301
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Data and Statistical Methods To Analyze the Human Microbiome. mSystems 2018; 3:mSystems00194-17. [PMID: 29556541 PMCID: PMC5850081 DOI: 10.1128/msystems.00194-17] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2017] [Accepted: 12/07/2017] [Indexed: 11/20/2022] Open
Abstract
The Waldron lab for computational biostatistics bridges the areas of cancer genomics and microbiome studies for public health, developing methods to exploit publicly available data resources and to integrate -omics studies. The Waldron lab for computational biostatistics bridges the areas of cancer genomics and microbiome studies for public health, developing methods to exploit publicly available data resources and to integrate -omics studies.
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302
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Abstract
The last few decades have witnessed an increasing interest in studying the human microbiome and its role in health and disease. The focus of those studies was mainly the characterization of changes in the composition of the microbial communities under different conditions. As a result of those studies, we now know that imbalance in the composition of the microbiome, also referred to as microbial dysbiosis, is directly linked to developing certain conditions. Dysbiosis of the oral microbiome is a prime example of how this imbalance leads to disease in the case of periodontal disease. However, there is considerable overlap in the phylogenetic profiles of microbial communities associated with active and inactive lesions, suggesting that the difference in periodontal status of those sites may not be explained solely by differences in the subgingival microbial composition. These findings suggest that differences in functional activities may be the essential elements that define the dysbiotic process. Researchers have recently begun to study gene expression of the oral microbiome in situ with the goal of identifying changes in functional activities that could explain the transition from health to disease. These initial results suggest that, rather than a specific composition, a better understanding of oral dysbiosis can be obtained from the study of functional activities of the microbial community. In this review, we give a summary of these initial studies, which have opened a new door to our understanding of the dynamics of the oral community during the dysbiotic process in the oral cavity.
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Affiliation(s)
- J Solbiati
- 1 Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, FL, USA
| | - J Frias-Lopez
- 1 Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, FL, USA
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303
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Wu WK, Chen CC, Panyod S, Chen RA, Wu MS, Sheen LY, Chang SC. Optimization of fecal sample processing for microbiome study - The journey from bathroom to bench. J Formos Med Assoc 2018; 118:545-555. [PMID: 29490879 DOI: 10.1016/j.jfma.2018.02.005] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 01/23/2018] [Accepted: 02/05/2018] [Indexed: 12/30/2022] Open
Abstract
Although great interest has been displayed by researchers in the contribution of gut microbiota to human health, there is still no standard protocol with consensus to guarantee the sample quality of metagenomic analysis. Here we reviewed existing methodology studies and present suggestions for optimizing research pipeline from fecal sample collection to DNA extraction. First, we discuss strategies of clinical metadata collection as common confounders for microbiome research. Second, we propose general principles for freshly collected fecal sample and its storage and share a DIY stool collection kit protocol based on the manual procedure of Human Microbiome Project (HMP). Third, we provide a useful information of collection kit with DNA stabilization buffers and compare their pros and cons for multi-omic study. Fourth, we offer technical strategies as well as information of novel tools for sample aliquoting before long-term storage. Fifth, we discuss the substantial impact of different DNA extraction protocols on technical variations of metagenomic analysis. And lastly, we point out the limitation of current methods and the unmet needs for better quality control of metagenomic analysis. We hope the information provided here will help investigators in this exciting field to advance their studies while avoiding experimental artifacts.
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Affiliation(s)
- Wei-Kai Wu
- Department of Internal Medicine, National Taiwan University Hospital Bei-Hu Branch, Taipei, Taiwan; Institute of Food Science and Technology, National Taiwan University, Taipei, Taiwan
| | - Chieh-Chang Chen
- Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Suraphan Panyod
- Institute of Food Science and Technology, National Taiwan University, Taipei, Taiwan; College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Rou-An Chen
- Institute of Food Science and Technology, National Taiwan University, Taipei, Taiwan
| | - Ming-Shiang Wu
- Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan; College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Lee-Yan Sheen
- Institute of Food Science and Technology, National Taiwan University, Taipei, Taiwan
| | - Shan-Chwen Chang
- Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan; College of Medicine, National Taiwan University, Taipei, Taiwan.
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304
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Mehta RS, Abu-Ali GS, Drew DA, Lloyd-Price J, Subramanian A, Lochhead P, Joshi AD, Ivey KL, Khalili H, Brown GT, DuLong C, Song M, Nguyen LH, Mallick H, Rimm EB, Izard J, Huttenhower C, Chan AT. Stability of the human faecal microbiome in a cohort of adult men. Nat Microbiol 2018; 3:347-355. [PMID: 29335554 PMCID: PMC6016839 DOI: 10.1038/s41564-017-0096-0] [Citation(s) in RCA: 169] [Impact Index Per Article: 28.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 12/11/2017] [Indexed: 12/30/2022]
Abstract
Characterizing the stability of the gut microbiome is important to exploit it as a therapeutic target and diagnostic biomarker. We metagenomically and metatranscriptomically sequenced the faecal microbiomes of 308 participants in the Health Professionals Follow-Up Study. Participants provided four stool samples-one pair collected 24-72 h apart and a second pair ~6 months later. Within-person taxonomic and functional variation was consistently lower than between-person variation over time. In contrast, metatranscriptomic profiles were comparably variable within and between subjects due to higher within-subject longitudinal variation. Metagenomic instability accounted for ~74% of corresponding metatranscriptomic instability. The rest was probably attributable to sources such as regulation. Among the pathways that were differentially regulated, most were consistently over- or under-transcribed at each time point. Together, these results suggest that a single measurement of the faecal microbiome can provide long-term information regarding organismal composition and functional potential, but repeated or short-term measures may be necessary for dynamic features identified by metatranscriptomics.
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Affiliation(s)
- Raaj S Mehta
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Galeb S Abu-Ali
- Biostatistics Department, Harvard T. H. Chan School of Public Health, Boston, MA, USA
- The Broad Institute, Cambridge, MA, USA
| | - David A Drew
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Jason Lloyd-Price
- Biostatistics Department, Harvard T. H. Chan School of Public Health, Boston, MA, USA
- The Broad Institute, Cambridge, MA, USA
| | - Ayshwarya Subramanian
- Biostatistics Department, Harvard T. H. Chan School of Public Health, Boston, MA, USA
- The Broad Institute, Cambridge, MA, USA
| | - Paul Lochhead
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Amit D Joshi
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Kerry L Ivey
- Department of Nutrition, Harvard T. H. Chan School of Public Health, Boston, MA, USA
- South Australian Health and Medical Research Institute, Infection and Immunity Theme, School of Medicine, Flinders University, Adelaide, Australia
| | - Hamed Khalili
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Gordon T Brown
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Casey DuLong
- Biostatistics Department, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Mingyang Song
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Long H Nguyen
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Himel Mallick
- Biostatistics Department, Harvard T. H. Chan School of Public Health, Boston, MA, USA
- The Broad Institute, Cambridge, MA, USA
| | - Eric B Rimm
- Department of Nutrition, Harvard T. H. Chan School of Public Health, Boston, MA, USA
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | | | - Curtis Huttenhower
- Biostatistics Department, Harvard T. H. Chan School of Public Health, Boston, MA, USA.
- The Broad Institute, Cambridge, MA, USA.
| | - Andrew T Chan
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA.
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305
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Schirmer M, Franzosa EA, Lloyd-Price J, McIver LJ, Schwager R, Poon TW, Ananthakrishnan AN, Andrews E, Barron G, Lake K, Prasad M, Sauk J, Stevens B, Wilson RG, Braun J, Denson LA, Kugathasan S, McGovern DPB, Vlamakis H, Xavier RJ, Huttenhower C. Dynamics of metatranscription in the inflammatory bowel disease gut microbiome. Nat Microbiol 2018; 3:337-346. [PMID: 29311644 PMCID: PMC6131705 DOI: 10.1038/s41564-017-0089-z] [Citation(s) in RCA: 315] [Impact Index Per Article: 52.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 11/28/2017] [Indexed: 02/07/2023]
Abstract
Inflammatory bowel disease (IBD) is a group of chronic diseases of the digestive tract that affects millions of people worldwide. Genetic, environmental and microbial factors have been implicated in the onset and exacerbation of IBD. However, the mechanisms associating gut microbial dysbioses and aberrant immune responses remain largely unknown. The integrative Human Microbiome Project seeks to close these gaps by examining the dynamics of microbiome functionality in disease by profiling the gut microbiomes of >100 individuals sampled over a 1-year period. Here, we present the first results based on 78 paired faecal metagenomes and metatranscriptomes, and 222 additional metagenomes from 59 patients with Crohn's disease, 34 with ulcerative colitis and 24 non-IBD control patients. We demonstrate several cases in which measures of microbial gene expression in the inflamed gut can be informative relative to metagenomic profiles of functional potential. First, although many microbial organisms exhibited concordant DNA and RNA abundances, we also detected species-specific biases in transcriptional activity, revealing predominant transcription of pathways by individual microorganisms per host (for example, by Faecalibacterium prausnitzii). Thus, a loss of these organisms in disease may have more far-reaching consequences than suggested by their genomic abundances. Furthermore, we identified organisms that were metagenomically abundant but inactive or dormant in the gut with little or no expression (for example, Dialister invisus). Last, certain disease-specific microbial characteristics were more pronounced or only detectable at the transcript level, such as pathways that were predominantly expressed by different organisms in patients with IBD (for example, Bacteroides vulgatus and Alistipes putredinis). This provides potential insights into gut microbial pathway transcription that can vary over time, inducing phenotypical changes that are complementary to those linked to metagenomic abundances. The study's results highlight the strength of analysing both the activity and the presence of gut microorganisms to provide insight into the role of the microbiome in IBD.
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Affiliation(s)
- Melanie Schirmer
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Eric A Franzosa
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Jason Lloyd-Price
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Lauren J McIver
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Randall Schwager
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Tiffany W Poon
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ashwin N Ananthakrishnan
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Boston, MA, USA
| | - Elizabeth Andrews
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Boston, MA, USA
| | - Gildardo Barron
- The F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Kathleen Lake
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Mahadev Prasad
- Division of Pediatric Gastroenterology, Emory University School of Medicine, Atlanta, GA, USA
| | - Jenny Sauk
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Boston, MA, USA
- Vatche and Tamar Manoukian Division of Digestive Disease, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Betsy Stevens
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Boston, MA, USA
| | - Robin G Wilson
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Boston, MA, USA
| | - Jonathan Braun
- Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Lee A Denson
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Subra Kugathasan
- Division of Pediatric Gastroenterology, Emory University School of Medicine, Atlanta, GA, USA
- Children's Healthcare of Atlanta, Atlanta, GA, USA
| | - Dermot P B McGovern
- The F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Hera Vlamakis
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ramnik J Xavier
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Boston, MA, USA.
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, USA.
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Curtis Huttenhower
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA.
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306
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Abu-Ali GS, Mehta RS, Lloyd-Price J, Mallick H, Branck T, Ivey KL, Drew DA, DuLong C, Rimm E, Izard J, Chan AT, Huttenhower C. Metatranscriptome of human faecal microbial communities in a cohort of adult men. Nat Microbiol 2018; 3:356-366. [PMID: 29335555 PMCID: PMC6557121 DOI: 10.1038/s41564-017-0084-4] [Citation(s) in RCA: 137] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 11/23/2017] [Indexed: 02/07/2023]
Abstract
The gut microbiome is intimately related to human health, but it is not yet known which functional activities are driven by specific microbes’ ecological configurations or transcription. We report a large-scale investigation of 372 human fecal metatranscriptomes and 929 metagenomes from a subset of 308 men in the Health Professionals Follow-up Study. We identified a metatranscriptomic “core” universally transcribed over time and across participants, often by different microbes. In contrast to the housekeeping functions enriched in this core, a “variable” metatranscriptome included specialized pathways that were differentially expressed both across participants and among microbes. Finally, longitudinal metagenomic profiles allowed ecological interaction network reconstruction, which remained stable over the six-month timespan, as did strain tracking within and between participants. These results provide an initial characterization of human fecal microbial ecology into core, subject-specific, microbe-specific, and temporally-variable transcription, and they differentiate metagenomically versus metatranscriptomically informative aspects of the human fecal microbiome.
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Affiliation(s)
- Galeb S Abu-Ali
- Biostatistics Department, Harvard T. H. Chan School of Public Health, Boston, MA, USA.,The Broad Institute, Cambridge, MA, USA
| | - Raaj S Mehta
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Jason Lloyd-Price
- Biostatistics Department, Harvard T. H. Chan School of Public Health, Boston, MA, USA.,The Broad Institute, Cambridge, MA, USA
| | - Himel Mallick
- Biostatistics Department, Harvard T. H. Chan School of Public Health, Boston, MA, USA.,The Broad Institute, Cambridge, MA, USA
| | - Tobyn Branck
- Biostatistics Department, Harvard T. H. Chan School of Public Health, Boston, MA, USA.,U.S. Army Natick Soldier Systems Center in Natick, Natick, MA, USA
| | - Kerry L Ivey
- Department of Nutrition, Harvard T. H. Chan School of Public Health, Boston, MA, USA.,South Australian Health and Medical Research Institute, Infection and Immunity Theme, School of Medicine, Flinders University, Adelaide, South Australia, Australia
| | - David A Drew
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Casey DuLong
- Biostatistics Department, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Eric Rimm
- Department of Nutrition, Harvard T. H. Chan School of Public Health, Boston, MA, USA.,Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | | | - Andrew T Chan
- The Broad Institute, Cambridge, MA, USA. .,Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA. .,Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA. .,Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.
| | - Curtis Huttenhower
- Biostatistics Department, Harvard T. H. Chan School of Public Health, Boston, MA, USA. .,The Broad Institute, Cambridge, MA, USA.
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307
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Li F, Neves ALA, Ghoshal B, Guan LL. Symposium review: Mining metagenomic and metatranscriptomic data for clues about microbial metabolic functions in ruminants. J Dairy Sci 2017; 101:5605-5618. [PMID: 29274958 DOI: 10.3168/jds.2017-13356] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 10/27/2017] [Indexed: 12/22/2022]
Abstract
Metagenomics and metatranscriptomics can capture the whole genome and transcriptome repertoire of microorganisms through sequencing total DNA/RNA from various environmental samples, providing both taxonomic and functional information with high resolution. The unique and complex rumen microbial ecosystem is receiving great research attention because the rumen microbiota coevolves with the host and equips ruminants with the ability to convert cellulosic plant materials to high-protein products for human consumption. To date, hundreds to thousands of microbial phylotypes have been identified in the rumen using culture-independent molecular-based approaches, and genomic information of rumen microorganisms is rapidly accumulating through the single genome sequencing. However, functional characteristics of the rumen microbiome have not been well described because there are numerous uncultivable microorganisms in the rumen. The advent of metagenomics and metatranscriptomics along with advanced bioinformatics methods can help us better understand mechanisms of the rumen fermentation, which is vital for improving nutrient utilization and animal productivity. Therefore, in this review, we summarize a general workflow to conduct rumen metagenomics and metatranscriptomics and discuss how the data can be interpreted to be useful information. Moreover, we review recent literatures studying associations between the rumen microbiome and host phenotypes (e.g., feed efficiency and methane emissions) using these approaches, aiming to provide a useful guide to include studying the rumen microbiome as one of the research objectives using these 2 approaches.
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Affiliation(s)
- Fuyong Li
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada T6G 2P5
| | - Andre L A Neves
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada T6G 2P5
| | - Bibaswan Ghoshal
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada T6G 2P5
| | - Le Luo Guan
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada T6G 2P5.
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308
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Feng J, Li B, Jiang X, Yang Y, Wells GF, Zhang T, Li X. Antibiotic resistome in a large-scale healthy human gut microbiota deciphered by metagenomic and network analyses. Environ Microbiol 2017; 20:355-368. [DOI: 10.1111/1462-2920.14009] [Citation(s) in RCA: 94] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Revised: 11/22/2017] [Accepted: 11/22/2017] [Indexed: 12/13/2022]
Affiliation(s)
- Jie Feng
- Division of Energy & Environment, Graduate School at Shenzhen; Tsinghua University; China
| | - Bing Li
- Division of Energy & Environment, Graduate School at Shenzhen; Tsinghua University; China
| | - Xiaotao Jiang
- Environmental Biotechnology Laboratory, Department of Civil Engineering; The University of Hong Kong; Hong Kong China
| | - Ying Yang
- South China Sea Resource Exploitation and Protection Collaborative Innovation Center, School of Marine Sciences; Sun Yat-sen University; Guangzhou China
| | - George F. Wells
- Department of Civil and Environmental Engineering; Northwestern University; Evanston IL USA
| | - Tong Zhang
- Environmental Biotechnology Laboratory, Department of Civil Engineering; The University of Hong Kong; Hong Kong China
| | - Xiaoyan Li
- Division of Energy & Environment, Graduate School at Shenzhen; Tsinghua University; China
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309
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Colonic Butyrate-Producing Communities in Humans: an Overview Using Omics Data. mSystems 2017; 2:mSystems00130-17. [PMID: 29238752 PMCID: PMC5715108 DOI: 10.1128/msystems.00130-17] [Citation(s) in RCA: 286] [Impact Index Per Article: 40.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 11/09/2017] [Indexed: 12/12/2022] Open
Abstract
Studies focusing on taxonomic compositions of the gut microbiota are plentiful, whereas its functional capabilities are still poorly understood. Specific key functions deserve detailed investigations, as they regulate microbiota-host interactions and promote host health and disease. The production of butyrate is among the top targets since depletion of this microbe-derived metabolite is linked to several emerging noncommunicable diseases and was shown to facilitate establishment of enteric pathogens by disrupting colonization resistance. In this study, we established a workflow to investigate in detail the composition of the polyphyletic butyrate-producing community from omics data extracting its biochemical and taxonomic diversity. By combining information from various publicly available data sets, we identified universal ecological key features of this functional group and shed light on its role in health and disease. Our results will assist the development of precision medicine to combat functional dysbiosis. Given the key role of butyrate for host health, understanding the ecology of intestinal butyrate-producing communities is a top priority for gut microbiota research. To this end, we performed a pooled analysis on 2,387 metagenomic/transcriptomic samples from 15 publicly available data sets that originated from three continents and encompassed eight diseases as well as specific interventions. For analyses, a gene catalogue was constructed from gene-targeted assemblies of all genes from butyrate synthesis pathways of all samples and from an updated reference database derived from genome screenings. We demonstrate that butyrate producers establish themselves within the first year of life and display high abundances (>20% of total bacterial community) in adults regardless of origin. Various bacteria form this functional group, exhibiting a biochemical diversity including different pathways and terminal enzymes, where one carbohydrate-fueled pathway was dominant with butyryl coenzyme A (CoA):acetate CoA transferase as the main terminal enzyme. Subjects displayed a high richness of butyrate producers, and 17 taxa, primarily members of the Lachnospiraceae and Ruminococcaceae along with some Bacteroidetes, were detected in >70% of individuals, encompassing ~85% of the total butyrate-producing potential. Most of these key taxa were also found to express genes for butyrate formation, indicating that butyrate producers occupy various niches in the gut ecosystem, concurrently synthesizing that compound. Furthermore, results from longitudinal analyses propose that diversity supports functional stability during ordinary life disturbances and during interventions such as antibiotic treatment. A reduction of the butyrate-producing potential along with community alterations was detected in various diseases, where patients suffering from cardiometabolic disorders were particularly affected. IMPORTANCE Studies focusing on taxonomic compositions of the gut microbiota are plentiful, whereas its functional capabilities are still poorly understood. Specific key functions deserve detailed investigations, as they regulate microbiota-host interactions and promote host health and disease. The production of butyrate is among the top targets since depletion of this microbe-derived metabolite is linked to several emerging noncommunicable diseases and was shown to facilitate establishment of enteric pathogens by disrupting colonization resistance. In this study, we established a workflow to investigate in detail the composition of the polyphyletic butyrate-producing community from omics data extracting its biochemical and taxonomic diversity. By combining information from various publicly available data sets, we identified universal ecological key features of this functional group and shed light on its role in health and disease. Our results will assist the development of precision medicine to combat functional dysbiosis.
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310
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Bost A, Franzenburg S, Adair KL, Martinson VG, Loeb G, Douglas AE. How gut transcriptional function of
Drosophila melanogaster
varies with the presence and composition of the gut microbiota. Mol Ecol 2017; 27:1848-1859. [DOI: 10.1111/mec.14413] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 10/28/2017] [Accepted: 10/30/2017] [Indexed: 12/26/2022]
Affiliation(s)
- Alyssa Bost
- Department of Entomology Cornell University Ithaca NY USA
| | | | - Karen L. Adair
- Department of Entomology Cornell University Ithaca NY USA
| | | | - Greg Loeb
- Department of Entomology Cornell University Ithaca NY USA
- Department of Entomology Cornell University Geneva NY USA
| | - Angela E. Douglas
- Department of Entomology Cornell University Ithaca NY USA
- Molecular Biology and Genetics Cornell University Ithaca NY USA
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311
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Traversi D, Rabbone I, Ignaccolo MG, Carletto G, Racca I, Vallini C, Andriolo V, Cadario F, Savastio S, Siliquini R, Cerutti F. Gut microbiota diversity and T1DM onset: Preliminary data of a case-control study. ACTA ACUST UNITED AC 2017. [DOI: 10.1016/j.humic.2017.11.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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312
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Mallick H, Ma S, Franzosa EA, Vatanen T, Morgan XC, Huttenhower C. Experimental design and quantitative analysis of microbial community multiomics. Genome Biol 2017; 18:228. [PMID: 29187204 PMCID: PMC5708111 DOI: 10.1186/s13059-017-1359-z] [Citation(s) in RCA: 116] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Studies of the microbiome have become increasingly sophisticated, and multiple sequence-based, molecular methods as well as culture-based methods exist for population-scale microbiome profiles. To link the resulting host and microbial data types to human health, several experimental design considerations, data analysis challenges, and statistical epidemiological approaches must be addressed. Here, we survey current best practices for experimental design in microbiome molecular epidemiology, including technologies for generating, analyzing, and integrating microbiome multiomics data. We highlight studies that have identified molecular bioactives that influence human health, and we suggest steps for scaling translational microbiome research to high-throughput target discovery across large populations.
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Affiliation(s)
- Himel Mallick
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Siyuan Ma
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Eric A Franzosa
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Tommi Vatanen
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Xochitl C Morgan
- Department of Microbiology and Immunology, The University of Otago, Dunedin, New Zealand
| | - Curtis Huttenhower
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
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313
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Chong J, Xia J. Computational Approaches for Integrative Analysis of the Metabolome and Microbiome. Metabolites 2017; 7:E62. [PMID: 29156542 PMCID: PMC5746742 DOI: 10.3390/metabo7040062] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 11/14/2017] [Accepted: 11/16/2017] [Indexed: 12/31/2022] Open
Abstract
The study of the microbiome, the totality of all microbes inhabiting the host or an environmental niche, has experienced exponential growth over the past few years. The microbiome contributes functional genes and metabolites, and is an important factor for maintaining health. In this context, metabolomics is increasingly applied to complement sequencing-based approaches (marker genes or shotgun metagenomics) to enable resolution of microbiome-conferred functionalities associated with health. However, analyzing the resulting multi-omics data remains a significant challenge in current microbiome studies. In this review, we provide an overview of different computational approaches that have been used in recent years for integrative analysis of metabolome and microbiome data, ranging from statistical correlation analysis to metabolic network-based modeling approaches. Throughout the process, we strive to present a unified conceptual framework for multi-omics integration and interpretation, as well as point out potential future directions.
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Affiliation(s)
- Jasmine Chong
- Institute of Parasitology, McGill University, Montreal, QC H3A 0G4, Canada.
| | - Jianguo Xia
- Institute of Parasitology, McGill University, Montreal, QC H3A 0G4, Canada.
- Department of Animal Science, McGill University, Montreal, QC H3A 0G4, Canada.
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314
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Rowe WPM, Baker-Austin C, Verner-Jeffreys DW, Ryan JJ, Micallef C, Maskell DJ, Pearce GP. Overexpression of antibiotic resistance genes in hospital effluents over time. J Antimicrob Chemother 2017; 72:1617-1623. [PMID: 28175320 PMCID: PMC5437528 DOI: 10.1093/jac/dkx017] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 01/09/2017] [Indexed: 12/11/2022] Open
Abstract
Objectives Effluents contain a diverse abundance of antibiotic resistance genes that augment the resistome of receiving aquatic environments. However, uncertainty remains regarding their temporal persistence, transcription and response to anthropogenic factors, such as antibiotic usage. We present a spatiotemporal study within a river catchment (River Cam, UK) that aims to determine the contribution of antibiotic resistance gene-containing effluents originating from sites of varying antibiotic usage to the receiving environment. Methods Gene abundance in effluents (municipal hospital and dairy farm) was compared against background samples of the receiving aquatic environment (i.e. the catchment source) to determine the resistome contribution of effluents. We used metagenomics and metatranscriptomics to correlate DNA and RNA abundance and identified differentially regulated gene transcripts. Results We found that mean antibiotic resistance gene and transcript abundances were correlated for both hospital ( ρ = 0.9, two-tailed P <0.0001) and farm ( ρ = 0.5, two-tailed P <0.0001) effluents and that two β-lactam resistance genes ( bla GES and bla OXA ) were overexpressed in all hospital effluent samples. High β-lactam resistance gene transcript abundance was related to hospital antibiotic usage over time and hospital effluents contained antibiotic residues. Conclusions We conclude that effluents contribute high levels of antibiotic resistance genes to the aquatic environment; these genes are expressed at significant levels and are possibly related to the level of antibiotic usage at the effluent source.
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Affiliation(s)
- Will P M Rowe
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK.,Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | | | | | - Jim J Ryan
- Environment, Health and Safety, GlaxoSmithKline, Ware, UK
| | - Christianne Micallef
- Pharmacy Department, Addenbrooke's Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Duncan J Maskell
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Gareth P Pearce
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
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315
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Zuñiga C, Zaramela L, Zengler K. Elucidation of complexity and prediction of interactions in microbial communities. Microb Biotechnol 2017; 10:1500-1522. [PMID: 28925555 PMCID: PMC5658597 DOI: 10.1111/1751-7915.12855] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 08/10/2017] [Accepted: 08/11/2017] [Indexed: 12/11/2022] Open
Abstract
Microorganisms engage in complex interactions with other members of the microbial community, higher organisms as well as their environment. However, determining the exact nature of these interactions can be challenging due to the large number of members in these communities and the manifold of interactions they can engage in. Various omic data, such as 16S rRNA gene sequencing, shotgun metagenomics, metatranscriptomics, metaproteomics and metabolomics, have been deployed to unravel the community structure, interactions and resulting community dynamics in situ. Interpretation of these multi-omic data often requires advanced computational methods. Modelling approaches are powerful tools to integrate, contextualize and interpret experimental data, thus shedding light on the underlying processes shaping the microbiome. Here, we review current methods and approaches, both experimental and computational, to elucidate interactions in microbial communities and to predict their responses to perturbations.
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Affiliation(s)
- Cristal Zuñiga
- Department of PediatricsUniversity of California, San Diego9500 Gilman DriveLa JollaCA92093‐0760USA
| | - Livia Zaramela
- Department of PediatricsUniversity of California, San Diego9500 Gilman DriveLa JollaCA92093‐0760USA
| | - Karsten Zengler
- Department of PediatricsUniversity of California, San Diego9500 Gilman DriveLa JollaCA92093‐0760USA
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316
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Crovadore J, Soljan V, Calmin G, Chablais R, Cochard B, Lefort F. Metatranscriptomic and metagenomic description of the bacterial nitrogen metabolism in waste water wet oxidation effluents. Heliyon 2017; 3:e00427. [PMID: 29062974 PMCID: PMC5647474 DOI: 10.1016/j.heliyon.2017.e00427] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 09/06/2017] [Accepted: 10/11/2017] [Indexed: 11/18/2022] Open
Abstract
Anaerobic digestion is a common method for reducing the amount of sludge solids in used waters and enabling biogas production. The wet oxidation process (WOX) improves anaerobic digestion by converting carbon into methane through oxidation of organic compounds. WOX produces effluents rich in ammonia, which must be removed to maintain the activity of methanogens. Ammonia removal from WOX could be biologically operated by aerobic granules. To this end, granulation experiments were conducted in 2 bioreactors containing an activated sludge (AS). For the first time, the dynamics of the microbial community structure and the expression levels of 7 enzymes of the nitrogen metabolism in such active microbial communities were followed in regard to time by metagenomics and metatranscriptomics. It was shown that bacterial communities adapt to the wet oxidation effluent by increasing the expression level of the nitrogen metabolism, suggesting that these biological activities could be a less costly alternative for the elimination of ammonia, resulting in a reduction of the use of chemicals and energy consumption in sewage plants. This study reached a strong sequencing depth (from 4.4 to 7.6 Gb) and enlightened a yet unknown diversity of the microorganisms involved in the nitrogen pathway. Moreover, this approach revealed the abundance and expression levels of specialised enzymes involved in nitrification, denitrification, ammonification, dissimilatory nitrate reduction to ammonium (DNRA) and nitrogen fixation processes in AS.
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Affiliation(s)
- Julien Crovadore
- Plants and pathogens group, Institute Land Nature and Environment, Hepia, HES-SO University of Applied Sciences and Arts Western Switzerland, 150 route de Presinge, 1254 Jussy, Switzerland
| | - Vice Soljan
- Puratis Sàrl, EPFL Innovation Park, Building C, 1015 Lausanne, Switzerland
| | - Gautier Calmin
- Faculty of Engineering and Architecture, HES-SO University of Applied Sciences and Arts Western Switzerland, Rue de la Jeunesse 1, 2800 Delémont, Switzerland
| | - Romain Chablais
- Plants and pathogens group, Institute Land Nature and Environment, Hepia, HES-SO University of Applied Sciences and Arts Western Switzerland, 150 route de Presinge, 1254 Jussy, Switzerland
| | - Bastien Cochard
- Plants and pathogens group, Institute Land Nature and Environment, Hepia, HES-SO University of Applied Sciences and Arts Western Switzerland, 150 route de Presinge, 1254 Jussy, Switzerland
| | - François Lefort
- Plants and pathogens group, Institute Land Nature and Environment, Hepia, HES-SO University of Applied Sciences and Arts Western Switzerland, 150 route de Presinge, 1254 Jussy, Switzerland
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317
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Klingenberg H, Meinicke P. How to normalize metatranscriptomic count data for differential expression analysis. PeerJ 2017; 5:e3859. [PMID: 29062598 PMCID: PMC5649605 DOI: 10.7717/peerj.3859] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 09/06/2017] [Indexed: 11/25/2022] Open
Abstract
Background Differential expression analysis on the basis of RNA-Seq count data has become a standard tool in transcriptomics. Several studies have shown that prior normalization of the data is crucial for a reliable detection of transcriptional differences. Until now it has not been clear whether and how the transcriptomic approach can be used for differential expression analysis in metatranscriptomics. Methods We propose a model for differential expression in metatranscriptomics that explicitly accounts for variations in the taxonomic composition of transcripts across different samples. As a main consequence the correct normalization of metatranscriptomic count data under this model requires the taxonomic separation of the data into organism-specific bins. Then the taxon-specific scaling of organism profiles yields a valid normalization and allows us to recombine the scaled profiles into a metatranscriptomic count matrix. This matrix can then be analyzed with statistical tools for transcriptomic count data. For taxon-specific scaling and recombination of scaled counts we provide a simple R script. Results When applying transcriptomic tools for differential expression analysis directly to metatranscriptomic data with an organism-independent (global) scaling of counts the resulting differences may be difficult to interpret. The differences may correspond to changing functional profiles of the contributing organisms but may also result from a variation of taxonomic abundances. Taxon-specific scaling eliminates this variation and therefore the resulting differences actually reflect a different behavior of organisms under changing conditions. In simulation studies we show that the divergence between results from global and taxon-specific scaling can be drastic. In particular, the variation of organism abundances can imply a considerable increase of significant differences with global scaling. Also, on real metatranscriptomic data, the predictions from taxon-specific and global scaling can differ widely. Our studies indicate that in real data applications performed with global scaling it might be impossible to distinguish between differential expression in terms of transcriptomic changes and differential composition in terms of changing taxonomic proportions. Conclusions As in transcriptomics, a proper normalization of count data is also essential for differential expression analysis in metatranscriptomics. Our model implies a taxon-specific scaling of counts for normalization of the data. The application of taxon-specific scaling consequently removes taxonomic composition variations from functional profiles and therefore provides a clear interpretation of the observed functional differences.
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Affiliation(s)
- Heiner Klingenberg
- Department of Bioinformatics, Institute of Microbiology and Genetics, University of Goettingen, Göttingen, Germany
| | - Peter Meinicke
- Department of Bioinformatics, Institute of Microbiology and Genetics, University of Goettingen, Göttingen, Germany
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318
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Costea PI, Zeller G, Sunagawa S, Pelletier E, Alberti A, Levenez F, Tramontano M, Driessen M, Hercog R, Jung FE, Kultima JR, Hayward MR, Coelho LP, Allen-Vercoe E, Bertrand L, Blaut M, Brown JRM, Carton T, Cools-Portier S, Daigneault M, Derrien M, Druesne A, de Vos WM, Finlay BB, Flint HJ, Guarner F, Hattori M, Heilig H, Luna RA, van Hylckama Vlieg J, Junick J, Klymiuk I, Langella P, Le Chatelier E, Mai V, Manichanh C, Martin JC, Mery C, Morita H, O'Toole PW, Orvain C, Patil KR, Penders J, Persson S, Pons N, Popova M, Salonen A, Saulnier D, Scott KP, Singh B, Slezak K, Veiga P, Versalovic J, Zhao L, Zoetendal EG, Ehrlich SD, Dore J, Bork P. Towards standards for human fecal sample processing in metagenomic studies. Nat Biotechnol 2017; 35:1069-1076. [PMID: 28967887 DOI: 10.1038/nbt.3960] [Citation(s) in RCA: 484] [Impact Index Per Article: 69.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 08/11/2017] [Indexed: 12/30/2022]
Abstract
Technical variation in metagenomic analysis must be minimized to confidently assess the contributions of microbiota to human health. Here we tested 21 representative DNA extraction protocols on the same fecal samples and quantified differences in observed microbial community composition. We compared them with differences due to library preparation and sample storage, which we contrasted with observed biological variation within the same specimen or within an individual over time. We found that DNA extraction had the largest effect on the outcome of metagenomic analysis. To rank DNA extraction protocols, we considered resulting DNA quantity and quality, and we ascertained biases in estimates of community diversity and the ratio between Gram-positive and Gram-negative bacteria. We recommend a standardized DNA extraction method for human fecal samples, for which transferability across labs was established and which was further benchmarked using a mock community of known composition. Its adoption will improve comparability of human gut microbiome studies and facilitate meta-analyses.
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Affiliation(s)
- Paul I Costea
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Georg Zeller
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Shinichi Sunagawa
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany.,Department of Biology, Institute of Microbiology, ETH Zurich, Zurich, Switzerland
| | - Eric Pelletier
- CEA - Institut François Jacob - Genoscope, Evry, France.,CNRS UMR-8030, Evry, France.,Université Evry Val d'Essonne, Evry, France
| | | | - Florence Levenez
- Metagenopolis, Institut National de la Recherche Agronomique, Jouy en Josas, France
| | - Melanie Tramontano
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Marja Driessen
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Rajna Hercog
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Ferris-Elias Jung
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Jens Roat Kultima
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Matthew R Hayward
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Luis Pedro Coelho
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Emma Allen-Vercoe
- Department of Molecular and Cellular Biology, The University of Guelph, Guelph, Ontario, Canada
| | | | - Michael Blaut
- Department of Gastrointestinal Microbiology, German Institute of Human Nutrition Potsdam-Rehbruecke, Nuthetal, Germany
| | - Jillian R M Brown
- School of Microbiology & APC Microbiome Institute, University College Cork, Cork, Ireland
| | | | | | - Michelle Daigneault
- Metagenopolis, Institut National de la Recherche Agronomique, Jouy en Josas, France
| | | | | | - Willem M de Vos
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, the Netherlands.,Immunobiology Research Program, Department of Bacteriology and Immunology, University of Helsinki, Helsinki, Finland
| | - B Brett Finlay
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Harry J Flint
- Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, UK
| | - Francisco Guarner
- Digestive System Research Unit, Vall d'Hebron Research Institute, Barcelona, Spain
| | - Masahira Hattori
- Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan.,Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
| | - Hans Heilig
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, the Netherlands
| | - Ruth Ann Luna
- Texas Children's Hospital, Feigin Center, Houston, Texas, USA
| | | | - Jana Junick
- Department of Gastrointestinal Microbiology, German Institute of Human Nutrition Potsdam-Rehbruecke, Nuthetal, Germany
| | - Ingeborg Klymiuk
- Center for Medical Research, Medical University of Graz, Graz, Austria
| | - Philippe Langella
- Metagenopolis, Institut National de la Recherche Agronomique, Jouy en Josas, France
| | | | - Volker Mai
- Department of Epidemiology, College of Public Health and Health Professions and College of Medicine, Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA
| | - Chaysavanh Manichanh
- Digestive System Research Unit, Vall d'Hebron Research Institute, Barcelona, Spain
| | - Jennifer C Martin
- Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, UK
| | | | - Hidetoshi Morita
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Paul W O'Toole
- School of Microbiology & APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Céline Orvain
- CEA - Institut François Jacob - Genoscope, Evry, France
| | - Kiran Raosaheb Patil
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
| | - John Penders
- School of Nutrition and Translational Research in Metabolism (NUTRIM) and Care and Public Health Research Institute (Caphri), Department of Medical Microbiology, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Søren Persson
- Unit of Foodborne Infections, Department of Bacteria, Parasites & Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Nicolas Pons
- Metagenopolis, Institut National de la Recherche Agronomique, Jouy en Josas, France
| | | | - Anne Salonen
- Immunobiology Research Program, Department of Bacteriology and Immunology, University of Helsinki, Helsinki, Finland
| | - Delphine Saulnier
- Department of Gastrointestinal Microbiology, German Institute of Human Nutrition Potsdam-Rehbruecke, Nuthetal, Germany
| | - Karen P Scott
- Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, UK
| | - Bhagirath Singh
- Centre for Human Immunology, Department of Microbiology & Immunology and Robarts Research Institute, University of Western Ontario, London, Ontario, Canada
| | - Kathleen Slezak
- Department of Gastrointestinal Microbiology, German Institute of Human Nutrition Potsdam-Rehbruecke, Nuthetal, Germany
| | | | | | - Liping Zhao
- Ministry of Education Key Laboratory for Systems Biomedicine, Shanghai Centre for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, PR China
| | - Erwin G Zoetendal
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, the Netherlands
| | - S Dusko Ehrlich
- Metagenopolis, Institut National de la Recherche Agronomique, Jouy en Josas, France.,King's College London, Centre for Host-Microbiome Interactions, Dental Institute Central Office, Guy's Hospital, London, UK
| | - Joel Dore
- Metagenopolis, Institut National de la Recherche Agronomique, Jouy en Josas, France
| | - Peer Bork
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany.,Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany.,Molecular Medicine Partnership Unit, Heidelberg, Germany.,Max-Delbrück-Centre for Molecular Medicine, Berlin, Germany
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319
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Levin BJ, Huang YY, Peck SC, Wei Y, Martínez-Del Campo A, Marks JA, Franzosa EA, Huttenhower C, Balskus EP. A prominent glycyl radical enzyme in human gut microbiomes metabolizes trans-4-hydroxy-l-proline. Science 2017; 355:355/6325/eaai8386. [PMID: 28183913 DOI: 10.1126/science.aai8386] [Citation(s) in RCA: 102] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 01/04/2017] [Indexed: 12/14/2022]
Abstract
The human microbiome encodes vast numbers of uncharacterized enzymes, limiting our functional understanding of this community and its effects on host health and disease. By incorporating information about enzymatic chemistry into quantitative metagenomics, we determined the abundance and distribution of individual members of the glycyl radical enzyme superfamily among the microbiomes of healthy humans. We identified many uncharacterized family members, including a universally distributed enzyme that enables commensal gut microbes and human pathogens to dehydrate trans-4-hydroxy-l-proline, the product of the most abundant human posttranslational modification. This "chemically guided functional profiling" workflow can therefore use ecological context to facilitate the discovery of enzymes in microbial communities.
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Affiliation(s)
- B J Levin
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA
| | - Y Y Huang
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA
| | - S C Peck
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA
| | - Y Wei
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - A Martínez-Del Campo
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA
| | - J A Marks
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA
| | - E A Franzosa
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA.,Broad Institute, Cambridge, MA 02139, USA
| | - C Huttenhower
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA.,Broad Institute, Cambridge, MA 02139, USA
| | - E P Balskus
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA. .,Broad Institute, Cambridge, MA 02139, USA
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320
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Kelly JR, Minuto C, Cryan JF, Clarke G, Dinan TG. Cross Talk: The Microbiota and Neurodevelopmental Disorders. Front Neurosci 2017; 11:490. [PMID: 28966571 PMCID: PMC5605633 DOI: 10.3389/fnins.2017.00490] [Citation(s) in RCA: 152] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 08/17/2017] [Indexed: 12/11/2022] Open
Abstract
Humans evolved within a microbial ecosystem resulting in an interlinked physiology. The gut microbiota can signal to the brain via the immune system, the vagus nerve or other host-microbe interactions facilitated by gut hormones, regulation of tryptophan metabolism and microbial metabolites such as short chain fatty acids (SCFA), to influence brain development, function and behavior. Emerging evidence suggests that the gut microbiota may play a role in shaping cognitive networks encompassing emotional and social domains in neurodevelopmental disorders. Drawing upon pre-clinical and clinical evidence, we review the potential role of the gut microbiota in the origins and development of social and emotional domains related to Autism spectrum disorders (ASD) and schizophrenia. Small preliminary clinical studies have demonstrated gut microbiota alterations in both ASD and schizophrenia compared to healthy controls. However, we await the further development of mechanistic insights, together with large scale longitudinal clinical trials, that encompass a systems level dimensional approach, to investigate whether promising pre-clinical and initial clinical findings lead to clinical relevance.
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Affiliation(s)
- John R Kelly
- Department of Psychiatry and Neurobehavioural Science, University College CorkCork, Ireland.,APC Microbiome Institute, University College CorkCork, Ireland
| | - Chiara Minuto
- Department of Psychiatry and Neurobehavioural Science, University College CorkCork, Ireland.,APC Microbiome Institute, University College CorkCork, Ireland
| | - John F Cryan
- APC Microbiome Institute, University College CorkCork, Ireland.,Department of Anatomy and Neuroscience, University College CorkCork, Ireland
| | - Gerard Clarke
- Department of Psychiatry and Neurobehavioural Science, University College CorkCork, Ireland.,APC Microbiome Institute, University College CorkCork, Ireland
| | - Timothy G Dinan
- Department of Psychiatry and Neurobehavioural Science, University College CorkCork, Ireland.,APC Microbiome Institute, University College CorkCork, Ireland
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321
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Cabral DJ, Wurster JI, Flokas ME, Alevizakos M, Zabat M, Korry BJ, Rowan AD, Sano WH, Andreatos N, Ducharme RB, Chan PA, Mylonakis E, Fuchs BB, Belenky P. The salivary microbiome is consistent between subjects and resistant to impacts of short-term hospitalization. Sci Rep 2017; 7:11040. [PMID: 28887570 PMCID: PMC5591268 DOI: 10.1038/s41598-017-11427-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 08/24/2017] [Indexed: 01/20/2023] Open
Abstract
In recent years, a growing amount of research has begun to focus on the oral microbiome due to its links with health and systemic disease. The oral microbiome has numerous advantages that make it particularly useful for clinical studies, including non-invasive collection, temporal stability, and lower complexity relative to other niches, such as the gut. Despite recent discoveries made in this area, it is unknown how the oral microbiome responds to short-term hospitalization. Previous studies have demonstrated that the gut microbiome is extremely sensitive to short-term hospitalization and that these changes are associated with significant morbidity and mortality. Here, we present a comprehensive pipeline for reliable bedside collection, sequencing, and analysis of the human salivary microbiome. We also develop a novel oral-specific mock community for pipeline validation. Using our methodology, we analyzed the salivary microbiomes of patients before and during hospitalization or azithromycin treatment to profile impacts on this community. Our findings indicate that azithromycin alters the diversity and taxonomic composition of the salivary microbiome; however, we also found that short-term hospitalization does not impact the richness or structure of this community, suggesting that the oral cavity may be less susceptible to dysbiosis during short-term hospitalization.
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Affiliation(s)
- Damien J Cabral
- Department of Molecular Microbiology and Immunology, Division of Biology and Medicine, Brown University, Providence, RI, 02912, USA
| | - Jenna I Wurster
- Department of Molecular Microbiology and Immunology, Division of Biology and Medicine, Brown University, Providence, RI, 02912, USA
| | - Myrto E Flokas
- Division of Infectious Diseases, Rhode Island Hospital, Alpert Medical School and Brown University, Providence, RI, 02903, USA
| | - Michail Alevizakos
- Division of Infectious Diseases, Rhode Island Hospital, Alpert Medical School and Brown University, Providence, RI, 02903, USA
| | - Michelle Zabat
- Department of Molecular Microbiology and Immunology, Division of Biology and Medicine, Brown University, Providence, RI, 02912, USA
| | - Benjamin J Korry
- Department of Molecular Microbiology and Immunology, Division of Biology and Medicine, Brown University, Providence, RI, 02912, USA
| | - Aislinn D Rowan
- Department of Molecular Microbiology and Immunology, Division of Biology and Medicine, Brown University, Providence, RI, 02912, USA
| | - William H Sano
- Department of Molecular Microbiology and Immunology, Division of Biology and Medicine, Brown University, Providence, RI, 02912, USA
| | - Nikolaos Andreatos
- Division of Infectious Diseases, Rhode Island Hospital, Alpert Medical School and Brown University, Providence, RI, 02903, USA
| | - R Bobby Ducharme
- Department of Medicine, Brown University, Providence, RI, 02903, USA
| | - Philip A Chan
- Department of Medicine, Brown University, Providence, RI, 02903, USA
| | - Eleftherios Mylonakis
- Division of Infectious Diseases, Rhode Island Hospital, Alpert Medical School and Brown University, Providence, RI, 02903, USA
| | - Beth Burgwyn Fuchs
- Division of Infectious Diseases, Rhode Island Hospital, Alpert Medical School and Brown University, Providence, RI, 02903, USA
| | - Peter Belenky
- Department of Molecular Microbiology and Immunology, Division of Biology and Medicine, Brown University, Providence, RI, 02912, USA.
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322
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Cohen LJ, Esterhazy D, Kim SH, Lemetre C, Aguilar RR, Gordon EA, Pickard AJ, Cross JR, Emiliano AB, Han SM, Chu J, Vila-Farres X, Kaplitt J, Rogoz A, Calle PY, Hunter C, Bitok JK, Brady SF. Commensal bacteria make GPCR ligands that mimic human signalling molecules. Nature 2017; 549:48-53. [PMID: 28854168 PMCID: PMC5777231 DOI: 10.1038/nature23874] [Citation(s) in RCA: 312] [Impact Index Per Article: 44.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 08/01/2017] [Indexed: 02/08/2023]
Abstract
Commensal bacteria are believed to have important roles in human health. The mechanisms by which they affect mammalian physiology remain poorly understood, but bacterial metabolites are likely to be key components of host interactions. Here we use bioinformatics and synthetic biology to mine the human microbiota for N-acyl amides that interact with G-protein-coupled receptors (GPCRs). We found that N-acyl amide synthase genes are enriched in gastrointestinal bacteria and the lipids that they encode interact with GPCRs that regulate gastrointestinal tract physiology. Mouse and cell-based models demonstrate that commensal GPR119 agonists regulate metabolic hormones and glucose homeostasis as efficiently as human ligands, although future studies are needed to define their potential physiological role in humans. Our results suggest that chemical mimicry of eukaryotic signalling molecules may be common among commensal bacteria and that manipulation of microbiota genes encoding metabolites that elicit host cellular responses represents a possible small-molecule therapeutic modality (microbiome-biosynthetic gene therapy).
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Affiliation(s)
- Louis J Cohen
- Laboratory of Genetically Encoded Small Molecules, Rockefeller University, New York, New York 10065, USA
- Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Daria Esterhazy
- Laboratory of Mucosal Immunology, Rockefeller University, New York, New York 10065, USA
| | - Seong-Hwan Kim
- Laboratory of Genetically Encoded Small Molecules, Rockefeller University, New York, New York 10065, USA
| | - Christophe Lemetre
- Laboratory of Genetically Encoded Small Molecules, Rockefeller University, New York, New York 10065, USA
| | - Rhiannon R Aguilar
- Laboratory of Genetically Encoded Small Molecules, Rockefeller University, New York, New York 10065, USA
| | - Emma A Gordon
- Laboratory of Genetically Encoded Small Molecules, Rockefeller University, New York, New York 10065, USA
| | - Amanda J Pickard
- Donald B. and Catherine C. Marron Cancer Metabolism Center, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Justin R Cross
- Donald B. and Catherine C. Marron Cancer Metabolism Center, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Ana B Emiliano
- Laboratory of Molecular Genetics, Rockefeller University, New York, New York 10065, USA
| | - Sun M Han
- Laboratory of Genetically Encoded Small Molecules, Rockefeller University, New York, New York 10065, USA
| | - John Chu
- Laboratory of Genetically Encoded Small Molecules, Rockefeller University, New York, New York 10065, USA
| | - Xavier Vila-Farres
- Laboratory of Genetically Encoded Small Molecules, Rockefeller University, New York, New York 10065, USA
| | - Jeremy Kaplitt
- Laboratory of Genetically Encoded Small Molecules, Rockefeller University, New York, New York 10065, USA
| | - Aneta Rogoz
- Laboratory of Mucosal Immunology, Rockefeller University, New York, New York 10065, USA
| | - Paula Y Calle
- Laboratory of Genetically Encoded Small Molecules, Rockefeller University, New York, New York 10065, USA
| | - Craig Hunter
- Comparative Biosciences Center, Rockefeller University, New York, New York 10065, USA
| | - J Kipchirchir Bitok
- Laboratory of Genetically Encoded Small Molecules, Rockefeller University, New York, New York 10065, USA
| | - Sean F Brady
- Laboratory of Genetically Encoded Small Molecules, Rockefeller University, New York, New York 10065, USA
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323
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Singer E, Wagner M, Woyke T. Capturing the genetic makeup of the active microbiome in situ. THE ISME JOURNAL 2017; 11:1949-1963. [PMID: 28574490 PMCID: PMC5563950 DOI: 10.1038/ismej.2017.59] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 03/02/2017] [Accepted: 03/10/2017] [Indexed: 12/21/2022]
Abstract
More than any other technology, nucleic acid sequencing has enabled microbial ecology studies to be complemented with the data volumes necessary to capture the extent of microbial diversity and dynamics in a wide range of environments. In order to truly understand and predict environmental processes, however, the distinction between active, inactive and dead microbial cells is critical. Also, experimental designs need to be sensitive toward varying population complexity and activity, and temporal as well as spatial scales of process rates. There are a number of approaches, including single-cell techniques, which were designed to study in situ microbial activity and that have been successively coupled to nucleic acid sequencing. The exciting new discoveries regarding in situ microbial activity provide evidence that future microbial ecology studies will indispensably rely on techniques that specifically capture members of the microbiome active in the environment. Herein, we review those currently used activity-based approaches that can be directly linked to shotgun nucleic acid sequencing, evaluate their relevance to ecology studies, and discuss future directions.
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Affiliation(s)
- Esther Singer
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Michael Wagner
- University of Vienna, Department of Microbial Ecology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Tanja Woyke
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
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324
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Feasibility of Metatranscriptome Analysis from Infant Gut Microbiota: Adaptation to Solid Foods Results in Increased Activity of Firmicutes at Six Months. Int J Microbiol 2017; 2017:9547063. [PMID: 28912815 PMCID: PMC5587937 DOI: 10.1155/2017/9547063] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Revised: 06/17/2017] [Accepted: 07/04/2017] [Indexed: 11/17/2022] Open
Abstract
Newborns are rapidly colonized by microbes and their intestinal tracts contain highly dynamic and rapidly developing microbial communities in the first months of life. In this study, we describe the feasibility of isolating mRNA from rapidly processed faecal samples and applying deep RNA-Seq analysis to provide insight into the active contributors of the microbial community in early life. Specific attention is given to the impact of removing rRNA from the mRNA on the phylogenetic and transcriptional profiling and its analysis depth. A breastfed baby was followed in the first six months of life during adaptation to solid food, dairy products, and formula. It was found that, in the weaning period, the total transcriptional activity of Actinobacteria, mainly represented by Bifidobacterium, decreased while that of Firmicutes increased over time. Moreover, Firmicutes and Actinobacteria, including the canonical Bifidobacteria as well as Collinsella, were found to be important contributors to carbohydrate fermentation and vitamin biosynthesis in the infant intestine. Finally, the expression of Lactobacillus rhamnosus-like genes was detected, likely following transfer from the mother who consumed L. rhamnosus GG. The study indicates that metatranscriptome analysis of the infant gut microbiota is feasible on infant stool samples and can be used to provide insight into the core activities of the developing community.
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325
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Zhang X, Chen W, Ning Z, Mayne J, Mack D, Stintzi A, Tian R, Figeys D. Deep Metaproteomics Approach for the Study of Human Microbiomes. Anal Chem 2017; 89:9407-9415. [PMID: 28749657 DOI: 10.1021/acs.analchem.7b02224] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Host-microbiome interactions have been shown to play important roles in human health and diseases. Most of the current studies of the microbiome have been performed by genomic approaches through next-generation sequencing. Technologies, such as metaproteomics, for functional analysis of the microbiome are needed to better understand the intricate host-microbiome interactions. However, significant efforts to improve the depth and resolution of gut metaproteomics are still required. In this study, we combined an efficient sample preparation technique, high resolution mass spectrometry, and metaproteomic bioinformatics tools to perform ultradeep metaproteomic analysis of human gut microbiome from stool. We reported the deepest analysis of the microbiome to date with an average of 20 558 protein groups identified per sample analysis. Moreover, strain resolution taxonomic and pathway analysis using deep metaproteomics revealed strain level variations, in particular for Faecalibacterium prausnitzii, in the microbiome from the different individuals. We also reported that the human proteins identified in stool samples are functionally enriched in extracellular region pathways and in particular those proteins involved in defense response against microbial organisms. Deep metaproteomics is a promising approach to perform in-depth microbiome analysis and simultaneously reveals both human and microbial changes that are not readily apparent using the standard genomic approaches.
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Affiliation(s)
- Xu Zhang
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa , Ottawa, Ontario, Canada , K1H 8M5
| | - Wendong Chen
- Department of Chemistry, Southern University of Science and Technology , Shenzhen 518055, Guangdong, China
| | - Zhibin Ning
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa , Ottawa, Ontario, Canada , K1H 8M5
| | - Janice Mayne
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa , Ottawa, Ontario, Canada , K1H 8M5
| | - David Mack
- Department of Paediatrics, Faculty of Medicine, University of Ottawa and Children's Hospital of Eastern Ontario Inflammatory Bowel Disease Centre and Research Institute , Ottawa, Ontario, Canada , K1H 8L1
| | - Alain Stintzi
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa , Ottawa, Ontario, Canada , K1H 8M5
| | - Ruijun Tian
- Department of Chemistry, Southern University of Science and Technology , Shenzhen 518055, Guangdong, China
| | - Daniel Figeys
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa , Ottawa, Ontario, Canada , K1H 8M5.,Canadian Institute for Advanced Research , Toronto, Ontario, Canada , M5G 1M1
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326
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Petersen LM, Bautista EJ, Nguyen H, Hanson BM, Chen L, Lek SH, Sodergren E, Weinstock GM. Community characteristics of the gut microbiomes of competitive cyclists. MICROBIOME 2017; 5:98. [PMID: 28797298 PMCID: PMC5553673 DOI: 10.1186/s40168-017-0320-4] [Citation(s) in RCA: 193] [Impact Index Per Article: 27.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2017] [Accepted: 08/01/2017] [Indexed: 05/04/2023]
Abstract
BACKGROUND Changes in diet and exercise can alter the gut microbiome of humans and mice; however, few studies to date have assessed the microbiomes of highly fit athletes. In this pilot study, we used metagenomic whole genome shotgun (mWGS) and metatranscriptomic (RNA-Seq) sequencing to show what organisms are both present and active in the gut microbiomes of both professional and amateur level competitive cyclists and to determine if any significant differences exist between these two groups. RESULTS Using mWGS sequencing data, we showed that the gut microbiomes of 33 cyclists split into three taxonomic clusters, characterized by either high Prevotella, high Bacteroides or a mix of many genera including Bacteroides, Prevotella, Eubacterium, Ruminococcus, and Akkermansia. While no significant correlations could be found between taxonomic cluster and being either a professional or amateur level cyclist, high abundance of the genus Prevotella (≥2.5%) was significantly correlated with time reported exercising during an average week. Increased abundance of Prevotella was correlated with a number of amino acid and carbohydrate metabolism pathways, including branched chain amino acid metabolism. Further analysis of the metatranscriptome revealed significant taxonomic differences when compared to the metagenome. There was increased abundance of Methanobrevibacter smithii transcripts in a number of professional cyclists in comparison to amateur cyclists and this archaeon had upregulation of genes involved in the production of methane. Furthermore, when methane metabolism was upregulated, there was similar upregulation of energy and carbohydrate metabolism pathways. CONCLUSIONS These results provide a framework for common constituents of the gut community in individuals who follow an exercise-rich lifestyle. These data also suggest how certain organisms such as M. smithii may beneficially influence the metabolic efficiency of the gut community in professional cyclists due to synergistic metabolic cross-feeding events.
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Affiliation(s)
- Lauren M. Petersen
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT 06032 USA
| | - Eddy J. Bautista
- Corporación Colombiana de Investigación Agropecuaria, Km 14 Vía Mosquera-Bogotá, Mosquera, Cundinamarca Colombia
| | - Hoan Nguyen
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT 06032 USA
| | - Blake M. Hanson
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT 06032 USA
| | - Lei Chen
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT 06032 USA
| | - Sai H. Lek
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT 06032 USA
| | - Erica Sodergren
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT 06032 USA
| | - George M. Weinstock
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT 06032 USA
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327
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Lackey KA, Williams JE, Price WJ, Carrothers JM, Brooker SL, Shafii B, McGuire MA, McGuire MK. Comparison of commercially-available preservatives for maintaining the integrity of bacterial DNA in human milk. J Microbiol Methods 2017; 141:73-81. [PMID: 28802721 DOI: 10.1016/j.mimet.2017.08.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2017] [Revised: 08/08/2017] [Accepted: 08/09/2017] [Indexed: 11/17/2022]
Abstract
BACKGROUND Inhibiting changes to bacteria in human milk between sample collection and analysis is necessary for unbiased characterization of the milk microbiome. Although cold storage is considered optimal, alternative preservation is sometimes necessary. RESEARCH AIM/QUESTION The objective of this study was to compare the effectiveness of several commercially-available preservatives with regard to maintaining bacterial DNA in human milk for delayed microbiome analysis. Specifically, we compared Life Technologies' RNAlater® stabilization solution, Biomatrica's DNAgard® Saliva, Advanced Instruments' Broad Spectrum Microtabs II™, and Norgen Biotek Corporation's Milk DNA Preservation and Isolation Kit. METHODS Aliquots of 8 pools of human milk were treated with each preservative. DNA was extracted immediately and at 1, 2, 4, and 6wk, during which time milk was held at 37°C. The V1-V3 region of the bacterial 16S rRNA gene was amplified and sequenced. Changes in bacterial community structure and diversity over time were evaluated. RESULTS Comparable to other studies, the most abundant genera were Streptococcus (33.3%), Staphylococcus (14.0%), Dyella (6.3%), Pseudomonas (3.0%), Veillonella (2.5%), Hafnia (2.0%), Prevotella (1.7%), Rhodococcus (1.6%), and Granulicatella (1.4%). Overall, use of Norgen's Milk DNA Preservation and Isolation Kit best maintained the consistency of the bacterial community structure. Total DNA, diversity, and evenness metrics were also highest in samples preserved with this method. CONCLUSIONS When collecting human milk for bacterial community analysis in field conditions where cold storage is not available, our results suggest that Norgen's Milk DNA Preservation and Isolation Kit may be a useful method, at least for a period of 2weeks.
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Affiliation(s)
- Kimberly A Lackey
- School of Biological Sciences, Washington State University, Pullman, WA, United States
| | - Janet E Williams
- Department and Animal and Veterinary Science, University of Idaho, Moscow, ID, United States
| | - William J Price
- Statistical Programs, University of Idaho, Moscow, ID, United States
| | - Janae M Carrothers
- School of Biological Sciences, Washington State University, Pullman, WA, United States
| | - Sarah L Brooker
- Department and Animal and Veterinary Science, University of Idaho, Moscow, ID, United States; Institute for Bioinformatics and Evolutionary Studies, Department of Biological Sciences, University of Idaho, Moscow, ID, United States
| | - Bahman Shafii
- Statistical Programs, University of Idaho, Moscow, ID, United States
| | - Mark A McGuire
- Department and Animal and Veterinary Science, University of Idaho, Moscow, ID, United States
| | - Michelle K McGuire
- School of Biological Sciences, Washington State University, Pullman, WA, United States; Paul G. Allen School for Global Animal Health, Washington State University, Pullman, WA, United States.
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328
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Fluoride Depletes Acidogenic Taxa in Oral but Not Gut Microbial Communities in Mice. mSystems 2017; 2:mSystems00047-17. [PMID: 28808691 PMCID: PMC5547758 DOI: 10.1128/msystems.00047-17] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 07/18/2017] [Indexed: 01/22/2023] Open
Abstract
Fluoridation of drinking water and dental products prevents dental caries primarily by inhibiting energy harvest in oral cariogenic bacteria (such as Streptococcus mutans and Streptococcus sanguinis), thus leading to their depletion. However, the extent to which oral and gut microbial communities are affected by host fluoride exposure has been underexplored. In this study, we modeled human fluoride exposures to municipal water and dental products by treating mice with low or high levels of fluoride over a 12-week period. We then used 16S rRNA gene amplicon and shotgun metagenomic sequencing to assess fluoride's effects on oral and gut microbiome composition and function. In both the low- and high-fluoride groups, several operational taxonomic units (OTUs) belonging to acidogenic bacterial genera (such as Parabacteroides, Bacteroides, and Bilophila) were depleted in the oral community. In addition, fluoride-associated changes in oral community composition resulted in depletion of gene families involved in central carbon metabolism and energy harvest (2-oxoglutarate ferredoxin oxidoreductase, succinate dehydrogenase, and the glyoxylate cycle). In contrast, fluoride treatment did not induce a significant shift in gut microbial community composition or function in our mouse model, possibly due to absorption in the upper gastrointestinal tract. Fluoride-associated perturbations thus appeared to have a selective effect on the composition of the oral but not gut microbial community in mice. Future studies will be necessary to understand possible implications of fluoride exposure for the human microbiome. IMPORTANCE Fluoride has been added to drinking water and dental products since the 1950s. The beneficial effects of fluoride on oral health are due to its ability to inhibit the growth of bacteria that cause dental caries. Despite widespread human consumption of fluoride, there have been only two studies of humans that considered the effect of fluoride on human-associated microbial communities, which are increasingly understood to play important roles in health and disease. Notably, neither of these studies included a true cross-sectional control lacking fluoride exposure, as study subjects continued baseline fluoride treatment in their daily dental hygiene routines. To our knowledge, this work (in mice) is the first controlled study to assess the independent effects of fluoride exposure on the oral and gut microbial communities. Investigating how fluoride interacts with host-associated microbial communities in this controlled setting represents an effort toward understanding how common environmental exposures may potentially influence health.
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329
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Tamburini S, Shen N, Wu HC, Clemente JC. The microbiome in early life: implications for health outcomes. Nat Med 2017; 22:713-22. [PMID: 27387886 DOI: 10.1038/nm.4142] [Citation(s) in RCA: 739] [Impact Index Per Article: 105.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 06/08/2016] [Indexed: 02/06/2023]
Abstract
Recent studies have characterized how host genetics, prenatal environment and delivery mode can shape the newborn microbiome at birth. Following this, postnatal factors, such as antibiotic treatment, diet or environmental exposure, further modulate the development of the infant's microbiome and immune system, and exposure to a variety of microbial organisms during early life has long been hypothesized to exert a protective effect in the newborn. Furthermore, epidemiological studies have shown that factors that alter bacterial communities in infants during childhood increase the risk for several diseases, highlighting the importance of understanding early-life microbiome composition. In this review, we describe how prenatal and postnatal factors shape the development of both the microbiome and the immune system. We also discuss the prospects of microbiome-mediated therapeutics and the need for more effective approaches that can reconfigure bacterial communities from pathogenic to homeostatic configurations.
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Affiliation(s)
- Sabrina Tamburini
- Icahn Institute for Genomics and Multiscale Biology. Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Nan Shen
- Icahn Institute for Genomics and Multiscale Biology. Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Han Chih Wu
- Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Department of Medicine, Division of Clinical Immunology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Jose C Clemente
- Icahn Institute for Genomics and Multiscale Biology. Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Department of Medicine, Division of Clinical Immunology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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330
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Integrated meta-omic analyses of the gastrointestinal tract microbiome in patients undergoing allogeneic hematopoietic stem cell transplantation. Transl Res 2017; 186:79-94.e1. [PMID: 28686852 DOI: 10.1016/j.trsl.2017.06.008] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Revised: 05/17/2017] [Accepted: 06/12/2017] [Indexed: 02/06/2023]
Abstract
In patients undergoing allogeneic hematopoietic stem cell transplantation (allo-HSCT), treatment-induced changes to the gastrointestinal tract (GIT) microbiome have been linked to adverse outcomes, most notably graft-versus-host disease (GvHD). However, it is presently unknown whether this relationship is causal or consequential. Here, we performed an integrated meta-omic analysis to probe deeper into the GIT microbiome changes during allo-HSCT and its accompanying treatments. We used 16S and 18S rRNA gene amplicon sequencing to resolve archaea, bacteria, and eukaryotes within the GIT microbiomes of 16 patients undergoing allo-HSCT for the treatment of hematologic malignancies. These results revealed a major shift in the GIT microbiome after allo-HSCT including a marked reduction in bacterial diversity, accompanied by only limited changes in eukaryotes and archaea. An integrated analysis of metagenomic and metatranscriptomic data was performed on samples collected from a patient before and after allo-HSCT for acute myeloid leukemia. This patient developed severe GvHD, leading to death 9 months after allo-HSCT. In addition to drastically decreased bacterial diversity, the post-treatment microbiome showed a higher overall number and higher expression levels of antibiotic resistance genes (ARGs). One specific Escherichia coli strain causing a paravertebral abscess was linked to GIT dysbiosis, suggesting loss of intestinal barrier integrity. The apparent selection for bacteria expressing ARGs suggests that prophylactic antibiotic administration may adversely affect the overall treatment outcome. We therefore assert that such analyses including information about the selection of pathogenic bacteria expressing ARGs may assist clinicians in "personalizing" regimens for individual patients to improve overall outcomes.
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331
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Vandeputte D, Tito RY, Vanleeuwen R, Falony G, Raes J. Practical considerations for large-scale gut microbiome studies. FEMS Microbiol Rev 2017; 41:S154-S167. [PMID: 28830090 PMCID: PMC7207147 DOI: 10.1093/femsre/fux027] [Citation(s) in RCA: 118] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 06/19/2017] [Indexed: 12/14/2022] Open
Abstract
First insights on the human gut microbiome have been gained from medium-sized, cross-sectional studies. However, given the modest portion of explained variance of currently identified covariates and the small effect size of gut microbiota modulation strategies, upscaling seems essential for further discovery and characterisation of the multiple influencing factors and their relative contribution. In order to guide future research projects and standardisation efforts, we here review currently applied collection and preservation methods for gut microbiome research. We discuss aspects such as sample quality, applicable omics techniques, user experience and time and cost efficiency. In addition, we evaluate the protocols of a large-scale microbiome cohort initiative, the Flemish Gut Flora Project, to give an idea of perspectives, and pitfalls of large-scale faecal sampling studies. Although cryopreservation can be regarded as the gold standard, freezing protocols generally require more resources due to cold chain management. However, here we show that much can be gained from an optimised transport chain and sample aliquoting before freezing. Other protocols can be useful as long as they preserve the microbial signature of a sample such that relevant conclusions can be drawn regarding the research question, and the obtained data are stable and reproducible over time.
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Affiliation(s)
- Doris Vandeputte
- KU Leuven, Department of Microbiology and Immunology, Rega Institute, Herestraat 49, B-3000 Leuven, Belgium
- VIB, Center for Microbiology, Herestraat 49, B-3000 Leuven, Belgium
- Microbiology Unit, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
| | - Raul Y. Tito
- KU Leuven, Department of Microbiology and Immunology, Rega Institute, Herestraat 49, B-3000 Leuven, Belgium
- VIB, Center for Microbiology, Herestraat 49, B-3000 Leuven, Belgium
- Microbiology Unit, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
| | - Rianne Vanleeuwen
- Universiteit Antwerpen, Productontwikkeling, Ambtmanstraat 1, B-2000 Antwerpen, Belgium
| | - Gwen Falony
- KU Leuven, Department of Microbiology and Immunology, Rega Institute, Herestraat 49, B-3000 Leuven, Belgium
- VIB, Center for Microbiology, Herestraat 49, B-3000 Leuven, Belgium
| | - Jeroen Raes
- KU Leuven, Department of Microbiology and Immunology, Rega Institute, Herestraat 49, B-3000 Leuven, Belgium
- VIB, Center for Microbiology, Herestraat 49, B-3000 Leuven, Belgium
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332
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Abstract
Colorectal cancer is the second-leading cause of cancer-related deaths in the United States and fourth-leading cause of cancer-related deaths worldwide. While cancer is largely considered to be a disease of genetic and environmental factors, increasing evidence has demonstrated a role for the microbiota (the microorganisms associated with the human body) in shaping inflammatory environments and promoting tumor growth and spread. Herein, we discuss both human data from meta'omics analyses and data from mechanistic studies in cell culture and animal models that support specific bacterial agents as potentiators of tumorigenesis-including Fusobacterium nucleatum, enterotoxigenic Bacteroides fragilis, and colibactin-producing Escherichia coli. Further, we consider how microbes can be used in diagnosing colorectal cancer and manipulating the tumor environment to encourage better patient outcomes in response to immunotherapy treatments.
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Affiliation(s)
- Caitlin A Brennan
- Departments of Immunology & Infectious Diseases and Genetics & Complex Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts 02115; ,
| | - Wendy S Garrett
- Departments of Immunology & Infectious Diseases and Genetics & Complex Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts 02115; , .,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115.,Cancer Program, Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142.,Department of Medicine, Harvard Medical School, Boston, Massachusetts 02115
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333
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Tanca A, Abbondio M, Palomba A, Fraumene C, Manghina V, Cucca F, Fiorillo E, Uzzau S. Potential and active functions in the gut microbiota of a healthy human cohort. MICROBIOME 2017; 5:79. [PMID: 28709472 PMCID: PMC5513205 DOI: 10.1186/s40168-017-0293-3] [Citation(s) in RCA: 97] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 06/28/2017] [Indexed: 05/20/2023]
Abstract
BACKGROUND The study of the gut microbiota (GM) is rapidly moving towards its functional characterization by means of shotgun meta-omics. In this context, there is still no consensus on which microbial functions are consistently and constitutively expressed in the human gut in physiological conditions. Here, we selected a cohort of 15 healthy subjects from a native and highly monitored Sardinian population and analyzed their GMs using shotgun metaproteomics, with the aim of investigating GM functions actually expressed in a healthy human population. In addition, shotgun metagenomics was employed to reveal GM functional potential and to compare metagenome and metaproteome profiles in a combined taxonomic and functional fashion. RESULTS Metagenomic and metaproteomic data concerning the taxonomic structure of the GM under study were globally comparable. On the contrary, a considerable divergence between genetic potential and functional activity of the human healthy GM was observed, with the metaproteome displaying a higher plasticity, compared to the lower inter-individual variability of metagenome profiles. The taxon-specific contribution to functional activities and metabolic tasks was also examined, giving insights into the peculiar role of several GM members in carbohydrate metabolism (including polysaccharide degradation, glycan transport, glycolysis, and short-chain fatty acid production). Noteworthy, Firmicutes-driven butyrogenesis (mainly due to Faecalibacterium spp.) was shown to be the metabolic activity with the highest expression rate and the lowest inter-individual variability in the study cohort, in line with the previously reported importance of the biosynthesis of this microbial product for the gut homeostasis. CONCLUSIONS Our results provide detailed and taxon-specific information regarding functions and pathways actively working in a healthy GM. The reported discrepancy between expressed functions and functional potential suggests that caution should be used before drawing functional conclusions from metagenomic data, further supporting metaproteomics as a fundamental approach to characterize the human GM metabolic functions and activities.
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Affiliation(s)
- Alessandro Tanca
- Porto Conte Ricerche, Science and Technology Park of Sardinia, S.P. 55 Porto Conte - Capo Caccia km 8,400, Località Tramariglio, 07041, Alghero, SS, Italy
| | - Marcello Abbondio
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Antonio Palomba
- Porto Conte Ricerche, Science and Technology Park of Sardinia, S.P. 55 Porto Conte - Capo Caccia km 8,400, Località Tramariglio, 07041, Alghero, SS, Italy
| | - Cristina Fraumene
- Porto Conte Ricerche, Science and Technology Park of Sardinia, S.P. 55 Porto Conte - Capo Caccia km 8,400, Località Tramariglio, 07041, Alghero, SS, Italy
| | - Valeria Manghina
- Porto Conte Ricerche, Science and Technology Park of Sardinia, S.P. 55 Porto Conte - Capo Caccia km 8,400, Località Tramariglio, 07041, Alghero, SS, Italy
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Francesco Cucca
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato, Cagliari, Italy
| | - Edoardo Fiorillo
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato, Cagliari, Italy
| | - Sergio Uzzau
- Porto Conte Ricerche, Science and Technology Park of Sardinia, S.P. 55 Porto Conte - Capo Caccia km 8,400, Località Tramariglio, 07041, Alghero, SS, Italy.
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy.
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Rojo D, Méndez-García C, Raczkowska BA, Bargiela R, Moya A, Ferrer M, Barbas C. Exploring the human microbiome from multiple perspectives: factors altering its composition and function. FEMS Microbiol Rev 2017; 41:453-478. [PMID: 28333226 PMCID: PMC5812509 DOI: 10.1093/femsre/fuw046] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 12/15/2016] [Indexed: 02/07/2023] Open
Abstract
Our microbiota presents peculiarities and characteristics that may be altered by multiple factors. The degree and consequences of these alterations depend on the nature, strength and duration of the perturbations as well as the structure and stability of each microbiota. The aim of this review is to sketch a very broad picture of the factors commonly influencing different body sites, and which have been associated with alterations in the human microbiota in terms of composition and function. To do so, first, a graphical representation of bacterial, fungal and archaeal genera reveals possible associations among genera affected by different factors. Then, the revision of sequence-based predictions provides associations with functions that become part of the active metabolism. Finally, examination of microbial metabolite contents and fluxes reveals whether metabolic alterations are a reflection of the differences observed at the level of population structure, and in the last step, link microorganisms to functions under perturbations that differ in nature and aetiology. The utilisation of complementary technologies and methods, with a special focus on metabolomics research, is thoroughly discussed to obtain a global picture of microbiota composition and microbiome function and to convey the urgent need for the standardisation of protocols.
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Affiliation(s)
- David Rojo
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad CEU San Pablo, Campus Montepríncipe, 28668 Madrid, Spain
| | | | - Beata Anna Raczkowska
- Department of Endocrinology, Diabetology and Internal Medicine, Medical University of Bialystok, 15-276 Bialystok, Poland
| | - Rafael Bargiela
- Institute of Catalysis, Consejo Superior de Investigaciones Científicas (CSIC), 28049 Madrid, Spain
| | - Andrés Moya
- Foundation for the Promotion of Health and Biomedical Research in the Valencian Community Public Health (FISABIO), 46020 Valencia, Spain
- Network Research Center for Epidemiology and Public Health (CIBER-ESP), 28029 Madrid, Spain
- Instituto Cavanilles de Biodiversidad y Biología Evolutiva, Universidad de Valencia, Paterna, 46980 Valencia, Spain
- These authors contributed equally to this work
| | - Manuel Ferrer
- Institute of Catalysis, Consejo Superior de Investigaciones Científicas (CSIC), 28049 Madrid, Spain
- Corresponding author: Institute of Catalysis, Consejo Superior de Investigaciones Científicas (CSIC), 28049 Madrid, Spain. Tel: (+34) 915854872; E-mail:
| | - Coral Barbas
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad CEU San Pablo, Campus Montepríncipe, 28668 Madrid, Spain
- These authors contributed equally to this work
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335
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Seidel DV, Azcárate-Peril MA, Chapkin RS, Turner ND. Shaping functional gut microbiota using dietary bioactives to reduce colon cancer risk. Semin Cancer Biol 2017; 46:191-204. [PMID: 28676459 DOI: 10.1016/j.semcancer.2017.06.009] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2017] [Revised: 06/20/2017] [Accepted: 06/23/2017] [Indexed: 12/18/2022]
Abstract
Colon cancer is a multifactorial disease associated with a variety of lifestyle factors. Alterations in the gut microbiota and the intestinal metabolome are noted during colon carcinogenesis, implicating them as critical contributors or results of the disease process. Diet is a known determinant of health, and as a modifier of the gut microbiota and its metabolism, a critical element in maintenance of intestinal health. This review summarizes recent evidence demonstrating the role and responses of the intestinal microbiota during colon tumorigenesis and the ability of dietary bioactive compounds and probiotics to impact colon health from the intestinal lumen to the epithelium and systemically. We first describe changes to the intestinal microbiome, metabolome, and epithelium associated with colon carcinogenesis. This is followed by a discussion of recent evidence indicating how specific classes of dietary bioactives, prebiotics, or probiotics affect colon carcinogenesis. Lastly, we briefly address the prospects of using multiple 'omics' techniques to integrate the effects of diet, host, and microbiota on colon tumorigenesis with the goal of more fully appreciating the interconnectedness of these systems and thus, how these approaches can be used to advance personalized nutrition strategies and nutrition research.
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Affiliation(s)
- Derek V Seidel
- Nutrition and Food Science Department, and Faculty of Genetics, Texas A&M University, College Station, TX 77843-2253, USA.
| | - M Andrea Azcárate-Peril
- Department of Medicine GI Division, University of North Carolina, Chapel Hill, NC 27599-7555, USA.
| | - Robert S Chapkin
- Nutrition and Food Science Department, and Faculty of Genetics, Texas A&M University, College Station, TX 77843-2253, USA.
| | - Nancy D Turner
- Nutrition and Food Science Department, and Faculty of Genetics, Texas A&M University, College Station, TX 77843-2253, USA.
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336
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Aitoro R, Paparo L, Amoroso A, Di Costanzo M, Cosenza L, Granata V, Di Scala C, Nocerino R, Trinchese G, Montella M, Ercolini D, Berni Canani R. Gut Microbiota as a Target for Preventive and Therapeutic Intervention against Food Allergy. Nutrients 2017; 9:nu9070672. [PMID: 28657607 PMCID: PMC5537787 DOI: 10.3390/nu9070672] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Revised: 06/15/2017] [Accepted: 06/23/2017] [Indexed: 12/24/2022] Open
Abstract
The gut microbiota plays a pivotal role in immune system development and function. Modification in the gut microbiota composition (dysbiosis) early in life is a critical factor affecting the development of food allergy. Many environmental factors including caesarean delivery, lack of breast milk, drugs, antiseptic agents, and a low-fiber/high-fat diet can induce gut microbiota dysbiosis, and have been associated with the occurrence of food allergy. New technologies and experimental tools have provided information regarding the importance of select bacteria on immune tolerance mechanisms. Short-chain fatty acids are crucial metabolic products of gut microbiota responsible for many protective effects against food allergy. These compounds are involved in epigenetic regulation of the immune system. These evidences provide a foundation for developing innovative strategies to prevent and treat food allergy. Here, we present an overview on the potential role of gut microbiota as the target of intervention against food allergy.
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Affiliation(s)
- Rosita Aitoro
- Department of Translational Medical Science-Pediatric Section, University of Naples "Federico II", 80131 Naples, Italy.
| | - Lorella Paparo
- Department of Translational Medical Science-Pediatric Section, University of Naples "Federico II", 80131 Naples, Italy.
| | - Antonio Amoroso
- Department of Translational Medical Science-Pediatric Section, University of Naples "Federico II", 80131 Naples, Italy.
| | - Margherita Di Costanzo
- Department of Translational Medical Science-Pediatric Section, University of Naples "Federico II", 80131 Naples, Italy.
| | - Linda Cosenza
- Department of Translational Medical Science-Pediatric Section, University of Naples "Federico II", 80131 Naples, Italy.
| | - Viviana Granata
- Department of Translational Medical Science-Pediatric Section, University of Naples "Federico II", 80131 Naples, Italy.
| | - Carmen Di Scala
- Department of Translational Medical Science-Pediatric Section, University of Naples "Federico II", 80131 Naples, Italy.
| | - Rita Nocerino
- Department of Translational Medical Science-Pediatric Section, University of Naples "Federico II", 80131 Naples, Italy.
| | - Giovanna Trinchese
- Department of Translational Medical Science-Pediatric Section, University of Naples "Federico II", 80131 Naples, Italy.
| | - Mariangela Montella
- Department of Translational Medical Science-Pediatric Section, University of Naples "Federico II", 80131 Naples, Italy.
| | - Danilo Ercolini
- Department of Agricultural Sciences, Division of Microbiology, University of Naples "Federico II", 80055 Portici, Italy.
- Task Force on Microbiome Studies, University of Naples "Federico II", 80131 Naples, Italy.
| | - Roberto Berni Canani
- Department of Translational Medical Science-Pediatric Section, University of Naples "Federico II", 80131 Naples, Italy.
- Task Force on Microbiome Studies, University of Naples "Federico II", 80131 Naples, Italy.
- European Laboratory for the Investigation of Food Induced Diseases, University of Naples "Federico II", 80131 Naples, Italy.
- CEINGE Advanced Biotechnologies, University of Naples "Federico II", 80131 Naples, Italy.
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337
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Wolff SM, Ellison MJ, Hao Y, Cockrum RR, Austin KJ, Baraboo M, Burch K, Lee HJ, Maurer T, Patil R, Ravelo A, Taxis TM, Truong H, Lamberson WR, Cammack KM, Conant GC. Diet shifts provoke complex and variable changes in the metabolic networks of the ruminal microbiome. MICROBIOME 2017; 5:60. [PMID: 28595639 PMCID: PMC5465553 DOI: 10.1186/s40168-017-0274-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Accepted: 05/02/2017] [Indexed: 06/07/2023]
Abstract
BACKGROUND Grazing mammals rely on their ruminal microbial symbionts to convert plant structural biomass into metabolites they can assimilate. To explore how this complex metabolic system adapts to the host animal's diet, we inferred a microbiome-level metabolic network from shotgun metagenomic data. RESULTS Using comparative genomics, we then linked this microbial network to that of the host animal using a set of interface metabolites likely to be transferred to the host. When the host sheep were fed a grain-based diet, the induced microbial metabolic network showed several critical differences from those seen on the evolved forage-based diet. Grain-based (e.g., concentrate) diets tend to be dominated by a smaller set of reactions that employ metabolites that are nearer in network space to the host's metabolism. In addition, these reactions are more central in the network and employ substrates with shorter carbon backbones. Despite this apparent lower complexity, the concentrate-associated metabolic networks are actually more dissimilar from each other than are those of forage-fed animals. Because both groups of animals were initially fed on a forage diet, we propose that the diet switch drove the appearance of a number of different microbial networks, including a degenerate network characterized by an inefficient use of dietary nutrients. We used network simulations to show that such disparate networks are not an unexpected result of a diet shift. CONCLUSION We argue that network approaches, particularly those that link the microbial network with that of the host, illuminate aspects of the structure of the microbiome not seen from a strictly taxonomic perspective. In particular, different diets induce predictable and significant differences in the enzymes used by the microbiome. Nonetheless, there are clearly a number of microbiomes of differing structure that show similar functional properties. Changes such as a diet shift uncover more of this type of diversity.
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Affiliation(s)
- Sara M Wolff
- Division of Animal Sciences, University of Missouri-Columbia, Columbia, MO, USA
| | - Melinda J Ellison
- Department of Animal and Veterinary Science, University of Idaho, Moscow, ID, USA
| | - Yue Hao
- Informatics Institute, University of Missouri-Columbia, Columbia, MO, USA
| | - Rebecca R Cockrum
- Department of Dairy Science, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Kathy J Austin
- Department of Animal Science, University of Wyoming, Laramie, WY, USA
| | - Michael Baraboo
- Department of Computer Science, Truman State University, Kirksville, MO, USA
| | - Katherine Burch
- Department of Psychology, Truman State University, Kirksville, MO, USA
| | - Hyuk Jin Lee
- Division of Biological Sciences, University of Missouri-Columbia, Columbia, MO, USA
| | - Taylor Maurer
- Department of Biology, Kenyon College, Gambier, Ohio, USA
| | - Rocky Patil
- Division of Animal Sciences, University of Missouri-Columbia, Columbia, MO, USA
| | - Andrea Ravelo
- Division of Biological Sciences, University of Missouri-Columbia, Columbia, MO, USA
| | - Tasia M Taxis
- National Animal Disease Center, ARS, USDA, Ames, IA, USA
| | - Huan Truong
- Informatics Institute, University of Missouri-Columbia, Columbia, MO, USA
| | - William R Lamberson
- Division of Animal Sciences, University of Missouri-Columbia, Columbia, MO, USA
| | - Kristi M Cammack
- Department of Animal Sciences, South Dakota State University, Brookings, SD, USA
| | - Gavin C Conant
- Division of Animal Sciences, University of Missouri-Columbia, Columbia, MO, USA.
- Informatics Institute, University of Missouri-Columbia, Columbia, MO, USA.
- Program in Genetics, North Carolina State University, Raleigh, NC, USA.
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA.
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA.
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338
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Comparison of Fecal Collection Methods for Microbiota Studies in Bangladesh. Appl Environ Microbiol 2017; 83:AEM.00361-17. [PMID: 28258145 DOI: 10.1128/aem.00361-17] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 02/27/2017] [Indexed: 12/17/2022] Open
Abstract
To our knowledge, fecal microbiota collection methods have not been evaluated in low- and middle-income countries. Therefore, we evaluated five different fecal sample collection methods for technical reproducibility, stability, and accuracy within the Health Effects of Arsenic Longitudinal Study (HEALS) in Bangladesh. Fifty participants from the HEALS provided fecal samples in the clinic which were aliquoted into no solution, 95% ethanol, RNAlater, postdevelopment fecal occult blood test (FOBT) cards, and fecal immunochemical test (FIT) tubes. Half of the aliquots were frozen immediately at -80°C (day 0) and the remaining samples were left at ambient temperature for 96 h and then frozen (day 4). Intraclass correlation coefficients (ICC) were calculated for the relative abundances of the top three phyla, for two alpha diversity measures, and for four beta diversity measures. The duplicate samples had relatively high ICCs for technical reproducibility at day 0 and day 4 (range, 0.79 to 0.99). The FOBT card and samples preserved in RNAlater and 95% ethanol had the highest ICCs for stability over 4 days. The FIT tube had lower stability measures overall. In comparison to the "gold standard" method using immediately frozen fecal samples with no solution, the ICCs for many of the microbial metrics were low, but the rank order appeared to be preserved as seen by the Spearman correlation. The FOBT cards, 95% ethanol, and RNAlater were effective fecal preservatives. These fecal collection methods are optimal for future cohort studies, particularly in low- and middle-income countries.IMPORTANCE The collection of fecal samples in prospective cohort studies is essential to provide the opportunity to study the effect of the human microbiota on numerous health conditions. However, these collection methods have not been adequately tested in low- and middle-income countries. We present estimates of technical reproducibility, stability at ambient temperature for 4 days, and accuracy comparing a "gold standard" for fecal samples in no solution, 95% ethanol, RNAlater, postdevelopment fecal occult blood test cards, and fecal immunochemical test tubes in a study conducted in Bangladesh. Fecal occult blood test cards and fecal samples stored in 95% ethanol or RNAlater adequately preserve fecal samples in this setting. Therefore, new studies in low- and middle-income countries should include collection of fecal samples using fecal occult blood test cards, 95% ethanol, or RNAlater for prospective cohort studies.
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339
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Repeated inoculation of cattle rumen with bison rumen contents alters the rumen microbiome and improves nitrogen digestibility in cattle. Sci Rep 2017; 7:1276. [PMID: 28455495 PMCID: PMC5430699 DOI: 10.1038/s41598-017-01269-3] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 03/28/2017] [Indexed: 11/23/2022] Open
Abstract
Future growth in demand for meat and milk, and the socioeconomic and environmental challenges that farmers face, represent a “grand challenge for humanity”. Improving the digestibility of crop residues such as straw could enhance the sustainability of ruminant production systems. Here, we investigated if transfer of rumen contents from bison to cattle could alter the rumen microbiome and enhance total tract digestibility of a barley straw-based diet. Beef heifers were adapted to the diet for 28 days prior to the experiment. After 46 days, ~70 percent of rumen contents were removed from each heifer and replaced with mixed rumen contents collected immediately after slaughter from 32 bison. This procedure was repeated 14 days later. Intake, chewing activity, total tract digestibility, ruminal passage rate, ruminal fermentation, and the bacterial and protozoal communities were examined before the first and after the second transfer. Overall, inoculation with bison rumen contents successfully altered the cattle rumen microbiome and metabolism, and increased protein digestibility and nitrogen retention, but did not alter fiber digestibility.
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340
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Abstract
The microbiome is a vital component to the evolution of a host and much of what we know about the microbiome derives from studies on humans and captive animals. But captivity alters the microbiome and mammals have unique biological adaptations that affect their microbiomes (e.g., milk). Birds represent over 30% of known tetrapod diversity and possess their own suite of adaptations relevant to the microbiome. In a previous study, we showed that 59 species of birds displayed immense variation in their microbiomes and host (bird) taxonomy and ecology were most correlated with the gut microbiome. In this Frontiers Focused Review, I put those results in a broader context by discussing how collecting and analyzing wild microbiomes contributes to the main goals of evolutionary biology and the specific ways that birds are unique microbial hosts. Finally, I outline some of the methodological considerations for adding microbiome sampling to the research of wild animals and urge researchers to do so. To truly understand the evolution of a host, we need to understand the millions of microorganisms that inhabit it as well: evolutionary biology needs wild microbiomes.
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Affiliation(s)
- Sarah M Hird
- Department of Molecular and Cell Biology, University of ConnecticutStorrs, CT, USA
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341
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Metatranscriptomic Profiling Reveals Linkages between the Active Rumen Microbiome and Feed Efficiency in Beef Cattle. Appl Environ Microbiol 2017; 83:AEM.00061-17. [PMID: 28235871 DOI: 10.1128/aem.00061-17] [Citation(s) in RCA: 187] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2017] [Accepted: 02/15/2017] [Indexed: 12/14/2022] Open
Abstract
Exploring compositional and functional characteristics of the rumen microbiome can improve the understanding of its role in rumen function and cattle feed efficiency. In this study, we applied metatranscriptomics to characterize the active rumen microbiomes of beef cattle with different feed efficiencies (efficient, n = 10; inefficient, n = 10) using total RNA sequencing. Active bacterial and archaeal compositions were estimated based on 16S rRNAs, and active microbial metabolic functions including carbohydrate-active enzymes (CAZymes) were assessed based on mRNAs from the same metatranscriptomic data sets. In total, six bacterial phyla (Proteobacteria, Firmicutes, Bacteroidetes, Spirochaetes, Cyanobacteria, and Synergistetes), eight bacterial families (Succinivibrionaceae, Prevotellaceae, Ruminococcaceae, Lachnospiraceae, Veillonellaceae, Spirochaetaceae, Dethiosulfovibrionaceae, and Mogibacteriaceae), four archaeal clades (Methanomassiliicoccales, Methanobrevibacter ruminantium, Methanobrevibacter gottschalkii, and Methanosphaera), 112 metabolic pathways, and 126 CAZymes were identified as core components of the active rumen microbiome. As determined by comparative analysis, three bacterial families (Lachnospiraceae, Lactobacillaceae, and Veillonellaceae) tended to be more abundant in low-feed-efficiency (inefficient) animals (P < 0.10), and one archaeal taxon (Methanomassiliicoccales) tended to be more abundant in high-feed-efficiency (efficient) cattle (P < 0.10). Meanwhile, 32 microbial metabolic pathways and 12 CAZymes were differentially abundant (linear discriminant analysis score of >2 with a P value of <0.05) between two groups. Among them, 30 metabolic pathways and 11 CAZymes were more abundant in the rumen of inefficient cattle, while 2 metabolic pathways and 1 CAZyme were more abundant in efficient animals. These findings suggest that the rumen microbiomes of inefficient cattle have more diverse activities than those of efficient cattle, which may be related to the host feed efficiency variation.IMPORTANCE This study applied total RNA-based metatranscriptomics and showed the linkage between the active rumen microbiome and feed efficiency (residual feed intake) in beef cattle. The data generated from the current study provide fundamental information on active rumen microbiome at both compositional and functional levels, which serve as a foundation to study rumen function and its role in cattle feed efficiency. The findings that the active rumen microbiome may contribute to variations in feed efficiency of beef cattle highlight the possibility of enhancing nutrient utilization and improve cattle feed efficiency through modification of rumen microbial functions.
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342
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Parmar KM, Gaikwad SL, Dhakephalkar PK, Kothari R, Singh RP. Intriguing Interaction of Bacteriophage-Host Association: An Understanding in the Era of Omics. Front Microbiol 2017; 8:559. [PMID: 28439260 PMCID: PMC5383658 DOI: 10.3389/fmicb.2017.00559] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 03/16/2017] [Indexed: 01/09/2023] Open
Abstract
Innovations in next-generation sequencing technology have introduced new avenues in microbial studies through “omics” approaches. This technology has considerably augmented the knowledge of the microbial world without isolation prior to their identification. With an enormous volume of bacterial “omics” data, considerable attempts have been recently invested to improve an insight into virosphere. The interplay between bacteriophages and their host has created a significant influence on the biogeochemical cycles, microbial diversity, and bacterial population regulation. This review highlights various concepts such as genomics, transcriptomics, proteomics, and metabolomics to infer the phylogenetic affiliation and function of bacteriophages and their impact on diverse microbial communities. Omics technologies illuminate the role of bacteriophage in an environment, the influences of phage proteins on the bacterial host and provide information about the genes important for interaction with bacteria. These investigations will reveal some of bio-molecules and biomarkers of the novel phage which demand to be unveiled.
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Affiliation(s)
| | | | | | - Ramesh Kothari
- Department of Biosciences, Saurashtra UniversityRajkot, India
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AlZahal O, Li F, Guan LL, Walker ND, McBride BW. Factors influencing ruminal bacterial community diversity and composition and microbial fibrolytic enzyme abundance in lactating dairy cows with a focus on the role of active dry yeast. J Dairy Sci 2017; 100:4377-4393. [PMID: 28390722 DOI: 10.3168/jds.2016-11473] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Accepted: 01/30/2017] [Indexed: 12/12/2022]
Abstract
The objective of the current study was to employ a DNA-based sequencing technology to study the effect of active dry yeast (ADY) supplementation, diet type, and sample location within the rumen on rumen bacterial community diversity and composition, and to use an RNA-based method to study the effect of ADY supplementation on rumen microbial metabolism during high-grain feeding (HG). Our previous report demonstrated that the supplementation of lactating dairy cows with ADY attenuated the effect of subacute ruminal acidosis. Therefore, we used samples from that study, where 16 multiparous, rumen-cannulated lactating Holstein cows were randomly assigned to 1 of 2 dietary treatments: ADY (Saccharomyces cerevisiae strain Y1242, 80 billion cfu/animal per day) or control (carrier only). Cows received a high-forage diet (77:23, forage:concentrate), then were abruptly switched to HG (49:51, forage:concentrate). Rumen bacterial community diversity and structure were highly influenced by diet and sampling location (fluid, solids, epimural). The transition to HG reduced bacterial diversity, but epimural bacteria maintained a greater diversity than fluid and solids. Analysis of molecular variance indicated a significant separation due to diet × sampling location, but not due to treatment. Across all samples, the analysis yielded 6,254 nonsingleton operational taxonomic units (OTU), which were classified into several phyla: mainly Firmicutes, Bacteroidetes, Fibrobacteres, Tenericutes, and Proteobacteria. High forage and solids were dominated by OTU from Fibrobacter, whereas HG and fluid were dominated by OTU from Prevotella. Epimural samples, however, were dominated in part by Campylobacter. Active dry yeast had no effect on bacterial community diversity or structure. The phylum SR1 was more abundant in all ADY samples regardless of diet or sampling location. Furthermore, on HG, OTU2 and OTU3 (both classified into Fibrobacter succinogenes) were more abundant with ADY in fluid and solids than control samples. This increase with ADY was paralleled by a reduction in prominent Prevotella OTU. Metatranscriptomic profiling of rumen microbiome conducted on random samples from the HG phase showed that ADY increased the abundance of the cellulase endo-β-1,4-glucanase and had a tendency to increase the hemicellulase α-glucuronidase. In conclusion, the shift from high forage to HG and sampling location had a more significant influence on ruminal bacterial community abundance and structure compared with ADY. However, evidence suggested that ADY can increase the abundance of some dominant anaerobic OTU belonging to F. succinogenes and phylum SR1. Further, microbial mRNA-based evidence suggested that ADY can increase the abundance of a specific microbial fibrolytic enzymes.
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Affiliation(s)
- Ousama AlZahal
- Department of Animal Biosciences, University of Guelph, Guelph, Ontario N1G 2W1, Canada.
| | - Fuyong Li
- Department of Agriculture, Food and Nutritional Science, University of Alberta, Edmonton T6G 2P5, Canada
| | - Le Luo Guan
- Department of Agriculture, Food and Nutritional Science, University of Alberta, Edmonton T6G 2P5, Canada
| | | | - Brian W McBride
- Department of Animal Biosciences, University of Guelph, Guelph, Ontario N1G 2W1, Canada
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344
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Argiroff WA, Zak DR, Lanser CM, Wiley MJ. Microbial Community Functional Potential and Composition Are Shaped by Hydrologic Connectivity in Riverine Floodplain Soils. MICROBIAL ECOLOGY 2017; 73:630-644. [PMID: 27807645 DOI: 10.1007/s00248-016-0883-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Accepted: 10/17/2016] [Indexed: 05/12/2023]
Abstract
Riverine floodplains are ecologically and economically valuable ecosystems that are heavily threatened by anthropogenic stressors. Microbial communities in floodplain soils mediate critical biogeochemical processes, yet we understand little about the relationship between these communities and variation in hydrologic connectivity related to land management or topography. Here, we present metagenomic evidence that differences among microbial communities in three floodplain soils correspond to a long-term gradient of hydrologic connectivity. Specifically, all strictly anaerobic taxa and metabolic pathways were positively associated with increased hydrologic connectivity and flooding frequency. In contrast, most aerobic taxa and all strictly aerobic pathways were negatively related to hydrologic connectivity and flooding frequency. Furthermore, the genetic potential to metabolize organic compounds tended to decrease as hydrologic connectivity increased, which may reflect either the observed concomitant decline of soil organic matter or the parallel increase in both anaerobic taxa and pathways. A decline in soil N, accompanied by an increased genetic potential for oligotrophic N acquisition subsystems, suggests that soil nutrients also shape microbial communities in these soils. We conclude that differences among floodplain soil microbial communities can be conceptualized along a gradient of hydrologic connectivity. Additionally, we show that these differences are likely due to connectivity-related variation in flooding frequency, soil organic matter, and soil N. Our findings are particularly relevant to the restoration and management of microbially mediated biogeochemical processes in riverine floodplain wetlands.
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Affiliation(s)
- William A Argiroff
- School of Natural Resources and Environment, University of Michigan, 440 Church St., Ann Arbor, MI, 48109, USA.
| | - Donald R Zak
- School of Natural Resources and Environment, University of Michigan, 440 Church St., Ann Arbor, MI, 48109, USA
- Department of Ecology and Evolutionary Biology, University of Michigan, 830 North University, Ann Arbor, MI, 48109, USA
| | - Christine M Lanser
- School of Natural Resources and Environment, University of Michigan, 440 Church St., Ann Arbor, MI, 48109, USA
| | - Michael J Wiley
- School of Natural Resources and Environment, University of Michigan, 440 Church St., Ann Arbor, MI, 48109, USA
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345
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Hatton JJ, Stevenson TJ, Buck CL, Duddleston KN. Diet affects arctic ground squirrel gut microbial metatranscriptome independent of community structure. Environ Microbiol 2017; 19:1518-1535. [PMID: 28251799 PMCID: PMC5417852 DOI: 10.1111/1462-2920.13712] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Revised: 02/24/2017] [Accepted: 02/24/2017] [Indexed: 12/24/2022]
Abstract
We examined the effect of diet on pre-hibernation fattening and the gut microbiota of captive arctic ground squirrels (Urocitellus parryii). We measured body composition across time and gut microbiota density, diversity and function prior to and after five-weeks on control, high-fat, low-fat (18%, 40% and 10% energy from fat, respectively), or restricted calorie (50% of control) diets. Squirrels fattened at the same rate and to the same degree on all diets. Additionally, we found no differences in gut microbiota diversity or short chain fatty acid production across time or with diet. Analysis of the gut microbial transcriptome indicated differences in community function among diet groups, but not across time, and revealed shifts in the relative contribution of function at a taxonomic level. Our results demonstrate that pre-hibernation fattening of arctic ground squirrels is robust to changes in diet and is accomplished by more than increased food intake. Although our analyses did not uncover a definitive link between host fattening and the gut microbiota, and suggest the squirrels may possess a gut microbial community structure that is unresponsive to dietary changes, studies manipulating diet earlier in the active season may yet uncover a relationship between host diet, fattening and gut microbiota.
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Affiliation(s)
| | | | - C. Loren Buck
- Northern Arizona University, Flagstaff, Arizona, 86011
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346
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Bicalho MLS, Machado VS, Higgins CH, Lima FS, Bicalho RC. Genetic and functional analysis of the bovine uterine microbiota. Part I: Metritis versus healthy cows. J Dairy Sci 2017; 100:3850-3862. [PMID: 28259404 DOI: 10.3168/jds.2016-12058] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 01/14/2017] [Indexed: 12/21/2022]
Abstract
Metritis is a uterine disease that affects 10 to 30% of all lactating dairy cows and has detrimental effects on reproductive performance, milk production, and survival. Data regarding the identity and abundance of bacterial genes governing traits such as virulence, antibiotic resistance, and stress responses could enable identification of previously unknown agents that play a role in metritis pathogenesis. Moreover, such knowledge could lead to the development of improved treatments or preventive methods. Therefore, the objectives of this study were to characterize the uterine microbial population and to differentiate, for the first time, the microbial functional diversity in cows with metritis versus healthy cows. In addition, we aimed to identify relationships between microbial genes and postpartum uterine health. Uterine swabs were collected from 24 cows within 3 to 12 d in milk; 12 cows were diagnosed with metritis and the other 12 were healthy. Metritis was defined as a watery, reddish or brownish uterine discharge having a fetid smell, and rectal temperature greater than 39.5°C. Cows with a clear and viscous uterine discharge, not fetid or mucopurulent, were classified as healthy. Microbial metagenomic DNA from uterine swab samples was subjected to whole-genome shotgun sequencing on the Illumina MiSeq platform (Illumina Inc., San Diego, CA). The MG-RAST server (metagenomic rapid annotations using subsystems technology; http://metagenomics.anl.gov/) and STAMP software (http://kiwi.cs.dal.ca/Software/STAMP) were used to detect statistically significant differences in the abundance of taxonomic and functional features between the uterine microbial metagenomes of metritic and healthy cows. Our results showed an increased abundance of Fusobacteria and Bacteroidetes in metritic cows, confirming the potential role of those 2 taxa in the pathogenesis of metritis. The MG-RAST analysis revealed a significantly higher abundance of genes for protein transport across the cytoplasmic membrane and type VI bacterial secretion systems in the metritic microbiota. Additionally, genes coding for resistance to acid stress were exclusive to the metritis microbiota, suggesting that microbial resistance to acid stress is important for microbial survival in the infected uterus. On the other hand, genes coding for adhesion molecules, bacteriocins, and antibacterial peptides were significantly associated with the uterine microbiota of healthy cows, as was tolerance to colicin E2.
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Affiliation(s)
- M L S Bicalho
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853
| | - V S Machado
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853
| | - C H Higgins
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853
| | - F S Lima
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853
| | - R C Bicalho
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853.
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347
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Pereira FC, Berry D. Microbial nutrient niches in the gut. Environ Microbiol 2017; 19:1366-1378. [PMID: 28035742 PMCID: PMC5412925 DOI: 10.1111/1462-2920.13659] [Citation(s) in RCA: 204] [Impact Index Per Article: 29.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 12/23/2016] [Accepted: 12/27/2016] [Indexed: 12/14/2022]
Abstract
The composition and function of the mammalian gut microbiota has been the subject of much research in recent years, but the principles underlying the assembly and structure of this complex community remain incompletely understood. Processes that shape the gut microbiota are thought to be mostly niche‐driven, with environmental factors such as the composition of available nutrients largely determining whether or not an organism can establish. The concept that the nutrient landscape dictates which organisms can successfully colonize and persist in the gut was first proposed in Rolf Freter's nutrient niche theory. In a situation where nutrients are perfectly mixed and there is balanced microbial growth, Freter postulated that an organism can only survive if it is able to utilize one or a few limiting nutrients more efficiently than its competitors. Recent experimental work indicates, however, that nutrients in the gut vary in space and time. We propose that in such a scenario, Freter's nutrient niche theory must be expanded to account for the co‐existence of microorganisms utilizing the same nutrients but in distinct sites or at different times, and that metabolic flexibility and mixed‐substrate utilization are common strategies for survival in the face of ever‐present nutrient fluctuations.
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Affiliation(s)
- Fátima C Pereira
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Althanstrasse 14, Vienna, 1090, Austria
| | - David Berry
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Althanstrasse 14, Vienna, 1090, Austria
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348
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Wang B, Yao M, Lv L, Ling Z, Li L. The Human Microbiota in Health and Disease. ENGINEERING 2017; 3:71-82. [DOI: 10.1016/j.eng.2017.01.008] [Citation(s) in RCA: 448] [Impact Index Per Article: 64.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/30/2023]
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349
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Liang C, Tseng HC, Chen HM, Wang WC, Chiu CM, Chang JY, Lu KY, Weng SL, Chang TH, Chang CH, Weng CT, Wang HM, Huang HD. Diversity and enterotype in gut bacterial community of adults in Taiwan. BMC Genomics 2017; 18:932. [PMID: 28198673 PMCID: PMC5310273 DOI: 10.1186/s12864-016-3261-6] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Background Gastrointestinal microbiota, particularly gut microbiota, is associated with human health. The biodiversity of gut microbiota is affected by ethnicities and environmental factors such as dietary habits or medicine intake, and three enterotypes of the human gut microbiome were announced in 2011. These enterotypes are not significantly correlated with gender, age, or body weight but are influenced by long-term dietary habits. However, to date, only two enterotypes (predominantly consisting of Bacteroides and Prevotella) have shown these characteristics in previous research; the third enterotype remains ambiguous. Understanding the enterotypes can improve the knowledge of the relationship between microbiota and human health. Results We obtained 181 human fecal samples from adults in Taiwan. Microbiota compositions were analyzed using next-generation sequencing (NGS) technology, which is a culture-independent method of constructing microbial community profiles by sequencing 16S ribosomal DNA (rDNA). In these samples, 17,675,898 sequencing reads were sequenced, and on average, 215 operational taxonomic units (OTUs) were identified for each sample. In this study, the major bacteria in the enterotypes identified from the fecal samples were Bacteroides, Prevotella, and Enterobacteriaceae, and their correlation with dietary habits was confirmed. A microbial interaction network in the gut was observed on the basis of the amount of short-chain fatty acids, pH value of the intestine, and composition of the bacterial community (enterotypes). Finally, a decision tree was derived to provide a predictive model for the three enterotypes. The accuracies of this model in training and independent testing sets were 97.2 and 84.0%, respectively. Conclusions We used NGS technology to characterize the microbiota and constructed a predictive model. The most significant finding was that Enterobacteriaceae, the predominant subtype, could be a new subtype of enterotypes in the Asian population. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3261-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Chao Liang
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, HsinChu, Taiwan
| | | | - Hui-Mei Chen
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, HsinChu, Taiwan
| | | | | | | | - Kuan-Yi Lu
- Health GeneTech Corporation, Taoyuan, Taiwan
| | - Shun-Long Weng
- Department of Obstetrics and Gynecology, Hsinchu Mackay Memorial Hospital, Hsinchu, Taiwan.,Mackay Medicine, Nursing and Management College, Taipei, Taiwan.,Department of Medicine, Mackay Medical College, New Taipei City, Taiwan
| | - Tzu-Hao Chang
- Graduate Institute of Biomedical Informatics, Taipei Medical University, Taipei, Taiwan
| | - Chao-Hsiang Chang
- School of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei, Taiwan
| | | | | | - Hsien-Da Huang
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, HsinChu, Taiwan. .,Department of Biological Science and Technology, National Chiao Tung University, HsinChu, Taiwan. .,Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung, Taiwan.
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350
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Embracing the gut microbiota: the new frontier for inflammatory and infectious diseases. Clin Transl Immunology 2017; 6:e125. [PMID: 28197336 PMCID: PMC5292562 DOI: 10.1038/cti.2016.91] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 11/27/2016] [Accepted: 12/04/2016] [Indexed: 02/07/2023] Open
Abstract
The gut microbiota provides essential signals for the development and appropriate function of the immune system. Through this critical contribution to immune fitness, the gut microbiota has a key role in health and disease. Recent advances in the technological applications to study microbial communities and their functions have contributed to a rapid increase in host-microbiota research. Although it still remains difficult to define a so-called 'normal' or 'healthy' microbial composition, alterations in the gut microbiota have been shown to influence the susceptibility of the host to different diseases. Current translational research combined with recent technological and computational advances have enabled in-depth study of the link between microbial composition and immune function, addressing the interplay between the gut microbiota and immune responses. As such, beneficial modulation of the gut microbiota is a promising clinical target for many prevalent diseases including inflammatory bowel disease, metabolic abnormalities such as obesity, reduced insulin sensitivity and low-grade inflammation, allergy and protective immunity against infections.
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