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Dorsey AF, Roach J, Burten RB, Azcarate-Peril MA, Thompson AL. Intestinal microbiota composition and efficacy of iron supplementation in Peruvian children. Am J Hum Biol 2024:e24058. [PMID: 38420749 DOI: 10.1002/ajhb.24058] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Revised: 02/15/2024] [Accepted: 02/16/2024] [Indexed: 03/02/2024] Open
Abstract
OBJECTIVE Despite repeated public health interventions, anemia prevalence among children remains a concern. We use an evolutionary medicine perspective to examine the intestinal microbiome as a pathway underlying the efficacy of iron-sulfate treatment. This study explores whether gut microbiota composition differs between anemic children who respond and do not respond to treatment at baseline and posttreatment and if specific microbiota taxa remain associated with response to iron supplementation after controlling for relevant inflammatory and pathogenic variables. METHODS Data come from 49 pre-school-aged anemic children living in San Juan de Lurigancho, Lima, Peru. We tested for differences in alpha and beta diversity using QIIME 2 and performed differential abundance testing in DESeq2 in R. We ran multivariate regression models to assess associations between abundance of specific taxa and response while controlling for relevant variables in Stata 17. RESULTS While we found no evidence for gut microbiota diversity associated with child response to iron treatment, we observed several differential abundance patterns between responders and non-responders at both timepoints. Additionally, we present support for a nonzero relationship between lower relative abundance of Barnesiellaceae and response to iron supplementation in samples collected before and after treatment. CONCLUSION While larger studies and more specific approaches are needed to understand the relationship between microbes and anemia in an epidemiological context, this study suggests that investigating nutritional status and pathogen exposure is key to better understanding the gut microbiome and impact of iron fortification.
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Affiliation(s)
- Achsah F Dorsey
- Department of Anthropology, University of Massachusetts, Amherst, Massachusetts, USA
| | - Jeff Roach
- Center for Gastrointestinal Biology and Disease (CGIBD), Department of Medicine, Division of Gastroenterology and Hepatology, School of Medicine, UNC Microbiome Core, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Rachel B Burten
- Graduate Program in Organismic and Evolutionary Biology, University of Massachusetts, Amherst, Massachusetts, USA
| | - M Andrea Azcarate-Peril
- Center for Gastrointestinal Biology and Disease (CGIBD), Department of Medicine, Division of Gastroenterology and Hepatology, School of Medicine, UNC Microbiome Core, University of North Carolina, Chapel Hill, North Carolina, USA
- Department of Nutrition, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Amanda L Thompson
- Department of Nutrition, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina, USA
- Department of Anthropology, University of North Carolina, Chapel Hill, North Carolina, USA
- Carolina Population Center, University of North Carolina, Chapel Hill, North Carolina, USA
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2
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Bhatt AP, Arnold JW, Awoniyi M, Sun S, Santiago VF, Quintela PH, Walsh K, Ngobeni R, Hansen B, Gulati A, Carroll IM, Azcarate-Peril MA, Fodor AA, Swann J, Bartelt LA. Giardia Antagonizes Beneficial Functions of Indigenous and Therapeutic Intestinal Bacteria during Malnutrition. bioRxiv 2024:2024.01.22.575921. [PMID: 38328247 PMCID: PMC10849499 DOI: 10.1101/2024.01.22.575921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Undernutrition in children commonly disrupts the structure and function of the small intestinal microbial community, leading to enteropathies, compromised metabolic health, and impaired growth and development. The mechanisms by which diet and microbes mediate the balance between commensal and pathogenic intestinal flora remain elusive. In a murine model of undernutrition, we investigated the direct interactions Giardia lamblia, a prevalent small intestinal pathogen, on indigenous microbiota and specifically on Lactobacillus strains known for their mucosal and growth homeostatic properties. Our research reveals that Giardia colonization shifts the balance of lactic acid bacteria, causing a relative decrease in Lactobacillus spp . and an increase in Bifidobacterium spp . This alteration corresponds with a decrease in multiple indicators of mucosal and nutritional homeostasis. Additionally, protein-deficient conditions coupled with Giardia infection exacerbate the rise of primary bile acids and susceptibility to bile acid-induced intestinal barrier damage. In epithelial cell monolayers, Lactobacillus spp . mitigated bile acid-induced permeability, showing strain-dependent protective effects. In vivo, L. plantarum, either alone or within a Lactobacillus spp consortium, facilitated growth in protein-deficient mice, an effect attenuated by Giardia , despite not inhibiting Lactobacillus colonization. These results highlight Giardia's potential role as a disruptor of probiotic functional activity, underscoring the imperative for further research into the complex interactions between parasites and bacteria under conditions of nutritional deficiency.
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3
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Templeton GB, Fefer G, Case BC, Roach J, Azcarate-Peril MA, Gruen ME, Callahan BJ, Olby NJ. Longitudinal Analysis of Canine Oral Microbiome Using Whole Genome Sequencing in Aging Companion Dogs. Animals (Basel) 2023; 13:3846. [PMID: 38136883 PMCID: PMC10740535 DOI: 10.3390/ani13243846] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Revised: 12/10/2023] [Accepted: 12/11/2023] [Indexed: 12/24/2023] Open
Abstract
Aged companion dogs have a high prevalence of periodontal disease and canine cognitive dysfunction syndrome (CCDS) and the two disorders are correlated. Similarly, periodontal disease and Alzheimer's Disease are correlated in people. However, little is known about the oral microbiota of aging dogs. The goal of this project was to characterize the longitudinal changes in oral microbiota in aged dogs. Oral swabs were taken from ten senior client-owned dogs on 2-3 occasions spanning 24 months and they underwent whole genome shotgun (WGS) sequencing. Cognitive status was established at each sampling time. A statistically significant increase in alpha diversity for bacterial and fungal species was observed between the first and last study visits. Bacteroidetes and proteobacteria were the most abundant bacterial phyla. Porphyromonas gulae was the most abundant bacterial species (11.6% of total reads). The species Lactobacillus gasseri had a statistically significant increase in relative abundance with age whereas Leptotrichia sp. oral taxon 212 had a statistically significant positive longitudinal association with cognition score. There is an increased fungal and bacterial alpha diversity in aging dogs over time and nearly universal oral dysbiosis. The role of the oral microbiota, particularly Leptotrichia and P. gulae and P. gingivalis, in aging and CCDS warrants further investigation.
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Affiliation(s)
- Ginger B. Templeton
- Department of Clinical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC 27607, USA (M.E.G.)
| | - Gilad Fefer
- Department of Clinical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC 27607, USA (M.E.G.)
| | - Beth C. Case
- Department of Clinical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC 27607, USA (M.E.G.)
| | - Jeff Roach
- Department of Medicine, Division of Gastroenterology and Hepatology, and UNC Microbiome Core, Center for Gastrointestinal Biology and Disease, School of Medicine, University of North Carolina, Chapel Hill, NC 27599, USA; (J.R.)
| | - M. Andrea Azcarate-Peril
- Department of Medicine, Division of Gastroenterology and Hepatology, and UNC Microbiome Core, Center for Gastrointestinal Biology and Disease, School of Medicine, University of North Carolina, Chapel Hill, NC 27599, USA; (J.R.)
| | - Margaret E. Gruen
- Department of Clinical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC 27607, USA (M.E.G.)
| | - Benjamin J. Callahan
- Department of Population Health and Pathobiology, North Carolina State University, Raleigh, NC 27607, USA;
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC 27695, USA
| | - Natasha J. Olby
- Department of Clinical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC 27607, USA (M.E.G.)
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4
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Dubey H, Roychoudhury R, Alex A, Best C, Liu S, White A, Carlson A, Azcarate-Peril MA, Mansfield LS, Knickmeyer R. Effect of Human Infant Gut Microbiota on Mouse Behavior, Dendritic Complexity, and Myelination. bioRxiv 2023:2023.10.24.563309. [PMID: 37961091 PMCID: PMC10634763 DOI: 10.1101/2023.10.24.563309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
The mammalian gut microbiome influences numerous developmental processes. In human infants it has been linked with cognition, social skills, hormonal responses to stress, and brain connectivity. Yet, these associations are not necessarily causal. The present study tested whether two microbial stool communities, common in human infants, affected behavior, myelination, dendritic morphology, and spine density when used to colonize mouse models. Humanized animals were more like specific-pathogen free mice than germ-free mice for most phenotypes, although in males, both humanized groups were less social. Both humanized groups had thinner myelin sheaths in the hippocampus, than did germ-free animals. Humanized animals were similar to each other except for dendritic morphology and spine density where one group had greater dendritic length in the prefrontal cortex, greater dendritic volume in the nucleus accumbens, and greater spine density in both regions, compared to the other. Results add to a body of literature suggesting the gut microbiome impacts brain development. Teaser Fecal transplants from human infants with highly abundant Bifidobacterium , an important inhabitant of the intestinal tract of breastfed newborns, may promote brain connectivity in mice.
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5
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Cho H, Qu Y, Liu C, Tang B, Lyu R, Lin BM, Roach J, Azcarate-Peril MA, Aguiar Ribeiro A, Love MI, Divaris K, Wu D. Comprehensive evaluation of methods for differential expression analysis of metatranscriptomics data. Brief Bioinform 2023; 24:bbad279. [PMID: 37738402 PMCID: PMC10516371 DOI: 10.1093/bib/bbad279] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 06/23/2023] [Accepted: 07/18/2023] [Indexed: 09/24/2023] Open
Abstract
Understanding the function of the human microbiome is important but the development of statistical methods specifically for the microbial gene expression (i.e. metatranscriptomics) is in its infancy. Many currently employed differential expression analysis methods have been designed for different data types and have not been evaluated in metatranscriptomics settings. To address this gap, we undertook a comprehensive evaluation and benchmarking of 10 differential analysis methods for metatranscriptomics data. We used a combination of real and simulated data to evaluate performance (i.e. type I error, false discovery rate and sensitivity) of the following methods: log-normal (LN), logistic-beta (LB), MAST, DESeq2, metagenomeSeq, ANCOM-BC, LEfSe, ALDEx2, Kruskal-Wallis and two-part Kruskal-Wallis. The simulation was informed by supragingival biofilm microbiome data from 300 preschool-age children enrolled in a study of childhood dental disease (early childhood caries, ECC), whereas validations were sought in two additional datasets from the ECC study and an inflammatory bowel disease study. The LB test showed the highest sensitivity in both small and large samples and reasonably controlled type I error. Contrarily, MAST was hampered by inflated type I error. Upon application of the LN and LB tests in the ECC study, we found that genes C8PHV7 and C8PEV7, harbored by the lactate-producing Campylobacter gracilis, had the strongest association with childhood dental disease. This comprehensive model evaluation offers practical guidance for selection of appropriate methods for rigorous analyses of differential expression in metatranscriptomics. Selection of an optimal method increases the possibility of detecting true signals while minimizing the chance of claiming false ones.
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Affiliation(s)
- Hunyong Cho
- Department of Biostatistics, University of North Carolina, Chapel Hill, NC, United States
| | - Yixiang Qu
- Department of Biostatistics, University of North Carolina, Chapel Hill, NC, United States
| | - Chuwen Liu
- Department of Biostatistics, University of North Carolina, Chapel Hill, NC, United States
| | - Boyang Tang
- Department of Statistics, University of Connecticut, Storrs, CT, United States
| | - Ruiqi Lyu
- School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States
| | - Bridget M Lin
- Department of Biostatistics, University of North Carolina, Chapel Hill, NC, United States
| | - Jeffrey Roach
- Research Computing, University of North Carolina, Chapel Hill, NC, United States
| | - M Andrea Azcarate-Peril
- Department of Medicine and Nutrition, University of North Carolina, Chapel Hill, NC, United States
| | - Apoena Aguiar Ribeiro
- Division of Diagnostic Sciences, University of North Carolina, Chapel Hill, NC, United States
| | - Michael I Love
- Department of Biostatistics, University of North Carolina, Chapel Hill, NC, United States
- Department of Genetics, University of North Carolina, Chapel Hill, NC, United States
| | - Kimon Divaris
- Division of Pediatric and Public Health, University of North Carolina, Chapel Hill, NC, United States
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, United States
| | - Di Wu
- Department of Biostatistics, University of North Carolina, Chapel Hill, NC, United States
- Division of Oral and Craniofacial Health Sciences, Adam School of Dentistry, University of North Carolina, Chapel Hill, NC, United States
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, United States
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6
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Ji M, Xu X, Xu Q, Hsiao YC, Martin C, Ukraintseva S, Popov V, Arbeev KG, Randall TA, Wu X, Garcia-Peterson LM, Liu J, Xu X, Andrea Azcarate-Peril M, Wan Y, Yashin AI, Anantharaman K, Lu K, Li JL, Shats I, Li X. Methionine restriction-induced sulfur deficiency impairs antitumour immunity partially through gut microbiota. Nat Metab 2023; 5:1526-1543. [PMID: 37537369 PMCID: PMC10513933 DOI: 10.1038/s42255-023-00854-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 06/30/2023] [Indexed: 08/05/2023]
Abstract
Restriction of methionine (MR), a sulfur-containing essential amino acid, has been reported to repress cancer growth and improve therapeutic responses in several preclinical settings. However, how MR impacts cancer progression in the context of the intact immune system is unknown. Here we report that while inhibiting cancer growth in immunocompromised mice, MR reduces T cell abundance, exacerbates tumour growth and impairs tumour response to immunotherapy in immunocompetent male and female mice. Mechanistically, MR reduces microbial production of hydrogen sulfide, which is critical for immune cell survival/activation. Dietary supplementation of a hydrogen sulfide donor or a precursor, or methionine, stimulates antitumour immunity and suppresses tumour progression. Our findings reveal an unexpected negative interaction between MR, sulfur deficiency and antitumour immunity and further uncover a vital role of gut microbiota in mediating this interaction. Our study suggests that any possible anticancer benefits of MR require careful consideration of both the microbiota and the immune system.
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Affiliation(s)
- Ming Ji
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Xiaojiang Xu
- Integrative Bioinformatics, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Qing Xu
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Yun-Chung Hsiao
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Cody Martin
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI, USA
| | - Svetlana Ukraintseva
- Social Science Research Institute, Duke University School of Medicine, Durham, NC, USA
| | - Vladimir Popov
- Social Science Research Institute, Duke University School of Medicine, Durham, NC, USA
| | - Konstantin G Arbeev
- Social Science Research Institute, Duke University School of Medicine, Durham, NC, USA
| | - Tom A Randall
- Integrative Bioinformatics, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Xiaoyue Wu
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Liz M Garcia-Peterson
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Juan Liu
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, USA
| | - Xin Xu
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - M Andrea Azcarate-Peril
- Department of Medicine, Division of Gastroenterology and Hepatology and Microbiome Core Facility, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Yisong Wan
- Department of Microbiology and Immunology and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Anatoliy I Yashin
- Social Science Research Institute, Duke University School of Medicine, Durham, NC, USA
| | | | - Kun Lu
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jian-Liang Li
- Integrative Bioinformatics, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Igor Shats
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Xiaoling Li
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA.
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7
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Wahl A, Yao W, Liao B, Chateau M, Richardson C, Ling L, Franks A, Senthil K, Doyon G, Li F, Frost J, Whitehurst CB, Pagano JS, Fletcher CA, Azcarate-Peril MA, Hudgens MG, Rogala AR, Tucker JD, McGowan I, Sartor RB, Garcia JV. A germ-free humanized mouse model shows the contribution of resident microbiota to human-specific pathogen infection. Nat Biotechnol 2023:10.1038/s41587-023-01906-5. [PMID: 37563299 DOI: 10.1038/s41587-023-01906-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 07/10/2023] [Indexed: 08/12/2023]
Abstract
Germ-free (GF) mice, which are depleted of their resident microbiota, are the gold standard for exploring the role of the microbiome in health and disease; however, they are of limited value in the study of human-specific pathogens because they do not support their replication. Here, we develop GF mice systemically reconstituted with human immune cells and use them to evaluate the role of the resident microbiome in the acquisition, replication and pathogenesis of two human-specific pathogens, Epstein-Barr virus (EBV) and human immunodeficiency virus (HIV). Comparison with conventional (CV) humanized mice showed that resident microbiota enhance the establishment of EBV infection and EBV-induced tumorigenesis and increase mucosal HIV acquisition and replication. HIV RNA levels were higher in plasma and tissues of CV humanized mice compared with GF humanized mice. The frequency of CCR5+ CD4+ T cells throughout the intestine was also higher in CV humanized mice, indicating that resident microbiota govern levels of HIV target cells. Thus, resident microbiota promote the acquisition and pathogenesis of two clinically relevant human-specific pathogens.
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Affiliation(s)
- Angela Wahl
- International Center for the Advancement of Translational Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Division of Infectious Diseases, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | - Wenbo Yao
- International Center for the Advancement of Translational Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Division of Infectious Diseases, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Baolin Liao
- International Center for the Advancement of Translational Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Division of Infectious Diseases, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, China
| | - Morgan Chateau
- International Center for the Advancement of Translational Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Division of Infectious Diseases, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Cara Richardson
- International Center for the Advancement of Translational Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Division of Infectious Diseases, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Lijun Ling
- International Center for the Advancement of Translational Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Division of Infectious Diseases, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Adrienne Franks
- International Center for the Advancement of Translational Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Division of Infectious Diseases, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Krithika Senthil
- International Center for the Advancement of Translational Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Division of Infectious Diseases, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Genevieve Doyon
- International Center for the Advancement of Translational Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Division of Infectious Diseases, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Fengling Li
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Josh Frost
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Division of Comparative Medicine, Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Christopher B Whitehurst
- Department of Pathology, Microbiology, and Immunology, New York Medical College, Valhalla, NY, USA
| | - Joseph S Pagano
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Craig A Fletcher
- Division of Comparative Medicine, Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - M Andrea Azcarate-Peril
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Division of Gastroenterology and Hepatology, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- UNC Microbiome Core, University of North Carolina, Chapel Hill, NC, USA
| | - Michael G Hudgens
- Department of Biostatistics, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Allison R Rogala
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Division of Comparative Medicine, Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Joseph D Tucker
- Division of Infectious Diseases, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Clinical Research Department, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Ian McGowan
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, University of Pittsburgh Medical School, Pittsburgh, PA, USA
- Orion Biotechnology, Ottawa, Ontario, Canada
| | - R Balfour Sartor
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Division of Gastroenterology and Hepatology, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - J Victor Garcia
- International Center for the Advancement of Translational Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Division of Infectious Diseases, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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8
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Cho H, Ren Z, Divaris K, Roach J, Lin BM, Liu C, Azcarate-Peril MA, Simancas-Pallares MA, Shrestha P, Orlenko A, Ginnis J, North KE, Zandona AGF, Ribeiro AA, Wu D, Koo H. Selenomonas sputigena acts as a pathobiont mediating spatial structure and biofilm virulence in early childhood caries. Nat Commun 2023; 14:2919. [PMID: 37217495 PMCID: PMC10202936 DOI: 10.1038/s41467-023-38346-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Accepted: 04/21/2023] [Indexed: 05/24/2023] Open
Abstract
Streptococcus mutans has been implicated as the primary pathogen in childhood caries (tooth decay). While the role of polymicrobial communities is appreciated, it remains unclear whether other microorganisms are active contributors or interact with pathogens. Here, we integrate multi-omics of supragingival biofilm (dental plaque) from 416 preschool-age children (208 males and 208 females) in a discovery-validation pipeline to identify disease-relevant inter-species interactions. Sixteen taxa associate with childhood caries in metagenomics-metatranscriptomics analyses. Using multiscale/computational imaging and virulence assays, we examine biofilm formation dynamics, spatial arrangement, and metabolic activity of Selenomonas sputigena, Prevotella salivae and Leptotrichia wadei, either individually or with S. mutans. We show that S. sputigena, a flagellated anaerobe with previously unknown role in supragingival biofilm, becomes trapped in streptococcal exoglucans, loses motility but actively proliferates to build a honeycomb-like multicellular-superstructure encapsulating S. mutans, enhancing acidogenesis. Rodent model experiments reveal an unrecognized ability of S. sputigena to colonize supragingival tooth surfaces. While incapable of causing caries on its own, when co-infected with S. mutans, S. sputigena causes extensive tooth enamel lesions and exacerbates disease severity in vivo. In summary, we discover a pathobiont cooperating with a known pathogen to build a unique spatial structure and heighten biofilm virulence in a prevalent human disease.
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Affiliation(s)
- Hunyong Cho
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Zhi Ren
- Biofilm Research Laboratories, Center for Innovation & Precision Dentistry, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Kimon Divaris
- Division of Pediatric and Public Health, Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Department of Epidemiology, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | - Jeffrey Roach
- UNC Information Technology Services and Research Computing, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- UNC Microbiome Core, Center for Gastrointestinal Biology and Disease, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Bridget M Lin
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Chuwen Liu
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - M Andrea Azcarate-Peril
- UNC Microbiome Core, Center for Gastrointestinal Biology and Disease, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Medicine, Division of Gastroenterology and Hepatology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Miguel A Simancas-Pallares
- Division of Pediatric and Public Health, Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Poojan Shrestha
- Division of Pediatric and Public Health, Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Epidemiology, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Alena Orlenko
- Artificial Intelligence Innovation Lab, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Jeannie Ginnis
- Division of Pediatric and Public Health, Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Kari E North
- Department of Epidemiology, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | - Apoena Aguiar Ribeiro
- Division of Diagnostic Sciences, Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Di Wu
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Division of Oral and Craniofacial Health Sciences, Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | - Hyun Koo
- Biofilm Research Laboratories, Center for Innovation & Precision Dentistry, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Department of Orthodontics, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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9
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Long ES, Penalver Bernabe B, Xia K, Azcarate-Peril MA, Carroll IM, Rackers HS, Grewen KM, Meltzer-Brody S, Kimmel MC. The microbiota-gut-brain axis and perceived stress in the perinatal period. Arch Womens Ment Health 2023; 26:227-234. [PMID: 36897389 PMCID: PMC10063483 DOI: 10.1007/s00737-023-01300-9] [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: 11/04/2022] [Accepted: 02/08/2023] [Indexed: 03/11/2023]
Abstract
Perinatal perceived stress can contribute to worse health outcomes for the parent-child dyad. Given the emerging relationship between the microbiota-gut-brain axis and stress, this study sought to elucidate connections between bowel symptoms and the gut microbiome in relation to perceived stress at three time points in the perinatal period: two during pregnancy and one postpartum. Ninety-five pregnant individuals participated in a prospective cohort study from April 2017 to November 2019. Researchers assessed Perceived Stress Scale-10 (PSS); bowel symptoms (according to the IBS Questionnaire); psychiatrist assessment of new onset or exacerbated depression and anxiety; and fecal samples analyzed for alpha diversity (measures of gut microbiome diversity utilizing Shannon, Observed OTUs, and Faith's PD) at each timepoint. Covariates included weeks of gestation and weeks postpartum. PSS scores were divided into "Perceived Self-Efficacy" and "Perceived Helplessness." Increased gut microbial diversity was associated with decreased bowel symptoms, decreased overall perceived stress, increased ability to cope with adversity, and decreased distress in the postpartum period. This study found a significant association between a less diverse microbial community, lower self-efficacy early in pregnancy, and greater bowel symptoms and perceived helplessness later in the perinatal period, relationships that may ultimately point to novel diagnostic methods and interventions for perceived stress based on the microbiota-gut-brain axis.
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Affiliation(s)
- Emily S Long
- Department of Psychiatry, University of North Carolina School of Medicine, Campus Box #7160, Chapel Hill, NC, 27599-7160, USA
| | - Beatriz Penalver Bernabe
- Department of Biomedical Engineering, College of Medicine, University of Illinois at Chicago, Chicago, IL, USA
| | - Kai Xia
- Department of Psychiatry, University of North Carolina School of Medicine, Campus Box #7160, Chapel Hill, NC, 27599-7160, USA
| | - M Andrea Azcarate-Peril
- Departments of Medicine and Nutrition, Microbiome Core, University of North Carolina, Chapel Hill, NC, USA
| | - Ian M Carroll
- Department of Nutrition, University of North Carolina Gillings School of Public Health, Chapel Hill, NC, USA
| | - Hannah S Rackers
- Department of Psychiatry, University of North Carolina School of Medicine, Campus Box #7160, Chapel Hill, NC, 27599-7160, USA
| | - Karen M Grewen
- Department of Psychiatry, University of North Carolina School of Medicine, Campus Box #7160, Chapel Hill, NC, 27599-7160, USA
| | - Samantha Meltzer-Brody
- Department of Psychiatry, University of North Carolina School of Medicine, Campus Box #7160, Chapel Hill, NC, 27599-7160, USA
| | - Mary C Kimmel
- Department of Psychiatry, University of North Carolina School of Medicine, Campus Box #7160, Chapel Hill, NC, 27599-7160, USA.
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10
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Liu M, Matuszek G, Azcarate-Peril MA, Loeser RF, Shea MK. An Exploratory Case-Control Study on the Associations of Bacterially-Derived Vitamin K Forms with the Intestinal Microbiome and Obesity-Related Osteoarthritis. Curr Dev Nutr 2023; 7:100049. [PMID: 37181928 PMCID: PMC10111584 DOI: 10.1016/j.cdnut.2023.100049] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 02/01/2023] [Accepted: 02/13/2023] [Indexed: 02/22/2023] Open
Abstract
Background Evidence suggests that natural metabolites produced by intestinal microorganisms may have beneficial or harmful effects on osteoarthritis (OA). This could include menaquinones, which are bacterially-synthesized, biologically-active vitamin K forms abundant in the intestinal microbiome. Objectives The overall goal of this study was to evaluate the association of intestinally-derived menaquinones with obesity-related OA. Methods This case-control study used data and biospecimens derived from a subgroup of Johnston County Osteoarthritis Study participants. Fecal menaquinone concentrations and microbial composition were determined in 52 obese participants with hand and knee OA and 42 age- and sex-matched obese participants without OA. The inter-relationships among fecal menaquinones were evaluated using principal component analysis. The differences in alpha and beta diversities and microbial composition across menaquinone clusters were evaluated using ANOVA. Results The samples were clustered into the following 3 groups: cluster 1 characterized by higher fecal menaquinone-9 and -10 concentrations, cluster 2 characterized by lower overall menaquinone concentrations, and cluster 3 characterized by higher menaquinone-12 and -13 concentrations. Overall, fecal menaquinone clusters did not differ between participants with or without OA (P = 0.707). Microbial diversity did not differ across the fecal menaquinone clusters (all F-test P > 0.12). However, the relative abundance of bacterial taxa differed among clusters, with higher abundance of Coprococcus, Prevotella, and Eggerthella in cluster 2 than in cluster 1; higher abundance of Oscillospira, Dorea, Eubacterium, and Bacteroides in cluster 3 than in cluster 1; and higher abundance of Prevotella, Sutterella, and Dorea in cluster 3 than in cluster 2 (all P < 0.001). Conclusion Menaquinones were variable and abundant in the human gut, but the fecal menaquinone clusters did not differ with OA status. Although the relative abundance of specific bacterial taxa differed among fecal menaquinone clusters, the relevance of these differences with respect to vitamin K status and human health is uncertain.
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Affiliation(s)
- Minying Liu
- USDA Human Nutrition Research Center on Aging at Tufts University, Boston, Massachusetts, USA
| | - Gregory Matuszek
- USDA Human Nutrition Research Center on Aging at Tufts University, Boston, Massachusetts, USA
| | - M Andrea Azcarate-Peril
- Division of Gastroenterology and Hepatology and UNC Microbiome Core, Center for Gastrointestinal Biology and Disease, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - Richard F. Loeser
- Division of Rheumatology, Allergy, and Immunology and the Thurston Arthritis Research Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - M Kyla Shea
- USDA Human Nutrition Research Center on Aging at Tufts University, Boston, Massachusetts, USA
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11
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Gookin JL, Hartley AN, Aicher KM, Mathews KG, Cullen R, Cullen JM, Callahan BJ, Stowe DM, Seiler GS, Jacob ME, Arnold JW, Azcarate-Peril MA, Stauffer SH. Gallbladder microbiota in healthy dogs and dogs with mucocele formation. PLoS One 2023; 18:e0281432. [PMID: 36763596 PMCID: PMC9916591 DOI: 10.1371/journal.pone.0281432] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 01/23/2023] [Indexed: 02/11/2023] Open
Abstract
To date studies have not investigated the culture-independent microbiome of bile from dogs, a species where aseptic collection of bile under ultrasound guidance is somewhat routine. Despite frequent collection of bile for culture-based diagnosis of bacterial cholecystitis, it is unknown whether bile from healthy dogs harbors uncultivable bacteria or a core microbiota. The answer to this question is critical to understanding the pathogenesis of biliary infection and as a baseline to exploration of other biliary diseases in dogs where uncultivable bacteria could play a pathogenic role. A pressing example of such a disease would be gallbladder mucocele formation in dogs. This prevalent and deadly condition is characterized by excessive secretion of abnormal mucus by the gallbladder epithelium that can eventually lead to rupture of the gallbladder or obstruction of bile flow. The cause of mucocele formation is unknown as is whether uncultivable, and therefore unrecognized, bacteria play any systematic role in pathogenesis. In this study we applied next-generation 16S rRNA gene sequencing to identify the culture-negative bacterial community of gallbladder bile from healthy dogs and gallbladder mucus from dogs with mucocele formation. Integral to our study was the use of 2 separate DNA isolations on each sample using different extraction methods and sequencing of negative control samples enabling recognition and curation of contaminating sequences. Microbiota findings were validated by simultaneous culture-based identification, cytological examination of bile, and fluorescence in-situ hybridization (FISH) performed on gallbladder mucosa. Using culture-dependent, cytological, FISH, and 16S rRNA sequencing approaches, results of our study do not support existence of a core microbiome in the bile of healthy dogs or gallbladder mucus from dogs with mucocele formation. Our findings further document how contaminating sequences can significantly contribute to the results of sequencing analysis when performed on samples with low bacterial biomass.
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Affiliation(s)
- Jody L. Gookin
- Department of Clinical Sciences, College of Veterinary Medicine and Comparative Medicine Institute, North Carolina State University, Raleigh, North Carolina, United States of America
- * E-mail:
| | - Ashley N. Hartley
- Department of Clinical Sciences, College of Veterinary Medicine and Comparative Medicine Institute, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Kathleen M. Aicher
- Department of Clinical Sciences, College of Veterinary Medicine and Comparative Medicine Institute, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Kyle G. Mathews
- Department of Clinical Sciences, College of Veterinary Medicine and Comparative Medicine Institute, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Rachel Cullen
- Department of Clinical Sciences, College of Veterinary Medicine and Comparative Medicine Institute, North Carolina State University, Raleigh, North Carolina, United States of America
| | - John M. Cullen
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Benjamin J. Callahan
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Devorah M. Stowe
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Gabriela S. Seiler
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Megan E. Jacob
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Jason W. Arnold
- Department of Medicine, Division of Gastroenterology and Hepatology, and UNC Microbiome Core, Center for Gastrointestinal Biology and Disease, School of Medicine, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - M. Andrea Azcarate-Peril
- Department of Medicine, Division of Gastroenterology and Hepatology, and UNC Microbiome Core, Center for Gastrointestinal Biology and Disease, School of Medicine, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Stephen H. Stauffer
- Department of Clinical Sciences, College of Veterinary Medicine and Comparative Medicine Institute, North Carolina State University, Raleigh, North Carolina, United States of America
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12
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Arbeeva L, Azcarate-Peril MA, Cui Y, Nelson AE, Loeser RF. Association of plasma microbial composition with a leaky gut in obesity-related osteoarthritis: An exploratory study. Osteoarthr Cartil Open 2022; 4:100317. [PMID: 36474790 PMCID: PMC9718202 DOI: 10.1016/j.ocarto.2022.100317] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 10/19/2022] [Accepted: 10/21/2022] [Indexed: 12/24/2022] Open
Abstract
Objective To examine the plasma microbiome for differences between obese individuals with and without osteoarthritis (OA) and its association with serum lipopolysaccharide (LPS). Design Blood samples from 70 participants with body mass index (BMI) ≥ 30kg/m2 and age ≥55 years, with (cases) or without (controls) hand plus knee OA, were analyzed for serum LPS and composition of the plasma microbiome. The Dirichlet-multinominal recursive partitioning model (DM-RPart) was applied to microbiome compositional data to test the hypothesis that LPS levels distinguish plasma microbiome, accounting for BMI and age. Results No significant differences in alpha diversity, or compositional differences between groups at the genus level, were seen between cases and controls (p = 0.11). β-Diversity was significantly associated with serum LPS levels (p = 0.01). DM-RPart resulted in an optimal tree with 3 divisions: 1) based on age (split at 69 years); 2) those older than 69 were split based on BMI; 3) those with BMI <39 kg/m2 were split based on LPS level (at 65 EU/ml). This resulted in 4 groups (nodes 2, and 5-7). Participants in node 2 were younger and the majority had no or mild OA. Those in nodes 5 and 6 were comparable in age and BMI but node 6 had higher LPS and more severe OA. Individuals in node 7 were older, had higher BMI, and the most severe OA. Conclusions Our results suggest a relationship between serum LPS and the plasma microbiome in a subgroup of obese individuals with hand plus knee OA that could reflect differences in intestinal permeability.
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Affiliation(s)
- Liubov Arbeeva
- Division of Rheumatology, Allergy and Immunology and the Thurston Arthritis Research Center, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - M. Andrea Azcarate-Peril
- Division of Gastroenterology and Hepatology and UNC Microbiome Core, Center for Gastrointestinal Biology and Disease, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Yang Cui
- Division of Rheumatology, Allergy and Immunology and the Thurston Arthritis Research Center, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Amanda E. Nelson
- Division of Rheumatology, Allergy and Immunology and the Thurston Arthritis Research Center, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Richard F. Loeser
- Division of Rheumatology, Allergy and Immunology and the Thurston Arthritis Research Center, University of North Carolina School of Medicine, Chapel Hill, NC, USA
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13
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Gookin JL, Strong SJ, Bruno-Bárcena JM, Stauffer SH, Williams S, Wassack E, Azcarate-Peril MA, Estrada M, Seguin A, Balzer J, Davidson G. Randomized placebo-controlled trial of feline-origin Enterococcus hirae probiotic effects on preventative health and fecal microbiota composition of fostered shelter kittens. Front Vet Sci 2022; 9:923792. [PMID: 36467638 PMCID: PMC9714445 DOI: 10.3389/fvets.2022.923792] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 04/19/2022] [Accepted: 11/02/2022] [Indexed: 10/29/2023] Open
Abstract
INTRODUCTION Diarrhea is the second most common cause of mortality in shelter kittens. Studies examining prevention strategies in this population are lacking. Probiotics are of particular interest but studies in cats are largely limited to healthy adults or those with induced disease. Only one study in domestic cats describes the use of host-derived bacteria as a probiotic. We previously identified Enterococcus hirae as a dominant species colonizing the small intestinal mucosa in healthy shelter kittens. Oral administration of a probiotic formulation of kitten-origin E. hirae (strain 1002-2) mitigated the increase in intestinal permeability and fecal water loss resulting from experimental enteropathogenic E. coli infection in purpose-bred kittens. Based on these findings, we hypothesized that administration of kitten-origin E. hirae to weaned fostered shelter kittens could provide a measurable preventative health benefit. METHODS We conducted a randomized, placebo-controlled, blinded clinical trial to determine the impact of a freeze-dried E. hirae probiotic on body weight gain, incidence of diarrhea, carriage of potential diarrheal pathogens, and composition of the intestinal microbiota in weaned fostered shelter kittens. RESULTS One-hundred thirty kittens completed the study. Fifty-eight kittens received the probiotic and 72 received the placebo. There were no significant differences in age, weight upon initiation of the study, number of days in the study, average daily gain in body weight, or weight at completion of the study. Kittens treated with E. hirae were 3.4 times less likely to develop diarrhea compared to kittens treated with placebo (odds ratio = 0.294, 95% CI 0.109-0.792, p = 0.022). A significant impact of E. hirae was not observed on the presence or abundance of 30 different bacterial, viral, protozoal, fungal, algal, and parasitic agents in feces examined by qPCR. With exception to a decrease in Megamonas, administration of the E. hirae probiotic did not alter the predominant bacterial phyla present in feces based on 16S rRNA gene amplicon sequencing. DISCUSSION Decreased incidence of diarrhea associated with preventative administration of E. hirae to foster kittens supports a rationale for use of E. hirae for disease prevention in this young population at high risk for intestinal disease though additional studies are warranted.
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Affiliation(s)
- Jody L Gookin
- Department of Clinical Sciences, College of Veterinary Medicine and Comparative Medicine Institute, North Carolina State University, Raleigh, NC, United States
| | - Sandra J Strong
- Department of Environmental Services, Wake County Animal Center, Raleigh, NC, United States
- Orange County Animal Services, Chapel Hill, NC, United States
| | - José M Bruno-Bárcena
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States
| | - Stephen H Stauffer
- Department of Clinical Sciences, College of Veterinary Medicine and Comparative Medicine Institute, North Carolina State University, Raleigh, NC, United States
| | - Shelby Williams
- Veterinary Hospital Pharmacy, College of Veterinary Medicine and Comparative Medicine Institute, North Carolina State University, Raleigh, NC, United States
- University of Wisconsin Veterinary Care, Madison, WI, United States
| | - Erica Wassack
- Veterinary Hospital Pharmacy, College of Veterinary Medicine and Comparative Medicine Institute, North Carolina State University, Raleigh, NC, United States
- Department of Clinical Sciences, College of Veterinary Medicine, Mississippi State University, Starkville, MS, United States
| | - M Andrea Azcarate-Peril
- Division of Gastroenterology and Hepatology, and UNC Microbiome Core, Department of Medicine, Center for Gastrointestinal Biology and Disease, School of Medicine, University of North Carolina, Chapel Hill, NC, United States
| | - Marko Estrada
- IDEXX Laboratories, Inc., West Sacramento, CA, United States
| | - Alexis Seguin
- IDEXX Laboratories, Inc., West Sacramento, CA, United States
| | - Joerg Balzer
- Vet Med Labor GmbH Division, IDEXX Laboratories, Inc., Kornwestheim, Germany
| | - Gigi Davidson
- Veterinary Hospital Pharmacy, College of Veterinary Medicine and Comparative Medicine Institute, North Carolina State University, Raleigh, NC, United States
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14
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Fan L, Zhu X, Sun S, Yu C, Huang X, Ness R, Dugan LL, Shu L, Seidner DL, Murff HJ, Fodor AA, Azcarate-Peril MA, Shrubsole MJ, Dai Q. Ca:Mg ratio, medium-chain fatty acids, and the gut microbiome. Clin Nutr 2022; 41:2490-2499. [PMID: 36223712 PMCID: PMC9588659 DOI: 10.1016/j.clnu.2022.08.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 08/04/2022] [Accepted: 08/31/2022] [Indexed: 12/26/2022]
Abstract
BACKGROUND & AIMS Ketogenic medium-chain fatty acids (MCFAs) with profound health benefits are commonly found in dairy products, palm kernel oil and coconut oil. We hypothesize that magnesium (Mg) supplementation leads to enhanced gut microbial production of MCFAs and, in turn, increased circulating MCFAs levels. METHODS We tested this hypothesis in the Personalized Prevention of Colorectal Cancer Trial (PPCCT) (NCT01105169), a double-blind 2 × 2 factorial randomized controlled trial enrolling 240 participants. Six 24-h dietary recalls were performed for all participants at the baseline and during the intervention period. Based on the baseline 24-h dietary recalls, the Mg treatment used a personalized dose of Mg supplementation that would reduce the calcium (Ca): Mg intake ratio to around 2.3. We measured plasma MCFAs, sugars, ketone bodies and tricarboxylic acid cycle (TCA cycle) metabolites using the Metabolon's global Precision Metabolomics™ LC-MS platform. Whole-genome shotgun metagenomics (WGS) sequencing was performed to assess microbiota in stool samples, rectal swabs, and rectal biopsies. RESULTS Personalized Mg treatment (mean dose 205.58 mg/day with a range from 77.25 to 389.55 mg/day) significantly increased the plasma levels of C7:0, C8:0, and combined C7:0 and C8:0 by 18.45%, 25.28%, and 24.20%, respectively, compared to 14.15%, 10.12%, and 12.62% decreases in the placebo arm. The effects remain significant after adjusting for age, sex, race and baseline level (P = 0.0126, P = 0.0162, and P = 0.0031, respectively) and FDR correction at 0.05 (q = 0.0324 for both C7:0 and C8:0). Mg treatment significantly reduced the plasma level of sucrose compared to the placebo arm (P = 0.0036 for multivariable-adjusted and P = 0.0216 for additional FDR correction model) whereas alterations in daily intakes of sucrose, fructose, glucose, maltose and C8:0 from baseline to the end of trial did not differ between two arms. Mediation analysis showed that combined C7:0 and C8:0 partially mediated the effects of Mg treatment on total and individual ketone bodies (P for indirect effect = 0.0045, 0.0043, and 0.03, respectively). The changes in plasma levels of C7:0 and C8:0 were significantly and positively correlated with the alterations in stool microbiome α diversity (r = 0.51, p = 0.0023 and r = 0.34, p = 0.0497, respectively) as well as in stool abundance for the signatures of MCFAs-related microbiota with acyl-ACP thioesterase gene producing C7:0 (r = 0.46, p = 0.0067) and C8:0 (r = 0.49, p = 0.003), respectively, following Mg treatment. CONCLUSIONS Optimizing Ca:Mg intake ratios to around 2.3 through 12-week personalized Mg supplementation leads to increased circulating levels of MCFAs (i.e. C7:0 and C8:0), which is attributed to enhanced production from gut microbial fermentation and, maybe, sucrose consumption.
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Affiliation(s)
- Lei Fan
- Department of Medicine, Division of Epidemiology, Vanderbilt Epidemiology Center, Vanderbilt University School of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Xiangzhu Zhu
- Department of Medicine, Division of Epidemiology, Vanderbilt Epidemiology Center, Vanderbilt University School of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Shan Sun
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Chang Yu
- Department of Biostatistics, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Xiang Huang
- Department of Medicine, Division of Epidemiology, Vanderbilt Epidemiology Center, Vanderbilt University School of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Reid Ness
- Department of Medicine, Division of Gastroenterology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Laura L Dugan
- Veterans Health Administration-Tennessee Valley Healthcare System Geriatric Research Education Clinical Center (GRECC), HSR&D Center, Vanderbilt University Medical Center, Nashville, TN, USA; Vanderbilt Brain Institute, Vanderbilt University, Nashville, TN, USA; Division of Geriatric Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Lihua Shu
- Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Douglas L Seidner
- Center for Human Nutrition, Department of Gastroenterology, Hepatology and Nutrition, Digestive Disease and Surgical Institute, Cleveland Clinic, OH, USA
| | - Harvey J Murff
- Veterans Health Administration-Tennessee Valley Healthcare System Geriatric Research Education Clinical Center (GRECC), HSR&D Center, Vanderbilt University Medical Center, Nashville, TN, USA; Division of Geriatric Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Anthony A Fodor
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - M Andrea Azcarate-Peril
- Department of Medicine, Division of Gastroenterology and Hepatology, and UNC Microbiome Core, Center for Gastrointestinal Biology and Disease, School of Medicine, University of North Carolina, Chapel Hill, NC, USA
| | - Martha J Shrubsole
- Department of Medicine, Division of Epidemiology, Vanderbilt Epidemiology Center, Vanderbilt University School of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Qi Dai
- Department of Medicine, Division of Epidemiology, Vanderbilt Epidemiology Center, Vanderbilt University School of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA.
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15
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Sanborn V, Aljumaah M, Azcarate-Peril MA, Gunstad J. Examining the cognitive benefits of probiotic supplementation in physically active older adults: A randomized clinical trial. Appl Physiol Nutr Metab 2022; 47:871-882. [PMID: 35617704 DOI: 10.1139/apnm-2021-0557] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The prevalence of dementia is projected to increase with the growing older adult population and prevention strategies are urgently needed. Two promising interventions include physical activity (PA) and probiotic supplementation, with initial findings suggesting their combined use may confer greater cognitive benefits than either intervention alone. However, no study has yet examined the effects of probiotic supplementation on cognitive function in healthy, physically active older adults. The present study used archival data from a randomized clinical trial including 127 physically active, middle-aged to older adults (avg age 64.3 years) with self-reported PA levels meeting or exceeding recommendations to investigate the effects of probiotic supplementation (Lactobacillus rhamnosus GG; L.GG) on cognitive outcomes. Repeated measures ANOVAs showed no significant changes in cognitive performance from baseline to follow up as an effect of L.GG consumption. These results suggest that probiotic supplementation may not improve cognitive function in persons already engaged in high levels of PA. Future research should include prospective studies to determine whether long-term use of probiotic supplementation may help prevent cognitive decline. Novelty: • Initial research shows promising cognitive benefits of combined physical activity and probiotics consumption. • L.GG did not lead to acute cognitive improvements for older adults already meeting physical activity guidelines. • Prospective studies examining prevention of cognitive decline with probiotics in healthy and clinical samples are much needed.
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Affiliation(s)
- Victoria Sanborn
- Kent State University, 4229, Psychological Sciences, 600 Hilltop Drive, Kent, Ohio, United States, 44242;
| | - Mashael Aljumaah
- University of North Carolina System, 2332, Department of Medicine, and UNC Microbiome Core, Center for Gastrointestinal Biology and Disease, Division of Gastroenterology and Hepatology, School of Medicine, Chapel Hill, North Carolina, United States.,North Carolina State University at Raleigh, 6798, Department of Plant and Microbial Biology, Raleigh, North Carolina, United States;
| | - M Andrea Azcarate-Peril
- University of North Carolina at Chapel Hill School of Medicine, 6797, Department of Medicine, and UNC Microbiome Core, Center for Gastrointestinal Biology and Disease, Division of Gastroenterology and Hepatology, Chapel Hill, North Carolina, United States;
| | - John Gunstad
- Kent State University College of Arts and Sciences, 142731, Psychological Sciences; Brain Health Research Institute, Kent, Ohio, United States;
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16
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Loeser RF, Arbeeva L, Kelley K, Fodor AA, Sun S, Ulici V, Longobardi L, Cui Y, Stewart DA, Sumner SJ, Azcarate-Peril MA, Sartor RB, Carroll IM, Renner JB, Jordan JM, Nelson AE. Association of Increased Serum Lipopolysaccharide, But Not Microbial Dysbiosis, With Obesity-Related Osteoarthritis. Arthritis Rheumatol 2022; 74:227-236. [PMID: 34423918 PMCID: PMC8795472 DOI: 10.1002/art.41955] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [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: 12/22/2020] [Revised: 07/19/2021] [Accepted: 08/19/2021] [Indexed: 02/03/2023]
Abstract
OBJECTIVE To test the hypothesis that an altered gut microbiota (dysbiosis) plays a role in obesity-associated osteoarthritis (OA). METHODS Stool and blood samples were collected from 92 participants with a body mass index (BMI) ≥30 kg/m2 , recruited from the Johnston County Osteoarthritis Project. OA patients (n = 50) had hand and knee OA (Kellgren/Lawrence [K/L] grade ≥2 or arthroplasty). Controls (n = 42) had no hand OA and a K/L grade of 0-1 for the knees. Compositional analysis of stool samples was carried out by 16S ribosomal RNA amplicon sequencing. Alpha- and beta-diversity and differences in taxa relative abundances were determined. Blood samples were used for multiplex cytokine analysis and measures of lipopolysaccharide (LPS) and LPS binding protein. Germ-free mice were gavaged with patient- or control-pooled fecal samples and fed a 40% fat, high-sucrose diet for 40 weeks. Knee OA was evaluated histologically. RESULTS On average, OA patients were slightly older than the controls, consisted of more women, and had a higher mean BMI, higher mean Western Ontario and McMaster Universities Osteoarthritis Index pain score, and higher mean K/L grade. There were no significant differences in α- or β-diversity or genus level composition between patients and controls. Patients had higher plasma levels of osteopontin (P = 0.01) and serum LPS (P < 0.0001) compared to controls. Mice transplanted with patient or control microbiota exhibited a significant difference in α-diversity (P = 0.02) and β-diversity, but no differences in OA severity were observed. CONCLUSION The lack of differences in the gut microbiota, but increased serum LPS levels, suggest the possibility that increased intestinal permeability allowing for greater absorption of LPS, rather than a dysbiotic microbiota, may contribute to the development of OA associated with obesity.
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Affiliation(s)
- Richard F. Loeser
- Division of Rheumatology, Allergy and Immunology and the Thurston Arthritis Research Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina,Corresponding author: Richard F. Loeser, Division of Rheumatology, Allergy and Immunology and the Thurston Arthritis Research Center, 3300 Thurston Building, Campus Box 7280, University of North Carolina School of Medicine, Chapel Hill, North Carolina, 27599, USA, Phone: 919-966-7042;
| | - Liubov Arbeeva
- Division of Rheumatology, Allergy and Immunology and the Thurston Arthritis Research Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Kathryn Kelley
- Division of Rheumatology, Allergy and Immunology and the Thurston Arthritis Research Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Anthony A. Fodor
- Dept. of Bioinformatics and Genomics, University of North Carolina-Charlotte, North Carolina
| | - Shan Sun
- Dept. of Bioinformatics and Genomics, University of North Carolina-Charlotte, North Carolina
| | - Veronica Ulici
- Division of Rheumatology, Allergy and Immunology and the Thurston Arthritis Research Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Lara Longobardi
- Division of Rheumatology, Allergy and Immunology and the Thurston Arthritis Research Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Yang Cui
- Division of Rheumatology, Allergy and Immunology and the Thurston Arthritis Research Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | | | - Susan J. Sumner
- Department of Nutrition, University of North Carolina, Chapel Hill, NC
| | - M. Andrea Azcarate-Peril
- Division of Gastroenterology and Hepatology and UNC Microbiome Core, Center for Gastrointestinal Biology and Disease, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - R. Balfour Sartor
- Division of Gastroenterology and Hepatology and Center for Gastrointestinal Biology and Disease, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Ian M. Carroll
- Department of Nutrition, University of North Carolina, Chapel Hill, NC
| | - Jordan B. Renner
- Department of Radiology and the Thurston Arthritis Research Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Joanne M. Jordan
- Division of Rheumatology, Allergy and Immunology and the Thurston Arthritis Research Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Amanda E. Nelson
- Division of Rheumatology, Allergy and Immunology and the Thurston Arthritis Research Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina
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17
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Rushing BR, McRitchie S, Arbeeva L, Nelson AE, Azcarate-Peril MA, Li YY, Qian Y, Pathmasiri W, Sumner SC, Loeser RF. Fecal metabolomics reveals products of dysregulated proteolysis and altered microbial metabolism in obesity-related osteoarthritis. Osteoarthritis Cartilage 2022; 30:81-91. [PMID: 34718137 PMCID: PMC8712415 DOI: 10.1016/j.joca.2021.10.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [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: 05/28/2021] [Revised: 09/16/2021] [Accepted: 10/13/2021] [Indexed: 02/07/2023]
Abstract
OBJECTIVE The objective of this exploratory study was to determine if perturbations in gut microbial composition and the gut metabolome could be linked to individuals with obesity and osteoarthritis (OA). METHODS Fecal samples were collected from obese individuals diagnosed with radiographic hand plus knee OA (n = 59), defined as involvement of at least 3 joints across both hands, and a Kellgren-Lawrence (KL) grade 2-4 (or total knee replacement) in at least one knee. Controls (n = 33) were without hand OA and with KL grade 0-1 knees. Fecal metabolomes were analyzed by a UHPLC/Q Exactive HFx mass spectrometer. Microbiome composition was determined in fecal samples by 16 S ribosomal RNA amplicon sequencing (rRNA-seq). Stepwise logistic regression models were built to determine microbiome and/or metabolic characteristics of OA. RESULTS Untargeted metabolomics analysis indicated that OA cases had significantly higher levels of di- and tripeptides and significant perturbations in microbial metabolites including propionic acid, indoles, and other tryptophan metabolites. Pathway analysis revealed several significantly perturbed pathways associated with OA including leukotriene metabolism, amino acid metabolism and fatty acid utilization. Logistic regression models selected metabolites associated with the gut microbiota and leaky gut syndrome as significant predictors of OA status, particularly when combined with the rRNA-seq data. CONCLUSIONS Adults with obesity and knee plus hand OA have distinct fecal metabolomes characterized by increased products of proteolysis, perturbations in leukotriene metabolism, and changes in microbial metabolites compared with controls. These metabolic perturbations indicate a possible role of dysregulated proteolysis in OA.
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Affiliation(s)
- Blake R. Rushing
- Department of Nutrition, University of North Carolina at Chapel Hill, Nutrition Research Institute, Kannapolis, NC, USA
| | - Susan McRitchie
- Department of Nutrition, University of North Carolina at Chapel Hill, Nutrition Research Institute, Kannapolis, NC, USA
| | - Liubov Arbeeva
- Department of Medicine, Division of Rheumatology, Allergy and Immunology and the Thurston Arthritis Research Center, University of North Carolina, Chapel Hill, NC, USA
| | - Amanda E. Nelson
- Department of Medicine, Division of Rheumatology, Allergy and Immunology and the Thurston Arthritis Research Center, University of North Carolina, Chapel Hill, NC, USA
| | - M. Andrea Azcarate-Peril
- Department of Medicine, Division of Gastroenterology and Hepatology and UNC Microbiome Core, Center for Gastrointestinal Biology and Disease, University of North Carolina, Chapel Hill, NC, USA
| | - Yuan-Yuan Li
- Department of Nutrition, University of North Carolina at Chapel Hill, Nutrition Research Institute, Kannapolis, NC, USA
| | - Yunzhi Qian
- Department of Nutrition, University of North Carolina at Chapel Hill, Nutrition Research Institute, Kannapolis, NC, USA
| | - Wimal Pathmasiri
- Department of Nutrition, University of North Carolina at Chapel Hill, Nutrition Research Institute, Kannapolis, NC, USA
| | - Susan C.J. Sumner
- Department of Nutrition, University of North Carolina at Chapel Hill, Nutrition Research Institute, Kannapolis, NC, USA,Corresponding authors: Richard F. Loeser, Division of Rheumatology, Allergy and Immunology and the Thurston Arthritis Research Center, 3300 Thurston Building, Campus Box 7280, University of North Carolina School of Medicine, Chapel Hill, North Carolina, 27599, USA, Phone: 919-966-7042; , Susan C.J. Sumner, Nutrition Research Institute, Department of Nutrition, UNC Chapel Hill, North Carolina, USA,
| | - Richard F. Loeser
- Department of Medicine, Division of Rheumatology, Allergy and Immunology and the Thurston Arthritis Research Center, University of North Carolina, Chapel Hill, NC, USA,Corresponding authors: Richard F. Loeser, Division of Rheumatology, Allergy and Immunology and the Thurston Arthritis Research Center, 3300 Thurston Building, Campus Box 7280, University of North Carolina School of Medicine, Chapel Hill, North Carolina, 27599, USA, Phone: 919-966-7042; , Susan C.J. Sumner, Nutrition Research Institute, Department of Nutrition, UNC Chapel Hill, North Carolina, USA,
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18
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Sun S, Zhu X, Huang X, Murff HJ, Ness RM, Seidner DL, Sorgen AA, Blakley IC, Yu C, Dai Q, Azcarate-Peril MA, Shrubsole MJ, Fodor AA. On the robustness of inference of association with the gut microbiota in stool, rectal swab and mucosal tissue samples. Sci Rep 2021; 11:14828. [PMID: 34290321 PMCID: PMC8295290 DOI: 10.1038/s41598-021-94205-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [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: 02/25/2021] [Accepted: 06/25/2021] [Indexed: 12/11/2022] Open
Abstract
The gut microbiota plays an important role in human health and disease. Stool, rectal swab and rectal mucosal tissue samples have been used in individual studies to survey the microbial community but the consequences of using these different sample types are not completely understood. In this study, we report differences in stool, rectal swab and rectal mucosal tissue microbial communities with shotgun metagenome sequencing of 1397 stool, swab and mucosal tissue samples from 240 participants. The taxonomic composition of stool and swab samples was distinct, but less different to each other than mucosal tissue samples. Functional profile differences between stool and swab samples are smaller, but mucosal tissue samples remained distinct from the other two types. When the taxonomic and functional profiles were used for inference in association with host phenotypes of age, sex, body mass index (BMI), antibiotics or non-steroidal anti-inflammatory drugs (NSAIDs) use, hypothesis testing using either stool or rectal swab gave broadly significantly correlated results, but inference performed on mucosal tissue samples gave results that were generally less consistent with either stool or swab. Our study represents an important resource for determination of how inference can change for taxa and pathways depending on the choice of where to sample within the human gut.
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Affiliation(s)
- Shan Sun
- grid.266859.60000 0000 8598 2218Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC USA
| | - Xiangzhu Zhu
- grid.412807.80000 0004 1936 9916Department of Medicine, Vanderbilt University Medical Center, Nashville, TN USA
| | - Xiang Huang
- grid.412807.80000 0004 1936 9916Department of Medicine, Vanderbilt University Medical Center, Nashville, TN USA
| | - Harvey J. Murff
- grid.412807.80000 0004 1936 9916Department of Medicine, Vanderbilt University Medical Center, Nashville, TN USA
| | - Reid M. Ness
- grid.412807.80000 0004 1936 9916Department of Medicine, Vanderbilt University Medical Center, Nashville, TN USA
| | - Douglas L. Seidner
- grid.239578.20000 0001 0675 4725Digestive Disease and Surgical Institute, Cleveland Clinic, Cleveland, OH USA
| | - Alicia A. Sorgen
- grid.266859.60000 0000 8598 2218Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC USA
| | - Ivory C. Blakley
- grid.266859.60000 0000 8598 2218Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC USA
| | - Chang Yu
- grid.412807.80000 0004 1936 9916Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN USA
| | - Qi Dai
- grid.412807.80000 0004 1936 9916Department of Medicine, Vanderbilt University Medical Center, Nashville, TN USA
| | - M. Andrea Azcarate-Peril
- grid.410711.20000 0001 1034 1720Department of Medicine and Microbiome Core Facility, School of Medicine, University of North Carolina, Chapel Hill, NC USA
| | - Martha J. Shrubsole
- grid.412807.80000 0004 1936 9916Department of Medicine, Vanderbilt University Medical Center, Nashville, TN USA
| | - Anthony A. Fodor
- grid.266859.60000 0000 8598 2218Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, 9331 Robert D. Snyder Rd, Room 361, Charlotte, NC 28223 USA
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19
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Fan L, Yu D, Zhu X, Zhang X, Huang X, Murff HJ, Azcarate-Peril MA, Shrubsole MJ, Dai Q. Abstract 2580: Synergistic effect of magnesium with metformin for the prevention of liver and colorectal cancer. Cancer Res 2021. [DOI: 10.1158/1538-7445.am2021-2580] [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
The obesity epidemic has dramatically increased the type 2 diabetes (T2D) prevalence in the US over the past two decades. Previous studies have relatively consistently found individuals with T2D are at increased risks of cancer, including liver and colorectal cancer in which insulin resistance may play an important role. However, the mechanism remains largely unknown. Metformin, the primary first-line medication for the treatment of T2D, has been shown to improve insulin resistance and be linked to a reduced risk of hepatocellular carcinoma (HCC) and colorectal cancer (CRC). Two recent Cell and Cell metabolism publications identified that imidazole propionate (ImP), a microbial metabolite of histidine, significantly increased in patients with T2D and causally induced insulin resistance in mice. Furthermore, the therapeutic effects of metformin on insulin resistance disappeared when ImP was elevated, indicating that ImP plays a key role in developing insulin resistance and resistance to metformin treatment. Our recent work together with a subsequent study from others demonstrated higher magnesium (Mg) intake is associated with a substantially reduced risk of HCC, HCC mortality and mortality from liver diseases. Accumulative evidence, including our prior work, has also linked higher Mg intake to a reduced risk of colorectal neoplasia. Previous studies found that the process of the histidine utilization (Hut) system to metabolize histidine in some bacterial taxa depends on concentrations of divalent metal ion Mg2+. We hypothesize that low availability of Mg2+ in gut microbiota could terminate the Hut system and increase the production of intermediate metabolites, including ImP, over other end products. This will lead to increased levels of ImP in the gut and, in turn, liver and circulation. We tested our hypothesis in the Personalized Prevention of Colorectal Cancer Trial (PPCCT) (registered at clinicaltrials.gov as NCT01105169), a precision-based randomized trial enrolling 240 participants at high risk of Mg deficiency. Among 68 participants (34 treatment/34 placebo), we found that compared to the placebo, Mg treatment significantly reduced ImP by 39.9% compared to a 6.0% increase in the placebo arm after adjustment for baseline ImP (P=0.02). However, we found Mg treatment did not significantly affect the levels of trans-urocanate, the precursor of ImP. Since Mg deficiency leads to insulin resistance and as high as 50% of patients with T2D have hypomagnesemia, Mg deficiency may lead to an increased risk of ImP and, in turn, resistance to metformin which subsequently increases risk of HCC and CRC. Thus, futures studies should evaluate whether the joint use of Mg supplementation and metformin synergistically maximizes the efficacy of metformin and minimizes the treatment resistance on insulin resistance and, subsequently, prevention of HCC and CRC.
Citation Format: Lei Fan, Danxia Yu, Xiangzhu Zhu, Xuehong Zhang, Xiang Huang, Harvey J. Murff, M. Andrea Azcarate-Peril, Martha J. Shrubsole, Qi Dai. Synergistic effect of magnesium with metformin for the prevention of liver and colorectal cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2580.
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Affiliation(s)
- Lei Fan
- 1Vanderbilt University Medical Center, Nashville, TN
| | - Danxia Yu
- 1Vanderbilt University Medical Center, Nashville, TN
| | - Xiangzhu Zhu
- 1Vanderbilt University Medical Center, Nashville, TN
| | | | - Xiang Huang
- 1Vanderbilt University Medical Center, Nashville, TN
| | | | | | | | - Qi Dai
- 1Vanderbilt University Medical Center, Nashville, TN
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20
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da Costa Rosa T, de Almeida Neves A, Azcarate-Peril MA, Divaris K, Wu D, Cho H, Moss K, Paster BJ, Chen T, B. Freitas-Fernandes L, Fidalgo TKS, Tadeu Lopes R, Valente AP, R. Arnold R, de Aguiar Ribeiro A. The bacterial microbiome and metabolome in caries progression and arrest. J Oral Microbiol 2021; 13:1886748. [PMID: 34188775 PMCID: PMC8211139 DOI: 10.1080/20002297.2021.1886748] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 10/07/2020] [Revised: 01/27/2021] [Accepted: 02/04/2021] [Indexed: 01/04/2023] Open
Abstract
Aim: This in vivo experimental study investigated bacterial microbiome and metabolome longitudinal changes associated with enamel caries lesion progression and arrest. Methods: We induced natural caries activity in three caries-free volunteers prior to four premolar extractions for orthodontic reasons. The experimental model included placement of a modified orthodontic band on smooth surfaces and a mesh on occlusal surfaces. We applied the caries-inducing protocol for 4- and 6-weeks, and subsequently promoted caries lesion arrest via a 2-week toothbrushing period. Lesions were verified clinically and quantitated via micro-CT enamel density measurements. The biofilm microbial composition was determined via 16S rRNA gene Illumina sequencing and NMR spectrometry was used for metabolomics. Results: Biofilm maturation and caries lesion progression were characterized by an increase in Gram-negative anaerobes, including Veillonella and Prevotella. Streptococcus was associated caries lesion progression, while a more equal distribution of Streptococcus, Bifidobacterium, Atopobium, Prevotella, Veillonella, and Saccharibacteria (TM7) characterized arrest. Lactate, acetate, pyruvate, alanine, valine, and sugars were more abundant in mature biofilms compared to newly formed biofilms. Conclusions: These longitudinal bacterial microbiome and metabolome results provide novel mechanistic insights into the role of the biofilm in caries progression and arrest and offer promising candidate biomarkers for validation in future studies.
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Affiliation(s)
| | - Aline de Almeida Neves
- Department of Pediatric Dentistry, Rio de Janeiro Federal University, Brazil
- Centre for Oral Clinical and Translational Sciences, King’s College London, London, UK
| | - M. Andrea Azcarate-Peril
- Microbiome Core Facility, University of North Carolina School of Medicine, Chapel Hill, USA
- Department of Medicine, Division of Gastroenterology and Hepatology, School of Medicine, University of North Carolina, Chapel Hill, USA
| | - Kimon Divaris
- Division of Pediatric and Public Health, Adams School of Dentistry, University of North Carolina, Chapel Hill, USA
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, USA
| | - Di Wu
- Division of Oral and Craniofacial Health Sciences, School of Dentistry, University of North Carolina, Chapel Hill, USA
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, USA
| | - Hunyong Cho
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, USA
| | - Kevin Moss
- Division of Oral and Craniofacial Health Sciences, School of Dentistry, University of North Carolina, Chapel Hill, USA
| | - Bruce J. Paster
- Department of Microbiology, Forsyth Institute, Cambridge, USA
- Department of Oral Medicine, Infection and Immunity, Harvard School of Dental Medicine, Boston, USA
| | - Tsute Chen
- Department of Microbiology, Forsyth Institute, Cambridge, USA
| | - Liana B. Freitas-Fernandes
- Department of Pediatric Dentistry, Rio de Janeiro Federal University, Brazil
- National Center for Nuclear Magnetic Resonance, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Tatiana K. S. Fidalgo
- National Center for Nuclear Magnetic Resonance, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Department of Preventive and Community Dentistry, School of Dentistry, Rio de Janeiro State University, Brazil
| | - Ricardo Tadeu Lopes
- Laboratory of Nuclear Instrumentation, Federal University of Rio de Janeiro, Rio De Janeiro, Brazil
| | - Ana Paula Valente
- National Center for Nuclear Magnetic Resonance, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Roland R. Arnold
- Division of Diagnostic Sciences, Adams School of Dentistry, University of North Carolina, Chapel Hill, USA
| | - Apoena de Aguiar Ribeiro
- Division of Diagnostic Sciences, Adams School of Dentistry, University of North Carolina, Chapel Hill, USA
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21
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Rushing B, McRitchie S, Arbeeva L, Nelson A, Azcarate-Peril MA, Li YY, Qian Y, Sumner S, Loeser R. Untargeted Fecal Metabolomics to Investigate the Role of the Microbiome and Nutrients in Osteoarthritis. Curr Dev Nutr 2021. [DOI: 10.1093/cdn/nzab033_047] [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: 11/14/2022] Open
Abstract
Abstract
Objectives
The objective of this study was to determine if perturbations in gut microbial composition and the gut metabolome could be linked to individuals with obesity and osteoarthritis (OA).
Methods
Fecal samples were collected from 92 participants with obesity recruited from the Johnston County Osteoarthritis Project. OA cases (n = 59) had radiographic hand plus knee OA, defined as involvement of at least 3 joints across both hands, and a Kellgren-Lawrence (KL) grade 2–4 in at least one knee. Controls (n = 33) were without hand OA and with KL grade 0–1 knees. Fecal metabolomes were analyzed by a UHPLC/Q Exactive HFx mass spectrometer. Microbiome composition was determined in fecal samples by 16S ribosomal RNA amplicon sequencing (rRNA-seq). Stepwise logistic regression models were built to determine predictors of OA status.
Spearman correlations were performed to determine associations between metabolites and microbiota in OA or healthy individuals.
Results
Untargeted metabolomics analysis indicated that OA cases had significantly higher levels of di- and tri-peptides (P < 0.05), and significant perturbations (P < 0.1) in microbial metabolites. Pathway analysis revealed several significantly perturbed pathways (P < 0.05) associated with OA, including leukotriene metabolism, amino acid metabolism and fatty acid utilization. Logistic regression models selected metabolites associated with the microbiota and leaky gut syndrome as significant predictors of OA status, particularly when combined with the 16S rRNA sequencing data. Omega-3/6 polyunsaturated fatty acids (PUFAs) levels were significantly correlated with the phyla Bacteriodetes and Firmicutes.
Conclusions
Adults with obesity and OA have distinct fecal metabolomes characterized by perturbations in microbial metabolites, PUFAs, and protein digestion compared with healthy controls. These metabolic perturbations suggest a role of intestinal inflammation and leaky gut in OA.
Funding Sources
Supported by the Arthritis Foundation, the National Center for Advancing Translational Sciences (NCATS) (UL1TR002489), and the National Institute of Arthritis and Musculoskeletal and Skin Diseases (P30AR072580).
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Affiliation(s)
- Blake Rushing
- UNC Nutrition Research Institute, University of North Carolina at Chapel Hill
| | | | | | | | | | | | | | - Susan Sumner
- UNC Nutrition Research Institute, University of North Carolina at Chapel Hill
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22
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Carlson AL, Xia K, Azcarate-Peril MA, Rosin SP, Fine JP, Mu W, Zopp JB, Kimmel MC, Styner MA, Thompson AL, Propper CB, Knickmeyer RC. Infant gut microbiome composition is associated with non-social fear behavior in a pilot study. Nat Commun 2021; 12:3294. [PMID: 34078892 PMCID: PMC8172562 DOI: 10.1038/s41467-021-23281-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 04/19/2021] [Indexed: 02/04/2023] Open
Abstract
Experimental manipulation of gut microbes in animal models alters fear behavior and relevant neurocircuitry. In humans, the first year of life is a key period for brain development, the emergence of fearfulness, and the establishment of the gut microbiome. Variation in the infant gut microbiome has previously been linked to cognitive development, but its relationship with fear behavior and neurocircuitry is unknown. In this pilot study of 34 infants, we find that 1-year gut microbiome composition (Weighted Unifrac; lower abundance of Bacteroides, increased abundance of Veillonella, Dialister, and Clostridiales) is significantly associated with increased fear behavior during a non-social fear paradigm. Infants with increased richness and reduced evenness of the 1-month microbiome also display increased non-social fear. This study indicates associations of the human infant gut microbiome with fear behavior and possible relationships with fear-related brain structures on the basis of a small cohort. As such, it represents an important step in understanding the role of the gut microbiome in the development of human fear behaviors, but requires further validation with a larger number of participants.
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Affiliation(s)
- Alexander L Carlson
- Frank Porter Graham Child Development Institute, University of North Carolina, Chapel Hill, NC, USA
| | - Kai Xia
- Department of Psychiatry, University of North Carolina, Chapel Hill, NC, USA
| | - M Andrea Azcarate-Peril
- Department of Medicine, University of North Carolina, Chapel Hill, NC, USA
- Microbiome Core Facility, University of North Carolina, Chapel Hill, NC, USA
| | - Samuel P Rosin
- Department of Biostatistics, University of North Carolina, Chapel Hill, NC, USA
| | - Jason P Fine
- Department of Biostatistics, University of North Carolina, Chapel Hill, NC, USA
| | - Wancen Mu
- Department of Biostatistics, University of North Carolina, Chapel Hill, NC, USA
| | - Jared B Zopp
- Department of Psychiatry, University of North Carolina, Chapel Hill, NC, USA
| | - Mary C Kimmel
- Department of Psychiatry, University of North Carolina, Chapel Hill, NC, USA
| | - Martin A Styner
- Department of Psychiatry, University of North Carolina, Chapel Hill, NC, USA
- Department of Computer Science, University of North Carolina, Chapel Hill, NC, USA
| | - Amanda L Thompson
- Department of Anthropology, University of North Carolina, Chapel Hill, NC, USA
- Department of Nutrition, University of North Carolina, Chapel Hill, NC, USA
| | - Cathi B Propper
- Frank Porter Graham Child Development Institute, University of North Carolina, Chapel Hill, NC, USA
| | - Rebecca C Knickmeyer
- Department of Psychiatry, University of North Carolina, Chapel Hill, NC, USA.
- Department of Pediatrics and Human Development, Michigan State University, East Lansing, MI, USA.
- Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI, USA.
- C-RAIND Fellow and Co-Director, Michigan State University, East Lansing, MI, USA.
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23
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Jahnke JR, Roach J, Azcarate-Peril MA, Thompson AL. Maternal precarity and HPA axis functioning shape infant gut microbiota and HPA axis development in humans. PLoS One 2021; 16:e0251782. [PMID: 34015045 PMCID: PMC8136730 DOI: 10.1371/journal.pone.0251782] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 05/03/2021] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Early life exposure to adverse environments, and maternal stress in particular, has been shown to increase risk for metabolic diseases and neurobehavioral disorders. While many studies have examined the hypothalamic-pituitary-adrenal axis (HPA axis) as the primary mechanism behind these relationships, emerging research on the brain-gut axis suggests that the microbiome may play a role. In this study, we tested the relationships among maternal precarity and HPA axis dysregulation during the peripartum period, infant gut microbiome composition, and infant HPA axis functioning. METHODS Data come from 25 mother-infant dyads in the Galápagos, Ecuador. Women completed surveys on precarity measures (food insecurity, low social support, depression, and stress) and gave salivary cortisol samples during and after pregnancy. Infant salivary cortisol and stool were collected in the postpartum. Statistical significance of differences in microbial diversity and relative abundance were assessed with respect to adjusted linear regression models. RESULTS Maternal precarity was associated with lower diversity and higher relative abundance of Enterobacteriaceae and Streptococcaceae and a lower relative abundance of Bifidobacterium and Lachnospiraceae. These patterns of colonization for Enterobacteriaceae and Bifidobacterium mirrored those found in infants with HPA axis dysregulation. Maternal HPA axis dysregulation during pregnancy was also associated with a greater relative abundance of Veillonella. CONCLUSIONS Overall, exposures to precarity and HPA axis dysregulation were associated with an increase in groups that include potentially pathogenic bacteria, including Enterobacteriaceae, Streptococcaceae, and Veillonella, and a decrease in potentially protective bacteria, including Bifidobacterium and Lachnospiraceae, as well as a decrease in overall diversity.
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Affiliation(s)
- Johanna R. Jahnke
- Department of Anthropology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Carolina Population Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Jeffrey Roach
- Research Computing Center, University of North Carolina, Chapel Hill, Chapel Hill, North Carolina, United States of America
- UNC Microbiome Core, Center for Gastrointestinal Biology and Disease, School of Medicine, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - M. Andrea Azcarate-Peril
- UNC Microbiome Core, Center for Gastrointestinal Biology and Disease, School of Medicine, University of North Carolina, Chapel Hill, North Carolina, United States of America
- Department of Medicine, Division of Gastroenterology and Hepatology, School of Medicine, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Amanda L. Thompson
- Department of Anthropology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Carolina Population Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Nutrition, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
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Arnold JW, Whittington HD, Dagher SF, Roach J, Azcarate-Peril MA, Bruno-Barcena JM. Safety and Modulatory Effects of Humanized Galacto-Oligosaccharides on the Gut Microbiome. Front Nutr 2021; 8:640100. [PMID: 33898497 PMCID: PMC8058378 DOI: 10.3389/fnut.2021.640100] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [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: 12/10/2020] [Accepted: 03/11/2021] [Indexed: 01/14/2023] Open
Abstract
Complex dietary carbohydrate structures including β(1–4) galacto-oligosaccharides (GOS) are resistant to digestion in the upper gastrointestinal (GI) tract and arrive intact to the colon where they benefit the host by selectively stimulating microbial growth. Studies have reported the beneficial impact of GOS (alone or in combination with other prebiotics) by serving as metabolic substrates for modulating the assembly of the infant gut microbiome while reducing GI infections. N-Acetyl-D-lactosamine (LacNAc, Galβ1,4GlcNAc) is found in breast milk as a free disaccharide. This compound is also found as a component of human milk oligosaccharides (HMOs), which have repeating and variably branched lactose and/or LacNAc units, often attached to sialic acid and fucose monosaccharides. Human glycosyl-hydrolases do not degrade most HMOs, indicating that these structures have evolved as natural prebiotics to drive the proper assembly of the infant healthy gut microbiota. Here, we sought to develop a novel enzymatic method for generating LacNAc-enriched GOS, which we refer to as humanized GOS (hGOS). We showed that the membrane-bound β-hexosyl transferase (rBHT) from Hamamotoa (Sporobolomyces) singularis was able to generate GOS and hGOS from lactose and N-Acetyl-glucosamine (GlcNAc). The enzyme catalyzed the regio-selective, repeated addition of galactose from lactose to GlcNAc forming the β-galactosyl linkage at the 4-position of the GlcNAc and at the 1-position of D-galactose generating, in addition to GOS, LacNAc, and Galactosyl-LacNAc trisaccharides which were produced by two sequential transgalactosylations. Humanized GOS is chemically distinct from HMOs, and its effects in vivo have yet to be determined. Thus, we evaluated its safety and demonstrated the prebiotic's ability to modulate the gut microbiome in 6-week-old C57BL/6J mice. Longitudinal analysis of gut microbiome composition of stool samples collected from mice fed a diet containing hGOS for 5 weeks showed a transient reduction in alpha diversity. Differences in microbiome community composition mostly within the Firmicutes phylum were observed between hGOS and GOS, compared to control-fed animals. In sum, our study demonstrated the biological synthesis of hGOS, and signaled its safety and ability to modulate the gut microbiome in vivo, promoting the growth of beneficial microorganisms, including Bifidobacterium and Akkermansia.
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Affiliation(s)
- Jason W Arnold
- Division of Gastroenterology and Hepatology, Department of Medicine, School of Medicine, University of North Carolina, Chapel Hill, NC, United States.,UNC Microbiome Core, Center for Gastrointestinal Biology and Disease, School of Medicine, University of North Carolina, Chapel Hill, NC, United States
| | - Hunter D Whittington
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States
| | - Suzanne F Dagher
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States
| | - Jeffery Roach
- UNC Microbiome Core, Center for Gastrointestinal Biology and Disease, School of Medicine, University of North Carolina, Chapel Hill, NC, United States.,UNC Information Technology Services and Research Computing, University of North Carolina, Chapel Hill, NC, United States
| | - M Andrea Azcarate-Peril
- Division of Gastroenterology and Hepatology, Department of Medicine, School of Medicine, University of North Carolina, Chapel Hill, NC, United States.,UNC Microbiome Core, Center for Gastrointestinal Biology and Disease, School of Medicine, University of North Carolina, Chapel Hill, NC, United States
| | - Jose M Bruno-Barcena
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States
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Arnold JW, Roach J, Fabela S, Moorfield E, Ding S, Blue E, Dagher S, Magness S, Tamayo R, Bruno-Barcena JM, Azcarate-Peril MA. Correction to: The pleiotropic effects of prebiotic galacto-oligosaccharides on the aging gut. Microbiome 2021; 9:56. [PMID: 33637107 PMCID: PMC7913251 DOI: 10.1186/s40168-021-01030-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
An amendment to this paper has been published and can be accessed via the original article.
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Affiliation(s)
- Jason W Arnold
- Department of Medicine, Division of Gastroenterology and Hepatology, School of Medicine, University of North Carolina, Chapel Hill, NC, USA
- UNC Microbiome Core, Center for Gastrointestinal Biology and Disease (CGIBD), School of Medicine, University of North Carolina, Chapel Hill, NC, USA
| | - Jeffery Roach
- UNC Microbiome Core, Center for Gastrointestinal Biology and Disease (CGIBD), School of Medicine, University of North Carolina, Chapel Hill, NC, USA
- UNC Information Technology Services and Research Computing, University of North Carolina, Chapel Hill, NC, USA
| | - Salvador Fabela
- Department of Medicine, Division of Gastroenterology and Hepatology, School of Medicine, University of North Carolina, Chapel Hill, NC, USA
- UNC Microbiome Core, Center for Gastrointestinal Biology and Disease (CGIBD), School of Medicine, University of North Carolina, Chapel Hill, NC, USA
- Current affiliation: Programa de Inmunología Molecular Microbiana. Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de Mexico, Mexico City, Mexico
| | - Emily Moorfield
- Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, NC, USA
| | - Shengli Ding
- Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, NC, USA
| | - Eric Blue
- Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, NC, USA
| | - Suzanne Dagher
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, USA
| | - Scott Magness
- Joint Department of Biomedical Engineering, University of North Carolina, Chapel Hill and North Carolina State University, Raleigh, NC, USA
| | - Rita Tamayo
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC, USA
| | - Jose M Bruno-Barcena
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, USA
| | - M Andrea Azcarate-Peril
- Department of Medicine, Division of Gastroenterology and Hepatology, School of Medicine, University of North Carolina, Chapel Hill, NC, USA.
- UNC Microbiome Core, Center for Gastrointestinal Biology and Disease (CGIBD), School of Medicine, University of North Carolina, Chapel Hill, NC, USA.
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Bierlein M, Hedgespeth BA, Azcarate-Peril MA, Stauffer SH, Gookin JL. Dysbiosis of fecal microbiota in cats with naturally occurring and experimentally induced Tritrichomonas foetus infection. PLoS One 2021; 16:e0246957. [PMID: 33606740 PMCID: PMC7894905 DOI: 10.1371/journal.pone.0246957] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 12/04/2020] [Accepted: 01/28/2021] [Indexed: 12/21/2022] Open
Abstract
The protozoal pathogen Tritrichomonas foetus infects the colon of domestic cats and is a major cause of chronic colitis and diarrhea. Treatment failure is common, but antibiotics may improve clinical signs in a subset of cats, leading researchers to question involvement of the colonic microbiota in disease pathogenesis. Studies performed in women with venereal Trichomonas vaginalis infections have revealed that dysbiosis of host microbiota contributes to pathogenicity with similar findings also found in mice with intestinal Tritrichomonas musculis The aim of this study was to characterize differences in the fecal microbiota of cats with and without naturally occurring T. foetus infection and in a group of kittens prior to and after experimentally induced infection. Archived fecal DNA from cats undergoing testing for T. foetus infection (n = 89) and experimentally infected kittens (n = 4; at pre-, 2 weeks, and 9 weeks post-infection) were analyzed by sequencing of 16S rRNA genes. Amongst the naturally infected population, the genera Megamonas and Helicobacter were significantly increased in prevalence and abundance in cats testing positive for T. foetus infection. In the group of four experimentally infected kittens, fecal samples post-infection had significantly lower abundance of genus Dialister and Megamonas and greater abundance of the class Betaproteobacteria and family Succinivibrionaceae. We hypothesize that T. foetus promotes dysbiosis by competition for fermentable substrates used by these bacteria and that metabolic byproducts may contribute to the pathogenesis of colonic inflammation and diarrhea. Future studies are warranted for the measurement of fecal concentrations of microbial and protozoal metabolites in cats with T. foetus infection for the identification of potential therapeutic targets.
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Affiliation(s)
- Metzere Bierlein
- Department of Clinical Sciences, College of Veterinary Medicine and Comparative Medicine Institute, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Barry A. Hedgespeth
- Department of Clinical Sciences, College of Veterinary Medicine and Comparative Medicine Institute, North Carolina State University, Raleigh, North Carolina, United States of America
| | - M. Andrea Azcarate-Peril
- Division of Gastroenterology and Hepatology, Department of Medicine, UNC Microbiome Core, Center for Gastrointestinal Biology and Disease, School of Medicine, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Stephen H. Stauffer
- Department of Clinical Sciences, College of Veterinary Medicine and Comparative Medicine Institute, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Jody L. Gookin
- Department of Clinical Sciences, College of Veterinary Medicine and Comparative Medicine Institute, North Carolina State University, Raleigh, North Carolina, United States of America
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Cunningham M, Azcarate-Peril MA, Barnard A, Benoit V, Grimaldi R, Guyonnet D, Holscher HD, Hunter K, Manurung S, Obis D, Petrova MI, Steinert RE, Swanson KS, van Sinderen D, Vulevic J, Gibson GR. Shaping the Future of Probiotics and Prebiotics. Trends Microbiol 2021; 29:667-685. [PMID: 33551269 DOI: 10.1016/j.tim.2021.01.003] [Citation(s) in RCA: 203] [Impact Index Per Article: 67.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Revised: 01/05/2021] [Accepted: 01/06/2021] [Indexed: 12/15/2022]
Abstract
Recent and ongoing developments in microbiome science are enabling new frontiers of research for probiotics and prebiotics. Novel types, mechanisms, and applications currently under study have the potential to change scientific understanding as well as nutritional and healthcare applications of these interventions. The expansion of related fields of microbiome-targeted interventions, and an evolving landscape for implementation across regulatory, policy, prescriber, and consumer spheres, portends an era of significant change. In this review we examine recent, emerging, and anticipated trends in probiotic and prebiotic science, and create a vision for broad areas of developing influence in the field.
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Affiliation(s)
- Marla Cunningham
- Department of Science and Innovation, Metagenics, PO Box 675, Virginia BC, QLD, 4014, Australia.
| | - M Andrea Azcarate-Peril
- UNC Departments of Medicine and Nutrition, Microbiome Core Facility, University of North Carolina, Chapel Hill, NC, USA
| | | | - Valerie Benoit
- Bell Institute of Health and Nutrition, General Mills, Minneapolis, MN, USA
| | | | - Denis Guyonnet
- Diana Nova, Symrise Nutrition, Clichy-la-Garenne, France
| | - Hannah D Holscher
- Department of Food Science and Human Nutrition and Division of Nutritional Sciences, University of Illinois, Urbana, IL, USA
| | - Kirsty Hunter
- Department of Sport Science, Nottingham Trent University, UK
| | - Sarmauli Manurung
- Emerging Sciences Research, Reckitt Benckiser, Nijmegen, The Netherlands
| | - David Obis
- Danone Nutricia Research, Palaiseau Cedex, France
| | | | - Robert E Steinert
- R&D Human Nutrition and Health, DSM Nutritional Products Ltd, Basel, Switzerland; Department of Surgery, Division of Visceral and Transplantation Surgery, University Hospital Zürich, Switzerland
| | - Kelly S Swanson
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Douwe van Sinderen
- Microbiology BioSciences Institute, University College Cork, Cork, Ireland
| | - Jelena Vulevic
- veMico Ltd, Reading, UK; Department of Food and Nutritional Sciences, University of Reading, Reading, UK
| | - Glenn R Gibson
- Department of Food and Nutritional Sciences, University of Reading, Reading, UK
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Smeekens J, Johnson-Weaver B, Hinton A, Azcarate-Peril MA, Moran T, Immormino R, Kesselring J, Steinbach E, Orgel K, Staats H, Burks AW, Mucha P, Ferris M, Kulis M. Food antigen sensitization in genetically-susceptible mice is influenced by fecal IgA, antigen absorption, and gut microbiome composition. J Allergy Clin Immunol 2021. [DOI: 10.1016/j.jaci.2020.12.516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Rosin S, Xia K, Azcarate-Peril MA, Carlson AL, Propper CB, Thompson AL, Grewen K, Knickmeyer RC. A preliminary study of gut microbiome variation and HPA axis reactivity in healthy infants. Psychoneuroendocrinology 2021; 124:105046. [PMID: 33254059 PMCID: PMC8121098 DOI: 10.1016/j.psyneuen.2020.105046] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [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: 04/03/2020] [Revised: 11/02/2020] [Accepted: 11/03/2020] [Indexed: 02/08/2023]
Abstract
The Hypothalamic Pituitary Adrenal (HPA) axis regulates hormonal responses to stress in both humans and animals and is dysregulated in a wide range of psychiatric disorders. There is strong evidence from rodent studies that gut microbial composition influences HPA axis development. In humans, variation in the gut microbiome has been associated with several psychological domains including depression and cognitive development, but studies focused on HPA axis development are still lacking. We tested whether differences in microbial composition are associated with HPA axis reactivity in a pilot study of 34 healthy human infants. HPA axis reactivity was assessed by measuring salivary cortisol in samples taken both before and after a heel stick, and 16S rRNA amplicon sequencing was used for identification and relative quantification of bacterial taxa. Subjects' alpha diversity levels showed a moderate positive association with their cortisol reactivity at one month of age. Exploratory genus-level analyses suggest that Staphylococcus, Prevotella, and genera in the order Lachnospiraceae may be related to cortisol reactivity at one month as well. The current study gives support for the endocrine pathway as a potential mediator in the microbiome-gut-brain axis during infancy, and as such provides motivation for future clinical work to support the development of stress-response systems through the manipulation of gut microbes.
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Affiliation(s)
- Samuel Rosin
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Kai Xia
- Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - M Andrea Azcarate-Peril
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Microbiome Core Facility, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Alexander L Carlson
- Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Cathi B Propper
- Frank Porter Graham Child Development Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Amanda L Thompson
- Department of Anthropology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Nutrition, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Karen Grewen
- Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Rebecca C Knickmeyer
- Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Pediatrics and Human Development, Michigan State University, East Lansing, MI, USA; Institute for Quantitative Health Sciences and Engineering, Michigan State University, East Lansing, MI, USA; C-RAIND Fellow, Michigan State University, East Lansing, MI, USA.
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Arnold JW, Roach J, Fabela S, Moorfield E, Ding S, Blue E, Dagher S, Magness S, Tamayo R, Bruno-Barcena JM, Azcarate-Peril MA. The pleiotropic effects of prebiotic galacto-oligosaccharides on the aging gut. Microbiome 2021; 9:31. [PMID: 33509277 PMCID: PMC7845053 DOI: 10.1186/s40168-020-00980-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 12/16/2020] [Indexed: 05/05/2023]
Abstract
BACKGROUND Prebiotic galacto-oligosaccharides (GOS) have an extensively demonstrated beneficial impact on intestinal health. In this study, we determined the impact of GOS diets on hallmarks of gut aging: microbiome dysbiosis, inflammation, and intestinal barrier defects ("leaky gut"). We also evaluated if short-term GOS feeding influenced how the aging gut responded to antibiotic challenges in a mouse model of Clostridioides difficile infection. Finally, we assessed if colonic organoids could reproduce the GOS responder-non-responder phenotypes observed in vivo. RESULTS Old animals had a distinct microbiome characterized by increased ratios of non-saccharolytic versus saccharolytic bacteria and, correspondingly, a lower abundance of β-galactosidases compared to young animals. GOS reduced the overall diversity, increased the abundance of specific saccharolytic bacteria (species of Bacteroides and Lactobacillus), increased the abundance of β-galactosidases in young and old animals, and increased the non-saccharolytic organisms; however, a robust, homogeneous bifidogenic effect was not observed. GOS reduced age-associated increased intestinal permeability and increased MUC2 expression and mucus thickness in old mice. Clyndamicin reduced the abundance Bifidobacterium while increasing Akkermansia, Clostridium, Coprococcus, Bacillus, Bacteroides, and Ruminococcus in old mice. The antibiotics were more impactful than GOS on modulating serum markers of inflammation. Higher serum levels of IL-17 and IL-6 were observed in control and GOS diets in the antibiotic groups, and within those groups, levels of IL-6 were higher in the GOS groups, regardless of age, and higher in the old compared to young animals in the control diet groups. RTqPCR revealed significantly increased gene expression of TNFα in distal colon tissue of old mice, which was decreased by the GOS diet. Colon transcriptomics analysis of mice fed GOS showed increased expression of genes involved in small-molecule metabolic processes and specifically the respirasome in old animals, which could indicate an increased oxidative metabolism and energetic efficiency. In young mice, GOS induced the expression of binding-related genes. The galectin gene Lgals1, a β-galactosyl-binding lectin that bridges molecules by their sugar moieties and is an important modulator of the immune response, and the PI3K-Akt and ECM-receptor interaction pathways were also induced in young mice. Stools from mice exhibiting variable bifidogenic response to GOS injected into colon organoids in the presence of prebiotics reproduced the response and non-response phenotypes observed in vivo suggesting that the composition and functionality of the microbiota are the main contributors to the phenotype. CONCLUSIONS Dietary GOS modulated homeostasis of the aging gut by promoting changes in microbiome composition and host gene expression, which was translated into decreased intestinal permeability and increased mucus production. Age was a determining factor on how prebiotics impacted the microbiome and expression of intestinal epithelial cells, especially apparent from the induction of galectin-1 in young but not old mice. Video abstract.
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Affiliation(s)
- Jason W Arnold
- Department of Medicine, Division of Gastroenterology and Hepatology, School of Medicine, University of North Carolina, Chapel Hill, NC, USA
- UNC Microbiome Core, Center for Gastrointestinal Biology and Disease (CGIBD), School of Medicine, University of North Carolina, Chapel Hill, NC, USA
| | - Jeffery Roach
- UNC Microbiome Core, Center for Gastrointestinal Biology and Disease (CGIBD), School of Medicine, University of North Carolina, Chapel Hill, NC, USA
- UNC Information Technology Services and Research Computing, University of North Carolina, Chapel Hill, NC, USA
| | - Salvador Fabela
- Department of Medicine, Division of Gastroenterology and Hepatology, School of Medicine, University of North Carolina, Chapel Hill, NC, USA
- UNC Microbiome Core, Center for Gastrointestinal Biology and Disease (CGIBD), School of Medicine, University of North Carolina, Chapel Hill, NC, USA
- Current affiliation: Programa de Inmunología Molecular Microbiana. Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de Mexico, Mexico City, Mexico
| | - Emily Moorfield
- Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, NC, USA
| | - Shengli Ding
- Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, NC, USA
| | - Eric Blue
- Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, NC, USA
| | - Suzanne Dagher
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, USA
| | - Scott Magness
- Joint Department of Biomedical Engineering, University of North Carolina, Chapel Hill and North Carolina State University, Raleigh, NC, USA
| | - Rita Tamayo
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC, USA
| | - Jose M Bruno-Barcena
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, USA
| | - M Andrea Azcarate-Peril
- Department of Medicine, Division of Gastroenterology and Hepatology, School of Medicine, University of North Carolina, Chapel Hill, NC, USA.
- UNC Microbiome Core, Center for Gastrointestinal Biology and Disease (CGIBD), School of Medicine, University of North Carolina, Chapel Hill, NC, USA.
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Smeekens JM, Johnson-Weaver BT, Hinton AL, Azcarate-Peril MA, Moran TP, Immormino RM, Kesselring JR, Steinbach EC, Orgel KA, Staats HF, Burks AW, Mucha PJ, Ferris MT, Kulis MD. Fecal IgA, Antigen Absorption, and Gut Microbiome Composition Are Associated With Food Antigen Sensitization in Genetically Susceptible Mice. Front Immunol 2021; 11:599637. [PMID: 33542716 PMCID: PMC7850988 DOI: 10.3389/fimmu.2020.599637] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 11/25/2020] [Indexed: 01/04/2023] Open
Abstract
Food allergy is a potentially fatal disease affecting 8% of children and has become increasingly common in the past two decades. Despite the prevalence and severe nature of the disease, the mechanisms underlying sensitization remain to be further elucidated. The Collaborative Cross is a genetically diverse panel of inbred mice that were specifically developed to study the influence of genetics on complex diseases. Using this panel of mouse strains, we previously demonstrated CC027/GeniUnc mice, but not C3H/HeJ mice, develop peanut allergy after oral exposure to peanut in the absence of a Th2-skewing adjuvant. Here, we investigated factors associated with sensitization in CC027/GeniUnc mice following oral exposure to peanut, walnut, milk, or egg. CC027/GeniUnc mice mounted antigen-specific IgE responses to peanut, walnut and egg, but not milk, while C3H/HeJ mice were not sensitized to any antigen. Naïve CC027/GeniUnc mice had markedly lower total fecal IgA compared to C3H/HeJ, which was accompanied by stark differences in gut microbiome composition. Sensitized CC027/GeniUnc mice had significantly fewer CD3+ T cells but higher numbers of CXCR5+ B cells and T follicular helper cells in the mesenteric lymph nodes compared to C3H/HeJ mice, which is consistent with their relative immunoglobulin production. After oral challenge to the corresponding food, peanut- and walnut-sensitized CC027/GeniUnc mice experienced anaphylaxis, whereas mice exposed to milk and egg did not. Ara h 2 was detected in serum collected post-challenge from peanut-sensitized mice, indicating increased absorption of this allergen, while Bos d 5 and Gal d 2 were not detected in mice exposed to milk and egg, respectively. Machine learning on the change in gut microbiome composition as a result of food protein exposure identified a unique signature in CC027/GeniUnc mice that experienced anaphylaxis, including the depletion of Akkermansia. Overall, these results demonstrate several factors associated with enteral sensitization in CC027/GeniUnc mice, including diminished total fecal IgA, increased allergen absorption and altered gut microbiome composition. Furthermore, peanuts and tree nuts may have inherent properties distinct from milk and eggs that contribute to allergy.
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Affiliation(s)
- Johanna M. Smeekens
- Department of Pediatrics, Division of Rheumatology, Allergy and Immunology, School of Medicine, University of North Carolina, Chapel Hill, NC, United States
- UNC Food Allergy Initiative, School of Medicine, University of North Carolina, Chapel Hill, NC, United States
| | | | - Andrew L. Hinton
- UNC Food Allergy Initiative, School of Medicine, University of North Carolina, Chapel Hill, NC, United States
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina, Chapel Hill, NC, United States
| | - M. Andrea Azcarate-Peril
- Department of Medicine, Division of Gastroenterology and Hepatology, University of North Carolina, Chapel Hill, NC, United States
- UNC Microbiome Core, Center for Gastrointestinal Biology and Disease, University of North Carolina, Chapel Hill, NC, United States
| | - Timothy P. Moran
- Department of Pediatrics, Division of Rheumatology, Allergy and Immunology, School of Medicine, University of North Carolina, Chapel Hill, NC, United States
| | - Robert M. Immormino
- Department of Pediatrics, Division of Rheumatology, Allergy and Immunology, School of Medicine, University of North Carolina, Chapel Hill, NC, United States
| | - Janelle R. Kesselring
- Department of Pediatrics, Division of Rheumatology, Allergy and Immunology, School of Medicine, University of North Carolina, Chapel Hill, NC, United States
- UNC Food Allergy Initiative, School of Medicine, University of North Carolina, Chapel Hill, NC, United States
| | - Erin C. Steinbach
- Department of Pediatrics, Division of Rheumatology, Allergy and Immunology, School of Medicine, University of North Carolina, Chapel Hill, NC, United States
| | - Kelly A. Orgel
- Department of Pediatrics, Division of Rheumatology, Allergy and Immunology, School of Medicine, University of North Carolina, Chapel Hill, NC, United States
- UNC Food Allergy Initiative, School of Medicine, University of North Carolina, Chapel Hill, NC, United States
| | - Herman F. Staats
- Department of Pathology, Duke University School of Medicine, Durham, NC, United States
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, United States
- Department of Immunology, Duke University School of Medicine, Durham, NC, United States
| | - A. Wesley Burks
- Department of Pediatrics, Division of Rheumatology, Allergy and Immunology, School of Medicine, University of North Carolina, Chapel Hill, NC, United States
- UNC Food Allergy Initiative, School of Medicine, University of North Carolina, Chapel Hill, NC, United States
| | - Peter J. Mucha
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina, Chapel Hill, NC, United States
- Department of Mathematics and Department of Applied Physical Sciences, University of North Carolina, Chapel Hill, NC, United States
| | - Martin T. Ferris
- Department of Genetics, School of Medicine, University of North Carolina, Chapel Hill, NC, United States
| | - Michael D. Kulis
- Department of Pediatrics, Division of Rheumatology, Allergy and Immunology, School of Medicine, University of North Carolina, Chapel Hill, NC, United States
- UNC Food Allergy Initiative, School of Medicine, University of North Carolina, Chapel Hill, NC, United States
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Fan L, Yu D, Zhu X, Huang X, Murff HJ, Azcarate-Peril MA, Shrubsole MJ, Dai Q. Magnesium and imidazole propionate. Clin Nutr ESPEN 2021; 41:436-438. [PMID: 33487303 DOI: 10.1016/j.clnesp.2020.12.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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: 11/11/2020] [Accepted: 12/17/2020] [Indexed: 12/20/2022]
Abstract
BACKGROUND & AIMS Circulating levels of imidazole propionate (ImP), a microbial metabolite of histidine, were higher in participants with type 2 diabetes (T2D) compared to those without and also induced insulin resistance. We hypothesize that low intake of magnesium (Mg) and/or low body Mg status in humans may lead to low Mg concentrations in gut microbiota, and, in turn, elevated microbial production of ImP and increased levels of circulating ImP. METHODS We tested this hypothesis in the Personalized Prevention of Colorectal Cancer Trial (PPCCT) (registered at clinicaltrials.gov as NCT01105169), a double-blind 2 × 2 factorial randomized controlled trial enrolling 240 participants at high risk of Mg deficiency. Among 68 participants (34 each in the treatment and placebo arms), we measured plasma metabolites using the untargeted Metabolon's global Precision Metabolomics™ LC-MS platform. RESULTS Mg treatment significantly reduced ImP by 39.9% compared to a 6.0% increase in the placebo arm (P = 0.02). We found the correlation coefficients were -0.12 (P = 0.32) and -0.31 (P < 0.01) between the change in ImP and changes in serum Mg and urinary Mg, respectively. In addition, we found Mg treatment increased circulating levels of propionic acid (InP) by 27.5% (P = 0.07) and reduced levels of glutarate by 17.9% (P = 0.04) compared to the placebo arm. CONCLUSIONS Further studies are needed to replicate these findings and to investigate whether Mg treatment specifically changes the production of ImP by microbiota. Also, future studies are warranted to confirm the effect of Mg treatment on glutarate and InP.
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Affiliation(s)
- Lei Fan
- Department of Medicine, Division of Epidemiology, Vanderbilt Epidemiology Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Danxia Yu
- Department of Medicine, Division of Epidemiology, Vanderbilt Epidemiology Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Xiangzhu Zhu
- Department of Medicine, Division of Epidemiology, Vanderbilt Epidemiology Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Xiang Huang
- Department of Medicine, Division of Epidemiology, Vanderbilt Epidemiology Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Harvey J Murff
- Veterans Health Administration-Tennessee Valley Healthcare System Geriatric Research Education Clinical Center (GRECC), HSR&D Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - M Andrea Azcarate-Peril
- Department of Medicine, Division of Gastroenterology and Hepatology, and UNC Microbiome Core, Center for Gastrointestinal Biology and Disease, School of Medicine, University of North Carolina, Chapel Hill, NC, USA
| | - Martha J Shrubsole
- Department of Medicine, Division of Epidemiology, Vanderbilt Epidemiology Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Qi Dai
- Department of Medicine, Division of Epidemiology, Vanderbilt Epidemiology Center, Vanderbilt University Medical Center, Nashville, TN, USA.
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Sanborn V, Azcarate-Peril MA, Updegraff J, Manderino L, Gunstad J. Randomized Clinical Trial Examining the Impact of Lactobacillus rhamnosus GG Probiotic Supplementation on Cognitive Functioning in Middle-aged and Older Adults. Neuropsychiatr Dis Treat 2020; 16:2765-2777. [PMID: 33223831 PMCID: PMC7671471 DOI: 10.2147/ndt.s270035] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 09/02/2020] [Indexed: 12/19/2022] Open
Abstract
PURPOSE The gut microbiome has been linked to cognitive function and appears to worsen with aging. Probiotic supplementation has been found to improve the health of the gut microbiome. As such, it is possible that probiotic supplementation may protect the aging brain. The current study examined the cognitive benefits of probiotic supplementation (Lactobacillus rhamnosus GG) in healthy middle-aged and older adults. MATERIALS AND METHODS The study was a double-blind, placebo-controlled, randomized clinical trial. Two hundred community-dwelling adults aged 52-75 were enrolled (mean age=64.3, SD=5.52). A three-month intervention involved daily consumption of probiotic or placebo. Independent sample t-tests, chi-squared tests, and repeated measure ANOVAs compared groups and examined changes over time. Primary outcome was change in NIH Toolbox Total Cognition Score from baseline to follow-up. RESULTS A total of 145 participants were examined in primary analyses (probiotic=77, placebo=68) and excluded persons due to discontinuation, low adherence, missing data, or outlier values. Established criteria (ie ≥1 subtest t-scores ≤35; n=19, n=23) were used to operationally define cognitive impairment. Repeated measures ANOVAs revealed that persons with cognitive impairment who consumed probiotics exhibited a greater total cognition score improvement than persons with cognitive impairment in the placebo group and cognitively intact persons in probiotic or placebo groups. CONCLUSION Lactobacillus rhamnosus GG probiotic supplementation was associated with improved cognitive performance in middle-aged and older adults with cognitive impairment. Probiotic supplementation may be a novel method for protecting cognitive health in aging.
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Affiliation(s)
- Victoria Sanborn
- Department of Psychological Sciences, Kent State University, Kent, OH, USA
| | - M Andrea Azcarate-Peril
- Department of Cell Biology and Physiology and Microbiome Core Facility, UNC School of Medicine, Chapel Hill, North Carolina, USA
| | - John Updegraff
- Department of Psychological Sciences, Kent State University, Kent, OH, USA
| | - Lisa Manderino
- Department of Psychological Sciences, Kent State University, Kent, OH, USA
| | - John Gunstad
- Department of Psychological Sciences, Kent State University, Kent, OH, USA
- Brain Health Research Institute, Kent State University, Kent, OH, USA
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Divaris K, Slade GD, Ferreira Zandona AG, Preisser JS, Ginnis J, Simancas-Pallares MA, Agler CS, Shrestha P, Karhade DS, Ribeiro ADA, Cho H, Gu Y, Meyer BD, Joshi AR, Azcarate-Peril MA, Basta PV, Wu D, North KE. Cohort Profile: ZOE 2.0-A Community-Based Genetic Epidemiologic Study of Early Childhood Oral Health. Int J Environ Res Public Health 2020; 17:E8056. [PMID: 33139633 PMCID: PMC7663650 DOI: 10.3390/ijerph17218056] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 10/28/2020] [Accepted: 10/29/2020] [Indexed: 02/06/2023]
Abstract
Early childhood caries (ECC) is an aggressive form of dental caries occurring in the first five years of life. Despite its prevalence and consequences, little progress has been made in its prevention and even less is known about individuals' susceptibility or genomic risk factors. The genome-wide association study (GWAS) of ECC ("ZOE 2.0") is a community-based, multi-ethnic, cross-sectional, genetic epidemiologic study seeking to address this knowledge gap. This paper describes the study's design, the cohort's demographic profile, data domains, and key oral health outcomes. Between 2016 and 2019, the study enrolled 8059 3-5-year-old children attending public preschools in North Carolina, United States. Participants resided in 86 of the state's 100 counties and racial/ethnic minorities predominated-for example, 48% (n = 3872) were African American, 22% white, and 20% (n = 1611) were Hispanic/Latino. Seventy-nine percent (n = 6404) of participants underwent clinical dental examinations yielding ECC outcome measures-ECC (defined at the established caries lesion threshold) prevalence was 54% and the mean number of decayed, missing, filled surfaces due to caries was eight. Nearly all (98%) examined children provided sufficient DNA from saliva for genotyping. The cohort's community-based nature and rich data offer excellent opportunities for addressing important clinical, epidemiologic, and biological questions in early childhood.
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Affiliation(s)
- Kimon Divaris
- Division of Pediatric and Public Health, Adams School of Dentistry, University of North Carolina-Chapel Hill, NC 27599-7450, USA; (G.D.S.); (J.G.); (M.A.S.-P.); (C.S.A.); (P.S.); (D.S.K.)
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina-Chapel Hill, NC 27599-7400, USA; (P.V.B.); (K.E.N.)
| | - Gary D. Slade
- Division of Pediatric and Public Health, Adams School of Dentistry, University of North Carolina-Chapel Hill, NC 27599-7450, USA; (G.D.S.); (J.G.); (M.A.S.-P.); (C.S.A.); (P.S.); (D.S.K.)
| | - Andrea G. Ferreira Zandona
- Department of Comprehensive Dentistry, School of Dental Medicine, Tufts University, Boston, MA 02111, USA;
| | - John S. Preisser
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina-Chapel Hill, NC 27599-7400, USA; (J.S.P.); (H.C.); (Y.G.); (D.W.)
| | - Jeannie Ginnis
- Division of Pediatric and Public Health, Adams School of Dentistry, University of North Carolina-Chapel Hill, NC 27599-7450, USA; (G.D.S.); (J.G.); (M.A.S.-P.); (C.S.A.); (P.S.); (D.S.K.)
| | - Miguel A. Simancas-Pallares
- Division of Pediatric and Public Health, Adams School of Dentistry, University of North Carolina-Chapel Hill, NC 27599-7450, USA; (G.D.S.); (J.G.); (M.A.S.-P.); (C.S.A.); (P.S.); (D.S.K.)
| | - Cary S. Agler
- Division of Pediatric and Public Health, Adams School of Dentistry, University of North Carolina-Chapel Hill, NC 27599-7450, USA; (G.D.S.); (J.G.); (M.A.S.-P.); (C.S.A.); (P.S.); (D.S.K.)
| | - Poojan Shrestha
- Division of Pediatric and Public Health, Adams School of Dentistry, University of North Carolina-Chapel Hill, NC 27599-7450, USA; (G.D.S.); (J.G.); (M.A.S.-P.); (C.S.A.); (P.S.); (D.S.K.)
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina-Chapel Hill, NC 27599-7400, USA; (P.V.B.); (K.E.N.)
| | - Deepti S. Karhade
- Division of Pediatric and Public Health, Adams School of Dentistry, University of North Carolina-Chapel Hill, NC 27599-7450, USA; (G.D.S.); (J.G.); (M.A.S.-P.); (C.S.A.); (P.S.); (D.S.K.)
| | - Apoena de Aguiar Ribeiro
- Division of Diagnostic Sciences, Adams School of Dentistry, University of North Carolina-Chapel Hill, NC 27599-7450, USA;
| | - Hunyong Cho
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina-Chapel Hill, NC 27599-7400, USA; (J.S.P.); (H.C.); (Y.G.); (D.W.)
| | - Yu Gu
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina-Chapel Hill, NC 27599-7400, USA; (J.S.P.); (H.C.); (Y.G.); (D.W.)
| | - Beau D. Meyer
- Division of Pediatric Dentistry, College of Dentistry, The Ohio State University, Columbus, OH 43210, USA;
| | - Ashwini R. Joshi
- Division of Surgery, School of Medicine, University of North Carolina-Chapel Hill, NC 27599-7050, USA;
| | - M. Andrea Azcarate-Peril
- Center for Gastrointestinal Biology and Disease, Division of Gastroenterology and Hepatology, and UNC Microbiome Core, Department of Medicine, School of Medicine, University of North Carolina-Chapel Hill, NC 27599-7555, USA;
| | - Patricia V. Basta
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina-Chapel Hill, NC 27599-7400, USA; (P.V.B.); (K.E.N.)
| | - Di Wu
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina-Chapel Hill, NC 27599-7400, USA; (J.S.P.); (H.C.); (Y.G.); (D.W.)
- Division of Oral and Craniofacial Health Sciences, Adams School of Dentistry, University of North Carolina-Chapel Hill, NC 27599-7450, USA
| | - Kari E. North
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina-Chapel Hill, NC 27599-7400, USA; (P.V.B.); (K.E.N.)
- Carolina Center for Genome Sciences, University of North Carolina-Chapel Hill, NC 27514, USA
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Sanborn VE, Azcarate-Peril MA, Gunstad J. Lactobacillus rhamnosus GG and HbA1c in middle age and older adults without type 2 diabetes mellitus: A preliminary randomized study. Diabetes Metab Syndr 2020; 14:907-909. [PMID: 32570015 DOI: 10.1016/j.dsx.2020.05.034] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [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: 11/05/2019] [Revised: 05/19/2020] [Accepted: 05/21/2020] [Indexed: 12/27/2022]
Abstract
BACKGROUND AND AIMS Probiotic supplementation improves glycemic control in persons with diabetes and the current study examined whether these benefits extend to healthy individuals. METHODS The current study was a 90-day placebo-controlled, double-blind, randomized clinical trial of Lactobacillus rhamnosus GG in healthy middle-aged and older adults. Fasting blood glucose and HbA1c were quantified at baseline and follow up. RESULTS ANCOVA controlling for baseline values showed group differences in follow up HbA1c [F (1,90) = 8.44, p = 0.005]; HbA1c values increased in the placebo group, though remained stable in the probiotic group. CONCLUSIONS If replicated, Lactobacillus rhamnosus GG may protect against changes in glycemic control.
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Affiliation(s)
| | - M Andrea Azcarate-Peril
- Department of Medicine, Division of Gastroenterology and Hepatology, and UNC Microbiome Core, Center for Gastrointestinal Biology and Disease, School of Medicine, University of North Carolina, Chapel Hill, NC, USA
| | - John Gunstad
- Department of Psychological Sciences, Kent State University, USA; Brain Health Research Institute, Kent State University, USA
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36
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Lee MK, Wyss AB, Carnes MU, Richards M, Parks CG, Beane Freeman LE, Thorne PS, Umbach DM, Azcarate-Peril MA, Peddada SD, London SJ. House dust microbiota in relation to adult asthma and atopy in a US farming population. J Allergy Clin Immunol 2020; 147:910-920. [PMID: 32615170 DOI: 10.1016/j.jaci.2020.06.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 06/18/2020] [Accepted: 06/22/2020] [Indexed: 02/08/2023]
Abstract
BACKGROUND Bacterial exposure from house dust has been associated with asthma and atopy in children but whether these relationships are present in adults remains unclear. OBJECTIVE We sought to examine associations of house dust microbiota with adult asthma, atopy, and hay fever. METHODS Vacuumed bedroom dust samples from the homes of 879 participants (average age, 62 years) in the Agricultural Lung Health Study, a case-control study of asthma nested within a farming cohort, were subjected to 16S rRNA amplicon sequencing to characterize bacterial communities. We defined current asthma and hay fever using questionnaires and current atopy by blood specific IgE level > 0.70 IU/mL to 1 or more of 10 common allergens. We used linear regression to examine whether overall within-sample bacterial diversity differed by outcome, microbiome regression-based kernel association test to evaluate whether between-sample bacterial community compositions differed by outcome, and analysis of composition of microbiomes to identify differentially abundant bacterial taxa. RESULTS Overall diversity of bacterial communities in house dust was similar by asthma status but was lower (P < .05) with atopy or hay fever. Many individual bacterial taxa were differentially abundant (false-discovery rate, <0.05) by asthma, atopy, or hay fever. Several taxa from Cyanobacteria, Bacteroidetes, and Fusobacteria were more abundant with asthma, atopy, or hay fever. In contrast, several taxa from Firmicutes were more abundant in homes of individuals with adequately controlled asthma (vs inadequately controlled asthma), individuals without atopy, or individuals without hay fever. CONCLUSIONS Microbial composition of house dust may influence allergic outcomes in adults.
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Affiliation(s)
- Mi Kyeong Lee
- Epidemiology Branch, National Institute of Environmental Health Sciences (NIEHS), National Institutes of Health (NIH), Department of Health and Human Services (DHHS), Research Triangle Park, NC
| | - Annah B Wyss
- Epidemiology Branch, National Institute of Environmental Health Sciences (NIEHS), National Institutes of Health (NIH), Department of Health and Human Services (DHHS), Research Triangle Park, NC
| | - Megan U Carnes
- Genomics in Public Health and Medicine Center, Biostatistics and Epidemiology Division, RTI International, Research Triangle Park, NC
| | | | - Christine G Parks
- Epidemiology Branch, National Institute of Environmental Health Sciences (NIEHS), National Institutes of Health (NIH), Department of Health and Human Services (DHHS), Research Triangle Park, NC
| | - Laura E Beane Freeman
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Rockville, Md
| | - Peter S Thorne
- Department of Occupational and Environmental Health, University of Iowa, Iowa City, Iowa
| | - David M Umbach
- Biostatistics and Computational Biology Branch, NIEHS, NIH, DHHS, Research Triangle Park, NC
| | - M Andrea Azcarate-Peril
- Department of Medicine and Microbiome Core, Center for Gastrointestinal Biology and Disease, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Shyamal D Peddada
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, Pa
| | - Stephanie J London
- Epidemiology Branch, National Institute of Environmental Health Sciences (NIEHS), National Institutes of Health (NIH), Department of Health and Human Services (DHHS), Research Triangle Park, NC.
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Trippe LH, Ribeiro AA, Azcarate-Peril MA, Preisser JS, Wang R, Zandona AF. Is Fluorescence Technology a Promising Tool for Detecting Infected Dentin in Deep Carious Lesions? Caries Res 2020; 54:205-217. [PMID: 32580204 DOI: 10.1159/000505643] [Citation(s) in RCA: 1] [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: 01/02/2019] [Accepted: 12/29/2019] [Indexed: 11/19/2022] Open
Abstract
The purpose of this study was to determine if the degree of fluorescence detected by fluorescence-aided caries excavation (FACE) correlates with dentin bacterial microbiome diversity, as assessed by 16S rRNA gene amplicon sequencing, and with traditional tactile dentin caries assessment. Unidentified human teeth were obtained from a dental facility. The included teeth had a carious lesion two-thirds into the dentin, verified by radiography, and were red-fluorescing (RF) using FACE technology (SIROInspect; Sirona, Bensheim, Germany). Two independent examiners performed visual/tactile assessment of the lesions. RF sites were sampled with a sterile spoon excavator and dentin characteristics were evaluated. Once RF dentin was removed, a second sample of pink-fluorescing (PF) dentin was obtained. After excavation with a sterile round bur to nonfluorescing (NF) dentin, a third sample was collected with a slow-speed round bur. The samples were processed at the UNC (University of North Carolina at Chapel Hill) Microbiome Core Facility. Out of 134 extracted teeth collected, 21 fit the inclusion criteria, yielding 61 dentin samples. RF samples had the highest number of observed operational taxonomic units (n = 154), followed by PF (n = 109) and NF (n = 100). RF carious dentin was primarily "soft," and NF dentin was assessed as "hard" 100% of the time by both examiners (rank correlation χ2: p < 0.001). However, approximately one-third of the tactile assessments of hard dentin still displayed some fluorescence, either pink or red. We concluded that the sampled fluorescing (RF and PF) and NF carious dentin layers displayed diverse bacterial taxa, and tactile assessments of soft, leathery, and hard corresponded with RF, PF, and NF.
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Affiliation(s)
- Leslie H Trippe
- Division of Comprehensive Oral Care, University of North Carolina Chapel Hill School of Dentistry, Chapel Hill, North Carolina, USA
| | - Apoena Aguiar Ribeiro
- Division of Diagnostic Sciences, School of Dentistry at University of North Carolina, Chapel Hill, North Carolina, USA,
| | - M Andrea Azcarate-Peril
- Departments of Medicine and Nutrition, and Microbiome Core, School of Medicine at University of North Carolina, Chapel Hill, North Carolina, USA
| | - John S Preisser
- Department of Biostatistics, Gillings School of Global Public Health at University of North Carolina, Chapel Hill, North Carolina, USA
| | - Rujin Wang
- Department of Biostatistics, Gillings School of Global Public Health at University of North Carolina, Chapel Hill, North Carolina, USA
| | - Andrea Ferreira Zandona
- Department of Comprehensive Care, Tufts University School of Dental Medicine, Boston, Massachusetts, USA
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Lei S, Twitchell EL, Ramesh AK, Bui T, Majette E, Tin CM, Avery R, Arango-Argoty G, Zhang L, Becker-Dreps S, Azcarate-Peril MA, Jiang X, Yuan L. Enhanced GII.4 human norovirus infection in gnotobiotic pigs transplanted with a human gut microbiota. J Gen Virol 2020; 100:1530-1540. [PMID: 31596195 DOI: 10.1099/jgv.0.001336] [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] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The role of commensal microbiota in enteric viral infections has been explored extensively, but the interaction between human gut microbiota (HGM) and human norovirus (HuNoV) is poorly understood. In this study, we established an HGM-Transplanted gnotobiotic (Gn) pig model of HuNoV infection and disease, using an infant stool as HGM transplant and a HuNoV GII.4/2006b strain for virus inoculation. Compared to germ-free Gn pigs, HuNoV inoculation in HGMT Gn pigs resulted in increased HuNoV shedding, characterized by significantly higher shedding titres on post inoculation day (PID) 3, 4, 6, 8 and 9, and significantly longer mean duration of virus shedding. In addition, virus titres were significantly higher in duodenum and distal ileum of HGMT Gn pigs on PID10, while comparable and transient HuNoV viremia was detected in both groups. 16S rRNA gene sequencing demonstrated that HuNoV infection dramatically altered intestinal microbiota in HGMT Gn pigs at the phylum (Proteobacteria, Firmicutes and Bacteroidetes) and genus (Enterococcus, Bifidobacterium, Clostridium, Ruminococcus, Anaerococcus, Bacteroides and Lactobacillus) levels. In summary, enhanced GII.4 HuNoV infection was observed in the presence of HGM, and host microbiota was susceptible to disruption upon HuNoV infection.
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Affiliation(s)
- Shaohua Lei
- Present address: Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.,Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, VA 24061, USA
| | - Erica L Twitchell
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, VA 24061, USA
| | - Ashwin K Ramesh
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, VA 24061, USA
| | - Tammy Bui
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, VA 24061, USA
| | - Elizabeth Majette
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, VA 24061, USA
| | - Christine M Tin
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, VA 24061, USA
| | - Roger Avery
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, VA 24061, USA
| | - Gustavo Arango-Argoty
- Department of Computer Science, College of Engineering, Virginia Tech, Blacksburg, VA 24061, USA
| | - Liqing Zhang
- Department of Computer Science, College of Engineering, Virginia Tech, Blacksburg, VA 24061, USA
| | - Sylvia Becker-Dreps
- Department of Family Medicine, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - M Andrea Azcarate-Peril
- Division of Gastroenterology and Hepatology, Department of Medicine, Microbiome Core Facility, Center for Gastrointestinal Biology and Disease, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Xi Jiang
- Division of Infectious Diseases, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Lijuan Yuan
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, VA 24061, USA
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Bhatt AP, Pellock SJ, Biernat KA, Walton WG, Wallace BD, Creekmore BC, Letertre MM, Swann JR, Wilson ID, Roques JR, Darr DB, Bailey ST, Montgomery SA, Roach JM, Azcarate-Peril MA, Sartor RB, Gharaibeh RZ, Bultman SJ, Redinbo MR. Targeted inhibition of gut bacterial β-glucuronidase activity enhances anticancer drug efficacy. Proc Natl Acad Sci U S A 2020; 117:7374-7381. [PMID: 32170007 PMCID: PMC7132129 DOI: 10.1073/pnas.1918095117] [Citation(s) in RCA: 106] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Irinotecan treats a range of solid tumors, but its effectiveness is severely limited by gastrointestinal (GI) tract toxicity caused by gut bacterial β-glucuronidase (GUS) enzymes. Targeted bacterial GUS inhibitors have been shown to partially alleviate irinotecan-induced GI tract damage and resultant diarrhea in mice. Here, we unravel the mechanistic basis for GI protection by gut microbial GUS inhibitors using in vivo models. We use in vitro, in fimo, and in vivo models to determine whether GUS inhibition alters the anticancer efficacy of irinotecan. We demonstrate that a single dose of irinotecan increases GI bacterial GUS activity in 1 d and reduces intestinal epithelial cell proliferation in 5 d, both blocked by a single dose of a GUS inhibitor. In a tumor xenograft model, GUS inhibition prevents intestinal toxicity and maintains the antitumor efficacy of irinotecan. Remarkably, GUS inhibitor also effectively blocks the striking irinotecan-induced bloom of Enterobacteriaceae in immune-deficient mice. In a genetically engineered mouse model of cancer, GUS inhibition alleviates gut damage, improves survival, and does not alter gut microbial composition; however, by allowing dose intensification, it dramatically improves irinotecan's effectiveness, reducing tumors to a fraction of that achieved by irinotecan alone, while simultaneously promoting epithelial regeneration. These results indicate that targeted gut microbial enzyme inhibitors can improve cancer chemotherapeutic outcomes by protecting the gut epithelium from microbial dysbiosis and proliferative crypt damage.
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Affiliation(s)
- Aadra P Bhatt
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3290
- Department of Medicine, Division of Gastroenterology and Hepatology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7555
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7555
| | - Samuel J Pellock
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3290
| | - Kristen A Biernat
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3290
| | - William G Walton
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3290
| | - Bret D Wallace
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3290
| | - Benjamin C Creekmore
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3290
| | - Marine M Letertre
- Computational and Systems Medicine, Department of Surgery & Cancer, Imperial College London, SW7 2AZ London, United Kingdom
| | - Jonathan R Swann
- Computational and Systems Medicine, Department of Surgery & Cancer, Imperial College London, SW7 2AZ London, United Kingdom
| | - Ian D Wilson
- Computational and Systems Medicine, Department of Surgery & Cancer, Imperial College London, SW7 2AZ London, United Kingdom
| | - Jose R Roques
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - David B Darr
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Sean T Bailey
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Stephanie A Montgomery
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7525
| | - Jeffrey M Roach
- Department of Medicine, Division of Gastroenterology and Hepatology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7555
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7555
| | - M Andrea Azcarate-Peril
- Department of Medicine, Division of Gastroenterology and Hepatology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7555
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7555
| | - R Balfour Sartor
- Department of Medicine, Division of Gastroenterology and Hepatology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7555
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7555
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Raad Z Gharaibeh
- Department of Medicine, Division of Gastroenterology, University of Florida, Gainesville, FL 32610
| | - Scott J Bultman
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7264
| | - Matthew R Redinbo
- Department of Biochemistry, Integrated Program for Biological and Genome Science, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3290;
- Department of Biophysics, Integrated Program for Biological and Genome Science, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3290
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Sanborn V, Azcarate-Peril MA, Gunstad J. The effects of medication adherence on study outcomes in randomized clinical trials: A role for cognitive dysfunction? Appl Neuropsychol Adult 2019; 28:641-646. [PMID: 31650861 DOI: 10.1080/23279095.2019.1680987] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Medication nonadherence is common and has been associated with poor health outcomes. Older adults are especially likely to be non-adherent to their medications, as they often have more medications to manage and are at greater risk for cognitive dysfunction. Though less frequently examined, the association between cognitive dysfunction and nonadherence also likely extends to clinical trials research. The current study used archival data to examine the potential impact of cognitive dysfunction on adherence to a nutritional supplement as part of a 90-day randomized clinical trial in neurologically healthy middle-aged and older adults. Results showed overall cognitive performance was predictive of adherence to capsule intake when controlling for polypharmacy [F(1,157) = 6.53, p < .01]. These results suggest that cognitive dysfunction may impact findings from RCTs through its adverse impact on adherence to study protocol, possibly leading to greater treatment variance, artificially reduced treatment effects, lower study power, and distorted study outcomes and conclusions. A better understanding of methodological and statistical approaches to account for these unwanted effects are needed.
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Affiliation(s)
- V Sanborn
- Department of Psychological Sciences, Kent State University, Kent, OH, USA
| | - M A Azcarate-Peril
- Department of Medicine, Division of Gastroenterology and Hepatology, and UNC Microbiome Core, Center for Gastrointestinal Biology and Disease, School of Medicine, University of North Carolina, Chapel Hill, NC, USA
| | - J Gunstad
- Department of Psychological Sciences, Kent State University, Kent, OH, USA.,Brain Health Research Institute, Kent State University, Kent, OH, USA
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Rothenberg SE, Wagner CL, Hamidi B, Alekseyenko AV, Andrea Azcarate-Peril M. Longitudinal changes during pregnancy in gut microbiota and methylmercury biomarkers, and reversal of microbe-exposure correlations. Environ Res 2019; 172:700-712. [PMID: 30903970 PMCID: PMC6675619 DOI: 10.1016/j.envres.2019.01.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [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: 07/12/2018] [Revised: 01/06/2019] [Accepted: 01/08/2019] [Indexed: 06/09/2023]
Abstract
OBJECTIVE Gut microorganisms contribute to the metabolism of environmental toxicants, including methylmercury (MeHg). Our main objective was to investigate whether associations between biomarkers for prenatal MeHg exposure and maternal gut microbiota differed between early and late gestation. METHODS Maternal blood and stool samples were collected during early (8.3-17 weeks, n=28) and late (27-36 weeks, n=24) gestation. Total mercury and MeHg concentrations were quantified in biomarkers, and inorganic mercury was estimated by subtraction. The diversity and structure of the gut microbiota were investigated using 16S rRNA gene profiling (n = 52). Biomarkers were dichotomized, and diversity patterns were compared between high/low mercury concentrations. Spearman's correlation was used to assess bivariate associations between MeHg biomarkers (stool, blood, and meconium), and 23 gut microbial taxa (genus or family level, >1% average relative abundance). RESULTS Within-person and between-person diversity patterns in gut microbiota differed between early/late gestation. The overall composition of the microbiome differed between high/low MeHg concentrations (in blood and stool) during early gestation, but not late gestation. Ten (of 23) taxa were significantly correlated with MeHg biomarkers (increasing or decreasing); however, associations differed, depending on whether the sample was collected during early or late gestation. A total of 43% of associations (69/161) reversed the direction of correlation between early/late gestation. CONCLUSIONS The time point at which a maternal fecal sample is collected may yield different associations between gut microorganisms and MeHg biomarkers, which may be due in part to remodeling of maternal microbiota during pregnancy. Our results suggest the effectiveness of dietary interventions to reduce prenatal MeHg exposure may differ between early and late gestation.
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Affiliation(s)
- Sarah E Rothenberg
- School of Biological and Population Health Sciences, Oregon State University, Corvallis, Oregon, USA.
| | - Carol L Wagner
- Department of Pediatrics, Medical University of South Carolina, Charleston, SC, USA
| | - Bashir Hamidi
- Department of Public Health Sciences, Medical University of South Carolina, Charleston, SC, USA
| | - Alexander V Alekseyenko
- Department of Public Health Sciences, Medical University of South Carolina, Charleston, SC, USA
| | - M Andrea Azcarate-Peril
- Division of Gastroenterology and Hepatology and Microbiome Core Facility, University of North Carolina, Chapel Hill, NC, USA
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Arnold JW, Simpson JB, Roach J, Bruno-Barcena JM, Azcarate-Peril MA. Prebiotics for Lactose Intolerance: Variability in Galacto-Oligosaccharide Utilization by Intestinal Lactobacillus rhamnosus. Nutrients 2018; 10:E1517. [PMID: 30332787 PMCID: PMC6213946 DOI: 10.3390/nu10101517] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 10/09/2018] [Accepted: 10/11/2018] [Indexed: 12/12/2022] Open
Abstract
Lactose intolerance, characterized by a decrease in host lactase expression, affects approximately 75% of the world population. Galacto-oligosaccharides (GOS) are prebiotics that have been shown to alleviate symptoms of lactose intolerance and to modulate the intestinal microbiota, promoting the growth of beneficial microorganisms. We hypothesized that mechanisms of GOS utilization by intestinal bacteria are variable, impacting efficacy and response, with differences occurring at the strain level. This study aimed to determine the mechanisms by which human-derived Lactobacillus rhamnosus strains metabolize GOS. Genomic comparisons between strains revealed differences in carbohydrate utilization components, including transporters, enzymes for degradation, and transcriptional regulation, despite a high overall sequence identity (>95%) between strains. Physiological and transcriptomics analyses showed distinct differences in carbohydrate metabolism profiles and GOS utilization between strains. A putative operon responsible for GOS utilization was identified and characterized by genetic disruption of the 6-phospho-β-galactosidase, which had a critical role in GOS utilization. Our findings highlight the importance of strain-specific bacterial metabolism in the selection of probiotics and synbiotics to alleviate symptoms of gastrointestinal disorders including lactose intolerance.
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Affiliation(s)
- Jason W Arnold
- Center for Gastrointestinal Biology and Disease, Division of Gastroenterology and Hepatology, and UNC Microbiome Core, Department of Medicine, School of Medicine, University of North Carolina, Chapel Hill, NC 27599, USA.
| | - Joshua B Simpson
- Center for Gastrointestinal Biology and Disease, Division of Gastroenterology and Hepatology, and UNC Microbiome Core, Department of Medicine, School of Medicine, University of North Carolina, Chapel Hill, NC 27599, USA.
| | - Jeffery Roach
- Research Computing, University of North Carolina, Chapel Hill, NC 27599, USA.
| | - Jose M Bruno-Barcena
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27607, USA.
| | - M Andrea Azcarate-Peril
- Center for Gastrointestinal Biology and Disease, Division of Gastroenterology and Hepatology, and UNC Microbiome Core, Department of Medicine, School of Medicine, University of North Carolina, Chapel Hill, NC 27599, USA.
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Ho NT, Li F, Lee-Sarwar KA, Tun HM, Brown BP, Pannaraj PS, Bender JM, Azad MB, Thompson AL, Weiss ST, Azcarate-Peril MA, Litonjua AA, Kozyrskyj AL, Jaspan HB, Aldrovandi GM, Kuhn L. Meta-analysis of effects of exclusive breastfeeding on infant gut microbiota across populations. Nat Commun 2018; 9:4169. [PMID: 30301893 PMCID: PMC6177445 DOI: 10.1038/s41467-018-06473-x] [Citation(s) in RCA: 230] [Impact Index Per Article: 38.3] [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: 04/04/2018] [Accepted: 08/28/2018] [Indexed: 02/07/2023] Open
Abstract
Previous studies on the differences in gut microbiota between exclusively breastfed (EBF) and non-EBF infants have provided highly variable results. Here we perform a meta-analysis of seven microbiome studies (1825 stool samples from 684 infants) to compare the gut microbiota of non-EBF and EBF infants across populations. In the first 6 months of life, gut bacterial diversity, microbiota age, relative abundances of Bacteroidetes and Firmicutes, and predicted microbial pathways related to carbohydrate metabolism are consistently higher in non-EBF than in EBF infants, whereas relative abundances of pathways related to lipid metabolism, vitamin metabolism, and detoxification are lower. Variation in predicted microbial pathways associated with non-EBF infants is larger among infants born by Caesarian section than among those vaginally delivered. Longer duration of exclusive breastfeeding is associated with reduced diarrhea-related gut microbiota dysbiosis. Furthermore, differences in gut microbiota between EBF and non-EBF infants persist after 6 months of age. Our findings elucidate some mechanisms of short and long-term benefits of exclusive breastfeeding across different populations.
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Affiliation(s)
- Nhan T Ho
- Gertrude H. Sergievsky Center, Columbia University, New York City, NY, 10032, USA
| | - Fan Li
- Department of Pediatrics, University of California, Los Angeles, CA, 90095, USA
| | - Kathleen A Lee-Sarwar
- Division of Rheumatology, Immunology and Allergy, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Hein M Tun
- Department of Pediatrics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, T6G 1C9, AB, Canada
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Bryan P Brown
- Duke University, Durham, NC, 27708, USA
- University of Cape Town Health Sciences Faculty, Institute of Infectious Disease and Molecular Medicine, Cape Town, 7701, South Africa
- Seattle Children's Research Institute, University of Washington, Seattle, WA, 98101, USA
| | - Pia S Pannaraj
- Children's Hospital Los Angeles, University of Southern California, Los Angeles, CA, 90027, USA
| | - Jeffrey M Bender
- Children's Hospital Los Angeles, University of Southern California, Los Angeles, CA, 90027, USA
| | - Meghan B Azad
- Children's Hospital Research Institute of Manitoba, Department of Pediatrics & Child Health, University of Manitoba, Winnipeg, R3E 3P4, Manitoba, Canada
| | - Amanda L Thompson
- Department of Anthropology, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Scott T Weiss
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - M Andrea Azcarate-Peril
- Department of Medicine, Division of Gastroenterology and Hepatology, School of Medicine, University of North Carolina, Chapel Hill, NC, 27599, USA
- Microbiome Core Facility, Center for Gastrointestinal Biology and Disease, School of Medicine, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Augusto A Litonjua
- Division of Pulmonary Medicine, Department of Pediatrics, University of Rochester Medical Center, Rochester, NY, 14642, USA
| | - Anita L Kozyrskyj
- Department of Pediatrics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, T6G 1C9, AB, Canada
| | - Heather B Jaspan
- University of Cape Town Health Sciences Faculty, Institute of Infectious Disease and Molecular Medicine, Cape Town, 7701, South Africa
- Seattle Children's Research Institute, University of Washington, Seattle, WA, 98101, USA
| | - Grace M Aldrovandi
- Department of Pediatrics, University of California, Los Angeles, CA, 90095, USA
| | - Louise Kuhn
- Gertrude H. Sergievsky Center, Columbia University, New York City, NY, 10032, USA.
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Jones RB, Zhu X, Moan E, Murff HJ, Dai Q, Shrubsole MJ, Fodor AA, Azcarate-Peril MA, Ness RM, Seidner DL. Abstract 3266: Measurement and comparison of the gut microbial communities in fecal, rectal swab, and mucosal samples. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-3266] [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: Studies evaluating the gut microbiome frequently use stool. However, stool, which is predominantly composed of luminal bacteria, may not adequately reflect mucosally adherent bacteria. The purpose of this study is to evaluate similarities and differences in gut bacterial measurements and stability in the microbial communities of three different types of samples that could be used to assess different niches of the gut microbiome: rectal swab, stool, and normal rectal mucosa samples.
Design: Sixty-eight participants were selected from a personalized chemoprevention trial population of individuals with previous colorectal adenomas who had donated stool, swab, and mucosal samples at baseline and three months later. 16S rRNA amplicon sequencing was conducted for 60 participants at two time points (n=120 stool and 120 swab). Whole-genome shotgun metagenomics DNA sequencing was conducted for 50 participants at two time points (n=100 stool, 28 swab, and 16 mucosal).
Results: In swab-stool comparisons, there were substantial taxa differences with some taxa varying largely by sample type (e.g., Thermaceae) while other taxa were predominantly associated with interindividual subject variation (e.g., Desulfovibrionaceae) or by both sample type and participant (e.g., Enterobacteriaceae). At species-level resolution (with WGS sequences) we observed that bacteria associated with colorectal tumors (Escherichia coli and Fusobacterium nucleatum) were of higher relative abundance in swab than stool. There were also statistically significant differences in other bacteria according to the sample type (e.g., Bifidobacterium longum, Bacteroides fragilis). Comparing all three sample types with whole-genome metagenome shotgun sequencing, swab samples were much closer to stool samples than mucosa samples, although all KEGG functional Level 1 and Level 2 pathways were significantly different across all sample types (e.g., transcription and environmental adaptation). However, the individual signature of participants was also observed and was largely stable between two time points. Thus, we found that while the distribution of some taxa was associated with these different sampling techniques, other taxa largely reflected individual differences in the microbial community that were insensitive to sampling technique.
Conclusion: There is substantial variability in the assessment of the gut microbial community according to the type of sample.
Citation Format: Roshonda B Jones, Xiangzhu Zhu, Emili Moan, Harvey J. Murff, Qi Dai, Martha J. Shrubsole, Anthony A. Fodor, M. Andrea Azcarate-Peril, Reid M. Ness, Douglas L. Seidner. Measurement and comparison of the gut microbial communities in fecal, rectal swab, and mucosal samples [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3266.
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Affiliation(s)
| | | | - Emili Moan
- 3North Carolina State University, Raleigh, NC
| | | | - Qi Dai
- 2Vanderbilt-Ingram Cancer Ctr., Nashville, TN
| | | | | | | | - Reid M. Ness
- 5Vanderbilt University Medical Center, Nashville, TN
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Lee MK, Carnes MU, Butz N, Azcarate-Peril MA, Richards M, Umbach DM, Thorne PS, Beane Freeman LE, Peddada SD, London SJ. Exposures Related to House Dust Microbiota in a U.S. Farming Population. Environ Health Perspect 2018; 126:067001. [PMID: 29863827 PMCID: PMC6084882 DOI: 10.1289/ehp3145] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 05/01/2018] [Accepted: 05/02/2018] [Indexed: 05/09/2023]
Abstract
BACKGROUND Environmental factors can influence the house dust microbiota, which may impact health outcomes. Little is known about how farming exposures impact the indoor microbiota. OBJECTIVE We aimed to identify exposures related to bacterial communities in house dust in a U.S. farming population. METHODS We used 16S rRNA amplicon sequencing to characterize bacterial communities in vacuumed dust samples from the bedrooms of a subset of 879 households of farmers and farmers' spouses enrolled in the Agricultural Lung Health Study (ALHS), a case-control study of asthma nested within the Agricultural Health Study (AHS) in North Carolina and Iowa. Information on current farming (past 12 mo), including both crop and animal farming, and other potential microbial sources was obtained via questionnaires. We used linear regression to evaluate associations between exposures and bacterial diversity within each sample, analysis of similarity (ANOSIM), and permutational multivariate analysis of variance (PERMANOVA) to identify exposures related to diversity between samples, and analysis of composition of microbiome to examine whether exposures related to diversity were also related to differential abundance of specific operational taxonomic units (OTUs). RESULTS Current farming was positively associated with bacterial diversity in house dust, with or without adjustment for nonfarm exposures related to diversity, including presence of indoor pets, home condition, and season of dust collection. Many taxa exhibited differential abundance related to farming. Some taxa in the phyla Chloroflexi and Verrucomicrobia were associated [false discovery rate (FDR)<0.05] with farming but not with other nonfarm factors. Many taxa correlated with the concentration of house dust of endotoxin, commonly studied as a general marker of exposure to the farming environment. CONCLUSIONS In this farming population, house dust microbiota differed by current farming status. Understanding the determinants of the indoor microbiota is the first step toward understanding potential relationships with health outcomes. https://doi.org/10.1289/EHP3145.
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Affiliation(s)
- Mi Kyeong Lee
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Dept. of Health and Human Services, Research Triangle Park, North Carolina, USA
| | - Megan U Carnes
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Dept. of Health and Human Services, Research Triangle Park, North Carolina, USA
| | - Natasha Butz
- Dept. of Medicine and Microbiome Core Facility, Center for Gastrointestinal Biology and Disease, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - M Andrea Azcarate-Peril
- Dept. of Medicine and Microbiome Core Facility, Center for Gastrointestinal Biology and Disease, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | | | - David M Umbach
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Dept. of Health and Human Services, Research Triangle Park, North Carolina, USA
| | - Peter S Thorne
- Department of Occupational and Environmental Health, University of Iowa, Iowa City, Iowa, USA
| | - Laura E Beane Freeman
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Dept. of Health and Human Services, Rockville, Maryland, USA
| | - Shyamal D Peddada
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Dept. of Health and Human Services, Research Triangle Park, North Carolina, USA
| | - Stephanie J London
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Dept. of Health and Human Services, Research Triangle Park, North Carolina, USA
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Williamson IA, Arnold JW, Samsa LA, Gaynor L, DiSalvo M, Cocchiaro JL, Carroll I, Azcarate-Peril MA, Rawls JF, Allbritton NL, Magness ST. A High-Throughput Organoid Microinjection Platform to Study Gastrointestinal Microbiota and Luminal Physiology. Cell Mol Gastroenterol Hepatol 2018; 6:301-319. [PMID: 30123820 PMCID: PMC6092482 DOI: 10.1016/j.jcmgh.2018.05.004] [Citation(s) in RCA: 139] [Impact Index Per Article: 23.2] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 05/14/2018] [Indexed: 12/16/2022]
Abstract
Background & Aims The human gut microbiota is becoming increasingly recognized as a key factor in homeostasis and disease. The lack of physiologically relevant in vitro models to investigate host-microbe interactions is considered a substantial bottleneck for microbiota research. Organoids represent an attractive model system because they are derived from primary tissues and embody key properties of the native gut lumen; however, access to the organoid lumen for experimental perturbation is challenging. Here, we report the development and validation of a high-throughput organoid microinjection system for cargo delivery to the organoid lumen and high-content sampling. Methods A microinjection platform was engineered using off-the-shelf and 3-dimensional printed components. Microinjection needles were modified for vertical trajectories and reproducible injection volumes. Computer vision (CVis) and microfabricated CellRaft Arrays (Cell Microsystems, Research Triangle Park, NC) were used to increase throughput and enable high-content sampling of mock bacterial communities. Modeling preformed using the COMSOL Multiphysics platform predicted a hypoxic luminal environment that was functionally validated by transplantation of fecal-derived microbial communities and monocultures of a nonsporulating anaerobe. Results CVis identified and logged locations of organoids suitable for injection. Reproducible loads of 0.2 nL could be microinjected into the organoid lumen at approximately 90 organoids/h. CVis analyzed and confirmed retention of injected cargos in approximately 500 organoids over 18 hours and showed the requirement to normalize for organoid growth for accurate assessment of barrier function. CVis analyzed growth dynamics of a mock community of green fluorescent protein- or Discosoma sp. red fluorescent protein-expressing bacteria, which grew within the organoid lumen even in the presence of antibiotics to control media contamination. Complex microbiota communities from fecal samples survived and grew in the colonoid lumen without appreciable changes in complexity. Conclusions High-throughput microinjection into organoids represents a next-generation in vitro approach to investigate gastrointestinal luminal physiology and the gastrointestinal microbiota.
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Key Words
- 2D, 2-dimensional
- 3D, 3-dimensional
- Anaerobic
- Barrier Function
- CAG, chicken beta-actin promoter with CMV enhancer
- CFU, colony-forming unit
- CRA, CellRaft Array
- CVis, computer vision
- EGFP, enhanced green fluorescent protein
- FITC, fluorescein isothiocyanate
- Fecal Microbiota
- GFP, green fluorescent protein
- GI, gastrointestinal
- HF, hydrogen fluoride
- High-Content Sampling
- High-Throughput
- Microinjection
- OUT, operational taxonomic unit
- Organoid
- PBS, phosphate-buffered saline
- PCR, polymerase chain reaction
- QIIME, Quantitative Insights Into Microbial Ecology
- WT, wild-type
- hiPS, Human Induced Pluripotent Stem Cell
- rRNA, ribosomal RNA
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Affiliation(s)
- Ian A. Williamson
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill/North Carolina State University, Chapel Hill, North Carolina
| | - Jason W. Arnold
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Leigh Ann Samsa
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill/North Carolina State University, Chapel Hill, North Carolina
| | - Liam Gaynor
- Graduate Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, Massachusetts
| | - Matthew DiSalvo
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill/North Carolina State University, Chapel Hill, North Carolina
| | - Jordan L. Cocchiaro
- Department of Molecular Genetics and Microbiology Medicine, Duke University, Durham, North Carolina
| | - Ian Carroll
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - M. Andrea Azcarate-Peril
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - John F. Rawls
- Department of Molecular Genetics and Microbiology Medicine, Duke University, Durham, North Carolina
| | - Nancy L. Allbritton
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill/North Carolina State University, Chapel Hill, North Carolina
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Scott T. Magness
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill/North Carolina State University, Chapel Hill, North Carolina
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
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Jones RB, Zhu X, Moan E, Murff HJ, Ness RM, Seidner DL, Sun S, Yu C, Dai Q, Fodor AA, Azcarate-Peril MA, Shrubsole MJ. Inter-niche and inter-individual variation in gut microbial community assessment using stool, rectal swab, and mucosal samples. Sci Rep 2018; 8:4139. [PMID: 29515151 PMCID: PMC5841359 DOI: 10.1038/s41598-018-22408-4] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [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: 10/11/2017] [Accepted: 02/22/2018] [Indexed: 12/21/2022] Open
Abstract
The purpose of this study is to evaluate similarities and differences in gut bacterial measurements and stability in the microbial communities of three different types of samples that could be used to assess different niches of the gut microbiome: rectal swab, stool, and normal rectal mucosa samples. In swab-stool comparisons, there were substantial taxa differences with some taxa varying largely by sample type (e.g. Thermaceae), inter-individual subject variation (e.g. Desulfovibrionaceae), or by both sample type and participant (e.g. Enterobacteriaceae). Comparing all three sample types with whole-genome metagenome shotgun sequencing, swab samples were much closer to stool samples than mucosa samples although all KEGG functional Level 1 and Level 2 pathways were significantly different across all sample types (e.g. transcription and environmental adaptation). However, the individual signature of participants was also observed and was largely stable between two time points. Thus, we found that while the distribution of some taxa was associated with these different sampling techniques, other taxa largely reflected individual differences in the microbial community that were insensitive to sampling technique. There is substantial variability in the assessment of the gut microbial community according to the type of sample.
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Affiliation(s)
- Roshonda B Jones
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Xiangzhu Zhu
- Department of Medicine, Division of Epidemiology, Vanderbilt Epidemiology Center, Vanderbilt University School of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Emili Moan
- Department of Statistics, North Carolina State University, Raleigh, NC, 27695, USA
| | - Harvey J Murff
- Department of Medicine, Division of Epidemiology, Vanderbilt Epidemiology Center, Vanderbilt University School of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Reid M Ness
- Department of Biostatistics, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Douglas L Seidner
- Department of Medicine, Division of Gastroenterology, Hepatology, and Nutrition, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Shan Sun
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Chang Yu
- Department of Biostatistics, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Qi Dai
- Department of Medicine, Division of Epidemiology, Vanderbilt Epidemiology Center, Vanderbilt University School of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Anthony A Fodor
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - M Andrea Azcarate-Peril
- Department of Medicine, and Microbiome Core Facility, School of Medicine, University of North Carolina, Chapel Hill, NC, USA
| | - Martha J Shrubsole
- Department of Medicine, Division of Epidemiology, Vanderbilt Epidemiology Center, Vanderbilt University School of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA.
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Arnold JW, Simpson JB, Roach J, Kwintkiewicz J, Azcarate-Peril MA. Intra-species Genomic and Physiological Variability Impact Stress Resistance in Strains of Probiotic Potential. Front Microbiol 2018; 9:242. [PMID: 29515537 PMCID: PMC5826259 DOI: 10.3389/fmicb.2018.00242] [Citation(s) in RCA: 21] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 01/31/2018] [Indexed: 12/28/2022] Open
Abstract
Large-scale microbiome studies have established that most of the diversity contained in the gastrointestinal tract is represented at the strain level; however, exhaustive genomic and physiological characterization of human isolates is still lacking. With increased use of probiotics as interventions for gastrointestinal disorders, genomic and functional characterization of novel microorganisms becomes essential. In this study, we explored the impact of strain-level genomic variability on bacterial physiology of two novel human Lactobacillus rhamnosus strains (AMC143 and AMC010) of probiotic potential in relation to stress resistance. The strains showed differences with known probiotic strains (L. rhamnosus GG, Lc705, and HN001) at the genomic level, including nucleotide polymorphisms, mutations in non-coding regulatory regions, and rearrangements of genomic architecture. Transcriptomics analysis revealed that gene expression profiles differed between strains when exposed to simulated gastrointestinal stresses, suggesting the presence of unique regulatory systems in each strain. In vitro physiological assays to test resistance to conditions mimicking the gut environment (acid, alkali, and bile stress) showed that growth of L. rhamnosus AMC143 was inhibited upon exposure to alkaline pH, while AMC010 and control strain LGG were unaffected. AMC143 also showed a significant survival advantage compared to the other strains upon bile exposure. Reverse transcription qPCR targeting the bile salt hydrolase gene (bsh) revealed that AMC143 expressed bsh poorly (a consequence of a deletion in the bsh promoter and truncation of bsh gene in AMC143), while AMC010 had significantly higher expression levels than AMC143 or LGG. Insertional inactivation of the bsh gene in AMC010 suggested that bsh could be detrimental to bacterial survival during bile stress. Together, these findings show that coupling of classical microbiology with functional genomics methods for the characterization of bacterial strains is critical for the development of novel probiotics, as variability between strains can dramatically alter bacterial physiology and functionality.
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Affiliation(s)
- Jason W. Arnold
- Division of Gastroenterology and Hepatology, Department of Medicine, Microbiome Core Facility, Center for Gastrointestinal Biology and Disease, School of Medicine, University of North Carolina, Chapel Hill, NC, United States
| | - Joshua B. Simpson
- Department of Chemistry, College of Arts and Sciences, University of North Carolina, Chapel Hill, NC, United States
| | - Jeffrey Roach
- Research Computing, University of North Carolina, Chapel Hill, NC, United States
| | - Jakub Kwintkiewicz
- Division of Gastroenterology and Hepatology, Department of Medicine, Microbiome Core Facility, Center for Gastrointestinal Biology and Disease, School of Medicine, University of North Carolina, Chapel Hill, NC, United States
| | - M. Andrea Azcarate-Peril
- Division of Gastroenterology and Hepatology, Department of Medicine, Microbiome Core Facility, Center for Gastrointestinal Biology and Disease, School of Medicine, University of North Carolina, Chapel Hill, NC, United States
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Carlson AL, Xia K, Azcarate-Peril MA, Goldman BD, Ahn M, Styner MA, Thompson AL, Geng X, Gilmore JH, Knickmeyer RC. Infant Gut Microbiome Associated With Cognitive Development. Biol Psychiatry 2018; 83:148-159. [PMID: 28793975 PMCID: PMC5724966 DOI: 10.1016/j.biopsych.2017.06.021] [Citation(s) in RCA: 290] [Impact Index Per Article: 48.3] [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: 11/21/2016] [Revised: 05/31/2017] [Accepted: 06/12/2017] [Indexed: 12/22/2022]
Abstract
BACKGROUND Studies in rodents provide compelling evidence that microorganisms inhabiting the gut influence neurodevelopment. In particular, experimental manipulations that alter intestinal microbiota impact exploratory and communicative behaviors and cognitive performance. In humans, the first years of life are a dynamic time in gut colonization and brain development, but little is known about the relationship between these two processes. METHODS We tested whether microbial composition at 1 year of age is associated with cognitive outcomes using the Mullen Scales of Early Learning and with global and regional brain volumes using structural magnetic resonance imaging at 1 and 2 years of age. Fecal samples were collected from 89 typically developing 1-year-olds. 16S ribosomal RNA amplicon sequencing was used for identification and relative quantification of bacterial taxa. RESULTS Cluster analysis identified 3 groups of infants defined by their bacterial composition. Mullen scores at 2 years of age differed significantly between clusters. In addition, higher alpha diversity was associated with lower scores on the overall composite score, visual reception scale, and expressive language scale at 2 years of age. Exploratory analyses of neuroimaging data suggest the gut microbiome has minimal effects on regional brain volumes at 1 and 2 years of age. CONCLUSIONS This is the first study to demonstrate associations between the gut microbiota and cognition in human infants. As such, it represents an essential first step in translating animal data into the clinic.
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Affiliation(s)
| | - Kai Xia
- Department of Psychiatry, University of North Carolina, Chapel Hill, NC, USA
| | - M. Andrea Azcarate-Peril
- Department of Medicine, University of North Carolina, Chapel Hill, NC, USA,Microbiome Core Facility, University of North Carolina, Chapel Hill, NC, USA
| | - Barbara D. Goldman
- Department of Psychology and Neuroscience, University of North Carolina, Chapel Hill, NC, USA,Frank Porter Graham Child Development Institute, University of North Carolina, Chapel Hill, NC, USA
| | - Mihye Ahn
- Department of Mathematics and Statistics, University of Nevada, Reno, NV, USA
| | - Martin A. Styner
- Department of Psychiatry, University of North Carolina, Chapel Hill, NC, USA,Department of Computer Science, University of North Carolina, Chapel Hill, NC, USA
| | - Amanda L. Thompson
- Department of Anthropology, University of North Carolina, Chapel Hill, NC, USA,Department of Nutrition, University of North Carolina, Chapel Hill, NC, USA
| | - Xiujuan Geng
- Department of Psychology Lab of Neuropsychology and Lab of Social Cognitive Affective Neuroscience, University of Hong Kong, Hong Kong,State Key Lab of Brain and Cognitive Sciences, University of Hong Kong, Hong Kong
| | - John H. Gilmore
- Department of Psychiatry, University of North Carolina, Chapel Hill, NC, USA
| | - Rebecca C. Knickmeyer
- Department of Psychiatry, University of North Carolina, Chapel Hill, NC, USA,Correspondence to: Rebecca C. Knickmeyer, Department of Psychiatry, 343 Medical Wings C, Campus Box #7160, University of North Carolina, Chapel Hill NC 27599-7160,
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Allali I, Arnold JW, Roach J, Cadenas MB, Butz N, Hassan HM, Koci M, Ballou A, Mendoza M, Ali R, Azcarate-Peril MA. A comparison of sequencing platforms and bioinformatics pipelines for compositional analysis of the gut microbiome. BMC Microbiol 2017; 17:194. [PMID: 28903732 PMCID: PMC5598039 DOI: 10.1186/s12866-017-1101-8] [Citation(s) in RCA: 149] [Impact Index Per Article: 21.3] [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: 11/06/2016] [Accepted: 08/29/2017] [Indexed: 12/16/2022] Open
Abstract
Background Advancements in Next Generation Sequencing (NGS) technologies regarding throughput, read length and accuracy had a major impact on microbiome research by significantly improving 16S rRNA amplicon sequencing. As rapid improvements in sequencing platforms and new data analysis pipelines are introduced, it is essential to evaluate their capabilities in specific applications. The aim of this study was to assess whether the same project-specific biological conclusions regarding microbiome composition could be reached using different sequencing platforms and bioinformatics pipelines. Results Chicken cecum microbiome was analyzed by 16S rRNA amplicon sequencing using Illumina MiSeq, Ion Torrent PGM, and Roche 454 GS FLX Titanium platforms, with standard and modified protocols for library preparation. We labeled the bioinformatics pipelines included in our analysis QIIME1 and QIIME2 (de novo OTU picking [not to be confused with QIIME version 2 commonly referred to as QIIME2]), QIIME3 and QIIME4 (open reference OTU picking), UPARSE1 and UPARSE2 (each pair differs only in the use of chimera depletion methods), and DADA2 (for Illumina data only). GS FLX+ yielded the longest reads and highest quality scores, while MiSeq generated the largest number of reads after quality filtering. Declines in quality scores were observed starting at bases 150–199 for GS FLX+ and bases 90–99 for MiSeq. Scores were stable for PGM-generated data. Overall microbiome compositional profiles were comparable between platforms; however, average relative abundance of specific taxa varied depending on sequencing platform, library preparation method, and bioinformatics analysis. Specifically, QIIME with de novo OTU picking yielded the highest number of unique species and alpha diversity was reduced with UPARSE and DADA2 compared to QIIME. Conclusions The three platforms compared in this study were capable of discriminating samples by treatment, despite differences in diversity and abundance, leading to similar biological conclusions. Our results demonstrate that while there were differences in depth of coverage and phylogenetic diversity, all workflows revealed comparable treatment effects on microbial diversity. To increase reproducibility and reliability and to retain consistency between similar studies, it is important to consider the impact on data quality and relative abundance of taxa when selecting NGS platforms and analysis tools for microbiome studies. Electronic supplementary material The online version of this article (10.1186/s12866-017-1101-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Imane Allali
- Department of Medicine, Division of Gastroenterology and Hepatology, and Microbiome Core Facility, Center for Gastrointestinal Biology and Disease, School of Medicine, University of North Carolina, Campus Box 7555, 332 Isaac Taylor Hall, Chapel Hill, NC, 27599-7545, USA.,Laboratory of Biochemistry & Immunology, Faculty of Sciences, Mohammed V University, Rabat, Morocco
| | - Jason W Arnold
- Department of Medicine, Division of Gastroenterology and Hepatology, and Microbiome Core Facility, Center for Gastrointestinal Biology and Disease, School of Medicine, University of North Carolina, Campus Box 7555, 332 Isaac Taylor Hall, Chapel Hill, NC, 27599-7545, USA
| | - Jeffrey Roach
- Research Computing, University of North Carolina, Chapel Hill, NC, USA
| | - Maria Belen Cadenas
- Department of Medicine, Division of Gastroenterology and Hepatology, and Microbiome Core Facility, Center for Gastrointestinal Biology and Disease, School of Medicine, University of North Carolina, Campus Box 7555, 332 Isaac Taylor Hall, Chapel Hill, NC, 27599-7545, USA
| | - Natasha Butz
- Department of Medicine, Division of Gastroenterology and Hepatology, and Microbiome Core Facility, Center for Gastrointestinal Biology and Disease, School of Medicine, University of North Carolina, Campus Box 7555, 332 Isaac Taylor Hall, Chapel Hill, NC, 27599-7545, USA
| | - Hosni M Hassan
- Department of Poultry Science, North Carolina State University, Raleigh, NC, USA
| | - Matthew Koci
- Department of Poultry Science, North Carolina State University, Raleigh, NC, USA
| | - Anne Ballou
- Department of Poultry Science, North Carolina State University, Raleigh, NC, USA
| | - Mary Mendoza
- Department of Poultry Science, North Carolina State University, Raleigh, NC, USA
| | - Rizwana Ali
- Department of Poultry Science, North Carolina State University, Raleigh, NC, USA
| | - M Andrea Azcarate-Peril
- Department of Medicine, Division of Gastroenterology and Hepatology, and Microbiome Core Facility, Center for Gastrointestinal Biology and Disease, School of Medicine, University of North Carolina, Campus Box 7555, 332 Isaac Taylor Hall, Chapel Hill, NC, 27599-7545, USA.
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