1
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Pereira GV, Boudaud M, Wolter M, Alexander C, De Sciscio A, Grant ET, Trindade BC, Pudlo NA, Singh S, Campbell A, Shan M, Zhang L, Yang Q, Willieme S, Kim K, Denike-Duval T, Fuentes J, Bleich A, Schmidt TM, Kennedy L, Lyssiotis CA, Chen GY, Eaton KA, Desai MS, Martens EC. Opposing diet, microbiome, and metabolite mechanisms regulate inflammatory bowel disease in a genetically susceptible host. Cell Host Microbe 2024; 32:527-542.e9. [PMID: 38513656 DOI: 10.1016/j.chom.2024.03.001] [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: 06/30/2023] [Revised: 12/18/2023] [Accepted: 03/01/2024] [Indexed: 03/23/2024]
Abstract
Inflammatory bowel diseases (IBDs) are chronic conditions characterized by periods of spontaneous intestinal inflammation and are increasing in industrialized populations. Combined with host genetics, diet and gut bacteria are thought to contribute prominently to IBDs, but mechanisms are still emerging. In mice lacking the IBD-associated cytokine, interleukin-10, we show that a fiber-deprived gut microbiota promotes the deterioration of colonic mucus, leading to lethal colitis. Inflammation starts with the expansion of natural killer cells and altered immunoglobulin-A coating of some bacteria. Lethal colitis is then driven by Th1 immune responses to increased activities of mucin-degrading bacteria that cause inflammation first in regions with thinner mucus. A fiber-free exclusive enteral nutrition diet also induces mucus erosion but inhibits inflammation by simultaneously increasing an anti-inflammatory bacterial metabolite, isobutyrate. Our findings underscore the importance of focusing on microbial functions-not taxa-contributing to IBDs and that some diet-mediated functions can oppose those that promote disease.
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Affiliation(s)
| | - Marie Boudaud
- Department of Infection and Immunity, Luxembourg Institute of Health, 4354 Esch-sur-Alzette, Luxembourg
| | - Mathis Wolter
- Department of Infection and Immunity, Luxembourg Institute of Health, 4354 Esch-sur-Alzette, Luxembourg; Faculty of Science, Technology and Medicine, University of Luxembourg, 4365 Esch-sur-Alzette, Luxembourg
| | - Celeste Alexander
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Alessandro De Sciscio
- Department of Infection and Immunity, Luxembourg Institute of Health, 4354 Esch-sur-Alzette, Luxembourg
| | - Erica T Grant
- Department of Infection and Immunity, Luxembourg Institute of Health, 4354 Esch-sur-Alzette, Luxembourg; Faculty of Science, Technology and Medicine, University of Luxembourg, 4365 Esch-sur-Alzette, Luxembourg
| | | | - Nicholas A Pudlo
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Shaleni Singh
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Austin Campbell
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Mengrou Shan
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA; Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
| | - Li Zhang
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA; Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
| | - Qinnan Yang
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Stéphanie Willieme
- Department of Infection and Immunity, Luxembourg Institute of Health, 4354 Esch-sur-Alzette, Luxembourg
| | - Kwi Kim
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Trisha Denike-Duval
- Unit for Laboratory Animal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Jaime Fuentes
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - André Bleich
- Institute for Laboratory Animal Science, Hanover Medical School, Hanover, Germany
| | - Thomas M Schmidt
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA; Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA; Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | - Lucy Kennedy
- Unit for Laboratory Animal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Costas A Lyssiotis
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA; Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
| | - Grace Y Chen
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Kathryn A Eaton
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Mahesh S Desai
- Department of Infection and Immunity, Luxembourg Institute of Health, 4354 Esch-sur-Alzette, Luxembourg; Odense Research Center for Anaphylaxis, Department of Dermatology and Allergy Center, Odense University Hospital, University of Southern Denmark, Odense, Denmark.
| | - Eric C Martens
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA.
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2
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Kuffa P, Pickard JM, Campbell A, Yamashita M, Schaus SR, Martens EC, Schmidt TM, Inohara N, Núñez G, Caruso R. Fiber-deficient diet inhibits colitis through the regulation of the niche and metabolism of a gut pathobiont. Cell Host Microbe 2023; 31:2007-2022.e12. [PMID: 37967555 PMCID: PMC10842462 DOI: 10.1016/j.chom.2023.10.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 09/26/2023] [Accepted: 10/18/2023] [Indexed: 11/17/2023]
Abstract
Exclusive enteral nutrition (EEN) with fiber-free diets is an effective steroid-sparing treatment to induce clinical remission in children with Crohn's disease (CD). However, the mechanism underlying the beneficial effects of EEN remains obscure. Using a model of microbiota-dependent colitis with the hallmarks of CD, we find that the administration of a fiber-free diet prevents the development of colitis and inhibits intestinal inflammation in colitic animals. Remarkably, fiber-free diet alters the intestinal localization of Mucispirillum schaedleri, a mucus-dwelling pathobiont, which is required for triggering disease. Mechanistically, the absence of dietary fiber reduces nutrient availability and impairs the dissimilatory nitrate reduction to ammonia (DNRA) metabolic pathway of Mucispirillum, leading to its exclusion from the mucus layer and disease remission. Thus, appropriate localization of the specific pathobiont in the mucus layer is critical for disease development, which is disrupted by fiber exclusion. These results suggest strategies to treat CD by targeting the intestinal niche and metabolism of disease-causing microbes.
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Affiliation(s)
- Peter Kuffa
- Department of Pathology and Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Joseph M Pickard
- Department of Pathology and Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Austin Campbell
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Misa Yamashita
- Department of Public Health and Preventive Medicine, Yamaguchi University Graduate School of Medicine, Ube, Yamaguchi 755-8505, Japan
| | - Sadie R Schaus
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Eric C Martens
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Thomas M Schmidt
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Naohiro Inohara
- Department of Pathology and Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Gabriel Núñez
- Department of Pathology and Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Roberta Caruso
- Department of Pathology and Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
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3
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Medeiros MCD, The S, Bellile E, Russo N, Schmitd L, Danella E, Singh P, Banerjee R, Bassis C, Murphy GR, Sartor MA, Lombaert I, Schmidt TM, Eisbruch A, Murdoch-Kinch CA, Rozek L, Wolf GT, Li G, Chen GY, D'Silva NJ. Salivary microbiome changes distinguish response to chemoradiotherapy in patients with oral cancer. Microbiome 2023; 11:268. [PMID: 38037123 PMCID: PMC10687843 DOI: 10.1186/s40168-023-01677-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 09/26/2023] [Indexed: 12/02/2023]
Abstract
BACKGROUND Oral squamous cell carcinoma (SCC) is associated with oral microbial dysbiosis. In this unique study, we compared pre- to post-treatment salivary microbiome in patients with SCC by 16S rRNA gene sequencing and examined how microbiome changes correlated with the expression of an anti-microbial protein. RESULTS Treatment of SCC was associated with a reduction in overall bacterial richness and diversity. There were significant changes in the microbial community structure, including a decrease in the abundance of Porphyromonaceae and Prevotellaceae and an increase in Lactobacillaceae. There were also significant changes in the microbial community structure before and after treatment with chemoradiotherapy, but not with surgery alone. In patients treated with chemoradiotherapy alone, several bacterial populations were differentially abundant between responders and non-responders before and after therapy. Microbiome changes were associated with a change in the expression of DMBT1, an anti-microbial protein in human saliva. Additionally, we found that salivary DMBT1, which increases after treatment, could serve as a post-treatment salivary biomarker that links to microbial changes. Specifically, post-treatment increases in human salivary DMBT1 correlated with increased abundance of Gemella spp., Pasteurellaceae spp., Lactobacillus spp., and Oribacterium spp. This is the first longitudinal study to investigate treatment-associated changes (chemoradiotherapy and surgery) in the oral microbiome in patients with SCC along with changes in expression of an anti-microbial protein in saliva. CONCLUSIONS The composition of the oral microbiota may predict treatment responses; salivary DMBT1 may have a role in modulating the oral microbiome in patients with SCC. After completion of treatment, 6 months after diagnosis, patients had a less diverse and less rich oral microbiome. Leptotrichia was a highly prevalent bacteria genus associated with disease. Expression of DMBT1 was higher after treatment and associated with microbiome changes, the most prominent genus being Gemella Video Abstract.
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Affiliation(s)
- Marcell Costa de Medeiros
- Periodontics and Oral Medicine, University of Michigan School of Dentistry, 1011 North University Ave, Room G018, Ann Arbor, MI, 48109-1078, USA
| | - Stephanie The
- Cancer Data Science Shared Resource, University of Michigan Medical School, 1500 E. Medical Center Dr, Ann Arbor, MI, USA
| | - Emily Bellile
- Cancer Data Science Shared Resource, University of Michigan Medical School, 1500 E. Medical Center Dr, Ann Arbor, MI, USA
| | - Nickole Russo
- Periodontics and Oral Medicine, University of Michigan School of Dentistry, 1011 North University Ave, Room G018, Ann Arbor, MI, 48109-1078, USA
| | - Ligia Schmitd
- Periodontics and Oral Medicine, University of Michigan School of Dentistry, 1011 North University Ave, Room G018, Ann Arbor, MI, 48109-1078, USA
| | - Erika Danella
- Periodontics and Oral Medicine, University of Michigan School of Dentistry, 1011 North University Ave, Room G018, Ann Arbor, MI, 48109-1078, USA
| | - Priyanka Singh
- Periodontics and Oral Medicine, University of Michigan School of Dentistry, 1011 North University Ave, Room G018, Ann Arbor, MI, 48109-1078, USA
| | - Rajat Banerjee
- Periodontics and Oral Medicine, University of Michigan School of Dentistry, 1011 North University Ave, Room G018, Ann Arbor, MI, 48109-1078, USA
| | - Christine Bassis
- Internal Medicine, University of Michigan Medical School, 1500 East Medical Center Drive, Ann Arbor, MI, 331248109, USA
| | - George R Murphy
- Biologic and Materials Sciences and Prosthodontics, University of Michigan School of Dentistry, 1011 N. University Ave, Ann Arbor, MI, USA
- Biointerfaces Institute, Ann Arbor, MI, USA
| | - Maureen A Sartor
- Computational Medicine and Bioinformatics, University of Michigan Medical School, 1500 E. Medical Center Dr, Ann Arbor, MI, USA
| | - Isabelle Lombaert
- Biologic and Materials Sciences and Prosthodontics, University of Michigan School of Dentistry, 1011 N. University Ave, Ann Arbor, MI, USA
- Biointerfaces Institute, Ann Arbor, MI, USA
| | - Thomas M Schmidt
- Microbiology and Immunology, University of Michigan Medical School, 1500 E. Medical Center Dr, Ann Arbor, MI, USA
| | - Avi Eisbruch
- Radiation Oncology, University of Michigan Medical School, 1500 E. Medical Center Dr, Ann Arbor, MI, USA
| | - Carol Anne Murdoch-Kinch
- Oral Pathology, Medicine and Radiology, Indiana University School of Dentistry, 1011 North Michigan St, Indianapolis, IN, USA
| | - Laura Rozek
- Environmental Health Sciences, University of Michigan Medical School, 1500 E. Medical Center Dr, Ann Arbor, MI, USA
| | - Gregory T Wolf
- Otolaryngology, University of Michigan Medical School, 1500 E. Medical Center Dr, Ann Arbor, MI, USA
| | - Gen Li
- Biostatistics, University of Michigan School of Public Health, University of Michigan Medical School, 1500 E. Medical Center Dr, Ann Arbor, MI, USA
| | - Grace Y Chen
- Internal Medicine, University of Michigan Medical School, 1500 East Medical Center Drive, Ann Arbor, MI, 331248109, USA.
| | - Nisha J D'Silva
- Periodontics and Oral Medicine, University of Michigan School of Dentistry, 1011 North University Ave, Room G018, Ann Arbor, MI, 48109-1078, USA.
- Pathology, University of Michigan Medical School, 1500 E. Medical Center Dr, Ann Arbor, MI, USA.
- Rogel Cancer Center, Ann Arbor, MI, USA.
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4
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Riwes MM, Golob JL, Magenau J, Shan M, Dick G, Braun T, Schmidt TM, Pawarode A, Anand S, Ghosh M, Maciejewski J, King D, Choi S, Yanik G, Geer M, Hillman E, Lyssiotis CA, Tewari M, Reddy P. Feasibility of a dietary intervention to modify gut microbial metabolism in patients with hematopoietic stem cell transplantation. Nat Med 2023; 29:2805-2813. [PMID: 37857710 PMCID: PMC10667101 DOI: 10.1038/s41591-023-02587-y] [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: 03/30/2023] [Accepted: 09/12/2023] [Indexed: 10/21/2023]
Abstract
Evaluation of the impact of dietary intervention on gastrointestinal microbiota and metabolites after allogeneic hematopoietic stem cell transplantation (HCT) is lacking. We conducted a feasibility study as the first of a two-phase trial. Ten adults received resistant potato starch (RPS) daily from day -7 to day 100. The primary objective was to test the feasibility of RPS and its effect on intestinal microbiome and metabolites, including the short-chain fatty acid butyrate. Feasibility met the preset goal of 60% or more, adhering to 70% or more doses; fecal butyrate levels were significantly higher when participants were on RPS than when they were not (P < 0.0001). An exploratory objective was to evaluate plasma metabolites. We observed longitudinal changes in plasma metabolites compared to baseline, which were independent of RPS (P < 0.0001). However, in recipients of RPS, the dominant plasma metabolites were more stable compared to historical controls with significant difference at engraftment (P < 0.05). These results indicate that RPS in recipients of allogeneic HCT is feasible; in this study, it was associated with significant alterations in intestinal and plasma metabolites. A phase 2 trial examining the effect of RPS on graft-versus-host disease in recipients of allogeneic HCT is underway. ClinicalTrials.gov registration: NCT02763033 .
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Affiliation(s)
- Mary M Riwes
- Department of Internal Medicine, Division of Hematology and Oncology, University of Michigan, Rogel Cancer Center, Ann Arbor, MI, USA.
| | - Jonathan L Golob
- Department of Internal Medicine, Division of Infectious Disease, University of Michigan, Ann Arbor, MI, USA
| | - John Magenau
- Department of Internal Medicine, Division of Hematology and Oncology, University of Michigan, Rogel Cancer Center, Ann Arbor, MI, USA
| | - Mengrou Shan
- Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
| | - Gregory Dick
- Department of Earth & Environmental Sciences, University of Michigan, Ann Arbor, MI, USA
| | - Thomas Braun
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
| | - Thomas M Schmidt
- Department of Internal Medicine, Division of Infectious Disease, University of Michigan, Ann Arbor, MI, USA
| | - Attaphol Pawarode
- Department of Internal Medicine, Division of Hematology and Oncology, University of Michigan, Rogel Cancer Center, Ann Arbor, MI, USA
| | - Sarah Anand
- Department of Internal Medicine, Division of Hematology and Oncology, University of Michigan, Rogel Cancer Center, Ann Arbor, MI, USA
| | - Monalisa Ghosh
- Department of Internal Medicine, Division of Hematology and Oncology, University of Michigan, Rogel Cancer Center, Ann Arbor, MI, USA
| | - John Maciejewski
- Department of Internal Medicine, Division of Hematology and Oncology, University of Michigan, Rogel Cancer Center, Ann Arbor, MI, USA
| | - Darren King
- Department of Internal Medicine, Division of Hematology and Oncology, University of Michigan, Rogel Cancer Center, Ann Arbor, MI, USA
| | - Sung Choi
- Department of Internal Medicine, Division of Hematology and Oncology, University of Michigan, Rogel Cancer Center, Ann Arbor, MI, USA
| | - Gregory Yanik
- Department of Internal Medicine, Division of Hematology and Oncology, University of Michigan, Rogel Cancer Center, Ann Arbor, MI, USA
| | - Marcus Geer
- Department of Internal Medicine, Division of Hematology and Oncology, University of Michigan, Rogel Cancer Center, Ann Arbor, MI, USA
| | - Ethan Hillman
- Department of Internal Medicine, Division of Infectious Disease, University of Michigan, Ann Arbor, MI, USA
| | - Costas A Lyssiotis
- Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
| | - Muneesh Tewari
- Department of Internal Medicine, Division of Hematology and Oncology, University of Michigan, Rogel Cancer Center, Ann Arbor, MI, USA
| | - Pavan Reddy
- Department of Internal Medicine, Division of Hematology and Oncology, University of Michigan, Rogel Cancer Center, Ann Arbor, MI, USA.
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA.
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5
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Campbell A, Gdanetz K, Schmidt AW, Schmidt TM. H 2 generated by fermentation in the human gut microbiome influences metabolism and competitive fitness of gut butyrate producers. Microbiome 2023; 11:133. [PMID: 37322527 PMCID: PMC10268494 DOI: 10.1186/s40168-023-01565-3] [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] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 05/03/2023] [Indexed: 06/17/2023]
Abstract
BACKGROUND Hydrogen gas (H2) is a common product of carbohydrate fermentation in the human gut microbiome and its accumulation can modulate fermentation. Concentrations of colonic H2 vary between individuals, raising the possibility that H2 concentration may be an important factor differentiating individual microbiomes and their metabolites. Butyrate-producing bacteria (butyrogens) in the human gut usually produce some combination of butyrate, lactate, formate, acetate, and H2 in branched fermentation pathways to manage reducing power generated during the oxidation of glucose to acetate and carbon dioxide. We predicted that a high concentration of intestinal H2 would favor the production of butyrate, lactate, and formate by the butyrogens at the expense of acetate, H2, and CO2. Regulation of butyrate production in the human gut is of particular interest due to its role as a mediator of colonic health through anti-inflammatory and anti-carcinogenic properties. RESULTS For butyrogens that contained a hydrogenase, growth under a high H2 atmosphere or in the presence of the hydrogenase inhibitor CO stimulated production of organic fermentation products that accommodate reducing power generated during glycolysis, specifically butyrate, lactate, and formate. Also as expected, production of fermentation products in cultures of Faecalibacterium prausnitzii strain A2-165, which does not contain a hydrogenase, was unaffected by H2 or CO. In a synthetic gut microbial community, addition of the H2-consuming human gut methanogen Methanobrevibacter smithii decreased butyrate production alongside H2 concentration. Consistent with this observation, M. smithii metabolic activity in a large human cohort was associated with decreased fecal butyrate, but only during consumption of a resistant starch dietary supplement, suggesting the effect may be most prominent when H2 production in the gut is especially high. Addition of M. smithii to the synthetic communities also facilitated the growth of E. rectale, resulting in decreased relative competitive fitness of F. prausnitzii. CONCLUSIONS H2 is a regulator of fermentation in the human gut microbiome. In particular, high H2 concentration stimulates production of the anti-inflammatory metabolite butyrate. By consuming H2, gut methanogenesis can decrease butyrate production. These shifts in butyrate production may also impact the competitive fitness of butyrate producers in the gut microbiome. Video Abstract.
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Affiliation(s)
- Austin Campbell
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Kristi Gdanetz
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI, 48824, USA
| | - Alexander W Schmidt
- Department of Internal Medicine, Division of Infectious Diseases, University of Michigan, MI, 48109, Ann Arbor, USA
| | - Thomas M Schmidt
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, 48109, USA.
- Department of Ecology & Evolutionary Biology, University of Michigan, MI, 48109, Ann Arbor, USA.
- Department of Internal Medicine, Division of Infectious Diseases, University of Michigan, MI, 48109, Ann Arbor, USA.
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6
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Pereira GV, Boudaud M, Wolter M, Alexander C, De Sciscio A, Grant ET, Trindade BC, Pudlo NA, Singh S, Campbell A, Shan M, Zhang L, Willieme S, Kim K, Denike-Duval T, Bleich A, Schmidt TM, Kennedy L, Lyssiotis CA, Chen GY, Eaton KA, Desai MS, Martens EC. Unravelling specific diet and gut microbial contributions to inflammatory bowel disease. Res Sq 2023:rs.3.rs-2518251. [PMID: 36993463 PMCID: PMC10055531 DOI: 10.21203/rs.3.rs-2518251/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Inflammatory bowel disease (IBD) is a chronic condition characterized by periods of spontaneous intestinal inflammation and is increasing in industrialized populations. Combined with host genetic predisposition, diet and gut bacteria are thought to be prominent features contributing to IBD, but little is known about the precise mechanisms involved. Here, we show that low dietary fiber promotes bacterial erosion of protective colonic mucus, leading to lethal colitis in mice lacking the IBD-associated cytokine, interleukin-10. Diet-induced inflammation is driven by mucin-degrading bacteria-mediated Th1 immune responses and is preceded by expansion of natural killer T cells and reduced immunoglobulin A coating of some bacteria. Surprisingly, an exclusive enteral nutrition diet, also lacking dietary fiber, reduced disease by increasing bacterial production of isobutyrate, which is dependent on the presence of a specific bacterial species, Eubacterium rectale. Our results illuminate a mechanistic framework using gnotobiotic mice to unravel the complex web of diet, host and microbial factors that influence IBD.
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Affiliation(s)
| | - Marie Boudaud
- Department of Infection and Immunity, Luxembourg Institute of Health, 4354 Esch-sur-Alzette, Luxembourg
| | - Mathis Wolter
- Department of Infection and Immunity, Luxembourg Institute of Health, 4354 Esch-sur-Alzette, Luxembourg
- Faculty of Science, Technology and Medicine, University of Luxembourg, 4365 Esch-sur-Alzette, Luxembourg
| | - Celeste Alexander
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Alessandro De Sciscio
- Department of Infection and Immunity, Luxembourg Institute of Health, 4354 Esch-sur-Alzette, Luxembourg
| | - Erica. T. Grant
- Department of Infection and Immunity, Luxembourg Institute of Health, 4354 Esch-sur-Alzette, Luxembourg
- Faculty of Science, Technology and Medicine, University of Luxembourg, 4365 Esch-sur-Alzette, Luxembourg
| | | | - Nicholas A. Pudlo
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Shaleni Singh
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Austin Campbell
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Mengrou Shan
- Dept. of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
- Dept. of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, Michigan, USA
| | - Li Zhang
- Dept. of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
- Dept. of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, Michigan, USA
| | - Stéphanie Willieme
- Department of Infection and Immunity, Luxembourg Institute of Health, 4354 Esch-sur-Alzette, Luxembourg
| | - Kwi Kim
- Dept. of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Trisha Denike-Duval
- Unit for Laboratory Animal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - André Bleich
- Institute for Laboratory Animal Science, Hanover Medical School, Hanover, Germany
| | - Thomas M. Schmidt
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
- Dept. of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
- Dept. of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Lucy Kennedy
- Unit for Laboratory Animal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Costas A. Lyssiotis
- Dept. of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
- Dept. of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, Michigan, USA
| | - Grace Y. Chen
- Dept. of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Kathryn A. Eaton
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Mahesh S. Desai
- Department of Infection and Immunity, Luxembourg Institute of Health, 4354 Esch-sur-Alzette, Luxembourg
- Odense Research Center for Anaphylaxis, Department of Dermatology and Allergy Center, Odense University Hospital, University of Southern Denmark, 5000 Odense, Denmark
| | - Eric C. Martens
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
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7
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Sugihara K, Kitamoto S, Saraithong P, Nagao-Kitamoto H, Hoostal M, McCarthy C, Rosevelt A, Muraleedharan CK, Gillilland MG, Imai J, Omi M, Bishu S, Kao JY, Alteri CJ, Barnich N, Schmidt TM, Nusrat A, Inohara N, Golob JL, Kamada N. Mucolytic bacteria license pathobionts to acquire host-derived nutrients during dietary nutrient restriction. Cell Rep 2022; 40:111093. [PMID: 35858565 PMCID: PMC10903618 DOI: 10.1016/j.celrep.2022.111093] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 04/26/2022] [Accepted: 06/21/2022] [Indexed: 12/26/2022] Open
Abstract
Pathobionts employ unique metabolic adaptation mechanisms to maximize their growth in disease conditions. Adherent-invasive Escherichia coli (AIEC), a pathobiont enriched in the gut mucosa of patients with inflammatory bowel disease (IBD), utilizes diet-derived L-serine to adapt to the inflamed gut. Therefore, the restriction of dietary L-serine starves AIEC and limits its fitness advantage. Here, we find that AIEC can overcome this nutrient limitation by switching the nutrient source from the diet to the host cells in the presence of mucolytic bacteria. During diet-derived L-serine restriction, the mucolytic symbiont Akkermansia muciniphila promotes the encroachment of AIEC to the epithelial niche by degrading the mucus layer. In the epithelial niche, AIEC acquires L-serine from the colonic epithelium and thus proliferates. Our work suggests that the indirect metabolic network between pathobionts and commensal symbionts enables pathobionts to overcome nutritional restriction and thrive in the gut.
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Affiliation(s)
- Kohei Sugihara
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Sho Kitamoto
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Prakaimuk Saraithong
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Hiroko Nagao-Kitamoto
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Matthew Hoostal
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Caroline McCarthy
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Alexandra Rosevelt
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | | | - Merritt G Gillilland
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Jin Imai
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Maiko Omi
- Department of Biologic and Materials Sciences and Prosthodontics, University of Michigan School of Dentistry, Ann Arbor, MI, USA
| | - Shrinivas Bishu
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - John Y Kao
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | | | - Nicolas Barnich
- M2iSH, UMR1071 Inserm/University Clermont Auvergne, Clermont-Ferrand, France
| | - Thomas M Schmidt
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Asma Nusrat
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Naohiro Inohara
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Jonathan L Golob
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Nobuhiko Kamada
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA; WPI Immunology Frontier Research Center, Osaka University, Suita, Osaka, Japan.
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8
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Schmidt TM. Stitching together a healthy gut microbiome with fiber. Cell Host Microbe 2022; 30:762-763. [PMID: 35679822 DOI: 10.1016/j.chom.2022.05.007] [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
Inter-individual variability in the gut microbiome confounds efforts to understand host responses to dietary fiber. In this issue of Cell Host & Microbe, Lancaster et al. report individual and generalized host and microbiome responses in an interventional study of fiber supplements, motivating consideration of an alternative classification of fiber.
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Affiliation(s)
- Thomas M Schmidt
- Departments of Internal Medicine and Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA.
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9
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Ostrowski MP, La Rosa SL, Kunath BJ, Robertson A, Pereira G, Hagen LH, Varghese NJ, Qiu L, Yao T, Flint G, Li J, McDonald SP, Buttner D, Pudlo NA, Schnizlein MK, Young VB, Brumer H, Schmidt TM, Terrapon N, Lombard V, Henrissat B, Hamaker B, Eloe-Fadrosh EA, Tripathi A, Pope PB, Martens EC. Mechanistic insights into consumption of the food additive xanthan gum by the human gut microbiota. Nat Microbiol 2022; 7:556-569. [PMID: 35365790 DOI: 10.1038/s41564-022-01093-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 02/24/2022] [Indexed: 12/13/2022]
Abstract
Processed foods often include food additives such as xanthan gum, a complex polysaccharide with unique rheological properties, that has established widespread use as a stabilizer and thickening agent. Xanthan gum's chemical structure is distinct from those of host and dietary polysaccharides that are more commonly expected to transit the gastrointestinal tract, and little is known about its direct interaction with the gut microbiota, which plays a central role in digestion of other dietary fibre polysaccharides. Here we show that the ability to digest xanthan gum is common in human gut microbiomes from industrialized countries and appears contingent on a single uncultured bacterium in the family Ruminococcaceae. Our data reveal that this primary degrader cleaves the xanthan gum backbone before processing the released oligosaccharides using additional enzymes. Some individuals harbour Bacteroides intestinalis that is incapable of consuming polymeric xanthan gum but grows on oligosaccharide products generated by the Ruminococcaceae. Feeding xanthan gum to germfree mice colonized with a human microbiota containing the uncultured Ruminococcaceae supports the idea that the additive xanthan gum can drive expansion of the primary degrader Ruminococcaceae, along with exogenously introduced B. intestinalis. Our work demonstrates the existence of a potential xanthan gum food chain involving at least two members of different phyla of gut bacteria and provides an initial framework for understanding how widespread consumption of a recently introduced food additive influences human microbiomes.
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Affiliation(s)
- Matthew P Ostrowski
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - Sabina Leanti La Rosa
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway.,Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
| | - Benoit J Kunath
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Andrew Robertson
- Life Sciences Institute: Natural Products Discovery Core, University of Michigan, Ann Arbor, MI, USA
| | - Gabriel Pereira
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - Live H Hagen
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | | | - Ling Qiu
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - Tianming Yao
- Department of Food Science and Whistler Center for Carbohydrate Research, Purdue University, West Lafayette, IN, USA
| | - Gabrielle Flint
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - James Li
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Sean P McDonald
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Duna Buttner
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - Nicholas A Pudlo
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - Matthew K Schnizlein
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - Vincent B Young
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA.,Department of Internal Medicine, Infectious Diseases Division, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Harry Brumer
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Thomas M Schmidt
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - Nicolas Terrapon
- Centre National de la Recherche Scientifique, Aix-Marseille Univ, Marseille, France.,Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Marseille, France
| | - Vincent Lombard
- Centre National de la Recherche Scientifique, Aix-Marseille Univ, Marseille, France.,Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Marseille, France
| | - Bernard Henrissat
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia.,Technical University of Denmark, DTU Bioengineering, Lyngby, Denmark
| | - Bruce Hamaker
- Department of Food Science and Whistler Center for Carbohydrate Research, Purdue University, West Lafayette, IN, USA
| | | | - Ashootosh Tripathi
- Life Sciences Institute: Natural Products Discovery Core, University of Michigan, Ann Arbor, MI, USA
| | - Phillip B Pope
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway. .,Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway.
| | - Eric C Martens
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA.
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10
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Pudlo NA, Pereira GV, Parnami J, Cid M, Markert S, Tingley JP, Unfried F, Ali A, Varghese NJ, Kim KS, Campbell A, Urs K, Xiao Y, Adams R, Martin D, Bolam DN, Becher D, Eloe-Fadrosh EA, Schmidt TM, Abbott DW, Schweder T, Hehemann JH, Martens EC. Diverse events have transferred genes for edible seaweed digestion from marine to human gut bacteria. Cell Host Microbe 2022; 30:314-328.e11. [PMID: 35240043 PMCID: PMC9096808 DOI: 10.1016/j.chom.2022.02.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Revised: 11/03/2021] [Accepted: 02/02/2022] [Indexed: 12/16/2022]
Abstract
Humans harbor numerous species of colonic bacteria that digest fiber polysaccharides in commonly consumed terrestrial plants. More recently in history, regional populations have consumed edible macroalgae seaweeds containing unique polysaccharides. It remains unclear how extensively gut bacteria have adapted to digest these nutrients. Here, we show that the ability of gut bacteria to digest seaweed polysaccharides is more pervasive than previously appreciated. Enrichment-cultured Bacteroides harbor previously discovered genes for seaweed degradation, which have mobilized into several members of this genus. Additionally, other examples of marine bacteria-derived genes, and their mobile DNA elements, are involved in gut microbial degradation of seaweed polysaccharides, including genes in gut-resident Firmicutes. Collectively, these results uncover multiple separate events that have mobilized the genes encoding seaweed-degrading-enzymes into gut bacteria. This work further underscores the metabolic plasticity of the human gut microbiome and global exchange of genes in the context of dietary selective pressures.
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Affiliation(s)
- Nicholas A Pudlo
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Jaagni Parnami
- Max Planck Institute for Marine Biology, Bremen, Germany
| | - Melissa Cid
- Max Planck Institute for Marine Biology, Bremen, Germany
| | - Stephanie Markert
- Pharmaceutical Biotechnology, University of Greifswald, 17487 Greifswald, Germany; Institute of Marine Biotechnology, 17489 Greifswald, Germany
| | - Jeffrey P Tingley
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, AB, Canada
| | - Frank Unfried
- Institute of Marine Biotechnology, 17489 Greifswald, Germany
| | - Ahmed Ali
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Kwi S Kim
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Austin Campbell
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Karthik Urs
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yao Xiao
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Ryan Adams
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Duña Martin
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA
| | - David N Bolam
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, UK
| | | | | | - Thomas M Schmidt
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - D Wade Abbott
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, AB, Canada
| | - Thomas Schweder
- Pharmaceutical Biotechnology, University of Greifswald, 17487 Greifswald, Germany; Institute of Marine Biotechnology, 17489 Greifswald, Germany
| | - Jan Hendrik Hehemann
- Max Planck Institute for Marine Biology, Bremen, Germany; University of Bremen, Center for Marine Environmental Sciences (MARUM), 28359 Bremen, Germany.
| | - Eric C Martens
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA.
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11
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Ashley SL, Sjoding MW, Popova AP, Cui TX, Hoostal MJ, Schmidt TM, Branton WR, Dieterle MG, Falkowski NR, Baker JM, Hinkle KJ, Konopka KE, Erb-Downward JR, Huffnagle GB, Dickson RP. Lung and gut microbiota are altered by hyperoxia and contribute to oxygen-induced lung injury in mice. Sci Transl Med 2020; 12:eaau9959. [PMID: 32801143 PMCID: PMC7732030 DOI: 10.1126/scitranslmed.aau9959] [Citation(s) in RCA: 85] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 06/14/2019] [Accepted: 01/21/2020] [Indexed: 12/27/2022]
Abstract
Inhaled oxygen, although commonly administered to patients with respiratory disease, causes severe lung injury in animals and is associated with poor clinical outcomes in humans. The relationship between hyperoxia, lung and gut microbiota, and lung injury is unknown. Here, we show that hyperoxia conferred a selective relative growth advantage on oxygen-tolerant respiratory microbial species (e.g., Staphylococcus aureus) as demonstrated by an observational study of critically ill patients receiving mechanical ventilation and experiments using neonatal and adult mouse models. During exposure of mice to hyperoxia, both lung and gut bacterial communities were altered, and these communities contributed to oxygen-induced lung injury. Disruption of lung and gut microbiota preceded lung injury, and variation in microbial communities correlated with variation in lung inflammation. Germ-free mice were protected from oxygen-induced lung injury, and systemic antibiotic treatment selectively modulated the severity of oxygen-induced lung injury in conventionally housed animals. These results suggest that inhaled oxygen may alter lung and gut microbial communities and that these communities could contribute to lung injury.
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Affiliation(s)
- Shanna L Ashley
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Michael W Sjoding
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
- Michigan Center for Integrative Research in Critical Care, Ann Arbor, MI, USA
| | - Antonia P Popova
- Division of Pediatric Pulmonology, Department of Pediatrics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Tracy X Cui
- Division of Pediatric Pulmonology, Department of Pediatrics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Matthew J Hoostal
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Thomas M Schmidt
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - William R Branton
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Michael G Dieterle
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Nicole R Falkowski
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Jennifer M Baker
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Kevin J Hinkle
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Kristine E Konopka
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - John R Erb-Downward
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Gary B Huffnagle
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
- Mary H. Weiser Food Allergy Center, University of Michigan, Ann Arbor, MI, USA
| | - Robert P Dickson
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA.
- Michigan Center for Integrative Research in Critical Care, Ann Arbor, MI, USA
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
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12
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Xavier JB, Young VB, Skufca J, Ginty F, Testerman T, Pearson AT, Macklin P, Mitchell A, Shmulevich I, Xie L, Caporaso JG, Crandall KA, Simone NL, Godoy-Vitorino F, Griffin TJ, Whiteson KL, Gustafson HH, Slade DJ, Schmidt TM, Walther-Antonio MRS, Korem T, Webb-Robertson BJM, Styczynski MP, Johnson WE, Jobin C, Ridlon JM, Koh AY, Yu M, Kelly L, Wargo JA. The Cancer Microbiome: Distinguishing Direct and Indirect Effects Requires a Systemic View. Trends Cancer 2020; 6:192-204. [PMID: 32101723 PMCID: PMC7098063 DOI: 10.1016/j.trecan.2020.01.004] [Citation(s) in RCA: 134] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 12/29/2019] [Accepted: 01/06/2020] [Indexed: 02/06/2023]
Abstract
The collection of microbes that live in and on the human body - the human microbiome - can impact on cancer initiation, progression, and response to therapy, including cancer immunotherapy. The mechanisms by which microbiomes impact on cancers can yield new diagnostics and treatments, but much remains unknown. The interactions between microbes, diet, host factors, drugs, and cell-cell interactions within the cancer itself likely involve intricate feedbacks, and no single component can explain all the behavior of the system. Understanding the role of host-associated microbial communities in cancer systems will require a multidisciplinary approach combining microbial ecology, immunology, cancer cell biology, and computational biology - a systems biology approach.
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Affiliation(s)
- Joao B Xavier
- Program for Computational and Systems Biology, Memorial Sloan-Kettering Cancer Center, New York, NY, USA.
| | - Vincent B Young
- Department of Internal Medicine, Division of Infectious Diseases, The University of Michigan Medical School, Ann Arbor, MI, USA
| | - Joseph Skufca
- Department of Mathematics, Clarkson University, Potsdam, NY, USA
| | | | - Traci Testerman
- Department of Pathology, Microbiology, and Immunology, University of South Carolina School of Medicine, Columbia, SC, USA
| | - Alexander T Pearson
- Section of Hematology/Oncology, Department of Medicine, Comprehensive Cancer Center, University of Chicago, Chicago, Illinois, IL, USA
| | - Paul Macklin
- Intelligent Systems Engineering, Indiana University, Bloomington, IN, USA
| | - Amir Mitchell
- Program in Systems Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | | | - Lei Xie
- Hunter College, Department of Computer Science, New York, NY, USA
| | - J Gregory Caporaso
- Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Keith A Crandall
- Computational Biology Institute, Milken Institute School of Public Health, George Washington University, Washington, DC, USA
| | - Nicole L Simone
- Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA
| | - Filipa Godoy-Vitorino
- Department of Microbiology and Medical Zoology, School of Medicine, University of Puerto Rico, San Juan, Puerto Rico
| | - Timothy J Griffin
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Katrine L Whiteson
- Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, CA, USA
| | - Heather H Gustafson
- Seattle Children's Research Institute, Ben Towne Center for Childhood Cancer Research, Seattle, WA, USA
| | - Daniel J Slade
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | | | - Marina R S Walther-Antonio
- Department of Surgery, Department of Obstetrics and Gynecology, and Microbiome Program, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Tal Korem
- Department of Systems Biology, Columbia University, New York, NY, USA
| | | | - Mark P Styczynski
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - W Evan Johnson
- Division of Computational Biomedicine, Boston University School of Medicine, Boston, MA, USA
| | - Christian Jobin
- Departments of Medicine, Anatomy, and Cell Biology, and of Infectious Diseases and Immunology, University of Florida, Gainesville, FL, USA
| | - Jason M Ridlon
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Andrew Y Koh
- University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Michael Yu
- Toyota Technological Institute at Chicago, Chicago, IL, USA
| | | | - Jennifer A Wargo
- The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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13
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Martiny JBH, Whiteson KL, Bohannan BJM, David LA, Hynson NA, McFall-Ngai M, Rawls JF, Schmidt TM, Abdo Z, Blaser MJ, Bordenstein S, Bréchot C, Bull CT, Dorrestein P, Eisen JA, Garcia-Pichel F, Gilbert J, Hofmockel KS, Holtz ML, Knight R, Mark Welch DB, McDonald D, Methé B, Mouncey NJ, Mueller NT, Pfister CA, Proctor L, Sachs JL. The emergence of microbiome centres. Nat Microbiol 2019; 5:2-3. [DOI: 10.1038/s41564-019-0644-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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14
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Golob JL, DeMeules MM, Loeffelholz T, Quinn ZZ, Dame MK, Silvestri SS, Wu MC, Schmidt TM, Fiedler TL, Hoostal MJ, Mielcarek M, Spence J, Pergam SA, Fredricks DN. Butyrogenic bacteria after acute graft-versus-host disease (GVHD) are associated with the development of steroid-refractory GVHD. Blood Adv 2019; 3:2866-2869. [PMID: 31585950 PMCID: PMC6784520 DOI: 10.1182/bloodadvances.2019000362] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 09/02/2019] [Indexed: 01/24/2023] Open
Abstract
The presence of butyrogenic bacteria after the onset of acute GVHD associates with subsequent steroid-refractory GVHD or chronic GVHD. Butyrate inhibits human colonic stem cells from forming an intact epithelial monolayer.
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Affiliation(s)
- Jonathan L Golob
- Division of Infectious Diseases, Department of Medicine, University of Michigan, Ann Arbor, MI
| | - Martha M DeMeules
- Infectious Disease Sciences, Vaccines and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Tillie Loeffelholz
- Infectious Disease Sciences, Vaccines and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Z Z Quinn
- Infectious Disease Sciences, Vaccines and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Michael K Dame
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI
| | | | | | - Thomas M Schmidt
- Division of Infectious Diseases, Department of Medicine, University of Michigan, Ann Arbor, MI
| | - Tina L Fiedler
- Infectious Disease Sciences, Vaccines and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Matthew J Hoostal
- Division of Infectious Diseases, Department of Medicine, University of Michigan, Ann Arbor, MI
| | - Marco Mielcarek
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA
- Division of Medical Oncology, Department of Medicine, University of Washington, Seattle, WA
| | - Jason Spence
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI
- Department of Biomedical Engineering, University of Michigan College of Engineering, Ann Arbor, MI; and
| | - Steven A Pergam
- Infectious Disease Sciences, Vaccines and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA
- Division of Allergy & Infectious Diseases, Department of Medicine, University of Washington, Seattle, WA
| | - David N Fredricks
- Infectious Disease Sciences, Vaccines and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA
- Division of Allergy & Infectious Diseases, Department of Medicine, University of Washington, Seattle, WA
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15
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Smith BJ, Miller RA, Ericsson AC, Harrison DC, Strong R, Schmidt TM. Changes in the gut microbiome and fermentation products concurrent with enhanced longevity in acarbose-treated mice. BMC Microbiol 2019; 19:130. [PMID: 31195972 PMCID: PMC6567620 DOI: 10.1186/s12866-019-1494-7] [Citation(s) in RCA: 177] [Impact Index Per Article: 35.4] [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: 09/20/2018] [Accepted: 05/17/2019] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Treatment with the α-glucosidase inhibitor acarbose increases median lifespan by approximately 20% in male mice and 5% in females. This longevity extension differs from dietary restriction based on a number of features, including the relatively small effects on weight and the sex-specificity of the lifespan effect. By inhibiting host digestion, acarbose increases the flux of starch to the lower digestive system, resulting in changes to the gut microbiota and their fermentation products. Given the documented health benefits of short-chain fatty acids (SCFAs), the dominant products of starch fermentation by gut bacteria, this secondary effect of acarbose could contribute to increased longevity in mice. To explore this hypothesis, we compared the fecal microbiome of mice treated with acarbose to control mice at three independent study sites. RESULTS Microbial communities and the concentrations of SCFAs in the feces of mice treated with acarbose were notably different from those of control mice. At all three study sites, the bloom of a single bacterial taxon was the most obvious response to acarbose treatment. The blooming populations were classified to the largely uncultured Bacteroidales family Muribaculaceae and were the same taxonomic unit at two of the three sites. Propionate concentrations in feces were consistently elevated in treated mice, while the concentrations of acetate and butyrate reflected a dependence on study site. Across all samples, Muribaculaceae abundance was strongly correlated with propionate and community composition was an important predictor of SCFA concentrations. Cox proportional hazards regression showed that the fecal concentrations of acetate, butyrate, and propionate were, together, predictive of mouse longevity even while controlling for sex, site, and acarbose. CONCLUSION We observed a correlation between fecal SCFAs and lifespan in mice, suggesting a role of the gut microbiota in the longevity-enhancing properties of acarbose. Treatment modulated the taxonomic composition and fermentation products of the gut microbiome, while the site-dependence of the responses illustrate the challenges facing reproducibility and interpretation in microbiome studies. These results motivate future studies exploring manipulation of the gut microbial community and its fermentation products for increased longevity, testing causal roles of SCFAs in the observed effects of acarbose.
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Affiliation(s)
- Byron J Smith
- Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, 48109 MI USA
| | - Richard A Miller
- Department of Pathology and Geriatrics Center, University of Michigan, Ann Arbor, 48109 MI USA
| | - Aaron C Ericsson
- University of Missouri Metagenomics Center, University of Missouri, Columbia, 65201 MO USA
| | | | - Randy Strong
- Department of Pharmacology, The University of Texas Health Science Center at San Antonio, San Antonio, 78229 TX USA
- Barshop Institute for Longevity and Aging Studies, San Antonio, 78245 TX USA
- Geriatric Research, Education and Clinical Center and Research Service, South Texas Veterans Health Care System, San Antonio, 78229 TX USA
| | - Thomas M Schmidt
- Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, 48109 MI USA
- Department of Internal Medicine, University of Michigan, Ann Arbor, 48109 MI USA
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16
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Hummel SL, Bassis C, Marolt C, Konerman M, Schmidt TM. GUT MICROBIOME DIFFERS BETWEEN HEART FAILURE WITH PRESERVED EJECTION FRACTION AND AGE-MATCHED CONTROLS. J Am Coll Cardiol 2019. [DOI: 10.1016/s0735-1097(19)31358-0] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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17
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Grate JW, Liu B, Kelly RT, Anheier NC, Schmidt TM. Microfluidic Sensors with Impregnated Fluorophores for Simultaneous Imaging of Spatial Structure and Chemical Oxygen Gradients. ACS Sens 2019; 4:317-325. [PMID: 30609370 DOI: 10.1021/acssensors.8b00924] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Interior surfaces of polystyrene microfluidic structures were impregnated with the oxygen sensing dye Pt(II) tetra(pentafluorophenyl)porphyrin (PtTFPP) using a solvent-induced fluorophore impregnation (SIFI) method. Using this technique, microfluidic oxygen sensors are obtained that enable simultaneous imaging of both chemical oxygen gradients and the physical structure of the microfluidic interior. A gentle method of fluorophore impregnation using acetonitrile solutions of PtTFPP at 50 °C was developed leading to a 10-μm-deep region containing fluorophore. This region is localized at the surface to sense oxygen in the interior fluid during use. Regions of the device that do not contact the interior fluid pathways lack fluorophores and are dark in fluorescent imaging. The technique was demonstrated on straight microchannel and pore network devices, the latter having pillars of 300 μm diameter spaced center to center at 340 μm providing pore throats of 40 μm. Sensing within channels or pores and imaging across the pore network devices were performed using a Lambert LIFA-P frequency domain fluorescence lifetime imaging system on a Leica microscope platform. Calibrations of different devices prepared by the SIFI method were indistinguishable. Gradient imaging showed fluorescent regions corresponding to the fluid pore network, dark pillars, and fluorescent lifetime varying across the gradient, thus providing both physical and chemical imaging. More generally, the SIFI technique can impregnate the interior surfaces of other polystyrene containers, such as cuvettes or cell and tissue culture containers, to enable sensing of interior conditions.
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Affiliation(s)
- Jay W. Grate
- Pacific Northwest
National Laboratory, P.O. Box 999, Richland, Washington 99352, United States
| | - Bingwen Liu
- Pacific Northwest
National Laboratory, P.O. Box 999, Richland, Washington 99352, United States
| | - Ryan T. Kelly
- Pacific Northwest
National Laboratory, P.O. Box 999, Richland, Washington 99352, United States
| | - Norman C. Anheier
- Pacific Northwest
National Laboratory, P.O. Box 999, Richland, Washington 99352, United States
| | - Thomas M. Schmidt
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan 48109, United States
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18
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Flowers SA, Baxter NT, Ward KM, Kraal AZ, McInnis MG, Schmidt TM, Ellingrod VL. Effects of Atypical Antipsychotic Treatment and Resistant Starch Supplementation on Gut Microbiome Composition in a Cohort of Patients with Bipolar Disorder or Schizophrenia. Pharmacotherapy 2019; 39:161-170. [PMID: 30620405 DOI: 10.1002/phar.2214] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
STUDY OBJECTIVE Previous studies identified shifts in gut microbiota associated with atypical antipsychotic (AAP) treatment that may link AAPs to metabolic burden. Dietary prebiotics such as resistant starch may be beneficial in obesity and glucose regulation, but little is known mechanistically about their ability to modify gut microbiota in AAP-treated individuals. This investigation was undertaken to delineate mechanistically the effects of AAP treatment and resistant starch supplementation on gut microbiota in a psychiatric population. DESIGN Cross-sectional cohort study. SETTING The study was performed in an outpatient setting. PATIENTS A total of 37 adults with a diagnosis of bipolar disorder or schizophrenia who were treated with an AAP (clozapine, olanzapine, risperidone, quetiapine, or ziprasidone [21 patients]) or lithium and/or lamotrigine (16 patients) for at least 6 months. INTERVENTION Patients in the AAP group received raw unmodified potato starch (resistant starch) daily for 14 days. MEASUREMENTS AND MAIN RESULTS Of the 37 patients, the mean ± SD age was 52.2 ± 12.5 years, and 57% were male. The primary outcome was gut microbiome DNA composition. Microbiome DNA obtained from stool samples from all patients was subject to 16S ribosomal RNA (rRNA) gene sequencing before and during resistant starch supplementation. Inter- and intragroup microbial diversity measures were performed by permutational multivariate analysis of variance and the Inverse Simpson Diversity Index, respectively. Differentially abundant organisms were detected by using linear discriminant analysis effect size. Although no significant difference in overall microbiota composition was detected at baseline between AAP users and nonusers, non-AAP users showed increased fractional representation of Alistipes. AAP-treated women exhibited decreased diversity compared with non-AAP-treated women. Although the microbiome of AAP-treated patients varied with resistant starch administration, an increased abundance of the Actinobacteria phylum was observed. CONCLUSION These data suggest that AAP treatment is associated with measurable differences in gut microbiota, particularly in female AAP-treated patients in whom reduced species richness was observed. Additionally, variable microbiome responses to resistant starch supplementation were seen, with a significant increase in starch degraders.
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Affiliation(s)
- Stephanie A Flowers
- Department of Pharmacy Practice, University of Illinois at Chicago, Chicago, Illinois
| | - Nielson T Baxter
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Kristen M Ward
- Department of Clinical Pharmacy, University of Michigan, Ann Arbor, Michigan
| | - A Zarina Kraal
- Department of Clinical Pharmacy, University of Michigan, Ann Arbor, Michigan
| | - Melvin G McInnis
- Department of Psychiatry, University of Michigan, Ann Arbor, Michigan
| | - Thomas M Schmidt
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Vicki L Ellingrod
- Department of Clinical Pharmacy, University of Michigan, Ann Arbor, Michigan
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19
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Baxter NT, Schmidt AW, Venkataraman A, Kim KS, Waldron C, Schmidt TM. Dynamics of Human Gut Microbiota and Short-Chain Fatty Acids in Response to Dietary Interventions with Three Fermentable Fibers. mBio 2019; 10:e02566-18. [PMID: 30696735 PMCID: PMC6355990 DOI: 10.1128/mbio.02566-18] [Citation(s) in RCA: 419] [Impact Index Per Article: 83.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 12/06/2018] [Indexed: 12/17/2022] Open
Abstract
Production of short-chain fatty acids (SCFAs), especially butyrate, in the gut microbiome is required for optimal health but is frequently limited by the lack of fermentable fiber in the diet. We attempted to increase butyrate production by supplementing the diets of 174 healthy young adults for 2 weeks with resistant starch from potatoes (RPS), resistant starch from maize (RMS), inulin from chicory root, or an accessible corn starch control. RPS resulted in the greatest increase in total SCFAs, including butyrate. Although the majority of microbiomes responded to RPS with increases in the relative abundance of bifidobacteria, those that responded with an increase in Ruminococcus bromii or Clostridium chartatabidum were more likely to yield higher butyrate concentrations, especially when their microbiota were replete with populations of the butyrate-producing species Eubacterium rectale RMS and inulin induced different changes in fecal communities, but they did not generate significant increases in fecal butyrate levels.IMPORTANCE These results reveal that not all fermentable fibers are equally capable of stimulating SCFA production, and they highlight the importance of the composition of an individual's microbiota in determining whether or not they respond to a specific dietary supplement. In particular, R. bromii or C. chartatabidum may be required for enhanced butyrate production in response to RS. Bifidobacteria, though proficient at degrading RS and inulin, may not contribute to the butyrogenic effect of those fermentable fibers in the short term.
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Affiliation(s)
- Nielson T Baxter
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Alexander W Schmidt
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Arvind Venkataraman
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Kwi S Kim
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Clive Waldron
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Thomas M Schmidt
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, USA
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20
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Singer BH, Dickson RP, Denstaedt SJ, Newstead MW, Kim K, Falkowski NR, Erb-Downward JR, Schmidt TM, Huffnagle GB, Standiford TJ. Bacterial Dissemination to the Brain in Sepsis. Am J Respir Crit Care Med 2018; 197:747-756. [PMID: 29232157 PMCID: PMC5855074 DOI: 10.1164/rccm.201708-1559oc] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [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: 08/01/2017] [Accepted: 12/12/2017] [Indexed: 12/11/2022] Open
Abstract
RATIONALE Sepsis causes brain dysfunction and neuroinflammation. It is unknown whether neuroinflammation in sepsis is initiated by dissemination of bacteria to the brain and sustained by persistent infection, or whether neuroinflammation is a sterile process resulting solely from circulating inflammatory mediators. OBJECTIVES To determine if gut bacteria translocate to the brain during sepsis, and are associated with neuroinflammation. METHODS Murine sepsis was induced using cecal ligation and puncture, and sepsis survivor mice were compared with sham and unoperated control animals. Brain tissue of patients who died of sepsis was compared with patients who died of noninfectious causes. Bacterial taxa were characterized by 16S ribosomal RNA gene sequencing in both murine and human brain specimens; compared among sepsis and nonsepsis groups; and correlated with levels of S100A8, a marker of neuroinflammation using permutational multivariate ANOVA. MEASUREMENTS AND MAIN RESULTS Viable gut-associated bacteria were enriched in the brains of mice 5 days after surviving abdominal sepsis (P < 0.01), and undetectable by 14 days. The community structure of brain-associated bacteria correlated with severity of neuroinflammation (P < 0.001). Furthermore, bacterial taxa detected in brains of humans who die of sepsis were distinct from those who died of noninfectious causes (P < 0.001) and correlated with S100A8/A9 expression (P < 0.05). CONCLUSIONS Although bacterial translocation is associated with acute neuroinflammation in murine sepsis, bacterial translocation did not result in chronic cerebral infection. Postmortem analysis of patients who die of sepsis suggests a role for bacteria in acute brain dysfunction in sepsis. Further work is needed to determine if modifying gut-associated bacterial communities modulates brain dysfunction after sepsis.
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Affiliation(s)
- Benjamin H. Singer
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, and
- Michigan Center for Integrative Research in Critical Care, Ann Arbor, Michigan
| | - Robert P. Dickson
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, and
- Michigan Center for Integrative Research in Critical Care, Ann Arbor, Michigan
| | - Scott J. Denstaedt
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, and
| | - Michael W. Newstead
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, and
| | - Kwi Kim
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan; and
| | - Nicole R. Falkowski
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, and
| | - John R. Erb-Downward
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, and
| | - Thomas M. Schmidt
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan; and
| | - Gary B. Huffnagle
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, and
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan; and
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21
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Kim YG, Sakamoto K, Seo SU, Pickard JM, Gillilland MG, Pudlo NA, Hoostal M, Li X, Wang TD, Feehley T, Stefka AT, Schmidt TM, Martens EC, Fukuda S, Inohara N, Nagler CR, Núñez G. Neonatal acquisition of Clostridia species protects against colonization by bacterial pathogens. Science 2017; 356:315-319. [PMID: 28428425 DOI: 10.1126/science.aag2029] [Citation(s) in RCA: 157] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Accepted: 03/28/2017] [Indexed: 12/18/2022]
Abstract
The high susceptibility of neonates to infections has been assumed to be due to immaturity of the immune system, but the mechanism remains unclear. By colonizing adult germ-free mice with the cecal contents of neonatal and adult mice, we show that the neonatal microbiota is unable to prevent colonization by two bacterial pathogens that cause mortality in neonates. The lack of colonization resistance occurred when Clostridiales were absent in the neonatal microbiota. Administration of Clostridiales, but not Bacteroidales, protected neonatal mice from pathogen infection and abrogated intestinal pathology upon pathogen challenge. Depletion of Clostridiales also abolished colonization resistance in adult mice. The neonatal bacteria enhanced the ability of protective Clostridiales to colonize the gut.
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Affiliation(s)
- Yun-Gi Kim
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA. .,Comprehensive Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Kei Sakamoto
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA.,Comprehensive Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Sang-Uk Seo
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA.,Comprehensive Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Joseph M Pickard
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA.,Comprehensive Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Merritt G Gillilland
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Nicholas A Pudlo
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Matthew Hoostal
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Xue Li
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Thomas D Wang
- Departments of Biomedical Engineering and Mechanical Engineering, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Taylor Feehley
- Department of Pathology and Committee on Immunology, University of Chicago, Chicago, IL 60637, USA
| | - Andrew T Stefka
- Department of Pathology and Committee on Immunology, University of Chicago, Chicago, IL 60637, USA
| | - Thomas M Schmidt
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA.,Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Eric C Martens
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Shinji Fukuda
- Institute for Advanced Biosciences, Keio University, Yamagata, Japan.,PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama 332-0012, Japan
| | - Naohiro Inohara
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Cathryn R Nagler
- Department of Pathology and Committee on Immunology, University of Chicago, Chicago, IL 60637, USA
| | - Gabriel Núñez
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA. .,Comprehensive Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA
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22
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Hill DR, Huang S, Nagy MS, Yadagiri VK, Fields C, Mukherjee D, Bons B, Dedhia PH, Chin AM, Tsai YH, Thodla S, Schmidt TM, Walk S, Young VB, Spence JR. Bacterial colonization stimulates a complex physiological response in the immature human intestinal epithelium. eLife 2017; 6:29132. [PMID: 29110754 PMCID: PMC5711377 DOI: 10.7554/elife.29132] [Citation(s) in RCA: 112] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 10/29/2017] [Indexed: 12/19/2022] Open
Abstract
The human gastrointestinal tract is immature at birth, yet must adapt to dramatic changes such as oral nutrition and microbial colonization. The confluence of these factors can lead to severe inflammatory disease in premature infants; however, investigating complex environment-host interactions is difficult due to limited access to immature human tissue. Here, we demonstrate that the epithelium of human pluripotent stem-cell-derived human intestinal organoids is globally similar to the immature human epithelium and we utilize HIOs to investigate complex host-microbe interactions in this naive epithelium. Our findings demonstrate that the immature epithelium is intrinsically capable of establishing a stable host-microbe symbiosis. Microbial colonization leads to complex contact and hypoxia driven responses resulting in increased antimicrobial peptide production, maturation of the mucus layer, and improved barrier function. These studies lay the groundwork for an improved mechanistic understanding of how colonization influences development of the immature human intestine.
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Affiliation(s)
- David R Hill
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, United States
| | - Sha Huang
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, United States
| | - Melinda S Nagy
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, United States
| | - Veda K Yadagiri
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, United States
| | - Courtney Fields
- Division of Infectious Disease, Department of Internal Medicine, University of Michigan, Ann Arbor, United States
| | - Dishari Mukherjee
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, United States
| | - Brooke Bons
- Division of Infectious Disease, Department of Internal Medicine, University of Michigan, Ann Arbor, United States
| | - Priya H Dedhia
- Department of Surgery, University of Michigan, Ann Arbor, United States
| | - Alana M Chin
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, United States
| | - Yu-Hwai Tsai
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, United States
| | - Shrikar Thodla
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, United States
| | - Thomas M Schmidt
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, United States
| | - Seth Walk
- Department of Microbiology and Immunology, Montana State University, Bozeman, United States
| | - Vincent B Young
- Division of Infectious Disease, Department of Internal Medicine, University of Michigan, Ann Arbor, United States
| | - Jason R Spence
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, United States.,Department of Cell andDevelopmental Biology, University of Michigan, Ann Arbor, United States
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23
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Roller BRK, Stoddard SF, Schmidt TM. Exploiting rRNA operon copy number to investigate bacterial reproductive strategies. Nat Microbiol 2016; 1:16160. [PMID: 27617693 PMCID: PMC5061577 DOI: 10.1038/nmicrobiol.2016.160] [Citation(s) in RCA: 219] [Impact Index Per Article: 27.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Accepted: 08/02/2016] [Indexed: 11/16/2022]
Abstract
The potential for rapid reproduction is a hallmark of microbial life, but microbes in nature must also survive and compete when growth is constrained by resource availability. Successful reproduction requires different strategies when resources are scarce compared to when they are abundant1,2, but a systematic framework for predicting these reproductive strategies in bacteria has not been available. Here we show that the number of ribosomal RNA operons (rrn) in bacterial genomes predicts two important components of reproduction – growth rate and growth efficiency – which are favored under contrasting regimes of resource availability3,4. We find that the maximum reproductive rate of bacteria doubles with a doubling of rrn copy number, while the efficiency of carbon use is inversely related to maximal growth rate and rrn copy number. We also identify a feasible explanation for these patterns: the rate and yield of protein synthesis mirror the overall pattern in maximum growth rate and growth efficiency. Furthermore, comparative analysis of genomes from 1,167 bacterial species reveals that rrn copy number predicts traits associated with resource availability, including chemotaxis and genome streamlining. Genome-wide patterns of orthologous gene content covary with rrn copy number, suggesting convergent evolution in response to resource availability. Our findings indicate that basic cellular processes adapt in contrasting ways to long-term differences in resource availability. They also establish a basis for predicting changes in bacterial community composition in response to resource perturbations using rrn copy number measurements5 or inferences6,7.
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Affiliation(s)
- Benjamin R K Roller
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan 48109, USA.,Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 48824, USA
| | - Steven F Stoddard
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Thomas M Schmidt
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan 48109, USA.,Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan 48109, USA.,Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan 48109, USA
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24
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Beck JM, Schloss PD, Venkataraman A, Twigg H, Jablonski KA, Bushman FD, Campbell TB, Charlson ES, Collman RG, Crothers K, Curtis JL, Drews KL, Flores SC, Fontenot AP, Foulkes MA, Frank I, Ghedin E, Huang L, Lynch SV, Morris A, Palmer BE, Schmidt TM, Sodergren E, Weinstock GM, Young VB. Multicenter Comparison of Lung and Oral Microbiomes of HIV-infected and HIV-uninfected Individuals. Am J Respir Crit Care Med 2016; 192:1335-44. [PMID: 26247840 DOI: 10.1164/rccm.201501-0128oc] [Citation(s) in RCA: 102] [Impact Index Per Article: 12.8] [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: 12/27/2022] Open
Abstract
RATIONALE Improved understanding of the lung microbiome in HIV-infected individuals could lead to better strategies for diagnosis, therapy, and prophylaxis of HIV-associated pneumonias. Differences in the oral and lung microbiomes in HIV-infected and HIV-uninfected individuals are not well defined. Whether highly active antiretroviral therapy influences these microbiomes is unclear. OBJECTIVES We determined whether oral and lung microbiomes differed in clinically healthy groups of HIV-infected and HIV-uninfected subjects. METHODS Participating sites in the Lung HIV Microbiome Project contributed bacterial 16S rRNA sequencing data from oral washes and bronchoalveolar lavages (BALs) obtained from HIV-uninfected individuals (n = 86), HIV-infected individuals who were treatment naive (n = 18), and HIV-infected individuals receiving antiretroviral therapy (n = 38). MEASUREMENTS AND MAIN RESULTS Microbial populations differed in the oral washes among the subject groups (Streptococcus, Actinomyces, Rothia, and Atopobium), but there were no individual taxa that differed among the BALs. Comparison of oral washes and BALs demonstrated similar patterns from HIV-uninfected individuals and HIV-infected individuals receiving antiretroviral therapy, with multiple taxa differing in abundance. The pattern observed from HIV-infected individuals who were treatment naive differed from the other two groups, with differences limited to Veillonella, Rothia, and Granulicatella. CD4 cell counts did not influence the oral or BAL microbiome in these relatively healthy, HIV-infected subjects. CONCLUSIONS The overall similarity of the microbiomes in participants with and without HIV infection was unexpected, because HIV-infected individuals with relatively preserved CD4 cell counts are at higher risk for lower respiratory tract infections, indicating impaired local immune function.
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Affiliation(s)
- James M Beck
- 1 Department of Medicine, University of Colorado Denver, Aurora, Colorado.,2 Veterans Affairs Eastern Colorado Health Care System, Denver, Colorado
| | - Patrick D Schloss
- 3 Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Arvind Venkataraman
- 3 Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Homer Twigg
- 4 Department of Medicine, Indiana University, Indianapolis, Indiana
| | - Kathleen A Jablonski
- 5 Department of Epidemiology and Biostatistics, George Washington University, Washington, District of Columbia
| | | | - Thomas B Campbell
- 1 Department of Medicine, University of Colorado Denver, Aurora, Colorado
| | - Emily S Charlson
- 7 Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Ronald G Collman
- 7 Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Kristina Crothers
- 8 Department of Medicine, University of Washington, Seattle, Washington
| | - Jeffrey L Curtis
- 3 Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan.,9 Veterans Affairs Ann Arbor Healthcare System, Ann Arbor, Michigan
| | - Kimberly L Drews
- 5 Department of Epidemiology and Biostatistics, George Washington University, Washington, District of Columbia
| | - Sonia C Flores
- 1 Department of Medicine, University of Colorado Denver, Aurora, Colorado
| | - Andrew P Fontenot
- 1 Department of Medicine, University of Colorado Denver, Aurora, Colorado
| | - Mary A Foulkes
- 5 Department of Epidemiology and Biostatistics, George Washington University, Washington, District of Columbia
| | - Ian Frank
- 7 Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Elodie Ghedin
- 10 Department of Computational and Systems Biology and
| | - Laurence Huang
- 11 Department of Medicine, University of California San Francisco, San Francisco, California; and
| | - Susan V Lynch
- 11 Department of Medicine, University of California San Francisco, San Francisco, California; and
| | - Alison Morris
- 12 Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Brent E Palmer
- 1 Department of Medicine, University of Colorado Denver, Aurora, Colorado
| | - Thomas M Schmidt
- 3 Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Erica Sodergren
- 13 The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut
| | | | - Vincent B Young
- 3 Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
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25
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Loudon AH, Venkataraman A, Van Treuren W, Woodhams DC, Parfrey LW, McKenzie VJ, Knight R, Schmidt TM, Harris RN. Vertebrate Hosts as Islands: Dynamics of Selection, Immigration, Loss, Persistence, and Potential Function of Bacteria on Salamander Skin. Front Microbiol 2016; 7:333. [PMID: 27014249 PMCID: PMC4793798 DOI: 10.3389/fmicb.2016.00333] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [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: 01/05/2016] [Accepted: 03/02/2016] [Indexed: 02/01/2023] Open
Abstract
Skin bacterial communities can protect amphibians from a fungal pathogen; however, little is known about how these communities are maintained. We used a neutral model of community ecology to identify bacteria that are maintained on salamanders by selection or by dispersal from a bacterial reservoir (soil) and ecological drift. We found that 75% (9/12) of bacteria that were consistent with positive selection, <1% of bacteria that were consistent with random dispersal and none of the bacteria that were consistent under negative selection had a 97% or greater match to antifungal isolates. Additionally we performed an experiment where salamanders were either provided or denied a bacterial reservoir and estimated immigration and loss (emigration and local extinction) rates of bacteria on salamanders in both treatments. Loss was strongly related to bacterial richness, suggesting competition is important for structuring the community. Bacteria closely related to antifungal isolates were more likely to persist on salamanders with or without a bacterial reservoir, suggesting they had a competitive advantage. Furthermore, over-represented and under-represented operational taxonomic units (OTUs) had similar persistence on salamanders when a bacterial reservoir was present. However, under-represented OTUs were less likely to persist in the absence of a bacterial reservoir, suggesting that the over-represented and under-represented bacteria were selected against or for on salamanders through time. Our findings from the neutral model, migration and persistence analyses show that bacteria that exhibit a high similarity to antifungal isolates persist on salamanders, which likely protect hosts against pathogens and improve fitness. This research is one of the first to apply ecological theory to investigate assembly of host associated-bacterial communities, which can provide insights for probiotic bioaugmentation as a conservation strategy against disease.
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Affiliation(s)
- Andrew H Loudon
- Department of Biology, James Madison University, Harrisonburg VA, USA
| | | | | | - Douglas C Woodhams
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder CO, USA
| | | | - Valerie J McKenzie
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder CO, USA
| | - Rob Knight
- BioFrontiers Institute, University of Colorado, Boulder CO, USA
| | - Thomas M Schmidt
- Department of Internal Medicine, University of Michigan, Ann Arbor MI, USA
| | - Reid N Harris
- Department of Biology, James Madison University, Harrisonburg VA, USA
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Rossander LH, Larsen-Olsen TT, Dam HF, Schmidt TM, Corazza M, Norrman K, Rajkovic I, Andreasen JW, Krebs FC. In situ X-ray scattering of perovskite solar cell active layers roll-to-roll coated on flexible substrates. CrystEngComm 2016. [DOI: 10.1039/c6ce00382f] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Abdalla LB, Padilha José E, Schmidt TM, Miwa RH, Fazzio A. Topological phase transitions of (BixSb1-x)2Se3 alloys by density functional theory. J Phys Condens Matter 2015; 27:255501. [PMID: 26045478 DOI: 10.1088/0953-8984/27/25/255501] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We have performed an ab initio total energy investigation of the topological phase transition, and the electronic properties of topologically protected surface states of (BixSb1-x)2Se3 alloys. In order to provide an accurate alloy concentration for the phase transition, we have considered the special quasirandom structures to describe the alloy system. The trivial → topological transition concentration was obtained by (i) the calculation of the band gap closing as a function of Bi concentration (x), and (ii) the calculation of the Z2 topological invariant number. We show that there is a topological phase transition, for x around 0.4, verified for both procedures (i) and (ii). We also show that in the concentration range 0.4 < x < 0.7, the alloy does not present any other band at the Fermi level besides the Dirac cone, where the Dirac point is far from the bulk states. This indicates that a possible suppression of the scattering process due to bulk states will occur.
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Affiliation(s)
- L B Abdalla
- Instituto de Física, Universidade de São Paulo, CP 66318, 05315-970, São Paulo, SP, Brazil
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Roller BRK, Schmidt TM. The physiology and ecological implications of efficient growth. ISME J 2015; 9:1481-7. [PMID: 25575305 DOI: 10.1038/ismej.2014.235] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2014] [Revised: 09/18/2014] [Accepted: 10/31/2014] [Indexed: 11/09/2022]
Abstract
The natural habitats of microbes are typically spatially structured with limited resources, so opportunities for unconstrained, balanced growth are rare. In these habitats, selection should favor microbes that are able to use resources most efficiently, that is, microbes that produce the most progeny per unit of resource consumed. On the basis of this assertion, we propose that selection for efficiency is a primary driver of the composition of microbial communities. In this article, we review how the quality and quantity of resources influence the efficiency of heterotrophic growth. A conceptual model proposing innate differences in growth efficiency between oligotrophic and copiotrophic microbes is also provided. We conclude that elucidation of the mechanisms underlying efficient growth will enhance our understanding of the selective pressures shaping microbes and will improve our capacity to manage microbial communities effectively.
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Affiliation(s)
- Benjamin R K Roller
- 1] Department of Microbiology and Molecular Genetics, East Lansing, MI, USA [2] Ecology, Evolutionary Biology and Behavior Program, Michigan State University, East Lansing, MI, USA [3] Departments of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Thomas M Schmidt
- 1] Departments of Internal Medicine, University of Michigan, Ann Arbor, MI, USA [2] Ecology and Evolutionary Biology, Ann Arbor, MI, USA [3] Microbiology and Immunology, Ann Arbor, MI, USA
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Schmidt TM, Frederiksen M, Bochenkov V, Sutherland DS. Exploring plasmonic coupling in hole-cap arrays. Beilstein J Nanotechnol 2015; 6:1-10. [PMID: 25671146 PMCID: PMC4311723 DOI: 10.3762/bjnano.6.1] [Citation(s) in RCA: 3] [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] [Subscribe] [Scholar Register] [Received: 06/07/2014] [Accepted: 12/02/2014] [Indexed: 06/02/2023]
Abstract
The plasmonic coupling between gold caps and holes in thin films was investigated experimentally and through finite-difference time-domain (FDTD) calculations. Sparse colloidal lithography combined with a novel thermal treatment was used to control the vertical spacing between caps and hole arrays and compared to separated arrays of holes or caps. Optical spectroscopy and FDTD simulations reveal strong coupling between the gold caps and both Bloch Wave-surface plasmon polariton (BW-SPP) modes and localized surface plasmon resonance (LSPR)-type resonances in hole arrays when they are in close proximity. The interesting and complex coupling between caps and hole arrays reveals the details of the field distribution for these simple to fabricate structures.
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Affiliation(s)
- Thomas M Schmidt
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus, Denmark
| | - Maj Frederiksen
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus, Denmark
| | - Vladimir Bochenkov
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus, Denmark
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russian Federation
| | - Duncan S Sutherland
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus, Denmark
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Carmody LA, Zhao J, Kalikin LM, LeBar W, Simon RH, Venkataraman A, Schmidt TM, Abdo Z, Schloss PD, LiPuma JJ. The daily dynamics of cystic fibrosis airway microbiota during clinical stability and at exacerbation. Microbiome 2015; 3:12. [PMID: 25834733 PMCID: PMC4381400 DOI: 10.1186/s40168-015-0074-9] [Citation(s) in RCA: 102] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Accepted: 02/24/2015] [Indexed: 05/21/2023]
Abstract
BACKGROUND Recent work indicates that the airways of persons with cystic fibrosis (CF) typically harbor complex bacterial communities. However, the day-to-day stability of these communities is unknown. Further, airway community dynamics during the days corresponding to the onset of symptoms of respiratory exacerbation have not been studied. RESULTS Using 16S rRNA amplicon sequencing of 95 daily sputum specimens collected from four adults with CF, we observed varying degrees of day-to-day stability in airway bacterial community structures during periods of clinical stability. Differences were observed between study subjects with respect to the degree of community changes at the onset of exacerbation. Decreases in the relative abundance of dominant taxa were observed in three subjects at exacerbation. We observed no relationship between total bacterial load and clinical status and detected no viruses by multiplex PCR. CONCLUSION CF airway microbial communities are relatively stable during periods of clinical stability. Changes in microbial community structure are associated with some, but not all, pulmonary exacerbations, supporting previous observations suggesting that distinct types of exacerbations occur in CF. Decreased abundance of species that are dominant at baseline suggests a role for less abundant taxa in some exacerbations. Daily sampling revealed patterns of change in microbial community structures that may prove useful in the prediction and management of CF pulmonary exacerbations.
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Affiliation(s)
- Lisa A Carmody
- />Department of Pediatrics and Communicable Diseases, University of Michigan Medical School, Ann Arbor, MI 48109 USA
| | - Jiangchao Zhao
- />Department of Pediatrics and Communicable Diseases, University of Michigan Medical School, Ann Arbor, MI 48109 USA
| | - Linda M Kalikin
- />Department of Pediatrics and Communicable Diseases, University of Michigan Medical School, Ann Arbor, MI 48109 USA
| | - William LeBar
- />Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109 USA
| | - Richard H Simon
- />Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109 USA
| | - Arvind Venkataraman
- />Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109 USA
| | - Thomas M Schmidt
- />Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109 USA
| | - Zaid Abdo
- />USDA-ARS, South Atlantic Area, Athens, GA USA
| | - Patrick D Schloss
- />Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109 USA
| | - John J LiPuma
- />Department of Pediatrics and Communicable Diseases, University of Michigan Medical School, Ann Arbor, MI 48109 USA
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Stoddard SF, Smith BJ, Hein R, Roller BRK, Schmidt TM. rrnDB: improved tools for interpreting rRNA gene abundance in bacteria and archaea and a new foundation for future development. Nucleic Acids Res 2014; 43:D593-8. [PMID: 25414355 PMCID: PMC4383981 DOI: 10.1093/nar/gku1201] [Citation(s) in RCA: 526] [Impact Index Per Article: 52.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Microbiologists utilize ribosomal RNA genes as molecular markers of taxonomy in surveys of microbial communities. rRNA genes are often co-located as part of an rrn operon, and multiple copies of this operon are present in genomes across the microbial tree of life. rrn copy number variability provides valuable insight into microbial life history, but introduces systematic bias when measuring community composition in molecular surveys. Here we present an update to the ribosomal RNA operon copy number database (rrnDB), a publicly available, curated resource for copy number information for bacteria and archaea. The redesigned rrnDB (http://rrndb.umms.med.umich.edu/) brings a substantial increase in the number of genomes described, improved curation, mapping of genomes to both NCBI and RDP taxonomies, and refined tools for querying and analyzing these data. With these changes, the rrnDB is better positioned to remain a comprehensive resource under the torrent of microbial genome sequencing. The enhanced rrnDB will contribute to the analysis of molecular surveys and to research linking genomic characteristics to life history.
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Affiliation(s)
- Steven F Stoddard
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Byron J Smith
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Robert Hein
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Benjamin R K Roller
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA
| | - Thomas M Schmidt
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA
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Philip Robertson G, Gross KL, Hamilton SK, Landis DA, Schmidt TM, Snapp SS, Swinton SM. Farming for Ecosystem Services: An Ecological Approach to Production Agriculture. Bioscience 2014; 64:404-415. [PMID: 26955069 PMCID: PMC4776676 DOI: 10.1093/biosci/biu037] [Citation(s) in RCA: 140] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
A balanced assessment of ecosystem services provided by agriculture requires a systems-level socioecological understanding of related management practices at local to landscape scales. The results from 25 years of observation and experimentation at the Kellogg Biological Station long-term ecological research site reveal services that could be provided by intensive row-crop ecosystems. In addition to high yields, farms could be readily managed to contribute clean water, biocontrol and other biodiversity benefits, climate stabilization, and long-term soil fertility, thereby helping meet society's need for agriculture that is economically and environmentally sustainable. Midwest farmers—especially those with large farms—appear willing to adopt practices that deliver these services in exchange for payments scaled to management complexity and farmstead benefit. Surveyed citizens appear willing to pay farmers for the delivery of specific services, such as cleaner lakes. A new farming for services paradigm in US agriculture seems feasible and could be environmentally significant.
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Affiliation(s)
- G Philip Robertson
- G. Philip Robertson ( ) is a professor at the Kellogg Biological Station (KBS) and in the Department of Plant, Soil, and Microbial Sciences at Michigan State University (MSU), in East Lansing. Katherine L. Gross is a professor at KBS and in the Department of Plant Biology at MSU. Stephen K. Hamilton is a professor at KBS and in the Department of Zoology at MSU. Douglas A. Landis is a professor in the Department of Entomology at MSU. Thomas M. Schmidt is a professor in the Department of Ecology and Evolutionary Biology at the University of Michigan, in Ann Arbor. Sieglinde S. Snapp is a professor at KBS and in the Department of Plant, Soil, and Microbial Sciences at MSU. Scott M. Swinton is a professor in the Department of Agricultural, Food, and Resource Economics at MSU. All of the authors are lead investigators with the KBS Long-Term Ecological Research Program
| | - Katherine L Gross
- G. Philip Robertson ( ) is a professor at the Kellogg Biological Station (KBS) and in the Department of Plant, Soil, and Microbial Sciences at Michigan State University (MSU), in East Lansing. Katherine L. Gross is a professor at KBS and in the Department of Plant Biology at MSU. Stephen K. Hamilton is a professor at KBS and in the Department of Zoology at MSU. Douglas A. Landis is a professor in the Department of Entomology at MSU. Thomas M. Schmidt is a professor in the Department of Ecology and Evolutionary Biology at the University of Michigan, in Ann Arbor. Sieglinde S. Snapp is a professor at KBS and in the Department of Plant, Soil, and Microbial Sciences at MSU. Scott M. Swinton is a professor in the Department of Agricultural, Food, and Resource Economics at MSU. All of the authors are lead investigators with the KBS Long-Term Ecological Research Program
| | - Stephen K Hamilton
- G. Philip Robertson ( ) is a professor at the Kellogg Biological Station (KBS) and in the Department of Plant, Soil, and Microbial Sciences at Michigan State University (MSU), in East Lansing. Katherine L. Gross is a professor at KBS and in the Department of Plant Biology at MSU. Stephen K. Hamilton is a professor at KBS and in the Department of Zoology at MSU. Douglas A. Landis is a professor in the Department of Entomology at MSU. Thomas M. Schmidt is a professor in the Department of Ecology and Evolutionary Biology at the University of Michigan, in Ann Arbor. Sieglinde S. Snapp is a professor at KBS and in the Department of Plant, Soil, and Microbial Sciences at MSU. Scott M. Swinton is a professor in the Department of Agricultural, Food, and Resource Economics at MSU. All of the authors are lead investigators with the KBS Long-Term Ecological Research Program
| | - Douglas A Landis
- G. Philip Robertson ( ) is a professor at the Kellogg Biological Station (KBS) and in the Department of Plant, Soil, and Microbial Sciences at Michigan State University (MSU), in East Lansing. Katherine L. Gross is a professor at KBS and in the Department of Plant Biology at MSU. Stephen K. Hamilton is a professor at KBS and in the Department of Zoology at MSU. Douglas A. Landis is a professor in the Department of Entomology at MSU. Thomas M. Schmidt is a professor in the Department of Ecology and Evolutionary Biology at the University of Michigan, in Ann Arbor. Sieglinde S. Snapp is a professor at KBS and in the Department of Plant, Soil, and Microbial Sciences at MSU. Scott M. Swinton is a professor in the Department of Agricultural, Food, and Resource Economics at MSU. All of the authors are lead investigators with the KBS Long-Term Ecological Research Program
| | - Thomas M Schmidt
- G. Philip Robertson ( ) is a professor at the Kellogg Biological Station (KBS) and in the Department of Plant, Soil, and Microbial Sciences at Michigan State University (MSU), in East Lansing. Katherine L. Gross is a professor at KBS and in the Department of Plant Biology at MSU. Stephen K. Hamilton is a professor at KBS and in the Department of Zoology at MSU. Douglas A. Landis is a professor in the Department of Entomology at MSU. Thomas M. Schmidt is a professor in the Department of Ecology and Evolutionary Biology at the University of Michigan, in Ann Arbor. Sieglinde S. Snapp is a professor at KBS and in the Department of Plant, Soil, and Microbial Sciences at MSU. Scott M. Swinton is a professor in the Department of Agricultural, Food, and Resource Economics at MSU. All of the authors are lead investigators with the KBS Long-Term Ecological Research Program
| | - Sieglinde S Snapp
- G. Philip Robertson ( ) is a professor at the Kellogg Biological Station (KBS) and in the Department of Plant, Soil, and Microbial Sciences at Michigan State University (MSU), in East Lansing. Katherine L. Gross is a professor at KBS and in the Department of Plant Biology at MSU. Stephen K. Hamilton is a professor at KBS and in the Department of Zoology at MSU. Douglas A. Landis is a professor in the Department of Entomology at MSU. Thomas M. Schmidt is a professor in the Department of Ecology and Evolutionary Biology at the University of Michigan, in Ann Arbor. Sieglinde S. Snapp is a professor at KBS and in the Department of Plant, Soil, and Microbial Sciences at MSU. Scott M. Swinton is a professor in the Department of Agricultural, Food, and Resource Economics at MSU. All of the authors are lead investigators with the KBS Long-Term Ecological Research Program
| | - Scott M Swinton
- G. Philip Robertson ( ) is a professor at the Kellogg Biological Station (KBS) and in the Department of Plant, Soil, and Microbial Sciences at Michigan State University (MSU), in East Lansing. Katherine L. Gross is a professor at KBS and in the Department of Plant Biology at MSU. Stephen K. Hamilton is a professor at KBS and in the Department of Zoology at MSU. Douglas A. Landis is a professor in the Department of Entomology at MSU. Thomas M. Schmidt is a professor in the Department of Ecology and Evolutionary Biology at the University of Michigan, in Ann Arbor. Sieglinde S. Snapp is a professor at KBS and in the Department of Plant, Soil, and Microbial Sciences at MSU. Scott M. Swinton is a professor in the Department of Agricultural, Food, and Resource Economics at MSU. All of the authors are lead investigators with the KBS Long-Term Ecological Research Program
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Werling BP, Dickson TL, Isaacs R, Gaines H, Gratton C, Gross KL, Liere H, Malmstrom CM, Meehan TD, Ruan L, Robertson BA, Robertson GP, Schmidt TM, Schrotenboer AC, Teal TK, Wilson JK, Landis DA. Perennial grasslands enhance biodiversity and multiple ecosystem services in bioenergy landscapes. Proc Natl Acad Sci U S A 2014; 111:1652-7. [PMID: 24474791 PMCID: PMC3910622 DOI: 10.1073/pnas.1309492111] [Citation(s) in RCA: 124] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Agriculture is being challenged to provide food, and increasingly fuel, for an expanding global population. Producing bioenergy crops on marginal lands--farmland suboptimal for food crops--could help meet energy goals while minimizing competition with food production. However, the ecological costs and benefits of growing bioenergy feedstocks--primarily annual grain crops--on marginal lands have been questioned. Here we show that perennial bioenergy crops provide an alternative to annual grains that increases biodiversity of multiple taxa and sustain a variety of ecosystem functions, promoting the creation of multifunctional agricultural landscapes. We found that switchgrass and prairie plantings harbored significantly greater plant, methanotrophic bacteria, arthropod, and bird diversity than maize. Although biomass production was greater in maize, all other ecosystem services, including methane consumption, pest suppression, pollination, and conservation of grassland birds, were higher in perennial grasslands. Moreover, we found that the linkage between biodiversity and ecosystem services is dependent not only on the choice of bioenergy crop but also on its location relative to other habitats, with local landscape context as important as crop choice in determining provision of some services. Our study suggests that bioenergy policy that supports coordinated land use can diversify agricultural landscapes and sustain multiple critical ecosystem services.
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Affiliation(s)
- Ben P. Werling
- Department of Entomology, Michigan State University, East Lansing, MI 48824
- Great Lakes Bioenergy Research Center, US Department of Energy, Michigan State University, East Lansing, MI 48824
| | - Timothy L. Dickson
- Great Lakes Bioenergy Research Center, US Department of Energy, Michigan State University, East Lansing, MI 48824
- Department of Biology, University of Nebraska at Omaha, Omaha, NE 68182
| | - Rufus Isaacs
- Department of Entomology, Michigan State University, East Lansing, MI 48824
- Great Lakes Bioenergy Research Center, US Department of Energy, Michigan State University, East Lansing, MI 48824
| | - Hannah Gaines
- Great Lakes Bioenergy Research Center, US Department of Energy, University of Wisconsin–Madison, Madison, WI 53706
- Department of Entomology, University of Wisconsin–Madison, Madison, WI 53706
| | - Claudio Gratton
- Great Lakes Bioenergy Research Center, US Department of Energy, University of Wisconsin–Madison, Madison, WI 53706
- Department of Entomology, University of Wisconsin–Madison, Madison, WI 53706
| | - Katherine L. Gross
- Great Lakes Bioenergy Research Center, US Department of Energy, Michigan State University, East Lansing, MI 48824
- W. K. Kellogg Biological Station, Michigan State University, Hickory Corners, MI 49060
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824
| | - Heidi Liere
- Great Lakes Bioenergy Research Center, US Department of Energy, University of Wisconsin–Madison, Madison, WI 53706
- Department of Entomology, University of Wisconsin–Madison, Madison, WI 53706
| | - Carolyn M. Malmstrom
- Great Lakes Bioenergy Research Center, US Department of Energy, Michigan State University, East Lansing, MI 48824
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824
| | - Timothy D. Meehan
- Great Lakes Bioenergy Research Center, US Department of Energy, University of Wisconsin–Madison, Madison, WI 53706
- Department of Entomology, University of Wisconsin–Madison, Madison, WI 53706
| | - Leilei Ruan
- Great Lakes Bioenergy Research Center, US Department of Energy, Michigan State University, East Lansing, MI 48824
- W. K. Kellogg Biological Station, Michigan State University, Hickory Corners, MI 49060
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824
| | - Bruce A. Robertson
- Great Lakes Bioenergy Research Center, US Department of Energy, Michigan State University, East Lansing, MI 48824
- Division of Science, Mathematics and Computing, Bard College, Annandale-on-Hudson, NY 12504
| | - G. Philip Robertson
- Great Lakes Bioenergy Research Center, US Department of Energy, Michigan State University, East Lansing, MI 48824
- W. K. Kellogg Biological Station, Michigan State University, Hickory Corners, MI 49060
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824
| | - Thomas M. Schmidt
- Great Lakes Bioenergy Research Center, US Department of Energy, Michigan State University, East Lansing, MI 48824
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109
| | - Abbie C. Schrotenboer
- Great Lakes Bioenergy Research Center, US Department of Energy, Michigan State University, East Lansing, MI 48824
- Department of Biology, Trinity Christian College, Palos Heights, IL 60463; and
| | - Tracy K. Teal
- Great Lakes Bioenergy Research Center, US Department of Energy, Michigan State University, East Lansing, MI 48824
- Department of Microbiology and Microbial Genetics, Michigan State University, East Lansing, MI 48824
| | - Julianna K. Wilson
- Department of Entomology, Michigan State University, East Lansing, MI 48824
- Great Lakes Bioenergy Research Center, US Department of Energy, Michigan State University, East Lansing, MI 48824
| | - Douglas A. Landis
- Department of Entomology, Michigan State University, East Lansing, MI 48824
- Great Lakes Bioenergy Research Center, US Department of Energy, Michigan State University, East Lansing, MI 48824
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Blasiak LC, Schmidt AW, Andriamiarinoro H, Mulaw T, Rasolomampianina R, Applequist WL, Birkinshaw C, Rejo-Fienena F, Lowry PP, Schmidt TM, Hill RT. Bacterial communities in Malagasy soils with differing levels of disturbance affecting botanical diversity. PLoS One 2014; 9:e85097. [PMID: 24465484 PMCID: PMC3896373 DOI: 10.1371/journal.pone.0085097] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [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: 08/14/2013] [Accepted: 11/22/2013] [Indexed: 11/18/2022] Open
Abstract
Madagascar is well-known for the exceptional biodiversity of its macro-flora and fauna, but the biodiversity of Malagasy microbial communities remains relatively unexplored. Understanding patterns of bacterial diversity in soil and their correlations with above-ground botanical diversity could influence conservation planning as well as sampling strategies to maximize access to bacterially derived natural products. We present the first detailed description of Malagasy soil bacterial communities from a targeted 16S rRNA gene survey of greater than 290,000 sequences generated using 454 pyrosequencing. Two sampling plots in each of three forest conservation areas were established to represent different levels of disturbance resulting from human impact through agriculture and selective exploitation of trees, as well as from natural impacts of cyclones. In parallel, we performed an in-depth characterization of the total vascular plant morphospecies richness within each plot. The plots representing different levels of disturbance within each forest did not differ significantly in bacterial diversity or richness. Changes in bacterial community composition were largest between forests rather than between different levels of impact within a forest. The largest difference in bacterial community composition with disturbance was observed at the Vohibe forest conservation area, and this difference was correlated with changes in both vascular plant richness and soil pH. These results provide the first survey of Malagasy soil bacterial diversity and establish a baseline of botanical diversity within important conservation areas.
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Affiliation(s)
- Leah C. Blasiak
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, Maryland, United States of America
| | - Alex W. Schmidt
- The Center for Microbial Sciences, University of Michigan, Ann Arbor, Michigan, United States of America
| | | | - Temesgen Mulaw
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, Maryland, United States of America
| | - Rado Rasolomampianina
- Laboratoire de Microbiologie de Environnement, Centre National de Recherches sur l′Environnement, Antananarivo, Madagascar
| | | | - Chris Birkinshaw
- Missouri Botanical Garden, St. Louis, Missouri, United States of America
| | - Félicitée Rejo-Fienena
- Laboratoire de Microbiologie de Environnement, Centre National de Recherches sur l′Environnement, Antananarivo, Madagascar
| | - Porter P. Lowry
- Missouri Botanical Garden, St. Louis, Missouri, United States of America
- Département Systématique et Évolution (UMR 7205), Muséum National d'Histoire Naturelle, Paris, France
| | - Thomas M. Schmidt
- The Center for Microbial Sciences, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Russell T. Hill
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, Maryland, United States of America
- * E-mail:
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Morris A, Beck JM, Schloss PD, Campbell TB, Crothers K, Curtis JL, Flores SC, Fontenot AP, Ghedin E, Huang L, Jablonski K, Kleerup E, Lynch SV, Sodergren E, Twigg H, Young VB, Bassis CM, Venkataraman A, Schmidt TM, Weinstock GM. Comparison of the respiratory microbiome in healthy nonsmokers and smokers. Am J Respir Crit Care Med 2013; 187:1067-75. [PMID: 23491408 DOI: 10.1164/rccm.201210-1913oc] [Citation(s) in RCA: 543] [Impact Index Per Article: 49.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
RATIONALE Results from 16S rDNA-encoding gene sequence-based, culture-independent techniques have led to conflicting conclusions about the composition of the lower respiratory tract microbiome. OBJECTIVES To compare the microbiome of the upper and lower respiratory tract in healthy HIV-uninfected nonsmokers and smokers in a multicenter cohort. METHODS Participants were nonsmokers and smokers without significant comorbidities. Oral washes and bronchoscopic alveolar lavages were collected in a standardized manner. Sequence analysis of bacterial 16S rRNA-encoding genes was performed, and the neutral model in community ecology was used to identify bacteria that were the most plausible members of a lung microbiome. MEASUREMENTS AND MAIN RESULTS Sixty-four participants were enrolled. Most bacteria identified in the lung were also in the mouth, but specific bacteria such as Enterobacteriaceae, Haemophilus, Methylobacterium, and Ralstonia species were disproportionally represented in the lungs compared with values predicted by the neutral model. Tropheryma was also in the lung, but not the mouth. Mouth communities differed between nonsmokers and smokers in species such as Porphyromonas, Neisseria, and Gemella, but lung bacterial populations did not. CONCLUSIONS This study is the largest to examine composition of the lower respiratory tract microbiome in healthy individuals and the first to use the neutral model to compare the lung to the mouth. Specific bacteria appear in significantly higher abundance in the lungs than would be expected if they originated from the mouth, demonstrating that the lung microbiome does not derive entirely from the mouth. The mouth microbiome differs in nonsmokers and smokers, but lung communities were not significantly altered by smoking.
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Affiliation(s)
- Alison Morris
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA.
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Young VB, Raffals LH, Huse SM, Vital M, Dai D, Schloss PD, Brulc JM, Antonopoulos DA, Arrieta RL, Kwon JH, Reddy KG, Hubert NA, Grim SL, Vineis JH, Dalal S, Morrison HG, Eren AM, Meyer F, Schmidt TM, Tiedje JM, Chang EB, Sogin ML. Multiphasic analysis of the temporal development of the distal gut microbiota in patients following ileal pouch anal anastomosis. Microbiome 2013; 1:9. [PMID: 24451366 PMCID: PMC3971607 DOI: 10.1186/2049-2618-1-9] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2012] [Accepted: 01/10/2013] [Indexed: 05/20/2023]
Abstract
BACKGROUND The indigenous gut microbiota are thought to play a crucial role in the development and maintenance of the abnormal inflammatory responses that are the hallmark of inflammatory bowel disease. Direct tests of the role of the gut microbiome in these disorders are typically limited by the fact that sampling of the microbiota generally occurs once disease has become manifest. This limitation could potentially be circumvented by studying patients who undergo total proctocolectomy with ileal pouch anal anastomosis (IPAA) for the definitive treatment of ulcerative colitis. A subset of patients who undergo IPAA develops an inflammatory condition known as pouchitis, which is thought to mirror the pathogenesis of ulcerative colitis. Following the development of the microbiome of the pouch would allow characterization of the microbial community that predates the development of overt disease. RESULTS We monitored the development of the pouch microbiota in four patients who underwent IPAA. Mucosal and luminal samples were obtained prior to takedown of the diverting ileostomy and compared to samples obtained 2, 4 and 8 weeks after intestinal continuity had been restored. Through the combined analysis of 16S rRNA-encoding gene amplicons, targeted 16S amplification and microbial cultivation, we observed major changes in structure and function of the pouch microbiota following ileostomy. There is a relative increase in anaerobic microorganisms with the capacity for fermentation of complex carbohydrates, which corresponds to the physical stasis of intestinal contents in the ileal pouch. Compared to the microbiome structure encountered in the colonic mucosa of healthy individuals, the pouch microbial community in three of the four individuals was quite distinct. In the fourth patient, a community that was much like that seen in a healthy colon was established, and this patient also had the most benign clinical course of the four patients, without the development of pouchitis 2 years after IPAA. CONCLUSIONS The microbiota that inhabit the ileal-anal pouch of patients who undergo IPAA for treatment of ulcerative colitis demonstrate significant structural and functional changes related to the restoration of fecal flow. Our preliminary results suggest once the pouch has assumed the physiologic role previously played by the intact colon, the precise structure and function of the pouch microbiome, relative to a normal colonic microbiota, will determine if there is establishment of a stable, healthy mucosal environment or the reinitiation of the pathogenic cascade that results in intestinal inflammation.
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Affiliation(s)
- Vincent B Young
- Department of Internal Medicine, Division of Infectious Diseases, Ann Arbor, MI, USA
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Laura H Raffals
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA
| | - Susan M Huse
- Josephine Bay Paul Center, Marine Biological Laboratory, Woods Hole, MA, USA
| | - Marius Vital
- Center for Microbial Ecology, Michigan State University, East Lansing, MI, USA
| | - Dongjuan Dai
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
| | - Patrick D Schloss
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Jennifer M Brulc
- Institute for Genomics and Systems Biology, Argonne National Laboratory, Argonne, IL, USA
| | | | - Rose L Arrieta
- Department of Medicine, Section of Gastroenterology, The University of Chicago, Knapp Center for Biomedical Discovery, Chicago, IL, USA
| | - John H Kwon
- Department of Medicine, Section of Gastroenterology, The University of Chicago, Knapp Center for Biomedical Discovery, Chicago, IL, USA
| | - K Gautham Reddy
- Department of Medicine, Section of Gastroenterology, The University of Chicago, Knapp Center for Biomedical Discovery, Chicago, IL, USA
| | - Nathaniel A Hubert
- Department of Medicine, Section of Gastroenterology, The University of Chicago, Knapp Center for Biomedical Discovery, Chicago, IL, USA
| | - Sharon L Grim
- Josephine Bay Paul Center, Marine Biological Laboratory, Woods Hole, MA, USA
| | - Joseph H Vineis
- Josephine Bay Paul Center, Marine Biological Laboratory, Woods Hole, MA, USA
| | - Sushila Dalal
- Department of Medicine, Section of Gastroenterology, The University of Chicago, Knapp Center for Biomedical Discovery, Chicago, IL, USA
| | - Hilary G Morrison
- Josephine Bay Paul Center, Marine Biological Laboratory, Woods Hole, MA, USA
| | - A Murat Eren
- Josephine Bay Paul Center, Marine Biological Laboratory, Woods Hole, MA, USA
| | - Folker Meyer
- Institute for Genomics and Systems Biology, Argonne National Laboratory, Argonne, IL, USA
| | - Thomas M Schmidt
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
| | - James M Tiedje
- Center for Microbial Ecology, Michigan State University, East Lansing, MI, USA
| | - Eugene B Chang
- Department of Medicine, Section of Gastroenterology, The University of Chicago, Knapp Center for Biomedical Discovery, Chicago, IL, USA
| | - Mitchell L Sogin
- Josephine Bay Paul Center, Marine Biological Laboratory, Woods Hole, MA, USA
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Vital M, Penton CR, Wang Q, Young VB, Antonopoulos DA, Sogin ML, Morrison HG, Raffals L, Chang EB, Huffnagle GB, Schmidt TM, Cole JR, Tiedje JM. A gene-targeted approach to investigate the intestinal butyrate-producing bacterial community. Microbiome 2013; 1:8. [PMID: 24451334 PMCID: PMC4126176 DOI: 10.1186/2049-2618-1-8] [Citation(s) in RCA: 112] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2012] [Accepted: 01/08/2013] [Indexed: 05/07/2023]
Abstract
BACKGROUND Butyrate, which is produced by the human microbiome, is essential for a well-functioning colon. Bacteria that produce butyrate are phylogenetically diverse, which hinders their accurate detection based on conventional phylogenetic markers. As a result, reliable information on this important bacterial group is often lacking in microbiome research. RESULTS In this study we describe a gene-targeted approach for 454 pyrotag sequencing and quantitative polymerase chain reaction for the final genes in the two primary bacterial butyrate synthesis pathways, butyryl-CoA:acetate CoA-transferase (but) and butyrate kinase (buk). We monitored the establishment and early succession of butyrate-producing communities in four patients with ulcerative colitis who underwent a colectomy with ileal pouch anal anastomosis and compared it with three control samples from healthy colons. All patients established an abundant butyrate-producing community (approximately 5% to 26% of the total community) in the pouch within the 2-month study, but patterns were distinctive among individuals. Only one patient harbored a community profile similar to the healthy controls, in which there was a predominance of but genes that are similar to reference genes from Acidaminococcus sp., Eubacterium sp., Faecalibacterium prausnitzii and Roseburia sp., and an almost complete absence of buk genes. Two patients were greatly enriched in buk genes similar to those of Clostridium butyricum and C. perfringens, whereas a fourth patient displayed abundant communities containing both genes. Most butyrate producers identified in previous studies were detected and the general patterns of taxa found were supported by 16S rRNA gene pyrotag analysis, but the gene-targeted approach provided more detail about the potential butyrate-producing members of the community. CONCLUSIONS The presented approach provides quantitative and genotypic insights into butyrate-producing communities and facilitates a more specific functional characterization of the intestinal microbiome. Furthermore, our analysis refines but and buk reference annotations found in central databases.
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Affiliation(s)
- Marius Vital
- Center for Microbial Ecology, Michigan State University, East Lansing, MI, USA
| | | | - Qiong Wang
- Center for Microbial Ecology, Michigan State University, East Lansing, MI, USA
| | - Vincent B Young
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | | | | | | | - Laura Raffals
- Knapp Center for Biomedical Discovery, University of Chicago, Chicago, IL, USA
| | - Eugene B Chang
- Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Gary B Huffnagle
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Thomas M Schmidt
- Center for Microbial Ecology, Michigan State University, East Lansing, MI, USA
| | - James R Cole
- Center for Microbial Ecology, Michigan State University, East Lansing, MI, USA
| | - James M Tiedje
- Center for Microbial Ecology, Michigan State University, East Lansing, MI, USA
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Shade A, Peter H, Allison SD, Baho DL, Berga M, Bürgmann H, Huber DH, Langenheder S, Lennon JT, Martiny JBH, Matulich KL, Schmidt TM, Handelsman J. Fundamentals of microbial community resistance and resilience. Front Microbiol 2012; 3:417. [PMID: 23267351 PMCID: PMC3525951 DOI: 10.3389/fmicb.2012.00417] [Citation(s) in RCA: 738] [Impact Index Per Article: 61.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2012] [Accepted: 11/19/2012] [Indexed: 12/20/2022] Open
Abstract
Microbial communities are at the heart of all ecosystems, and yet microbial community behavior in disturbed environments remains difficult to measure and predict. Understanding the drivers of microbial community stability, including resistance (insensitivity to disturbance) and resilience (the rate of recovery after disturbance) is important for predicting community response to disturbance. Here, we provide an overview of the concepts of stability that are relevant for microbial communities. First, we highlight insights from ecology that are useful for defining and measuring stability. To determine whether general disturbance responses exist for microbial communities, we next examine representative studies from the literature that investigated community responses to press (long-term) and pulse (short-term) disturbances in a variety of habitats. Then we discuss the biological features of individual microorganisms, of microbial populations, and of microbial communities that may govern overall community stability. We conclude with thoughts about the unique insights that systems perspectives – informed by meta-omics data – may provide about microbial community stability.
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Affiliation(s)
- Ashley Shade
- Department of Molecular, Cellular and Developmental Biology, Yale University New Haven, CT, USA
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Theis KR, Schmidt TM, Holekamp KE. Evidence for a bacterial mechanism for group-specific social odors among hyenas. Sci Rep 2012; 2:615. [PMID: 22937224 PMCID: PMC3431069 DOI: 10.1038/srep00615] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2012] [Accepted: 08/10/2012] [Indexed: 02/01/2023] Open
Abstract
Symbiotic microbes can benefit their animal hosts by enhancing the diversity of communication signals available to them. The fermentation hypothesis for chemical recognition posits that 1) fermentative bacteria in specialized mammalian scent glands generate odorants that mammals co-opt to communicate with one another, and 2) that variation in scent gland odors is due to underlying variation in the structure of bacterial communities within scent glands. For example, group-specific social odors are suggested to be due to members of the same social group harboring more similar bacterial communities in their scent glands than do members of different social groups. We used 16S rRNA gene surveys to show that 1) the scent secretions of spotted hyenas are densely populated by fermentative bacteria whose closest relatives are well-documented odor producers, and that 2) these bacterial communities are more similar among hyenas from the same social group than among those from different groups.
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Affiliation(s)
- Kevin R Theis
- Department of Microbiology & Molecular Genetics, Michigan State University, East Lansing, MI, USA.
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Young VB, Kahn SA, Schmidt TM, Chang EB. Studying the Enteric Microbiome in Inflammatory Bowel Diseases: Getting through the Growing Pains and Moving Forward. Front Microbiol 2011; 2:144. [PMID: 21772835 PMCID: PMC3131521 DOI: 10.3389/fmicb.2011.00144] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2011] [Accepted: 06/16/2011] [Indexed: 01/01/2023] Open
Abstract
In this commentary, we will review some of the early efforts aimed at understanding the role of the enteric microbiota in the causality of inflammatory bowel diseases. By examining these studies and drawing on our own experiences bridging clinical gastroenterology and microbial ecology as part of the NIH-funded Human Microbiome Project (Turnbaugh et al., 2007), we hope to help define some of the “growing pains” that have hampered these initial efforts. It is our sincere hope that this discussion will help advance future efforts in this area by identifying current challenges and limitations and by suggesting strategies to overcome these obstacles.
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Affiliation(s)
- Vincent B Young
- Department of Medicine, University of Michigan Ann Arbor, MI, USA
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Abstract
An intrinsic artifact of 454-based pyrosequencing leads to artificial overrepresentation of >10% of the original DNA sequencing templates. This artificial amplification of sequences is unbiased with regard to position on the pyrosequencing plate or sequence identity, and it occurs in all currently available 454 technologies. The amplified sequences start at the same position and are identical (duplicates), or vary in length, or contain a sequencing discrepancy. If the abundance of any sequence in a data set is going to be enumerated, either for comparative community analysis, transcriptional analysis or other applications, it is important to remove these artificial replicates before analysis. A web-based tool that incorporates the clustering algorithm cd-hit was developed to identify and remove artificially replicated sequences in 454-based pyrosequencing data sets. This tool cannot be used for data sets that have an initial amplification step before the standard pyrosequencing procedure, because artificial replicates cannot be distinguished from expected replication due to polymerase chain reaction (PCR) amplification, e.g., in sequencing of amplified gene "tags." This protocol provides details on how to use the replicate filter and obtain a file of unique sequences for use in metagenomic or transcriptomic analyses.
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Affiliation(s)
- Tracy K Teal
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA.
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Tang X, Schmidt TM, Perez-Leighton CE, Kofuji P. Inwardly rectifying potassium channel Kir4.1 is responsible for the native inward potassium conductance of satellite glial cells in sensory ganglia. Neuroscience 2010; 166:397-407. [PMID: 20074622 DOI: 10.1016/j.neuroscience.2010.01.005] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2009] [Accepted: 01/05/2010] [Indexed: 12/31/2022]
Abstract
Satellite glial cells (SGCs) surround primary afferent neurons in sensory ganglia, and increasing evidence has implicated the K(+) channels of SGCs in affecting or regulating sensory ganglion excitability. The inwardly rectifying K(+) (Kir) channel Kir4.1 is highly expressed in several types of glial cells in the central nervous system (CNS) where it has been implicated in extracellular K(+) concentration buffering. Upon neuronal activity, the extracellular K(+) concentration increases, and if not corrected, causes neuronal depolarization and uncontrolled changes in neuronal excitability. Recently, it has been demonstrated that knockdown of Kir4.1 expression in trigeminal ganglia leads to neuronal hyperexcitability in this ganglia and heightened nociception. Thus, we investigated the contribution of Kir4.1 to the membrane K(+) conductance of SGCs in neonatal and adult mouse trigeminal and dorsal root ganglia. Whole cell patch clamp recordings were performed in conjunction with immunocytochemistry and quantitative transcript analysis in various mouse lines. We found that in wild-type mice, the inward K(+) conductance of SGCs is blocked almost completely with extracellular barium, cesium and desipramine, consistent with a conductance mediated by Kir channels. We then utilized mouse lines in which genetic ablation led to partial or complete loss of Kir4.1 expression to assess the role of this channel subunit in SGCs. The inward K(+) currents of SGCs in Kir4.1+/- mice were decreased by about half while these currents were almost completely absent in Kir4.1-/- mice. These findings in combination with previous reports support the notion that Kir4.1 is the principal Kir channel type in SGCs. Therefore Kir4.1 emerges as a key regulator of SGC function and possibly neuronal excitability in sensory ganglia.
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Affiliation(s)
- X Tang
- Department of Neuroscience, University of Minnesota, 6-145 Jackson Hall, 321 Church Street SE, Minneapolis, MN 55455, USA
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Abstract
Metagenomics is providing an unprecedented view of the taxonomic diversity, metabolic potential and ecological role of microbial communities in biomes as diverse as the mammalian gastrointestinal tract, the marine water column and soils. However, we have found a systematic error in metagenomes generated by 454-based pyrosequencing that leads to an overestimation of gene and taxon abundance; between 11% and 35% of sequences in a typical metagenome are artificial replicates. Here we document the error in several published and original datasets and offer a web-based solution (http://microbiomes.msu.edu/replicates) for identifying and removing these artifacts.
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Affiliation(s)
- Vicente Gomez-Alvarez
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
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Schmidt TM, Miwa RH. An ab initio study of energetic stability and electronic confinement for different structural phases of ZnO nanowires. Nanotechnology 2009; 20:215202. [PMID: 19423926 DOI: 10.1088/0957-4484/20/21/215202] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
We performed an ab initio total energy investigation of hexagonal (wurtzite and graphitic) and zinc blende ZnO nanowires (NWs) aligned along the [0001] and [111] directions, respectively, as a function of the NW diameter. We have considered unpassivated and (hydrogen) passivated NW surfaces. For the unpassivated system, we find that the wurtzite phase represents the energetically most favorable configuration. The width of the energy bandgap of wurtzite ZnO NWs increases by reducing the NW diameter, which is in accordance with the one-dimensional confinement effect. In contrast, this property fails in the zinc blende and graphitic NWs. In the former it is due to the high density of surface states within the fundamental bandgap, while in the latter system the energy bandgap becomes indirect and increases slowly by reducing the NW diameter. Our total energy results indicate that the hydrogen-passivated ZnO NWs are more stable than the unpassivated ones. For thin hydrogen-passivated NWs, we find that the graphitic phase becomes more stable than the wurtzite. For NW diameters around 2 nm, the graphitic and wurtzite phases present similar formation energies, while for larger diameters the wurtzite NWs become energetically more favorable. Finally, comparing the behavior and the positions of the valence and conduction band edges for the unpassivated ZnO NWs, we proposed the formation of type II band alignment for a hypothetical wurtzite/graphitic NW heterojunction.
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Affiliation(s)
- T M Schmidt
- Instituto de Física, Universidade Federal de Uberlândia, Uberlândia, MG, Brazil.
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Abstract
The community of microbes that inhabits the mammalian intestinal tract exists in a symbiosis with their host. The structure of this community represents the combined effects of selection pressure on the part of the host and on the part of the microbes themselves. Through recent advances in the field of microbial ecology we are beginning to understand the forces that shape this complex community. We will review what is known about the interaction between the host and the indigenous microbial community. Following this discussion we will introduce methods that have been used to study the structure, function and dynamics of this community.
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Affiliation(s)
- Vincent B Young
- Department of Medicine, Division of Infectious Diseases, The University of Michigan, Ann Arbor, Michigan 48109, USA.
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Abstract
A dramatic exception to the general pattern of single-copy genes in bacterial and archaeal genomes is the presence of 1–15 copies of each ribosomal RNA encoding gene. The original version of the Ribosomal RNA Database (rrnDB) cataloged estimates of the number of 16S rRNA-encoding genes; the database now includes the number of genes encoding each of the rRNAs (5S, 16S and 23S), an internally transcribed spacer region, and the number of tRNA genes. The rrnDB has been used largely by microbiologists to predict the relative rate at which microbial populations respond to favorable growth conditions, and to interpret 16S rRNA-based surveys of microbial communities. To expand the functionality of the rrnDB (http://ribosome.mmg.msu.edu/rrndb/index.php), the search engine has been redesigned to allow database searches based on 16S rRNA gene copy number, specific organisms or taxonomic subsets of organisms. The revamped database also computes average gene copy numbers for any collection of entries selected. Curation tools now permit rapid updates, resulting in an expansion of the database to include data for 785 bacterial and 69 archaeal strains. The rrnDB continues to serve as the authoritative, curated source that documents the phylogenetic distribution of rRNA and tRNA genes in microbial genomes.
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Affiliation(s)
- Zarraz May-Ping Lee
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA
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Jackson JH, Schmidt TM, Herring PA. A systems approach to model natural variation in reactive properties of bacterial ribosomes. BMC Syst Biol 2008; 2:62. [PMID: 18620602 PMCID: PMC2488324 DOI: 10.1186/1752-0509-2-62] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2008] [Accepted: 07/13/2008] [Indexed: 11/26/2022]
Abstract
Background Natural variation in protein output from translation in bacteria and archaea may be an organism-specific property of the ribosome. This paper adopts a systems approach to model the protein output as a measure of specific ribosome reactive properties in a ribosome-mediated translation apparatus. We use the steady-state assumption to define a transition state complex for the ribosome, coupled with mRNA, tRNA, amino acids and reaction factors, as a subsystem that allows a focus on the completed translational output as a measure of specific properties of the ribosome. Results In analogy to the steady-state reaction of an enzyme complex, we propose a steady-state translation complex for mRNA from any gene, and derive a maximum specific translation activity, Ta(max), as a property of the ribosomal reaction complex. Ta(max) has units of a-protein output per time per a-specific mRNA. A related property of the ribosome, T˜a(max), has units of a-protein per time per total RNA with the relationship T˜a(max) = ρa Ta(max), where ρa represents the fraction of total RNA committed to translation output of Pa from gene a message. Ta(max) as a ribosome property is analogous to kcat for a purified enzyme, and T˜a(max) is analogous to enzyme specific activity in a crude extract. Conclusion Analogy to an enzyme reaction complex led us to a ribosome reaction model for measuring specific translation activity of a bacterial ribosome. We propose to use this model to design experimental tests of our hypothesis that specific translation activity is a ribosomal property that is subject to natural variation and natural selection much like Vmax and Km for any specific enzyme.
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Affiliation(s)
- Julius H Jackson
- Department of Microbiology & Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA.
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Abstract
The effects of surface passivation on the electronic and structural properties of InP nanowires have been investigated by first-principles calculations. We compare the properties of nanowires whose surfaces have been passivated in several ways, always by H atoms and OH radicals. Taking as the initial reference nanowires that are fully passivated by H atoms, we find that the exchange of these atoms at the surface by OH radicals is always energetically favorable. A nanowire fully passivated by OH radicals is about 2.5 eV per passivated dangling bond more stable than a nanowire fully passivated by H atoms. However, the energetically most stable passivated surface is predicted to have all In atoms bonded to OH radicals and all P atoms bonded to H atoms. This mixed passivation is 2.66 eV per passivated dangling bond more stable than a nanowire fully passivated by H atoms. Our results show that, in comparison with the fully H-saturated nanowire, the fully OH-saturated nanowire has a smaller energy band gap and localized states near the energy band edges. Also, more interestingly, concerning optical applications, the most stable H+OH passivated nanowire has a well-defined energy band gap, only 10% smaller than the H-saturated nanowire energy gap, and few localized states always close to the valence band maximum.
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Affiliation(s)
- M Dionízio Moreira
- Instituto de Física, Universidade Federal Fluminense, Campus da Praia Vermelha, Niterói, Rio de Janeiro, CEP 24210-340, Brazil
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Eichorst SA, Breznak JA, Schmidt TM. Isolation and characterization of soil bacteria that define Terriglobus gen. nov., in the phylum Acidobacteria. Appl Environ Microbiol 2007; 73:2708-17. [PMID: 17293520 PMCID: PMC1855589 DOI: 10.1128/aem.02140-06] [Citation(s) in RCA: 198] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacteria in the phylum Acidobacteria are widely distributed and abundant in soils, but their ecological roles are poorly understood, owing in part to a paucity of cultured representatives. In a molecular survey of acidobacterial diversity at the Michigan State University Kellogg Biological Station Long-Term Ecological Research site, 27% of acidobacterial 16S rRNA gene clones in a never-tilled, successional plant community belonged to subdivision 1, whose relative abundance varied inversely with soil pH. Strains of subdivision 1 were isolated from these never-tilled soils using low-nutrient medium incubated for 3 to 4 weeks under elevated levels of carbon dioxide, which resulted in a slightly acidified medium that matched the pH optima of the strains (between 5 and 6). Colonies were approximately 1 mm in diameter and either white or pink, the latter due to a carotenoid(s) that was synthesized preferentially under 20% instead of 2% oxygen. Strains were gram-negative, aerobic, chemo-organotrophic, nonmotile rods that produced an extracellular matrix. All strains contained either one or two copies of the 16S rRNA encoding gene, which along with a relatively slow doubling time (10 to 15 h at ca. 23 degrees C) is suggestive of an oligotrophic lifestyle. Six of the strains are sufficiently similar to one another, but distinct from previously named Acidobacteria, to warrant creation of a new genus, Terriglobus, with Terriglobus roseus defined as the type species. The physiological and nutritional characteristics of Terriglobus are consistent with its potential widespread distribution in soil.
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MESH Headings
- Bacterial Typing Techniques
- Blotting, Southern
- Carbon/metabolism
- Carotenoids/biosynthesis
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Extracellular Matrix
- Fatty Acids/analysis
- Fatty Acids/chemistry
- Genes, rRNA/genetics
- Gram-Negative Aerobic Rods and Cocci/classification
- Gram-Negative Aerobic Rods and Cocci/cytology
- Gram-Negative Aerobic Rods and Cocci/isolation & purification
- Gram-Negative Aerobic Rods and Cocci/physiology
- Molecular Sequence Data
- Movement
- Phylogeny
- Pigments, Biological/biosynthesis
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/genetics
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
- Soil Microbiology
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Affiliation(s)
- Stephanie A Eichorst
- Michigan State University, Department of Microbiology and Molecular Genetics, 6180 Biomedical and Physical Sciences Building, East Lansing, MI 48824-4320, USA
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50
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Abstract
Protein synthesis is the predominant activity of growing bacteria; the protein synthesis system accounts for more than one-half the cell's dry mass and consumes most of the cell's energy during rapid growth. Translation has been studied extensively using model organisms, and the translational apparatus is qualitatively similar in terms of structure and function across all known forms of life. However, little is known about variation between organisms in translational performance. Using measurements of macromolecular content in a phylogenetically diverse collection of bacteria with contrasting ecological strategies, we found that the translational power (the rate of protein synthesis normalized to the mass of the protein synthesis system) is three- to fourfold higher among bacteria that respond rapidly to nutrient availability than among bacteria that respond slowly. An analysis of codon use in completely sequenced bacterial genomes confirmed that the selective forces acting on translation vary with the ecological strategy. We propose that differences in translational power result from ecologically based variation among microbes in the relative importance of two competing benefits: reducing the biomass invested in the protein synthesis system and reducing the energetic expense of protein synthesis.
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Affiliation(s)
- Les Dethlefsen
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824-4320, USA
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