6101
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Aw W, Fukuda S. The Role of Integrated Omics in Elucidating the Gut Microbiota Health Potentials. ACTA ACUST UNITED AC 2015. [DOI: 10.1007/978-3-319-23213-3_4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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6102
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Abstract
PURPOSE OF REVIEW With depressive disorders the leading source of disability globally, the identification of new targets for prevention and management is imperative. A rapidly emerging field of research suggests that the microbiome-gut-brain axis is of substantial relevance to mood and behaviour. Similarly, unhealthy diet has recently emerged as a significant correlate of and risk factor for depression. This review provides evidence for the gut microbiota as a key factor mediating the link between diet and depressive illness. RECENT FINDINGS The development of new technologies is affording a better understanding of how diet influences gut microbiota composition and activity and how this may, in turn, influence depressive illness. New interventions are also suggesting the possible utility of pre and probiotic formulations and fermented food in influencing mental health. SUMMARY Although in its early stages, the emerging field of research focused on the human microbiome suggests an important role for the gut microbiota in influencing brain development, behaviour and mood in humans. The recognition that the gut microbiota interacts bidirectionally with other environmental risk factors, such as diet and stress, suggests promise in the development of interventions targeting the gut microbiota for the prevention and treatment of common mental health disorders.
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6103
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Engen PA, Green SJ, Voigt RM, Forsyth CB, Keshavarzian A. The Gastrointestinal Microbiome: Alcohol Effects on the Composition of Intestinal Microbiota. Alcohol Res 2015; 37:223-36. [PMID: 26695747 PMCID: PMC4590619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The excessive use of alcohol is a global problem causing many adverse pathological health effects and a significant financial health care burden. This review addresses the effect of alcohol consumption on the microbiota in the gastrointestinal tract (GIT). Although data are limited in humans, studies highlight the importance of changes in the intestinal microbiota in alcohol-related disorders. Alcohol-induced changes in the GIT microbiota composition and metabolic function may contribute to the well-established link between alcohol-induced oxidative stress, intestinal hyperpermeability to luminal bacterial products, and the subsequent development of alcoholic liver disease (ALD), as well as other diseases. In addition, clinical and preclinical data suggest that alcohol-related disorders are associated with quantitative and qualitative dysbiotic changes in the intestinal microbiota and may be associated with increased GIT inflammation, intestinal hyperpermeability resulting in endotoxemia, systemic inflammation, and tissue damage/organ pathologies including ALD. Thus, gut-directed interventions, such as probiotic and synbiotic modulation of the intestinal microbiota, should be considered and evaluated for prevention and treatment of alcohol-associated pathologies.
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6104
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Frese SA, Parker K, Calvert CC, Mills DA. Diet shapes the gut microbiome of pigs during nursing and weaning. MICROBIOME 2015; 3:28. [PMID: 26167280 PMCID: PMC4499176 DOI: 10.1186/s40168-015-0091-8] [Citation(s) in RCA: 311] [Impact Index Per Article: 34.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Accepted: 06/06/2015] [Indexed: 05/21/2023]
Abstract
BACKGROUND The newborn mammal is rapidly colonized by a complex microbial community, whose importance for host health is becoming increasingly clear. Understanding the forces that shape the early community, especially during the nursing period, is critical to gain insight into how this consortium of microbes is assembled. Pigs present an attractive model for nursing humans, given physiological and compositional similarity of pig and human milk and the utility of pigs in experimental studies. However, there is a paucity of data examining the gut microbiome in nursing pigs from birth through weaning using modern molecular methods and fewer experimental studies that examine the impact of diet on these microbial communities. RESULTS We characterized the fecal microbiome of pigs from birth through 7 weeks of age, during which the animals were transitioned from an exclusive diet of sow milk to a starter diet composed of plant and animal-based components. Microbial communities were clearly distinguishable based on diet, being relatively stable absent dietary changes. Metagenomic sequencing was used to characterize a subset of animals before and after weaning, which identified glycan degradation pathways differing significantly between diets. Predicted enzymes active on milk-derived glycans that are otherwise indigestible to the host animal were enriched in the microbial metagenome of milk-fed animals. In contrast, the bacterial metagenome of weaned animals was enriched in functional pathways involved in plant glycan deconstruction and consumption. CONCLUSIONS The gut microbiome in young pigs is dramatically shaped by the composition of dietary glycans, reflected by the different functional capacities of the microbiome before and after weaning.
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Affiliation(s)
- Steven A. Frese
- />Department of Food Science and Technology, University of California Davis, Davis, CA 95616 USA
- />Foods for Health Institute, University of California Davis, Davis, CA 95616 USA
| | - Kent Parker
- />Department of Animal Science, University of California Davis, Davis, CA 95616 USA
| | - C. Chris Calvert
- />Department of Animal Science, University of California Davis, Davis, CA 95616 USA
| | - David A. Mills
- />Department of Food Science and Technology, University of California Davis, Davis, CA 95616 USA
- />Foods for Health Institute, University of California Davis, Davis, CA 95616 USA
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6105
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Valdés L, Cuervo A, Salazar N, Ruas-Madiedo P, Gueimonde M, González S. The relationship between phenolic compounds from diet and microbiota: impact on human health. Food Funct 2015; 6:2424-39. [DOI: 10.1039/c5fo00322a] [Citation(s) in RCA: 142] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The human intestinal tract is home to a complex microbial community called microbiota.
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Affiliation(s)
- L. Valdés
- Department of Microbiology and Biochemistry of Dairy Products
- Instituto de Productos Lácteos de Asturias – Consejo Superior de Investigaciones Científicas (IPLA-CSIC)
- Pase Río Linares s/n
- 33300 Villaviciosa
- Spain
| | - A. Cuervo
- Department of Functional Biology
- University of Oviedo
- Facultad de Medicina
- Oviedo
- Spain
| | - N. Salazar
- Department of Microbiology and Biochemistry of Dairy Products
- Instituto de Productos Lácteos de Asturias – Consejo Superior de Investigaciones Científicas (IPLA-CSIC)
- Pase Río Linares s/n
- 33300 Villaviciosa
- Spain
| | - P. Ruas-Madiedo
- Department of Microbiology and Biochemistry of Dairy Products
- Instituto de Productos Lácteos de Asturias – Consejo Superior de Investigaciones Científicas (IPLA-CSIC)
- Pase Río Linares s/n
- 33300 Villaviciosa
- Spain
| | - M. Gueimonde
- Department of Microbiology and Biochemistry of Dairy Products
- Instituto de Productos Lácteos de Asturias – Consejo Superior de Investigaciones Científicas (IPLA-CSIC)
- Pase Río Linares s/n
- 33300 Villaviciosa
- Spain
| | - S. González
- Department of Functional Biology
- University of Oviedo
- Facultad de Medicina
- Oviedo
- Spain
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6106
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Tilg H, Gao B. Dietary saturated lipids in alcoholic liver disease: new microbiota-targeting bullets? Gastroenterology 2015; 148:16-9. [PMID: 25451649 DOI: 10.1053/j.gastro.2014.11.023] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Herbert Tilg
- Department of Internal Medicine I, Endocrinology, Gastroenterology & Metabolism, Medical University Innsbruck, Innsbruck, Austria.
| | - Bin Gao
- Laboratory of Liver Diseases, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, Maryland.
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6107
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Daft JG, Ptacek T, Kumar R, Morrow C, Lorenz RG. Cross-fostering immediately after birth induces a permanent microbiota shift that is shaped by the nursing mother. MICROBIOME 2015; 3:17. [PMID: 25969735 PMCID: PMC4427954 DOI: 10.1186/s40168-015-0080-y] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Accepted: 04/03/2015] [Indexed: 05/15/2023]
Abstract
BACKGROUND Current research has led to the appreciation that there are differences in the commensal microbiota between healthy individuals and individuals that are predisposed to disease. Treatments to reverse disease pathogenesis through the manipulation of the gastrointestinal (GI) microbiota are now being explored. Normalizing microbiota between different strains of mice in the same study is also needed to better understand disease pathogenesis. Current approaches require repeated delivery of bacteria and large numbers of animals and vary in treatment start time. A method is needed that can shift the microbiota of predisposed individuals to a healthy microbiota at an early age and sustain this shift through the lifetime of the individual. RESULTS We tested cross-fostering of pups within 48 h of birth as a means to permanently shift the microbiota from birth. Taxonomical analysis revealed that the nursing mother was the critical factor in determining bacterial colonization, instead of the birth mother. Data was evaluated using bacterial 16S rDNA sequences from fecal pellets and sequencing was performed on an Illumina Miseq using a 251 bp paired-end library. CONCLUSIONS The results show that cross-fostering is an effective means to induce an early and maintained shift in the commensal microbiota. This will allow for the evaluation of a prolonged microbial shift and its effects on disease pathogenesis. Cross-fostering will also eliminate variation within control models by normalizing the commensal microbiota between different strains of mice.
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Affiliation(s)
- Joseph G Daft
- />Department of Pathology, University of Alabama at Birmingham, 1825 University Blvd, SHEL 602, Birmingham, AL USA
- />Comprehensive Diabetes Center, University of Alabama at Birmingham, 1825 University Boulevard, SHEL 1207, Birmingham, AL USA
| | - Travis Ptacek
- />Department of Microbiology, University of Alabama at Birmingham, 3201 1st Avenue North, Birmingham, AL USA
- />Center for Clinical and Translational Science, University of Alabama at Birmingham, 1924 7th Avenue South, Birmingham, AL USA
| | - Ranjit Kumar
- />Center for Clinical and Translational Science, University of Alabama at Birmingham, 1924 7th Avenue South, Birmingham, AL USA
| | - Casey Morrow
- />Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, 1918 University Boulevard, Birmingham, AL USA
| | - Robin G Lorenz
- />Department of Pathology, University of Alabama at Birmingham, 1825 University Blvd, SHEL 602, Birmingham, AL USA
- />Comprehensive Diabetes Center, University of Alabama at Birmingham, 1825 University Boulevard, SHEL 1207, Birmingham, AL USA
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6108
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Baxter NT, Wan JJ, Schubert AM, Jenior ML, Myers P, Schloss PD. Intra- and interindividual variations mask interspecies variation in the microbiota of sympatric peromyscus populations. Appl Environ Microbiol 2015; 81:396-404. [PMID: 25362056 PMCID: PMC4272734 DOI: 10.1128/aem.02303-14] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Accepted: 10/22/2014] [Indexed: 02/06/2023] Open
Abstract
Using populations of two sympatric Peromyscus species, we characterized the importance of the host species, physiology, environment, diet, and other factors in shaping the structure and dynamics of their gut microbiota. We performed a capture-mark-release experiment in which we obtained 16S rRNA gene sequence data from 49 animals at multiple time points. In addition, we performed 18S rRNA gene sequencing of the same samples to characterize the diet of each individual. Our analysis could not distinguish between the two species of Peromyscus on the basis of the structures of their microbiotas. However, we did observe a set of bacterial populations that were found in every animal. Most notable were abundant representatives of the genera Lactobacillus and Helicobacter. When we combined the 16S and 18S rRNA gene sequence analyses, we were unable to distinguish the communities on the basis of the animal's diet. Furthermore, there were no discernible differences in the structure of the gut communities based on the capture site or their developmental or physiological status. Finally, in contrast to humans, where each individual has a unique microbiota when sampled over years, among the animals captured in this study, the uniqueness of each microbiota was lost within a week of the original sampling. Wild populations provide an opportunity to study host-microbiota interactions as they originally evolved, and the ability to perform natural experiments will facilitate a greater understanding of the factors that shape the structure and function of the gut microbiota.
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Affiliation(s)
- Nielson T Baxter
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
| | - Judy J Wan
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Alyxandria M Schubert
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
| | - Matthew L Jenior
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
| | - Philip Myers
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Patrick D Schloss
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
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6109
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Abstract
The question whether dietary habits and lifestyle have influence on the course of multiple sclerosis (MS) is still a matter of debate, and at present, MS therapy is not associated with any information on diet and lifestyle. Here we show that dietary factors and lifestyle may exacerbate or ameliorate MS symptoms by modulating the inflammatory status of the disease both in relapsing-remitting MS and in primary-progressive MS. This is achieved by controlling both the metabolic and inflammatory pathways in the human cell and the composition of commensal gut microbiota. What increases inflammation are hypercaloric Western-style diets, characterized by high salt, animal fat, red meat, sugar-sweetened drinks, fried food, low fiber, and lack of physical exercise. The persistence of this type of diet upregulates the metabolism of human cells toward biosynthetic pathways including those of proinflammatory molecules and also leads to a dysbiotic gut microbiota, alteration of intestinal immunity, and low-grade systemic inflammation. Conversely, exercise and low-calorie diets based on the assumption of vegetables, fruit, legumes, fish, prebiotics, and probiotics act on nuclear receptors and enzymes that upregulate oxidative metabolism, downregulate the synthesis of proinflammatory molecules, and restore or maintain a healthy symbiotic gut microbiota. Now that we know the molecular mechanisms by which dietary factors and exercise affect the inflammatory status in MS, we can expect that a nutritional intervention with anti-inflammatory food and dietary supplements can alleviate possible side effects of immune-modulatory drugs and the symptoms of chronic fatigue syndrome and thus favor patient wellness.
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Affiliation(s)
- Paolo Riccio
- Department of Sciences, University of Basilicata, Potenza, Italy
| | - Rocco Rossano
- Department of Sciences, University of Basilicata, Potenza, Italy
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6110
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Plé C, Adouard N, Breton J, Dewulf J, Pot B, Bonnarme P, Foligné B. Designing specific cheese-ripening ecosystems to shape the immune effects of dairy products? J Funct Foods 2015. [DOI: 10.1016/j.jff.2014.11.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
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6111
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Repeated cooking and freezing of whole wheat flour increases resistant starch with beneficial impacts on in vitro fecal fermentation properties. J Funct Foods 2015. [DOI: 10.1016/j.jff.2014.11.023] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
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6112
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Weingarden A, González A, Vázquez-Baeza Y, Weiss S, Humphry G, Berg-Lyons D, Knights D, Unno T, Bobr A, Kang J, Khoruts A, Knight R, Sadowsky MJ. Dynamic changes in short- and long-term bacterial composition following fecal microbiota transplantation for recurrent Clostridium difficile infection. MICROBIOME 2015; 3:10. [PMID: 25825673 PMCID: PMC4378022 DOI: 10.1186/s40168-015-0070-0] [Citation(s) in RCA: 179] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Accepted: 01/29/2015] [Indexed: 05/22/2023]
Abstract
BACKGROUND Fecal microbiota transplantation (FMT) is an effective treatment for recurrent Clostridium difficile infection (CDI) that often fails standard antibiotic therapy. Despite its widespread recent use, however, little is known about the stability of the fecal microbiota following FMT. RESULTS Here we report on short- and long-term changes and provide kinetic visualization of fecal microbiota composition in patients with multiply recurrent CDI that were refractory to antibiotic therapy and treated using FMT. Fecal samples were collected from four patients before and up to 151 days after FMT, with daily collections until 28 days and weekly collections until 84 days post-FMT. The composition of fecal bacteria was characterized using high throughput 16S rRNA gene sequence analysis, compared to microbiota across body sites in the Human Microbiome Project (HMP) database, and visualized in a movie-like, kinetic format. FMT resulted in rapid normalization of bacterial fecal sample composition from a markedly dysbiotic state to one representative of normal fecal microbiota. While the microbiome appeared most similar to the donor implant material 1 day post-FMT, the composition diverged variably at later time points. The donor microbiota composition also varied over time. However, both post-FMT and donor samples remained within the larger cloud of fecal microbiota characterized as healthy by the HMP. CONCLUSIONS Dynamic behavior is an intrinsic property of normal fecal microbiota and should be accounted for in comparing microbial communities among normal individuals and those with disease states. This also suggests that more frequent sample analyses are needed in order to properly assess success of FMT procedures.
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Affiliation(s)
- Alexa Weingarden
- />Department of Soil, Water, and Climate, and Microbial and Plant Genomics Institute, University of Minnesota, St Paul, MN USA
- />BioTechnology Institute, 1479 Gortner Ave, 140 Gortner Labs, St. Paul, MN 55108 USA
| | - Antonio González
- />BioFrontiers Institute, University of Colorado, Boulder, CO USA
| | | | - Sophie Weiss
- />Department of Chemical and Biological Engineering, University of Colorado, Boulder, CO USA
| | - Gregory Humphry
- />Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, USA
| | - Donna Berg-Lyons
- />Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, USA
| | - Dan Knights
- />Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN USA
- />BioTechnology Institute, 1479 Gortner Ave, 140 Gortner Labs, St. Paul, MN 55108 USA
| | - Tatsuya Unno
- />BioTechnology Institute, 1479 Gortner Ave, 140 Gortner Labs, St. Paul, MN 55108 USA
| | - Aleh Bobr
- />Division of Gastroenterology, Department of Medicine, Center for Immunology, University of Minnesota, Minneapolis, MN USA
| | - Johnthomas Kang
- />BioTechnology Institute, 1479 Gortner Ave, 140 Gortner Labs, St. Paul, MN 55108 USA
- />Division of Gastroenterology, Department of Medicine, Center for Immunology, University of Minnesota, Minneapolis, MN USA
| | - Alexander Khoruts
- />BioTechnology Institute, 1479 Gortner Ave, 140 Gortner Labs, St. Paul, MN 55108 USA
- />Division of Gastroenterology, Department of Medicine, Center for Immunology, University of Minnesota, Minneapolis, MN USA
| | - Rob Knight
- />BioFrontiers Institute, University of Colorado, Boulder, CO USA
- />Department of Chemistry & Biochemistry, University of Colorado, Boulder, CO USA
- />Howard Hughes Medical Institute, Boulder, CO USA
| | - Michael J Sadowsky
- />Department of Soil, Water, and Climate, and Microbial and Plant Genomics Institute, University of Minnesota, St Paul, MN USA
- />BioTechnology Institute, 1479 Gortner Ave, 140 Gortner Labs, St. Paul, MN 55108 USA
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6113
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Cătoi AF, Pârvu A, Mureşan A, Busetto L. Metabolic Mechanisms in Obesity and Type 2 Diabetes: Insights from Bariatric/Metabolic Surgery. Obes Facts 2015; 8:350-63. [PMID: 26584027 PMCID: PMC5644813 DOI: 10.1159/000441259] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 09/17/2015] [Indexed: 12/11/2022] Open
Abstract
Obesity and the related diabetes epidemics represent a real concern worldwide. Bariatric/metabolic surgery emerged in last years as a valuable therapeutic option for obesity and related diseases, including type 2 diabetes mellitus (T2DM). The complicated network of mechanisms involved in obesity and T2DM have not completely defined yet. There is still a debate on which would be the first metabolic defect leading to metabolic deterioration: insulin resistance or hyperinsulinemia? Insight into the metabolic effects of bariatric/metabolic surgery has revealed that, beyond weight loss and food restriction, other mechanisms can be activated by the rearrangements of the gastrointestinal tract, such as the incretinic/anti-incretinic system, changes in bile acid composition and flow, and modifications of gut microbiota; all of them possibly involved in the remission of T2DM. The complete elucidation of these mechanisms will lead to a better understanding of the pathogenesis of this disease. Our aim was to review some of the metabolic mechanisms involved in the development of T2DM in obese patients as well as in the remission of this condition in patients submitted to bariatric/metabolic surgery.
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Affiliation(s)
- Adriana Florinela Cătoi
- Department of Functional Biosciences, Faculty of Medicine, ‘Iuliu Haţieganu’ University of Medicine and Pharmacy, Cluj-Napoca, Romania, Italy
| | - Alina Pârvu
- Department of Functional Biosciences, Faculty of Medicine, ‘Iuliu Haţieganu’ University of Medicine and Pharmacy, Cluj-Napoca, Romania, Italy
| | - Adriana Mureşan
- Department of Functional Biosciences, Faculty of Medicine, ‘Iuliu Haţieganu’ University of Medicine and Pharmacy, Cluj-Napoca, Romania, Italy
| | - Luca Busetto
- Department of Medicine, University of Padova, Padova, Italy
- *Dr. Luca Busetto, Clinica Medica 3, Policlinico Universitario, Via Giustiniani 2, 30100 Padova, Italy
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6114
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Abstract
: The human intestinal microbiome plays a critical role in human health and disease, including the pathogenesis of inflammatory bowel disease (IBD). Numerous studies have identified altered bacterial diversity and abundance at varying taxonomic levels through biopsies and fecal samples of patients with IBD and diseased model animals. However, inconsistent observations regarding the microbial compositions of such patients have hindered the efforts in assessing the etiological role of specific bacterial species in the pathophysiology of IBD. These observations highlight the importance of minimizing the confounding factors associated with IBD and the need for a standardized methodology to analyze well-defined microbial sampling sources in early IBD diagnosis. Furthermore, establishing the linkage between microbiota compositions with their function within the host system can provide new insights on the pathogenesis of IBD. Such research has been greatly facilitated by technological advances that include functional metagenomics coupled with proteomic and metabolomic profiling. This review provides updates on the composition of the microbiome in IBD and emphasizes microbiota dysbiosis-involved mechanisms. We highlight functional roles of specific bacterial groups in the development and management of IBD. Functional analyses of the microbiome may be the key to understanding the role of microbiota in the development and chronicity of IBD and reveal new strategies for therapeutic intervention.
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6115
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Burokas A, Moloney RD, Dinan TG, Cryan JF. Microbiota regulation of the Mammalian gut-brain axis. ADVANCES IN APPLIED MICROBIOLOGY 2015; 91:1-62. [PMID: 25911232 DOI: 10.1016/bs.aambs.2015.02.001] [Citation(s) in RCA: 184] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The realization that the microbiota-gut-brain axis plays a critical role in health and disease has emerged over the past decade. The brain-gut axis is a bidirectional communication system between the central nervous system (CNS) and the gastrointestinal tract. Regulation of the microbiota-brain-gut axis is essential for maintaining homeostasis, including that of the CNS. The routes of this communication are not fully elucidated but include neural, humoral, immune, and metabolic pathways. A number of approaches have been used to interrogate this axis including the use of germ-free animals, probiotic agents, antibiotics, or animals exposed to pathogenic bacterial infections. Together, it is clear that the gut microbiota can be a key regulator of mood, cognition, pain, and obesity. Understanding microbiota-brain interactions is an exciting area of research which may contribute new insights into individual variations in cognition, personality, mood, sleep, and eating behavior, and how they contribute to a range of neuropsychiatric diseases ranging from affective disorders to autism and schizophrenia. Finally, the concept of psychobiotics, bacterial-based interventions with mental health benefit, is also emerging.
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Affiliation(s)
- Aurelijus Burokas
- Laboratory of Neurogastroenterology, Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
| | - Rachel D Moloney
- Laboratory of Neurogastroenterology, Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
| | - Timothy G Dinan
- Laboratory of Neurogastroenterology, Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland; Department of Psychiatry, University College Cork, Cork, Ireland
| | - John F Cryan
- Laboratory of Neurogastroenterology, Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland
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6116
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Bello González T, van Passel M, Tims S, Fuentes S, De Vos W, Smidt H, Belzer C. Application of the Human Intestinal Tract Chip to the non-human primate gut microbiota. Benef Microbes 2015; 6:271-6. [DOI: 10.3920/bm2014.0087] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The human intestinal microbiota is responsible for various health-related functions, and its diversity can be readily mapped with the 16S ribosomal RNA targeting Human Intestinal Tract (HIT) Chip. Here we characterise distal gut samples from chimpanzees, gorillas and marmosets, and compare them with human gut samples. Our results indicated applicability of the HITChip platform can be extended to chimpanzee and gorilla faecal samples for analysis of microbiota composition and enterotypes, but not to the evolutionary more distant marmosets.
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Affiliation(s)
- T.D.J. Bello González
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, the Netherlands
| | - M.W.J. van Passel
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, the Netherlands
- National Institute for Public Health and the Environment, Postbus 1, 3720 BA Bilthoven, the Netherlands
| | - S. Tims
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, the Netherlands
| | - S. Fuentes
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, the Netherlands
| | - W.M. De Vos
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, the Netherlands
- Department of Veterinary Biosciences, Helsinki University, P.O. Box 66, 00014 Helsinki, Finland
- Department of Bacteriology and Immunology, Helsinki University, P.O. Box 21, 00014 Helsinki, Finland
| | - H. Smidt
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, the Netherlands
| | - C. Belzer
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, the Netherlands
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6117
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Abstract
The microbiome, of which the bacterial component alone (microbiota), is estimated to include 10 times more cells than human cells of the body, blooms immediately after birth and evolves in composition and complexity throughout childhood. The gut microbiome has a profound impact on gastrointestinal tract development, maintenance of mucosal surface integrity, and contributes to the nutritional status of the host and thus plays a pivotal role in health and disease. New technologies have enabled the detailed characterization of normal microbial symbionts and dysbiosis-disease associations. This review summarizes the stepwise establishment of the intestinal microbiota, influential environmental factors, and how this may be perturbed in preterm very-low-birth-weight infants. The contribution of the microbiota to provision of energy and nutrients for intestinal development and the nutritional status of the host are reviewed. In addition, the crucial role of the gut microbiota in maintaining mucosal integrity is explored along with how its breakdown can lead to sepsis, necrotizing enterocolitis, and systemic inflammatory response syndrome. Finally, the role of enteral feeding type (human milk, formula, and nutrient fortification) in mediating these processes is discussed, and guidance is provided for nutritional strategies to promote health in these fragile infants.
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6118
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Abstract
The human intestine houses an astounding number and species of microorganisms, estimated at more than 10(14) gut microbiota and composed of over a thousand species. An individual's profile of microbiota is continually influenced by a variety of factors including but not limited to genetics, age, sex, diet, and lifestyle. Although each person's microbial profile is distinct, the relative abundance and distribution of bacterial species is similar among healthy individuals, aiding in the maintenance of one's overall health. Consequently, the ability of gut microbiota to bidirectionally communicate with the brain, known as the gut-brain axis, in the modulation of human health is at the forefront of current research. At a basic level, the gut microbiota interacts with the human host in a mutualistic relationship - the host intestine provides the bacteria with an environment to grow and the bacterium aids in governing homeostasis within the host. Therefore, it is reasonable to think that the lack of healthy gut microbiota may also lead to a deterioration of these relationships and ultimately disease. Indeed, a dysfunction in the gut-brain axis has been elucidated by a multitude of studies linked to neuropsychological, metabolic, and gastrointestinal disorders. For instance, altered microbiota has been linked to neuropsychological disorders including depression and autism spectrum disorder, metabolic disorders such as obesity, and gastrointestinal disorders including inflammatory bowel disease and irritable bowel syndrome. Fortunately, studies have also indicated that gut microbiota may be modulated with the use of probiotics, antibiotics, and fecal microbiota transplants as a prospect for therapy in microbiota-associated diseases. This modulation of gut microbiota is currently a growing area of research as it just might hold the key to treatment.
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Affiliation(s)
- Linghong Zhou
- Department of Psychiatry and Behavioural Neurosciences, McMaster University, Hamilton, ON, Canada
| | - Jane A Foster
- Department of Psychiatry and Behavioural Neurosciences, McMaster University, Hamilton, ON, Canada ; Brain-Body Institute, St Joseph's Healthcare, Hamilton, ON, Canada
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6119
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Hubert J, Nesvorná M, Kopecký J, Ságová-Marečková M, Poltronieri P. Carpoglyphus lactis
(Acari: Astigmata) from various dried fruits differed in associated micro-organisms. J Appl Microbiol 2014; 118:470-84. [DOI: 10.1111/jam.12714] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Revised: 11/18/2014] [Accepted: 11/30/2014] [Indexed: 11/28/2022]
Affiliation(s)
- J. Hubert
- Crop Research Institute; Prague Czech Republic
| | - M. Nesvorná
- Crop Research Institute; Prague Czech Republic
| | - J. Kopecký
- Crop Research Institute; Prague Czech Republic
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6120
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Mao L, Franke J. Symbiosis, dysbiosis, and rebiosis-The value of metaproteomics in human microbiome monitoring. Proteomics 2014; 15:1142-51. [DOI: 10.1002/pmic.201400329] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Revised: 09/02/2014] [Accepted: 10/08/2014] [Indexed: 01/01/2023]
Affiliation(s)
- Lei Mao
- Department of Life Science Engineering; HTW Berlin - University of Applied Sciences; Germany
| | - Jacqueline Franke
- Department of Life Science Engineering; HTW Berlin - University of Applied Sciences; Germany
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6121
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Raskov H, Pommergaard HC, Burcharth J, Rosenberg J. Colorectal carcinogenesis-update and perspectives. World J Gastroenterol 2014; 20:18151-18164. [PMID: 25561783 PMCID: PMC4277953 DOI: 10.3748/wjg.v20.i48.18151] [Citation(s) in RCA: 116] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/28/2014] [Revised: 08/18/2014] [Accepted: 09/30/2014] [Indexed: 02/06/2023] Open
Abstract
Colorectal cancer (CRC) is a very common malignancy in the Western World and despite advances in surgery, chemotherapy and screening, it is still the second leading cause of cancer deaths in this part of the world. Numerous factors are found important in the development of CRC including colonocyte metbolism, high risk luminal environment, inflammation, as well as lifestyle factors such as diet, tobacco, and alchohol consumption. In recent years focus has turned towards the genetics and molecular biology of CRC and several interesting and promising correlations and pathways have been discovered. The major genetic pathways of CRC are the Chromosome Instability Pathway representing the pathway of sporadic CRC through the K-ras, APC, and P53 mutations, and the Microsatellite Instability Pathway representing the pathway of hereditary non-polyposis colon cancer through mutations in mismatch repair genes. To identify early cancers, screening programs have been initiated, and the leading strategy has been the use of faecal occult blood testing followed by colonoscopy in positive cases. Regarding the treatment of colorectal cancer, significant advances have been made in the recent decade. The molecular targets of CRC include at least two important cell surface receptors: the epidermal growth factor receptor and the vascular endothelial growth factor receptor. The genetic and molecular knowledge of CRC has widen the scientific and clinical perspectives of diagnosing and treatment. However, despite significant advances in the understanding and treatment of CRC, results from targeted therapy are still not convincing. Future studies will determine the role for this new treatment modality.
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6122
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Carmody RN, Gerber GK, Luevano JM, Gatti DM, Somes L, Svenson KL, Turnbaugh PJ. Diet dominates host genotype in shaping the murine gut microbiota. Cell Host Microbe 2014; 17:72-84. [PMID: 25532804 DOI: 10.1016/j.chom.2014.11.010] [Citation(s) in RCA: 737] [Impact Index Per Article: 73.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Revised: 10/03/2014] [Accepted: 11/07/2014] [Indexed: 12/30/2022]
Abstract
Mammals exhibit marked interindividual variations in their gut microbiota, but it remains unclear if this is primarily driven by host genetics or by extrinsic factors like dietary intake. To address this, we examined the effect of dietary perturbations on the gut microbiota of five inbred mouse strains, mice deficient for genes relevant to host-microbial interactions (MyD88(-/-), NOD2(-/-), ob/ob, and Rag1(-/-)), and >200 outbred mice. In each experiment, consumption of a high-fat, high-sugar diet reproducibly altered the gut microbiota despite differences in host genotype. The gut microbiota exhibited a linear dose response to dietary perturbations, taking an average of 3.5 days for each diet-responsive bacterial group to reach a new steady state. Repeated dietary shifts demonstrated that most changes to the gut microbiota are reversible, while also uncovering bacteria whose abundance depends on prior consumption. These results emphasize the dominant role that diet plays in shaping interindividual variations in host-associated microbial communities.
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Affiliation(s)
- Rachel N Carmody
- FAS Center for Systems Biology, Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA; Department of Microbiology and Immunology, Hooper Foundation, University of California, San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143, USA
| | - Georg K Gerber
- Center for Clinical and Translational Metagenomics, Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, 221 Longwood Avenue, Boston, MA 02115, USA
| | - Jesus M Luevano
- FAS Center for Systems Biology, Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA
| | - Daniel M Gatti
- The Jackson Laboratory, 610 Main Street, Bar Harbor, ME 04609, USA
| | - Lisa Somes
- The Jackson Laboratory, 610 Main Street, Bar Harbor, ME 04609, USA
| | - Karen L Svenson
- The Jackson Laboratory, 610 Main Street, Bar Harbor, ME 04609, USA
| | - Peter J Turnbaugh
- FAS Center for Systems Biology, Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA; Department of Microbiology and Immunology, Hooper Foundation, University of California, San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143, USA.
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6123
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Brüssow H. Microbiota and the human nature: know thyself. Environ Microbiol 2014; 17:10-5. [DOI: 10.1111/1462-2920.12693] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Accepted: 10/24/2014] [Indexed: 12/27/2022]
Affiliation(s)
- Harald Brüssow
- Nutrition and Health Research; Nestlé Research Center; Lausanne 26 Lausanne CH-1000 Switzerland
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6124
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Potter JD. Nutritional epidemiology--there's life in the old dog yet! Cancer Epidemiol Biomarkers Prev 2014; 24:323-30. [PMID: 25515549 DOI: 10.1158/1055-9965.epi-14-1327] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Consideration is given to the idea that the nutritional epidemiology of cancer is dead, as some in the media have claimed. The basis for the claim does not lie in science nor has anyone with relevant knowledge made such a statement-although that, too, has been claimed. Evidence is adduced for the importance of past achievements of nutritional epidemiology. Attention is similarly drawn to recent contributions. In particular, I note the state of play of cancer and plant foods, fat and breast cancer, meat and cancer, vegetarians, intervention studies, migrant studies, and westernization of diet and lifestyle. Some next steps and some currently important questions are outlined.
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Affiliation(s)
- John D Potter
- Centre for Public Health Research, Massey University, Wellington, New Zealand. Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington.
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6125
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Lam W, Jiang Z, Guan F, Hu R, Liu SH, Chu E, Cheng YC. The number of intestinal bacteria is not critical for the enhancement of antitumor activity and reduction of intestinal toxicity of irinotecan by the Chinese herbal medicine PHY906 (KD018). Altern Ther Health Med 2014; 14:490. [PMID: 25510341 PMCID: PMC4302098 DOI: 10.1186/1472-6882-14-490] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2014] [Accepted: 12/11/2014] [Indexed: 12/19/2022]
Abstract
Background The four-herb Chinese medicine PHY906(KD018) has been shown to both enhance the in vivo antitumor activity of irinotecan (CPT-11) against colon cancer tumor allografts and alleviate intestinal toxicity caused by CPT-11. Methods Since intestinal bacteria can metabolize CPT-11 and PHY906, we investigated whether intestinal bacteria play a critical role in the in vivo activity of PHY906 in murine Colon-38 tumor-bearing mice. Intestinal bacteria were depleted using streptomycin/neomycin for 10 days before and during treatment with PHY906 and/or CPT-11. qPCR using 16S DNA group-specific primers was used to quantify the levels of the major intestinal bacteria. Results Both PHY906 and antibiotic treatment changed the profile of intestinal bacteria species: Lactobacillus/Enterococcus, Bacteroides, Clostridium leptum, and E. rectale/C. coccoides. Antibiotic treatment did not alter the ability of PHY906 to enhance the antitumor activity of CPT-11. Antibiotic treatment alone partially reduced animal body weight loss in CPT-11-treated mice. However, PHY906 treatment was able to protect against the body weight loss in the CPT-11/antibiotic treatment group. H&E and PCNA staining of intestine showed that antibiotic treatment partially reduced the intestinal damage caused by CPT-11 but not as effectively as PHY906 treatment. Antibiotic treatment plus PHY906 conferred the most effective protection of intestine histological structure against damage by CPT-11. Both PHY906 and antibiotic treatment inhibited CPT-11-associated inflammatory processes, including infiltration of the intestine by neutrophils, MCP1 and TNF-alpha mRNA expression in the intestine, and expression of pro-inflammatory cytokines G-CSF and MCP1 proteins in the plasma. However, whereas antibiotic treatment suppressed the mRNA expression of two important intestinal progenitor/stem cell markers, Olfm4 and Lgr5, PHY906 treatment resulted in enhanced expression of these two stem cell markers. Conclusions Alterations in the population of intestinal bacteria did not affect the abilities of PHY906 to enhance CPT-11 antitumor activity or reduce the intestinal toxicity associated with CPT-11 treatment. The major species of intestinal bacteria do not appear to play a role in PHY906’s enhancement of the therapeutic index of CPT-11 in tumor-bearing mice. Thus, patients with different intestinal bacterial profiles may still benefit from PHY906 treatment alongside CPT-11.
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6126
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The gut microbiota of Colombians differs from that of Americans, Europeans and Asians. BMC Microbiol 2014; 14:311. [PMID: 25495462 PMCID: PMC4275940 DOI: 10.1186/s12866-014-0311-6] [Citation(s) in RCA: 150] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Accepted: 11/25/2014] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND The composition of the gut microbiota has recently been associated with health and disease, particularly with obesity. Some studies suggested a higher proportion of Firmicutes and a lower proportion of Bacteroidetes in obese compared to lean people; others found discordant patterns. Most studies, however, focused on Americans or Europeans, giving a limited picture of the gut microbiome. To determine the generality of previous observations and expand our knowledge of the human gut microbiota, it is important to replicate studies in overlooked populations. Thus, we describe here, for the first time, the gut microbiota of Colombian adults via the pyrosequencing of the 16S ribosomal DNA (rDNA), comparing it with results obtained in Americans, Europeans, Japanese and South Koreans, and testing the generality of previous observations concerning changes in Firmicutes and Bacteroidetes with increasing body mass index (BMI). RESULTS We found that the composition of the gut microbiota of Colombians was significantly different from that of Americans, Europeans and Asians. The geographic origin of the population explained more variance in the composition of this bacterial community than BMI or gender. Concerning changes in Firmicutes and Bacteroidetes with obesity, in Colombians we found a tendency in Firmicutes to diminish with increasing BMI, whereas no change was observed in Bacteroidetes. A similar result was found in Americans. A more detailed inspection of the Colombian dataset revealed that five fiber-degrading bacteria, including Akkermansia, Dialister, Oscillospira, Ruminococcaceae and Clostridiales, became less abundant in obese subjects. CONCLUSION We contributed data from unstudied Colombians that showed that the geographic origin of the studied population had a greater impact on the composition of the gut microbiota than BMI or gender. Any strategy aiming to modulate or control obesity via manipulation of this bacterial community should consider this effect.
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6127
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Abstract
The human gut harbours diverse and abundant microbes, forming a complex ecological system that interacts with host and environmental factors. In this article, we summarise recent advances in microbiome studies across both Western and non-Western populations, either in cross-sectional or longitudinal surveys, and over various age groups, revealing a considerable diversity and variability in the human gut microbiome. Of all the exogenous factors affecting gut microbiome, a long-term diet appears to have the largest effect to date. Recent research on the effects of dietary interventions has shown that the gut microbiome can change dramatically with diet; however, the gut microbiome is generally resilient, and short-term dietary intervention is not typically successful in treating obesity and malnutrition. Understanding the dynamics of the gut microbiome under different conditions will help us diagnose and treat many diseases that are now known to be associated with microbial communities.
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6128
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Lukens JR, Gurung P, Vogel P, Johnson GR, Carter RA, McGoldrick DJ, Bandi SR, Calabrese CR, Vande Walle L, Lamkanfi M, Kanneganti TD. Dietary modulation of the microbiome affects autoinflammatory disease. Nature 2014; 516:246-9. [PMID: 25274309 PMCID: PMC4268032 DOI: 10.1038/nature13788] [Citation(s) in RCA: 229] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Accepted: 08/22/2014] [Indexed: 12/12/2022]
Abstract
The incidences of chronic inflammatory disorders have increased considerably over the past three decades. Recent shifts in dietary consumption may have contributed importantly to this surge, but how dietary consumption modulates inflammatory disease is poorly defined. Pstpip2(cmo) mice, which express a homozygous Leu98Pro missense mutation in the Pombe Cdc15 homology family protein PSTPIP2 (proline-serine-threonine phosphatase interacting protein 2), spontaneously develop osteomyelitis that resembles chronic recurrent multifocal osteomyelitis in humans. Recent reports demonstrated a crucial role for interleukin-1β (IL-1β) in osteomyelitis, but deletion of the inflammasome components caspase-1 and NLRP3 failed to rescue Pstpip2(cmo) mice from inflammatory bone disease. Thus, the upstream mechanisms controlling IL-1β production in Pstpip2(cmo) mice remain to be identified. In addition, the environmental factors driving IL-1β-dependent inflammatory bone erosion are unknown. Here we show that the intestinal microbiota of diseased Pstpip2(cmo) mice was characterized by an outgrowth of Prevotella. Notably, Pstpip2(cmo) mice that were fed a diet rich in fat and cholesterol maintained a normal body weight, but were markedly protected against inflammatory bone disease and bone erosion. Diet-induced protection against osteomyelitis was accompanied by marked reductions in intestinal Prevotella levels and significantly reduced pro-IL-1β expression in distant neutrophils. Furthermore, pro-IL-1β expression was also decreased in Pstpip2(cmo) mice treated with antibiotics, and in wild-type mice that were kept under germ-free conditions. We further demonstrate that combined deletion of caspases 1 and 8 was required for protection against IL-1β-dependent inflammatory bone disease, whereas the deletion of either caspase alone or of elastase or neutrophil proteinase 3 failed to prevent inflammatory disease. Collectively, this work reveals diet-associated changes in the intestinal microbiome as a crucial factor regulating inflammasome- and caspase-8-mediated maturation of IL-1β and osteomyelitis in Pstpip2(cmo) mice.
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Affiliation(s)
- John R. Lukens
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Prajwal Gurung
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Peter Vogel
- Animal Resources Center and the Veterinary Pathology Core, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Gordon R. Johnson
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Robert A. Carter
- Hartwell Center for Bioinformatics and Biotechnology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Daniel J. McGoldrick
- Hartwell Center for Bioinformatics and Biotechnology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Srinivasa R.A.O. Bandi
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | | | - Lieselotte Vande Walle
- Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium
- Department of Biochemistry, Ghent University; B-9000 Ghent, Belgium
| | - Mohamed Lamkanfi
- Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium
- Department of Biochemistry, Ghent University; B-9000 Ghent, Belgium
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6129
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Lang JM, Eisen JA, Zivkovic AM. The microbes we eat: abundance and taxonomy of microbes consumed in a day's worth of meals for three diet types. PeerJ 2014; 2:e659. [PMID: 25538865 PMCID: PMC4266855 DOI: 10.7717/peerj.659] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2014] [Accepted: 10/18/2014] [Indexed: 12/21/2022] Open
Abstract
Far more attention has been paid to the microbes in our feces than the microbes in our food. Research efforts dedicated to the microbes that we eat have historically been focused on a fairly narrow range of species, namely those which cause disease and those which are thought to confer some “probiotic” health benefit. Little is known about the effects of ingested microbial communities that are present in typical American diets, and even the basic questions of which microbes, how many of them, and how much they vary from diet to diet and meal to meal, have not been answered. We characterized the microbiota of three different dietary patterns in order to estimate: the average total amount of daily microbes ingested via food and beverages, and their composition in three daily meal plans representing three different dietary patterns. The three dietary patterns analyzed were: (1) the Average American (AMERICAN): focused on convenience foods, (2) USDA recommended (USDA): emphasizing fruits and vegetables, lean meat, dairy, and whole grains, and (3) Vegan (VEGAN): excluding all animal products. Meals were prepared in a home kitchen or purchased at restaurants and blended, followed by microbial analysis including aerobic, anaerobic, yeast and mold plate counts as well as 16S rRNA PCR survey analysis. Based on plate counts, the USDA meal plan had the highest total amount of microbes at 1.3 × 109 CFU per day, followed by the VEGAN meal plan and the AMERICAN meal plan at 6 × 106 and 1.4 × 106 CFU per day respectively. There was no significant difference in diversity among the three dietary patterns. Individual meals clustered based on taxonomic composition independent of dietary pattern. For example, meals that were abundant in Lactic Acid Bacteria were from all three dietary patterns. Some taxonomic groups were correlated with the nutritional content of the meals. Predictive metagenome analysis using PICRUSt indicated differences in some functional KEGG categories across the three dietary patterns and for meals clustered based on whether they were raw or cooked. Further studies are needed to determine the impact of ingested microbes on the intestinal microbiota, the extent of variation across foods, meals and diets, and the extent to which dietary microbes may impact human health. The answers to these questions will reveal whether dietary microbes, beyond probiotics taken as supplements—i.e., ingested with food—are important contributors to the composition, inter-individual variation, and function of our gut microbiota.
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Affiliation(s)
- Jenna M Lang
- Genome Center, University of California , Davis, CA , USA
| | - Jonathan A Eisen
- Genome Center, Evolution and Ecology, Medical Microbiology and Immunology, University of California , Davis, CA , USA
| | - Angela M Zivkovic
- Department of Nutrition, University of California , Davis, CA , USA ; Foods for Health Institute, University of California , Davis, CA , USA
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6130
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Investigation of the impact of increased dietary insoluble fiber through the feeding of distillers dried grains with solubles (DDGS) on the incidence and severity of Brachyspira-associated colitis in pigs. PLoS One 2014; 9:e114741. [PMID: 25485776 PMCID: PMC4259391 DOI: 10.1371/journal.pone.0114741] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Accepted: 11/13/2014] [Indexed: 01/10/2023] Open
Abstract
Diet has been implicated as a major factor impacting clinical disease expression of swine dysentery and Brachyspira hyodysenteriae colonization. However, the impact of diet on novel pathogenic strongly beta-hemolytic Brachyspira spp. including “B. hampsonii” has yet to be investigated. In recent years, distillers dried grains with solubles (DDGS), a source of insoluble dietary fiber, has been increasingly included in diets of swine. A randomized complete block experiment was used to examine the effect of increased dietary fiber through the feeding of DDGS on the incidence of Brachyspira-associated colitis in pigs. One hundred 4-week-old pigs were divided into five groups based upon inocula (negative control, Brachyspira intermedia, Brachyspira pilosicoli, B. hyodysenteriae or “B. hampsonii”) and fed one of two diets containing no (diet 1) or 30% (diet 2) DDGS. The average days to first positive culture and days post inoculation to the onset of clinical dysentery in the B. hyodysenteriae groups was significantly shorter for diet 2 when compared to diet 1 (P = 0.04 and P = 0.0009, respectively). A similar difference in the average days to first positive culture and days post inoculation to the onset of clinical dysentery was found when comparing the “B. hampsonii” groups. In this study, pigs receiving 30% DDGS shed on average one day prior to and developed swine dysentery nearly twice as fast as pigs receiving 0% DDGS. Accordingly, these data suggest a reduction in insoluble fiber through reducing or eliminating DDGS in swine rations should be considered an integral part of any effective disease elimination strategy for swine dysentery.
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6131
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Scheperjans F, Aho V, Pereira PAB, Koskinen K, Paulin L, Pekkonen E, Haapaniemi E, Kaakkola S, Eerola‐Rautio J, Pohja M, Kinnunen E, Murros K, Auvinen P. Gut microbiota are related to Parkinson's disease and clinical phenotype. Mov Disord 2014; 30:350-8. [DOI: 10.1002/mds.26069] [Citation(s) in RCA: 1068] [Impact Index Per Article: 106.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Revised: 08/21/2014] [Accepted: 10/08/2014] [Indexed: 12/11/2022] Open
Affiliation(s)
- Filip Scheperjans
- Department of NeurologyHelsinki University Central Hospitaland Department of Neurological SciencesUniversity of HelsinkiHelsinki Finland
| | - Velma Aho
- Institute of Biotechnology, DNA Sequencing and Genomics Laboratory, University of HelsinkiHelsinki Finland
| | - Pedro A. B. Pereira
- Institute of Biotechnology, DNA Sequencing and Genomics Laboratory, University of HelsinkiHelsinki Finland
| | - Kaisa Koskinen
- Institute of Biotechnology, DNA Sequencing and Genomics Laboratory, University of HelsinkiHelsinki Finland
| | - Lars Paulin
- Institute of Biotechnology, DNA Sequencing and Genomics Laboratory, University of HelsinkiHelsinki Finland
| | - Eero Pekkonen
- Department of NeurologyHelsinki University Central Hospitaland Department of Neurological SciencesUniversity of HelsinkiHelsinki Finland
| | - Elena Haapaniemi
- Department of NeurologyHelsinki University Central Hospitaland Department of Neurological SciencesUniversity of HelsinkiHelsinki Finland
| | - Seppo Kaakkola
- Department of NeurologyHelsinki University Central Hospitaland Department of Neurological SciencesUniversity of HelsinkiHelsinki Finland
| | - Johanna Eerola‐Rautio
- Department of NeurologyHelsinki University Central Hospitaland Department of Neurological SciencesUniversity of HelsinkiHelsinki Finland
| | - Marjatta Pohja
- Department of NeurologyHelsinki University Central Hospitaland Department of Neurological SciencesUniversity of HelsinkiHelsinki Finland
| | - Esko Kinnunen
- Department of NeurologyHyvinkää HospitalHyvinkää Finland
| | - Kari Murros
- Department of NeurologyHelsinki University Central Hospitaland Department of Neurological SciencesUniversity of HelsinkiHelsinki Finland
| | - Petri Auvinen
- Institute of Biotechnology, DNA Sequencing and Genomics Laboratory, University of HelsinkiHelsinki Finland
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6132
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Flores GE, Caporaso JG, Henley JB, Rideout JR, Domogala D, Chase J, Leff JW, Vázquez-Baeza Y, Gonzalez A, Knight R, Dunn RR, Fierer N. Temporal variability is a personalized feature of the human microbiome. Genome Biol 2014; 15:531. [PMID: 25517225 PMCID: PMC4252997 DOI: 10.1186/s13059-014-0531-y] [Citation(s) in RCA: 269] [Impact Index Per Article: 26.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Accepted: 11/05/2014] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND It is now apparent that the complex microbial communities found on and in the human body vary across individuals. What has largely been missing from previous studies is an understanding of how these communities vary over time within individuals. To the extent to which it has been considered, it is often assumed that temporal variability is negligible for healthy adults. Here we address this gap in understanding by profiling the forehead, gut (fecal), palm, and tongue microbial communities in 85 adults, weekly over 3 months. RESULTS We found that skin (forehead and palm) varied most in the number of taxa present, whereas gut and tongue communities varied more in the relative abundances of taxa. Within each body habitat, there was a wide range of temporal variability across the study population, with some individuals harboring more variable communities than others. The best predictor of these differences in variability across individuals was microbial diversity; individuals with more diverse gut or tongue communities were more stable in composition than individuals with less diverse communities. CONCLUSIONS Longitudinal sampling of a relatively large number of individuals allowed us to observe high levels of temporal variability in both diversity and community structure in all body habitats studied. These findings suggest that temporal dynamics may need to be considered when attempting to link changes in microbiome structure to changes in health status. Furthermore, our findings show that, not only is the composition of an individual's microbiome highly personalized, but their degree of temporal variability is also a personalized feature.
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Affiliation(s)
- Gilberto E Flores
- />Department of Biology, California State University, Northridge, Northridge, CA 91330-8303 USA
| | - J Gregory Caporaso
- />Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011 USA
- />Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ 86011 USA
| | - Jessica B Henley
- />Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, CO 80309 USA
| | - Jai Ram Rideout
- />Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ 86011 USA
- />Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Daniel Domogala
- />Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011 USA
| | - John Chase
- />Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011 USA
| | - Jonathan W Leff
- />Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, CO 80309 USA
- />Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309 USA
| | | | - Antonio Gonzalez
- />BioFrontiers Institute, University of Colorado, Boulder, CO 80309 USA
| | - Rob Knight
- />BioFrontiers Institute, University of Colorado, Boulder, CO 80309 USA
- />Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309 USA
- />Howard Hughes Medical Institute, University of Colorado, Boulder, CO 80309 USA
| | - Robert R Dunn
- />Department of Biological Sciences and Keck Center for Behavioral Biology, North Carolina State University, Raleigh, NC 27607 USA
| | - Noah Fierer
- />Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, CO 80309 USA
- />Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309 USA
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6133
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Ohland CL, Jobin C. Microbial activities and intestinal homeostasis: A delicate balance between health and disease. Cell Mol Gastroenterol Hepatol 2014; 1:28-40. [PMID: 25729763 PMCID: PMC4339954 DOI: 10.1016/j.jcmgh.2014.11.004] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The concept that the intestinal microbiota modulates numerous physiological processes including immune development and function, nutrition and metabolism as well as pathogen exclusion is relatively well established in the scientific community. The molecular mechanisms driving these various effects and the events leading to the establishment of a "healthy" microbiome are slowly emerging. The objective of this review is to bring into focus important aspects of microbial/host interactions in the intestine and to discuss key molecular mechanisms controlling health and disease states. We will discuss recent evidence on how microbes interact with the host and one another and their impact on intestinal homeostasis.
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Affiliation(s)
| | - Christian Jobin
- Department of Medicine, University of Florida, Gainesville, Florida
- Department of Infectious Diseases and Pathology, University of Florida, Gainesville, Florida
- Correspondence Address correspondence to: Christian Jobin, PhD, Department of Medicine, University of Florida, 2033 Mowry Road, Office 461, Gainesville, Florida 32610. fax: (352) 392-3944.
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6134
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Diet and feeding pattern affect the diurnal dynamics of the gut microbiome. Cell Metab 2014; 20:1006-17. [PMID: 25470548 PMCID: PMC4255146 DOI: 10.1016/j.cmet.2014.11.008] [Citation(s) in RCA: 581] [Impact Index Per Article: 58.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Revised: 09/16/2014] [Accepted: 11/12/2014] [Indexed: 12/15/2022]
Abstract
The gut microbiome and daily feeding/fasting cycle influence host metabolism and contribute to obesity and metabolic diseases. However, fundamental characteristics of this relationship between the feeding/fasting cycle and the gut microbiome are unknown. Our studies show that the gut microbiome is highly dynamic, exhibiting daily cyclical fluctuations in composition. Diet-induced obesity dampens the daily feeding/fasting rhythm and diminishes many of these cyclical fluctuations. Time-restricted feeding (TRF), in which feeding is consolidated to the nocturnal phase, partially restores these cyclical fluctuations. Furthermore, TRF, which protects against obesity and metabolic diseases, affects bacteria shown to influence host metabolism. Cyclical changes in the gut microbiome from feeding/fasting rhythms contribute to the diversity of gut microflora and likely represent a mechanism by which the gut microbiome affects host metabolism. Thus, feeding pattern and time of harvest, in addition to diet, are important parameters when assessing the microbiome's contribution to host metabolism.
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6135
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Knights D, Silverberg MS, Weersma RK, Gevers D, Dijkstra G, Huang H, Tyler AD, van Sommeren S, Imhann F, Stempak JM, Huang H, Vangay P, Al-Ghalith GA, Russell C, Sauk J, Knight J, Daly MJ, Huttenhower C, Xavier RJ. Complex host genetics influence the microbiome in inflammatory bowel disease. Genome Med 2014; 6:107. [PMID: 25587358 PMCID: PMC4292994 DOI: 10.1186/s13073-014-0107-1] [Citation(s) in RCA: 269] [Impact Index Per Article: 26.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Accepted: 11/13/2014] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Human genetics and host-associated microbial communities have been associated independently with a wide range of chronic diseases. One of the strongest associations in each case is inflammatory bowel disease (IBD), but disease risk cannot be explained fully by either factor individually. Recent findings point to interactions between host genetics and microbial exposures as important contributors to disease risk in IBD. These include evidence of the partial heritability of the gut microbiota and the conferral of gut mucosal inflammation by microbiome transplant even when the dysbiosis was initially genetically derived. Although there have been several tests for association of individual genetic loci with bacterial taxa, there has been no direct comparison of complex genome-microbiome associations in large cohorts of patients with an immunity-related disease. METHODS We obtained 16S ribosomal RNA (rRNA) gene sequences from intestinal biopsies as well as host genotype via Immunochip in three independent cohorts totaling 474 individuals. We tested for correlation between relative abundance of bacterial taxa and number of minor alleles at known IBD risk loci, including fine mapping of multiple risk alleles in the Nucleotide-binding oligomerization domain-containing protein 2 (NOD2) gene exon. We identified host polymorphisms whose associations with bacterial taxa were conserved across two or more cohorts, and we tested related genes for enrichment of host functional pathways. RESULTS We identified and confirmed in two cohorts a significant association between NOD2 risk allele count and increased relative abundance of Enterobacteriaceae, with directionality of the effect conserved in the third cohort. Forty-eight additional IBD-related SNPs have directionality of their associations with bacterial taxa significantly conserved across two or three cohorts, implicating genes enriched for regulation of innate immune response, the JAK-STAT cascade, and other immunity-related pathways. CONCLUSIONS These results suggest complex interactions between genetically altered host functional pathways and the structure of the microbiome. Our findings demonstrate the ability to uncover novel associations from paired genome-microbiome data, and they suggest a complex link between host genetics and microbial dysbiosis in subjects with IBD across independent cohorts.
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Affiliation(s)
- Dan Knights
- />Department of Computer Science and Engineering, University of Minnesota, Minneapolis, Minnesota 55455 USA
- />Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142 USA
- />Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02114 USA
- />Biotechnology Institute, University of Minnesota, St. Paul, Minnesota 55108 USA
| | - Mark S Silverberg
- />Zane Cohen Centre for Digestive Diseases, Mount Sinai Hospital IBD Group, University of Toronto, Toronto, Ontario M5G 1X5 Canada
| | - Rinse K Weersma
- />Department of Gastroenterology and Hepatology, University Medical Center Groningen, Groningen, 9700RB The Netherlands
| | - Dirk Gevers
- />Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142 USA
| | - Gerard Dijkstra
- />Department of Gastroenterology and Hepatology, University Medical Center Groningen, Groningen, 9700RB The Netherlands
| | - Hailiang Huang
- />Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts 02114 USA
| | - Andrea D Tyler
- />Zane Cohen Centre for Digestive Diseases, Mount Sinai Hospital IBD Group, University of Toronto, Toronto, Ontario M5G 1X5 Canada
| | - Suzanne van Sommeren
- />Department of Gastroenterology and Hepatology, University Medical Center Groningen, Groningen, 9700RB The Netherlands
- />Department of Genetics, University Medical Center Groningen, Groningen, 9700RB The Netherlands
| | - Floris Imhann
- />Department of Gastroenterology and Hepatology, University Medical Center Groningen, Groningen, 9700RB The Netherlands
- />Department of Genetics, University Medical Center Groningen, Groningen, 9700RB The Netherlands
| | - Joanne M Stempak
- />Zane Cohen Centre for Digestive Diseases, Mount Sinai Hospital IBD Group, University of Toronto, Toronto, Ontario M5G 1X5 Canada
| | - Hu Huang
- />Biomedical Informatics and Computational Biology, University of Minnesota, Minneapolis, Minnesota 55455 USA
| | - Pajau Vangay
- />Biomedical Informatics and Computational Biology, University of Minnesota, Minneapolis, Minnesota 55455 USA
| | - Gabriel A Al-Ghalith
- />Biomedical Informatics and Computational Biology, University of Minnesota, Minneapolis, Minnesota 55455 USA
| | - Caitlin Russell
- />Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02114 USA
- />Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02114 USA
| | - Jenny Sauk
- />Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02114 USA
| | - Jo Knight
- />Department of Psychiatry, University of Toronto, Toronto, Ontario M5T 1R8 Canada
| | - Mark J Daly
- />Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142 USA
- />Department of Medicine, Analytic and Translational Genetics Unit, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02114 USA
- />Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142 USA
| | - Curtis Huttenhower
- />Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142 USA
- />Biostatistics Department, Harvard School of Public Health, Boston, Massachusetts 02115 USA
| | - Ramnik J Xavier
- />Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142 USA
- />Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02114 USA
- />Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02114 USA
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6136
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Pereira DIA, Aslam MF, Frazer DM, Schmidt A, Walton GE, McCartney AL, Gibson GR, Anderson GJ, Powell JJ. Dietary iron depletion at weaning imprints low microbiome diversity and this is not recovered with oral Nano Fe(III). Microbiologyopen 2014; 4:12-27. [PMID: 25461615 PMCID: PMC4335973 DOI: 10.1002/mbo3.213] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Revised: 07/31/2014] [Accepted: 08/01/2014] [Indexed: 12/31/2022] Open
Abstract
Alterations in the gut microbiota have been recently linked to oral iron. We conducted two feeding studies including an initial diet-induced iron-depletion period followed by supplementation with nanoparticulate tartrate-modified ferrihydrite (Nano Fe(III): considered bioavailable to host but not bacteria) or soluble ferrous sulfate (FeSO4: considered bioavailable to both host and bacteria). We applied denaturing gradient gel electrophoresis and fluorescence in situ hybridization for study-1 and 454-pyrosequencing of fecal 16S rRNA in study-2. In study-1, the within-community microbial diversity increased with FeSO4 (P = 0.0009) but not with Nano Fe(III) supplementation. This was confirmed in study-2, where we also showed that iron depletion at weaning imprinted significantly lower within- and between-community microbial diversity compared to mice weaned onto the iron-sufficient reference diet (P < 0.0001). Subsequent supplementation with FeSO4 partially restored the within-community diversity (P = 0.006 in relation to the continuously iron-depleted group) but not the between-community diversity, whereas Nano Fe(III) had no effect. We conclude that (1) dietary iron depletion at weaning imprints low diversity in the microbiota that is not, subsequently, easily recovered; (2) in the absence of gastrointestinal disease iron supplementation does not negatively impact the microbiota; and (3) Nano Fe(III) is less available to the gut microbiota.
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Affiliation(s)
- Dora I A Pereira
- MRC Human Nutrition Research, Elsie Widdowson Laboratory, Cambridge, United Kingdom
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6137
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Kendig DM, Hurst NR, Bradley ZL, Mahavadi S, Kuemmerle JF, Lyall V, DeSimone J, Murthy KS, Grider JR. Activation of the umami taste receptor (T1R1/T1R3) initiates the peristaltic reflex and pellet propulsion in the distal colon. Am J Physiol Gastrointest Liver Physiol 2014; 307:G1100-7. [PMID: 25324508 PMCID: PMC4254958 DOI: 10.1152/ajpgi.00251.2014] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Intraluminal nutrients in the gut affect the peristaltic reflex, although the mechanism is not well defined. Recent evidence supports the presence of taste receptors and their signaling components in enteroendocrine cells, although their function is unclear. This study aimed to determine if nutrients modify colonic motility through activation of taste receptors. Colonic sections were immunostained for the umami taste receptor T1R1/T1R3, which mediates the response to umami ligands, such as monosodium glutamate (MSG), in taste cells. Ascending contraction, descending relaxation, and calcitonin gene-related peptide release were measured in three-chamber flat-sheet preparations of rat colon in response to MSG alone or with inosine 5'-monophosphate (IMP). Velocity of artificial fecal pellet propulsion was measured by video recording in guinea pig distal colon. T1R1/T1R3 receptors were present in enteroendocrine cells of colonic sections from human, rat, mouse, and guinea pig. MSG initiated ascending contraction and descending relaxation components of the peristaltic reflex and calcitonin gene-related peptide release in flat-sheet preparations. IMP augmented the MSG-induced effects, suggesting activation of T1R1/T1R3 receptors. In T1R1(-/-) mice, mucosal stroking, but not MSG, elicited a peristaltic reflex. Intraluminal perfusion of MSG enhanced the velocity of artificial fecal pellet propulsion, which was also augmented by IMP. Propulsion was also increased by l-cysteine, but not l-tryptophan, supporting a role of T1R1/T1R3 receptors. We conclude that T1R1/T1R3 activation by luminal MSG or l-cysteine elicits a peristaltic reflex and CGRP release and increases the velocity of pellet propulsion in distal colon. This mechanism may explain how nutrients regulate colonic propulsion.
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Affiliation(s)
- Derek M. Kendig
- 1Department of Physiology and Biophysics, Virginia Commonwealth University School of Medicine, Richmond, Virginia; and
| | - Norman R. Hurst
- 1Department of Physiology and Biophysics, Virginia Commonwealth University School of Medicine, Richmond, Virginia; and
| | - Zachary L. Bradley
- 1Department of Physiology and Biophysics, Virginia Commonwealth University School of Medicine, Richmond, Virginia; and
| | - Sunila Mahavadi
- 1Department of Physiology and Biophysics, Virginia Commonwealth University School of Medicine, Richmond, Virginia; and
| | - John F. Kuemmerle
- 1Department of Physiology and Biophysics, Virginia Commonwealth University School of Medicine, Richmond, Virginia; and ,2Department of Medicine, VCU Program in Enteric Neuromuscular Sciences, Virginia Commonwealth University School of Medicine, Richmond, Virginia
| | - Vijay Lyall
- 1Department of Physiology and Biophysics, Virginia Commonwealth University School of Medicine, Richmond, Virginia; and
| | - John DeSimone
- 1Department of Physiology and Biophysics, Virginia Commonwealth University School of Medicine, Richmond, Virginia; and
| | - Karnam S. Murthy
- 1Department of Physiology and Biophysics, Virginia Commonwealth University School of Medicine, Richmond, Virginia; and ,2Department of Medicine, VCU Program in Enteric Neuromuscular Sciences, Virginia Commonwealth University School of Medicine, Richmond, Virginia
| | - John R. Grider
- 1Department of Physiology and Biophysics, Virginia Commonwealth University School of Medicine, Richmond, Virginia; and ,2Department of Medicine, VCU Program in Enteric Neuromuscular Sciences, Virginia Commonwealth University School of Medicine, Richmond, Virginia
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6138
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Abstract
Humans have coevolved with their microbes over thousands of years, but this relationship, is now being dramatically affected by shifts in the collective human microbiome resulting from changes in the environment and societal norms. Resulting perturbations of intestinal host-microbe interactions can lead to miscues and altered host responses that increase the risk of pathogenic processes and promote “western” disorders such as inflammatory bowel diseases, cancers, obesity, diabetes, autism, and asthma. Given the current challenges and limitations in gene therapy, approaches that can reshape the gut microbiome represent a reasonable strategy for restoring the balance between host and microbes. In this review and commentary, we highlight recent progress in our understanding of the intestinal microbiome in the context of health and diseases, focusing on mechanistic concepts that underlie the complex relationships between host and microbes. Despite these gains, many challenges lie ahead that make it difficult to close the gap between the basic sciences and clinical application. We will discuss the potential therapeutic strategies that can be used to manipulate the gut microbiota, recognizing that the promise of pharmabiotics (“bugs to drugs”) is unlikely to be completely fulfilled without a greater understanding of enteric microbiota and its impact on mammalian physiology. By leveraging the knowledge gained through these studies, we will be prepared to enter the era of personalized medicine where clinical inventions can be custom-tailored to individual patients to achieve better outcomes.
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6139
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Leone VA, Cham CM, Chang EB. Diet, gut microbes, and genetics in immune function: can we leverage our current knowledge to achieve better outcomes in inflammatory bowel diseases? Curr Opin Immunol 2014; 31:16-23. [PMID: 25214301 PMCID: PMC4253729 DOI: 10.1016/j.coi.2014.08.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Revised: 08/08/2014] [Accepted: 08/24/2014] [Indexed: 02/06/2023]
Abstract
Autoimmune disorders, particularly inflammatory bowel diseases (IBD), are increasing at an alarming frequency. While the exact cause remains elusive, studies have examined how the immune system is shaped in the context of genetic susceptibility, gut microbes, and environmental pressures, including dietary intake. Shifts towards a Westernized high fat, high carbohydrate diet result in changes to gut microbiota structure and function that may aid in triggering and perpetuating autoimmunity by promoting the emergence of pathobionts leading to altered immune activation. This review summarizes our current understanding of dietary-induced changes in gut microbiota on autoimmunity in the context of IBD. We provide a framework for leveraging this knowledge to develop new dietary, microbial and immune-based modulation strategies for individualized risk assessment and improving clinical outcomes.
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Affiliation(s)
- Vanessa A Leone
- University of Chicago, Department of Medicine, Gastroenterology, Hepatology and Nutrition, United States
| | - Candace M Cham
- University of Chicago, Department of Medicine, Gastroenterology, Hepatology and Nutrition, United States
| | - Eugene B Chang
- University of Chicago, Department of Medicine, Gastroenterology, Hepatology and Nutrition, United States.
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6140
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John C, Werner P, Worthmann A, Wegner K, Tödter K, Scheja L, Rohn S, Heeren J, Fischer M. A liquid chromatography-tandem mass spectrometry-based method for the simultaneous determination of hydroxy sterols and bile acids. J Chromatogr A 2014; 1371:184-95. [DOI: 10.1016/j.chroma.2014.10.064] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Revised: 10/20/2014] [Accepted: 10/21/2014] [Indexed: 01/07/2023]
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6141
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Zeller G, Tap J, Voigt AY, Sunagawa S, Kultima JR, Costea PI, Amiot A, Böhm J, Brunetti F, Habermann N, Hercog R, Koch M, Luciani A, Mende DR, Schneider MA, Schrotz-King P, Tournigand C, Tran Van Nhieu J, Yamada T, Zimmermann J, Benes V, Kloor M, Ulrich CM, von Knebel Doeberitz M, Sobhani I, Bork P. Potential of fecal microbiota for early-stage detection of colorectal cancer. Mol Syst Biol 2014; 10:766. [PMID: 25432777 PMCID: PMC4299606 DOI: 10.15252/msb.20145645] [Citation(s) in RCA: 762] [Impact Index Per Article: 76.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Several bacterial species have been implicated in the development of colorectal carcinoma (CRC), but CRC-associated changes of fecal microbiota and their potential for cancer screening remain to be explored. Here, we used metagenomic sequencing of fecal samples to identify taxonomic markers that distinguished CRC patients from tumor-free controls in a study population of 156 participants. Accuracy of metagenomic CRC detection was similar to the standard fecal occult blood test (FOBT) and when both approaches were combined, sensitivity improved > 45% relative to the FOBT, while maintaining its specificity. Accuracy of metagenomic CRC detection did not differ significantly between early- and late-stage cancer and could be validated in independent patient and control populations (N = 335) from different countries. CRC-associated changes in the fecal microbiome at least partially reflected microbial community composition at the tumor itself, indicating that observed gene pool differences may reveal tumor-related host-microbe interactions. Indeed, we deduced a metabolic shift from fiber degradation in controls to utilization of host carbohydrates and amino acids in CRC patients, accompanied by an increase of lipopolysaccharide metabolism.
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Affiliation(s)
- Georg Zeller
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Julien Tap
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany Department of Gastroenterology and LIC-EA4393-EC2M3, APHP and UPEC Université Paris-Est Créteil, Créteil, France
| | - Anita Y Voigt
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany Department of Applied Tumor Biology, Institute of Pathology University Hospital Heidelberg, Heidelberg, Germany Clinical Cooperation Unit Applied Tumor Biology, German Cancer Research Center (DKFZ), Heidelberg, Germany Molecular Medicine Partnership Unit (MMPU), University Hospital Heidelberg and European Molecular Biology Laboratory, Heidelberg, Germany
| | - Shinichi Sunagawa
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Jens Roat Kultima
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Paul I Costea
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Aurélien Amiot
- Department of Gastroenterology and LIC-EA4393-EC2M3, APHP and UPEC Université Paris-Est Créteil, Créteil, France
| | - Jürgen Böhm
- Division of Preventive Oncology, National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Francesco Brunetti
- Department of Surgery, APHP and UPEC Université Paris-Est Créteil, Créteil, France
| | - Nina Habermann
- Division of Preventive Oncology, National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Rajna Hercog
- Genomics Core Facility, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Moritz Koch
- Department of General, Visceral and Transplantation Surgery, University Hospital Heidelberg, Heidelberg, Germany
| | - Alain Luciani
- Department of Radiology, APHP and UPEC Université Paris-Est Créteil, Créteil, France
| | - Daniel R Mende
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Martin A Schneider
- Department of General, Visceral and Transplantation Surgery, University Hospital Heidelberg, Heidelberg, Germany
| | - Petra Schrotz-King
- Division of Preventive Oncology, National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Christophe Tournigand
- Department of Medical Oncology, APHP and UPEC Université Paris-Est Créteil, Créteil, France
| | - Jeanne Tran Van Nhieu
- Department of Pathology and LIC-EA4393-EC2M3, APHP and UPEC Université Paris-Est Créteil, Créteil, France
| | - Takuji Yamada
- Department of Biological Information, Tokyo Institute of Technology, Tokyo, Japan
| | - Jürgen Zimmermann
- Genomics Core Facility, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Vladimir Benes
- Genomics Core Facility, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Matthias Kloor
- Department of Applied Tumor Biology, Institute of Pathology University Hospital Heidelberg, Heidelberg, Germany Clinical Cooperation Unit Applied Tumor Biology, German Cancer Research Center (DKFZ), Heidelberg, Germany Molecular Medicine Partnership Unit (MMPU), University Hospital Heidelberg and European Molecular Biology Laboratory, Heidelberg, Germany
| | - Cornelia M Ulrich
- Division of Preventive Oncology, National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany German Cancer Research Center (DKFZ), Heidelberg, Germany Fred Hutchinson Cancer Research Center (FHCRC), Seattle, WA, USA
| | - Magnus von Knebel Doeberitz
- Department of Applied Tumor Biology, Institute of Pathology University Hospital Heidelberg, Heidelberg, Germany Clinical Cooperation Unit Applied Tumor Biology, German Cancer Research Center (DKFZ), Heidelberg, Germany Molecular Medicine Partnership Unit (MMPU), University Hospital Heidelberg and European Molecular Biology Laboratory, Heidelberg, Germany
| | - Iradj Sobhani
- Department of Gastroenterology and LIC-EA4393-EC2M3, APHP and UPEC Université Paris-Est Créteil, Créteil, France
| | - Peer Bork
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany Molecular Medicine Partnership Unit (MMPU), University Hospital Heidelberg and European Molecular Biology Laboratory, Heidelberg, Germany Max Delbrück Centre for Molecular Medicine, Berlin, Germany
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6142
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Redinbo MR. The microbiota, chemical symbiosis, and human disease. J Mol Biol 2014; 426:3877-91. [PMID: 25305474 PMCID: PMC4252811 DOI: 10.1016/j.jmb.2014.09.011] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Revised: 09/07/2014] [Accepted: 09/19/2014] [Indexed: 02/07/2023]
Abstract
Our understanding of mammalian-microbial mutualism has expanded by combing microbial sequencing with evolving molecular and cellular methods, as well as unique model systems. Here, the recent literature linking the microbiota to diseases of three of the key mammalian mucosal epithelial compartments-nasal, lung, and gastrointestinal tract-is reviewed with a focus on new knowledge about the taxa, species, proteins, and chemistry that promote health and impact progression toward disease. The information presented is further organized by specific diseases now associated with the microbiota: Staphylococcus aureus infection and rhinosinusitis in the nasal-sinus mucosa, as well as cystic fibrosis, chronic obstructive pulmonary disorder, and asthma in the pulmonary tissues. For the vast and microbially dynamic gastrointestinal compartment, several disorders are considered, including obesity, atherosclerosis, Crohn's disease, ulcerative colitis, drug toxicity, and even autism. Our appreciation of the chemical symbiosis ongoing between human systems and the microbiota continues to grow and suggests new opportunities for modulating this symbiosis using designed interventions.
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Affiliation(s)
- Matthew R Redinbo
- Department of Chemistry, Department of Biochemistry and Biophysics, Department of Microbiology and Immunology, College of Arts and Sciences, Integrative Program for Biological and Genome Sciences, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3290, USA.
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6143
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The microbiome of New World vultures. Nat Commun 2014; 5:5498. [PMID: 25423494 DOI: 10.1038/ncomms6498] [Citation(s) in RCA: 195] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Accepted: 10/03/2014] [Indexed: 12/11/2022] Open
Abstract
Vultures are scavengers that fill a key ecosystem niche, in which they have evolved a remarkable tolerance to bacterial toxins in decaying meat. Here we report the first deep metagenomic analysis of the vulture microbiome. Through face and gut comparisons of 50 vultures representing two species, we demonstrate a remarkably conserved low diversity of gut microbial flora. The gut samples contained an average of 76 operational taxonomic units (OTUs) per specimen, compared with 528 OTUs on the facial skin. Clostridia and Fusobacteria, widely pathogenic to other vertebrates, dominate the vulture's gut microbiota. We reveal a likely faecal-oral-gut route for their origin. DNA of prey species detectable on facial swabs was completely degraded in the gut samples from most vultures, suggesting that the gastrointestinal tracts of vultures are extremely selective. Our findings show a strong adaption of vultures and their bacteria to their food source, exemplifying a specialized host-microbial alliance.
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6144
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Wang L, Conlon MA, Christophersen CT, Sorich MJ, Angley MT. Gastrointestinal microbiota and metabolite biomarkers in children with autism spectrum disorders. Biomark Med 2014; 8:331-44. [PMID: 24712423 DOI: 10.2217/bmm.14.12] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Autism spectrum disorder (ASD) is a neurodevelopmental disorder. Many affected individuals also display symptoms of gastrointestinal (GI) disturbance, suggesting GI factors may play an important role in the pathogenesis of ASD and/or related complications. The current review will focus on evidence supporting a role for the GI microbiota and their fermentation products in the etiology and/or symptoms of ASD, and their potential use as biomarkers. GI-related biomarkers could potentially enable early identification of ASD at risk of GI disturbance, and thereby guide targeted interventions, potentially improving the health and quality of life of affected individuals.
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Affiliation(s)
- Lv Wang
- Sansom Institute for Health Research, University of South Australia, GPO Box 2471, Adelaide, SA 5001, Australia
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6145
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Gut brain axis: diet microbiota interactions and implications for modulation of anxiety and depression. Curr Opin Biotechnol 2014; 32:35-41. [PMID: 25448230 DOI: 10.1016/j.copbio.2014.10.007] [Citation(s) in RCA: 185] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Revised: 10/07/2014] [Accepted: 10/15/2014] [Indexed: 12/11/2022]
Abstract
The human gut microbiome is composed of an enormous number of microorganisms, generally regarded as commensal bacteria. Without this inherent microbial community, we would be unable to digest plant polysaccharides and would have trouble extracting lipids from our diet. Resident gut bacteria are an important contributor to healthy metabolism and there is significant evidence linking gut microbiota and metabolic disorders such as obesity and diabetes. In the past few years, neuroscience research has demonstrated the importance of microbiota in the development of brain systems that are vital to both stress reactivity and stress-related behaviours. Here we review recent literature that examines the impact of diet-induced changes in the microbiota on stress-related behaviours including anxiety and depression.
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6146
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Shah R, Kellermayer R. Microbiome associations of therapeutic enteral nutrition. Nutrients 2014; 6:5298-311. [PMID: 25421531 PMCID: PMC4245590 DOI: 10.3390/nu6115298] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Revised: 10/08/2014] [Accepted: 10/21/2014] [Indexed: 12/19/2022] Open
Abstract
One of the most effective forms of therapeutic enteral nutrition is designated as “exclusive enteral nutrition” (EEN). EEN constitutes the monotonous enteral delivery of complete liquid nutrition and has been most explored in the treatment Crohn’s disease (CD), a form of inflammatory bowel disease. While EEN’s mechanisms of action are not clearly understood, it has been shown to modify the composition of the intestinal microbiome, an important component of CD pathogenesis. The current literature on the intestinal microbiome in healthy individuals and CD patients is reviewed with respect to EEN therapy. Further investigations in this field are needed to better understand the role and potential for EEN in chronic human disorders.
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Affiliation(s)
- Rajesh Shah
- Department of Internal Medicine, Section of Gastroenterology, Baylor College of Medicine, Houston, TX, 77030, USA.
| | - Richard Kellermayer
- Department of Pediatrics, Section of Gastroenterology, Baylor College of Medicine and Texas Children's Hospital, Houston, TX, 77030, USA.
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6147
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Festi D, Schiumerini R, Eusebi LH, Marasco G, Taddia M, Colecchia A. Gut microbiota and metabolic syndrome. World J Gastroenterol 2014; 20:16079-16094. [PMID: 25473159 PMCID: PMC4239493 DOI: 10.3748/wjg.v20.i43.16079] [Citation(s) in RCA: 331] [Impact Index Per Article: 33.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Revised: 06/20/2014] [Accepted: 07/16/2014] [Indexed: 02/06/2023] Open
Abstract
Gut microbiota exerts a significant role in the pathogenesis of the metabolic syndrome, as confirmed by studies conducted both on humans and animal models. Gut microbial composition and functions are strongly influenced by diet. This complex intestinal “superorganism” seems to affect host metabolic balance modulating energy absorption, gut motility, appetite, glucose and lipid metabolism, as well as hepatic fatty storage. An impairment of the fine balance between gut microbes and host’s immune system could culminate in the intestinal translocation of bacterial fragments and the development of “metabolic endotoxemia”, leading to systemic inflammation and insulin resistance. Diet induced weight-loss and bariatric surgery promote significant changes of gut microbial composition, that seem to affect the success, or the inefficacy, of treatment strategies. Manipulation of gut microbiota through the administration of prebiotics or probiotics could reduce intestinal low grade inflammation and improve gut barrier integrity, thus, ameliorating metabolic balance and promoting weight loss. However, further evidence is needed to better understand their clinical impact and therapeutic use.
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6148
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The Metabolism of Polysaccharide from Atractylodes macrocephala Koidz and Its Effect on Intestinal Microflora. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2014; 2014:926381. [PMID: 25505927 PMCID: PMC4258363 DOI: 10.1155/2014/926381] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Accepted: 11/06/2014] [Indexed: 12/16/2022]
Abstract
An active polysaccharide from the rhizome of Atractylodes macrocephala Koidz (PAM) was identified to improve and adjust disordered intestinal flora. High-performance gel permeation chromatography (HPGPC) and gas chromatography-mass spectrometry (GC-MS) were employed to identify the components of PAM as rhamnose, glucose, mannose, xylose, and galactose at a ratio of 0.03 : 0.25 : 0.15 : 0.41 : 0.15. PAM metabolized in gastrointestinal tract when incubated with artificial gastric and intestinal juices. Anaerobic incubation of PAM on intestinal flora confirmed that PAM promoted the ability of intestinal bacteria to digest reducing sugar. Based on the Shannon index and similarity coefficient index of enterobacterial repetitive intergenic consensus-PCR (ERIC-PCR) fingerprinting of the total intestinal bacteria DNA, we concluded that PAM can significantly improve disordered intestinal flora and may be used as an oral adjuvant to regulate intestinal flora.
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6149
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Ohtani N. Microbiome and cancer. Semin Immunopathol 2014; 37:65-72. [PMID: 25404117 DOI: 10.1007/s00281-014-0457-1] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Accepted: 11/03/2014] [Indexed: 02/07/2023]
Abstract
The human intestine is believed to contain approximately 100 trillion intestinal (gut) microbiota, comprising about 500-1000 different species. These intestinal microbiota exist in a symbiotic relationship with their host, by metabolizing compounds that the host is unable to utilize and controlling the immune balance of the host's body. However, the composition of the intestinal microbiota is known to vary, depending on diet, nutrition status, and other factors. The recently developed meta-omics microbial data and the technical progress for the metabolome analysis provide a substantial understanding of the role of intestinal microbes and their metabolism. Interestingly, accumulating evidence suggests that the intestinal microbiota contributes to the onset of colorectal cancer, not only via the pro-carcinogenic activities of specific pathogens but also via the influence of the bacterial metabolites. Moreover, since the gut microbial metabolites circulate in the host's body, it has been increasingly recognized that the intestinal microbiota are involved in the pathogenesis of diseases not only in the intestine but also in the organs located distant from the intestine. We recently found that metabolites from obesity-induced intestinal microbiota promoted liver cancer, and elucidated the underlying molecular mechanism. In this review, I first summarize the general understanding on the carcinogenic process by bacterial metabolites, and then discuss on the association between intestinal microbiota and colorectal cancer. In the last part, I will introduce our recent findings on liver cancer promotion by a metabolite of the obesity-induced intestinal microbiota.
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Affiliation(s)
- Naoko Ohtani
- Department of Applied Bioscience, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda-shi, Chiba, Japan,
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6150
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Klein-Jöbstl D, Schornsteiner E, Mann E, Wagner M, Drillich M, Schmitz-Esser S. Pyrosequencing reveals diverse fecal microbiota in Simmental calves during early development. Front Microbiol 2014; 5:622. [PMID: 25452753 PMCID: PMC4233928 DOI: 10.3389/fmicb.2014.00622] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Accepted: 10/31/2014] [Indexed: 01/01/2023] Open
Abstract
From birth to the time after weaning the gastrointestinal microbiota of calves must develop into a stable, autochthonous community accompanied by pivotal changes of anatomy and physiology of the gastrointestinal tract. The aim of this pilot study was to examine the fecal microbiota of six Simmental dairy calves to investigate time-dependent dynamics of the microbial community. Calves were followed up from birth until after weaning according to characteristic timepoints during physiological development of the gastrointestinal tract. Pyrosequencing of 16S rRNA gene amplicons from 35 samples yielded 253,528 reads clustering into 5410 operational taxonomic units based on 0.03 16S rRNA distance. Operational taxonomic units were assigned to 296 genera and 17 phyla with Bacteroidetes, Firmicutes, and Proteobacteria being most abundant. An age-dependent increasing diversity and species richness was observed. Highest similarities between fecal microbial communities were found around weaning compared with timepoints from birth to the middle of the milk feeding period. Principal coordinate analysis revealed a high variance particularly in samples taken at the middle of the milk feeding period (at the age of approximately 40 days) compared to earlier timepoints, confirming a unique individual development of the fecal microbiota of each calf. This study provides first deep insights into the composition of the fecal microbiota of Simmental dairy calves and might be a basis for future more detailed studies.
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Affiliation(s)
- Daniela Klein-Jöbstl
- Clinical Unit for Herd Health Management, Department for Farm Animals and Veterinary Public Health, University Clinic for Ruminants, University of Veterinary Medicine Vienna Vienna, Austria ; Research Cluster "Animal Gut Health," University of Veterinary Medicine Vienna Vienna, Austria
| | - Elisa Schornsteiner
- Department for Farm Animals and Veterinary Public Health, Institute for Milk Hygiene, Milk Technology and Food Science, University of Veterinary Medicine Vienna Vienna, Austria
| | - Evelyne Mann
- Research Cluster "Animal Gut Health," University of Veterinary Medicine Vienna Vienna, Austria ; Department for Farm Animals and Veterinary Public Health, Institute for Milk Hygiene, Milk Technology and Food Science, University of Veterinary Medicine Vienna Vienna, Austria
| | - Martin Wagner
- Research Cluster "Animal Gut Health," University of Veterinary Medicine Vienna Vienna, Austria ; Department for Farm Animals and Veterinary Public Health, Institute for Milk Hygiene, Milk Technology and Food Science, University of Veterinary Medicine Vienna Vienna, Austria
| | - Marc Drillich
- Clinical Unit for Herd Health Management, Department for Farm Animals and Veterinary Public Health, University Clinic for Ruminants, University of Veterinary Medicine Vienna Vienna, Austria
| | - Stephan Schmitz-Esser
- Research Cluster "Animal Gut Health," University of Veterinary Medicine Vienna Vienna, Austria ; Department for Farm Animals and Veterinary Public Health, Institute for Milk Hygiene, Milk Technology and Food Science, University of Veterinary Medicine Vienna Vienna, Austria
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