1
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Chang HW, Lee EM, Wang Y, Zhou C, Pruss KM, Henrissat S, Chen RY, Kao C, Hibberd MC, Lynn HM, Webber DM, Crane M, Cheng J, Rodionov DA, Arzamasov AA, Castillo JJ, Couture G, Chen Y, Balcazo NP, Lebrilla CB, Terrapon N, Henrissat B, Ilkayeva O, Muehlbauer MJ, Newgard CB, Mostafa I, Das S, Mahfuz M, Osterman AL, Barratt MJ, Ahmed T, Gordon JI. Prevotella copri and microbiota members mediate the beneficial effects of a therapeutic food for malnutrition. Nat Microbiol 2024; 9:922-937. [PMID: 38503977 PMCID: PMC10994852 DOI: 10.1038/s41564-024-01628-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 01/31/2024] [Indexed: 03/21/2024]
Abstract
Microbiota-directed complementary food (MDCF) formulations have been designed to repair the gut communities of malnourished children. A randomized controlled trial demonstrated that one formulation, MDCF-2, improved weight gain in malnourished Bangladeshi children compared to a more calorically dense standard nutritional intervention. Metagenome-assembled genomes from study participants revealed a correlation between ponderal growth and expression of MDCF-2 glycan utilization pathways by Prevotella copri strains. To test this correlation, here we use gnotobiotic mice colonized with defined consortia of age- and ponderal growth-associated gut bacterial strains, with or without P. copri isolates closely matching the metagenome-assembled genomes. Combining gut metagenomics and metatranscriptomics with host single-nucleus RNA sequencing and gut metabolomic analyses, we identify a key role of P. copri in metabolizing MDCF-2 glycans and uncover its interactions with other microbes including Bifidobacterium infantis. P. copri-containing consortia mediated weight gain and modulated energy metabolism within intestinal epithelial cells. Our results reveal structure-function relationships between MDCF-2 and members of the gut microbiota of malnourished children with potential implications for future therapies.
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Affiliation(s)
- Hao-Wei Chang
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Evan M Lee
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO, USA
| | - Yi Wang
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Cyrus Zhou
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO, USA
| | - Kali M Pruss
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Suzanne Henrissat
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO, USA
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille University, Marseille, France
| | - Robert Y Chen
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO, USA
| | - Clara Kao
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO, USA
| | - Matthew C Hibberd
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Hannah M Lynn
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO, USA
| | - Daniel M Webber
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Marie Crane
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO, USA
| | - Jiye Cheng
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO, USA
| | - Dmitry A Rodionov
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Aleksandr A Arzamasov
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Juan J Castillo
- Department of Chemistry, University of California, Davis, CA, USA
| | - Garret Couture
- Department of Chemistry, University of California, Davis, CA, USA
| | - Ye Chen
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO, USA
- Department of Chemistry, University of California, Davis, CA, USA
| | - Nikita P Balcazo
- Department of Chemistry, University of California, Davis, CA, USA
| | | | - Nicolas Terrapon
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille University, Marseille, France
| | - Bernard Henrissat
- Department of Biotechnology and Biomedicine (DTU Bioengineering), Technical University of Denmark, Lyngby, Denmark
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Olga Ilkayeva
- Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, NC, USA
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC, USA
- Department of Medicine, Duke University Medical Center, Durham, NC, USA
| | - Michael J Muehlbauer
- Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, NC, USA
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC, USA
| | - Christopher B Newgard
- Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, NC, USA
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC, USA
- Department of Medicine, Duke University Medical Center, Durham, NC, USA
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC, USA
| | - Ishita Mostafa
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Subhasish Das
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Mustafa Mahfuz
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Andrei L Osterman
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Michael J Barratt
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Tahmeed Ahmed
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Jeffrey I Gordon
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA.
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA.
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2
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Hibberd MC, Webber DM, Rodionov DA, Henrissat S, Chen RY, Zhou C, Lynn HM, Wang Y, Chang HW, Lee EM, Lelwala-Guruge J, Kazanov MD, Arzamasov AA, Leyn SA, Lombard V, Terrapon N, Henrissat B, Castillo JJ, Couture G, Bacalzo NP, Chen Y, Lebrilla CB, Mostafa I, Das S, Mahfuz M, Barratt MJ, Osterman AL, Ahmed T, Gordon JI. Bioactive glycans in a microbiome-directed food for children with malnutrition. Nature 2024; 625:157-165. [PMID: 38093016 PMCID: PMC10764277 DOI: 10.1038/s41586-023-06838-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 11/06/2023] [Indexed: 12/26/2023]
Abstract
Evidence is accumulating that perturbed postnatal development of the gut microbiome contributes to childhood malnutrition1-4. Here we analyse biospecimens from a randomized, controlled trial of a microbiome-directed complementary food (MDCF-2) that produced superior rates of weight gain compared with a calorically more dense conventional ready-to-use supplementary food in 12-18-month-old Bangladeshi children with moderate acute malnutrition4. We reconstructed 1,000 bacterial genomes (metagenome-assembled genomes (MAGs)) from the faecal microbiomes of trial participants, identified 75 MAGs of which the abundances were positively associated with ponderal growth (change in weight-for-length Z score (WLZ)), characterized changes in MAG gene expression as a function of treatment type and WLZ response, and quantified carbohydrate structures in MDCF-2 and faeces. The results reveal that two Prevotella copri MAGs that are positively associated with WLZ are the principal contributors to MDCF-2-induced expression of metabolic pathways involved in utilizing the component glycans of MDCF-2. The predicted specificities of carbohydrate-active enzymes expressed by their polysaccharide-utilization loci are correlated with (1) the in vitro growth of Bangladeshi P. copri strains, possessing varying degrees of polysaccharide-utilization loci and genomic conservation with these MAGs, in defined medium containing different purified glycans representative of those in MDCF-2, and (2) the levels of faecal carbohydrate structures in the trial participants. These associations suggest that identifying bioactive glycan structures in MDCFs metabolized by growth-associated bacterial taxa will help to guide recommendations about their use in children with acute malnutrition and enable the development of additional formulations.
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Affiliation(s)
- Matthew C Hibberd
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St Louis, MO, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Daniel M Webber
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St Louis, MO, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Dmitry A Rodionov
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Suzanne Henrissat
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St Louis, MO, USA
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille University, Marseille, France
| | - Robert Y Chen
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St Louis, MO, USA
| | - Cyrus Zhou
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St Louis, MO, USA
| | - Hannah M Lynn
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St Louis, MO, USA
| | - Yi Wang
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St Louis, MO, USA
| | - Hao-Wei Chang
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St Louis, MO, USA
| | - Evan M Lee
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St Louis, MO, USA
| | - Janaki Lelwala-Guruge
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St Louis, MO, USA
| | - Marat D Kazanov
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
| | - Aleksandr A Arzamasov
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Semen A Leyn
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Vincent Lombard
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille University, Marseille, France
| | - Nicolas Terrapon
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille University, Marseille, France
| | - Bernard Henrissat
- Department of Biotechnology and Biomedicine (DTU Bioengineering), Technical University of Denmark, Lyngby, Denmark
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Juan J Castillo
- Department of Chemistry, University of California, Davis, Davis, CA, USA
| | - Garret Couture
- Department of Chemistry, University of California, Davis, Davis, CA, USA
| | - Nikita P Bacalzo
- Department of Chemistry, University of California, Davis, Davis, CA, USA
| | - Ye Chen
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St Louis, MO, USA
- Department of Chemistry, University of California, Davis, Davis, CA, USA
| | - Carlito B Lebrilla
- Department of Chemistry, University of California, Davis, Davis, CA, USA
| | - Ishita Mostafa
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Subhasish Das
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Mustafa Mahfuz
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Michael J Barratt
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St Louis, MO, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Andrei L Osterman
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Tahmeed Ahmed
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Jeffrey I Gordon
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA.
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St Louis, MO, USA.
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA.
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3
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Browne HP, Iqbal NT, Osman M, Tigoi C, Lawley TD, Gordon JI, Ahmed T, Kariuki S. Boosting microbiome science worldwide could save millions of children's lives. Nature 2024; 625:237-240. [PMID: 38191714 PMCID: PMC10810019 DOI: 10.1038/d41586-024-00017-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2024]
Abstract
Studies of the microbes living on and in our bodies are conducted mainly in a few rich countries, squandering opportunities to improve the health of people globally.
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4
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Chang HW, Lee EM, Wang Y, Zhou C, Pruss KM, Henrissat S, Chen RY, Kao C, Hibberd MC, Lynn HM, Webber DM, Crane M, Cheng J, Rodionov DA, Arzamasov AA, Castillo JJ, Couture G, Chen Y, Balcazo NP, Lebrilla CB, Terrapon N, Henrissat B, Ilkayeva O, Muehlbauer MJ, Newgard CB, Mostafa I, Das S, Mahfuz M, Osterman AL, Barratt MJ, Ahmed T, Gordon JI. Prevotella copri-related effects of a therapeutic food for malnutrition. bioRxiv 2023:2023.08.11.553030. [PMID: 37645712 PMCID: PMC10461977 DOI: 10.1101/2023.08.11.553030] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Preclinical and clinical studies are providing evidence that the healthy growth of infants and children reflects, in part, healthy development of their gut microbiomes1-5. This process of microbial community assembly and functional maturation is perturbed in children with acute malnutrition. Gnotobiotic animals, colonized with microbial communities from children with severe and moderate acute malnutrition, have been used to develop microbiome-directed complementary food (MDCF) formulations for repairing the microbiomes of these children during the weaning period5. Bangladeshi children with moderate acute malnutrition (MAM) participating in a previously reported 3-month-long randomized controlled clinical study of one such formulation, MDCF-2, exhibited significantly improved weight gain compared to a commonly used nutritional intervention despite the lower caloric density of the MDCF6. Characterizing the 'metagenome assembled genomes' (MAGs) of bacterial strains present in the microbiomes of study participants revealed a significant correlation between accelerated ponderal growth and the expression by two Prevotella copri MAGs of metabolic pathways involved in processing of MDCF-2 glycans1. To provide a direct test of these relationships, we have now performed 'reverse translation' experiments using a gnotobiotic mouse model of mother-to-offspring microbiome transmission. Mice were colonized with defined consortia of age- and ponderal growth-associated gut bacterial strains cultured from Bangladeshi infants/children in the study population, with or without P. copri isolates resembling the MAGs. By combining analyses of microbial community assembly, gene expression and processing of glycan constituents of MDCF-2 with single nucleus RNA-Seq and mass spectrometric analyses of the intestine, we establish a principal role for P. copri in mediating metabolism of MDCF-2 glycans, characterize its interactions with other consortium members including Bifidobacterium longum subsp. infantis, and demonstrate the effects of P. copri-containing consortia in mediating weight gain and modulating the activities of metabolic pathways involved in lipid, amino acid, carbohydrate plus other facets of energy metabolism within epithelial cells positioned at different locations in intestinal crypts and villi. Together, the results provide insights into structure/function relationships between MDCF-2 and members of the gut communities of malnourished children; they also have implications for developing future prebiotic, probiotic and/or synbiotic therapeutics for microbiome restoration in children with already manifest malnutrition, or who are at risk for this pervasive health challenge.
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Affiliation(s)
- Hao-Wei Chang
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110 USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110 USA
| | - Evan M. Lee
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110 USA
| | - Yi Wang
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110 USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110 USA
| | - Cyrus Zhou
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110 USA
| | - Kali M. Pruss
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110 USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110 USA
| | - Suzanne Henrissat
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110 USA
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille University, F-13288, Marseille, France
| | - Robert Y. Chen
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110 USA
| | - Clara Kao
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110 USA
| | - Matthew C. Hibberd
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110 USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110 USA
| | - Hannah M. Lynn
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110 USA
| | - Daniel M. Webber
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110 USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110 USA
| | - Marie Crane
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110 USA
| | - Jiye Cheng
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110 USA
| | - Dmitry A. Rodionov
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037 USA
| | - Aleksandr A. Arzamasov
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037 USA
| | - Juan J. Castillo
- Department of Chemistry, University of California, Davis, CA 95616 USA
| | - Garret Couture
- Department of Chemistry, University of California, Davis, CA 95616 USA
| | - Ye Chen
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110 USA
- Department of Chemistry, University of California, Davis, CA 95616 USA
| | - Nikita P. Balcazo
- Department of Chemistry, University of California, Davis, CA 95616 USA
| | | | - Nicolas Terrapon
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille University, F-13288, Marseille, France
| | - Bernard Henrissat
- Department of Biotechnology and Biomedicine (DTU Bioengineering), Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Olga Ilkayeva
- Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, NC 27710 USA
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC 27710 USA
- Department of Medicine, Duke University Medical Center, Durham, NC, 27710 USA
| | - Michael J. Muehlbauer
- Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, NC 27710 USA
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC 27710 USA
| | - Christopher B. Newgard
- Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, NC 27710 USA
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC 27710 USA
- Department of Medicine, Duke University Medical Center, Durham, NC, 27710 USA
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC 27710 USA
| | - Ishita Mostafa
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh
| | - Subhasish Das
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh
| | - Mustafa Mahfuz
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh
| | - Andrei L. Osterman
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037 USA
| | - Michael J. Barratt
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110 USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110 USA
| | - Tahmeed Ahmed
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh
| | - Jeffrey I. Gordon
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110 USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110 USA
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5
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Beller ZW, Wesener DA, Seebeck TR, Guruge JL, Byrne AE, Henrissat S, Terrapon N, Henrissat B, Rodionov DA, Osterman AL, Suarez C, Bacalzo NP, Chen Y, Couture G, Lebrilla CB, Zhang Z, Eastlund ER, McCann CH, Davis GD, Gordon JI. Inducible CRISPR-targeted "knockdown" of human gut Bacteroides in gnotobiotic mice discloses glycan utilization strategies. Proc Natl Acad Sci U S A 2023; 120:e2311422120. [PMID: 37733741 PMCID: PMC10523453 DOI: 10.1073/pnas.2311422120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 08/08/2023] [Indexed: 09/23/2023] Open
Abstract
Understanding how members of the human gut microbiota prioritize nutrient resources is one component of a larger effort to decipher the mechanisms defining microbial community robustness and resiliency in health and disease. This knowledge is foundational for development of microbiota-directed therapeutics. To model how bacteria prioritize glycans in the gut, germfree mice were colonized with 13 human gut bacterial strains, including seven saccharolytic Bacteroidaceae species. Animals were fed a Western diet supplemented with pea fiber. After community assembly, an inducible CRISPR-based system was used to selectively and temporarily reduce the absolute abundance of Bacteroides thetaiotaomicron or B. cellulosilyticus by 10- to 60-fold. Each knockdown resulted in specific, reproducible increases in the abundances of other Bacteroidaceae and dynamic alterations in their expression of genes involved in glycan utilization. Emergence of these "alternate consumers" was associated with preservation of community saccharolytic activity. Using an inducible system for CRISPR base editing in vitro, we disrupted translation of transporters critical for utilizing dietary polysaccharides in Phocaeicola vulgatus, a B. cellulosilyticus knockdown-responsive taxon. In vitro and in vivo tests of the resulting P. vulgatus mutants allowed us to further characterize mechanisms associated with its increased fitness after knockdown. In principle, the approach described can be applied to study utilization of a range of nutrients and to preclinical efforts designed to develop therapeutic strategies for precision manipulation of microbial communities.
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Affiliation(s)
- Zachary W. Beller
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO63110
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO63110
| | - Darryl A. Wesener
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO63110
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO63110
| | - Timothy R. Seebeck
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO63110
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO63110
- Genome Engineering R&D, MilliporeSigma, the Life Science business Merck KGaA, Darmstadt, Germany, St. Louis, MO63103
| | - Janaki L. Guruge
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO63110
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO63110
| | - Alexandra E. Byrne
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO63110
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO63110
| | - Suzanne Henrissat
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO63110
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO63110
- Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique and Aix-Marseille University, 13288Marseille, France
| | - Nicolas Terrapon
- Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique and Aix-Marseille University, 13288Marseille, France
| | - Bernard Henrissat
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. LyngbyDK-2800, Denmark
- Department of Biological Sciences, King Abdulaziz University, Jeddah21589, Saudi Arabia
| | - Dmitry A. Rodionov
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA92037
| | - Andrei L. Osterman
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA92037
| | - Chris Suarez
- Department of Chemistry, University of California, Davis, CA95616
| | | | - Ye Chen
- Department of Chemistry, University of California, Davis, CA95616
| | - Garret Couture
- Department of Chemistry, University of California, Davis, CA95616
| | | | - Zhigang Zhang
- Genome Engineering R&D, MilliporeSigma, the Life Science business Merck KGaA, Darmstadt, Germany, St. Louis, MO63103
| | - Erik R. Eastlund
- Genome Engineering R&D, MilliporeSigma, the Life Science business Merck KGaA, Darmstadt, Germany, St. Louis, MO63103
| | - Caitlin H. McCann
- Genome Engineering R&D, MilliporeSigma, the Life Science business Merck KGaA, Darmstadt, Germany, St. Louis, MO63103
| | - Gregory D. Davis
- Genome Engineering R&D, MilliporeSigma, the Life Science business Merck KGaA, Darmstadt, Germany, St. Louis, MO63103
| | - Jeffrey I. Gordon
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO63110
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO63110
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6
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Hibberd MC, Webber DM, Rodionov DA, Henrissat S, Chen RY, Zhou C, Lynn HM, Wang Y, Chang HW, Lee EM, Lelwala-Guruge J, Kazanov MD, Arzamasov AA, Leyn SA, Lombard V, Terrapon N, Henrissat B, Castillo JJ, Couture G, Bacalzo NP, Chen Y, Lebrilla CB, Mostafa I, Das S, Mahfuz M, Barratt MJ, Osterman AL, Ahmed T, Gordon JI. Bioactive glycans in a microbiome-directed food for malnourished children. medRxiv 2023:2023.08.14.23293998. [PMID: 37645824 PMCID: PMC10462212 DOI: 10.1101/2023.08.14.23293998] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Evidence is accumulating that perturbed postnatal development of the gut microbiome contributes to childhood malnutrition1-4. Designing effective microbiome-directed therapeutic foods to repair these perturbations requires knowledge about how food components interact with the microbiome to alter its expressed functions. Here we use biospecimens from a randomized, controlled trial of a microbiome-directed complementary food prototype (MDCF-2) that produced superior rates of weight gain compared to a conventional ready-to-use supplementary food (RUSF) in 12-18-month-old Bangladeshi children with moderate acute malnutrition (MAM)4. We reconstructed 1000 bacterial genomes (metagenome-assembled genomes, MAGs) present in their fecal microbiomes, identified 75 whose abundances were positively associated with weight gain (change in weight-for-length Z score, WLZ), characterized gene expression changes in these MAGs as a function of treatment type and WLZ response, and used mass spectrometry to quantify carbohydrate structures in MDCF-2 and feces. The results reveal treatment-induced changes in expression of carbohydrate metabolic pathways in WLZ-associated MAGs. Comparing participants consuming MDCF-2 versus RUSF, and MDCF-2-treated children in the upper versus lower quartiles of WLZ responses revealed that two Prevotella copri MAGs positively associated with WLZ were principal contributors to MDCF-2-induced expression of metabolic pathways involved in utilization of its component glycans. Moreover, the predicted specificities of carbohydrate active enzymes expressed by polysaccharide utilization loci (PULs) in these two MAGs correlate with the (i) in vitro growth of Bangladeshi P. copri strains, possessing differing degrees of PUL and overall genomic content similarity to these MAGs, cultured in defined medium containing different purified glycans representative of those in MDCF-2, and (ii) levels of carbohydrate structures identified in feces from clinical trial participants. In the accompanying paper5, we use a gnotobiotic mouse model colonized with age- and WLZ-associated bacterial taxa cultured from this study population, and fed diets resembling those consumed by study participants, to directly test the relationship between P. copri, MDCF-2 glycan metabolism, host ponderal growth responses, and intestinal gene expression and metabolism. The ability to identify bioactive glycan structures in MDCFs that are metabolized by growth-associated bacterial taxa will help guide recommendations about use of this MDCF for children with acute malnutrition representing different geographic locales and ages, as well as enable development of bioequivalent, or more efficacious, formulations composed of culturally acceptable and affordable ingredients.
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Affiliation(s)
- Matthew C. Hibberd
- Edison Family Center for Genome Sciences and Systems Biology,
Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington
University School of Medicine, St. Louis, MO 63110 USA
- Department of Pathology and Immunology, Washington University
School of Medicine, St. Louis, MO 63110 USA
| | - Daniel M. Webber
- Edison Family Center for Genome Sciences and Systems Biology,
Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington
University School of Medicine, St. Louis, MO 63110 USA
- Department of Pathology and Immunology, Washington University
School of Medicine, St. Louis, MO 63110 USA
| | - Dmitry A. Rodionov
- Infectious and Inflammatory Disease Center, Sanford Burnham
Prebys Medical Discovery Institute, La Jolla, CA 92037 USA
| | - Suzanne Henrissat
- Edison Family Center for Genome Sciences and Systems Biology,
Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington
University School of Medicine, St. Louis, MO 63110 USA
- Architecture et Fonction des Macromolécules Biologiques,
CNRS, Aix-Marseille University, F-13288, Marseille, France
| | - Robert Y. Chen
- Edison Family Center for Genome Sciences and Systems Biology,
Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington
University School of Medicine, St. Louis, MO 63110 USA
| | - Cyrus Zhou
- Edison Family Center for Genome Sciences and Systems Biology,
Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington
University School of Medicine, St. Louis, MO 63110 USA
| | - Hannah M. Lynn
- Edison Family Center for Genome Sciences and Systems Biology,
Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington
University School of Medicine, St. Louis, MO 63110 USA
| | - Yi Wang
- Edison Family Center for Genome Sciences and Systems Biology,
Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington
University School of Medicine, St. Louis, MO 63110 USA
| | - Hao-Wei Chang
- Edison Family Center for Genome Sciences and Systems Biology,
Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington
University School of Medicine, St. Louis, MO 63110 USA
| | - Evan M. Lee
- Edison Family Center for Genome Sciences and Systems Biology,
Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington
University School of Medicine, St. Louis, MO 63110 USA
| | - Janaki Lelwala-Guruge
- Edison Family Center for Genome Sciences and Systems Biology,
Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington
University School of Medicine, St. Louis, MO 63110 USA
| | - Marat D. Kazanov
- Faculty of Engineering and Natural Sciences, Sabanci University,
Istanbul, Turkey, 34956
| | - Aleksandr A. Arzamasov
- Infectious and Inflammatory Disease Center, Sanford Burnham
Prebys Medical Discovery Institute, La Jolla, CA 92037 USA
| | - Semen A. Leyn
- Infectious and Inflammatory Disease Center, Sanford Burnham
Prebys Medical Discovery Institute, La Jolla, CA 92037 USA
| | - Vincent Lombard
- Architecture et Fonction des Macromolécules Biologiques,
CNRS, Aix-Marseille University, F-13288, Marseille, France
| | - Nicolas Terrapon
- Architecture et Fonction des Macromolécules Biologiques,
CNRS, Aix-Marseille University, F-13288, Marseille, France
| | - Bernard Henrissat
- Department of Biotechnology and Biomedicine (DTU Bioengineering),
Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
- Department of Biological Sciences, King Abdulaziz University,
Jeddah, Saudi Arabia
| | - Juan J. Castillo
- Department of Chemistry, University of California, Davis, CA
95616, USA
| | - Garret Couture
- Department of Chemistry, University of California, Davis, CA
95616, USA
| | - Nikita P. Bacalzo
- Department of Chemistry, University of California, Davis, CA
95616, USA
| | - Ye Chen
- Edison Family Center for Genome Sciences and Systems Biology,
Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington
University School of Medicine, St. Louis, MO 63110 USA
- Department of Chemistry, University of California, Davis, CA
95616, USA
| | | | - Ishita Mostafa
- International Centre for Diarrhoeal Disease Research,
Bangladesh (icddr,b), Dhaka 1212, Bangladesh
| | - Subhasish Das
- International Centre for Diarrhoeal Disease Research,
Bangladesh (icddr,b), Dhaka 1212, Bangladesh
| | - Mustafa Mahfuz
- International Centre for Diarrhoeal Disease Research,
Bangladesh (icddr,b), Dhaka 1212, Bangladesh
| | - Michael J. Barratt
- Edison Family Center for Genome Sciences and Systems Biology,
Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington
University School of Medicine, St. Louis, MO 63110 USA
- Department of Pathology and Immunology, Washington University
School of Medicine, St. Louis, MO 63110 USA
| | - Andrei L. Osterman
- Infectious and Inflammatory Disease Center, Sanford Burnham
Prebys Medical Discovery Institute, La Jolla, CA 92037 USA
| | - Tahmeed Ahmed
- International Centre for Diarrhoeal Disease Research,
Bangladesh (icddr,b), Dhaka 1212, Bangladesh
| | - Jeffrey I. Gordon
- Edison Family Center for Genome Sciences and Systems Biology,
Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington
University School of Medicine, St. Louis, MO 63110 USA
- Department of Pathology and Immunology, Washington University
School of Medicine, St. Louis, MO 63110 USA
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7
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Seo DO, O’Donnell D, Jain N, Ulrich JD, Herz J, Li Y, Lemieux M, Cheng J, Hu H, Serrano JR, Bao X, Franke E, Karlsson M, Meier M, Deng S, Desai C, Dodiya H, Lelwala-Guruge J, Handley SA, Kipnis J, Sisodia SS, Gordon JI, Holtzman DM. ApoE isoform- and microbiota-dependent progression of neurodegeneration in a mouse model of tauopathy. Science 2023; 379:eadd1236. [PMID: 36634180 PMCID: PMC9901565 DOI: 10.1126/science.add1236] [Citation(s) in RCA: 69] [Impact Index Per Article: 69.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Accepted: 11/22/2022] [Indexed: 01/13/2023]
Abstract
Tau-mediated neurodegeneration is a hallmark of Alzheimer's disease. Primary tauopathies are characterized by pathological tau accumulation and neuronal and synaptic loss. Apolipoprotein E (ApoE)-mediated neuroinflammation is involved in the progression of tau-mediated neurodegeneration, and emerging evidence suggests that the gut microbiota regulates neuroinflammation in an APOE genotype-dependent manner. However, evidence of a causal link between the microbiota and tau-mediated neurodegeneration is lacking. In this study, we characterized a genetically engineered mouse model of tauopathy expressing human ApoE isoforms reared under germ-free conditions or after perturbation of their gut microbiota with antibiotics. Both of these manipulations reduced gliosis, tau pathology, and neurodegeneration in a sex- and ApoE isoform-dependent manner. The findings reveal mechanistic and translationally relevant interrelationships between the microbiota, neuroinflammation, and tau-mediated neurodegeneration.
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Affiliation(s)
- Dong-oh Seo
- Department of Neurology, Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO. USA
| | - David O’Donnell
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO. USA; Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO. USA
| | - Nimansha Jain
- Department of Neurology, Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO. USA
| | - Jason D. Ulrich
- Department of Neurology, Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO. USA
| | - Jasmin Herz
- Center for Brain Immunology and Glia (BIG), Washington University School of Medicine, St. Louis, MO. USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO. USA
| | - Yuhao Li
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, MO. USA
| | - Mackenzie Lemieux
- Center for Brain Immunology and Glia (BIG), Washington University School of Medicine, St. Louis, MO. USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO. USA
| | - Jiye Cheng
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO. USA; Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO. USA
| | - Hao Hu
- Department of Neurology, Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO. USA
| | - Javier R. Serrano
- Department of Neurology, Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO. USA
| | - Xin Bao
- Department of Neurology, Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO. USA
| | - Emily Franke
- Department of Neurology, Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO. USA
| | - Maria Karlsson
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO. USA; Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO. USA
| | - Martin Meier
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO. USA; Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO. USA
| | - Su Deng
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO. USA; Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO. USA
| | - Chandani Desai
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO. USA; Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO. USA
| | - Hemraj Dodiya
- Department of Neurobiology, The University of Chicago, Chicago, IL, 60637, USA
| | - Janaki Lelwala-Guruge
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO. USA; Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO. USA
| | - Scott A. Handley
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO. USA
| | - Jonathan Kipnis
- Center for Brain Immunology and Glia (BIG), Washington University School of Medicine, St. Louis, MO. USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO. USA
| | - Sangram S. Sisodia
- Department of Neurobiology, The University of Chicago, Chicago, IL, 60637, USA
| | - Jeffrey I. Gordon
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO. USA; Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO. USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO. USA
| | - David M. Holtzman
- Department of Neurology, Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO. USA
- Knight Alzheimer Disease Research Center, Washington University School of Medicine, St. Louis, MO. USA
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8
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Lawenius L, Cowardin C, Grahnemo L, Scheffler JM, Horkeby K, Engdahl C, Wu J, Vandenput L, Koskela A, Tukkanen J, Coward E, Hveem K, Langhammer A, Abrahamsson S, Gordon JI, Sjögren K, Ohlsson C. Transplantation of gut microbiota from old mice into young healthy mice reduces lean mass but not bone mass. Gut Microbes 2023; 15:2236755. [PMID: 37475479 PMCID: PMC10364652 DOI: 10.1080/19490976.2023.2236755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 06/27/2023] [Accepted: 07/10/2023] [Indexed: 07/22/2023] Open
Abstract
Aging is associated with low bone and lean mass as well as alterations in the gut microbiota (GM). In this study, we determined whether the reduced bone mass and relative lean mass observed in old mice could be transferred to healthy young mice by GM transplantation (GMT). GM from old (21-month-old) and young adult (5-month-old) donors was used to colonize germ-free (GF) mice in three separate studies involving still growing 5- or 11-week-old recipients and 17-week-old recipients with minimal bone growth. The GM of the recipient mice was similar to that of the donors, demonstrating successful GMT. GM from old mice did not have statistically significant effects on bone mass or bone strength, but significantly reduced the lean mass percentage of still growing recipient mice when compared with recipients of GM from young adult mice. The levels of propionate in the cecum of mice receiving old donor GM were significantly lower than those in mice receiving young adult donor GM. Bacteroides ovatus was enriched in the microbiota of recipient mice harboring GM from young adult donors. The presence of B. ovatus was not only significantly associated with high lean mass percentage in mice, but also with lean mass adjusted for fat mass in the large human HUNT cohort. In conclusion, GM from old mice reduces lean mass percentage but not bone mass in young, healthy, still growing recipient mice. Future studies are warranted to determine whether GM from young mice improves the musculoskeletal phenotype of frail elderly recipient mice.
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Affiliation(s)
- Lina Lawenius
- Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, Sahlgrenska Osteoporosis Centre, Centre for Bone and Arthritis Research at the Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Carrie Cowardin
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University in St. Louis, St. Louis, MO, USA
| | - Louise Grahnemo
- Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, Sahlgrenska Osteoporosis Centre, Centre for Bone and Arthritis Research at the Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Julia M. Scheffler
- Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, Sahlgrenska Osteoporosis Centre, Centre for Bone and Arthritis Research at the Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Rheumatology and Inflammation Research, Institute of Medicine, Sahlgrenska Osteoporosis Centre, Centre for Bone and Arthritis Research at the Sahlgrenska Academy, Sahlgrenska Academy University of Gothenburg, Gothenburg, Sweden
| | - Karin Horkeby
- Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, Sahlgrenska Osteoporosis Centre, Centre for Bone and Arthritis Research at the Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Cecilia Engdahl
- Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, Sahlgrenska Osteoporosis Centre, Centre for Bone and Arthritis Research at the Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Rheumatology and Inflammation Research, Institute of Medicine, Sahlgrenska Osteoporosis Centre, Centre for Bone and Arthritis Research at the Sahlgrenska Academy, Sahlgrenska Academy University of Gothenburg, Gothenburg, Sweden
| | - Jianyao Wu
- Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, Sahlgrenska Osteoporosis Centre, Centre for Bone and Arthritis Research at the Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Liesbeth Vandenput
- Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, Sahlgrenska Osteoporosis Centre, Centre for Bone and Arthritis Research at the Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Antti Koskela
- Department of Anatomy and Cell Biology, Faculty of Medicine, Institute of Cancer Research and Translational Medicine, University of Oulu, Oulu, Finland
| | - Juha Tukkanen
- Department of Anatomy and Cell Biology, Faculty of Medicine, Institute of Cancer Research and Translational Medicine, University of Oulu, Oulu, Finland
| | - Eivind Coward
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
| | - Kristian Hveem
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
- HUNT Research Centre, Department of Public Health and Nursing, Norwegian University of Science and Technology, Levanger, Norway
| | - Arnulf Langhammer
- HUNT Research Centre, Department of Public Health and Nursing, Norwegian University of Science and Technology, Levanger, Norway
| | - Sanna Abrahamsson
- Bioinformatics and Data Centre, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Jeffrey I. Gordon
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University in St. Louis, St. Louis, MO, USA
| | - Klara Sjögren
- Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, Sahlgrenska Osteoporosis Centre, Centre for Bone and Arthritis Research at the Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Claes Ohlsson
- Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, Sahlgrenska Osteoporosis Centre, Centre for Bone and Arthritis Research at the Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Drug Treatment, Region Västra Götaland, Sahlgrenska University Hospital, Gothenburg, Sweden
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9
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Seo D, O'Donnell D, Jain N, Ulrich JD, Herz J, Lemieux M, Stanley JG, Franke E, Serrano JR, Bao X, Karlsson M, Meier M, Desai C, Lelwala‐Guruge J, Li Y, Shi Y, Wang C, Cheng J, de Lima KA, Dodiya HB, Hibberd M, Griffin N, Handley S, Kipnis J, Sisodia SS, Gordon JI, Holtzman DM. Gut microbiota regulates neuroinflammation and progression of neurodegeneration in a mouse model of tauopathy. Alzheimers Dement 2022. [DOI: 10.1002/alz.062080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Dong‐oh Seo
- Washington University in St. Louis St. Louis MO USA
| | | | | | | | - Jasmin Herz
- Washington University in St. Louis St. Louis MO USA
| | | | | | - Emily Franke
- Washington University in St. Louis St. Louis MO USA
| | | | - Xin Bao
- Washington University in St. Louis St. Louis MO USA
| | | | - Marty Meier
- Washington University in St. Louis St. Louis MO USA
| | | | | | - Yuhao Li
- Washington University in St. Louis St. Louis MO USA
| | - Yang Shi
- Washington University in St. Louis St. Louis MO USA
| | - Chao Wang
- Washington University in St. Louis St. Louis MO USA
| | - Jiye Cheng
- Washington University in St. Louis St. Louis MO USA
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10
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Zaydman MA, Little AA, Haro F, Aksianiuk V, Buchser WJ, DiAntonio A, Gordon JI, Milbrandt J, Raman AS. Defining hierarchical protein interaction networks from spectral analysis of bacterial proteomes. eLife 2022; 11:74104. [PMID: 35976223 PMCID: PMC9427106 DOI: 10.7554/elife.74104] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 08/17/2022] [Indexed: 11/25/2022] Open
Abstract
Cellular behaviors emerge from layers of molecular interactions: proteins interact to form complexes, pathways, and phenotypes. We show that hierarchical networks of protein interactions can be defined from the statistical pattern of proteome variation measured across thousands of diverse bacteria and that these networks reflect the emergence of complex bacterial phenotypes. Our results are validated through gene-set enrichment analysis and comparison to existing experimentally derived databases. We demonstrate the biological utility of our approach by creating a model of motility in Pseudomonas aeruginosa and using it to identify a protein that affects pilus-mediated motility. Our method, SCALES (Spectral Correlation Analysis of Layered Evolutionary Signals), may be useful for interrogating genotype-phenotype relationships in bacteria.
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Affiliation(s)
- Mark A Zaydman
- Department of Pathology, Washington University in St. Louis, St Louis, United States
| | - Alexander A Little
- Duchossois Family Institute, University of Chicago, Chicago, United States
| | - Fidel Haro
- Duchossois Family Institute, University of Chicago, Chicago, United States
| | - Valeryia Aksianiuk
- Duchossois Family Institute, University of Chicago, Chicago, United States
| | - William J Buchser
- Department of Genetics, Washington University in St. Louis, St Louis, United States
| | - Aaron DiAntonio
- Department of Developmental Biology, Washington University in St. Louis, St Louis, United States
| | - Jeffrey I Gordon
- Department of Pathology, Washington University in St. Louis, St Louis, United States
| | - Jeffrey Milbrandt
- Department of Genetics, Washington University in St. Louis, St Louis, United States
| | - Arjun S Raman
- Duchossois Family Institute, University of Chicago, Chicago, United States
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11
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Han ND, Cheng J, Delannoy-Bruno O, Webber D, Terrapon N, Henrissat B, Rodionov DA, Arzamasov AA, Osterman AL, Hayashi DK, Meynier A, Vinoy S, Desai C, Marion S, Barratt MJ, Heath AC, Gordon JI. Microbial liberation of N-methylserotonin from orange fiber in gnotobiotic mice and humans. Cell 2022; 185:3056-3057. [PMID: 35931022 PMCID: PMC9469646 DOI: 10.1016/j.cell.2022.07.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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12
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Mostafa I, Fahim SM, Das S, Gazi MA, Hasan MM, Saqeeb KN, Mahfuz M, Lynn HB, Barratt MJ, Gordon JI, Ahmed T. Developing shelf-stable Microbiota Directed Complementary Food (MDCF) prototypes for malnourished children: study protocol for a randomized, single-blinded, clinical study. BMC Pediatr 2022; 22:385. [PMID: 35778675 PMCID: PMC9247958 DOI: 10.1186/s12887-022-03436-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 06/22/2022] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND Childhood undernutrition is a major public health concern that needs special attention to achieve 2025 global nutrition targets. Moderate acute malnutrition (MAM), manifest as wasting (low weight-for-height), affects 33 million children under 5, yet there are currently no global guidelines for its treatment. We recently performed a randomized-controlled clinical study of a microbiota-directed complementary food formulation (MDCF-2) in 12-18-month-old Bangladeshi children with MAM. The results revealed that MDCF-2, freshly prepared each day, produced a significantly greater improvement in ponderal growth than a standard ready-to-use supplementary food (RUSF), an effect that is associated with repair of the disrupted gut microbial community development that occurs in children with MAM. To test the generalizability of these results in acutely malnourished children at other sites, there is a pressing need for a packaged, shelf-stable, organoleptically-acceptable formulation that is bioequivalent to MDCF-2. This report describes the protocol for a clinical study to evaluate candidate formulations designed to meet these criteria. METHODS A randomized single-blind study will be conducted in 8-12-month-old Bangladeshi children with MAM to compare the efficacy of alternative shelf-stable MDCF prototypes versus the current MDCF-2 formulation that is produced fresh each day. V4-16S rDNA amplicon and shotgun sequencing datasets will be generated from faecal DNA samples collected from each child enrolled in each group prior to, during, and after treatment to determine the abundances of MDCF-2-responsive bacterial taxa. Efficacy will be assessed by quantifying the change in representation of MDCF-2-responsive gut bacterial taxa after 4-weeks of treatment with freshly prepared MDCF-2 compared to their changes in abundance after treatment with the prototype MDCFs. Equivalence will be defined as the absence of a statistically significant difference, after 4-weeks of treatment, in the representation of faecal bacterial taxa associated with the response to MDCF-2 in participants receiving a test MDCF. DISCUSSION This trial aims to establish acceptability and equivalence with respect to microbiota repair, of scalable, shelf-stable formulations of MDCF-2 in 8-12-month-old Bangladeshi children with moderate acute malnutrition. TRIAL REGISTRATION ClinicalTrials.gov (NCT05094024). The trial has been registered before starting enrolment on 23 October 2021.
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Affiliation(s)
- Ishita Mostafa
- grid.414142.60000 0004 0600 7174Nutrition and Clinical Services Division, icddr,b, Dhaka, 1212 Bangladesh ,grid.502801.e0000 0001 2314 6254Faculty of Medicine and Health Technology, University of Tampere, Tampere, Finland
| | | | - Subhasish Das
- grid.414142.60000 0004 0600 7174Nutrition and Clinical Services Division, icddr,b, Dhaka, 1212 Bangladesh ,grid.9654.e0000 0004 0372 3343Liggins Institute, University of Auckland, Auckland, New Zealand
| | - Md Amran Gazi
- grid.414142.60000 0004 0600 7174Nutrition and Clinical Services Division, icddr,b, Dhaka, 1212 Bangladesh
| | - Md. Mehedi Hasan
- grid.414142.60000 0004 0600 7174Nutrition and Clinical Services Division, icddr,b, Dhaka, 1212 Bangladesh
| | - Kazi Nazmus Saqeeb
- grid.414142.60000 0004 0600 7174Nutrition and Clinical Services Division, icddr,b, Dhaka, 1212 Bangladesh
| | - Mustafa Mahfuz
- grid.414142.60000 0004 0600 7174Nutrition and Clinical Services Division, icddr,b, Dhaka, 1212 Bangladesh ,grid.502801.e0000 0001 2314 6254Faculty of Medicine and Health Technology, University of Tampere, Tampere, Finland
| | - Hannah B. Lynn
- grid.4367.60000 0001 2355 7002The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO USA ,grid.4367.60000 0001 2355 7002Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO USA
| | - Michael J. Barratt
- grid.4367.60000 0001 2355 7002The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO USA ,grid.4367.60000 0001 2355 7002Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO USA ,grid.4367.60000 0001 2355 7002Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO USA
| | - Jeffrey I. Gordon
- grid.4367.60000 0001 2355 7002The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO USA ,grid.4367.60000 0001 2355 7002Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO USA ,grid.4367.60000 0001 2355 7002Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO USA
| | - Tahmeed Ahmed
- grid.414142.60000 0004 0600 7174Nutrition and Clinical Services Division, icddr,b, Dhaka, 1212 Bangladesh ,grid.414142.60000 0004 0600 7174Office of the Executive Director, icddr,b, Dhaka, Bangladesh ,grid.34477.330000000122986657Department of Global Health, University of Washington, Seattle, Washington, USA ,grid.52681.380000 0001 0746 8691Department of Public Health Nutrition, James P Grant School of Public Health, BRAC University, Dhaka, Bangladesh
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13
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Han ND, Cheng J, Delannoy-Bruno O, Webber D, Terrapon N, Henrissat B, Rodionov DA, Arzamasov AA, Osterman AL, Hayashi DK, Meynier A, Vinoy S, Desai C, Marion S, Barratt MJ, Heath AC, Gordon JI. Microbial liberation of N-methylserotonin from orange fiber in gnotobiotic mice and humans. Cell 2022; 185:2495-2509.e11. [PMID: 35764090 DOI: 10.1016/j.cell.2022.06.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 11/23/2021] [Accepted: 06/03/2022] [Indexed: 12/13/2022]
Abstract
Plant fibers in byproduct streams produced by non-harsh food processing methods represent biorepositories of diverse, naturally occurring, and physiologically active biomolecules. To demonstrate one approach for their characterization, mass spectrometry of intestinal contents from gnotobiotic mice, plus in vitro studies, revealed liberation of N-methylserotonin from orange fibers by human gut microbiota members including Bacteroides ovatus. Functional genomic analyses of B. ovatus strains grown under permissive and non-permissive N-methylserotonin "mining" conditions revealed polysaccharide utilization loci that target pectins whose expression correlate with strain-specific liberation of this compound. N-methylserotonin, orally administered to germ-free mice, reduced adiposity, altered liver glycogenesis, shortened gut transit time, and changed expression of genes that regulate circadian rhythm in the liver and colon. In human studies, dose-dependent, orange-fiber-specific fecal accumulation of N-methylserotonin positively correlated with levels of microbiome genes encoding enzymes that digest pectic glycans. Identifying this type of microbial mining activity has potential therapeutic implications.
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Affiliation(s)
- Nathan D Han
- The Edison Family Center for Genome Sciences and Systems Biology, St. Louis, MO 63110, USA; Center for Gut Microbiome and Nutrition Research, St. Louis, MO 63110, USA
| | - Jiye Cheng
- The Edison Family Center for Genome Sciences and Systems Biology, St. Louis, MO 63110, USA; Center for Gut Microbiome and Nutrition Research, St. Louis, MO 63110, USA
| | - Omar Delannoy-Bruno
- The Edison Family Center for Genome Sciences and Systems Biology, St. Louis, MO 63110, USA; Center for Gut Microbiome and Nutrition Research, St. Louis, MO 63110, USA
| | - Daniel Webber
- The Edison Family Center for Genome Sciences and Systems Biology, St. Louis, MO 63110, USA; Center for Gut Microbiome and Nutrition Research, St. Louis, MO 63110, USA; Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Nicolas Terrapon
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille University, 13288 Marseille, France
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille University, 13288 Marseille, France; Department of Biotechnology and Biomedicine (DTU Bioengineering), Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Dmitry A Rodionov
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Aleksandr A Arzamasov
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Andrei L Osterman
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | | | | | | | - Chandani Desai
- The Edison Family Center for Genome Sciences and Systems Biology, St. Louis, MO 63110, USA; Center for Gut Microbiome and Nutrition Research, St. Louis, MO 63110, USA
| | - Stacey Marion
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Michael J Barratt
- The Edison Family Center for Genome Sciences and Systems Biology, St. Louis, MO 63110, USA; Center for Gut Microbiome and Nutrition Research, St. Louis, MO 63110, USA; Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Andrew C Heath
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Jeffrey I Gordon
- The Edison Family Center for Genome Sciences and Systems Biology, St. Louis, MO 63110, USA; Center for Gut Microbiome and Nutrition Research, St. Louis, MO 63110, USA.
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14
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Abstract
Forty-five percent of deaths among children under 5 years of age are associated with undernutrition. Globally, almost 200 million children exhibit the two major forms of undernutrition-wasting (low weight-for-height) or stunting (low height-for-age), with many affected by both. Undernutrition is not due to food insecurity alone. Growing evidence indicates that perturbed postnatal gut microbiome development contributes to its pathogenesis. This perspective focuses on defining and repairing these defects in gut microbiome development. We describe an approach that involves the analysis of well-phenotyped human cohorts, followed by preclinical studies using gnotobiotic animals colonized with microbiota from these cohorts. Additionally, these models can be used to identify therapeutic targets and candidates that can then be tested clinically. Furthermore, introducing pretreatment microbiota from trial participants into gnotobiotic animals and re-enacting trial conditions allow mechanisms to be dissected. We highlight these recent advances as well as gaps in existing knowledge that present opportunities for future research.
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Affiliation(s)
- Michael J. Barratt
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University in St. Louis, St. Louis, MO 63110,Center for Gut Microbiome Research, Washington University in St. Louis, St. Louis, MO 63110
| | - Tahmeed Ahmed
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh
| | - Jeffrey I. Gordon
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University in St. Louis, St. Louis, MO 63110,Center for Gut Microbiome Research, Washington University in St. Louis, St. Louis, MO 63110
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15
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Barratt MJ, Nuzhat S, Ahsan K, Frese SA, Arzamasov AA, Sarker SA, Islam MM, Palit P, Islam MR, Hibberd MC, Nakshatri S, Cowardin CA, Guruge JL, Byrne AE, Venkatesh S, Sundaresan V, Henrick B, Duar RM, Mitchell RD, Casaburi G, Prambs J, Flannery R, Mahfuz M, Rodionov DA, Osterman AL, Kyle D, Ahmed T, Gordon JI. Bifidobacterium infantis treatment promotes weight gain in Bangladeshi infants with severe acute malnutrition. Sci Transl Med 2022; 14:eabk1107. [PMID: 35417188 PMCID: PMC9516695 DOI: 10.1126/scitranslmed.abk1107] [Citation(s) in RCA: 49] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Disrupted development of the gut microbiota is a contributing cause of childhood malnutrition. Bifidobacterium longum subspecies infantis is a prominent early colonizer of the infant gut that consumes human milk oligosaccharides (HMOs). We found that the absolute abundance of Bifidobacterium infantis is lower in 3- to 24-month-old Bangladeshi infants with severe acute malnutrition (SAM) compared to their healthy age-matched counterparts. A single-blind, placebo-controlled trial (SYNERGIE) was conducted in 2- to 6-month-old Bangladeshi infants with SAM. A commercial U.S. donor-derived B. infantis strain (EVC001) was administered daily with or without the HMO lacto-N-neotetraose for 28 days. This intervention increased fecal B. infantis abundance in infants with SAM, although to levels still 10- to 100-fold lower than in untreated healthy controls. EVC001 treatment promoted weight gain that was associated with reduced intestinal inflammation markers in infants with SAM. We cultured fecal B. infantis strains from Bangladeshi infants and colonized gnotobiotic mice with these cultured strains. The gnotobiotic mice were fed a diet representative of that consumed by 6-month-old Bangladeshi infants, with or without HMO supplementation. One B. infantis strain, Bg_2D9, expressing two gene clusters involved in uptake and utilization of N-glycans and plant-derived polysaccharides, exhibited superior fitness over EVC001. The fitness advantage of Bg_2D9 was confirmed in a gnotobiotic mouse model of mother-to-infant gut microbiota transmission where dams received a pretreatment fecal community from a SAM infant in the SYNERGIE trial. Whether Bg_2D9 is superior to EVC001 for treating malnourished infants who consume a diet with limited breastmilk requires further clinical testing.
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Affiliation(s)
- Michael J. Barratt
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110 USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110 USA
| | - Sharika Nuzhat
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh
| | - Kazi Ahsan
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110 USA
| | - Steven A. Frese
- Evolve BioSystems, Inc., Davis, CA 95618 USA
- Department of Food Science and Technology, University of Nebraska, Lincoln, NE 68588 USA
| | - Aleksandr A. Arzamasov
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037 USA
| | - Shafiqul Alam Sarker
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh
| | - M. Munirul Islam
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh
| | - Parag Palit
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh
| | - Md Ridwan Islam
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh
| | - Matthew C. Hibberd
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110 USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110 USA
| | - Swetha Nakshatri
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110 USA
| | - Carrie A. Cowardin
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110 USA
| | - Janaki L. Guruge
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110 USA
| | - Alexandra E. Byrne
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110 USA
| | - Siddarth Venkatesh
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110 USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110 USA
| | - Vinaik Sundaresan
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110 USA
| | - Bethany Henrick
- Evolve BioSystems, Inc., Davis, CA 95618 USA
- Department of Food Science and Technology, University of Nebraska, Lincoln, NE 68588 USA
| | | | | | | | | | | | - Mustafa Mahfuz
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh
| | - Dmitry A. Rodionov
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037 USA
- A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow 127994 Russia
| | - Andrei L. Osterman
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037 USA
| | - David Kyle
- Evolve BioSystems, Inc., Davis, CA 95618 USA
| | - Tahmeed Ahmed
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh
| | - Jeffrey I. Gordon
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110 USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110 USA
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16
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Vinjamuri A, Davis JCC, Totten SM, Wu LD, Klein LD, Martin M, Quinn EA, Scelza B, Breakey A, Gurven M, Jasienska G, Kaplan H, Valeggia C, Hinde K, Smilowitz JT, Bernstein RM, Zivkovic AM, Barratt MJ, Gordon JI, Underwood MA, Mills DA, German JB, Lebrilla CB. Human Milk Oligosaccharide Compositions Illustrate Global Variations in Early Nutrition. J Nutr 2022; 152:1239-1253. [PMID: 35179194 PMCID: PMC9071347 DOI: 10.1093/jn/nxac027] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 01/26/2022] [Accepted: 02/01/2022] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Human milk oligosaccharides (HMOs) are an abundant class of compounds found in human milk and have been linked to the development of the infant, and specifically the brain, immune system, and gut microbiome. OBJECTIVES Advanced analytical methods were used to obtain relative quantitation of many structures in approximately 2000 samples from over 1000 mothers in urban, semirural, and rural sites across geographically diverse countries. METHODS LC-MS-based analytical methods were used to profile the compounds with broad structural coverage and quantitative information. The profiles revealed their structural heterogeneity and their potential biological roles. Comparisons of HMO compositions were made between mothers of different age groups, lactation periods, infant sexes, and residing geographical locations. RESULTS A common behavior found among all sites was a decrease in HMO abundances during lactation until approximately postnatal month 6, where they remained relatively constant. The greatest variations in structural abundances were associated with the presence of α(1,2)-fucosylated species. Genomic analyses of the mothers were not performed; instead, milk was phenotyped according to the abundances of α(1,2)-fucosylated structures. Mothers from the South American sites tended to have higher proportions of phenotypic secretors [mothers with relatively high concentrations of α(1,2)-fucosylated structures] in their populations compared to the rest of the globe, with Bolivia at ∼100% secretors, Peru at ∼97%, Brazil at ∼90%, and Argentina at ∼85%. Conversely, the cohort sampled in Africa manifested the lowest proportion of secretors (South Africa ∼ 63%, the Gambia ∼ 64%, and Malawi ∼ 75%). Furthermore, we compared total abundances of HMOs in secretors compared with nonsecretors and found that nonsecretors have lower abundances of HMOs compared to secretors, regardless of geographical location. We also observed compositional differences of the 50+ most abundant HMOs between milk types and geographical locations. CONCLUSIONS This study represents the largest structural HMO study to date and reveals the general behavior of HMOs during lactation among different populations.
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Affiliation(s)
- Anita Vinjamuri
- Department of Chemistry, University of California, Davis, CA, USA,Foods for Health Institute, University of California, Davis, CA, USA
| | - Jasmine C C Davis
- Department of Chemistry, University of California, Davis, CA, USA,Foods for Health Institute, University of California, Davis, CA, USA
| | - Sarah M Totten
- Department of Chemistry, University of California, Davis, CA, USA,Foods for Health Institute, University of California, Davis, CA, USA
| | - Lauren D Wu
- Department of Chemistry, University of California, Davis, CA, USA,Foods for Health Institute, University of California, Davis, CA, USA
| | - Laura D Klein
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Melanie Martin
- Department of Anthropology, University of Washington, Seattle, WA, USA
| | - E A Quinn
- Department of Anthropology, Washington University in St. Louis, St. Louis, MO, USA
| | - Brooke Scelza
- Department of Anthropology, University of California Los Angeles, Los Angeles, CA, USA
| | | | - Michael Gurven
- Department of Anthropology, University of California Santa Barbara, Santa Barbara, CA, USA
| | - Grazyna Jasienska
- Department of Environmental Health, Faculty of Health Sciences, Jagiellonian University Medical College, Krakow, Poland
| | | | | | - Katie Hinde
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ,
USA
| | - Jennifer T Smilowitz
- Foods for Health Institute, University of California, Davis, CA, USA,Department of Food Science and Technology, University of California, Davis, CA, USA
| | - Robin M Bernstein
- Department of Anthropology, University of Colorado, Boulder, CO, USA,Institute of Behavioral Science, University of Colorado, Boulder, CO, USA
| | - Angela M Zivkovic
- Foods for Health Institute, University of California, Davis, CA, USA,Department of Nutrition, University of California, Davis, CA, USA
| | - Michael J Barratt
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis MO,
USA,Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, MO, USA
| | - Jeffrey I Gordon
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis MO,
USA,Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, MO, USA
| | - Mark A Underwood
- Foods for Health Institute, University of California, Davis, CA, USA,Department of Pediatrics, University of California, Davis, CA, USA
| | - David A Mills
- Foods for Health Institute, University of California, Davis, CA, USA,Department of Food Science and Technology, University of California, Davis, CA, USA
| | - J Bruce German
- Foods for Health Institute, University of California, Davis, CA, USA,Department of Food Science and Technology, University of California, Davis, CA, USA
| | - Carlito B Lebrilla
- Department of Chemistry, University of California, Davis, CA, USA,Foods for Health Institute, University of California, Davis, CA, USA
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17
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Seo D, Stanley JG, Shi Y, Wang C, Serrano JR, Bao X, O'Donnell D, Lelwala‐Guruge J, Griffin N, Meier M, Dodiya HB, Sisodia SS, Gordon JI, Holtzman DM. Evidence that the gut microbiota regulates progression of neurodegeneration in a mouse model of tauopathy, in a sex‐ and ApoE isoform‐dependent manner. Alzheimers Dement 2021. [DOI: 10.1002/alz.049741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Dong‐oh Seo
- Washington University in St. Louis St. Louis MO USA
| | | | - Yang Shi
- Washington University in St. Louis St. Louis MO USA
| | - Chao Wang
- Washington University in St. Louis, School of Medicine St. Louis MO USA
| | | | - Xin Bao
- Washington University in St. Louis St. Louis MO USA
| | | | | | | | - Marty Meier
- Washington University in St. Louis St. Louis MO USA
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18
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Delannoy-Bruno O, Desai C, Raman AS, Chen RY, Hibberd MC, Cheng J, Han N, Castillo JJ, Couture G, Lebrilla CB, Barve RA, Lombard V, Henrissat B, Leyn SA, Rodionov DA, Osterman AL, Hayashi DK, Meynier A, Vinoy S, Kirbach K, Wilmot T, Heath AC, Klein S, Barratt MJ, Gordon JI. Evaluating microbiome-directed fibre snacks in gnotobiotic mice and humans. Nature 2021; 595:91-95. [PMID: 34163075 PMCID: PMC8324079 DOI: 10.1038/s41586-021-03671-4] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 05/25/2021] [Indexed: 02/06/2023]
Abstract
Changing food preferences brought about by westernization that have deleterious health effects1,2-combined with myriad forces that are contributing to increased food insecurity-are catalysing efforts to identify more nutritious and affordable foods3. Consumption of dietary fibre can help to prevent cardiovascular disease, type 2 diabetes and obesity4-6. A substantial number of reports have explored the effects of dietary fibre on the gut microbial community7-9. However, the microbiome is complex, dynamic and exhibits considerable intra- and interpersonal variation in its composition and functions. The large number of potential interactions between the components of the microbiome makes it challenging to define the mechanisms by which food ingredients affect community properties. Here we address the question of how foods containing different fibre preparations can be designed to alter functions associated with specific components of the microbiome. Because a marked increase in snack consumption is associated with westernization, we formulated snack prototypes using plant fibres from different sustainable sources that targeted distinct features of the gut microbiomes of individuals with obesity when transplanted into gnotobiotic mice. We used these snacks to supplement controlled diets that were consumed by adult individuals with obesity or who were overweight. Fibre-specific changes in their microbiomes were linked to changes in their plasma proteomes indicative of an altered physiological state.
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Affiliation(s)
- Omar Delannoy-Bruno
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St Louis, MO, USA
| | - Chandani Desai
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St Louis, MO, USA
| | - Arjun S Raman
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St Louis, MO, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Robert Y Chen
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St Louis, MO, USA
| | - Matthew C Hibberd
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St Louis, MO, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Jiye Cheng
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St Louis, MO, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Nathan Han
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St Louis, MO, USA
| | - Juan J Castillo
- Department of Chemistry, University of California, Davis, CA, USA
| | - Garret Couture
- Department of Chemistry, University of California, Davis, CA, USA
| | | | - Ruteja A Barve
- Department of Genetics, Washington University School of Medicine, St Louis, MO, USA
| | - Vincent Lombard
- Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique and Aix-Marseille Université, Marseille, France
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique and Aix-Marseille Université, Marseille, France
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Semen A Leyn
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Dmitry A Rodionov
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
- A. A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
| | - Andrei L Osterman
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | | | | | | | - Kyleigh Kirbach
- Department of Medicine, Washington University School of Medicine, St Louis, MO, USA
| | - Tara Wilmot
- Department of Medicine, Washington University School of Medicine, St Louis, MO, USA
| | - Andrew C Heath
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO, USA
| | - Samuel Klein
- Department of Medicine, Washington University School of Medicine, St Louis, MO, USA
| | - Michael J Barratt
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St Louis, MO, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Jeffrey I Gordon
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA.
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St Louis, MO, USA.
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA.
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19
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Rouhani S, Griffin NW, Yori PP, Gehrig JL, Olortegui MP, Salas MS, Trigoso DR, Moulton LH, Houpt ER, Barratt MJ, Kosek MN, Gordon JI. Diarrhea as a Potential Cause and Consequence of Reduced Gut Microbial Diversity Among Undernourished Children in Peru. Clin Infect Dis 2021; 71:989-999. [PMID: 31773127 PMCID: PMC7053391 DOI: 10.1093/cid/ciz905] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2019] [Accepted: 09/13/2019] [Indexed: 12/18/2022] Open
Abstract
Background Detrimental effects of diarrhea on child growth and survival are well documented, but details of the underlying mechanisms remain poorly understood. Recent evidence demonstrates that perturbations to normal development of the gut microbiota in early life may contribute to growth faltering and susceptibility to related childhood diseases. We assessed associations between diarrhea, gut microbiota configuration, and childhood growth in the Peruvian Amazon. Methods Growth, diarrhea incidence, illness, pathogen infection, and antibiotic exposure were assessed monthly in a birth cohort of 271 children aged 0–24 months. Gut bacterial diversity and abundances of specific bacterial taxa were quantified by sequencing 16S rRNA genes in fecal samples collected at 6, 12, 18, and 24 months. Linear and generalized linear models were used to determine whether diarrhea was associated with altered microbiota and, in turn, if features of the microbiota were associated with the subsequent risk of diarrhea. Results Diarrheal frequency, duration, and severity were negatively associated with bacterial diversity and richness (P < .05). Children born stunted (length-for-age z-score [LAZ] ≤ −2) who were also severely stunted (LAZ ≤ −3) at the time of sampling exhibited the greatest degree of diarrhea-associated reductions in bacterial diversity and the slowest recovery of bacterial diversity after episodes of diarrhea. Increased bacterial diversity was predictive of reduced subsequent diarrhea from age 6 to 18 months. Conclusions Persistent, severe growth faltering may reduce the gut microbiota's resistance and resilience to diarrhea, leading to greater losses of diversity and longer recovery times. This phenotype, in turn, denotes an increased risk of future diarrheal disease and growth faltering.
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Affiliation(s)
- Saba Rouhani
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Nicholas W Griffin
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, Washington.,Center for Gut Microbiome and Nutrition Research, St. Louis, Missouri
| | - Pablo Peñataro Yori
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland.,Asociación Benéfica Preferred Reporting Items for Systematic Reviews and Meta-analyses, Iquitos, Peru
| | - Jeanette L Gehrig
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, Washington.,Center for Gut Microbiome and Nutrition Research, St. Louis, Missouri
| | - Maribel Paredes Olortegui
- Asociación Benéfica Preferred Reporting Items for Systematic Reviews and Meta-analyses, Iquitos, Peru
| | - Mery Siguas Salas
- Asociación Benéfica Preferred Reporting Items for Systematic Reviews and Meta-analyses, Iquitos, Peru
| | - Dixner Rengifo Trigoso
- Asociación Benéfica Preferred Reporting Items for Systematic Reviews and Meta-analyses, Iquitos, Peru
| | | | - Eric R Houpt
- University of Virginia, Charlottesville, Virginia
| | - Michael J Barratt
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, Washington.,Center for Gut Microbiome and Nutrition Research, St. Louis, Missouri
| | - Margaret N Kosek
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland.,University of Virginia, Charlottesville, Virginia
| | - Jeffrey I Gordon
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, Washington.,Center for Gut Microbiome and Nutrition Research, St. Louis, Missouri
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20
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Chen RY, Mostafa I, Hibberd MC, Das S, Mahfuz M, Naila NN, Islam M, Huq S, Alam M, Zaman MU, Raman AS, Webber D, Zhou C, Sundaresan V, Ahsan K, Meier MF, Barratt MJ, Ahmed T, Gordon JI. A Microbiota-Directed Food Intervention for Undernourished Children. N Engl J Med 2021; 384:1517-1528. [PMID: 33826814 PMCID: PMC7993600 DOI: 10.1056/nejmoa2023294] [Citation(s) in RCA: 124] [Impact Index Per Article: 41.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
BACKGROUND More than 30 million children worldwide have moderate acute malnutrition. Current treatments have limited effectiveness, and much remains unknown about the pathogenesis of this condition. Children with moderate acute malnutrition have perturbed development of their gut microbiota. METHODS In this study, we provided a microbiota-directed complementary food prototype (MDCF-2) or a ready-to-use supplementary food (RUSF) to 123 slum-dwelling Bangladeshi children with moderate acute malnutrition between the ages of 12 months and 18 months. The supplementation was given twice daily for 3 months, followed by 1 month of monitoring. We obtained weight-for-length, weight-for-age, and length-for-age z scores and mid-upper-arm circumference values at baseline and every 2 weeks during the intervention period and at 4 months. We compared the rate of change of these related phenotypes between baseline and 3 months and between baseline and 4 months. We also measured levels of 4977 proteins in plasma and 209 bacterial taxa in fecal samples. RESULTS A total of 118 children (59 in each study group) completed the intervention. The rates of change in the weight-for-length and weight-for-age z scores are consistent with a benefit of MDCF-2 on growth over the course of the study, including the 1-month follow-up. Receipt of MDCF-2 was linked to the magnitude of change in levels of 70 plasma proteins and of 21 associated bacterial taxa that were positively correlated with the weight-for-length z score (P<0.001 for comparisons of both protein and bacterial taxa). These proteins included mediators of bone growth and neurodevelopment. CONCLUSIONS These findings provide support for MDCF-2 as a dietary supplement for young children with moderate acute malnutrition and provide insight into mechanisms by which this targeted manipulation of microbiota components may be linked to growth. (Supported by the Bill and Melinda Gates Foundation and the National Institutes of Health; ClinicalTrials.gov number, NCT04015999.).
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Affiliation(s)
- Robert Y. Chen
- Edison Family Center for Genome Sciences and Systems Biology, Washington
University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington University
School of Medicine, St. Louis, MO 63110 USA
| | - Ishita Mostafa
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b),
Dhaka 1212, Bangladesh
| | - Matthew C. Hibberd
- Edison Family Center for Genome Sciences and Systems Biology, Washington
University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington University
School of Medicine, St. Louis, MO 63110 USA
- Department of Pathology and Immunology, Washington University in St. Louis
School of Medicine, St Louis, MO 63110 USA
| | - Subhasish Das
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b),
Dhaka 1212, Bangladesh
| | - Mustafa Mahfuz
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b),
Dhaka 1212, Bangladesh
| | - Nurun N. Naila
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b),
Dhaka 1212, Bangladesh
| | - Md.Munirul Islam
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b),
Dhaka 1212, Bangladesh
| | - Sayeeda Huq
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b),
Dhaka 1212, Bangladesh
| | - Md.Ashraful Alam
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b),
Dhaka 1212, Bangladesh
| | - Mahabub Uz Zaman
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b),
Dhaka 1212, Bangladesh
| | - Arjun S. Raman
- Edison Family Center for Genome Sciences and Systems Biology, Washington
University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington University
School of Medicine, St. Louis, MO 63110 USA
- Department of Pathology and Immunology, Washington University in St. Louis
School of Medicine, St Louis, MO 63110 USA
| | - Daniel Webber
- Edison Family Center for Genome Sciences and Systems Biology, Washington
University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington University
School of Medicine, St. Louis, MO 63110 USA
- Department of Pathology and Immunology, Washington University in St. Louis
School of Medicine, St Louis, MO 63110 USA
| | - Cyrus Zhou
- Edison Family Center for Genome Sciences and Systems Biology, Washington
University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington University
School of Medicine, St. Louis, MO 63110 USA
| | - Vinaik Sundaresan
- Edison Family Center for Genome Sciences and Systems Biology, Washington
University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington University
School of Medicine, St. Louis, MO 63110 USA
| | - Kazi Ahsan
- Edison Family Center for Genome Sciences and Systems Biology, Washington
University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington University
School of Medicine, St. Louis, MO 63110 USA
| | - Martin F. Meier
- Edison Family Center for Genome Sciences and Systems Biology, Washington
University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington University
School of Medicine, St. Louis, MO 63110 USA
| | - Michael J. Barratt
- Edison Family Center for Genome Sciences and Systems Biology, Washington
University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington University
School of Medicine, St. Louis, MO 63110 USA
- Department of Pathology and Immunology, Washington University in St. Louis
School of Medicine, St Louis, MO 63110 USA
| | - Tahmeed Ahmed
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b),
Dhaka 1212, Bangladesh
| | - Jeffrey I. Gordon
- Edison Family Center for Genome Sciences and Systems Biology, Washington
University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington University
School of Medicine, St. Louis, MO 63110 USA
- Department of Pathology and Immunology, Washington University in St. Louis
School of Medicine, St Louis, MO 63110 USA
- Address correspondence to:
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21
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Patnode ML, Guruge JL, Castillo JJ, Couture GA, Lombard V, Terrapon N, Henrissat B, Lebrilla CB, Gordon JI. Strain-level functional variation in the human gut microbiota based on bacterial binding to artificial food particles. Cell Host Microbe 2021; 29:664-673.e5. [PMID: 33571448 DOI: 10.1016/j.chom.2021.01.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 12/07/2020] [Accepted: 01/18/2021] [Indexed: 01/26/2023]
Abstract
Greater understanding of the spatial relationships between members of the human gut microbiota and available nutrients is needed to gain deeper insights about community dynamics and expressed functions. Therefore, we generated a panel of artificial food particles with each type composed of microscopic paramagnetic beads coated with a fluorescent barcode and one of 60 different dietary or host glycan preparations. Analysis of 160 Bacteroides and Parabacteroides strains disclosed diverse strain-specific and glycan-specific binding phenotypes. We identified carbohydrate structures that correlated with binding by specific bacterial strains in vitro and noted strain-specific differences in the catabolism of glycans that mediate adhesion. Mixed in vitro cultures revealed that these adhesion phenotypes are maintained in more complex communities. Additionally, orally administering glycan beads to gnotobiotic mice confirmed specificity in glycan binding. This approach should facilitate analyses of how strains occupying the same physical niche interact, and it should advance the development of synbiotics, more nutritious foods, and microbiota-based diagnostics.
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Affiliation(s)
- Michael L Patnode
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA; Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Janaki L Guruge
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA; Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Juan J Castillo
- Department of Chemistry, University of California, Davis, CA 95616, USA
| | - Garret A Couture
- Department of Chemistry, University of California, Davis, CA 95616, USA
| | - Vincent Lombard
- Architecture et Fonction des Macromolécules Biologiques, UMR7257 Centre National de la Recherche Scientifique and Aix-Marseille Université, USC1408 Institut National de la Recherche Agronomique, 13288 Marseille cedex 9, France
| | - Nicolas Terrapon
- Architecture et Fonction des Macromolécules Biologiques, UMR7257 Centre National de la Recherche Scientifique and Aix-Marseille Université, USC1408 Institut National de la Recherche Agronomique, 13288 Marseille cedex 9, France
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, UMR7257 Centre National de la Recherche Scientifique and Aix-Marseille Université, USC1408 Institut National de la Recherche Agronomique, 13288 Marseille cedex 9, France; Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | | | - Jeffrey I Gordon
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA; Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110, USA.
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22
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Wesener DA, Beller ZW, Peters SL, Rajabi A, Dimartino G, Giannone RJ, Hettich RL, Gordon JI. Microbiota functional activity biosensors for characterizing nutrient metabolism in vivo. eLife 2021; 10:e64478. [PMID: 33684031 PMCID: PMC7939548 DOI: 10.7554/elife.64478] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 02/01/2021] [Indexed: 12/12/2022] Open
Abstract
Methods for measuring gut microbiota biochemical activities in vivo are needed to characterize its functional states in health and disease. To illustrate one approach, an arabinan-containing polysaccharide was isolated from pea fiber, its structure defined, and forward genetic and proteomic analyses used to compare its effects, versus unfractionated pea fiber and sugar beet arabinan, on a human gut bacterial strain consortium in gnotobiotic mice. We produced 'Microbiota Functional Activity Biosensors' (MFABs) consisting of glycans covalently linked to the surface of fluorescent paramagnetic microscopic glass beads. Three MFABs, each containing a unique glycan/fluorophore combination, were simultaneously orally gavaged into gnotobiotic mice, recovered from their intestines, and analyzed to directly quantify bacterial metabolism of structurally distinct arabinans in different human diet contexts. Colocalizing pea-fiber arabinan and another polysaccharide (glucomannan) on the bead surface enhanced in vivo degradation of glucomannan. MFABs represent a potentially versatile platform for developing new prebiotics and more nutritious foods.
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Affiliation(s)
- Darryl A Wesener
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of MedicineSt. LouisUnited States
- Center for Gut Microbiome and Nutrition Research, Washington University School of MedicineSt. LouisUnited States
| | - Zachary W Beller
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of MedicineSt. LouisUnited States
- Center for Gut Microbiome and Nutrition Research, Washington University School of MedicineSt. LouisUnited States
| | - Samantha L Peters
- Chemical Sciences Division, Oak Ridge National LaboratoryOak RidgeUnited States
| | - Amir Rajabi
- Mondelez InternationalDeerfieldUnited States
| | | | - Richard J Giannone
- Chemical Sciences Division, Oak Ridge National LaboratoryOak RidgeUnited States
| | - Robert L Hettich
- Chemical Sciences Division, Oak Ridge National LaboratoryOak RidgeUnited States
| | - Jeffrey I Gordon
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of MedicineSt. LouisUnited States
- Center for Gut Microbiome and Nutrition Research, Washington University School of MedicineSt. LouisUnited States
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23
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Rouhani S, Griffin NW, Yori PP, Olortegui MP, Siguas Salas M, Rengifo Trigoso D, Moulton LH, Houpt ER, Barratt MJ, Kosek MN, Gordon JI. Gut Microbiota Features Associated With Campylobacter Burden and Postnatal Linear Growth Deficits in a Peruvian Birth Cohort. Clin Infect Dis 2020; 71:1000-1007. [PMID: 31773126 PMCID: PMC7428392 DOI: 10.1093/cid/ciz906] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2019] [Accepted: 09/13/2019] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Campylobacter infection is associated with impaired growth of children, even in the absence of symptoms. To examine the underlying mechanisms, we evaluated associations between Campylobacter infection, linear growth, and fecal microbial community features in a prospective birth cohort of 271 children with a high burden of diarrhea and stunting in the Amazonian lowlands of Peru. METHODS Campylobacter was identified using a broadly reactive, genus-specific enzyme-linked immunosorbent assay. 16S rRNA-based analyses were used to identify bacterial taxa in fecal samples at ages 6, 12, 18, and 24 months (N = 928). Associations between infection, growth, and gut microbial community composition were investigated using multiple linear regression adjusting for within-child correlations, age, and breastfeeding. Indicator species analyses identified taxa specifically associated with Campylobacter burden. RESULTS Ninety-three percent (251) of children had Campylobacter present in asymptomatic fecal samples during the follow-up period. A 10% increase in the proportion of stools infected was associated with mean reductions of 0.02 length-for-age z scores (LAZ) at 3, 6, and 9 months thereafter (P < .01). We identified 13 bacterial taxa indicative of cumulative Campylobacter burden and 14 taxa significantly associated with high or low burden of enteroaggregative Escherichia coli, norovirus, or Giardia. CONCLUSIONS Campylobacter infection is common in this cohort and associated with changes in microbial community composition. These results support the notion that disruptions to the fecal microbiota may help explain the observed effects of asymptomatic infections on growth in early life.
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Affiliation(s)
- Saba Rouhani
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Nicholas W Griffin
- Edison Family Center for Genome Sciences and Systems Biology, St. Louis, Missouri, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Pablo Peñataro Yori
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
- Asociación Benéfica Proyectos en Informática Medicina y Salud, Iquitos, Peru
| | | | - Mery Siguas Salas
- Asociación Benéfica Proyectos en Informática Medicina y Salud, Iquitos, Peru
| | | | - Lawrence H Moulton
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Eric R Houpt
- University of Virginia, Charlottesville, Virginia, USA
| | - Michael J Barratt
- Edison Family Center for Genome Sciences and Systems Biology, St. Louis, Missouri, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Margaret N Kosek
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
- University of Virginia, Charlottesville, Virginia, USA
| | - Jeffrey I Gordon
- Edison Family Center for Genome Sciences and Systems Biology, St. Louis, Missouri, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, Missouri, USA
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24
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Chen RY, Kung VL, Das S, Hossain MS, Hibberd MC, Guruge J, Mahfuz M, Begum SMKN, Rahman MM, Fahim SM, Gazi MA, Haque MR, Sarker SA, Mazumder RN, Luccia BD, Ahsan K, Kennedy E, Santiago-Borges J, Rodionov DA, Leyn SA, Osterman AL, Barratt MJ, Ahmed T, Gordon JI. Duodenal Microbiota in Stunted Undernourished Children with Enteropathy. N Engl J Med 2020; 383:321-333. [PMID: 32706533 PMCID: PMC7289524 DOI: 10.1056/nejmoa1916004] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
BACKGROUND Environmental enteric dysfunction (EED) is an enigmatic disorder of the small intestine that is postulated to play a role in childhood undernutrition, a pressing global health problem. Defining the incidence of this disorder, its pathophysiological features, and its contribution to impaired linear and ponderal growth has been hampered by the difficulty in directly sampling the small intestinal mucosa and microbial community (microbiota). METHODS In this study, among 110 young children (mean age, 18 months) with linear growth stunting who were living in an urban slum in Dhaka, Bangladesh, and had not benefited from a nutritional intervention, we performed endoscopy in 80 children who had biopsy-confirmed EED and available plasma and duodenal samples. We quantified the levels of 4077 plasma proteins and 2619 proteins in duodenal biopsy samples obtained from these children. The levels of bacterial strains in microbiota recovered from duodenal aspirate from each child were determined with the use of culture-independent methods. In addition, we obtained 21 plasma samples and 27 fecal samples from age-matched healthy children living in the same area. Young germ-free mice that had been fed a Bangladeshi diet were colonized with bacterial strains cultured from the duodenal aspirates. RESULTS Of the bacterial strains that were obtained from the children, the absolute levels of a shared group of 14 taxa (which are not typically classified as enteropathogens) were negatively correlated with linear growth (length-for-age z score, r = -0.49; P = 0.003) and positively correlated with duodenal proteins involved in immunoinflammatory responses. The representation of these 14 duodenal taxa in fecal microbiota was significantly different from that in samples obtained from healthy children (P<0.001 by permutational multivariate analysis of variance). Enteropathy of the small intestine developed in gnotobiotic mice that had been colonized with cultured duodenal strains obtained from children with EED. CONCLUSIONS These results provide support for a causal relationship between growth stunting and components of the small intestinal microbiota and enteropathy and offer a rationale for developing therapies that target these microbial contributions to EED. (Funded by the Bill and Melinda Gates Foundation and others; ClinicalTrials.gov number, NCT02812615.).
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Affiliation(s)
- Robert Y. Chen
- Edison Family Center for Genome Sciences and Systems
Biology, Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research,
Washington University School of Medicine, St. Louis, MO 63110 USA
| | - Vanderlene L. Kung
- Edison Family Center for Genome Sciences and Systems
Biology, Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research,
Washington University School of Medicine, St. Louis, MO 63110 USA
- Department of Pathology and Immunology, Washington
University School of Medicine, St. Louis, MO 63110 USA
| | - Subhasish Das
- International Centre for Diarrhoeal Disease Research,
Bangladesh (icddr,b), Dhaka 1212, Bangladesh
| | - Md. Shabab Hossain
- International Centre for Diarrhoeal Disease Research,
Bangladesh (icddr,b), Dhaka 1212, Bangladesh
| | - Matthew C. Hibberd
- Edison Family Center for Genome Sciences and Systems
Biology, Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research,
Washington University School of Medicine, St. Louis, MO 63110 USA
- Department of Pathology and Immunology, Washington
University School of Medicine, St. Louis, MO 63110 USA
| | - Janaki Guruge
- Edison Family Center for Genome Sciences and Systems
Biology, Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research,
Washington University School of Medicine, St. Louis, MO 63110 USA
| | - Mustafa Mahfuz
- International Centre for Diarrhoeal Disease Research,
Bangladesh (icddr,b), Dhaka 1212, Bangladesh
| | | | - M. Masudur Rahman
- Sheikh Russel National Gastroliver Institute and Hospital,
Dhaka 1210, Bangladesh
| | - Shah Mohammad Fahim
- International Centre for Diarrhoeal Disease Research,
Bangladesh (icddr,b), Dhaka 1212, Bangladesh
| | - Md. Amran Gazi
- International Centre for Diarrhoeal Disease Research,
Bangladesh (icddr,b), Dhaka 1212, Bangladesh
| | - M. Rashidul Haque
- International Centre for Diarrhoeal Disease Research,
Bangladesh (icddr,b), Dhaka 1212, Bangladesh
| | - Shafiqul Alam Sarker
- International Centre for Diarrhoeal Disease Research,
Bangladesh (icddr,b), Dhaka 1212, Bangladesh
| | - R. N. Mazumder
- International Centre for Diarrhoeal Disease Research,
Bangladesh (icddr,b), Dhaka 1212, Bangladesh
| | - Blanda Di Luccia
- Edison Family Center for Genome Sciences and Systems
Biology, Washington University School of Medicine, St. Louis, MO 63110 USA
- Department of Pathology and Immunology, Washington
University School of Medicine, St. Louis, MO 63110 USA
| | - Kazi Ahsan
- Edison Family Center for Genome Sciences and Systems
Biology, Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research,
Washington University School of Medicine, St. Louis, MO 63110 USA
| | - Elizabeth Kennedy
- Edison Family Center for Genome Sciences and Systems
Biology, Washington University School of Medicine, St. Louis, MO 63110 USA
| | - Jesus Santiago-Borges
- Edison Family Center for Genome Sciences and Systems
Biology, Washington University School of Medicine, St. Louis, MO 63110 USA
| | - Dmitry A. Rodionov
- A. A. Kharkevich Institute for Information Transmission
Problems, Russian Academy of Sciences, Moscow 127994, Russia
- Infectious and Inflammatory Disease Center, Sanford
Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037 US
| | - Semen A. Leyn
- A. A. Kharkevich Institute for Information Transmission
Problems, Russian Academy of Sciences, Moscow 127994, Russia
- Infectious and Inflammatory Disease Center, Sanford
Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037 US
| | - Andrei L. Osterman
- Infectious and Inflammatory Disease Center, Sanford
Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037 US
| | - Michael J. Barratt
- Edison Family Center for Genome Sciences and Systems
Biology, Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research,
Washington University School of Medicine, St. Louis, MO 63110 USA
- Department of Pathology and Immunology, Washington
University School of Medicine, St. Louis, MO 63110 USA
| | - Tahmeed Ahmed
- International Centre for Diarrhoeal Disease Research,
Bangladesh (icddr,b), Dhaka 1212, Bangladesh
| | - Jeffrey I. Gordon
- Edison Family Center for Genome Sciences and Systems
Biology, Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research,
Washington University School of Medicine, St. Louis, MO 63110 USA
- Department of Pathology and Immunology, Washington
University School of Medicine, St. Louis, MO 63110 USA
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25
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Di Luccia B, Ahern PP, Griffin NW, Cheng J, Guruge JL, Byrne AE, Rodionov DA, Leyn SA, Osterman AL, Ahmed T, Colonna M, Barratt MJ, Delahaye NF, Gordon JI. Combined Prebiotic and Microbial Intervention Improves Oral Cholera Vaccination Responses in a Mouse Model of Childhood Undernutrition. Cell Host Microbe 2020; 27:899-908.e5. [PMID: 32348782 DOI: 10.1016/j.chom.2020.04.008] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 03/18/2020] [Accepted: 04/08/2020] [Indexed: 12/11/2022]
Abstract
Undernourished children in low-income countries often exhibit poor responses to oral vaccination. Perturbed microbiota development is linked to undernutrition, but whether and how microbiota changes affect vaccine responsiveness remains unclear. Here, we show that gnotobiotic mice colonized with microbiota from undernourished Bangladeshi children and fed a Bangladeshi diet exhibited microbiota-dependent differences in mucosal IgA responses to oral vaccination with cholera toxin (CT). Supplementation with a nutraceutical consisting of spirulina, amaranth, flaxseed, and micronutrients augmented CT-IgA production. Mice initially colonized with a microbiota associated with poor CT responses exhibited improved immunogenicity upon invasion of bacterial taxa from cagemates colonized with a more "responsive" microbiota. Additionally, a consortium of five cultured bacterial invaders conferred augmented CT-IgA responses in mice fed the supplemented diet and colonized with the "hypo-responsive" community. These results provide preclinical proof-of-concept that diet and microbiota influence mucosal immune responses to CT vaccination and identify a candidate synbiotic formulation.
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Affiliation(s)
- Blanda Di Luccia
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA; Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Philip P Ahern
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA; Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Nicholas W Griffin
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA; Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Jiye Cheng
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA; Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Janaki L Guruge
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA; Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Alexandra E Byrne
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA; Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Dmitry A Rodionov
- A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow 127994, Russia; Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Semen A Leyn
- A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow 127994, Russia; Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Andrei L Osterman
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Tahmeed Ahmed
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh
| | - Marco Colonna
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Michael J Barratt
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA; Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110, USA
| | | | - Jeffrey I Gordon
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA; Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110, USA.
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26
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Raman AS, Gehrig JL, Venkatesh S, Chang HW, Hibberd MC, Subramanian S, Kang G, Bessong PO, Lima AAM, Kosek MN, Petri WA, Rodionov DA, Arzamasov AA, Leyn SA, Osterman AL, Huq S, Mostafa I, Islam M, Mahfuz M, Haque R, Ahmed T, Barratt MJ, Gordon JI. A sparse covarying unit that describes healthy and impaired human gut microbiota development. Science 2020; 365:365/6449/eaau4735. [PMID: 31296739 PMCID: PMC6683326 DOI: 10.1126/science.aau4735] [Citation(s) in RCA: 111] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 04/24/2019] [Accepted: 06/07/2019] [Indexed: 12/30/2022]
Abstract
Characterizing the organization of the human gut microbiota is a formidable challenge given the number of possible interactions between its components. Using a statistical approach initially applied to financial markets, we measured temporally conserved covariance among bacterial taxa in the microbiota of healthy members of a Bangladeshi birth cohort sampled from 1 to 60 months of age. The results revealed an “ecogroup” of 15 covarying bacterial taxa that provide a concise description of microbiota development in healthy children from this and other low-income countries, and a means for monitoring community repair in undernourished children treated with therapeutic foods. Features of ecogroup population dynamics were recapitulated in gnotobiotic piglets as they transitioned from exclusive milk feeding to a fully weaned state consuming a representative Bangladeshi diet.
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Affiliation(s)
- Arjun S Raman
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA.,Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Jeanette L Gehrig
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA.,Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Siddarth Venkatesh
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA.,Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Hao-Wei Chang
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA.,Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Matthew C Hibberd
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA.,Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Sathish Subramanian
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA.,Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Gagandeep Kang
- Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | - Pascal O Bessong
- HIV/AIDS and Global Health Research Programme, Department of Microbiology, University of Venda, Thohoyandou 0950, South Africa
| | - Aldo A M Lima
- Center for Global Health, Department of Physiology and Pharmacology, Clinical Research Unit and Institute of Biomedicine, School of Medicine, Federal University of Ceará, Fortaleza, CE 60430270, Brazil
| | - Margaret N Kosek
- Department of International Health, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA.,AB PRISMA, Ramirez Hurtado 622, Iquitos, Peru
| | - William A Petri
- Departments of Medicine, Microbiology, and Pathology, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Dmitry A Rodionov
- A. A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow 127994, Russia.,Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Aleksandr A Arzamasov
- A. A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow 127994, Russia.,Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Semen A Leyn
- A. A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow 127994, Russia.,Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Andrei L Osterman
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Sayeeda Huq
- International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka 1212, Bangladesh
| | - Ishita Mostafa
- International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka 1212, Bangladesh
| | - Munirul Islam
- International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka 1212, Bangladesh
| | - Mustafa Mahfuz
- International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka 1212, Bangladesh
| | - Rashidul Haque
- International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka 1212, Bangladesh
| | - Tahmeed Ahmed
- International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka 1212, Bangladesh
| | - Michael J Barratt
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA.,Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Jeffrey I Gordon
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA. .,Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110, USA
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27
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Affiliation(s)
- Lars Bode
- Department of Pediatrics and Larsson-Rosenquist Foundation, Mother-Milk-Infant Center of Research Excellence, University of California, San Diego, La Jolla, CA, USA.
| | - Arjun S Raman
- The Edison Family Center for Genome Sciences and Systems Biology, and the Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO, USA
| | - Simon H Murch
- Warwick Medical School, University of Warwick, Coventry, UK
| | - Nigel C Rollins
- Departments of Maternal, Newborn, Child, and Adolescent Health and Ageing, World Health Organization, Geneva, Switzerland
| | - Jeffrey I Gordon
- The Edison Family Center for Genome Sciences and Systems Biology, and the Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO, USA.
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28
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Mostafa I, Nahar NN, Islam MM, Huq S, Mustafa M, Barratt M, Gordon JI, Ahmed T. Proof-of-concept study of the efficacy of a microbiota-directed complementary food formulation (MDCF) for treating moderate acute malnutrition. BMC Public Health 2020; 20:242. [PMID: 32066412 PMCID: PMC7027293 DOI: 10.1186/s12889-020-8330-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 02/06/2020] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Childhood undernutrition remains a significant global health challenge accounting for over half of all under 5 child mortality. Moderate acute malnutrition (MAM), which leads to wasting [weight-for-length z-scores (WLZ) between - 2 and - 3], affects 33 million children under 5 globally and more than 2 million in Bangladesh alone. We have previously reported that acute malnutrition in this population is associated with gut microbiota immaturity, and in a small, 1-month pre-proof-of-concept (POC) study demonstrated that a microbiota-directed complementary food formulation (MDCF-2) was able to repair this immaturity, promote weight gain and increase plasma biomarkers and mediators of healthy growth. Here we describe the design controlled feeding study that tests whether MDCF-2 exhibits superior efficacy (ponderal growth, host biomarkers of a biological state) than a conventional Ready-to-use Supplementary Food (RUSF) in children with MAM over intervention period of 3 months. METHODS Two separate cohorts of 12-18-month-old children will be enrolled: 124 with primary MAM, and 124 with MAM after having been treated for severe acute malnutrition (post-SAM MAM). We have established several field sites in an urban slum located in the Mirpur district of Dhaka, Bangladesh and at a rural site, Kurigram in the north of Bangladesh. The two groups of children receiving MDCF-2 and RUSF will be compared at baseline (pre-intervention), after 1 month, at the end of intervention (3 months), 1 month after cessation of intervention, and every 6 months thereafter for 4 years. DISCUSSION This study will determine whether daily, controlled administration of MDCF-2 for 3 months provides superior improvements in weight gain, microbiota repair, and elevated levels of key plasma biomarkers/mediators of healthy growth compared to the control RUSF formulation. The pathogenesis of MAM is poorly defined and there are currently no WHO-approved treatments; results from the current study of children with primary MAM and post-SAM MAM will shed light on the effects of the gut microbiota on childhood growth/development and will provide a knowledge base that may help improve complementary feeding practices. TRIAL REGISTRATION The primary MAM and post-SAM MAM trials are registered in Clintrials.gov (NCT04015999 and NCT04015986, registered on July 11, 2019, retrospectively registered).
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Affiliation(s)
- Ishita Mostafa
- Nutrition and Clinical Services Division (NCSD), International Centre for Diarrhoeal Disease Research, Bangladesh (icddr, b), 68, Shaheed Tajuddin Ahmed Sarani Mohakhali, Dhaka, 1212, Bangladesh.
| | - Naila Nurun Nahar
- Nutrition and Clinical Services Division (NCSD), International Centre for Diarrhoeal Disease Research, Bangladesh (icddr, b), 68, Shaheed Tajuddin Ahmed Sarani Mohakhali, Dhaka, 1212, Bangladesh
| | - Md Munirul Islam
- Nutrition and Clinical Services Division (NCSD), International Centre for Diarrhoeal Disease Research, Bangladesh (icddr, b), 68, Shaheed Tajuddin Ahmed Sarani Mohakhali, Dhaka, 1212, Bangladesh
| | - Sayeeda Huq
- Nutrition and Clinical Services Division (NCSD), International Centre for Diarrhoeal Disease Research, Bangladesh (icddr, b), 68, Shaheed Tajuddin Ahmed Sarani Mohakhali, Dhaka, 1212, Bangladesh
| | - Mahfuz Mustafa
- Nutrition and Clinical Services Division (NCSD), International Centre for Diarrhoeal Disease Research, Bangladesh (icddr, b), 68, Shaheed Tajuddin Ahmed Sarani Mohakhali, Dhaka, 1212, Bangladesh
| | - Michael Barratt
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO, USA
| | - Jeffrey I Gordon
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO, USA
| | - Tahmeed Ahmed
- Nutrition and Clinical Services Division (NCSD), International Centre for Diarrhoeal Disease Research, Bangladesh (icddr, b), 68, Shaheed Tajuddin Ahmed Sarani Mohakhali, Dhaka, 1212, Bangladesh
- James P. Grant School of Public Health, BRAC University, Mohakhali, Dhaka, 1212, Bangladesh
- Department of Global Health, University of Washington, Seattle, WA, USA
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29
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Feng L, Raman AS, Hibberd MC, Cheng J, Griffin NW, Peng Y, Leyn SA, Rodionov DA, Osterman AL, Gordon JI. Identifying determinants of bacterial fitness in a model of human gut microbial succession. Proc Natl Acad Sci U S A 2020; 117:2622-2633. [PMID: 31969452 PMCID: PMC7007522 DOI: 10.1073/pnas.1918951117] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Human gut microbiota development has been associated with healthy growth but understanding the determinants of community assembly and composition is a formidable challenge. We cultured bacteria from serially collected fecal samples from a healthy infant; 34 sequenced strains containing 103,102 genes were divided into two consortia representing earlier and later stages in community assembly during the first six postnatal months. The two consortia were introduced alone (singly), or sequentially in different order, or simultaneously into young germ-free mice fed human infant formula. The pattern of fitness of bacterial strains observed across the different colonization conditions indicated that later-phase strains substantially outcompete earlier-phase strains, although four early-phase members persist. Persistence was not determined by order of introduction, suggesting that priority effects are not prominent in this model. To characterize succession in the context of the metabolic potential of consortium members, we performed in silico reconstructions of metabolic pathways involved in carbohydrate utilization and amino acid and B-vitamin biosynthesis, then quantified the fitness (abundance) of strains in serially collected fecal samples and their transcriptional responses to different histories of colonization. Applying feature-reduction methods disclosed a set of metabolic pathways whose presence and/or expression correlates with strain fitness and that enable early-stage colonizers to survive during introduction of later colonizers. The approach described can be used to test the magnitude of the contribution of identified metabolic pathways to fitness in different community contexts, study various ecological processes thought to govern community assembly, and facilitate development of microbiota-directed therapeutics.
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Affiliation(s)
- Lihui Feng
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110
| | - Arjun S Raman
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110
| | - Matthew C Hibberd
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110;
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110
| | - Jiye Cheng
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110
| | - Nicholas W Griffin
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110
| | - Yangqing Peng
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110
| | - Semen A Leyn
- A. A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, 127994 Moscow, Russia
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037
| | - Dmitry A Rodionov
- A. A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, 127994 Moscow, Russia
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037
| | - Andrei L Osterman
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037
| | - Jeffrey I Gordon
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110;
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110
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30
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Halatchev IG, O’Donnell D, Hibberd MC, Gordon JI. Applying indirect open-circuit calorimetry to study energy expenditure in gnotobiotic mice harboring different human gut microbial communities. Microbiome 2019; 7:158. [PMID: 31831058 PMCID: PMC6909537 DOI: 10.1186/s40168-019-0769-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 11/11/2019] [Indexed: 06/10/2023]
Abstract
Given the increasing use of gnotobiotic mouse models for deciphering the effects of human microbial communities on host biology, there is a need to develop new methods for characterizing these animals while maintaining their isolation from environmental microbes. We describe a method for performing open-circuit indirect calorimetry on gnotobiotic mice colonized with gut microbial consortia obtained from different human donors. In this illustrative case, cultured collections of gut bacterial strains were obtained from obese and lean co-twins. The approach allows microbial contributions to host energy homeostasis to be characterized.
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Affiliation(s)
- Ilia G. Halatchev
- The Edison Family Center for Genome Sciences and Systems Biology, St. Louis, USA
- Center for Gut Microbiome and Nutrition Research, St. Louis, USA
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110 USA
| | - David O’Donnell
- The Edison Family Center for Genome Sciences and Systems Biology, St. Louis, USA
- Center for Gut Microbiome and Nutrition Research, St. Louis, USA
| | - Matthew C. Hibberd
- The Edison Family Center for Genome Sciences and Systems Biology, St. Louis, USA
- Center for Gut Microbiome and Nutrition Research, St. Louis, USA
| | - Jeffrey I. Gordon
- The Edison Family Center for Genome Sciences and Systems Biology, St. Louis, USA
- Center for Gut Microbiome and Nutrition Research, St. Louis, USA
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31
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Wang Y, Chiang IL, Ohara TE, Fujii S, Cheng J, Muegge BD, Ver Heul A, Han ND, Lu Q, Xiong S, Chen F, Lai CW, Janova H, Wu R, Whitehurst CE, VanDussen KL, Liu TC, Gordon JI, Sibley LD, Stappenbeck TS. Long-Term Culture Captures Injury-Repair Cycles of Colonic Stem Cells. Cell 2019; 179:1144-1159.e15. [PMID: 31708126 PMCID: PMC6904908 DOI: 10.1016/j.cell.2019.10.015] [Citation(s) in RCA: 114] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 07/15/2019] [Accepted: 10/16/2019] [Indexed: 02/07/2023]
Abstract
The colonic epithelium can undergo multiple rounds of damage and repair, often in response to excessive inflammation. The responsive stem cell that mediates this process is unclear, in part because of a lack of in vitro models that recapitulate key epithelial changes that occur in vivo during damage and repair. Here, we identify a Hopx+ colitis-associated regenerative stem cell (CARSC) population that functionally contributes to mucosal repair in mouse models of colitis. Hopx+ CARSCs, enriched for fetal-like markers, transiently arose from hypertrophic crypts known to facilitate regeneration. Importantly, we established a long-term, self-organizing two-dimensional (2D) epithelial monolayer system to model the regenerative properties and responses of Hopx+ CARSCs. This system can reenact the "homeostasis-injury-regeneration" cycles of epithelial alterations that occur in vivo. Using this system, we found that hypoxia and endoplasmic reticulum stress, insults commonly present in inflammatory bowel diseases, mediated the cyclic switch of cellular status in this process.
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Affiliation(s)
- Yi Wang
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - I-Ling Chiang
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Takahiro E Ohara
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Satoru Fujii
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Jiye Cheng
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA; The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Brian D Muegge
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Aaron Ver Heul
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Nathan D Han
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA; The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Qiuhe Lu
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Shanshan Xiong
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Feidi Chen
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Chin-Wen Lai
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Hana Janova
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Renee Wu
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Charles E Whitehurst
- Boehringer Ingelheim Pharmaceuticals, Immunology and Respiratory Disease Research, Ridgefield, CT 06877, USA
| | - Kelli L VanDussen
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Ta-Chiang Liu
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Jeffrey I Gordon
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA; The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - L David Sibley
- Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Thaddeus S Stappenbeck
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA.
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32
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Thackray LB, Handley SA, Gorman MJ, Poddar S, Bagadia P, Briseño CG, Theisen DJ, Tan Q, Hykes BL, Lin H, Lucas TM, Desai C, Gordon JI, Murphy KM, Virgin HW, Diamond MS. Oral Antibiotic Treatment of Mice Exacerbates the Disease Severity of Multiple Flavivirus Infections. Cell Rep 2019; 22:3440-3453.e6. [PMID: 29590614 PMCID: PMC5908250 DOI: 10.1016/j.celrep.2018.03.001] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Revised: 02/15/2018] [Accepted: 02/28/2018] [Indexed: 12/22/2022] Open
Abstract
Although the outcome of flavivirus infection can vary from asymptomatic to lethal, environmental factors modulating disease severity are poorly defined. Here, we observed increased susceptibility of mice to severe West Nile (WNV), Dengue, and Zika virus infections after treatment with oral antibiotics (Abx) that depleted the gut microbiota. Abx treatment impaired the development of optimal T cell responses, with decreased levels of WNV-specific CD8+ T cells associated with increased infection and immunopathology. Abx treatments that resulted in enhanced WNV susceptibility generated changes in the overall structure of the gut bacterial community and in the abundance of specific bacterial taxa. As little as 3 days of treatment with ampicillin was sufficient to alter host immunity and WNV outcome. Our results identify oral Abx therapy as a potential environmental determinant of systemic viral disease, and they raise the possibility that perturbation of the gut microbiota may have deleterious consequences for subsequent flavivirus infections.
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Affiliation(s)
- Larissa B Thackray
- Department of Medicine, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Scott A Handley
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Matthew J Gorman
- Department of Medicine, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Subhajit Poddar
- Department of Medicine, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Prachi Bagadia
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Carlos G Briseño
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Derek J Theisen
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Qing Tan
- Department of Medicine, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Barry L Hykes
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Hueylie Lin
- Department of Medicine, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Tiffany M Lucas
- Department of Medicine, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Chandni Desai
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Jeffrey I Gordon
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, Saint Louis, MO 63110, USA; Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Kenneth M Murphy
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA; Howard Hughes Medical Institute, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Herbert W Virgin
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA; Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Michael S Diamond
- Department of Medicine, Washington University School of Medicine, Saint Louis, MO 63110, USA; Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA; Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, MO 63110, USA; The Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, Saint Louis, MO 63110, USA.
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33
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Wolf AR, Wesener DA, Cheng J, Houston-Ludlam AN, Beller ZW, Hibberd MC, Giannone RJ, Peters SL, Hettich RL, Leyn SA, Rodionov DA, Osterman AL, Gordon JI. Bioremediation of a Common Product of Food Processing by a Human Gut Bacterium. Cell Host Microbe 2019; 26:463-477.e8. [PMID: 31585844 DOI: 10.1016/j.chom.2019.09.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 08/23/2019] [Accepted: 09/06/2019] [Indexed: 02/07/2023]
Abstract
Dramatic increases in processed food consumption represent a global health threat. Maillard reaction products (MRPs), which are common in processed foods, form upon heat-induced reaction of amino acids with reducing sugars and include advanced glycation end products with deleterious health effects. To examine how processed foods affect the microbiota, we fed gnotobiotic mice, colonized with 54 phylogenetically diverse human gut bacterial strains, defined sugar-rich diets containing whey as the protein source or a matched amino acid mixture. Whey or ϵ-fructoselysine, an MRP in whey and many processed foods, selectively increases Collinsella intestinalis absolute abundance and induces Collinsella expression of genomic loci directing import and metabolism of ϵ-fructoselysine to innocuous products. This locus is repressed by glucose in C. aerofaciens, whose abundance decreases with whey, but is not repressed in C. intestinalis. Identifying gut organisms responding to and degrading potentially harmful processed food components has implications for food science, microbiome science, and public health.
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Affiliation(s)
- Ashley R Wolf
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, Saint Louis, MO 63110, USA; Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Darryl A Wesener
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, Saint Louis, MO 63110, USA; Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Jiye Cheng
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, Saint Louis, MO 63110, USA; Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Alexandra N Houston-Ludlam
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Zachary W Beller
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, Saint Louis, MO 63110, USA; Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Matthew C Hibberd
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, Saint Louis, MO 63110, USA; Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Richard J Giannone
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Samantha L Peters
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Robert L Hettich
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Semen A Leyn
- A. A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, 127994, Russia; Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Dmitry A Rodionov
- A. A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, 127994, Russia; Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Andrei L Osterman
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Jeffrey I Gordon
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, Saint Louis, MO 63110, USA; Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, Saint Louis, MO 63110, USA.
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34
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Iqbal NT, Syed S, Sadiq K, Khan MN, Iqbal J, Ma JZ, Umrani F, Ahmed S, Maier EA, Denson LA, Haberman Y, McNeal MM, Setchell KDR, Zhao X, Qureshi S, Shen L, Moskaluk CA, Liu TC, Yilmaz O, Brown DE, Barratt MJ, Kung VL, Gordon JI, Moore SR, Ali SA. Study of Environmental Enteropathy and Malnutrition (SEEM) in Pakistan: protocols for biopsy based biomarker discovery and validation. BMC Pediatr 2019; 19:247. [PMID: 31331393 PMCID: PMC6643315 DOI: 10.1186/s12887-019-1564-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 05/31/2019] [Indexed: 12/26/2022] Open
Abstract
Background Environmental Enteropathy (EE), characterized by alterations in intestinal structure, function, and immune activation, is believed to be an important contributor to childhood undernutrition and its associated morbidities, including stunting. Half of all global deaths in children < 5 years are attributable to under-nutrition, making the study of EE an area of critical priority. Methods Community based intervention study, divided into two sub-studies, 1) Longitudinal analyses and 2) Biopsy studies for identification of EE features via omics analyses. Birth cohorts in Matiari, Pakistan established: moderately or severely malnourished (weight for height Z score (WHZ) < − 2) children, and well-nourished (WHZ > 0) children. Blood, urine, and fecal samples, for evaluation of potential biomarkers, will be collected at various time points from all participants (longitudinal analyses). Participants will receive appropriate educational and nutritional interventions; non-responders will undergo further evaluation to determine eligibility for further workup, including upper gastrointestinal endoscopy. Histopathological changes in duodenal biopsies will be compared with duodenal biopsies obtained from USA controls who have celiac disease, Crohn’s disease, or who were found to have normal histopathology. RNA-Seq will be employed to characterize mucosal gene expression across groups. Duodenal biopsies, luminal aspirates from the duodenum, and fecal samples will be analyzed to define microbial community composition (omic analyses). The relationship between histopathology, mucosal gene expression, and community configuration will be assessed using a variety of bioinformatic tools to gain better understanding of disease pathogenesis and to identify mechanism-based biomarkers. Ethical review committees at all collaborating institutions have approved this study. All results will be made available to the scientific community. Discussion Operational and ethical constraints for safely obtaining intestinal biopsies from children in resource-poor settings have led to a paucity of human tissue-based investigations to understand and reverse EE in vulnerable populations. Furthermore, EE biomarkers have rarely been correlated with gold standard histopathological confirmation. The Study of Environmental Enteropathy and Malnutrition (SEEM) is designed to better understand the pathophysiology, predictors, biomarkers, and potential management strategies of EE to inform strategies to eradicate this debilitating pathology and accelerate progress towards the 2030 Sustainable Development Goals. Trial registration Retrospectively registered; clinicaltrials.gov ID NCT03588013. Electronic supplementary material The online version of this article (10.1186/s12887-019-1564-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Najeeha T Iqbal
- Department of Paediatrics and Child Health, Aga Khan University, Karachi, Pakistan.,Department of Biological and Biomedical Sciences, Aga Khan University, Karachi, Pakistan
| | - Sana Syed
- Department of Paediatrics and Child Health, Aga Khan University, Karachi, Pakistan.,Department of Pediatrics, University of Virginia, Charlottesville, VA, USA
| | - Kamran Sadiq
- Department of Paediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Marium N Khan
- Department of Pediatrics, University of Virginia, Charlottesville, VA, USA
| | - Junaid Iqbal
- Department of Paediatrics and Child Health, Aga Khan University, Karachi, Pakistan.,Department of Biological and Biomedical Sciences, Aga Khan University, Karachi, Pakistan
| | - Jennie Z Ma
- Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA
| | - Fayaz Umrani
- Department of Paediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Sheraz Ahmed
- Department of Paediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Elizabeth A Maier
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Lee A Denson
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Yael Haberman
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Monica M McNeal
- Division of Infectious Diseases, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Kenneth D R Setchell
- Clinical Mass Spectrometry, Division of Pathology and Laboratory Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Xueheng Zhao
- Clinical Mass Spectrometry, Division of Pathology and Laboratory Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Shahida Qureshi
- Department of Paediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Lanlan Shen
- Department of Pediatrics, Baylor College of Medicine, USDA/ARS Children's Nutrition Research Center, Houston, TX, USA
| | | | - Ta-Chiang Liu
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Omer Yilmaz
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Koch Institute for Integrative Cancer Research at MIT and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Donald E Brown
- Data Science Institute, University of Virginia, Charlottesville, VA, USA
| | - Michael J Barratt
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Vanderlene L Kung
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Jeffrey I Gordon
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Sean R Moore
- Department of Pediatrics, University of Virginia, Charlottesville, VA, USA.
| | - S Asad Ali
- Department of Paediatrics and Child Health, Aga Khan University, Karachi, Pakistan.
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35
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Gehrig JL, Venkatesh S, Chang HW, Hibberd MC, Kung VL, Cheng J, Chen RY, Subramanian S, Cowardin CA, Meier MF, O'Donnell D, Talcott M, Spears LD, Semenkovich CF, Henrissat B, Giannone RJ, Hettich RL, Ilkayeva O, Muehlbauer M, Newgard CB, Sawyer C, Head RD, Rodionov DA, Arzamasov AA, Leyn SA, Osterman AL, Hossain MI, Islam M, Choudhury N, Sarker SA, Huq S, Mahmud I, Mostafa I, Mahfuz M, Barratt MJ, Ahmed T, Gordon JI. Effects of microbiota-directed foods in gnotobiotic animals and undernourished children. Science 2019; 365:eaau4732. [PMID: 31296738 PMCID: PMC6683325 DOI: 10.1126/science.aau4732] [Citation(s) in RCA: 234] [Impact Index Per Article: 46.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 04/24/2019] [Accepted: 06/07/2019] [Indexed: 12/16/2022]
Abstract
To examine the contributions of impaired gut microbial community development to childhood undernutrition, we combined metabolomic and proteomic analyses of plasma samples with metagenomic analyses of fecal samples to characterize the biological state of Bangladeshi children with severe acute malnutrition (SAM) as they transitioned, after standard treatment, to moderate acute malnutrition (MAM) with persistent microbiota immaturity. Host and microbial effects of microbiota-directed complementary food (MDCF) prototypes targeting weaning-phase bacterial taxa underrepresented in SAM and MAM microbiota were characterized in gnotobiotic mice and gnotobiotic piglets colonized with age- and growth-discriminatory bacteria. A randomized, double-blind controlled feeding study identified a lead MDCF that changes the abundances of targeted bacteria and increases plasma biomarkers and mediators of growth, bone formation, neurodevelopment, and immune function in children with MAM.
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Affiliation(s)
- Jeanette L Gehrig
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Siddarth Venkatesh
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Hao-Wei Chang
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Matthew C Hibberd
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Vanderlene L Kung
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Jiye Cheng
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Robert Y Chen
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Sathish Subramanian
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Carrie A Cowardin
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Martin F Meier
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - David O'Donnell
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Michael Talcott
- Division of Comparative Medicine, Washington University, St. Louis, MO 63110, USA
| | - Larry D Spears
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Clay F Semenkovich
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique and Aix-Marseille Université, 13288 Marseille cedex 9, France
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Richard J Giannone
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Robert L Hettich
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Olga Ilkayeva
- Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, NC 27710, USA
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Michael Muehlbauer
- Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, NC 27710, USA
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Christopher B Newgard
- Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, NC 27710, USA
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC 27710, USA
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC 27710, USA
- Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA
| | - Christopher Sawyer
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
- Genome Technology Access Center, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Richard D Head
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
- Genome Technology Access Center, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Dmitry A Rodionov
- A. A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow 127994, Russia
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Aleksandr A Arzamasov
- A. A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow 127994, Russia
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Semen A Leyn
- A. A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow 127994, Russia
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Andrei L Osterman
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Md Iqbal Hossain
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh
| | - Munirul Islam
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh
| | - Nuzhat Choudhury
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh
| | - Shafiqul Alam Sarker
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh
| | - Sayeeda Huq
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh
| | - Imteaz Mahmud
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh
| | - Ishita Mostafa
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh
| | - Mustafa Mahfuz
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh
| | - Michael J Barratt
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Tahmeed Ahmed
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh
| | - Jeffrey I Gordon
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA.
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110, USA
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36
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Schriefer AE, Cliften PF, Hibberd MC, Sawyer C, Brown-Kennerly V, Burcea L, Klotz E, Crosby SD, Gordon JI, Head RD. A multi-amplicon 16S rRNA sequencing and analysis method for improved taxonomic profiling of bacterial communities. J Microbiol Methods 2018; 154:6-13. [PMID: 30273610 DOI: 10.1016/j.mimet.2018.09.019] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 09/26/2018] [Accepted: 09/27/2018] [Indexed: 12/24/2022]
Abstract
Metagenomic sequencing of bacterial samples has become the gold standard for profiling microbial populations, but 16S rRNA profiling remains widely used due to advantages in sample throughput, cost, and sensitivity even though the approach is hampered by primer bias and lack of specificity. We hypothesized that a hybrid approach, that combined targeted PCR amplification with high-throughput sequencing of multiple regions of the genome, would capture many of the advantages of both approaches. We developed a method that identifies and quantifies members of bacterial communities through simultaneous analysis of multiple variable regions of the bacterial 16S rRNA gene. The method combines high-throughput microfluidics for PCR amplification, short read DNA sequencing, and a custom algorithm named MVRSION (Multiple 16S Variable Region Species-Level IdentificatiON) for optimizing taxonomic assignment. MVRSION performance was compared to single variable region analyses (V3 or V4) of five synthetic mixtures of human gut bacterial strains using existing software (QIIME), and the results of community profiling by shotgun sequencing (COPRO-Seq) of fecal DNA samples collected from gnotobiotic mice colonized with a defined, phylogenetically diverse consortium of human gut bacterial strains. Positive predictive values for MVRSION ranged from 65%-91% versus 44%-61% for single region QIIME analyses (p < .01, p < .001), while the abundance estimate r2 for MVRSION compared to COPRO-Seq was 0.77 vs. 0.46 and 0.45 for V3-QIIME and V4-QIIME, respectively. MVRSION represents a generally applicable tool for taxonomic classification that is superior to single-region 16S rRNA methods, resource efficient, highly scalable for assessing the microbial composition of up to thousands of samples concurrently, with multiple applications ranging from whole community profiling to targeted tracking of organisms of interest in diverse habitats as a function of specified variables/perturbations.
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Affiliation(s)
- Andrew E Schriefer
- Genome Technology Access Center, Department of Genetics, Washington University School of Medicine, 63110 St. Louis, MO, USA.
| | - Paul F Cliften
- Genome Technology Access Center, Department of Genetics, Washington University School of Medicine, 63110 St. Louis, MO, USA.
| | - Matthew C Hibberd
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA; Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110, USA.
| | - Christopher Sawyer
- Genome Technology Access Center, Department of Genetics, Washington University School of Medicine, 63110 St. Louis, MO, USA.
| | | | - Lauren Burcea
- Genome Technology Access Center, Department of Genetics, Washington University School of Medicine, 63110 St. Louis, MO, USA.
| | - Elliott Klotz
- Genome Technology Access Center, Department of Genetics, Washington University School of Medicine, 63110 St. Louis, MO, USA.
| | - Seth D Crosby
- Genome Technology Access Center, Department of Genetics, Washington University School of Medicine, 63110 St. Louis, MO, USA.
| | - Jeffrey I Gordon
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA; Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110, USA.
| | - Richard D Head
- Genome Technology Access Center, Department of Genetics, Washington University School of Medicine, 63110 St. Louis, MO, USA.
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37
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Abstract
Analytic advances are enabling more precise definitions of the molecular composition of key food staples incorporated into contemporary diets and how the nutrient landscapes of these staples vary as a function of cultivar and food processing methods. This knowledge, combined with insights about the interrelationship between consumer microbiota configurations and biotransformation of food ingredients, should have a number of effects on agriculture, food production, and strategies for improving the nutritional value of foods and health status. These effects include decision-making about which cultivars of current or future food staples to incorporate into existing and future food systems, and which components of waste streams from current or future food manufacturing processes have nutritional value that is worth capturing. They can also guide which technologies should be applied, or need to be developed, to produce foods that support efficient microbial biotransformation of their ingredients into metabolic products that sustain health.
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Affiliation(s)
- Michael J Barratt
- Center for Genome Sciences and Systems Biology, Washington University in St. Louis, St. Louis, MO 63110, USA; Center for Gut Microbiome and Nutrition Research, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Carlito Lebrilla
- Department of Chemistry, University of California, Davis, Davis, CA 95616, USA
| | - Howard-Yana Shapiro
- Department of Plant Sciences, College of Agricultural and Environmental Sciences, University of California, Davis, Davis, CA 95616, USA; World Agroforestry Centre, Nairobi 00100, Kenya
| | - Jeffrey I Gordon
- Center for Genome Sciences and Systems Biology, Washington University in St. Louis, St. Louis, MO 63110, USA; Center for Gut Microbiome and Nutrition Research, Washington University in St. Louis, St. Louis, MO 63110, USA.
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38
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An J, Wang L, Patnode ML, Ridaura VK, Haldeman JM, Stevens RD, Ilkayeva O, Bain JR, Muehlbauer MJ, Glynn EL, Thomas S, Muoio D, Summers SA, Vath JE, Hughes TE, Gordon JI, Newgard CB. Physiological mechanisms of sustained fumagillin-induced weight loss. JCI Insight 2018. [PMID: 29515039 DOI: 10.1172/jci.insight.99453] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Current obesity interventions suffer from lack of durable effects and undesirable complications. Fumagillin, an inhibitor of methionine aminopeptidase-2, causes weight loss by reducing food intake, but with effects on weight that are superior to pair-feeding. Here, we show that feeding of rats on a high-fat diet supplemented with fumagillin (HF/FG) suppresses the aggressive feeding observed in pair-fed controls (HF/PF) and alters expression of circadian genes relative to the HF/PF group. Multiple indices of reduced energy expenditure are observed in HF/FG but not HF/PF rats. HF/FG rats also exhibit changes in gut hormones linked to food intake, increased energy harvest by gut microbiota, and caloric spilling in the urine. Studies in gnotobiotic mice reveal that effects of fumagillin on energy expenditure but not feeding behavior may be mediated by the gut microbiota. In sum, fumagillin engages weight loss-inducing behavioral and physiologic circuits distinct from those activated by simple caloric restriction.
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Affiliation(s)
- Jie An
- Sarah W. Stedman Nutrition and Metabolism Center, Duke Molecular Physiology Institute, Departments of Pharmacology and Cancer Biology and Medicine, Duke University Medical Center, Durham, North Carolina, USA
| | - Liping Wang
- Sarah W. Stedman Nutrition and Metabolism Center, Duke Molecular Physiology Institute, Departments of Pharmacology and Cancer Biology and Medicine, Duke University Medical Center, Durham, North Carolina, USA
| | - Michael L Patnode
- Center for Genome Sciences and Systems Biology and.,Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Vanessa K Ridaura
- Center for Genome Sciences and Systems Biology and.,Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Jonathan M Haldeman
- Sarah W. Stedman Nutrition and Metabolism Center, Duke Molecular Physiology Institute, Departments of Pharmacology and Cancer Biology and Medicine, Duke University Medical Center, Durham, North Carolina, USA
| | - Robert D Stevens
- Sarah W. Stedman Nutrition and Metabolism Center, Duke Molecular Physiology Institute, Departments of Pharmacology and Cancer Biology and Medicine, Duke University Medical Center, Durham, North Carolina, USA
| | - Olga Ilkayeva
- Sarah W. Stedman Nutrition and Metabolism Center, Duke Molecular Physiology Institute, Departments of Pharmacology and Cancer Biology and Medicine, Duke University Medical Center, Durham, North Carolina, USA
| | - James R Bain
- Sarah W. Stedman Nutrition and Metabolism Center, Duke Molecular Physiology Institute, Departments of Pharmacology and Cancer Biology and Medicine, Duke University Medical Center, Durham, North Carolina, USA
| | - Michael J Muehlbauer
- Sarah W. Stedman Nutrition and Metabolism Center, Duke Molecular Physiology Institute, Departments of Pharmacology and Cancer Biology and Medicine, Duke University Medical Center, Durham, North Carolina, USA
| | - Erin L Glynn
- Sarah W. Stedman Nutrition and Metabolism Center, Duke Molecular Physiology Institute, Departments of Pharmacology and Cancer Biology and Medicine, Duke University Medical Center, Durham, North Carolina, USA
| | - Steven Thomas
- Sarah W. Stedman Nutrition and Metabolism Center, Duke Molecular Physiology Institute, Departments of Pharmacology and Cancer Biology and Medicine, Duke University Medical Center, Durham, North Carolina, USA
| | - Deborah Muoio
- Sarah W. Stedman Nutrition and Metabolism Center, Duke Molecular Physiology Institute, Departments of Pharmacology and Cancer Biology and Medicine, Duke University Medical Center, Durham, North Carolina, USA
| | - Scott A Summers
- Sarah W. Stedman Nutrition and Metabolism Center, Duke Molecular Physiology Institute, Departments of Pharmacology and Cancer Biology and Medicine, Duke University Medical Center, Durham, North Carolina, USA
| | | | | | - Jeffrey I Gordon
- Center for Genome Sciences and Systems Biology and.,Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Christopher B Newgard
- Sarah W. Stedman Nutrition and Metabolism Center, Duke Molecular Physiology Institute, Departments of Pharmacology and Cancer Biology and Medicine, Duke University Medical Center, Durham, North Carolina, USA
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39
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Wagner VE, Dey N, Guruge J, Hsiao A, Ahern PP, Semenkovich NP, Blanton LV, Cheng J, Griffin N, Stappenbeck TS, Ilkayeva O, Newgard CB, Petri W, Haque R, Ahmed T, Gordon JI. Effects of a gut pathobiont in a gnotobiotic mouse model of childhood undernutrition. Sci Transl Med 2017; 8:366ra164. [PMID: 27881825 DOI: 10.1126/scitranslmed.aah4669] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 11/04/2016] [Indexed: 12/21/2022]
Abstract
To model how interactions among enteropathogens and gut microbial community members contribute to undernutrition, we colonized gnotobiotic mice fed representative Bangladeshi diets with sequenced bacterial strains cultured from the fecal microbiota of two 24-month-old Bangladeshi children: one healthy and the other underweight. The undernourished donor's bacterial collection contained an enterotoxigenic Bacteroides fragilis strain (ETBF), whereas the healthy donor's bacterial collection contained two nontoxigenic strains of B. fragilis (NTBF). Analyses of mice harboring either the unmanipulated culture collections or systematically manipulated versions revealed that ETBF was causally related to weight loss in the context of its native community but not when introduced into the healthy donor's community. This phenotype was transmissible from the dams to their offspring and was associated with derangements in host energy metabolism manifested by impaired tricarboxylic acid cycle activity and decreased acyl-coenzyme A utilization. NTBF reduced ETBF's expression of its enterotoxin and mitigated the effects of ETBF on the transcriptomes of other healthy donor community members. These results illustrate how intraspecific (ETBF-NTBF) and interspecific interactions influence the effects of harboring B. fragilis.
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Affiliation(s)
- Vitas E Wagner
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA.,Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Neelendu Dey
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA.,Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110, USA.,Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Janaki Guruge
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA.,Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Ansel Hsiao
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA.,Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Philip P Ahern
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA.,Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Nicholas P Semenkovich
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA.,Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Laura V Blanton
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA.,Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Jiye Cheng
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA.,Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Nicholas Griffin
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA.,Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Thaddeus S Stappenbeck
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Olga Ilkayeva
- Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, NC 27710, USA
| | - Christopher B Newgard
- Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, NC 27710, USA.,Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC 27710, USA.,Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC 27710, USA.,Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA
| | - William Petri
- Departments of Medicine, Microbiology, and Pathology, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Rashidul Haque
- International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka 1212, Bangladesh
| | - Tahmeed Ahmed
- International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka 1212, Bangladesh
| | - Jeffrey I Gordon
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA. .,Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110, USA
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40
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Cervantes-Barragan L, Chai JN, Tianero MD, Di Luccia B, Ahern PP, Merriman J, Cortez VS, Caparon MG, Donia MS, Gilfillan S, Cella M, Gordon JI, Hsieh CS, Colonna M. Lactobacillus reuteri induces gut intraepithelial CD4 +CD8αα + T cells. Science 2017; 357. [PMID: 28775213 PMCID: PMC5687812 DOI: 10.1126/science.aah5825 10.1126/science.aah5825] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The small intestine contains CD4+CD8αα+ double-positive intraepithelial lymphocytes (DP IELs), which originate from intestinal CD4+ T cells through down-regulation of the transcription factor Thpok and have regulatory functions. DP IELs are absent in germ-free mice, which suggests that their differentiation depends on microbial factors. We found that DP IEL numbers in mice varied in different vivaria, correlating with the presence of Lactobacillus reuteri This species induced DP IELs in germ-free mice and conventionally-raised mice lacking these cells. L. reuteri did not shape the DP-IEL-TCR (TCR, T cell receptor) repertoire but generated indole derivatives of tryptophan that activated the aryl-hydrocarbon receptor in CD4+ T cells, allowing Thpok down-regulation and differentiation into DP IELs. Thus, L. reuteri, together with a tryptophan-rich diet, can reprogram intraepithelial CD4+ T cells into immunoregulatory T cells.
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Affiliation(s)
- Luisa Cervantes-Barragan
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO 63110
| | - Jiani N. Chai
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO 63110,Department of Internal Medicine, Washington University School of Medicine, St Louis, MO 63110
| | - Ma. Diarey Tianero
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Blanda Di Luccia
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO 63110
| | - Philip P. Ahern
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA,Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Joseph Merriman
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO 63110
| | - Victor S. Cortez
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO 63110
| | - Michael G Caparon
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO 63110
| | - Mohamed S Donia
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Susan Gilfillan
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO 63110
| | - Marina Cella
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO 63110
| | - Jeffrey I. Gordon
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA,Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Chyi-Song Hsieh
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO 63110,Department of Internal Medicine, Washington University School of Medicine, St Louis, MO 63110
| | - Marco Colonna
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO 63110,Correspondence to: Marco Colonna, Department of Pathology and Immunology, Washington University School of Medicine, 660 S. Euclid St Louis, MO 63110. Tel: 314-362-0367; FAX: 314-747-0809;
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41
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Mahfuz M, Das S, Mazumder RN, Masudur Rahman M, Haque R, Bhuiyan MMR, Akhter H, Sarker MSA, Mondal D, Muaz SSA, Karim ASMB, Borowitz SM, Moskaluk CA, Barratt MJ, Petri WA, Gordon JI, Ahmed T. Bangladesh Environmental Enteric Dysfunction (BEED) study: protocol for a community-based intervention study to validate non-invasive biomarkers of environmental enteric dysfunction. BMJ Open 2017; 7:e017768. [PMID: 28801442 PMCID: PMC5724211 DOI: 10.1136/bmjopen-2017-017768] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
INTRODUCTION Environmental enteric dysfunction (EED) is a subacute inflammatory condition of the small intestinal mucosa with unclear aetiology that may account for more than 40% of all cases of stunting. Currently, there are no universally accepted protocols for the diagnosis, treatment and ultimately prevention of EED. The Bangladesh Environmental Enteric Dysfunction (BEED) study is designed to validate non-invasive biomarkers of EED with small intestinal biopsy, better understand disease pathogenesis and identify potential therapeutic targets for interventions designed to control EED and stunting. METHODS AND ANALYSIS The BEED study is a community-based intervention where participants are recruited from three cohorts: stunted children aged 12-18 months (length for age Z-score (LAZ) <-2), at risk of stunting children aged 12-18 months (LAZ <-1 to -2) and malnourished adults aged 18-45 years (body mass index <18.5 kg/m2). After screening, participants eligible for study provide faecal, urine and plasma specimens to quantify the levels of candidate EED biomarkers before and after receiving a nutritional intervention. Participants who fail to respond to nutritional therapy are considered as the candidates for upper gastrointestinal endoscopy with biopsy. Histopathological scoring for EED will be performed on biopsies obtained from several locations within the proximal small intestine. Candidate EED biomarkers will be correlated with nutritional status, the results of histochemical and immunohistochemical analyses of epithelial and lamina propria cell populations, plus assessments of microbial community structure. ETHICS AND DISSEMINATION Ethics approval was obtained in all participating institutes. Results of this study will be submitted for publication in peer-reviewed journals. TRIAL REGISTRATION NUMBER ClinicalTrials.gov ID: NCT02812615. Registered on 21 June 2016.
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Affiliation(s)
- Mustafa Mahfuz
- Nutrition and Clinical Services Division (NCSD), International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Subhasish Das
- Nutrition and Clinical Services Division (NCSD), International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Ramendra Nath Mazumder
- Nutrition and Clinical Services Division (NCSD), International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - M Masudur Rahman
- Department of Gastroenterology, Dhaka Medical College and Hospital, Dhaka, Bangladesh
| | - Rashidul Haque
- Nutrition and Clinical Services Division (NCSD), International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | | | | | - Md. Shafiqul Alam Sarker
- Nutrition and Clinical Services Division (NCSD), International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Dinesh Mondal
- Nutrition and Clinical Services Division (NCSD), International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Syed Shafi Ahmed Muaz
- Department of Paediatric Gastroenterology, Hepatology & Nutrition, Dhaka Shishu Hospital, Dhaka, Bangladesh
| | - A S M Bazlul Karim
- Department of Paediatric Gastroenterology & Nutrition, Bangabandhu Sheikh Mujib Medical University (BSMMU), Dhaka, Bangladesh
| | - Stephen M Borowitz
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia, USA
| | - Christopher A Moskaluk
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia, USA
| | - Michael J Barratt
- Center for Genome Sciences and Systems Biology, Washington University, St Louis, Missouri, USA
- Center for Gut Microbiome and Nutrition Research, Washington University, St. Louis, Missouri, USA
| | - William A Petri
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia, USA
| | - Jeffrey I Gordon
- Center for Genome Sciences and Systems Biology, Washington University, St Louis, Missouri, USA
- Center for Gut Microbiome and Nutrition Research, Washington University, St. Louis, Missouri, USA
| | - Tahmeed Ahmed
- Nutrition and Clinical Services Division (NCSD), International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
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42
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Cervantes-Barragan L, Chai JN, Tianero MD, Di Luccia B, Ahern PP, Merriman J, Cortez VS, Caparon MG, Donia MS, Gilfillan S, Cella M, Gordon JI, Hsieh CS, Colonna M. Lactobacillus reuteri induces gut intraepithelial CD4 +CD8αα + T cells. Science 2017; 357:806-810. [PMID: 28775213 DOI: 10.1126/science.aah5825] [Citation(s) in RCA: 494] [Impact Index Per Article: 70.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2016] [Revised: 04/05/2017] [Accepted: 07/11/2017] [Indexed: 12/17/2022]
Abstract
The small intestine contains CD4+CD8αα+ double-positive intraepithelial lymphocytes (DP IELs), which originate from intestinal CD4+ T cells through down-regulation of the transcription factor Thpok and have regulatory functions. DP IELs are absent in germ-free mice, which suggests that their differentiation depends on microbial factors. We found that DP IEL numbers in mice varied in different vivaria, correlating with the presence of Lactobacillus reuteri This species induced DP IELs in germ-free mice and conventionally-raised mice lacking these cells. L. reuteri did not shape the DP-IEL-TCR (TCR, T cell receptor) repertoire but generated indole derivatives of tryptophan that activated the aryl-hydrocarbon receptor in CD4+ T cells, allowing Thpok down-regulation and differentiation into DP IELs. Thus, L. reuteri, together with a tryptophan-rich diet, can reprogram intraepithelial CD4+ T cells into immunoregulatory T cells.
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Affiliation(s)
- Luisa Cervantes-Barragan
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Jiani N Chai
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA.,Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Ma Diarey Tianero
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Blanda Di Luccia
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Philip P Ahern
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA.,Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Joseph Merriman
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Victor S Cortez
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Michael G Caparon
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Mohamed S Donia
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Susan Gilfillan
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Marina Cella
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Jeffrey I Gordon
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA.,Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Chyi-Song Hsieh
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA.,Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Marco Colonna
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA.
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43
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Ma H, Sales VM, Wolf AR, Subramanian S, Matthews TJ, Chen M, Sharma A, Gall W, Kulik W, Cohen DE, Adachi Y, Griffin NW, Gordon JI, Patti ME, Isganaitis E. Attenuated Effects of Bile Acids on Glucose Metabolism and Insulin Sensitivity in a Male Mouse Model of Prenatal Undernutrition. Endocrinology 2017; 158. [PMID: 28637315 PMCID: PMC5551557 DOI: 10.1210/en.2017-00288] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Prenatal undernutrition and low birth weight are associated with risk of type 2 diabetes and obesity. Prenatal caloric restriction results in low birth weight, glucose intolerance, obesity, and reduced plasma bile acids (BAs) in offspring mice. Because BAs can regulate systemic metabolism and glucose homeostasis, we hypothesized that BA supplementation could prevent diet-induced obesity and glucose intolerance in this model of developmental programming. Pregnant dams were food restricted by 50% from gestational days 12.5 to 18.5. Offspring of both undernourished (UN) and control (C) dams given unrestricted diets were weaned to high-fat diets with or without supplementation with 0.25% w/w ursodeoxycholic acid (UDCA), yielding four experimental groups: C, UN, C + UDCA, and UN + UDCA. Glucose homeostasis, BA composition, liver and intestinal gene expression, and microbiota composition were analyzed in the four groups. Although UDCA supplementation ameliorated diet-induced obesity in C mice, there was no effect in UN mice. UDCA similarly lowered fasting insulin, and improved glucose tolerance, pyruvate tolerance, and liver steatosis in C, but not UN, animals. BA composition differed significantly, and liver and ileal expression of genes involved in BA metabolism (Cyp7b1, Shp) were differentially induced by UDCA in C vs UN animals. Bacterial taxa in fecal microbiota correlated with treatment groups and metabolic parameters. In conclusion, prenatal undernutrition alters responsiveness to the metabolic benefits of BA supplementation, with resistance to the weight-lowering and insulin-sensitizing effects of UDCA supplementation. Our findings suggest that BA metabolism may be a previously unrecognized contributor to developmentally programmed diabetes risk.
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Affiliation(s)
- Huijuan Ma
- Research Division, Joslin Diabetes Center and Harvard Medical School, Boston, Massachusetts 02115
- Department of Endocrinology and Metabolism, Hebei General Hospital, Shijiazhuang, Hebei, 050051, China
| | - Vicencia M Sales
- Research Division, Joslin Diabetes Center and Harvard Medical School, Boston, Massachusetts 02115
| | - Ashley R Wolf
- Center for Genome Sciences and Systems Biology, and Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, Missouri 63110
| | - Sathish Subramanian
- Center for Genome Sciences and Systems Biology, and Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, Missouri 63110
| | - Tucker J Matthews
- Research Division, Joslin Diabetes Center and Harvard Medical School, Boston, Massachusetts 02115
| | - Michael Chen
- Research Division, Joslin Diabetes Center and Harvard Medical School, Boston, Massachusetts 02115
| | - Aparna Sharma
- Research Division, Joslin Diabetes Center and Harvard Medical School, Boston, Massachusetts 02115
| | - Walt Gall
- Metabolon, Durham, North Carolina 27713
| | - Wim Kulik
- Laboratory of Genetic Metabolic Diseases, Departments of Pediatrics and Clinical Chemistry, University of Amsterdam, 1105 AZ Amsterdam-Zuidoost, The Netherlands
| | - David E Cohen
- Division of Gastroenterology and Hepatology, Joan & Sanford I. Weill Department of Medicine, Weill Cornell Medical College, New York, New York 10021
| | - Yusuke Adachi
- Research Division, Joslin Diabetes Center and Harvard Medical School, Boston, Massachusetts 02115
| | - Nicholas W Griffin
- Center for Genome Sciences and Systems Biology, and Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, Missouri 63110
| | - Jeffrey I Gordon
- Center for Genome Sciences and Systems Biology, and Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, Missouri 63110
| | - Mary-Elizabeth Patti
- Research Division, Joslin Diabetes Center and Harvard Medical School, Boston, Massachusetts 02115
| | - Elvira Isganaitis
- Research Division, Joslin Diabetes Center and Harvard Medical School, Boston, Massachusetts 02115
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44
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Abstract
Ongoing efforts to develop microbiota-directed foods (MDF) provide potentially new ways for improving health status. A MDF could alter the structural and functional configuration of a consumer’s gut microbial community, provide substrates for microbial transformation to biomolecules necessary for a healthy state, or act through a combination of these mechanisms. The development of MDFs promises to expand our view of ‘essential nutrients’ and prompt questions about how they should be classified and regulated.
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Affiliation(s)
- Jonathan M Green
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
- Institute for Public Health, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Michael J Barratt
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Michael Kinch
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Jeffrey I Gordon
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA.
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110, USA
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Spaulding CN, Klein RD, Ruer S, Kau AL, Schreiber HL, Cusumano ZT, Dodson KW, Pinkner JS, Fremont DH, Janetka JW, Remaut H, Gordon JI, Hultgren SJ. Selective depletion of uropathogenic E. coli from the gut by a FimH antagonist. Nature 2017; 546:528-532. [PMID: 28614296 PMCID: PMC5654549 DOI: 10.1038/nature22972] [Citation(s) in RCA: 172] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 05/22/2017] [Indexed: 12/19/2022]
Abstract
Urinary tract infections (UTI) caused by uropathogenic E. coli (UPEC) affect 150 million people annually1,2. Despite effective antibiotic therapy, 30–50% of patients experience recurrent UTI (rUTI)1. Additionally, the growing prevelance of UPEC resistant to last-line antibiotic treatments, and more recently carbapenems and colistin, make UTIs a prime example of the antibiotic-resistance crisis and emphasize the need for new approaches to treat and prevent bacterial infections3–5. UPEC strains establish reservoirs in the gut from which they are shed in the feces, can colonize the peri-urethral area or vagina and subsequently ascend through the urethra to the urinary tract, where they cause UTI6. UPEC isolates encode up to 16 distinct chaperone-usher pathway (CUP) pili and each pilus type likely enables colonization of a habitat in the host or environment7. For example, the type 1 pilus adhesin, FimH, binds mannose on the bladder surface, mediating bladder colonization. However, little is known regarding the mechanisms underlying UPEC persistence in the gut5. Using a mouse model, we found that F17-like and type 1 pili promote intestinal colonization and show distinct binding to epithelial cells distributed along colonic crypts. Phylogenomic and structural analyses reveal that F17-like pili are closely related to pilus types carried by intestinal pathogens, but are restricted to extra-intestinal pathogenic E. coli. Moreover, we show that targeting FimH with a high-affinity inhibitor, mannoside M4284, reduces intestinal colonization of genetically diverse UPEC isolates, while simultaneously treating UTI, without significantly disrupting the the structural configuration of the gut microbiota. By selectively depleting the intestinal UPEC reservoir, mannosides could significantly reduce the rate of UTI and rUTI.
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Affiliation(s)
- Caitlin N Spaulding
- Department of Molecular Microbiology, Washington University in St Louis, St Louis, Missouri 63110, USA.,Center for Women's Infectious Disease Research (CWIDR), Washington University in St Louis, St Louis, Missouri 63110, USA
| | - Roger D Klein
- Department of Molecular Microbiology, Washington University in St Louis, St Louis, Missouri 63110, USA.,Center for Women's Infectious Disease Research (CWIDR), Washington University in St Louis, St Louis, Missouri 63110, USA
| | - Ségolène Ruer
- Structural and Molecular Microbiology, VIB Center for Structural Biology, VIB, Pleinlaan 2, 1050 Brussels, Belgium.,Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Andrew L Kau
- Center for Women's Infectious Disease Research (CWIDR), Washington University in St Louis, St Louis, Missouri 63110, USA.,Department of Medicine, Washington University in St Louis, St Louis, Missouri 63110, USA
| | - Henry L Schreiber
- Department of Molecular Microbiology, Washington University in St Louis, St Louis, Missouri 63110, USA.,Center for Women's Infectious Disease Research (CWIDR), Washington University in St Louis, St Louis, Missouri 63110, USA.,The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Zachary T Cusumano
- Department of Molecular Microbiology, Washington University in St Louis, St Louis, Missouri 63110, USA.,Center for Women's Infectious Disease Research (CWIDR), Washington University in St Louis, St Louis, Missouri 63110, USA
| | - Karen W Dodson
- Department of Molecular Microbiology, Washington University in St Louis, St Louis, Missouri 63110, USA.,Center for Women's Infectious Disease Research (CWIDR), Washington University in St Louis, St Louis, Missouri 63110, USA
| | - Jerome S Pinkner
- Department of Molecular Microbiology, Washington University in St Louis, St Louis, Missouri 63110, USA.,Center for Women's Infectious Disease Research (CWIDR), Washington University in St Louis, St Louis, Missouri 63110, USA
| | - Daved H Fremont
- Department of Molecular Microbiology, Washington University in St Louis, St Louis, Missouri 63110, USA.,Department of Pathology and Immunology, Washington University in St Louis, St Louis, Missouri 63110, USA.,Department of Biochemistry and Molecular Biophysics, Washington University in St Louis, St Louis, Missouri 63110, USA
| | - James W Janetka
- Center for Women's Infectious Disease Research (CWIDR), Washington University in St Louis, St Louis, Missouri 63110, USA.,Department of Biochemistry and Molecular Biophysics, Washington University in St Louis, St Louis, Missouri 63110, USA
| | - Han Remaut
- Structural and Molecular Microbiology, VIB Center for Structural Biology, VIB, Pleinlaan 2, 1050 Brussels, Belgium.,Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Jeffrey I Gordon
- Center for Genome Sciences and Systems Biology, Washington University in St Louis, St Louis, Missouri 63110, USA.,Center for Gut Microbiome and Nutrition Research, Washington University in St Louis, St Louis, Missouri 63110, USA
| | - Scott J Hultgren
- Department of Molecular Microbiology, Washington University in St Louis, St Louis, Missouri 63110, USA.,Center for Women's Infectious Disease Research (CWIDR), Washington University in St Louis, St Louis, Missouri 63110, USA
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Hibberd MC, Wu M, Rodionov DA, Li X, Cheng J, Griffin NW, Barratt MJ, Giannone RJ, Hettich RL, Osterman AL, Gordon JI. The effects of micronutrient deficiencies on bacterial species from the human gut microbiota. Sci Transl Med 2017; 9:eaal4069. [PMID: 28515336 PMCID: PMC5524138 DOI: 10.1126/scitranslmed.aal4069] [Citation(s) in RCA: 147] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 03/14/2017] [Indexed: 12/13/2022]
Abstract
Vitamin and mineral (micronutrient) deficiencies afflict 2 billion people. Although the impact of these imbalances on host biology has been studied extensively, much less is known about their effects on the gut microbiota of developing or adult humans. Therefore, we established a community of cultured, sequenced human gut-derived bacterial species in gnotobiotic mice and fed the animals a defined micronutrient-sufficient diet, followed by a derivative diet devoid of vitamin A, folate, iron, or zinc, followed by return to the sufficient diet. Acute vitamin A deficiency had the largest effect on bacterial community structure and metatranscriptome, with Bacteroides vulgatus, a prominent responder, increasing its abundance in the absence of vitamin A. Applying retinol selection to a library of 30,300 B. vulgatus transposon mutants revealed that disruption of acrR abrogated retinol sensitivity. Genetic complementation studies, microbial RNA sequencing, and transcription factor-binding assays disclosed that AcrR is a repressor of an adjacent AcrAB-TolC efflux system. Retinol efflux measurements in wild-type and acrR-mutant strains plus treatment with a pharmacologic inhibitor of the efflux system revealed that AcrAB-TolC is a determinant of retinol and bile acid sensitivity in B. vulgatus Acute vitamin A deficiency was associated with altered bile acid metabolism in vivo, raising the possibility that retinol, bile acid metabolites, and AcrAB-TolC interact to influence the fitness of B. vulgatus and perhaps other microbiota members. This type of preclinical model can help to develop mechanistic insights about the effects of, and more effective treatment strategies for micronutrient deficiencies.
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Affiliation(s)
- Matthew C Hibberd
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Meng Wu
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Dmitry A Rodionov
- A. A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow 127994, Russia
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Xiaoqing Li
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Jiye Cheng
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Nicholas W Griffin
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Michael J Barratt
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Richard J Giannone
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Robert L Hettich
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Andrei L Osterman
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Jeffrey I Gordon
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA.
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110, USA
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Griffin NW, Ahern PP, Cheng J, Heath AC, Ilkayeva O, Newgard CB, Fontana L, Gordon JI. Prior Dietary Practices and Connections to a Human Gut Microbial Metacommunity Alter Responses to Diet Interventions. Cell Host Microbe 2016; 21:84-96. [PMID: 28041931 DOI: 10.1016/j.chom.2016.12.006] [Citation(s) in RCA: 106] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 09/22/2016] [Accepted: 11/29/2016] [Indexed: 12/22/2022]
Abstract
Ensuring that gut microbiota respond consistently to prescribed dietary interventions, irrespective of prior dietary practices (DPs), is critical for effective nutritional therapy. To address this, we identified DP-associated gut bacterial taxa in individuals either practicing chronic calorie restriction with adequate nutrition (CRON) or without dietary restrictions (AMER). When transplanted into gnotobiotic mice, AMER and CRON microbiota responded predictably to CRON and AMER diets but with variable response strengths. An individual's microbiota is connected to other individuals' communities ("metacommunity") by microbial exchange. Sequentially cohousing AMER-colonized mice with two different groups of CRON-colonized mice simulated metacommunity effects, resulting in enhanced responses to a CRON diet intervention and changes in several metabolic features in AMER animals. This response was driven by an influx of CRON DP-associated taxa. Certain DPs may impair responses to dietary interventions, necessitating the introduction of diet-responsive bacterial lineages present in other individuals and identified using the strategies described.
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Affiliation(s)
- Nicholas W Griffin
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA; Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Philip P Ahern
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA; Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Jiye Cheng
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA; Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Andrew C Heath
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Olga Ilkayeva
- Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, NC 27701, USA; Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC 27701, USA
| | - Christopher B Newgard
- Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, NC 27701, USA; Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC 27701, USA; Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC 27701, USA; Department of Medicine, Duke University Medical Center, Durham, NC 27701, USA
| | - Luigi Fontana
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Clinical and Experimental Sciences, Brescia University Medical School, Brescia, Italy; CEINGE Biotecnologie Avanzate, Napoli 80145, Italy
| | - Jeffrey I Gordon
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA; Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110, USA.
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Bäckhed F, Ley RE, Sonnenburg JL, Gordon JI. The human intestinal microbiota and its relationship to energy balance. Scandinavian Journal of Food and Nutrition 2016. [DOI: 10.1080/17482970601066546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Fredrik Bäckhed
- Center for Genome SciencesSchool of Medicine, Washington UniversitySt LouisMissouriUSA
| | - Ruth E. Ley
- Center for Genome SciencesSchool of Medicine, Washington UniversitySt LouisMissouriUSA
| | - Justin L. Sonnenburg
- Center for Genome SciencesSchool of Medicine, Washington UniversitySt LouisMissouriUSA
| | - Jeffrey I. Gordon
- Center for Genome SciencesSchool of Medicine, Washington UniversitySt LouisMissouriUSA
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49
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Blanton LV, Charbonneau MR, Salih T, Barratt MJ, Venkatesh S, Ilkaveya O, Subramanian S, Manary MJ, Trehan I, Jorgensen JM, Fan YM, Henrissat B, Leyn SA, Rodionov DA, Osterman AL, Maleta KM, Newgard CB, Ashorn P, Dewey KG, Gordon JI. Gut bacteria that prevent growth impairments transmitted by microbiota from malnourished children. Science 2016; 351:351/6275/aad3311. [PMID: 26912898 DOI: 10.1126/science.aad3311] [Citation(s) in RCA: 482] [Impact Index Per Article: 60.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Undernourished children exhibit impaired development of their gut microbiota. Transplanting microbiota from 6- and 18-month-old healthy or undernourished Malawian donors into young germ-free mice that were fed a Malawian diet revealed that immature microbiota from undernourished infants and children transmit impaired growth phenotypes. The representation of several age-discriminatory taxa in recipient animals correlated with lean body mass gain; liver, muscle, and brain metabolism; and bone morphology. Mice were cohoused shortly after receiving microbiota from healthy or severely stunted and underweight infants; age- and growth-discriminatory taxa from the microbiota of the former were able to invade that of the latter, which prevented growth impairments in recipient animals. Adding two invasive species, Ruminococcus gnavus and Clostridium symbiosum, to the microbiota from undernourished donors also ameliorated growth and metabolic abnormalities in recipient animals. These results provide evidence that microbiota immaturity is causally related to undernutrition and reveal potential therapeutic targets and agents.
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Affiliation(s)
- Laura V Blanton
- Center for Genome Sciences and Systems Biology and Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Mark R Charbonneau
- Center for Genome Sciences and Systems Biology and Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Tarek Salih
- Center for Genome Sciences and Systems Biology and Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Michael J Barratt
- Center for Genome Sciences and Systems Biology and Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Siddarth Venkatesh
- Center for Genome Sciences and Systems Biology and Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Olga Ilkaveya
- Sarah W. Stedman Nutrition and Metabolism Centerand Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Sathish Subramanian
- Center for Genome Sciences and Systems Biology and Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Mark J Manary
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA. School of Public Health and Family Medicine, College of Medicine, University of Malawi, Chichiri, Blantyre 3, Malawi
| | - Indi Trehan
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA. Department of Paediatrics and Child Health, College of Medicine, University of Malawi, Chichiri, Blantyre 3, Malawi
| | - Josh M Jorgensen
- Department of Nutrition and Program in International and Community Nutrition, University of California-Davis, Davis, CA 95616, USA
| | - Yue-Mei Fan
- Department for International Health, University of Tampere School of Medicine, Tampere 33014, Finland
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique and Aix-Marseille Université, 13288 Marseille Cedex 9, France. Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Semen A Leyn
- A. A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow 127994, Russia
| | - Dmitry A Rodionov
- A. A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow 127994, Russia. Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Andrei L Osterman
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Kenneth M Maleta
- School of Public Health and Family Medicine, College of Medicine, University of Malawi, Chichiri, Blantyre 3, Malawi
| | - Christopher B Newgard
- Sarah W. Stedman Nutrition and Metabolism Centerand Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC 27710, USA. Department of Pharmacology and Cancer Biology and Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA
| | - Per Ashorn
- Department for International Health, University of Tampere School of Medicine, Tampere 33014, Finland. Department of Pediatrics, Tampere University Hospital, Tampere 33521, Finland
| | - Kathryn G Dewey
- Department of Nutrition and Program in International and Community Nutrition, University of California-Davis, Davis, CA 95616, USA
| | - Jeffrey I Gordon
- Center for Genome Sciences and Systems Biology and Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63108, USA
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50
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Agre P, Bertozzi C, Bissell M, Campbell KP, Cummings RD, Desai UR, Estes M, Flotte T, Fogleman G, Gage F, Ginsburg D, Gordon JI, Hart G, Hascall V, Kiessling L, Kornfeld S, Lowe J, Magnani J, Mahal LK, Medzhitov R, Roberts RJ, Sackstein R, Sarkar R, Schnaar R, Schwartz N, Varki A, Walt D, Weissman I. Training the next generation of biomedical investigators in glycosciences. J Clin Invest 2016; 126:405-8. [PMID: 26829621 DOI: 10.1172/jci85905] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
This position statement originated from a working group meeting convened on April 15, 2015, by the NHLBI and incorporates follow-up contributions by the participants as well as other thought leaders subsequently consulted, who together represent research fields relevant to all branches of the NIH. The group was deliberately composed not only of individuals with a current research emphasis in the glycosciences, but also of many experts from other fields, who evinced a strong interest in being involved in the discussions. The original goal was to discuss the value of creating centers of excellence for training the next generation of biomedical investigators in the glycosciences. A broader theme that emerged was the urgent need to bring the glycosciences back into the mainstream of biology by integrating relevant education into the curricula of medical, graduate, and postgraduate training programs, thus generating a critical sustainable workforce that can advance the much-needed translation of glycosciences into a more complete understanding of biology and the enhanced practice of medicine.
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