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La Reau AJ, Strom NB, Filvaroff E, Mavrommatis K, Ward TL, Knights D. Author Correction: Shallow shotgun sequencing reduces technical variation in microbiome analysis. Sci Rep 2024; 14:6116. [PMID: 38480754 PMCID: PMC10937960 DOI: 10.1038/s41598-024-56475-7] [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: 03/17/2024] Open
Affiliation(s)
- Alex J La Reau
- Diversigen, Inc., 600 County Road D, West, Suite 8, New Brighton, MN, 55112, USA.
| | - Noah B Strom
- Diversigen, Inc., 600 County Road D, West, Suite 8, New Brighton, MN, 55112, USA
| | - Ellen Filvaroff
- Bristol Myers Squibb, 1500 Owens St, Suite 600, San Francisco, CA, 94158, USA
| | | | - Tonya L Ward
- Diversigen, Inc., 600 County Road D, West, Suite 8, New Brighton, MN, 55112, USA
| | - Dan Knights
- Diversigen, Inc., 600 County Road D, West, Suite 8, New Brighton, MN, 55112, USA.
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, 55455, USA.
- Biotechnology Institute, College of Biological Sciences, University of Minnesota, Minneapolis, MN, 55455, USA.
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2
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Allert M, Ferretti P, Johnson KE, Heisel T, Gonia S, Knights D, Fields DA, Albert FW, Demerath EW, Gale CA, Blekhman R. Assembly, stability, and dynamics of the infant gut microbiome are linked to bacterial strains and functions in mother's milk. bioRxiv 2024:2024.01.28.577594. [PMID: 38328166 PMCID: PMC10849666 DOI: 10.1101/2024.01.28.577594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
The establishment of the gut microbiome in early life is critical for healthy infant development. Although human milk is recommended as the sole source of nutrition for the human infant, little is known about how variation in milk composition, and especially the milk microbiome, shapes the microbial communities in the infant gut. Here, we quantified the similarity between the maternal milk and the infant gut microbiome using 507 metagenomic samples collected from 195 mother-infant pairs at one, three, and six months postpartum. We found that the microbial taxonomic overlap between milk and the infant gut was driven by bifidobacteria, in particular by B. longum. Infant stool samples dominated by B. longum also showed higher temporal stability compared to samples dominated by other species. We identified two instances of strain sharing between maternal milk and the infant gut, one involving a commensal (B. longum) and one a pathobiont (K. pneumoniae). In addition, strain sharing between unrelated infants was higher among infants born at the same hospital compared to infants born in different hospitals, suggesting a potential role of the hospital environment in shaping the infant gut microbiome composition. The infant gut microbiome at one month compared to six months of age was enriched in metabolic pathways associated with de-novo molecule biosynthesis, suggesting that early colonisers might be more versatile and metabolically independent compared to later colonizers. Lastly, we found a significant overlap in antimicrobial resistance genes carriage between the mother's milk and their infant's gut microbiome. Taken together, our results suggest that the human milk microbiome has an important role in the assembly, composition, and stability of the infant gut microbiome.
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Affiliation(s)
- Mattea Allert
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN, USA
| | - Pamela Ferretti
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Kelsey E Johnson
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN, USA
| | - Timothy Heisel
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA
| | - Sara Gonia
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA
| | - Dan Knights
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA
- BioTechnology Institute, College of Biological Sciences, University of Minnesota, Minneapolis, MN, USA
| | - David A Fields
- Department of Pediatrics, the University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Frank W Albert
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN, USA
| | - Ellen W Demerath
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN, USA
| | - Cheryl A Gale
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA
| | - Ran Blekhman
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
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3
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Kamer O, Rinott E, Tsaban G, Kaplan A, Yaskolka Meir A, Zelicha H, Knights D, Tuohy K, Fava F, Uwe Scholz M, Ziv O, Rubin E, Blüher M, Stumvoll M, Ceglarek U, Clément K, Koren O, Hu FB, Stampfer MJ, Wang DD, Youngster I, Shai I. Successful weight regain attenuation by autologous fecal microbiota transplantation is associated with non-core gut microbiota changes during weight loss; randomized controlled trial. Gut Microbes 2023; 15:2264457. [PMID: 37796016 PMCID: PMC10557561 DOI: 10.1080/19490976.2023.2264457] [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: 04/23/2023] [Accepted: 09/25/2023] [Indexed: 10/06/2023] Open
Abstract
We previously reported that autologous-fecal-microbiota-transplantation (aFMT), following 6 m of lifestyle intervention, attenuated subsequent weight regain and insulin rebound for participants consuming a high-polyphenol green-Mediterranean diet. Here, we explored whether specific changes in the core (abundant) vs. non-core (low-abundance) gut microbiome taxa fractions during the weight-loss phase (0-6 m) were differentially associated with weight maintenance following aFMT. Eighty-two abdominally obese/dyslipidemic participants (age = 52 years; 6 m weightloss = -8.3 kg) who provided fecal samples (0 m, 6 m) were included. Frozen 6 m's fecal samples were processed into 1 g, opaque and odorless aFMT capsules. Participants were randomly assigned to receive 100 capsules containing their own fecal microbiota or placebo over 8 m-14 m in ten administrations (adherence rate > 90%). Gut microbiome composition was evaluated using shotgun metagenomic sequencing. Non-core taxa were defined as ≤ 66% prevalence across participants. Overall, 450 species were analyzed. At baseline, 13.3% were classified as core, and Firmicutes presented the highest core proportion by phylum. During 6 m weight-loss phase, abundance of non-core species changed more than core species (P < .0001). Subject-specific changes in core and non-core taxa fractions were strongly correlated (Jaccard Index; r = 0.54; P < .001). Following aFMT treatment, only participants with a low 6 m change in core taxa, and a high change in non-core taxa, avoided 8-14 m weight regain (aFMT = -0.58 ± 2.4 kg, corresponding placebo group = 3.18 ± 3.5 kg; P = .02). In a linear regression model, low core/high non-core 6 m change was the only combination that was significantly associated with attenuated 8-14 m weight regain (P = .038; P = .002 for taxa patterns/treatment intervention interaction). High change in non-core, low-abundance taxa during weight-loss might mediate aFMT treatment success for weight loss maintenance.ClinicalTrials.gov: NCT03020186.
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Affiliation(s)
- Omer Kamer
- Faculty of Health Sciences, Ben-Gurion University of the Negev, The International Center of Health, Innovation & Nutrition On the memory of Manya Igel, Beer-Sheva, Israel
| | - Ehud Rinott
- Department of Medicine, Hebrew University and Hadassah Medical Center, Jerusalem, Israel
| | - Gal Tsaban
- Faculty of Health Sciences, Ben-Gurion University of the Negev, The International Center of Health, Innovation & Nutrition On the memory of Manya Igel, Beer-Sheva, Israel
| | - Alon Kaplan
- Faculty of Health Sciences, Ben-Gurion University of the Negev, The International Center of Health, Innovation & Nutrition On the memory of Manya Igel, Beer-Sheva, Israel
| | - Anat Yaskolka Meir
- Faculty of Health Sciences, Ben-Gurion University of the Negev, The International Center of Health, Innovation & Nutrition On the memory of Manya Igel, Beer-Sheva, Israel
| | - Hila Zelicha
- Faculty of Health Sciences, Ben-Gurion University of the Negev, The International Center of Health, Innovation & Nutrition On the memory of Manya Igel, Beer-Sheva, Israel
| | - Dan Knights
- BioTechnology Institute, University of Minnesota, St Paul, USA
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, USA
| | - Kieran Tuohy
- Department of Food Quality and Nutrition, Research and Innovation Centre, Fondazione Edmund Mach, Trento, Italy
- School of Food Science & Nutrition, University of Leeds, Leeds, UK
| | - Francesca Fava
- Department of Food Quality and Nutrition, Research and Innovation Centre, Fondazione Edmund Mach, Trento, Italy
| | - Matthias Uwe Scholz
- Department of Food Quality and Nutrition, Research and Innovation Centre, Fondazione Edmund Mach, Trento, Italy
| | - Oren Ziv
- Azrieli Faculty of Medicine, Bar Ilan University, Safed, Israel
| | - Elad Rubin
- Azrieli Faculty of Medicine, Bar Ilan University, Safed, Israel
| | - Matthias Blüher
- Department of Medicine, University of Leipzig, Leipzig, Germany
- Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG) of the Helmholtz Zentrum München at the University of Leipzig and University Hospital Leipzig, Leipzig, Germany
| | - Michael Stumvoll
- Department of Medicine, University of Leipzig, Leipzig, Germany
- Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG) of the Helmholtz Zentrum München at the University of Leipzig and University Hospital Leipzig, Leipzig, Germany
| | - Uta Ceglarek
- Department of Medicine, University of Leipzig, Leipzig, Germany
| | - Karine Clément
- Inserm, Nutrition and obesities: systemic approaches, nutriOmicsn Research Unit, Nutrition Department, Pitié-Salpêtrière Hospital, Assistance-Publique Hopitaux de Paris, Sorbonne University, Paris, France
| | - Omry Koren
- Azrieli Faculty of Medicine, Bar Ilan University, Safed, Israel
| | - Frank B. Hu
- Harvard T.H. Chan School of Public Health, Boston, USA
- Department of Medicine, Channing Division of Network Medicine, Department of Medicine, Harvard Medical School and Brigham and Women’s Hospital, Boston, USA
| | - Meir J. Stampfer
- Harvard T.H. Chan School of Public Health, Boston, USA
- Department of Medicine, Channing Division of Network Medicine, Department of Medicine, Harvard Medical School and Brigham and Women’s Hospital, Boston, USA
| | - Dong D. Wang
- Harvard T.H. Chan School of Public Health, Boston, USA
| | - Ilan Youngster
- Pediatric Division and Center for Microbiome Research, Shamir Medical Center, Be’er Ya’akov, Israel
- Sackler School of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Iris Shai
- Faculty of Health Sciences, Ben-Gurion University of the Negev, The International Center of Health, Innovation & Nutrition On the memory of Manya Igel, Beer-Sheva, Israel
- Harvard T.H. Chan School of Public Health, Boston, USA
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Vangay P, Ward T, Lucas S, Beura LK, Sabas D, Abramson M, Till L, Hoops SL, Kashyap P, Hunter RC, Masopust D, Knights D. Industrialized human gut microbiota increases CD8+ T cells and mucus thickness in humanized mouse gut. Gut Microbes 2023; 15:2266627. [PMID: 37853762 PMCID: PMC10588527 DOI: 10.1080/19490976.2023.2266627] [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] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 09/29/2023] [Indexed: 10/20/2023] Open
Abstract
Immigration to a highly industrialized nation has been associated with metabolic disease and simultaneous shifts in microbiota composition, but the underlying mechanisms are challenging to test in human studies. Here, we conducted a pilot study to assess the differential effects of human gut microbiota collected from the United States (US) and rural Thailand on the murine gut mucosa and immune system. Colonization of germ-free mice with microbiota from US individuals resulted in an increased accumulation of innate-like CD8 T cells in the small intestine lamina propria and intra-epithelial compartments when compared to colonization with microbiota from Thai individuals. Both TCRγδ and CD8αα T cells showed a marked increase in mice receiving Western microbiota and, interestingly, this phenotype was also associated with an increase in intestinal mucus thickness. Serendipitously, an accidentally infected group of mice corroborated this association between elevated inflammatory response and increased mucus thickness. These results suggest that Western-associated human gut microbes contribute to a pro-inflammatory immune response.
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Affiliation(s)
- Pajau Vangay
- Bioinformatics and Computational Biology Program, University of Minnesota, Minneapolis, MN, USA
| | - Tonya Ward
- BioTechnology Institute, University of Minnesota, Minneapolis, MN, USA
| | - Sarah Lucas
- Department of Biology, Syracuse University, Syracuse, NY, USA
| | - Lalit K. Beura
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI, USA
| | - Dominique Sabas
- Department of Food Science and Nutrition, University of Minnesota, Minneapolis, MN, USA
| | - Max Abramson
- Department of Neuroscience, Macalester College, St. Paul, MN, USA
- Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Lisa Till
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Mayo Clinic, Rochester, MN, USA
| | - Susan L. Hoops
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Purna Kashyap
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Mayo Clinic, Rochester, MN, USA
| | - Ryan C. Hunter
- Department of Biology, Syracuse University, Syracuse, NY, USA
| | - David Masopust
- Department of Biology, Syracuse University, Syracuse, NY, USA
| | - Dan Knights
- Bioinformatics and Computational Biology Program, University of Minnesota, Minneapolis, MN, USA
- BioTechnology Institute, University of Minnesota, Minneapolis, MN, USA
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA
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5
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Hoops SL, Knights D. LMdist: Local Manifold distance accurately measures beta diversity in ecological gradients. Bioinformatics 2023; 39:btad727. [PMID: 38060267 PMCID: PMC10713119 DOI: 10.1093/bioinformatics/btad727] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 05/11/2023] [Revised: 11/07/2023] [Accepted: 12/06/2023] [Indexed: 12/08/2023] Open
Abstract
MOTIVATION Differentiating ecosystems poses a complex, high-dimensional problem constrained by capturing relevant variation across species profiles. Researchers use pairwise distances and subsequent dimensionality reduction to highlight variation in a few dimensions. Despite popularity in analysis of ecological data, these low-dimensional visualizations can contain geometric abnormalities such as "arch" and "horseshoe" effects, potentially obscuring the impact of environmental gradients. These abnormalities appear in ordination but are in fact a product of oversaturated large pairwise distances. RESULTS We present Local Manifold distance (LMdist), an unsupervised algorithm which adjusts pairwise beta diversity measures to better represent true ecological distances between samples. Beta diversity measures can have a bounded dynamic range in depicting long environmental gradients with high species turnover. Using a graph structure, LMdist projects pairwise distances onto a manifold and traverses the manifold surface to adjust pairwise distances at the upper end of the beta diversity measure's dynamic range. This allows for values beyond the range of the original measure. Not all datasets will have oversaturated pairwise distances, nor will capture variation that resembles a manifold, so LMdist adjusts only those pairwise values which may be undervalued in the presence of a sampled gradient. The adjusted distances serve as input for ordination and statistical testing. We demonstrate on real and simulated data that LMdist effectively recovers distances along known gradients and along complex manifolds such as the Swiss roll dataset. LMdist enables more powerful statistical tests for gradient effects and reveals variation orthogonal to the gradient. AVAILABILITY AND IMPLEMENTATION Available on GitHub at https://github.com/knights-lab/LMdist.
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Affiliation(s)
- Susan L Hoops
- Department of Computer Science and Engineering, College of Science and Engineering, University of Minnesota, Minneapolis, MN 55455, United States
| | - Dan Knights
- Department of Computer Science and Engineering, College of Science and Engineering, University of Minnesota, Minneapolis, MN 55455, United States
- BioTechnology Institute, College of Biological Sciences, University of Minnesota, Saint Paul, MN 55108, United States
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Johnson KE, Heisel T, Fields DA, Isganaitis E, Jacobs KM, Knights D, Lock EF, Rudolph MC, Gale CA, Schleiss MR, Albert FW, Demerath EW, Blekhman R. Human Cytomegalovirus in breast milk is associated with milk composition, the infant gut microbiome, and infant growth. bioRxiv 2023:2023.07.19.549370. [PMID: 37503212 PMCID: PMC10370112 DOI: 10.1101/2023.07.19.549370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Human cytomegalovirus (CMV) is a highly prevalent herpesvirus that is often transmitted to the neonate via breast milk. Postnatal CMV transmission can have negative health consequences for preterm and immunocompromised infants, but any effects on healthy term infants are thought to be benign. Furthermore, the impact of CMV on the composition of the hundreds of bioactive factors in human milk has not been tested. Here, we utilize a cohort of exclusively breastfeeding full term mother-infant pairs to test for differences in the milk transcriptome and metabolome associated with CMV, and the impact of CMV in breast milk on the infant gut microbiome and infant growth. We find upregulation of the indoleamine 2,3- dioxygenase (IDO) tryptophan-to-kynurenine metabolic pathway in CMV+ milk samples, and that CMV+ milk is associated with decreased Bifidobacterium in the infant gut. Our data indicate a complex relationship between milk CMV, milk kynurenine, and infant growth; with kynurenine positively correlated, and CMV viral load negatively correlated, with infant weight-for-length at 1 month of age. These results suggest CMV transmission, CMV-related changes in milk composition, or both may be modulators of full term infant development.
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Affiliation(s)
- Kelsey E Johnson
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, USA
| | - Timothy Heisel
- Division of Neonatology, Department of Pediatrics, University of Minnesota Medical School, Minneapolis, MN, USA
| | - David A Fields
- Department of Pediatrics, Diabetes-Endocrinology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Elvira Isganaitis
- Pediatric, Adolescent and Young Adult Unit, Joslin Diabetes Center, Harvard Medical School, Boston, MA, USA
| | - Katherine M Jacobs
- Department of Obstetrics, Gynecology and Women's Health, Division of Maternal-Fetal Medicine, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Dan Knights
- BioTechnology Institute, College of Biological Sciences, University of Minnesota, Minneapolis, MN, USA
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Eric F Lock
- Division of Biostatistics, University of Minnesota School of Public Health, Minneapolis, MN, USA
| | - Michael C Rudolph
- Harold Hamm Diabetes Center, Department of Physiology, Oklahoma University Health Sciences Center, Oklahoma City, OK, USA
| | - Cheryl A Gale
- Division of Neonatology, Department of Pediatrics, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Mark R Schleiss
- Division of Pediatric Infectious Diseases and Immunology, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Frank W Albert
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, USA
| | - Ellen W Demerath
- Division of Epidemiology and Community Health, University of Minnesota School of Public Health, Minneapolis, MN, USA
| | - Ran Blekhman
- Section of Genetic Medicine, Division of Biological Sciences, University of Chicago, Chicago, IL, USA
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7
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La Reau AJ, Strom NB, Filvaroff E, Mavrommatis K, Ward TL, Knights D. Shallow shotgun sequencing reduces technical variation in microbiome analysis. Sci Rep 2023; 13:7668. [PMID: 37169816 PMCID: PMC10175443 DOI: 10.1038/s41598-023-33489-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 04/13/2023] [Indexed: 05/13/2023] Open
Abstract
The microbiome is known to play a role in many human diseases, but identifying key microbes and their functions generally requires large studies due to the vast number of species and genes, and the high levels of intra-individual and inter-individual variation. 16S amplicon sequencing of the rRNA gene is commonly used for large studies due to its comparatively low sequencing cost, but it has poor taxonomic and functional resolution. Deep shotgun sequencing is a more accurate and comprehensive alternative for small studies, but can be cost-prohibitive for biomarker discovery in large populations. Shallow or moderate-depth shotgun metagenomics may serve as a viable alternative to 16S sequencing for large-scale and/or dense longitudinal studies, but only if resolution and reproducibility are comparable. Here we applied both 16S and shallow shotgun stool microbiome sequencing to a cohort of 5 subjects sampled twice daily and weekly, with technical replication at the DNA extraction and the library preparation/sequencing steps, for a total of 80 16S samples and 80 shallow shotgun sequencing samples. We found that shallow shotgun sequencing produced lower technical variation and higher taxonomic resolution than 16S sequencing, at a much lower cost than deep shotgun sequencing. These findings suggest that shallow shotgun sequencing provides a more specific and more reproducible alternative to 16S sequencing for large-scale microbiome studies where costs prohibit deep shotgun sequencing and where bacterial species are expected to have good coverage in whole-genome reference databases.
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Affiliation(s)
- Alex J La Reau
- Diversigen, Inc., 600 County Road D, West, Suite 8, New Brighton, MN, 55112, USA.
| | - Noah B Strom
- Diversigen, Inc., 600 County Road D, West, Suite 8, New Brighton, MN, 55112, USA
| | - Ellen Filvaroff
- Bristol Myers Squibb, 1500 Owens St, Suite 600, San Francisco, CA, 94158, USA
| | | | - Tonya L Ward
- Diversigen, Inc., 600 County Road D, West, Suite 8, New Brighton, MN, 55112, USA
| | - Dan Knights
- Diversigen, Inc., 600 County Road D, West, Suite 8, New Brighton, MN, 55112, USA.
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, 55455, USA.
- Biotechnology Institute, College of Biological Sciences, University of Minnesota, Minneapolis, MN, 55455, USA.
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Johnson KE, Heisel T, Allert M, Fürst A, Yerabandi N, Knights D, Jacobs KM, Lock EF, Bode L, Fields DA, Rudolph MC, Gale CA, Albert FW, Demerath EW, Blekhman R. Human milk variation is shaped by maternal genetics and impacts the infant gut microbiome. bioRxiv 2023:2023.01.24.525211. [PMID: 36747843 PMCID: PMC9900818 DOI: 10.1101/2023.01.24.525211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Human milk is a complex mix of nutritional and bioactive components that provide complete nutrition for the infant. However, we lack a systematic knowledge of the factors shaping milk composition and how milk variation influences infant health. Here, we used multi-omic profiling to characterize interactions between maternal genetics, milk gene expression, milk composition, and the infant fecal microbiome in 242 exclusively breastfeeding mother-infant pairs. We identified 487 genetic loci associated with milk gene expression unique to the lactating mammary gland, including loci that impacted breast cancer risk and human milk oligosaccharide concentration. Integrative analyses uncovered connections between milk gene expression and infant gut microbiome, including an association between the expression of inflammation-related genes with IL-6 concentration in milk and the abundance of Bifidobacteria in the infant gut. Our results show how an improved understanding of the genetics and genomics of human milk connects lactation biology with maternal and infant health.
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Affiliation(s)
- Kelsey E Johnson
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, USA
| | - Timothy Heisel
- Division of Neonatology, Department of Pediatrics, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Mattea Allert
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, USA
| | - Annalee Fürst
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Nikhila Yerabandi
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Dan Knights
- BioTechnology Institute, College of Biological Sciences, University of Minnesota, Minneapolis, MN, USA
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Katherine M Jacobs
- Department of Obstetrics, Gynecology and Women's Health, Division of Maternal-Fetal Medicine, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Eric F Lock
- Division of Biostatistics, University of Minnesota School of Public Health, Minneapolis, MN, USA
| | - Lars Bode
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
- Human Milk Institute (HMI) and Mother-Milk-Infant Center of Research Excellence (MOMI CORE), University of California, San Diego, La Jolla, CA, USA
| | - David A Fields
- Department of Pediatrics, the University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Michael C Rudolph
- Harold Hamm Diabetes Center, Department of Physiology, the University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Cheryl A Gale
- Division of Neonatology, Department of Pediatrics, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Frank W Albert
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, USA
| | - Ellen W Demerath
- Division of Epidemiology and Community Health, University of Minnesota School of Public Health, Minneapolis, MN, USA
| | - Ran Blekhman
- Section of Genetic Medicine, Division of Biological Sciences, University of Chicago, Chicago, IL, USA
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9
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Heisel T, Johnson AJ, Gonia S, Dillon A, Skalla E, Haapala J, Jacobs KM, Nagel E, Pierce S, Fields D, Demerath E, Knights D, Gale CA. Bacterial, fungal, and interkingdom microbiome features of exclusively breastfeeding dyads are associated with infant age, antibiotic exposure, and birth mode. Front Microbiol 2022; 13:1050574. [PMID: 36466688 PMCID: PMC9714262 DOI: 10.3389/fmicb.2022.1050574] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 10/26/2022] [Indexed: 11/19/2022] Open
Abstract
The composition and function of early life gut bacterial communities (microbiomes) have been proposed to modulate health for the long term. In addition to bacteria, fungi (mycobiomes) also colonize the early life gut and have been implicated in health disorders such as asthma and obesity. Despite the potential importance of mycobiomes in health, there has been a lack of study regarding fungi and their interkingdom interactions with bacteria during infancy. The goal of this study was to obtain a more complete understanding of microbial communities thought to be relevant for the early life programming of health. Breastmilk and infant feces were obtained from a unique cohort of healthy, exclusively breastfeeding dyads recruited as part of the Mothers and Infants Linked for Healthy Growth (MILk) study with microbial taxa characterized using amplicon-based sequencing approaches. Bacterial and fungal communities in breastmilk were both distinct from those of infant feces, consistent with niche-specific microbial community development. Nevertheless, overlap was observed among sample types (breastmilk, 1-month feces, 6-month feces) with respect to the taxa that were the most prevalent and abundant. Self-reported antibacterial antibiotic exposure was associated with micro- as well as mycobiome variation, which depended upon the subject receiving antibiotics (mother or infant), timing of exposure (prenatal, peri- or postpartum), and sample type. In addition, birth mode was associated with bacterial and fungal community variation in infant feces, but not breastmilk. Correlations between bacterial and fungal taxa abundances were identified in all sample types. For infant feces, congruency between bacterial and fungal communities was higher for older infants, consistent with the idea of co-maturation of bacterial and fungal gut communities. Interkingdom connectedness also tended to be higher in older infants. Additionally, higher interkingdom connectedness was associated with Cesarean section birth and with antibiotic exposure for microbial communities of both breastmilk and infant feces. Overall, these results implicate infant age, birth mode, and antibiotic exposure in bacterial, fungal and interkingdom relationship variation in early-life-relevant microbiomes, expanding the current literature beyond bacteria.
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Affiliation(s)
- Timothy Heisel
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, United States
| | - Abigail J. Johnson
- School of Public Health, University of Minnesota, Minneapolis, MN, United States
| | - Sara Gonia
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, United States
| | - Abrielle Dillon
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, United States
| | - Emily Skalla
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, United States,School of Public Health, University of Minnesota, Minneapolis, MN, United States
| | - Jacob Haapala
- School of Public Health, University of Minnesota, Minneapolis, MN, United States,HealthPartners Institute, Minneapolis, MN, United States
| | - Katherine M. Jacobs
- Department of Obstetrics, Gynecology, and Women’s Health, University of Minnesota, Minneapolis, MN, United States
| | - Emily Nagel
- School of Public Health, University of Minnesota, Minneapolis, MN, United States
| | - Stephanie Pierce
- College of Medicine, University of Oklahoma, Oklahoma City, OK, United States
| | - David Fields
- College of Medicine, University of Oklahoma, Oklahoma City, OK, United States
| | - Ellen Demerath
- School of Public Health, University of Minnesota, Minneapolis, MN, United States
| | - Dan Knights
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, United States
| | - Cheryl A. Gale
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, United States,*Correspondence: Cheryl A. Gale,
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Bantle A, Alvear A, Knights D, Chow L, Johnson A. Weight Loss Associated With Time Restricted Eating Is Not Reflected in Changes in the Human Gut Microbiome. Curr Dev Nutr 2022. [PMCID: PMC9194336 DOI: 10.1093/cdn/nzac069.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Abstract
Objectives
Time-restricted eating (TRE) is a novel approach to obesity treatment that recently received attention. Very limited data exist regarding gut microbiome changes during TRE interventions in humans. Our objective was to characterize the gut microbiome of human participants before and after a 12-week TRE intervention.
Methods
In a randomized controlled trial of an 8-hour TRE intervention in human participants over 12 weeks, Chow, et al. demonstrated reduction in weight, lean mass, and visceral fat with TRE compared to control. Stool samples were collected before and after the intervention by study participants using home kits, placed in RNAlater Stabilization Solution (Ambion), and kept < at room temperature for < 7 days before storage in a −80°C freezer. Samples were submitted as a batch to the University of Minnesota Genomics Center for DNA extraction, amplification, and shotgun metagenomic DNA sequencing (Illumina HiSeq platform). Quality-controlled sequences were aligned to the GTDB Genome Taxonomy Database (https://gtdb.ecogenomic.org).
Results
Sixteen study participants provided stool samples which were used in this analysis (8 TRE and 8 control). Participants undergoing the TRE intervention successfully restricted their eating window (mean ± SD 15.3 ± 0.8 hours at baseline to 9.3 ± 1.7 hours during intervention, p < 0.001). The control group's eating window remained unchanged. Weight loss, visceral fat loss, and BMI reduction were significantly greater for the TRE group. There was no significant effect of the TRE intervention on alpha diversity (Shannon index, Simpson index, and number of taxa, linear mixed models), beta diversity (Bray-curtis, PERMANOVA), or overall microbiome composition controlling for weight change and visceral fat change.
Conclusions
Our analyses did not show any difference in gut microbiome composition or diversity indices in participants completing a TRE intervention as compared to control, but are limited by small sample size, short study duration, and stool-sampling at only two study timepoints.
Funding Sources
This work was supported by the University of Minnesota and grants from the National Institute of Diabetes and Digestive and Kidney Diseases and National Center for Advancing Translational Sciences.
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Priya S, Burns MB, Ward T, Mars RAT, Adamowicz B, Lock EF, Kashyap PC, Knights D, Blekhman R. Identification of shared and disease-specific host gene-microbiome associations across human diseases using multi-omic integration. Nat Microbiol 2022; 7:780-795. [PMID: 35577971 PMCID: PMC9159953 DOI: 10.1038/s41564-022-01121-z] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [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] [Received: 03/01/2021] [Accepted: 04/06/2022] [Indexed: 12/19/2022]
Abstract
While gut microbiome and host gene regulation independently contribute to gastrointestinal disorders, it is unclear how the two may interact to influence host pathophysiology. Here we developed a machine learning-based framework to jointly analyse paired host transcriptomic (n = 208) and gut microbiome (n = 208) profiles from colonic mucosal samples of patients with colorectal cancer, inflammatory bowel disease and irritable bowel syndrome. We identified associations between gut microbes and host genes that depict shared as well as disease-specific patterns. We found that a common set of host genes and pathways implicated in gastrointestinal inflammation, gut barrier protection and energy metabolism are associated with disease-specific gut microbes. Additionally, we also found that mucosal gut microbes that have been implicated in all three diseases, such as Streptococcus, are associated with different host pathways in each disease, suggesting that similar microbes can affect host pathophysiology in a disease-specific manner through regulation of different host genes. Our framework can be applied to other diseases for the identification of host gene-microbiome associations that may influence disease outcomes.
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Affiliation(s)
- Sambhawa Priya
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, USA
- Bioinformatics and Computational Biology, University of Minnesota, Minneapolis, MN, USA
| | - Michael B Burns
- Department of Biology, Loyola University Chicago, Chicago, IL, USA
| | - Tonya Ward
- BioTechnology Institute, College of Biological Sciences, University of Minnesota, Minneapolis, MN, USA
| | - Ruben A T Mars
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Mayo Clinic, Rochester, MN, USA
| | - Beth Adamowicz
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, USA
| | - Eric F Lock
- Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, MN, USA
| | - Purna C Kashyap
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Mayo Clinic, Rochester, MN, USA
| | - Dan Knights
- BioTechnology Institute, College of Biological Sciences, University of Minnesota, Minneapolis, MN, USA
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Ran Blekhman
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, USA.
- Department of Ecology, Evolution, and Behavior, University of Minnesota, Minneapolis, MN, USA.
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12
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Deehan EC, Zhang Z, Riva A, Armet AM, Perez-Muñoz ME, Nguyen NK, Krysa JA, Seethaler B, Zhao YY, Cole J, Li F, Hausmann B, Spittler A, Nazare JA, Delzenne NM, Curtis JM, Wismer WV, Proctor SD, Bakal JA, Bischoff SC, Knights D, Field CJ, Berry D, Prado CM, Walter J. Elucidating the role of the gut microbiota in the physiological effects of dietary fiber. Microbiome 2022; 10:77. [PMID: 35562794 PMCID: PMC9107176 DOI: 10.1186/s40168-022-01248-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 02/16/2022] [Indexed: 05/12/2023]
Abstract
BACKGROUND Dietary fiber is an integral part of a healthy diet, but questions remain about the mechanisms that underlie effects and the causal contributions of the gut microbiota. Here, we performed a 6-week exploratory trial in adults with excess weight (BMI: 25-35 kg/m2) to compare the effects of a high-dose (females: 25 g/day; males: 35 g/day) supplement of fermentable corn bran arabinoxylan (AX; n = 15) with that of microbiota-non-accessible microcrystalline cellulose (MCC; n = 16). Obesity-related surrogate endpoints and biomarkers of host-microbiome interactions implicated in the pathophysiology of obesity (trimethylamine N-oxide, gut hormones, cytokines, and measures of intestinal barrier integrity) were assessed. We then determined whether clinical outcomes could be predicted by fecal microbiota features or mechanistic biomarkers. RESULTS AX enhanced satiety after a meal and decreased homeostatic model assessment of insulin resistance (HOMA-IR), while MCC reduced tumor necrosis factor-α and fecal calprotectin. Machine learning models determined that effects on satiety could be predicted by fecal bacterial taxa that utilized AX, as identified by bioorthogonal non-canonical amino acid tagging. Reductions in HOMA-IR and calprotectin were associated with shifts in fecal bile acids, but correlations were negative, suggesting that the benefits of fiber may not be mediated by their effects on bile acid pools. Biomarkers of host-microbiome interactions often linked to bacterial metabolites derived from fiber fermentation (short-chain fatty acids) were not affected by AX supplementation when compared to non-accessible MCC. CONCLUSION This study demonstrates the efficacy of purified dietary fibers when used as supplements and suggests that satietogenic effects of AX may be linked to bacterial taxa that ferment the fiber or utilize breakdown products. Other effects are likely microbiome independent. The findings provide a basis for fiber-type specific therapeutic applications and their personalization. TRIAL REGISTRATION Clinicaltrials.gov, NCT02322112 , registered on July 3, 2015. Video Abstract.
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Affiliation(s)
- Edward C. Deehan
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta Canada
| | - Zhengxiao Zhang
- Department of Medicine, University of Alberta, Edmonton, Alberta Canada
- College of Food and Biological Engineering, Jimei University, Xiamen, Fujian China
| | - Alessandra Riva
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Anissa M. Armet
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta Canada
| | - Maria Elisa Perez-Muñoz
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta Canada
| | - Nguyen K. Nguyen
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta Canada
| | - Jacqueline A. Krysa
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta Canada
- Metabolic and Cardiovascular Disease Laboratory, University of Alberta, Edmonton, Alberta Canada
| | - Benjamin Seethaler
- Institute of Nutritional Medicine, University of Hohenheim, Stuttgart, Germany
| | - Yuan-Yuan Zhao
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta Canada
| | - Janis Cole
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta Canada
| | - Fuyong Li
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta Canada
| | - Bela Hausmann
- Joint Microbiome Facility of the Medical University of Vienna and University of Vienna, Vienna, Austria
- Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - Andreas Spittler
- Core Facility Flow Cytometry and Department of Surgery, Research Lab, Medical University of Vienna, Vienna, Austria
| | - Julie-Anne Nazare
- Centre de Recherche en Nutrition Humaine Rhône-Alpes, Univ-Lyon, CarMeN Laboratory, INSERM, INRA, INSA Lyon, Université Claude Bernard Lyon 1, Hospices Civils de Lyon, F-CRIN/FORCE Network, Pierre-Bénite, France
| | - Nathalie M. Delzenne
- Metabolism and Nutrition Research Group, Louvain Drug Research Institute, Université Catholique de Louvain, Brussels, Belgium
| | - Jonathan M. Curtis
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta Canada
| | - Wendy V. Wismer
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta Canada
| | - Spencer D. Proctor
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta Canada
- Metabolic and Cardiovascular Disease Laboratory, University of Alberta, Edmonton, Alberta Canada
| | - Jeffrey A. Bakal
- Patient Health Outcomes Research and Clinical Effectiveness Unit, Division of General Internal Medicine, University of Alberta, Edmonton, Alberta Canada
| | - Stephan C. Bischoff
- Institute of Nutritional Medicine, University of Hohenheim, Stuttgart, Germany
| | - Dan Knights
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, Minnesota USA
- BioTechnology Institute, University of Minnesota, Saint Paul, Minnesota USA
| | - Catherine J. Field
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta Canada
| | - David Berry
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
- Joint Microbiome Facility of the Medical University of Vienna and University of Vienna, Vienna, Austria
| | - Carla M. Prado
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta Canada
| | - Jens Walter
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta Canada
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta Canada
- APC Microbiome Ireland, School of Microbiology, and Department of Medicine, University College Cork – National University of Ireland, Cork, Ireland
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13
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Samara J, Moossavi S, Alshaikh B, Ortega VA, Pettersen VK, Ferdous T, Hoops SL, Soraisham A, Vayalumkal J, Dersch-Mills D, Gerber JS, Mukhopadhyay S, Puopolo K, Tompkins TA, Knights D, Walter J, Amin H, Arrieta MC. Supplementation with a probiotic mixture accelerates gut microbiome maturation and reduces intestinal inflammation in extremely preterm infants. Cell Host Microbe 2022; 30:696-711.e5. [PMID: 35550672 DOI: 10.1016/j.chom.2022.04.005] [Citation(s) in RCA: 57] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 02/08/2022] [Accepted: 04/11/2022] [Indexed: 11/19/2022]
Abstract
Probiotics are increasingly administered to premature infants to prevent necrotizing enterocolitis and neonatal sepsis. However, their effects on gut microbiome assembly and immunity are poorly understood. Using a randomized intervention trial in extremely premature infants, we tested the effects of a probiotic product containing four strains of Bifidobacterium species autochthonous to the infant gut and one Lacticaseibacillus strain on the compositional and functional trajectory of microbiome. Daily administration of the mixture accelerated the transition into a mature, term-like microbiome with higher stability and species interconnectivity. Besides infant age, Bifidobacterium strains and stool metabolites were the best predictors of microbiome maturation, and structural equation modeling confirmed probiotics as a major determinant for the trajectory of microbiome assembly. Bifidobacterium-driven microbiome maturation was also linked to an anti-inflammatory intestinal immune milieu. This demonstrates that Bifidobacterium strains are ecosystem engineers that lead to an acceleration of microbiome maturation and immunological consequences in extremely premature infants.
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Affiliation(s)
- Jumana Samara
- Department of Physiology and Pharmacology, Snyder Institute for Chronic Diseases, University of Calgary, Calgary, AB, Canada; Department of Pediatrics, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada; International Microbiome Centre, University of Calgary, Calgary, AB, Canada; Health Sciences Centre, Winnipeg, MB, Canada
| | - Shirin Moossavi
- Department of Physiology and Pharmacology, Snyder Institute for Chronic Diseases, University of Calgary, Calgary, AB, Canada; Department of Pediatrics, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada; International Microbiome Centre, University of Calgary, Calgary, AB, Canada; Microbiome and Microbial Ecology Interest Group (MMEIG), Universal Scientific Education and Research Network (USERN), Calgary, Canada
| | - Belal Alshaikh
- Department of Pediatrics, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada; Calgary Zone Section of Neonatology, Calgary, AB, Canada
| | - Van A Ortega
- Department of Physiology and Pharmacology, Snyder Institute for Chronic Diseases, University of Calgary, Calgary, AB, Canada; Department of Pediatrics, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada; International Microbiome Centre, University of Calgary, Calgary, AB, Canada
| | - Veronika Kuchařová Pettersen
- Department of Physiology and Pharmacology, Snyder Institute for Chronic Diseases, University of Calgary, Calgary, AB, Canada; Department of Pediatrics, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada; International Microbiome Centre, University of Calgary, Calgary, AB, Canada; Department of Medical Biology, UiT The Arctic University of Norway, Tromsø, Norway
| | - Tahsin Ferdous
- Department of Physiology and Pharmacology, Snyder Institute for Chronic Diseases, University of Calgary, Calgary, AB, Canada; Department of Pediatrics, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada; International Microbiome Centre, University of Calgary, Calgary, AB, Canada
| | - Suzie L Hoops
- Biotechnology Institute and Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Amuchou Soraisham
- Department of Pediatrics, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada; Calgary Zone Section of Neonatology, Calgary, AB, Canada
| | - Joseph Vayalumkal
- Department of Pediatrics, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada
| | - Deonne Dersch-Mills
- Department of Pediatrics, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada; Calgary Zone Section of Neonatology, Calgary, AB, Canada
| | - Jeffrey S Gerber
- Division of Infectious Diseases, Children's Hospital of Philadelphia, Philadelphia, PA, USA; Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Sagori Mukhopadhyay
- Newborn Care at Children's Hospital of Philadelphia, Philadelphia, PA, USA; Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Karen Puopolo
- Newborn Care at Children's Hospital of Philadelphia, Philadelphia, PA, USA; Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | | | - Dan Knights
- Biotechnology Institute and Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Jens Walter
- School of Microbiology, Department of Medicine, and APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Harish Amin
- Department of Pediatrics, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada; Calgary Zone Section of Neonatology, Calgary, AB, Canada
| | - Marie-Claire Arrieta
- Department of Physiology and Pharmacology, Snyder Institute for Chronic Diseases, University of Calgary, Calgary, AB, Canada; Department of Pediatrics, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada; International Microbiome Centre, University of Calgary, Calgary, AB, Canada.
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Haq IU, Hillmann B, Moran M, Willard S, Knights D, Fixen KR, Schilling JS. Bacterial communities associated with wood rot fungi that use distinct decomposition mechanisms. ISME Commun 2022; 2:26. [PMID: 37938255 PMCID: PMC9723729 DOI: 10.1038/s43705-022-00108-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 02/08/2022] [Accepted: 02/10/2022] [Indexed: 05/11/2023]
Abstract
Wood decomposer fungi are grouped by how they extract sugars from lignocellulose. Brown rot fungi selectively degrade cellulose and hemicellulose, leaving lignin intact, and white rot fungi degrade all components. Many trees are susceptible to both rot types, giving carbon in Earth's woody biomass, specifically lignin, a flexible fate that is affected not only by the fungal decomposition mechanism but also the associated microbial community. However, little is understood about how rot type may influence the microbial community in decaying wood. In this study, we quantified bacterial communities associated with Fomes fomentarius (white rot) and Fomitopsis betulina (brown rot) found on a shared tree host species, birch (Betula papyrifera). We collected 25 wood samples beneath sporocarps of F. fomentarius (n = 13) and F. betulina (n = 12) on standing dead trees, and coupled microbial DNA sequencing with chemical signatures of rot type (pH and lignin removal). We found that bacterial communities for both fungi were dominated by Proteobacteria, a commonly reported association. However, rot type exerted significant influence on less abundant taxa in ways that align logically with fungal traits. Amplicon sequence variants (ASVs) were enriched in Firmicutes in white-rotted wood, and were enriched in Alphaproteobacteria, Actinobacteria and Acidobacteria in lower pH brown rot. Our results suggest that wood decomposer strategies may exert significant selection effects on bacteria, or vice versa, among less-abundant taxa that have been overlooked when using abundance as the only measure of influence.
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Affiliation(s)
- Irshad Ul Haq
- Department of Plant and Microbial Biology, College of Biological Sciences, University of Minnesota, St. Paul, MN, USA
- Biotechnology Institute, College of Biological Sciences, University of Minnesota, Minneapolis, MN, USA
| | - Benjamin Hillmann
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Molly Moran
- Department of Plant and Microbial Biology, College of Biological Sciences, University of Minnesota, St. Paul, MN, USA
| | - Samuel Willard
- Department of Life Sciences, Imperial College London, London, UK
| | - Dan Knights
- Biotechnology Institute, College of Biological Sciences, University of Minnesota, Minneapolis, MN, USA
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Kathryn R Fixen
- Department of Plant and Microbial Biology, College of Biological Sciences, University of Minnesota, St. Paul, MN, USA
- Biotechnology Institute, College of Biological Sciences, University of Minnesota, Minneapolis, MN, USA
| | - Jonathan S Schilling
- Department of Plant and Microbial Biology, College of Biological Sciences, University of Minnesota, St. Paul, MN, USA.
- Biotechnology Institute, College of Biological Sciences, University of Minnesota, Minneapolis, MN, USA.
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15
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Rinott E, Meir AY, Tsaban G, Zelicha H, Kaplan A, Knights D, Tuohy K, Scholz MU, Koren O, Stampfer MJ, Wang DD, Shai I, Youngster I. The effects of the Green-Mediterranean diet on cardiometabolic health are linked to gut microbiome modifications: a randomized controlled trial. Genome Med 2022; 14:29. [PMID: 35264213 PMCID: PMC8908597 DOI: 10.1186/s13073-022-01015-z] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [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] [Received: 04/29/2021] [Accepted: 01/24/2022] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Previous studies have linked the Mediterranean diet (MED) with improved cardiometabolic health, showing preliminary evidence for a mediating role of the gut microbiome. We recently suggested the Green-Mediterranean (Green-MED) diet as an improved version of the healthy MED diet, with increased consumption of plant-based foods and reduced meat intake. Here, we investigated the effects of MED interventions on the gut microbiota and cardiometabolic markers, and the interplay between the two, during the initial weight loss phase of the DIRECT-PLUS trial. METHODS In the DIRECT-PLUS study, 294 participants with abdominal obesity/dyslipidemia were prospectively randomized to one of three intervention groups: healthy dietary guidelines (standard science-based nutritional counseling), MED, and Green-MED. Both isocaloric MED and Green-MED groups were supplemented with 28g/day walnuts. The Green-MED group was further provided with daily polyphenol-rich green tea and Mankai aquatic plant (new plant introduced to a western population). Gut microbiota was profiled by 16S rRNA for all stool samples and shotgun sequencing for a select subset of samples. RESULTS Both MED diets induced substantial changes in the community structure of the gut microbiome, with the Green-MED diet leading to more prominent compositional changes, largely driven by the low abundant, "non-core," microorganisms. The Green-MED diet was associated with specific microbial changes, including enrichments in the genus Prevotella and enzymatic functions involved in branched-chain amino acid degradation, and reductions in the genus Bifidobacterium and enzymatic functions responsible for branched-chain amino acid biosynthesis. The MED and Green-MED diets were also associated with stepwise beneficial changes in body weight and cardiometabolic biomarkers, concomitantly with the increased plant intake and reduced meat intake. Furthermore, while the level of adherence to the Green-MED diet and its specific green dietary components was associated with the magnitude of changes in microbiome composition, changes in gut microbial features appeared to mediate the association between adherence to the Green-MED and body weight and cardiometabolic risk reduction. CONCLUSIONS Our findings support a mediating role of the gut microbiome in the beneficial effects of the Green-MED diet enriched with Mankai and green tea on cardiometabolic risk factors. TRIAL REGISTRATION The study was registered on ClinicalTrial.gov ( NCT03020186 ) on January 13, 2017.
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Affiliation(s)
- Ehud Rinott
- Faculty of Health Sciences, Ben-Gurion University of the Negev, 84105, Beer-Sheva, Israel
| | - Anat Yaskolka Meir
- Faculty of Health Sciences, Ben-Gurion University of the Negev, 84105, Beer-Sheva, Israel
| | - Gal Tsaban
- Faculty of Health Sciences, Ben-Gurion University of the Negev, 84105, Beer-Sheva, Israel
| | - Hila Zelicha
- Faculty of Health Sciences, Ben-Gurion University of the Negev, 84105, Beer-Sheva, Israel
| | - Alon Kaplan
- Faculty of Health Sciences, Ben-Gurion University of the Negev, 84105, Beer-Sheva, Israel
| | - Dan Knights
- BioTechnology Institute, University of Minnesota, Saint Paul, MN, 55108, USA
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Kieran Tuohy
- Department of Food Quality and Nutrition, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, San Michele all'Adige, 38016, Trento, Italy
- University of Leeds, School of Food Science and Nutrition, Leeds, LS2 9JT, UK
| | - Matthias Uwe Scholz
- Department of Food Quality and Nutrition, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, San Michele all'Adige, 38016, Trento, Italy
| | - Omry Koren
- Azrieli Faculty of Medicine, Bar Ilan University, Safed, Israel
| | - Meir J Stampfer
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Harvard T.H. Chan School of Public Health, Boston, USA
| | - Dong D Wang
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Iris Shai
- The Health & Nutrition Innovative International Research Center, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel.
| | - Ilan Youngster
- Pediatric Division and Center for Microbiome Research, Shamir Medical Center, Be'er Ya'akov, Israel.
- Sackler School of Medicine, Tel-Aviv University, Tel-Aviv, Israel.
- Pediatric Infectious Diseases Unit and the Center for Microbiome Research, Shamir Medical Center, 70300, Zerifin, Israel.
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16
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Gomes-Neto JC, Pavlovikj N, Cano C, Abdalhamid B, Al-Ghalith GA, Loy JD, Knights D, Iwen PC, Chaves BD, Benson AK. Heuristic and Hierarchical-Based Population Mining of Salmonella enterica Lineage I Pan-Genomes as a Platform to Enhance Food Safety. Front Sustain Food Syst 2021. [DOI: 10.3389/fsufs.2021.725791] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The recent incorporation of bacterial whole-genome sequencing (WGS) into Public Health laboratories has enhanced foodborne outbreak detection and source attribution. As a result, large volumes of publicly available datasets can be used to study the biology of foodborne pathogen populations at an unprecedented scale. To demonstrate the application of a heuristic and agnostic hierarchical population structure guided pan-genome enrichment analysis (PANGEA), we used populations of S. enterica lineage I to achieve two main objectives: (i) show how hierarchical population inquiry at different scales of resolution can enhance ecological and epidemiological inquiries; and (ii) identify population-specific inferable traits that could provide selective advantages in food production environments. Publicly available WGS data were obtained from NCBI database for three serovars of Salmonella enterica subsp. enterica lineage I (S. Typhimurium, S. Newport, and S. Infantis). Using the hierarchical genotypic classifications (Serovar, BAPS1, ST, cgMLST), datasets from each of the three serovars showed varying degrees of clonal structuring. When the accessory genome (PANGEA) was mapped onto these hierarchical structures, accessory loci could be linked with specific genotypes. A large heavy-metal resistance mobile element was found in the Monophasic ST34 lineage of S. Typhimurium, and laboratory testing showed that Monophasic isolates have on average a higher degree of copper resistance than the Biphasic ones. In S. Newport, an extra sugE gene copy was found among most isolates of the ST45 lineage, and laboratory testing of multiple isolates confirmed that isolates of S. Newport ST45 were on average less sensitive to the disinfectant cetylpyridimium chloride than non-ST45 isolates. Lastly, data-mining of the accessory genomic content of S. Infantis revealed two cryptic Ecotypes with distinct accessory genomic content and distinct ecological patterns. Poultry appears to be the major reservoir for Ecotype 1, and temporal analysis further suggested a recent ecological succession, with Ecotype 2 apparently being displaced by Ecotype 1. Altogether, the use of a heuristic hierarchical-based population structure analysis that includes bacterial pan-genomes (core and accessory genomes) can (1) improve genomic resolution for mapping populations and accessing epidemiological patterns; and (2) define lineage-specific informative loci that may be associated with survival in the food chain.
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Mihindukulasuriya KA, Mars RAT, Johnson AJ, Ward T, Priya S, Lekatz HR, Kalari KR, Droit L, Zheng T, Blekhman R, D'Amato M, Farrugia G, Knights D, Handley SA, Kashyap PC. Multi-Omics Analyses Show Disease, Diet, and Transcriptome Interactions With the Virome. Gastroenterology 2021; 161:1194-1207.e8. [PMID: 34245762 PMCID: PMC8463486 DOI: 10.1053/j.gastro.2021.06.077] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [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: 04/16/2021] [Revised: 06/21/2021] [Accepted: 06/30/2021] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS The gut virome includes eukaryotic viruses and bacteriophages that can shape the gut bacterial community and elicit host responses. The virome can be implicated in diseases, such as irritable bowel syndrome (IBS), where gut bacteria play an important role in pathogenesis. We provide a comprehensive and longitudinal characterization of the virome, including DNA and RNA viruses and paired multi-omics data in a cohort of healthy subjects and patients with IBS. METHODS We selected 2 consecutive stool samples per subject from a longitudinal study cohort and performed metagenomic sequencing on DNA and RNA viruses after enriching for viral-like particles. Viral sequence abundance was evaluated over time, as well as in the context of diet, bacterial composition and function, metabolite levels, colonic gene expression, host genetics, and IBS subsets. RESULTS We found that the gut virome was temporally stable and correlated with the colonic transcriptome. We identified IBS-subset-specific changes in phage populations; Microviridae, Myoviridae, and Podoviridae species were elevated in diarrhea-predominant IBS, and other Microviridae and Myoviridae species were elevated in constipation-predominant IBS compared to healthy controls. We identified correlations between subsets of the virome and bacterial composition (unclassifiable "dark matter" and phages) and diet (eukaryotic viruses). CONCLUSIONS We found that the gut virome is stable over time but varies among subsets of patients with IBS. It can be affected by diet and potentially influences host function via interactions with gut bacteria and/or altering host gene expression.
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Affiliation(s)
| | - Ruben A T Mars
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Abigail J Johnson
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minneapolis, Minnesota
| | - Tonya Ward
- BioTechnology Institute, College of Biological Sciences, University of Minnesota, Minneapolis, Minnesota
| | - Sambhawa Priya
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota
| | - Heather R Lekatz
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Krishna R Kalari
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
| | - Lindsay Droit
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, Missouri
| | - Tenghao Zheng
- School of Biological Sciences, Monash University, Clayton, Victoria, Australia
| | - Ran Blekhman
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota
| | - Mauro D'Amato
- Gastrointestinal Genetics Laboratory, CIC bioGUNE, Basque Research and Technology Alliance, Derio, Spain; Ikerbasque, Basque Foundation for Science, Bilbao, Spain
| | - Gianrico Farrugia
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Dan Knights
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minneapolis, Minnesota; Department of Computer Science and Engineering, University of Minnesota, Minneapolis, Minnesota.
| | - Scott A Handley
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, Missouri.
| | - Purna C Kashyap
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota; Department of Medicine and Physiology, Mayo Clinic, Rochester, Minnesota.
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18
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Benny PA, Al-Akwaa FM, Dirkx C, Schlueter RJ, Wolfgruber TK, Chern IY, Hoops S, Knights D, Garmire LX. Placentas delivered by pre-pregnant obese women have reduced abundance and diversity in the microbiome. FASEB J 2021; 35:e21524. [PMID: 33742690 PMCID: PMC8251846 DOI: 10.1096/fj.202002184rr] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [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: 12/02/2020] [Revised: 02/26/2021] [Accepted: 02/26/2021] [Indexed: 12/12/2022]
Abstract
Maternal pre‐pregnancy obesity may have an impact on both maternal and fetal health. We examined the microbiome recovered from placentas in a multi‐ethnic maternal pre‐pregnant obesity cohort, through an optimized microbiome protocol to enrich low bacterial biomass samples. We found that the microbiomes recovered from the placentas of obese pre‐pregnant mothers are less abundant and less diverse when compared to those from mothers of normal pre‐pregnancy weight. Microbiome richness also decreases from the maternal side to the fetal side, demonstrating heterogeneity by geolocation within the placenta. In summary, our study shows that the microbiomes recovered from the placentas are associated with pre‐pregnancy obesity. Importance Maternal pre‐pregnancy obesity may have an impact on both maternal and fetal health. The placenta is an important organ at the interface of the mother and fetus, and supplies nutrients to the fetus. We report that the microbiomes enriched from the placentas of obese pre‐pregnant mothers are less abundant and less diverse when compared to those from mothers of normal pre‐pregnancy weight. More over, the microbiomes also vary by geolocation within the placenta.
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Affiliation(s)
- Paula A Benny
- Department of Epidemiology, University of Hawaii Cancer Center, Honolulu, HI, USA
| | - Fadhl M Al-Akwaa
- Department of Computational Medicine and Bioinformatics, North Campus Research Complex, University of Michigan, Ann Arbor, MI, USA
| | - Corbin Dirkx
- University of Minnesota Genomics Center, University of Minnesota- Twin Cities, Minneapolis, MN, USA
| | - Ryan J Schlueter
- Department of Obstetrics and Gynaecology, University of Hawaii, Honolulu, HI, USA
| | - Thomas K Wolfgruber
- Department of Epidemiology, University of Hawaii Cancer Center, Honolulu, HI, USA
| | - Ingrid Y Chern
- Department of Obstetrics and Gynaecology, University of Hawaii, Honolulu, HI, USA
| | - Suzie Hoops
- BioTechnology Institute, College of Biological Sciences, University of Minnesota, Minneapolis, MN, USA.,Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Dan Knights
- BioTechnology Institute, College of Biological Sciences, University of Minnesota, Minneapolis, MN, USA.,Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Lana X Garmire
- Department of Computational Medicine and Bioinformatics, North Campus Research Complex, University of Michigan, Ann Arbor, MI, USA
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19
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Khuat LT, Le CT, Pai CCS, Shields-Cutler RR, Holtan SG, Rashidi A, Parker SL, Knights D, Luna JI, Dunai C, Wang Z, Sturgill IR, Stoffel KM, Merleev AA, More SK, Maverakis E, Raybould HE, Chen M, Canter RJ, Monjazeb AM, Dave M, Ferrara JLM, Levine JE, Longo DL, Abedi M, Blazar BR, Murphy WJ. Obesity induces gut microbiota alterations and augments acute graft-versus-host disease after allogeneic stem cell transplantation. Sci Transl Med 2021; 12:12/571/eaay7713. [PMID: 33239390 DOI: 10.1126/scitranslmed.aay7713] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 01/22/2020] [Accepted: 06/02/2020] [Indexed: 12/22/2022]
Abstract
The efficacy of allogeneic hematopoietic stem cell transplantation (allo-HSCT) is limited by acute and chronic graft-versus-host disease (GVHD). The impact of obesity on allo-HSCT outcomes is poorly understood. Here, we report that obesity had a negative and selective impact on acute gut GVHD after allo-HSCT in mice with diet-induced obesity (DIO). These animals exhibited increased gut permeability, endotoxin translocation across the gut, and radiation-induced gastrointestinal damage after allo-HSCT. After allo-HSCT, both male and female DIO mouse recipients showed increased proinflammatory cytokine production and expression of the GVHD marker ST2 (IL-33R) and MHC class II molecules; they also exhibited decreased survival associated with acute severe gut GVHD. This rapid-onset, obesity-associated gut GVHD depended on donor CD4+ T cells and occurred even with a minor MHC mismatch between donor and recipient animals. Retrospective analysis of clinical cohorts receiving allo-HSCT transplants from unrelated donors revealed that recipients with a high body mass index (BMI, >30) had reduced survival and higher serum ST2 concentrations compared with nonobese transplant recipients. Assessment of both DIO mice and allo-HSCT recipients with a high BMI revealed reduced gut microbiota diversity and decreased Clostridiaceae abundance. Prophylactic antibiotic treatment protected DIO mouse recipients from endotoxin translocation across the gut and increased inflammatory cytokine production, as well as gut pathology and mortality, but did not protect against later development of chronic skin GVHD. These results suggest that obesity-induced alterations of the gut microbiota may affect GVHD after allo-HSCT in DIO mice, which could be ameliorated by prophylactic antibiotic treatment.
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Affiliation(s)
- Lam T Khuat
- Department of Dermatology, School of Medicine, University of California, Davis, Sacramento, CA 95817, USA
| | - Catherine T Le
- Department of Dermatology, School of Medicine, University of California, Davis, Sacramento, CA 95817, USA
| | - Chien-Chun Steven Pai
- Department of Dermatology, School of Medicine, University of California, Davis, Sacramento, CA 95817, USA
| | | | - Shernan G Holtan
- Blood and Marrow Transplant Program, University of Minnesota, Minneapolis, MN 55455, USA
| | - Armin Rashidi
- Blood and Marrow Transplant Program, University of Minnesota, Minneapolis, MN 55455, USA
| | - Sarah L Parker
- Department of Internal Medicine, University of Minnesota, Minneapolis, MN 55455, USA
| | - Dan Knights
- Department of Computer Science and Engineering, Biotechnology Institute, University of Minnesota, Minneapolis, MN 55455, USA
| | - Jesus I Luna
- Department of Dermatology, School of Medicine, University of California, Davis, Sacramento, CA 95817, USA
| | - Cordelia Dunai
- Department of Dermatology, School of Medicine, University of California, Davis, Sacramento, CA 95817, USA
| | - Ziming Wang
- Department of Dermatology, School of Medicine, University of California, Davis, Sacramento, CA 95817, USA
| | - Ian R Sturgill
- Department of Dermatology, School of Medicine, University of California, Davis, Sacramento, CA 95817, USA
| | - Kevin M Stoffel
- Department of Dermatology, School of Medicine, University of California, Davis, Sacramento, CA 95817, USA
| | - Alexander A Merleev
- Department of Dermatology, School of Medicine, University of California, Davis, Sacramento, CA 95817, USA
| | - Shyam K More
- Division of Gastroenterology, Department of Internal Medicine, School of Medicine, University of California, Davis, Sacramento, CA 95817, USA
| | - Emanual Maverakis
- Department of Dermatology, School of Medicine, University of California, Davis, Sacramento, CA 95817, USA
| | - Helen E Raybould
- Department of Anatomy, Physiology, and Cell Biology, School of Veterinary Medicine, University of California, Davis, Davis, CA 95616, USA
| | - Mingyi Chen
- Department of Pathology and Laboratory Medicine, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Robert J Canter
- Division of Surgical Oncology, Department of Surgery, School of Medicine, University of California, Davis, Sacramento, CA 95817, USA
| | - Arta M Monjazeb
- Department of Radiation Oncology, School of Medicine, University of California, Davis, Sacramento, CA 95817, USA
| | - Maneesh Dave
- Division of Gastroenterology, Department of Internal Medicine, School of Medicine, University of California, Davis, Sacramento, CA 95817, USA
| | - James L M Ferrara
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - John E Levine
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Dan L Longo
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Mehrdad Abedi
- Department of Internal Medicine, School of Medicine, University of California, Davis, Sacramento, CA 95817, USA
| | - Bruce R Blazar
- Masonic Cancer Center and Division of Blood and Marrow Transplantation, Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA
| | - William J Murphy
- Department of Dermatology, School of Medicine, University of California, Davis, Sacramento, CA 95817, USA. .,Department of Internal Medicine, School of Medicine, University of California, Davis, Sacramento, CA 95817, USA
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20
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Abstract
Abstract
Objectives
Health outcomes in previous fiber intervention studies have been variable, potentially due to differences in gut microbiome composition. This study aimed to determine if the effect of fiber intervention on the microbiome differs by initial microbiome or the quantity of fiber provided.
Methods
This study was designed as a randomized, un-blinded, cross-over trial of fiber cereal dosage. The cross-over design tested the effect of two 2-week long interventions with a High (28g) and Low (14g) level of daily supplemental fiber from whole wheat and bran cereal. Analysis was also completed on the overall study as a single arm, non-randomized, intervention of fiber cereal. The study enrolled 31 healthy adults. The microbiome was assessed at baseline and after intervention for changes in diversity, composition, and stability.
Results
Across all individuals, fiber intervention increased microbiome alpha-diversity (paired t-test, P = 0.047), but the microbiome was otherwise resistant to the effects of the intervention. Increasing fiber dose (High v. Low) was not associated with consistent changes in beta-diversity (linear mixed models). Approximately 20% of subjects were identified as responders based on beta diversity effect size. At baseline, responders had higher Prevotella copri and lower Bacteroides abundance than non-responders (Wilcoxon rank sum, qval < 0.05). In responders, fiber intake caused increased abundance of Bacteroides and Alistipes and reduced Prevotella (paired Wilcoxon, q < 0.2). In all subjects, fiber intervention decreased microbiome stability (paired Wilcoxon signed rank test, P = 0.006). In responders, there was a significant effect of the fiber level on stability, with higher fiber further lowering stability (linear mixed model, P = 0.05).
Conclusions
Our data suggest a responder/non-responder microbiome signature for this whole wheat and bran fiber cereal. We find that many effects were not additive by dosage level. Overall, microbiome diversity was increased and stability was decreased during the fiber cereal intervention and in responders this was dose dependent; the clinical implications of the impact of changes in stability remain unknown, and it is possible that the microbiome would stabilize in a longer intervention study. ClinicalTrials.gov identifier: NCT03623308.
Funding Sources
General Mills, Inc.
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Affiliation(s)
- Abigail Johnson
- Division of Epidemiology & Community Health, School of Public Health, University of Minnesota, Minneapolis, MN
| | - Mo Houtti
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN
| | - Anna Saboe
- BioTechnology Institute, College of Biological Sciences, University of Minnesota
| | - Katie Koecher
- Bell Institute of Health and Nutrition, General Mills Inc
| | - Ravi Menon
- Bell Institute of Health and Nutrition, General Mills Inc
| | - Dan Knights
- BioTechnology Institute, College of Biological Sciences, University of Minnesota
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21
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Bajaj JS, Sikaroodi M, Shamsaddini A, Henseler Z, Santiago-Rodriguez T, Acharya C, Fagan A, Hylemon PB, Fuchs M, Gavis E, Ward T, Knights D, Gillevet PM. Interaction of bacterial metagenome and virome in patients with cirrhosis and hepatic encephalopathy. Gut 2021; 70:1162-1173. [PMID: 32998876 DOI: 10.1136/gutjnl-2020-322470] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 08/18/2020] [Accepted: 08/30/2020] [Indexed: 02/06/2023]
Abstract
OBJECTIVE Altered bacterial composition is associated with disease progression in cirrhosis but the role of virome, especially phages, is unclear. DESIGN Cross-sectional and pre/post rifaximin cohorts were enrolled. Cross-sectional: controls and cirrhotic outpatients (compensated, on lactulose (Cirr-L), on rifaximin (Cirr-LR)) were included and followed for 90-day hospitalisations. Pre/post: compensated cirrhotics underwent stool collection pre/post 8 weeks of rifaximin. Stool metagenomics for bacteria and phages and their correlation networks were analysed in controls versus cirrhosis, within cirrhotics, hospitalised/not and pre/post rifaximin. RESULTS Cross-sectional: 40 controls and 163 cirrhotics (63 compensated, 43 Cirr-L, 57 Cirr-LR) were enrolled. Cirr-L/LR groups were similar on model for end-stage liver disease (MELD) score but Cirr-L developed greater hospitalisations versus Cirr-LR (56% vs 30%, p=0.008). Bacterial alpha/beta diversity worsened from controls through Cirr-LR. While phage alpha diversity was similar, beta diversity was different between groups. Autochthonous bacteria linked negatively, pathobionts linked positively with MELD but only modest phage-MELD correlations were seen. Phage-bacterial correlation network complexity was highest in controls, lowest in Cirr-L and increased in Cirr-LR. Microviridae and Faecalibacterium phages were linked with autochthonous bacteria in Cirr-LR, but not Cirr-L hospitalised patients had greater pathobionts, lower commensal bacteria and phages focused on Streptococcus, Lactococcus and Myoviridae. Pre/post: No changes in alpha/beta diversity of phages or bacteria were seen postrifaximin. Phage-bacterial linkages centred around urease-producing Streptococcus species collapsed postrifaximin. CONCLUSION Unlike bacteria, faecal phages are sparsely linked with cirrhosis characteristics and 90-day outcomes. Phage and bacterial linkages centred on urease-producing, ammonia-generating Streptococcus species were affected by disease progression and rifaximin therapy and were altered in patients who experienced 90-day hospitalisations.
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Affiliation(s)
- Jasmohan S Bajaj
- Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and Central Virginia Veterans Healthcare System, Richmond, Virginia, USA
| | - Masoumeh Sikaroodi
- Microbiome Analysis Center, George Mason University, Manassas, Virginia, USA
| | | | | | | | - Chathur Acharya
- Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and Central Virginia Veterans Healthcare System, Richmond, Virginia, USA
| | - Andrew Fagan
- Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and Central Virginia Veterans Healthcare System, Richmond, Virginia, USA
| | - Phillip B Hylemon
- Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and Central Virginia Veterans Healthcare System, Richmond, Virginia, USA
| | - Michael Fuchs
- Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and Central Virginia Veterans Healthcare System, Richmond, Virginia, USA
| | - Edith Gavis
- Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and Central Virginia Veterans Healthcare System, Richmond, Virginia, USA
| | - Tonya Ward
- Diversigen, New Brighton, Minnesota, USA
| | - Dan Knights
- Diversigen, New Brighton, Minnesota, USA.,Department of Computer Science and Engineering, U, University of Minnesota, Minneapolis, MN, USA.,Minnesota Biotechnology Institute, University of Minnesota, Minneapolis, MN, USA
| | - Patrick M Gillevet
- Microbiome Analysis Center, George Mason University, Manassas, Virginia, USA
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22
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Rinott E, Youngster I, Yaskolka Meir A, Tsaban G, Zelicha H, Kaplan A, Knights D, Tuohy K, Fava F, Scholz MU, Ziv O, Rubin E, Tirosh A, Rudich A, Blüher M, Stumvoll M, Ceglarek U, Clement K, Koren O, Wang DD, Hu FB, Stampfer MJ, Shai I. Effects of Diet-Modulated Autologous Fecal Microbiota Transplantation on Weight Regain. Gastroenterology 2021; 160:158-173.e10. [PMID: 32860791 PMCID: PMC7755729 DOI: 10.1053/j.gastro.2020.08.041] [Citation(s) in RCA: 74] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Revised: 08/10/2020] [Accepted: 08/20/2020] [Indexed: 12/30/2022]
Abstract
BACKGROUND & AIMS We evaluated the efficacy and safety of diet-modulated autologous fecal microbiota transplantation (aFMT) for treatment of weight regain after the weight-loss phase. METHODS In the DIRECT PLUS (Dietary Intervention Randomized Controlled Trial Polyphenols-Unprocessed) weight-loss trial (May 2017 through July 2018), abdominally obese or dyslipidemic participants in Israel were randomly assigned to healthy dietary guidelines, Mediterranean diet, and green-Mediterranean diet weight-loss groups. All groups received free gym membership and physical activity guidelines. Both isocaloric Mediterranean groups consumed 28 g/d walnuts (+440 mg/d polyphenols provided). The green-Mediterranean dieters also consumed green tea (3-4 cups/d) and a Wolffia globosa (Mankai strain, 100 g/d) green shake (+800 mg/d polyphenols provided). After 6 months (weight-loss phase), 90 eligible participants (mean age, 52 years; mean weight loss, 8.3 kg) provided a fecal sample that was processed into aFMT by frozen, opaque, and odorless capsules. The participants were then randomly assigned to groups that received 100 capsules containing their own fecal microbiota or placebo until month 14. The primary outcome was regain of the lost weight over the expected weight-regain phase (months 6-14). Secondary outcomes were gastrointestinal symptoms, waist circumference, glycemic status, and changes in the gut microbiome, as measured by metagenomic sequencing and 16s ribosomal RNA. We validated the results in a parallel in vivo study of mice specifically fed with Mankai compared with control chow diet. RESULTS Of the 90 participants in the aFMT trial, 96% ingested at least 80 of 100 oral aFMT or placebo frozen capsules during the transplantation period. No aFMT-related adverse events or symptoms were observed. For the primary outcome, although no significant differences in weight regain were observed among the participants in the different lifestyle interventions during months 6-14 (aFMT, 30.4% vs placebo, 40.6%; P = .28), aFMT significantly attenuated weight regain in the green-Mediterranean group (aFMT, 17.1%, vs placebo, 50%; P = .02), but not in the dietary guidelines (P = .57) or Mediterranean diet (P = .64) groups (P for the interaction = .03). Accordingly, aFMT attenuated waist circumference gain (aFMT, 1.89 cm vs placebo, 5.05 cm; P = .01) and insulin rebound (aFMT, -1.46 ± 3.6 μIU/mL vs placebo, 1.64 ± 4.7 μIU/mL; P = .04) in the green-Mediterranean group but not in the dietary guidelines or Mediterranean diet (P for the interaction = .04 and .03, respectively). The green-Mediterranean diet was the only intervention to induce a significant change in microbiome composition during the weight-loss phase, and to prompt preservation of weight-loss-associated specific bacteria and microbial metabolic pathways (mainly microbial sugar transport) after the aFMT. In mice, Mankai-modulated aFMT in the weight-loss phase compared with control diet aFMT, significantly prevented weight regain and resulted in better glucose tolerance during a high-fat diet-induced regain phase (all, P < .05). CONCLUSIONS Autologous FMT, collected during the weight-loss phase and administrated in the regain phase, might preserve weight loss and glycemic control, and is associated with specific microbiome signatures. A high-polyphenols, green plant-based or Mankai diet better optimizes the microbiome for an aFMT procedure. ClinicalTrials.gov number, NCT03020186.
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Affiliation(s)
- Ehud Rinott
- Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Ilan Youngster
- Pediatric Division and Center for Microbiome Research, Shamir Medical Center, Be'er Ya'akov, Israel; Sackler School of Medicine, Tel-Aviv University, Tel-Aviv, Israel.
| | - Anat Yaskolka Meir
- Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Gal Tsaban
- Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Hila Zelicha
- Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Alon Kaplan
- Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Dan Knights
- BioTechnology Institute, University of Minnesota, St Paul, Minnesota; Department of Computer Science and Engineering, University of Minnesota, Minneapolis, Minnesota
| | - Kieran Tuohy
- Department of Food Quality and Nutrition, Research and Innovation Centre, Fondazione Edmund Mach, Trento, Italy
| | - Francesca Fava
- Department of Food Quality and Nutrition, Research and Innovation Centre, Fondazione Edmund Mach, Trento, Italy
| | - Matthias Uwe Scholz
- Department of Food Quality and Nutrition, Research and Innovation Centre, Fondazione Edmund Mach, Trento, Italy
| | - Oren Ziv
- Azrieli Faculty of Medicine, Bar Ilan University, Safed, Israel
| | - Elad Rubin
- Azrieli Faculty of Medicine, Bar Ilan University, Safed, Israel
| | - Amir Tirosh
- Division of Endocrinology, Diabetes and Metabolism, Sheba Medical Center, Tel-Hashomer, Israel; Sackler School of Medicine, Tel-Aviv University, Tel-Aviv, Israel; Division of Endocrinology, Diabetes, and Hypertension, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Assaf Rudich
- Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | | | | | - Uta Ceglarek
- Department of Medicine, University of Leipzig, German
| | - Karine Clement
- Sorbonne University/Inserm, NutriOmics Research Unit, Nutrition Department, Pitié-Salpêtrière Hospital, Assistance-Publique Hopitaux de Paris, Paris, France
| | - Omry Koren
- Azrieli Faculty of Medicine, Bar Ilan University, Safed, Israel
| | - Dong D Wang
- Harvard T.H. Chan School of Public Health, Cambridge, Massachusetts
| | - Frank B Hu
- Harvard T.H. Chan School of Public Health, Cambridge, Massachusetts; Channing Division of Network Medicine, Department of Medicine, Harvard Medical School and Brigham and Women's Hospital, Boston, Massachusetts
| | - Meir J Stampfer
- Harvard T.H. Chan School of Public Health, Cambridge, Massachusetts; Channing Division of Network Medicine, Department of Medicine, Harvard Medical School and Brigham and Women's Hospital, Boston, Massachusetts
| | - Iris Shai
- Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel; Harvard T.H. Chan School of Public Health, Cambridge, Massachusetts.
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23
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Hillmann B, Al-Ghalith GA, Shields-Cutler RR, Zhu Q, Knight R, Knights D. SHOGUN: a modular, accurate and scalable framework for microbiome quantification. Bioinformatics 2020; 36:4088-4090. [PMID: 32365167 DOI: 10.1093/bioinformatics/btaa277] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 04/24/2020] [Indexed: 11/12/2022] Open
Abstract
SUMMARY The software pipeline SHOGUN profiles known taxonomic and gene abundances of short-read shotgun metagenomics sequencing data. The pipeline is scalable, modular and flexible. Data analysis and transformation steps can be run individually or together in an automated workflow. Users can easily create new reference databases and can select one of three DNA alignment tools, ranging from ultra-fast low-RAM k-mer-based database search to fully exhaustive gapped DNA alignment, to best fit their analysis needs and computational resources. The pipeline includes an implementation of a published method for taxonomy assignment disambiguation with empirical Bayesian redistribution. The software is installable via the conda resource management framework, has plugins for the QIIME2 and QIITA packages and produces both taxonomy and gene abundance profile tables with a single command, thus promoting convenient and reproducible metagenomics research. AVAILABILITY AND IMPLEMENTATION https://github.com/knights-lab/SHOGUN.
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Affiliation(s)
- Benjamin Hillmann
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, 55455 Minnesota, USA
| | - Gabriel A Al-Ghalith
- Bioinformatics and Computational Biology, University of Minnesota, Minneapolis, 55455 Minnesota, USA
| | | | - Qiyun Zhu
- Department of Pediatrics, University of California San Diego, San Diego, 92161 5 California, USA
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, San Diego, 92161 5 California, USA.,Department of Computer of Science and Engineering, University of California San Diego, San Diego, 92093 California, USA.,Center for Microbiome Innovation, University of California San Diego, San Diego, 92093 California, USA
| | - Dan Knights
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, 55455 Minnesota, USA.,Bioinformatics and Computational Biology, University of Minnesota, Minneapolis, 55455 Minnesota, USA.,Biotechnology Institute, University of Minnesota, Minneapolis, 55455 Minnesota, USA
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Turner G, Smith M, Hoeschen AL, Wilson JA, Kennedy J, Abramson M, Cao Q, El Jurdi N, MacMillan ML, Weisdorf DJ, Blazar BR, Khoruts A, Shields-Cutler RR, Knights D, Holtan SG, Rashidi A. Shotgun sequencing of the faecal microbiome to predict response to steroids in patients with lower gastrointestinal acute graft-versus-host disease: An exploratory analysis. Br J Haematol 2020; 192:e69-e73. [PMID: 33222185 DOI: 10.1111/bjh.17238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 10/22/2020] [Accepted: 10/25/2020] [Indexed: 11/30/2022]
Affiliation(s)
- Gavin Turner
- College of Biological Sciences, BioTechnology Institute, University of Minnesota, St. Paul, MN, USA
| | - Madeline Smith
- College of Biological Sciences, BioTechnology Institute, University of Minnesota, St. Paul, MN, USA
| | - Andrea L Hoeschen
- Clinical Trials Office, Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
| | | | - Jessica Kennedy
- College of Biological Sciences, BioTechnology Institute, University of Minnesota, St. Paul, MN, USA
| | - Max Abramson
- Department of Biology, Macalester College, St. Paul, MN, USA
| | - Qing Cao
- Biostatistics and Informatics, Clinical and Translational Science Institute, University of Minnesota, Minneapolis, MN, USA
| | - Najla El Jurdi
- Division of Hematology, Oncology, and Transplantation, Department of Medicine, University of Minnesota, Minneapolis, MN, USA
| | - Margaret L MacMillan
- Blood and Marrow Transplant Program, Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA
| | - Daniel J Weisdorf
- Division of Hematology, Oncology, and Transplantation, Department of Medicine, University of Minnesota, Minneapolis, MN, USA
| | - Bruce R Blazar
- Blood and Marrow Transplant Program, Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA
| | - Alexander Khoruts
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, University of Minnesota, Minneapolis, MN, USA
| | | | - Dan Knights
- College of Biological Sciences, BioTechnology Institute, University of Minnesota, St. Paul, MN, USA
| | - Shernan G Holtan
- Division of Hematology, Oncology, and Transplantation, Department of Medicine, University of Minnesota, Minneapolis, MN, USA
| | - Armin Rashidi
- Division of Hematology, Oncology, and Transplantation, Department of Medicine, University of Minnesota, Minneapolis, MN, USA
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Santiago-Rodriguez TM, Garoutte A, Adams E, Nasser W, Ross MC, La Reau A, Henseler Z, Ward T, Knights D, Petrosino JF, Hollister EB. Metagenomic Information Recovery from Human Stool Samples Is Influenced by Sequencing Depth and Profiling Method. Genes (Basel) 2020; 11:E1380. [PMID: 33233349 PMCID: PMC7700633 DOI: 10.3390/genes11111380] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 11/17/2020] [Accepted: 11/18/2020] [Indexed: 12/20/2022] Open
Abstract
Sequencing of the 16S rRNA gene (16S) has long been a go-to method for microbiome characterization due to its accessibility and lower cost compared to shotgun metagenomic sequencing (SMS). However, 16S sequencing rarely provides species-level resolution and cannot provide direct assessment of other taxa (e.g., viruses and fungi) or functional gene content. Shallow shotgun metagenomic sequencing (SSMS) has emerged as an approach to bridge the gap between 16S sequencing and deep metagenomic sequencing. SSMS is cost-competitive with 16S sequencing, while also providing species-level resolution and functional gene content insights. In the present study, we evaluated the effects of sequencing depth on marker gene-mapping- and alignment-based annotation of bacteria in healthy human stool samples. The number of identified taxa decreased with lower sequencing depths, particularly with the marker gene-mapping-based approach. Other annotations, including viruses and pathways, also showed a depth-dependent effect on feature recovery. These results refine the understanding of the suitability and shortcomings of SSMS, as well as annotation tools for metagenomic analyses in human stool samples. Results may also translate to other sample types and may open the opportunity to explore the effect of sequencing depth and annotation method.
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Affiliation(s)
| | - Aaron Garoutte
- Diversigen Inc., Houston, TX 77021, USA; (A.G.); (E.A.); (W.N.); (J.F.P.); (E.B.H.)
| | - Emmase Adams
- Diversigen Inc., Houston, TX 77021, USA; (A.G.); (E.A.); (W.N.); (J.F.P.); (E.B.H.)
| | - Waleed Nasser
- Diversigen Inc., Houston, TX 77021, USA; (A.G.); (E.A.); (W.N.); (J.F.P.); (E.B.H.)
| | - Matthew C. Ross
- Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, TX 77030, USA;
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Alex La Reau
- Diversigen Inc., Saint Paul, MN 55112, USA; (A.L.R.); (Z.H.); (T.W.); (D.K.)
| | - Zachariah Henseler
- Diversigen Inc., Saint Paul, MN 55112, USA; (A.L.R.); (Z.H.); (T.W.); (D.K.)
| | - Tonya Ward
- Diversigen Inc., Saint Paul, MN 55112, USA; (A.L.R.); (Z.H.); (T.W.); (D.K.)
| | - Dan Knights
- Diversigen Inc., Saint Paul, MN 55112, USA; (A.L.R.); (Z.H.); (T.W.); (D.K.)
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN 55455, USA
- Biotechnology Institute, College of Biological Sciences, University of Minnesota, Minneapolis, MN 55455, USA
| | - Joseph F. Petrosino
- Diversigen Inc., Houston, TX 77021, USA; (A.G.); (E.A.); (W.N.); (J.F.P.); (E.B.H.)
- Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, TX 77030, USA;
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Emily B. Hollister
- Diversigen Inc., Houston, TX 77021, USA; (A.G.); (E.A.); (W.N.); (J.F.P.); (E.B.H.)
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26
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Mars RAT, Yang Y, Ward T, Houtti M, Priya S, Lekatz HR, Tang X, Sun Z, Kalari KR, Korem T, Bhattarai Y, Zheng T, Bar N, Frost G, Johnson AJ, van Treuren W, Han S, Ordog T, Grover M, Sonnenburg J, D'Amato M, Camilleri M, Elinav E, Segal E, Blekhman R, Farrugia G, Swann JR, Knights D, Kashyap PC. Longitudinal Multi-omics Reveals Subset-Specific Mechanisms Underlying Irritable Bowel Syndrome. Cell 2020; 183:1137-1140. [PMID: 33186523 DOI: 10.1016/j.cell.2020.10.040] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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27
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Rengarajan S, Knoop KA, Rengarajan A, Chai JN, Grajales-Reyes JG, Samineni VK, Russler-Germain EV, Ranganathan P, Fasano A, Sayuk GS, Gereau RW, Kau AL, Knights D, Kashyap PC, Ciorba MA, Newberry RD, Hsieh CS. A Potential Role for Stress-Induced Microbial Alterations in IgA-Associated Irritable Bowel Syndrome with Diarrhea. Cell Rep Med 2020; 1. [PMID: 33196055 PMCID: PMC7659537 DOI: 10.1016/j.xcrm.2020.100124] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Stress is a known trigger for flares of inflammatory bowel disease (IBD) and irritable bowel syndrome (IBS); however, this process is not well understood. Here, we find that restraint stress in mice leads to signs of diarrhea, fecal dysbiosis, and a barrier defect via the opening of goblet-cell associated passages. Notably, stress increases host immunity to gut bacteria as assessed by immunoglobulin A (IgA)-bound gut bacteria. Stress-induced microbial changes are necessary and sufficient to elicit these effects. Moreover, similar to mice, many diarrhea-predominant IBS (IBS-D) patients from two cohorts display increased antibacterial immunity as assessed by IgA-bound fecal bacteria. This antibacterial IgA response in IBS-D correlates with somatic symptom severity and was distinct from healthy controls or IBD patients. These findings suggest that stress may play an important role in patients with IgA-associated IBS-D by disrupting the intestinal microbial community that alters gastrointestinal function and host immunity to commensal bacteria. Stress in mice causes diarrhea, dysbiosis, barrier defect, increased antibacterial IgA Stress-induced microbial changes are sufficient to elicit the above effects IBS-D patients from two cohorts display increased and unique antibacterial IgA Antibacterial IgA in IBS-D correlates with patient symptom severity
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Affiliation(s)
- Sunaina Rengarajan
- Department of Internal Medicine, Division of Rheumatology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Kathryn A Knoop
- Department of Internal Medicine, Division of Gastroenterology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Arvind Rengarajan
- Department of Internal Medicine, Division of Gastroenterology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Jiani N Chai
- Department of Internal Medicine, Division of Rheumatology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Jose G Grajales-Reyes
- Washington University Pain Center and Department of Anesthesiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Vijay K Samineni
- Washington University Pain Center and Department of Anesthesiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Emilie V Russler-Germain
- Department of Internal Medicine, Division of Rheumatology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Prabha Ranganathan
- Department of Internal Medicine, Division of Rheumatology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Alessio Fasano
- Center for Celiac Research and Treatment and Division of Pediatric Gastroenterology and Nutrition, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Gregory S Sayuk
- Department of Internal Medicine, Division of Gastroenterology, Washington University School of Medicine, St. Louis, MO 63110, USA.,Gastroenterology Section, John Cochran Veterans Affairs Medical Center, St. Louis, MO 63125, USA
| | - Robert W Gereau
- Washington University Pain Center and Department of Anesthesiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Andrew L Kau
- Center for Women's Infectious Disease Research and Department of Internal Medicine, Division of Allergy and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Dan Knights
- Biomedical Informatics and Computational Biology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Purna C Kashyap
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN 55905, USA
| | - Matthew A Ciorba
- Department of Internal Medicine, Division of Gastroenterology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Rodney D Newberry
- Department of Internal Medicine, Division of Gastroenterology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Chyi-Song Hsieh
- Department of Internal Medicine, Division of Rheumatology, Washington University School of Medicine, St. Louis, MO 63110, USA.,Lead Contact
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Mars RAT, Yang Y, Ward T, Houtti M, Priya S, Lekatz HR, Tang X, Sun Z, Kalari KR, Korem T, Bhattarai Y, Zheng T, Bar N, Frost G, Johnson AJ, van Treuren W, Han S, Ordog T, Grover M, Sonnenburg J, D'Amato M, Camilleri M, Elinav E, Segal E, Blekhman R, Farrugia G, Swann JR, Knights D, Kashyap PC. Longitudinal Multi-omics Reveals Subset-Specific Mechanisms Underlying Irritable Bowel Syndrome. Cell 2020; 182:1460-1473.e17. [PMID: 32916129 DOI: 10.1016/j.cell.2020.08.007] [Citation(s) in RCA: 171] [Impact Index Per Article: 42.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 05/25/2020] [Accepted: 07/31/2020] [Indexed: 12/15/2022]
Abstract
The gut microbiome has been implicated in multiple human chronic gastrointestinal (GI) disorders. Determining its mechanistic role in disease has been difficult due to apparent disconnects between animal and human studies and lack of an integrated multi-omics view of disease-specific physiological changes. We integrated longitudinal multi-omics data from the gut microbiome, metabolome, host epigenome, and transcriptome in the context of irritable bowel syndrome (IBS) host physiology. We identified IBS subtype-specific and symptom-related variation in microbial composition and function. A subset of identified changes in microbial metabolites correspond to host physiological mechanisms that are relevant to IBS. By integrating multiple data layers, we identified purine metabolism as a novel host-microbial metabolic pathway in IBS with translational potential. Our study highlights the importance of longitudinal sampling and integrating complementary multi-omics data to identify functional mechanisms that can serve as therapeutic targets in a comprehensive treatment strategy for chronic GI diseases. VIDEO ABSTRACT.
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Affiliation(s)
- Ruben A T Mars
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN 55905, USA
| | - Yi Yang
- Department of Metabolism, Digestion and Reproduction, Imperial College, London SW7 2AZ, UK
| | - Tonya Ward
- BioTechnology Institute, College of Biological Sciences, University of Minnesota, Minneapolis, MN 55455, USA
| | - Mo Houtti
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - Sambhawa Priya
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Heather R Lekatz
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN 55905, USA
| | - Xiaojia Tang
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Zhifu Sun
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Krishna R Kalari
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Tal Korem
- Department of Systems Biology, Columbia University, New York, NY 10032, USA; CIFAR Azrieli Global Scholars program, CIFAR, Toronto, ON M5G 1M1, Canada
| | - Yogesh Bhattarai
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN 55905, USA
| | - Tenghao Zheng
- School of Biological Sciences, Monash University, Clayton, 3800 VIC, Australia
| | - Noam Bar
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Gary Frost
- Department of Metabolism, Digestion and Reproduction, Imperial College, London SW7 2AZ, UK
| | - Abigail J Johnson
- BioTechnology Institute, College of Biological Sciences, University of Minnesota, Minneapolis, MN 55455, USA
| | - Will van Treuren
- Department of Microbiology and Immunology, Center for Human Microbiome Studies, Stanford University, Stanford, CA 94305, USA
| | - Shuo Han
- Department of Microbiology and Immunology, Center for Human Microbiome Studies, Stanford University, Stanford, CA 94305, USA
| | - Tamas Ordog
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN 55905, USA
| | - Madhusudan Grover
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN 55905, USA; Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN 55905, USA
| | - Justin Sonnenburg
- Department of Microbiology and Immunology, Center for Human Microbiome Studies, Stanford University, Stanford, CA 94305, USA
| | - Mauro D'Amato
- School of Biological Sciences, Monash University, Clayton, 3800 VIC, Australia
| | - Michael Camilleri
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN 55905, USA; Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN 55905, USA
| | - Eran Elinav
- Department of Immunology, Weizmann Institute of Science, Rehovot 76100, Israel; Division of Cancer-Microbiome Research, DKFZ, 69120 Heidelberg, Germany
| | - Eran Segal
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Ran Blekhman
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Gianrico Farrugia
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN 55905, USA; Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN 55905, USA
| | - Jonathan R Swann
- Department of Metabolism, Digestion and Reproduction, Imperial College, London SW7 2AZ, UK; School of Human Development and Health, Faculty of Medicine, University of Southampton, Southampton SO17 1BJ, UK
| | - Dan Knights
- BioTechnology Institute, College of Biological Sciences, University of Minnesota, Minneapolis, MN 55455, USA; Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Purna C Kashyap
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN 55905, USA; Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN 55905, USA.
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Prizment AE, Staley C, Onyeaghala GC, Vivek S, Thyagarajan B, Straka RJ, Demmer RT, Knights D, Meyer KA, Shaukat A, Sadowsky MJ, Church TR. Randomised clinical study: oral aspirin 325 mg daily vs placebo alters gut microbial composition and bacterial taxa associated with colorectal cancer risk. Aliment Pharmacol Ther 2020; 52:976-987. [PMID: 32770859 PMCID: PMC7719064 DOI: 10.1111/apt.16013] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 03/30/2020] [Accepted: 07/14/2020] [Indexed: 12/21/2022]
Abstract
BACKGROUND Aspirin is associated with decreased risk of colorectal cancer (CRC), potentially by modulating the gut microbiome. AIMS To evaluate the effect of aspirin on the gut microbiome in a double-blinded, randomised placebo-controlled pilot trial. METHODS Healthy volunteers aged 50-75 received a standard dose of aspirin (325 mg, N = 30) or placebo (N = 20) once daily for 6 weeks and provided stool samples every 3 weeks for 12 weeks. Serial measurements of gut microbial community composition and bacterial abundance were derived from 16S rRNA sequences. Linear discriminant analysis of effect size (LEfSe) was tested for between-arm differences in bacterial abundance. Mixed-effect regression with binomial distribution estimated the effect of aspirin use on changes in the relative abundance of individual bacterial taxa via an interaction term (treatment × time). RESULTS Over the study period, there were differences in microbial composition in the aspirin vs placebo arm. After treatment, four taxa were differentially abundant across arms: Prevotella, Veillonella, Clostridium XlVa and Clostridium XVIII clusters. Of pre-specified bacteria associated with CRC (n = 8) or aspirin intake (n = 4) in published studies, interactions were significant for four taxa, suggesting relative increases in Akkermansia, Prevotella and Ruminococcaceae and relative decreases in Parabacteroides, Bacteroides and Dorea in the aspirin vs placebo arm. CONCLUSION Compared to placebo, aspirin intake influenced several microbial taxa (Ruminococcaceae, Clostridium XlVa, Parabacteroides and Dorea) in a direction consistent with a priori hypothesis based on their association with CRC. This suggests that aspirin may influence CRC development through an effect on the gut microbiome. The findings need replication in a larger trial.
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30
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Nguyen NK, Deehan EC, Zhang Z, Jin M, Baskota N, Perez-Muñoz ME, Cole J, Tuncil YE, Seethaler B, Wang T, Laville M, Delzenne NM, Bischoff SC, Hamaker BR, Martínez I, Knights D, Bakal JA, Prado CM, Walter J. Gut microbiota modulation with long-chain corn bran arabinoxylan in adults with overweight and obesity is linked to an individualized temporal increase in fecal propionate. Microbiome 2020; 8:118. [PMID: 32814582 PMCID: PMC7439537 DOI: 10.1186/s40168-020-00887-w] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Accepted: 06/30/2020] [Indexed: 05/19/2023]
Abstract
BACKGROUND Variability in the health effects of dietary fiber might arise from inter-individual differences in the gut microbiota's ability to ferment these substrates into beneficial metabolites. Our understanding of what drives this individuality is vastly incomplete and will require an ecological perspective as microbiomes function as complex inter-connected communities. Here, we performed a parallel two-arm, exploratory randomized controlled trial in 31 adults with overweight and class-I obesity to characterize the effects of long-chain, complex arabinoxylan (n = 15) at high supplementation doses (female: 25 g/day; male: 35 g/day) on gut microbiota composition and short-chain fatty acid production as compared to microcrystalline cellulose (n = 16, non-fermentable control), and integrated the findings using an ecological framework. RESULTS Arabinoxylan resulted in a global shift in fecal bacterial community composition, reduced α-diversity, and the promotion of specific taxa, including operational taxonomic units related to Bifidobacterium longum, Blautia obeum, and Prevotella copri. Arabinoxylan further increased fecal propionate concentrations (p = 0.012, Friedman's test), an effect that showed two distinct groupings of temporal responses in participants. The two groups showed differences in compositional shifts of the microbiota (p ≤ 0.025, PERMANOVA), and multiple linear regression (MLR) analyses revealed that the propionate response was predictable through shifts and, to a lesser degree, baseline composition of the microbiota. Principal components (PCs) derived from community data were better predictors in MLR models as compared to single taxa, indicating that arabinoxylan fermentation is the result of multi-species interactions within microbiomes. CONCLUSION This study showed that long-chain arabinoxylan modulates both microbiota composition and the output of health-relevant SCFAs, providing information for a more targeted application of this fiber. Variation in propionate production was linked to both compositional shifts and baseline composition, with PCs derived from shifts of the global microbial community showing the strongest associations. These findings constitute a proof-of-concept for the merit of an ecological framework that considers features of the wider gut microbial community for the prediction of metabolic outcomes of dietary fiber fermentation. This provides a basis to personalize the use of dietary fiber in nutritional application and to stratify human populations by relevant gut microbiota features to account for the inconsistent health effects in human intervention studies. TRIAL REGISTRATION Clinicaltrials.gov, NCT02322112 , registered on July 3, 2015. Video Abstract.
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Affiliation(s)
- Nguyen K. Nguyen
- Department of Agricultural, Food & Nutritional Science, University of Alberta, Edmonton, AB T6G 2E1 Canada
| | - Edward C. Deehan
- Department of Agricultural, Food & Nutritional Science, University of Alberta, Edmonton, AB T6G 2E1 Canada
| | - Zhengxiao Zhang
- Department of Medicine, University of Alberta, Edmonton, AB T6G 2E1 Canada
| | - Mingliang Jin
- Department of Agricultural, Food & Nutritional Science, University of Alberta, Edmonton, AB T6G 2E1 Canada
- School of Life Science, Northwestern Polytechnical University, Xi’an, 710072 People’s Republic of China
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058 People’s Republic of China
| | - Nami Baskota
- Department of Agricultural, Food & Nutritional Science, University of Alberta, Edmonton, AB T6G 2E1 Canada
| | - Maria Elisa Perez-Muñoz
- Department of Agricultural, Food & Nutritional Science, University of Alberta, Edmonton, AB T6G 2E1 Canada
| | - Janis Cole
- Department of Agricultural, Food & Nutritional Science, University of Alberta, Edmonton, AB T6G 2E1 Canada
| | - Yunus E. Tuncil
- Food Engineering Department, Ordu University, 52200 Ordu, Turkey
- Whistler Center for Carbohydrate Research and Department of Food Science, Purdue University, West Lafayette, IN 47907 USA
| | - Benjamin Seethaler
- Institute of Nutritional Medicine, University of Hohenheim, 70593 Stuttgart, Germany
| | - Ting Wang
- Patient Health Outcomes Research and Clinical Effectiveness Unit, University of Alberta, Edmonton, AB T6G 2E1 Canada
| | - Martine Laville
- Centre de Recherche en Nutrition Humaine Rhône-Alpes and Centre Européen Nutrition Santé, 69310 Pierre Bénite, France
| | - Nathalie M. Delzenne
- Metabolism and Nutrition Research Group, Louvain Drug Research Institute, Université catholique de Louvain, 1200 Brussels, Belgium
| | - Stephan C. Bischoff
- Institute of Nutritional Medicine, University of Hohenheim, 70593 Stuttgart, Germany
| | - Bruce R. Hamaker
- Whistler Center for Carbohydrate Research and Department of Food Science, Purdue University, West Lafayette, IN 47907 USA
| | - Inés Martínez
- Department of Agricultural, Food & Nutritional Science, University of Alberta, Edmonton, AB T6G 2E1 Canada
| | - Dan Knights
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN 55455 USA
- BioTechnology Institute, University of Minnesota, Saint Paul, MN 55455 USA
| | - Jeffrey A. Bakal
- Patient Health Outcomes Research and Clinical Effectiveness Unit, University of Alberta, Edmonton, AB T6G 2E1 Canada
| | - Carla M. Prado
- Department of Agricultural, Food & Nutritional Science, University of Alberta, Edmonton, AB T6G 2E1 Canada
| | - Jens Walter
- Department of Agricultural, Food & Nutritional Science, University of Alberta, Edmonton, AB T6G 2E1 Canada
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E1 Canada
- School of Microbiology, Department of Medicine, and APC Microbiome Institute, University College Cork–National University of Ireland, Cork, T12 YT20 Ireland
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Abstract
Intense recent interest in understanding how the human gut microbiome influences health has kindled a concomitant interest in linking dietary choices to microbiome variation. Diet is known to be a driver of microbiome variation, and yet the precise mechanisms by which certain dietary components modulate the microbiome, and by which the microbiome produces byproducts and secondary metabolites from dietary components, are not well-understood. Interestingly, despite the influence of diet on the gut microbiome, the majority of microbiome studies published to date contain little or no analysis of dietary intake. Although an increasing number of microbiome studies are now collecting some form of dietary data or even performing diet interventions, there are no clear standards in the microbiome field for how to collect diet data or how to design a diet-microbiome study. In this article, we review the current practices in diet-microbiome analysis and study design and make several recommendations for best practices to provoke broader discussion in the field. We recommend that microbiome studies include multiple consecutive microbiome samples per study timepoint or phase and multiple days of dietary history prior to each microbiome sample whenever feasible. We find evidence that direct effects of diet on the microbiome are likely to be observable within days, while the length of an intervention required for observing microbiome-mediated effects on the host phenotype or host biomarkers, depending on the outcome, may be much longer, on the order of weeks or months. Finally, recent studies demonstrating that diet-microbiome interactions are personalized suggest that diet-microbiome studies should either include longitudinal sampling within individuals to identify personalized responses, or should include an adequate number of participants spanning a range of microbiome types to identify generalized responses.
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Affiliation(s)
- Abigail J Johnson
- BioTechnology Institute, College of Biological Sciences, University of Minnesota, Minneapolis, MN, United States
| | - Jack Jingyuan Zheng
- Department of Nutrition, University of California, Davis, Davis, CA, United States
| | - Jea Woo Kang
- Department of Nutrition, University of California, Davis, Davis, CA, United States
| | - Anna Saboe
- BioTechnology Institute, College of Biological Sciences, University of Minnesota, Minneapolis, MN, United States
| | - Dan Knights
- BioTechnology Institute, College of Biological Sciences, University of Minnesota, Minneapolis, MN, United States.,Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, United States
| | - Angela M Zivkovic
- Department of Nutrition, University of California, Davis, Davis, CA, United States
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Tompkins K, Nelson A, Litzau L, Everett B, Houtti M, Pornschloegl L, Lemmex A, Swanson L, Aird E, Evans R, Knights D, Gordon W. Uncovering and Exploiting HUH‐endonuclease ssDNA Recognition for Protein‐DNA Bioconjugation. FASEB J 2020. [DOI: 10.1096/fasebj.2020.34.s1.03070] [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: 11/11/2022]
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33
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Zhu L, Clayton JB, Suhr Van Haute MJ, Yang Q, Hassenstab HR, Mustoe AC, Knights D, Benson AK, French JA. Sex Bias in Gut Microbiome Transmission in Newly Paired Marmosets (Callithrix jacchus). mSystems 2020; 5:e00910-19. [PMID: 32209720 PMCID: PMC7093826 DOI: 10.1128/msystems.00910-19] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 03/10/2020] [Indexed: 01/28/2023] Open
Abstract
Social behavior can alter the microbiome composition via transmission among social partners, but there have been few controlled experimental studies of gut microbiome transmission among social partners in primates. We collected longitudinal fecal samples from eight unrelated male-female pairs of marmoset monkeys prior to pairing and for 8 weeks following pairing. We then sequenced 16S rRNA to characterize the changes in the gut microbiome that resulted from the pairing. Marmoset pairs had a higher similarity in gut microbiome communities after pairing than before pairing. We discovered sex differences in the degrees of change in gut microbiome communities following pairing. Specifically, the gut microbiome communities in males exhibited greater dissimilarity from the prepairing stage (baseline) than the gut microbiome communities in females. Conversely, females showed a gradual stabilization in the rate of the gut microbiome community turnover. Importantly, we found that the male fecal samples harbored more female-source gut microbes after pairing, especially early in pairing (paired test, P < 0.05), possibly linked to sex bias in the frequencies of social behavior. From this controlled study, we report for the first time that pair-living primates undergo significant changes in gut microbiome during pairing and that females transmit more microbes to their partners than males do. The potential biases influencing which microbes are transmitted on the basis of sex and whether they are due to sex biases in other behavioral or physiological features need to be widely investigated in other nonhuman primates and humans in the future.IMPORTANCE In this controlled study, we collected longitudinal fecal samples from 16 male and female marmoset monkeys for 2 weeks prior to and for 8 weeks after pairing in male-female dyads. We report for the first time that marmoset monkeys undergo significant changes to the gut microbiome following pairing and that these changes are sex-biased; i.e., females transmit more microbes to their social partners than males do. Marmosets exhibit pair bonding behavior such as spatial proximity, physical contact, and grooming, and sex biases in these behavioral patterns may contribute to the observed sex bias in social transmission of gut microbiomes.
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Affiliation(s)
- Lifeng Zhu
- Department of Biology, University of Nebraska at Omaha, Omaha, Nebraska, USA
- Nebraska Food for Health Center, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Jonathan B Clayton
- Department of Biology, University of Nebraska at Omaha, Omaha, Nebraska, USA
- Nebraska Food for Health Center, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Mallory J Suhr Van Haute
- Nebraska Food for Health Center, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Qinnan Yang
- Nebraska Food for Health Center, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Haley R Hassenstab
- Department of Biology, University of Nebraska at Omaha, Omaha, Nebraska, USA
| | - Aaryn C Mustoe
- Department of Biology, University of Nebraska at Omaha, Omaha, Nebraska, USA
- Nebraska Food for Health Center, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
- Department of Psychology, University of Nebraska at Omaha, Omaha, Nebraska, USA
| | - Dan Knights
- BioTechnology Institute, College of Biological Sciences, University of Minnesota, Minneapolis, Minnesota, USA
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, Minnesota, USA
| | - Andrew K Benson
- Nebraska Food for Health Center, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Jeffrey A French
- Department of Biology, University of Nebraska at Omaha, Omaha, Nebraska, USA
- Nebraska Food for Health Center, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
- Department of Psychology, University of Nebraska at Omaha, Omaha, Nebraska, USA
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34
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Johnson AJ, Vangay P, Al-Ghalith GA, Hillmann BM, Ward TL, Shields-Cutler RR, Kim AD, Shmagel AK, Syed AN, Walter J, Menon R, Koecher K, Knights D. Daily Sampling Reveals Personalized Diet-Microbiome Associations in Humans. Cell Host Microbe 2019; 25:789-802.e5. [PMID: 31194939 DOI: 10.1016/j.chom.2019.05.005] [Citation(s) in RCA: 357] [Impact Index Per Article: 71.4] [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: 10/06/2018] [Revised: 01/31/2019] [Accepted: 05/09/2019] [Indexed: 02/06/2023]
Abstract
Diet is a key determinant of human gut microbiome variation. However, the fine-scale relationships between daily food choices and human gut microbiome composition remain unexplored. Here, we used multivariate methods to integrate 24-h food records and fecal shotgun metagenomes from 34 healthy human subjects collected daily over 17 days. Microbiome composition depended on multiple days of dietary history and was more strongly associated with food choices than with conventional nutrient profiles, and daily microbial responses to diet were highly personalized. Data from two subjects consuming only meal replacement beverages suggest that a monotonous diet does not induce microbiome stability in humans, and instead, overall dietary diversity associates with microbiome stability. Our work provides key methodological insights for future diet-microbiome studies and suggests that food-based interventions seeking to modulate the gut microbiota may need to be tailored to the individual microbiome. Trial Registration: ClinicalTrials.gov: NCT03610477.
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Affiliation(s)
- Abigail J Johnson
- BioTechnology Institute, University of Minnesota, Saint Paul, MN 55108, USA
| | - Pajau Vangay
- Bioinformatics and Computational Biology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Gabriel A Al-Ghalith
- Bioinformatics and Computational Biology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Benjamin M Hillmann
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | | | | | - Austin D Kim
- Department of Mathematics, Statistics, and Computer Science, Macalester College, St. Paul, MN 55105, USA
| | - Anna Konstantinovna Shmagel
- Division of Rheumatic and Autoimmune Diseases, Department of Medicine, University of Minnesota, Minneapolis, MN 55455, USA
| | - Arzang N Syed
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | -
- Microbial Engineering Program, Biotechnology Institute, University of Minnesota, Minneapolis, MN 55455, USA
| | - Jens Walter
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada
| | - Ravi Menon
- Bell Institute of Health & Nutrition, General Mills Inc, Minneapolis, MN 55427, USA
| | - Katie Koecher
- Bell Institute of Health & Nutrition, General Mills Inc, Minneapolis, MN 55427, USA
| | - Dan Knights
- BioTechnology Institute, University of Minnesota, Saint Paul, MN 55108, USA; Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN 55455, USA.
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35
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Zhu Q, Mai U, Pfeiffer W, Janssen S, Asnicar F, Sanders JG, Belda-Ferre P, Al-Ghalith GA, Kopylova E, McDonald D, Kosciolek T, Yin JB, Huang S, Salam N, Jiao JY, Wu Z, Xu ZZ, Cantrell K, Yang Y, Sayyari E, Rabiee M, Morton JT, Podell S, Knights D, Li WJ, Huttenhower C, Segata N, Smarr L, Mirarab S, Knight R. Phylogenomics of 10,575 genomes reveals evolutionary proximity between domains Bacteria and Archaea. Nat Commun 2019; 10:5477. [PMID: 31792218 PMCID: PMC6889312 DOI: 10.1038/s41467-019-13443-4] [Citation(s) in RCA: 121] [Impact Index Per Article: 24.2] [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: 06/08/2019] [Accepted: 11/06/2019] [Indexed: 11/10/2022] Open
Abstract
Rapid growth of genome data provides opportunities for updating microbial evolutionary relationships, but this is challenged by the discordant evolution of individual genes. Here we build a reference phylogeny of 10,575 evenly-sampled bacterial and archaeal genomes, based on a comprehensive set of 381 markers, using multiple strategies. Our trees indicate remarkably closer evolutionary proximity between Archaea and Bacteria than previous estimates that were limited to fewer "core" genes, such as the ribosomal proteins. The robustness of the results was tested with respect to several variables, including taxon and site sampling, amino acid substitution heterogeneity and saturation, non-vertical evolution, and the impact of exclusion of candidate phyla radiation (CPR) taxa. Our results provide an updated view of domain-level relationships.
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Affiliation(s)
- Qiyun Zhu
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Uyen Mai
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
| | - Wayne Pfeiffer
- San Diego Supercomputer Center, University of California San Diego, La Jolla, CA, USA
| | - Stefan Janssen
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Algorithmic Bioinformatics, Department of Biology and Chemistry, Justus Liebig University Gießen, Giessen, Germany
| | | | - Jon G Sanders
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Pedro Belda-Ferre
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Gabriel A Al-Ghalith
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Evguenia Kopylova
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Daniel McDonald
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Tomasz Kosciolek
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - John B Yin
- Department of Electrical and Computer Engineering, University of California San Diego, La Jolla, CA, USA
- Department of Mathematics, University of California San Diego, La Jolla, CA, USA
| | - Shi Huang
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Single-Cell Center, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China
| | - Nimaichand Salam
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Jian-Yu Jiao
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Zijun Wu
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Zhenjiang Z Xu
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Kalen Cantrell
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Yimeng Yang
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Erfan Sayyari
- Department of Electrical and Computer Engineering, University of California San Diego, La Jolla, CA, USA
| | - Maryam Rabiee
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
| | - James T Morton
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
| | - Sheila Podell
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Dan Knights
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Curtis Huttenhower
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Nicola Segata
- Department CIBIO, University of Trento, Trento, Italy
| | - Larry Smarr
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
- California Institute for Telecommunications and Information Technology, University of California San Diego, La Jolla, CA, USA
| | - Siavash Mirarab
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA.
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA.
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA.
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36
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Bolyen E, Rideout JR, Dillon MR, Bokulich NA, Abnet CC, Al-Ghalith GA, Alexander H, Alm EJ, Arumugam M, Asnicar F, Bai Y, Bisanz JE, Bittinger K, Brejnrod A, Brislawn CJ, Brown CT, Callahan BJ, Caraballo-Rodríguez AM, Chase J, Cope EK, Da Silva R, Diener C, Dorrestein PC, Douglas GM, Durall DM, Duvallet C, Edwardson CF, Ernst M, Estaki M, Fouquier J, Gauglitz JM, Gibbons SM, Gibson DL, Gonzalez A, Gorlick K, Guo J, Hillmann B, Holmes S, Holste H, Huttenhower C, Huttley GA, Janssen S, Jarmusch AK, Jiang L, Kaehler BD, Kang KB, Keefe CR, Keim P, Kelley ST, Knights D, Koester I, Kosciolek T, Kreps J, Langille MGI, Lee J, Ley R, Liu YX, Loftfield E, Lozupone C, Maher M, Marotz C, Martin BD, McDonald D, McIver LJ, Melnik AV, Metcalf JL, Morgan SC, Morton JT, Naimey AT, Navas-Molina JA, Nothias LF, Orchanian SB, Pearson T, Peoples SL, Petras D, Preuss ML, Pruesse E, Rasmussen LB, Rivers A, Robeson MS, Rosenthal P, Segata N, Shaffer M, Shiffer A, Sinha R, Song SJ, Spear JR, Swafford AD, Thompson LR, Torres PJ, Trinh P, Tripathi A, Turnbaugh PJ, Ul-Hasan S, van der Hooft JJJ, Vargas F, Vázquez-Baeza Y, Vogtmann E, von Hippel M, Walters W, Wan Y, Wang M, Warren J, Weber KC, Williamson CHD, Willis AD, Xu ZZ, Zaneveld JR, Zhang Y, Zhu Q, Knight R, Caporaso JG. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat Biotechnol 2019; 37:852-857. [PMID: 31341288 DOI: 10.1038/s41587-019-0209-9] [Citation(s) in RCA: 8051] [Impact Index Per Article: 1610.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Evan Bolyen
- Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Jai Ram Rideout
- Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Matthew R Dillon
- Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Nicholas A Bokulich
- Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Christian C Abnet
- Metabolic Epidemiology Branch, National Cancer Institute, Rockville, MD, USA
| | - Gabriel A Al-Ghalith
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Harriet Alexander
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA.,Department of Population Health and Reproduction, University of California, Davis, Davis, CA, USA
| | - Eric J Alm
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.,Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Manimozhiyan Arumugam
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Yang Bai
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.,Centre of Excellence for Plant and Microbial Sciences (CEPAMS), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences & John Innes Centre, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jordan E Bisanz
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
| | - Kyle Bittinger
- Division of Gastroenterology and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Hepatology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Asker Brejnrod
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Colin J Brislawn
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - C Titus Brown
- Department of Population Health and Reproduction, University of California, Davis, Davis, CA, USA
| | - Benjamin J Callahan
- Department of Population Health & Pathobiology, North Carolina State University, Raleigh, NC, USA.,Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
| | - Andrés Mauricio Caraballo-Rodríguez
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
| | - John Chase
- Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Emily K Cope
- Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA.,Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Ricardo Da Silva
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
| | | | - Pieter C Dorrestein
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
| | - Gavin M Douglas
- Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Daniel M Durall
- Irving K. Barber School of Arts and Sciences, University of British Columbia, Kelowna, British Columbia, Canada
| | - Claire Duvallet
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Christian F Edwardson
- A. Watson Armour III Center for Animal Health and Welfare, Aquarium Microbiome Project, John G. Shedd Aquarium, Chicago, IL, USA
| | - Madeleine Ernst
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA.,Department of Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Mehrbod Estaki
- Department of Biology, University of British Columbia Okanagan, Okanagan, British Columbia, Canada
| | - Jennifer Fouquier
- Computational Bioscience Program, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.,Department of Medicine, Division of Biomedical Informatics and Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Julia M Gauglitz
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
| | - Sean M Gibbons
- Institute for Systems Biology, Seattle, WA, USA.,eScience Institute, University of Washington, Seattle, WA, USA
| | - Deanna L Gibson
- Irving K. Barber School of Arts and Sciences, Department of Biology, University of British Columbia, Kelowna, British Columbia, Canada.,Department of Medicine, University of British Columbia, Kelowna, British Columbia, Canada
| | - Antonio Gonzalez
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Kestrel Gorlick
- Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Jiarong Guo
- Center for Microbial Ecology, Michigan State University, East Lansing, MI, USA
| | - Benjamin Hillmann
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Susan Holmes
- Statistics Department, Stanford University, Palo Alto, CA, USA
| | - Hannes Holste
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.,Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
| | - Curtis Huttenhower
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Gavin A Huttley
- Research School of Biology, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Stefan Janssen
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Heinrich-Heine University Dusseldorf, Dusseldorf, Germany
| | - Alan K Jarmusch
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
| | - Lingjing Jiang
- Department of Family Medicine and Public Health, University of California San Diego, La Jolla, CA, USA
| | - Benjamin D Kaehler
- Research School of Biology, The Australian National University, Canberra, Australian Capital Territory, Australia.,School of Science, University of New South Wales, Canberra, Australian Capital Territory, Australia
| | - Kyo Bin Kang
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA.,College of Pharmacy, Sookmyung Women's University, Seoul, Republic of Korea
| | - Christopher R Keefe
- Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Paul Keim
- Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Scott T Kelley
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Dan Knights
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA.,Biotechnology Institute, University of Minnesota, Saint Paul, MN, USA
| | - Irina Koester
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA.,Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Tomasz Kosciolek
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Jorden Kreps
- Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Morgan G I Langille
- Department of Pharmacology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Joslynn Lee
- Science Education, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Ruth Ley
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen, Germany.,Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Yong-Xin Liu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.,Centre of Excellence for Plant and Microbial Sciences (CEPAMS), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences & John Innes Centre, Beijing, China
| | - Erikka Loftfield
- Metabolic Epidemiology Branch, National Cancer Institute, Rockville, MD, USA
| | - Catherine Lozupone
- Department of Medicine, Division of Biomedical Informatics and Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Massoud Maher
- Department of Computer Science & Engineering, University of California San Diego, La Jolla, CA, USA
| | - Clarisse Marotz
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Bryan D Martin
- Department of Statistics, University of Washington, Seattle, WA, USA
| | - Daniel McDonald
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Lauren J McIver
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Alexey V Melnik
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
| | - Jessica L Metcalf
- Department of Animal Science, Colorado State University, Fort Collins, CO, USA
| | - Sydney C Morgan
- Irving K. Barber School of Arts and Sciences, Unit 2 (Biology), University of British Columbia, Kelowna, British Columbia, Canada
| | - Jamie T Morton
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.,Department of Computer Science & Engineering, University of California San Diego, La Jolla, CA, USA
| | - Ahmad Turan Naimey
- Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Jose A Navas-Molina
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.,Department of Computer Science & Engineering, University of California San Diego, La Jolla, CA, USA.,Google LLC, Mountain View, CA, USA
| | - Louis Felix Nothias
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
| | - Stephanie B Orchanian
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Talima Pearson
- Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Samuel L Peoples
- School of Information Studies, Syracuse University, Syracuse, NY, USA.,School of STEM, University of Washington Bothell, Bothell, WA, USA
| | - Daniel Petras
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
| | - Mary Lai Preuss
- Department of Biological Sciences, Webster University, St. Louis, MO, USA
| | - Elmar Pruesse
- Department of Medicine, Division of Biomedical Informatics and Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Lasse Buur Rasmussen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Adam Rivers
- Agricultural Research Service, Genomics and Bioinformatics Research Unit, United States Department of Agriculture, Gainesville, FL, USA
| | - Michael S Robeson
- College of Medicine, Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Patrick Rosenthal
- Department of Biological Sciences, Webster University, St. Louis, MO, USA
| | - Nicola Segata
- Centre for Integrative Biology, University of Trento, Trento, Italy
| | - Michael Shaffer
- Computational Bioscience Program, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.,Department of Medicine, Division of Biomedical Informatics and Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Arron Shiffer
- Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Rashmi Sinha
- Metabolic Epidemiology Branch, National Cancer Institute, Rockville, MD, USA
| | - Se Jin Song
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - John R Spear
- Department of Civil and Environmental Engineering, Colorado School of Mines, Golden, CO, USA
| | - Austin D Swafford
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Luke R Thompson
- Department of Biological Sciences and Northern Gulf Institute, University of Southern Mississippi, Hattiesburg, MS, USA.,Ocean Chemistry and Ecosystems Division, Atlantic Oceanographic and Meteorological Laboratory, National Oceanic and Atmospheric Administration, La Jolla, CA, USA
| | - Pedro J Torres
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Pauline Trinh
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, USA
| | - Anupriya Tripathi
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA.,Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.,Division of Biological Sciences, University of California San Diego, San Diego, CA, USA
| | - Peter J Turnbaugh
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
| | - Sabah Ul-Hasan
- Quantitative and Systems Biology Graduate Program, University of California Merced, Merced, CA, USA
| | | | - Fernando Vargas
- Division of Biological Sciences, University of California San Diego, San Diego, CA, USA
| | | | - Emily Vogtmann
- Metabolic Epidemiology Branch, National Cancer Institute, Rockville, MD, USA
| | - Max von Hippel
- Department of Mathematics, University of Arizona, Tucson, AZ, USA
| | - William Walters
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Yunhu Wan
- Metabolic Epidemiology Branch, National Cancer Institute, Rockville, MD, USA
| | - Mingxun Wang
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
| | - Jonathan Warren
- National Laboratory Service, Environment Agency, Starcross, UK
| | - Kyle C Weber
- Agricultural Research Service, Genomics and Bioinformatics Research Unit, United States Department of Agriculture, Gainesville, FL, USA.,College of Agriculture and Life Sciences, University of Florida, Gainesville, FL, USA
| | | | - Amy D Willis
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Zhenjiang Zech Xu
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Jesse R Zaneveld
- School of STEM, Division of Biological Sciences, University of Washington Bothell, Bothell, WA, USA
| | | | - Qiyun Zhu
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.,Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA.,Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
| | - J Gregory Caporaso
- Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA. .,Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA.
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37
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Le Bastard Q, Vangay P, Batard E, Knights D, Montassier E. US Immigration Is Associated With Rapid and Persistent Acquisition of Antibiotic Resistance Genes in the Gut. Clin Infect Dis 2019; 71:419-421. [DOI: 10.1093/cid/ciz1087] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 10/30/2019] [Indexed: 12/21/2022] Open
Abstract
Abstract
Little is known about the effect of human migration on gut microbiome antibiotic resistance gene (ARG) carriage. Using deep shotgun stool metagenomics analysis, we found a rapid increase in gut microbiome ARG richness and abundance in women from 2 independent ethnic groups relocating from Thailand to the United States.
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Affiliation(s)
- Quentin Le Bastard
- MiHAR Laboratory, Université de Nantes, Nantes, France
- Emergency Department, Nantes University Hospital, Nantes, France
| | - Pajau Vangay
- Bioinformatics and Computational Biology Program, University of Minnesota, Minneapolis, Minnesota, USA
| | - Eric Batard
- MiHAR Laboratory, Université de Nantes, Nantes, France
- Emergency Department, Nantes University Hospital, Nantes, France
| | - Dan Knights
- Bioinformatics and Computational Biology Program, University of Minnesota, Minneapolis, Minnesota, USA
- Biotechnology Institute, University of Minnesota, Minneapolis, Minnesota, USA
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, Minnesota, USA
| | - Emmanuel Montassier
- MiHAR Laboratory, Université de Nantes, Nantes, France
- Emergency Department, Nantes University Hospital, Nantes, France
- EA3826 Thérapeutiques Anti-infectieuses, Institut de Recherche en Santé 2 Nantes Biotech, Medical University of Nantes, Nantes, France
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38
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Bolyen E, Rideout JR, Dillon MR, Bokulich NA, Abnet CC, Al-Ghalith GA, Alexander H, Alm EJ, Arumugam M, Asnicar F, Bai Y, Bisanz JE, Bittinger K, Brejnrod A, Brislawn CJ, Brown CT, Callahan BJ, Caraballo-Rodríguez AM, Chase J, Cope EK, Da Silva R, Diener C, Dorrestein PC, Douglas GM, Durall DM, Duvallet C, Edwardson CF, Ernst M, Estaki M, Fouquier J, Gauglitz JM, Gibbons SM, Gibson DL, Gonzalez A, Gorlick K, Guo J, Hillmann B, Holmes S, Holste H, Huttenhower C, Huttley GA, Janssen S, Jarmusch AK, Jiang L, Kaehler BD, Kang KB, Keefe CR, Keim P, Kelley ST, Knights D, Koester I, Kosciolek T, Kreps J, Langille MGI, Lee J, Ley R, Liu YX, Loftfield E, Lozupone C, Maher M, Marotz C, Martin BD, McDonald D, McIver LJ, Melnik AV, Metcalf JL, Morgan SC, Morton JT, Naimey AT, Navas-Molina JA, Nothias LF, Orchanian SB, Pearson T, Peoples SL, Petras D, Preuss ML, Pruesse E, Rasmussen LB, Rivers A, Robeson MS, Rosenthal P, Segata N, Shaffer M, Shiffer A, Sinha R, Song SJ, Spear JR, Swafford AD, Thompson LR, Torres PJ, Trinh P, Tripathi A, Turnbaugh PJ, Ul-Hasan S, van der Hooft JJJ, Vargas F, Vázquez-Baeza Y, Vogtmann E, von Hippel M, Walters W, Wan Y, Wang M, Warren J, Weber KC, Williamson CHD, Willis AD, Xu ZZ, Zaneveld JR, Zhang Y, Zhu Q, Knight R, Caporaso JG. Author Correction: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat Biotechnol 2019; 37:1091. [PMID: 31399723 DOI: 10.1038/s41587-019-0252-6] [Citation(s) in RCA: 281] [Impact Index Per Article: 56.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Affiliation(s)
- Evan Bolyen
- Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Jai Ram Rideout
- Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Matthew R Dillon
- Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Nicholas A Bokulich
- Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Christian C Abnet
- Metabolic Epidemiology Branch, National Cancer Institute, Rockville, MD, USA
| | - Gabriel A Al-Ghalith
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Harriet Alexander
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA.,Department of Population Health and Reproduction, University of California, Davis, Davis, CA, USA
| | - Eric J Alm
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.,Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Manimozhiyan Arumugam
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Yang Bai
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.,Centre of Excellence for Plant and Microbial Sciences (CEPAMS), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences & John Innes Centre, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jordan E Bisanz
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
| | - Kyle Bittinger
- Division of Gastroenterology and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Hepatology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Asker Brejnrod
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Colin J Brislawn
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - C Titus Brown
- Department of Population Health and Reproduction, University of California, Davis, Davis, CA, USA
| | - Benjamin J Callahan
- Department of Population Health & Pathobiology, North Carolina State University, Raleigh, NC, USA.,Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
| | - Andrés Mauricio Caraballo-Rodríguez
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
| | - John Chase
- Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Emily K Cope
- Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA.,Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Ricardo Da Silva
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
| | | | - Pieter C Dorrestein
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
| | - Gavin M Douglas
- Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Daniel M Durall
- Irving K. Barber School of Arts and Sciences, University of British Columbia, Kelowna, British Columbia, Canada
| | - Claire Duvallet
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Christian F Edwardson
- A. Watson Armour III Center for Animal Health and Welfare, Aquarium Microbiome Project, John G. Shedd Aquarium, Chicago, IL, USA
| | - Madeleine Ernst
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA.,Department of Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Mehrbod Estaki
- Department of Biology, University of British Columbia Okanagan, Okanagan, British Columbia, Canada
| | - Jennifer Fouquier
- Computational Bioscience Program, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.,Department of Medicine, Division of Biomedical Informatics and Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Julia M Gauglitz
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
| | - Sean M Gibbons
- Institute for Systems Biology, Seattle, WA, USA.,eScience Institute, University of Washington, Seattle, WA, USA
| | - Deanna L Gibson
- Irving K. Barber School of Arts and Sciences, Department of Biology, University of British Columbia, Kelowna, British Columbia, Canada.,Department of Medicine, University of British Columbia, Kelowna, British Columbia, Canada
| | - Antonio Gonzalez
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Kestrel Gorlick
- Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Jiarong Guo
- Center for Microbial Ecology, Michigan State University, East Lansing, MI, USA
| | - Benjamin Hillmann
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Susan Holmes
- Statistics Department, Stanford University, Palo Alto, CA, USA
| | - Hannes Holste
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.,Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
| | - Curtis Huttenhower
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Gavin A Huttley
- Research School of Biology, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Stefan Janssen
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Heinrich-Heine University Dusseldorf, Dusseldorf, Germany
| | - Alan K Jarmusch
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
| | - Lingjing Jiang
- Department of Family Medicine and Public Health, University of California San Diego, La Jolla, CA, USA
| | - Benjamin D Kaehler
- Research School of Biology, The Australian National University, Canberra, Australian Capital Territory, Australia.,School of Science, University of New South Wales, Canberra, Australian Capital Territory, Australia
| | - Kyo Bin Kang
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA.,College of Pharmacy, Sookmyung Women's University, Seoul, Republic of Korea
| | - Christopher R Keefe
- Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Paul Keim
- Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Scott T Kelley
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Dan Knights
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA.,Biotechnology Institute, University of Minnesota, Saint Paul, MN, USA
| | - Irina Koester
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA.,Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Tomasz Kosciolek
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Jorden Kreps
- Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Morgan G I Langille
- Department of Pharmacology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Joslynn Lee
- Science Education, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Ruth Ley
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen, Germany.,Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Yong-Xin Liu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.,Centre of Excellence for Plant and Microbial Sciences (CEPAMS), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences & John Innes Centre, Beijing, China
| | - Erikka Loftfield
- Metabolic Epidemiology Branch, National Cancer Institute, Rockville, MD, USA
| | - Catherine Lozupone
- Department of Medicine, Division of Biomedical Informatics and Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Massoud Maher
- Department of Computer Science & Engineering, University of California San Diego, La Jolla, CA, USA
| | - Clarisse Marotz
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Bryan D Martin
- Department of Statistics, University of Washington, Seattle, WA, USA
| | - Daniel McDonald
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Lauren J McIver
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Alexey V Melnik
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
| | - Jessica L Metcalf
- Department of Animal Science, Colorado State University, Fort Collins, CO, USA
| | - Sydney C Morgan
- Irving K. Barber School of Arts and Sciences, Unit 2 (Biology), University of British Columbia, Kelowna, British Columbia, Canada
| | - Jamie T Morton
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.,Department of Computer Science & Engineering, University of California San Diego, La Jolla, CA, USA
| | - Ahmad Turan Naimey
- Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Jose A Navas-Molina
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.,Department of Computer Science & Engineering, University of California San Diego, La Jolla, CA, USA.,Google LLC, Mountain View, CA, USA
| | - Louis Felix Nothias
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
| | - Stephanie B Orchanian
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Talima Pearson
- Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Samuel L Peoples
- School of Information Studies, Syracuse University, Syracuse, NY, USA.,School of STEM, University of Washington Bothell, Bothell, WA, USA
| | - Daniel Petras
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
| | - Mary Lai Preuss
- Department of Biological Sciences, Webster University, St. Louis, MO, USA
| | - Elmar Pruesse
- Department of Medicine, Division of Biomedical Informatics and Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Lasse Buur Rasmussen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Adam Rivers
- Agricultural Research Service, Genomics and Bioinformatics Research Unit, United States Department of Agriculture, Gainesville, FL, USA
| | - Michael S Robeson
- College of Medicine, Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Patrick Rosenthal
- Department of Biological Sciences, Webster University, St. Louis, MO, USA
| | - Nicola Segata
- Centre for Integrative Biology, University of Trento, Trento, Italy
| | - Michael Shaffer
- Computational Bioscience Program, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.,Department of Medicine, Division of Biomedical Informatics and Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Arron Shiffer
- Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Rashmi Sinha
- Metabolic Epidemiology Branch, National Cancer Institute, Rockville, MD, USA
| | - Se Jin Song
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - John R Spear
- Department of Civil and Environmental Engineering, Colorado School of Mines, Golden, CO, USA
| | - Austin D Swafford
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Luke R Thompson
- Department of Biological Sciences and Northern Gulf Institute, University of Southern Mississippi, Hattiesburg, MS, USA.,Ocean Chemistry and Ecosystems Division, Atlantic Oceanographic and Meteorological Laboratory, National Oceanic and Atmospheric Administration, La Jolla, CA, USA
| | - Pedro J Torres
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Pauline Trinh
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, USA
| | - Anupriya Tripathi
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA.,Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.,Division of Biological Sciences, University of California San Diego, San Diego, CA, USA
| | - Peter J Turnbaugh
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
| | - Sabah Ul-Hasan
- Quantitative and Systems Biology Graduate Program, University of California Merced, Merced, CA, USA
| | | | - Fernando Vargas
- Division of Biological Sciences, University of California San Diego, San Diego, CA, USA
| | | | - Emily Vogtmann
- Metabolic Epidemiology Branch, National Cancer Institute, Rockville, MD, USA
| | - Max von Hippel
- Department of Mathematics, University of Arizona, Tucson, AZ, USA
| | - William Walters
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Yunhu Wan
- Metabolic Epidemiology Branch, National Cancer Institute, Rockville, MD, USA
| | - Mingxun Wang
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
| | - Jonathan Warren
- National Laboratory Service, Environment Agency, Starcross, UK
| | - Kyle C Weber
- Agricultural Research Service, Genomics and Bioinformatics Research Unit, United States Department of Agriculture, Gainesville, FL, USA.,College of Agriculture and Life Sciences, University of Florida, Gainesville, FL, USA
| | | | - Amy D Willis
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Zhenjiang Zech Xu
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Jesse R Zaneveld
- School of STEM, Division of Biological Sciences, University of Washington Bothell, Bothell, WA, USA
| | | | - Qiyun Zhu
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.,Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA.,Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
| | - J Gregory Caporaso
- Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA. .,Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA.
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Rashidi A, Ebadi M, Shields-Cutler RR, Kruziki K, Manias DA, Barnes AMT, DeFor TE, Ferrieri P, Young JAH, Knights D, Blazar BR, Weisdorf DJ, Dunny GM. Early E. casseliflavus gut colonization and outcomes of allogeneic hematopoietic cell transplantation. PLoS One 2019; 14:e0220850. [PMID: 31393924 PMCID: PMC6687141 DOI: 10.1371/journal.pone.0220850] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [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: 03/15/2019] [Accepted: 07/24/2019] [Indexed: 12/25/2022] Open
Abstract
Gut dysbiosis has been associated with worse allogeneic hematopoietic cell transplantation (allo-HCT) outcomes. We reported an association between intrinsically vancomycin-resistant enterococci (iVRE: E. gallinarum and E. casseliflavus) gut colonization and lower post-transplant mortality. In this study, using an expanded cohort, we evaluated whether our previously observed association is species-specific. We included allo-HCT recipients with ≥1 positive rectal swab or stool culture for iVRE between days -14 and +14 of transplant. To investigate whether iVRE modulate the gut microbiota, we performed agar diffusion assays. To investigate whether iVRE differ in their ability to activate the aryl hydrocarbon receptor, we analyzed iVRE genomes for enzymes in the shikimate and tryptophan pathways. Sixty six (23 E. casseliflavus and 43 E. gallinarum) of the 908 allograft recipients (2011-2017) met our inclusion criteria. Overall survival was significantly higher in patients with E. casseliflavus (91% vs. 62% at 3 years, P = 0.04). In multivariable analysis, E. casseliflavus gut colonization was significantly associated with reduced all-cause mortality (hazard ratio 0.20, 95% confidence interval 0.04-0.91, P = 0.04). While agar assays were largely unremarkable, genome mining predicted that E. casseliflavus encodes a larger number of enzymes in the tryptophan metabolism pathway. In conclusion, E. casseliflavus gut colonization is associated with reduced post-HCT morality. Further research is needed to understand the mechanisms for this association.
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Affiliation(s)
- Armin Rashidi
- Division of Hematology, Oncology, and Transplantation, Department of Medicine, University of Minnesota, Minneapolis, MN, United States of America
| | - Maryam Ebadi
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, University of Minnesota, Minneapolis, MN, United States of America
| | - Robin R. Shields-Cutler
- BioTechnology Institute, College of Biological Sciences, University of Minnesota, MN, United States of America
- Department of Biology, Macalester College, Saint Paul, MN, United States of America
| | - Kathryn Kruziki
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN, United States of America
| | - Dawn A. Manias
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN, United States of America
| | - Aaron M. T. Barnes
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN, United States of America
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, United States of America
| | - Todd E. DeFor
- Biostatistics Core, Masonic Cancer Center, University of Minnesota, Minneapolis, MN, United States of America
| | - Patricia Ferrieri
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, United States of America
| | - Jo-Anne H. Young
- Division of Infectious Disease and International Medicine, Department of Medicine, University of Minnesota, Minneapolis, MN, United States of America
| | - Dan Knights
- BioTechnology Institute, College of Biological Sciences, University of Minnesota, MN, United States of America
| | - Bruce R. Blazar
- Division of Blood and Marrow Transplantation, Department of Pediatrics, University of Minnesota, Minneapolis, MN, United States of America
| | - Daniel J. Weisdorf
- Division of Hematology, Oncology, and Transplantation, Department of Medicine, University of Minnesota, Minneapolis, MN, United States of America
| | - Gary M. Dunny
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN, United States of America
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40
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Vangay P, Johnson AJ, Ward TL, Al-Ghalith GA, Shields-Cutler RR, Hillmann BM, Lucas SK, Beura LK, Thompson EA, Till LM, Batres R, Paw B, Pergament SL, Saenyakul P, Xiong M, Kim AD, Kim G, Masopust D, Martens EC, Angkurawaranon C, McGready R, Kashyap PC, Culhane-Pera KA, Knights D. US Immigration Westernizes the Human Gut Microbiome. Cell 2019; 175:962-972.e10. [PMID: 30388453 DOI: 10.1016/j.cell.2018.10.029] [Citation(s) in RCA: 404] [Impact Index Per Article: 80.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Revised: 09/10/2018] [Accepted: 10/12/2018] [Indexed: 12/26/2022]
Abstract
Many US immigrant populations develop metabolic diseases post immigration, but the causes are not well understood. Although the microbiome plays a role in metabolic disease, there have been no studies measuring the effects of US immigration on the gut microbiome. We collected stool, dietary recalls, and anthropometrics from 514 Hmong and Karen individuals living in Thailand and the United States, including first- and second-generation immigrants and 19 Karen individuals sampled before and after immigration, as well as from 36 US-born European American individuals. Using 16S and deep shotgun metagenomic DNA sequencing, we found that migration from a non-Western country to the United States is associated with immediate loss of gut microbiome diversity and function in which US-associated strains and functions displace native strains and functions. These effects increase with duration of US residence and are compounded by obesity and across generations.
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Affiliation(s)
- Pajau Vangay
- Bioinformatics and Computational Biology Program, University of Minnesota, Minneapolis, MN 55455, USA
| | - Abigail J Johnson
- Biotechnology Institute, University of Minnesota, Minneapolis, MN 55455, USA
| | - Tonya L Ward
- Biotechnology Institute, University of Minnesota, Minneapolis, MN 55455, USA
| | - Gabriel A Al-Ghalith
- Bioinformatics and Computational Biology Program, University of Minnesota, Minneapolis, MN 55455, USA
| | | | - Benjamin M Hillmann
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - Sarah K Lucas
- Center for Immunology, Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Lalit K Beura
- Center for Immunology, Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Emily A Thompson
- Center for Immunology, Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Lisa M Till
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Mayo Clinic, Rochester, MN 55902, USA
| | - Rodolfo Batres
- Somali, Latino, and Hmong Partnership for Health and Wellness, West Side Community Health Services, St. Paul, MN 55106, USA
| | - Bwei Paw
- Somali, Latino, and Hmong Partnership for Health and Wellness, West Side Community Health Services, St. Paul, MN 55106, USA
| | - Shannon L Pergament
- Somali, Latino, and Hmong Partnership for Health and Wellness, West Side Community Health Services, St. Paul, MN 55106, USA
| | - Pimpanitta Saenyakul
- Somali, Latino, and Hmong Partnership for Health and Wellness, West Side Community Health Services, St. Paul, MN 55106, USA
| | - Mary Xiong
- Somali, Latino, and Hmong Partnership for Health and Wellness, West Side Community Health Services, St. Paul, MN 55106, USA
| | - Austin D Kim
- Department of Mathematics, Statistics, and Computer Science, Macalester College, St. Paul, MN 55105, USA
| | - Grant Kim
- College of Biological Sciences, University of Minnesota, Minneapolis, MN 55455, USA
| | - David Masopust
- Center for Immunology, Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Eric C Martens
- Department of Microbiology & Immunology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Chaisiri Angkurawaranon
- Department of Family Medicine, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Rose McGready
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot 63110, Thailand; Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Oxford OX3 7BN, UK
| | - Purna C Kashyap
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Mayo Clinic, Rochester, MN 55902, USA
| | - Kathleen A Culhane-Pera
- Somali, Latino, and Hmong Partnership for Health and Wellness, West Side Community Health Services, St. Paul, MN 55106, USA
| | - Dan Knights
- Bioinformatics and Computational Biology Program, University of Minnesota, Minneapolis, MN 55455, USA; Biotechnology Institute, University of Minnesota, Minneapolis, MN 55455, USA; Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN 55455, USA.
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Prizment AE, Menk J, Staley C, Vivek S, Onyeaghala G, Thyagarajan B, Demmer R, Knights D, Meyer K, Shaukat A, Khorutz A, Sadowsky MJ, Straka RJ, Church T. Abstract 5060: Effect of aspirin on gut microbiome in a pilot randomized double-blind trial. Cancer Res 2019. [DOI: 10.1158/1538-7445.am2019-5060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Aspirin use is associated with decreased risk of colorectal cancer (CRC), possibly by modulating the gut microbiome. We conducted a pilot double-blind randomized trial to evaluate the effect of aspirin on the gut microbiome. (ClinicalTrials.gov NCT02761486).
Methods: Fifty healthy individuals 50-75 years old were randomized (3:2) to receive a daily standard dose of aspirin (325 mg, N=30) or placebo (lactose, N=20) for 6 weeks followed by a 6-week washout. Stool specimens were collected at baseline, 3, 6, 9, and 12 weeks, and analyzed using 16S ribosomal RNA gene sequencing (V4 region) and Mothur software [ver. 1.35.1]. Fifteen genera associated with CRC were pre-specified from a published meta-analysis of the gut microbiome and CRC [Shah, 2017]. Among these 15 genera, eight genera, which were present in >10% of subjects at baseline in our study, were examined. Additionally, we examined four taxa previously associated with aspirin in a cross-sectional study of non-steroidal anti-inflammatory drugs and the gut microbiome [Rogers, 2016]. Mixed-effects logistic regression was used to estimate associations between aspirin use and changes in the relative abundance of taxa from pre- to post-treatment (baseline to week 6) via an interaction term (treatment*time). Log of odds ratio (β estimate) and P-values for the interaction term comparing aspirin to placebo for week 6 versus baseline are presented.
Results and conclusions. Out of the 8 pre-specified genera found to be associated with CRC in the meta-analysis, the interaction term was significant for 3 genera: Parabacteroides (β =-0.43, P<0.0001), Dorea (β =-1.56, P=0.02), and Akkermansia (β =0.30, P=0.009). These results suggest that aspirin decreases the relative abundance of two bacteria increased in CRC cases compared to non-cases - Parabacteroides and Dorea., while it increases the relative abundance of Akkermansia, which has been associated with anti-cancer immune response and improved survival of CRC patients. The following taxa that were previously associated with aspirin [Rogers, 2016] were also associated with aspirin in the present trial: family Ruminococcaceae (β= 0.33, P<0.0001), genera Bacteroides (β= -0.39; P<0.0001) and Prevotella (β= 0.51; P<0.0001). Our study suggests that aspirin changes the relative abundances of several gut bacteria previously shown to be associated with CRC.
Citation Format: Anna E. Prizment, Jeremiah Menk, Christopher Staley, Sithara Vivek, Guillaume Onyeaghala, Bharat Thyagarajan, Ryan Demmer, Dan Knights, Kathie Meyer, Aasma Shaukat, Alexander Khorutz, Michael J. Sadowsky, Robert J. Straka, Timothy Church. Effect of aspirin on gut microbiome in a pilot randomized double-blind trial [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 5060.
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Johnson A, Vangay P, Knights D. Dietary Patterns Correspond with Microbiome Composition (FS07-02-19). Curr Dev Nutr 2019. [DOI: 10.1093/cdn/nzz040.fs07-02-19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Objectives
Previous studies have defined dietary patterns for comparison with microbiome features using factor analysis from food frequency questionnaires. In this study, we applied a new tree-based method to directly define dietary patterns from 24-hour food records. We aimed to determine if these patterns corresponded with microbial features.
Methods
Daily fecal samples and daily 24-hour food records (ASA24–2016) were collected from 32 healthy adults over 17 days. Dietary patterns were derived using all reported foods for each subject. Foods were arranged into a tree structure using USDA food groups. Tree-based weighted Unifrac food distances (QIIME 1.9.1) were used for principal coordinate analysis to define five dietary patterns. Each pattern was named after its most influential food groups. Average microbiome composition was determined from metagenomic sequencing. Dietary patterns were compared with subjects’ average microbiome composition using correlation analysis. Spearman correlations were corrected for multiple comparisons within each taxonomy level. Constrained redundancy analysis (RDA) was used to determine the explanatory power of dietary patterns.
Results
Four of the five most discriminatory dietary patterns (DPs) were associated with microbial taxa (A). DP1 was positively correlated with an unclassified family in the order Burkholderiales and negatively correlated with the species Lachnospiraceae bacterium TF01–11. DP3, DP4, DP5 were most representative of a western diet. DP3 was negatively correlated with family Pasteurellaceae. DP4 was positively correlated with family Erysipelotrichaceae and negatively correlated with family Sutterellaceae. DP5 was positively correlated with members of class Bacteroidia including two specific Bacteroides speciesHMSC073E02 and HMSC067B03. Constrained RDA using the five dietary patterns revealed a gradient of Phylum Bacteroidetes along an axis driven by DP3, DP4, and DP5 (B).
Conclusions
The dietary patterns derived using our tree-based method reveal relationships between diet microbial taxa. In agreement with previous studies, our tree-based patterns show that the western diet corresponds to increased Bacteroidetes, demonstrating the utility of this method.
Funding Sources
Funding for this study was provided by General Mills.
Supporting Tables, Images and/or Graphs
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Saffouri GB, Shields-Cutler RR, Chen J, Yang Y, Lekatz HR, Hale VL, Cho JM, Battaglioli EJ, Bhattarai Y, Thompson KJ, Kalari KK, Behera G, Berry JC, Peters SA, Patel R, Schuetz AN, Faith JJ, Camilleri M, Sonnenburg JL, Farrugia G, Swann JR, Grover M, Knights D, Kashyap PC. Small intestinal microbial dysbiosis underlies symptoms associated with functional gastrointestinal disorders. Nat Commun 2019; 10:2012. [PMID: 31043597 PMCID: PMC6494866 DOI: 10.1038/s41467-019-09964-7] [Citation(s) in RCA: 129] [Impact Index Per Article: 25.8] [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: 10/04/2018] [Accepted: 04/03/2019] [Indexed: 12/18/2022] Open
Abstract
Small intestinal bacterial overgrowth (SIBO) has been implicated in symptoms associated with functional gastrointestinal disorders (FGIDs), though mechanisms remain poorly defined and treatment involves non-specific antibiotics. Here we show that SIBO based on duodenal aspirate culture reflects an overgrowth of anaerobes, does not correspond with patient symptoms, and may be a result of dietary preferences. Small intestinal microbial composition, on the other hand, is significantly altered in symptomatic patients and does not correspond with aspirate culture results. In a pilot interventional study we found that switching from a high fiber diet to a low fiber, high simple sugar diet triggered FGID-related symptoms and decreased small intestinal microbial diversity while increasing small intestinal permeability. Our findings demonstrate that characterizing small intestinal microbiomes in patients with gastrointestinal symptoms may allow a more targeted antibacterial or a diet-based approach to treatment.
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Affiliation(s)
- George B Saffouri
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, 55902, USA
| | - Robin R Shields-Cutler
- BioTechnology Institute, College of Biological Sciences, University of Minnesota, Minneapolis, MN, 55455, USA
- Department of Biology, Macalester College, Saint Paul, MN, 55105, USA
| | - Jun Chen
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN, 55902, USA
| | - Yi Yang
- Computational and Systems Medicine Section of the Department of Surgery and Cancer, Imperial College, (London), UK
| | - Heather R Lekatz
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, 55902, USA
| | - Vanessa L Hale
- Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, OH, 43210, USA
| | - Janice M Cho
- Division of Internal Medicine, Mayo Clinic, Rochester, MN, 55902, USA
| | - Eric J Battaglioli
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, 55902, USA
| | - Yogesh Bhattarai
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, 55902, USA
| | - Kevin J Thompson
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN, 55902, USA
| | - Krishna K Kalari
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN, 55902, USA
| | - Gaurav Behera
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, 55902, USA
| | - Jonathan C Berry
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, 55902, USA
| | - Stephanie A Peters
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, 55902, USA
| | - Robin Patel
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, 55902, USA
| | - Audrey N Schuetz
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, 55902, USA
| | - Jeremiah J Faith
- Department of Genetics and Genomic Sciences, Medicine, and Clinical Immunology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Michael Camilleri
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, 55902, USA
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN, 55902, USA
| | - Justin L Sonnenburg
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, 94305, USA
| | - Gianrico Farrugia
- Division of Gastroenterology, Mayo Clinic, Jacksonville, FL, 32224, USA
| | - Jonathan R Swann
- Computational and Systems Medicine Section of the Department of Surgery and Cancer, Imperial College, (London), UK
| | - Madhusudan Grover
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, 55902, USA
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN, 55902, USA
| | - Dan Knights
- BioTechnology Institute, College of Biological Sciences, University of Minnesota, Minneapolis, MN, 55455, USA
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Purna C Kashyap
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, 55902, USA.
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN, 55902, USA.
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Vangay P, Hillmann BM, Knights D. Microbiome Learning Repo (ML Repo): A public repository of microbiome regression and classification tasks. Gigascience 2019; 8:giz042. [PMID: 31042284 PMCID: PMC6493971 DOI: 10.1093/gigascience/giz042] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [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: 08/21/2018] [Revised: 02/24/2019] [Accepted: 03/26/2019] [Indexed: 01/05/2023] Open
Abstract
The use of machine learning in high-dimensional biological applications, such as the human microbiome, has grown exponentially in recent years, but algorithm developers often lack the domain expertise required for interpretation and curation of the heterogeneous microbiome datasets. We present Microbiome Learning Repo (ML Repo, available at https://knights-lab.github.io/MLRepo/), a public, web-based repository of 33 curated classification and regression tasks from 15 published human microbiome datasets. We highlight the use of ML Repo in several use cases to demonstrate its wide application, and we expect it to be an important resource for algorithm developers.
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Affiliation(s)
- Pajau Vangay
- Bioinformatics and Computational Biology, University of Minnesota, 200 Union Street SE, Minneapolis, MN 55455
| | - Benjamin M Hillmann
- Department of Computer Science and Engineering, University of Minnesota, 200 Union Street SE, Minneapolis, MN 55455
| | - Dan Knights
- Bioinformatics and Computational Biology, University of Minnesota, 200 Union Street SE, Minneapolis, MN 55455
- Department of Computer Science and Engineering, University of Minnesota, 200 Union Street SE, Minneapolis, MN 55455
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Muñiz Pedrogo DA, Chen J, Hillmann B, Jeraldo P, Al-Ghalith G, Taneja V, Davis JM, Knights D, Nelson H, Faubion WA, Raffals L, Kashyap PC. An Increased Abundance of Clostridiaceae Characterizes Arthritis in Inflammatory Bowel Disease and Rheumatoid Arthritis: A Cross-sectional Study. Inflamm Bowel Dis 2019; 25:902-913. [PMID: 30321331 PMCID: PMC6458525 DOI: 10.1093/ibd/izy318] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Indexed: 12/13/2022]
Abstract
BACKGROUND Inflammatory bowel diseases (IBDs) are a group of heterogeneous inflammatory conditions affecting the gastrointestinal tract. Although there is considerable evidence linking the gut microbiota to intestinal inflammation, there is limited knowledge on its potential role in the development of extraintestinal manifestations of IBD. METHODS Four groups of patients were included: IBD-associated arthropathy (IBD-A); IBD without arthropathy (IBD-N); rheumatoid arthritis (RA); and non-IBD, nonarthritis controls. DNA from stool samples was isolated and sequenced using the Illumina platform. Paired-end reads were quality-controlled using SHI7 and processed with SHOGUN. Abundance and diversity analyses were performed using QIIME, and compositional biomarker identification was performed using LEfSe. RESULTS One hundred eighty patients were included in the analysis. IBD-A was associated with an increased abundance of microbial tyrosine degradation pathways when compared with IBD-N (P = 0.02), whereas IBD-A and RA patients both shared an increased abundance of Clostridiaceae when compared with controls (P = 0.045). We found that history of bowel surgery was a significant source of variability (P = 0.001) among all IBD patients and was associated with decreased alpha diversity and increased abundance of Enterobacteriaceae (P = 0.004). CONCLUSIONS An increased abundance of gut microbial tyrosine degradation pathways was associated with IBD-A. An increased abundance of Clostridiaceae was shared by both IBD-A and RA patients and suggests a potentially common microbial link for inflammatory arthritis. The increased abundance of Enterobacteriaceae, previously reported in IBD, may be due to the effects of previous bowel surgery and highlights the importance of controlling for this variable in future studies.
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Affiliation(s)
- David A Muñiz Pedrogo
- Center for Clinical and Translational Science, Mayo Clinic, Rochester, Minnesota,University of Puerto Rico School of Medicine, San Juan, Puerto Rico
| | - Jun Chen
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
| | - Benjamin Hillmann
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, Minnesota
| | | | - Gabriel Al-Ghalith
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, Minnesota
| | - Veena Taneja
- Department of Immunology, Mayo Clinic, Rochester, Minnesota
| | - John M Davis
- Division of Rheumatology, Mayo Clinic, Rochester, Minnesota
| | - Dan Knights
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, Minnesota
| | - Heidi Nelson
- Department of Surgery, Mayo Clinic, Rochester, Minnesota
| | - William A Faubion
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Laura Raffals
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Purna C Kashyap
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota,Address correspondence to: Purna C. Kashyap, MBBS, Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN 55905 ()
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Clayton JB, Shields-Cutler RR, Hoops SL, Al-Ghalith GA, Sha JCM, Johnson TJ, Knights D. Bacterial community structure and function distinguish gut sites in captive red-shanked doucs (Pygathrix nemaeus). Am J Primatol 2019; 81:e22977. [PMID: 30997937 DOI: 10.1002/ajp.22977] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 03/22/2019] [Accepted: 04/01/2019] [Indexed: 12/12/2022]
Abstract
The mammalian order primates contains wide species diversity. Members of the subfamily Colobinae are unique amongst extant primates in that their gastrointestinal systems more closely resemble those of ruminants than other members of the primate order. In the growing literature surrounding nonhuman primate microbiomes, analysis of microbial communities has been limited to the hindgut, since few studies have captured data on other gut sites, including the foregut of colobine primates. In this study, we used the red-shanked douc (Pygathrix nemaeus) as a model for colobine primates to study the relationship between gastrointestinal bacterial community structure and gut site within and between subjects. We analyzed fecal and pregastric stomach content samples, representative of the hindgut and foregut respectively, using 16S recombinant DNA (rDNA) sequencing and identified microbiota using closed-reference operational taxonomic unit (OTU) picking against the GreenGenes database. Our results show divergent bacterial communities clearly distinguish the foregut and hindgut microbiomes. We found higher bacterial biodiversity and a higher Firmicutes:Bacteroides ratio in the hindgut as opposed to the foregut. These gut sites showed strong associations with bacterial function. Specifically, energy metabolism was upregulated in the hindgut, whereas detoxification was increased in the foregut. Our results suggest a red-shanked douc's foregut microbiome is no more concordant with its own hindgut than it is with any other red-shanked douc's hindgut microbiome, thus reinforcing the notion that the bacterial communities of the foregut and hindgut are distinctly unique. OPEN PRACTICES: This article has been awarded Open Materials and Open Data badges. All materials and data are publicly accessible via the IRIS Repository at https://www.iris-database.org/iris/app/home/detail?id=york:934328. Learn more about the Open Practices badges from the Center for Open Science: https://osf.io/tvyxz/wiki.
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Affiliation(s)
- Jonathan B Clayton
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, Minnesota.,GreenViet Biodiversity Conservation Center, Danang, Vietnam.,Primate Microbiome Project, University of Minnesota, Minneapolis, Minnesota.,Biotechnology Institute, University of Minnesota, Saint Paul, Minnesota
| | - Robin R Shields-Cutler
- Biotechnology Institute, University of Minnesota, Saint Paul, Minnesota.,Department of Biology, Macalester College, St. Paul, Minnesota
| | - Susan L Hoops
- Biotechnology Institute, University of Minnesota, Saint Paul, Minnesota
| | - Gabriel A Al-Ghalith
- Bioinformatics and Computational Biology, University of Minnesota, Minneapolis, Minnesota
| | - John C M Sha
- School of Sociology and Anthropology, Sun Yat-Sen University, Guangzhou, China
| | - Timothy J Johnson
- Primate Microbiome Project, University of Minnesota, Minneapolis, Minnesota.,Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, Mennisota.,Mid-Central Research and Outreach Center, University of Minnesota, Willmar, Minnesota
| | - Dan Knights
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, Minnesota.,Primate Microbiome Project, University of Minnesota, Minneapolis, Minnesota.,Biotechnology Institute, University of Minnesota, Saint Paul, Minnesota
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Aschard H, Laville V, Tchetgen ET, Knights D, Imhann F, Seksik P, Zaitlen N, Silverberg MS, Cosnes J, Weersma RK, Xavier R, Beaugerie L, Skurnik D, Sokol H. Genetic effects on the commensal microbiota in inflammatory bowel disease patients. PLoS Genet 2019; 15:e1008018. [PMID: 30849075 PMCID: PMC6426259 DOI: 10.1371/journal.pgen.1008018] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [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: 09/12/2018] [Revised: 03/20/2019] [Accepted: 02/13/2019] [Indexed: 12/16/2022] Open
Abstract
Several bacteria in the gut microbiota have been shown to be associated with inflammatory bowel disease (IBD), and dozens of IBD genetic variants have been identified in genome-wide association studies. However, the role of the microbiota in the etiology of IBD in terms of host genetic susceptibility remains unclear. Here, we studied the association between four major genetic variants associated with an increased risk of IBD and bacterial taxa in up to 633 IBD cases. We performed systematic screening for associations, identifying and replicating associations between NOD2 variants and two taxa: the Roseburia genus and the Faecalibacterium prausnitzii species. By exploring the overall association patterns between genes and bacteria, we found that IBD risk alleles were significantly enriched for associations concordant with bacteria-IBD associations. To understand the significance of this pattern in terms of the study design and known effects from the literature, we used counterfactual principles to assess the fitness of a few parsimonious gene-bacteria-IBD causal models. Our analyses showed evidence that the disease risk of these genetic variants were likely to be partially mediated by the microbiome. We confirmed these results in extensive simulation studies and sensitivity analyses using the association between NOD2 and F. prausnitzii as a case study.
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Affiliation(s)
- Hugues Aschard
- Centre de Bioinformatique, Biostatistique et Biologie Intégrative (C3BI), Institut Pasteur, Paris, France
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
- * E-mail: (HA); (DS); (HS)
| | - Vincent Laville
- Centre de Bioinformatique, Biostatistique et Biologie Intégrative (C3BI), Institut Pasteur, Paris, France
| | - Eric Tchetgen Tchetgen
- Department of Statistics, The Wharton School at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Dan Knights
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, Minnesota, United States of America
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
- Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States of America
- Biotechnology Institute, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Floris Imhann
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - Philippe Seksik
- Department of Gastroenterology, Saint Antoine Hospital, Paris, France
| | - Noah Zaitlen
- Department of Medicine, University of California, San Francisco, California, United States of America
| | - Mark S. Silverberg
- Zane Cohen Centre for Digestive Diseases, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Jacques Cosnes
- Department of Gastroenterology, Saint Antoine Hospital, Paris, France
- Sorbonne Université, Paris, France
| | - Rinse K. Weersma
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - Ramnik Xavier
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
- Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States of America
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Laurent Beaugerie
- Department of Gastroenterology, Saint Antoine Hospital, Paris, France
- Sorbonne Université, Paris, France
| | - David Skurnik
- Division of Infectious Diseases, Harvard Medical School, Boston, Massachusetts, United States of America
- Massachusetts Technology and Analytics, Brookline, Massachusetts, United States of America
- Department of Microbiology, Necker Hospital and University Paris Descartes, Paris, France
- INSERM U1151-Equipe 11, Institut Necker-Enfants Malades, Paris, France
- * E-mail: (HA); (DS); (HS)
| | - Harry Sokol
- Department of Gastroenterology, Saint Antoine Hospital, Paris, France
- Sorbonne Université, Paris, France
- Micalis Institute, AgroParisTech, Jouy-en-Josas, France
- INSERM CRSA UMRS U938, Paris, France
- * E-mail: (HA); (DS); (HS)
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Clayton JB, Danzeisen JL, Johnson TJ, Trent AM, Hayer SS, Murphy T, Wuenschmann A, Elder M, Shen Z, Mannion A, Bryant E, Knights D, Fox JG. Characterization of Campylobacter jejuni, Campylobacter upsaliensis, and a novel Campylobacter sp. in a captive non-human primate zoological collection. J Med Primatol 2018; 48:114-122. [PMID: 30536921 DOI: 10.1111/jmp.12393] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [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: 07/24/2018] [Revised: 10/04/2018] [Accepted: 10/24/2018] [Indexed: 11/30/2022]
Abstract
BACKGROUND The aim of this study was to longitudinally investigate the prevalence and characterization of Campylobacter spp. from non-human primates primate (NHP) with a history of endemic diarrhea housed at Como Park Zoo. METHODS Fecal samples from 33 symptom-free NHP belonging to eight different species were collected weekly for 9 weeks. Species-level characterization and phylogenetic analysis of isolates included biochemical testing and 16S rRNA sequencing. RESULTS Campylobacter spp. were isolated from the feces of 42% (14/33) of the primates. Three Campylobacter spp. (C upsaliensis, C jejuni, and novel Campylobacter sp.) were identified from three NHP species. A possible positive host Campylobacter species-specificity was observed. However, no statistical association was observed between the isolation of Campylobacter spp. and age and sex of the animal. CONCLUSIONS The study revealed the value of conducting repeated fecal sampling to establish the overall prevalence of Campylobacter in zoo-maintained NHP; it also importantly identifies a novel Campylobacter sp. isolated from white-faced saki monkeys.
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Affiliation(s)
- Jonathan B Clayton
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota.,GreenViet Biodiversity Conservation Center, Danang, Vietnam.,Primate Microbiome Project, Minneapolis, Minnesota
| | - Jessica L Danzeisen
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota
| | - Timothy J Johnson
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota.,Primate Microbiome Project, Minneapolis, Minnesota.,Mid-Central Research and Outreach Center, University of Minnesota, Willmar, Minnesota
| | - Ava M Trent
- Department of Veterinary Population Medicine, University of Minnesota, Saint Paul, Minnesota
| | - Shivdeep S Hayer
- Department of Veterinary Population Medicine, University of Minnesota, Saint Paul, Minnesota
| | - Tami Murphy
- Como Park Zoo & Conservatory, Saint Paul, Minnesota
| | - Arno Wuenschmann
- Veterinary Diagnostic Laboratory, University of Minnesota, Saint Paul, Minnesota
| | - Megan Elder
- Como Park Zoo & Conservatory, Saint Paul, Minnesota
| | - Zeli Shen
- Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Anthony Mannion
- Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Erin Bryant
- Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Dan Knights
- Primate Microbiome Project, Minneapolis, Minnesota.,Department of Computer Science and Engineering, University of Minnesota, Minneapolis, Minnesota.,Biotechnology Institute, University of Minnesota, Saint Paul, Minnesota.,Biomedical Informatics and Computational Biology, University of Minnesota, Minneapolis, Minnesota
| | - James G Fox
- Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, Massachusetts
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Wu JF, Muthusamy A, Al-Ghalith GA, Knights D, Guo B, Wu B, Remmel RP, Schladt DP, Alegre ML, Oetting WS, Jacobson PA, Israni AK. Urinary microbiome associated with chronic allograft dysfunction in kidney transplant recipients. Clin Transplant 2018; 32:e13436. [PMID: 30372560 PMCID: PMC6984979 DOI: 10.1111/ctr.13436] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [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: 06/20/2018] [Revised: 09/14/2018] [Accepted: 10/21/2018] [Indexed: 02/07/2023]
Abstract
BACKGROUND We performed a study to identify differences in the urinary microbiome associated with chronic allograft dysfunction (CAD) and compared the urinary microbiome of male and female transplant recipients with CAD. METHODS This case-control study enrolled 67 patients within the Deterioration of Kidney Allograft Function (DeKAF) Genomics cohort at two transplant centers. CAD was defined as a greater than 25% rise in serum creatinine relative to a 3 month post-transplant baseline. Urine samples from patients with and without CAD were analyzed using 16S V4 bacterial ribosomal DNA sequences. RESULTS Corynebacterium was more prevalent in female and male patients with CAD compared to non-CAD female patients (P = 0.0005). A total 21 distinct Operational Taxonomic Unit (OTUs) were identified as significantly different when comparing CAD and non-CAD patients using Kruskal-Wallis (P < 0.01). A subset analysis of female patients with CAD compared to non-CAD females identified similar differentially abundant OTUs, including the genera Corynebacterium and Staphylococcus (Kruskal-Wallis; P = 0.01; P = 0.004, respectively). Male CAD vs female CAD analysis showed greater abundance of phylum Proteobacteria in males. CONCLUSION There were differences in the urinary microbiome when comparing female and male CAD patients with their female non-CAD counterparts and these differences persisted in the subset analysis limited to female patients only.
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Affiliation(s)
- Jennifer F. Wu
- Department of Medicine, Nephrology Division, Hennepin Healthcare, Minneapolis, MN
| | | | | | - Dan Knights
- Department of Computer Science and Biotechnology Institute, University of Minnesota, Minneapolis, MN
| | - Bin Guo
- Division of Biostatistics, University of Minnesota, Minneapolis, MN
| | - Baolin Wu
- Division of Biostatistics, University of Minnesota, Minneapolis, MN
| | - Rory P. Remmel
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN
| | | | - Maria-Luisa Alegre
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL
| | - William S. Oetting
- Department of Experimental and Clinical Pharmacology, University of Minnesota, Minneapolis, MN
| | - Pamala A. Jacobson
- Department of Experimental and Clinical Pharmacology, University of Minnesota, Minneapolis, MN
| | - Ajay K. Israni
- Department of Medicine, Nephrology Division, Hennepin Healthcare, Minneapolis, MN
- Hennepin Healthcare Research Institute, Minneapolis, MN
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Lynch J, Tang K, Priya S, Sands J, Sands M, Tang E, Mukherjee S, Knights D, Blekhman R. HOMINID: a framework for identifying associations between host genetic variation and microbiome composition. Gigascience 2018; 6:1-7. [PMID: 29126115 PMCID: PMC5740987 DOI: 10.1093/gigascience/gix107] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Accepted: 10/31/2017] [Indexed: 02/02/2023] Open
Abstract
Recent studies have uncovered a strong effect of host genetic variation on the composition of host-associated microbiota. Here, we present HOMINID, a computational approach based on Lasso linear regression, that given host genetic variation and microbiome taxonomic composition data, identifies host single nucleotide polymorphisms (SNPs) that are correlated with microbial taxa abundances. Using simulated data, we show that HOMINID has accuracy in identifying associated SNPs and performs better compared with existing methods. We also show that HOMINID can accurately identify the microbial taxa that are correlated with associated SNPs. Lastly, by using HOMINID on real data of human genetic variation and microbiome composition, we identified 13 human SNPs in which genetic variation is correlated with microbiome taxonomic composition across body sites. In conclusion, HOMINID is a powerful method to detect host genetic variants linked to microbiome composition and can facilitate discovery of mechanisms controlling host-microbiome interactions.
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Affiliation(s)
- Joshua Lynch
- Department of Genetics, Cell Biology, and Development, University of Minnesota, 321 Church St SE, 6-160 Jackson Hall, Minneapolis MN 55455, USA.,Department of Ecology, Evolution, and Behavior, University of Minnesota, 1479 Gortner Ave, 140 Gortner Lab, Saint Paul MN 55108, USA
| | - Karen Tang
- Department of Genetics, Cell Biology, and Development, University of Minnesota, 321 Church St SE, 6-160 Jackson Hall, Minneapolis MN 55455, USA.,Department of Ecology, Evolution, and Behavior, University of Minnesota, 1479 Gortner Ave, 140 Gortner Lab, Saint Paul MN 55108, USA
| | - Sambhawa Priya
- Department of Genetics, Cell Biology, and Development, University of Minnesota, 321 Church St SE, 6-160 Jackson Hall, Minneapolis MN 55455, USA.,Department of Ecology, Evolution, and Behavior, University of Minnesota, 1479 Gortner Ave, 140 Gortner Lab, Saint Paul MN 55108, USA
| | - Joanna Sands
- Department of Genetics, Cell Biology, and Development, University of Minnesota, 321 Church St SE, 6-160 Jackson Hall, Minneapolis MN 55455, USA.,Department of Ecology, Evolution, and Behavior, University of Minnesota, 1479 Gortner Ave, 140 Gortner Lab, Saint Paul MN 55108, USA
| | - Margaret Sands
- Department of Genetics, Cell Biology, and Development, University of Minnesota, 321 Church St SE, 6-160 Jackson Hall, Minneapolis MN 55455, USA.,Department of Ecology, Evolution, and Behavior, University of Minnesota, 1479 Gortner Ave, 140 Gortner Lab, Saint Paul MN 55108, USA
| | - Evan Tang
- Department of Genetics, Cell Biology, and Development, University of Minnesota, 321 Church St SE, 6-160 Jackson Hall, Minneapolis MN 55455, USA.,Department of Ecology, Evolution, and Behavior, University of Minnesota, 1479 Gortner Ave, 140 Gortner Lab, Saint Paul MN 55108, USA
| | - Sayan Mukherjee
- Departments of Statistical Science, Mathematics, and Computer Science, Duke University, 112 Old Chemistry, Box 90251, Durham NC 27708, USA
| | - Dan Knights
- Department of Computer Science and Engineering, University of Minnesota, 200 Union St SE, 4-192 Keller Hall, Minneapolis MN 55455, USA.,Biotechnology Institute, University of Minnesota, 1479 Gortner Ave, 140 Gortner Lab, Saint Paul MN 55108, USA
| | - Ran Blekhman
- Department of Genetics, Cell Biology, and Development, University of Minnesota, 321 Church St SE, 6-160 Jackson Hall, Minneapolis MN 55455, USA.,Department of Ecology, Evolution, and Behavior, University of Minnesota, 1479 Gortner Ave, 140 Gortner Lab, Saint Paul MN 55108, USA
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