401
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An evaluation of the accuracy and speed of metagenome analysis tools. Sci Rep 2016; 6:19233. [PMID: 26778510 PMCID: PMC4726098 DOI: 10.1038/srep19233] [Citation(s) in RCA: 188] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 12/04/2015] [Indexed: 12/19/2022] Open
Abstract
Metagenome studies are becoming increasingly widespread, yielding important insights into microbial communities covering diverse environments from terrestrial and aquatic ecosystems to human skin and gut. With the advent of high-throughput sequencing platforms, the use of large scale shotgun sequencing approaches is now commonplace. However, a thorough independent benchmark comparing state-of-the-art metagenome analysis tools is lacking. Here, we present a benchmark where the most widely used tools are tested on complex, realistic data sets. Our results clearly show that the most widely used tools are not necessarily the most accurate, that the most accurate tool is not necessarily the most time consuming, and that there is a high degree of variability between available tools. These findings are important as the conclusions of any metagenomics study are affected by errors in the predicted community composition and functional capacity. Data sets and results are freely available from http://www.ucbioinformatics.org/metabenchmark.html
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402
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Addis MF, Tanca A, Uzzau S, Oikonomou G, Bicalho RC, Moroni P. The bovine milk microbiota: insights and perspectives from -omics studies. MOLECULAR BIOSYSTEMS 2016; 12:2359-72. [DOI: 10.1039/c6mb00217j] [Citation(s) in RCA: 134] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Recent findings and future perspectives of -omics studies on the bovine milk microbiota, focusing on its impact on animal health.
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Affiliation(s)
- M. F. Addis
- Porto Conte Ricerche
- SP 55 Porto Conte/Capo Caccia
- 07041 Alghero
- Italy
| | - A. Tanca
- Porto Conte Ricerche
- SP 55 Porto Conte/Capo Caccia
- 07041 Alghero
- Italy
| | - S. Uzzau
- Porto Conte Ricerche
- SP 55 Porto Conte/Capo Caccia
- 07041 Alghero
- Italy
- Università degli Studi di Sassari
| | - G. Oikonomou
- Epidemiology and Population Health
- Institute of Infection and Global Health
- University of Liverpool
- Liverpool
- UK
| | - R. C. Bicalho
- Cornell University
- Department of Population Medicine and Diagnostic Sciences
- College of Veterinary Medicine
- Ithaca
- USA
| | - P. Moroni
- Cornell University
- Department of Population Medicine and Diagnostic Sciences
- College of Veterinary Medicine
- Ithaca
- USA
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403
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Fabijanić M, Vlahoviček K. Big Data, Evolution, and Metagenomes: Predicting Disease from Gut Microbiota Codon Usage Profiles. Methods Mol Biol 2016; 1415:509-531. [PMID: 27115650 DOI: 10.1007/978-1-4939-3572-7_26] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Metagenomics projects use next-generation sequencing to unravel genetic potential in microbial communities from a wealth of environmental niches, including those associated with human body and relevant to human health. In order to understand large datasets collected in metagenomics surveys and interpret them in context of how a community metabolism as a whole adapts and interacts with the environment, it is necessary to extend beyond the conventional approaches of decomposing metagenomes into microbial species' constituents and performing analysis on separate components. By applying concepts of translational optimization through codon usage adaptation on entire metagenomic datasets, we demonstrate that a bias in codon usage present throughout the entire microbial community can be used as a powerful analytical tool to predict for community lifestyle-specific metabolism. Here we demonstrate this approach combined with machine learning, to classify human gut microbiome samples according to the pathological condition diagnosed in the human host.
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Affiliation(s)
- Maja Fabijanić
- Bioinformatics Group, Division of Biology, Department of Molecular Biology, Faculty of Science, University of Zagreb, Rooseveltov trg 6, Zagreb, Croatia
| | - Kristian Vlahoviček
- Bioinformatics Group, Division of Biology, Department of Molecular Biology, Faculty of Science, University of Zagreb, Rooseveltov trg 6, Zagreb, Croatia.
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404
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Wu H, Tremaroli V, Bäckhed F. Linking Microbiota to Human Diseases: A Systems Biology Perspective. Trends Endocrinol Metab 2015; 26:758-770. [PMID: 26555600 DOI: 10.1016/j.tem.2015.09.011] [Citation(s) in RCA: 92] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Revised: 09/28/2015] [Accepted: 09/28/2015] [Indexed: 12/19/2022]
Abstract
The human gut microbiota encompasses a densely populated ecosystem that provides essential functions for host development, immune maturation, and metabolism. Alterations to the gut microbiota have been observed in numerous diseases, including human metabolic diseases such as obesity, type 2 diabetes (T2D), and irritable bowel syndrome, and some animal experiments have suggested causality. However, few studies have validated causality in humans and the underlying mechanisms remain largely to be elucidated. We discuss how systems biology approaches combined with new experimental technologies may disentangle some of the mechanistic details in the complex interactions of diet, microbiota, and host metabolism and may provide testable hypotheses for advancing our current understanding of human-microbiota interaction.
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Affiliation(s)
- Hao Wu
- The Wallenberg Laboratory, Department of Molecular and Clinical Medicine, University of Gothenburg, 41345 Gothenburg, Sweden
| | - Valentina Tremaroli
- The Wallenberg Laboratory, Department of Molecular and Clinical Medicine, University of Gothenburg, 41345 Gothenburg, Sweden
| | - Fredrik Bäckhed
- The Wallenberg Laboratory, Department of Molecular and Clinical Medicine, University of Gothenburg, 41345 Gothenburg, Sweden; Novo Nordisk Foundation Center for Basic Metabolic Research, Section for Metabolic Receptology and Enteroendocrinology, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark.
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405
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Nozhevnikova AN, Botchkova EA, Plakunov VK. Multi-species biofilms in ecology, medicine, and biotechnology. Microbiology (Reading) 2015. [DOI: 10.1134/s0026261715060107] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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406
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Leung RKK, Wu YK. Circulating microbial RNA and health. Sci Rep 2015; 5:16814. [PMID: 26576508 PMCID: PMC4649493 DOI: 10.1038/srep16814] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Accepted: 10/15/2015] [Indexed: 12/22/2022] Open
Abstract
Measurement of health indicators in the blood is a commonly performed diagnostic procedure. Two blood studies one involving extended observations on the health of an individual by integrative Personal Omics Profiling (iPOP), and the other tracking the impact of Left Ventricular Assist Device (LVAD) placement on nine heart failure patients were examined for the association of change in health status with change in microbial RNA species. Decrease in RNA expression ratios of human to bacteria and viruses accompanying deteriorated conditions was evident in both studies. Despite large between-subject variations in bacterial composition before LVAD implantation among all the patients, on day 180 after the implantation they manifested apparent between-subject bacterial similarity. In the iPOP study three periods, namely, pre-respiratory syncytial virus (RSV) infection with normal blood glucose level, RSV infection with normal blood glucose level, and post-RSV infection with high blood glucose level could be defined. The upsurge of Enterobacteria phage PhiX 174 sensu lato and Escherichia coli gene expression, in which membrane transporters, membrane receptors for environment signalling, carbohydrate catabolic genes and carbohydrate-active enzymes were enriched only throughout the second period, which suggests a potentially overlooked microbial response to or modulation of the host blood glucose level.
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Affiliation(s)
- Ross Ka-Kit Leung
- Stanley Ho Centre for Emerging Infectious Diseases, The Chinese University of Hong Kong, Shatin, NT, Hong Kong, The People's Republic of China.,Division of Genomics and Bioinformatics, CUHK-BGI Innovation Institute of Trans-omics, The Chinese University of Hong Kong Shatin, N.T., Hong Kong, The People's Republic of China
| | - Ying-Kit Wu
- Stanley Ho Centre for Emerging Infectious Diseases, The Chinese University of Hong Kong, Shatin, NT, Hong Kong, The People's Republic of China.,Division of Genomics and Bioinformatics, CUHK-BGI Innovation Institute of Trans-omics, The Chinese University of Hong Kong Shatin, N.T., Hong Kong, The People's Republic of China
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407
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Morgun A, Dzutsev A, Dong X, Greer RL, Sexton DJ, Ravel J, Schuster M, Hsiao W, Matzinger P, Shulzhenko N. Uncovering effects of antibiotics on the host and microbiota using transkingdom gene networks. Gut 2015; 64:1732-43. [PMID: 25614621 PMCID: PMC5166700 DOI: 10.1136/gutjnl-2014-308820] [Citation(s) in RCA: 190] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Accepted: 12/22/2014] [Indexed: 12/12/2022]
Abstract
OBJECTIVE Despite widespread use of antibiotics for the treatment of life-threatening infections and for research on the role of commensal microbiota, our understanding of their effects on the host is still very limited. DESIGN Using a popular mouse model of microbiota depletion by a cocktail of antibiotics, we analysed the effects of antibiotics by combining intestinal transcriptome together with metagenomic analysis of the gut microbiota. In order to identify specific microbes and microbial genes that influence the host phenotype in antibiotic-treated mice, we developed and applied analysis of the transkingdom network. RESULTS We found that most antibiotic-induced alterations in the gut can be explained by three factors: depletion of the microbiota; direct effects of antibiotics on host tissues and the effects of remaining antibiotic-resistant microbes. Normal microbiota depletion mostly led to downregulation of different aspects of immunity. The two other factors (antibiotic direct effects on host tissues and antibiotic-resistant microbes) primarily inhibited mitochondrial gene expression and amounts of active mitochondria, increasing epithelial cell death. By reconstructing and analysing the transkingdom network, we discovered that these toxic effects were mediated by virulence/quorum sensing in antibiotic-resistant bacteria, a finding further validated using in vitro experiments. CONCLUSIONS In addition to revealing mechanisms of antibiotic-induced alterations, this study also describes a new bioinformatics approach that predicts microbial components that regulate host functions and establishes a comprehensive resource on what, why and how antibiotics affect the gut in a widely used mouse model of microbiota depletion by antibiotics.
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Affiliation(s)
- Andrey Morgun
- College of Pharmacy, Oregon State University, Corvallis, Oregon,
USA,Ghost Lab, National Institute of Allergy and Infectious Diseases,
National Institutes of Health, Bethesda, Maryland, USA
| | - Amiran Dzutsev
- Cancer and Inflammation Program, National Cancer Institute/Leidos
Biomedical Research, Inc., Frederick, Maryland, USA
| | - Xiaoxi Dong
- College of Pharmacy, Oregon State University, Corvallis, Oregon,
USA
| | - Renee L Greer
- College of Veterinary Medicine, Oregon State University, Corvallis,
Oregon, USA
| | - D Joseph Sexton
- Department of Microbiology, Oregon State University, Corvallis,
Oregon, USA
| | - Jacques Ravel
- Institute for Genome Sciences, University of Maryland School of
Medicine, Baltimore, Maryland, USA
| | - Martin Schuster
- Department of Microbiology, Oregon State University, Corvallis,
Oregon, USA
| | - William Hsiao
- University of British Columbia, Vancouver, British Columbia,
Canada
| | - Polly Matzinger
- Ghost Lab, National Institute of Allergy and Infectious Diseases,
National Institutes of Health, Bethesda, Maryland, USA
| | - Natalia Shulzhenko
- College of Veterinary Medicine, Oregon State University, Corvallis,
Oregon, USA,Ghost Lab, National Institute of Allergy and Infectious Diseases,
National Institutes of Health, Bethesda, Maryland, USA
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408
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Library preparation methodology can influence genomic and functional predictions in human microbiome research. Proc Natl Acad Sci U S A 2015; 112:14024-9. [PMID: 26512100 DOI: 10.1073/pnas.1519288112] [Citation(s) in RCA: 130] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Observations from human microbiome studies are often conflicting or inconclusive. Many factors likely contribute to these issues including small cohort sizes, sample collection, and handling and processing differences. The field of microbiome research is moving from 16S rDNA gene sequencing to a more comprehensive genomic and functional representation through whole-genome sequencing (WGS) of complete communities. Here we performed quantitative and qualitative analyses comparing WGS metagenomic data from human stool specimens using the Illumina Nextera XT and Illumina TruSeq DNA PCR-free kits, and the KAPA Biosystems Hyper Prep PCR and PCR-free systems. Significant differences in taxonomy are observed among the four different next-generation sequencing library preparations using a DNA mock community and a cell control of known concentration. We also revealed biases in error profiles, duplication rates, and loss of reads representing organisms that have a high %G+C content that can significantly impact results. As with all methods, the use of benchmarking controls has revealed critical differences among methods that impact sequencing results and later would impact study interpretation. We recommend that the community adopt PCR-free-based approaches to reduce PCR bias that affects calculations of abundance and to improve assemblies for accurate taxonomic assignment. Furthermore, the inclusion of a known-input cell spike-in control provides accurate quantitation of organisms in clinical samples.
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409
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Britton LE, Cassidy JP, O'Donovan J, Gordon SV, Markey B. Potential application of emerging diagnostic techniques to the diagnosis of bovine Johne's disease (paratuberculosis). Vet J 2015; 209:32-9. [PMID: 26831164 DOI: 10.1016/j.tvjl.2015.10.033] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Revised: 05/15/2015] [Accepted: 10/10/2015] [Indexed: 12/19/2022]
Abstract
Mycobacterium avium subspecies paratuberculosis (MAP) causes Johne's disease (paratuberculosis), a chronic wasting disease in cattle with important welfare, economic and potential public health implications. Current tests are unable to recognise all stages of the disease, which makes it difficult to diagnose and control. This review explores emerging diagnostic techniques that could complement and enhance the diagnosis of MAP infection, including bacteriophage analysis, new MAP-specific antigens, host protein expression in response to infection, transcriptomic studies, analysis of microRNAs and investigation of the gastrointestinal microbiome. It emphasises the inherent challenges of diagnosing bovine Johne's disease and investigates novel areas which may have the potential both to advance our understanding of the immunopathology of MAP infection and to augment current diagnostic tests.
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Affiliation(s)
| | | | - Jim O'Donovan
- Department of Agriculture, Food and the Marine, Model Farm Road, Cork, Ireland
| | | | - Bryan Markey
- University College Dublin, Belfield, Dublin, Ireland
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410
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Kelly JR, Kennedy PJ, Cryan JF, Dinan TG, Clarke G, Hyland NP. Breaking down the barriers: the gut microbiome, intestinal permeability and stress-related psychiatric disorders. Front Cell Neurosci 2015; 9:392. [PMID: 26528128 PMCID: PMC4604320 DOI: 10.3389/fncel.2015.00392] [Citation(s) in RCA: 636] [Impact Index Per Article: 70.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 09/21/2015] [Indexed: 12/12/2022] Open
Abstract
The emerging links between our gut microbiome and the central nervous system (CNS) are regarded as a paradigm shift in neuroscience with possible implications for not only understanding the pathophysiology of stress-related psychiatric disorders, but also their treatment. Thus the gut microbiome and its influence on host barrier function is positioned to be a critical node within the brain-gut axis. Mounting preclinical evidence broadly suggests that the gut microbiota can modulate brain development, function and behavior by immune, endocrine and neural pathways of the brain-gut-microbiota axis. Detailed mechanistic insights explaining these specific interactions are currently underdeveloped. However, the concept that a "leaky gut" may facilitate communication between the microbiota and these key signaling pathways has gained traction. Deficits in intestinal permeability may underpin the chronic low-grade inflammation observed in disorders such as depression and the gut microbiome plays a critical role in regulating intestinal permeability. In this review we will discuss the possible role played by the gut microbiota in maintaining intestinal barrier function and the CNS consequences when it becomes disrupted. We will draw on both clinical and preclinical evidence to support this concept as well as the key features of the gut microbiota which are necessary for normal intestinal barrier function.
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Affiliation(s)
- John R Kelly
- Laboratory of Neurogastroenterology, APC Microbiome Institute, University College Cork Cork, Ireland ; Department of Psychiatry and Neurobehavioural Science, University College Cork Cork, Ireland
| | - Paul J Kennedy
- Laboratory of Neurogastroenterology, APC Microbiome Institute, University College Cork Cork, Ireland
| | - John F Cryan
- Laboratory of Neurogastroenterology, APC Microbiome Institute, University College Cork Cork, Ireland ; Department of Anatomy and Neuroscience, University College Cork Cork, Ireland
| | - Timothy G Dinan
- Laboratory of Neurogastroenterology, APC Microbiome Institute, University College Cork Cork, Ireland ; Department of Psychiatry and Neurobehavioural Science, University College Cork Cork, Ireland
| | - Gerard Clarke
- Laboratory of Neurogastroenterology, APC Microbiome Institute, University College Cork Cork, Ireland ; Department of Psychiatry and Neurobehavioural Science, University College Cork Cork, Ireland
| | - Niall P Hyland
- Laboratory of Neurogastroenterology, APC Microbiome Institute, University College Cork Cork, Ireland ; Department of Pharmacology and Therapeutics, University College Cork Cork, Ireland
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411
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Kelly JR, Kennedy PJ, Cryan JF, Dinan TG, Clarke G, Hyland NP. Breaking down the barriers: the gut microbiome, intestinal permeability and stress-related psychiatric disorders. Front Cell Neurosci 2015. [DOI: 10.3389/fncel.2015.00392 order by 1-- -] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023] Open
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412
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Kelly JR, Kennedy PJ, Cryan JF, Dinan TG, Clarke G, Hyland NP. Breaking down the barriers: the gut microbiome, intestinal permeability and stress-related psychiatric disorders. Front Cell Neurosci 2015. [DOI: 10.3389/fncel.2015.00392 order by 8029-- -] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023] Open
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413
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Kelly JR, Kennedy PJ, Cryan JF, Dinan TG, Clarke G, Hyland NP. Breaking down the barriers: the gut microbiome, intestinal permeability and stress-related psychiatric disorders. Front Cell Neurosci 2015. [DOI: 10.3389/fncel.2015.00392 order by 8029-- #] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023] Open
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414
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Kelly JR, Kennedy PJ, Cryan JF, Dinan TG, Clarke G, Hyland NP. Breaking down the barriers: the gut microbiome, intestinal permeability and stress-related psychiatric disorders. Front Cell Neurosci 2015. [DOI: 10.3389/fncel.2015.00392 order by 1-- gadu] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023] Open
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415
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Kelly JR, Kennedy PJ, Cryan JF, Dinan TG, Clarke G, Hyland NP. Breaking down the barriers: the gut microbiome, intestinal permeability and stress-related psychiatric disorders. Front Cell Neurosci 2015. [DOI: 10.3389/fncel.2015.00392 order by 8029-- awyx] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023] Open
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416
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Kelly JR, Kennedy PJ, Cryan JF, Dinan TG, Clarke G, Hyland NP. Breaking down the barriers: the gut microbiome, intestinal permeability and stress-related psychiatric disorders. Front Cell Neurosci 2015. [DOI: 10.3389/fncel.2015.00392 order by 1-- #] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023] Open
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417
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Kelly JR, Kennedy PJ, Cryan JF, Dinan TG, Clarke G, Hyland NP. Breaking down the barriers: the gut microbiome, intestinal permeability and stress-related psychiatric disorders. Front Cell Neurosci 2015. [DOI: 10.3389/fncel.2015.00392 and 1880=1880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023] Open
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418
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Montalban-Arques A, De Schryver P, Bossier P, Gorkiewicz G, Mulero V, Gatlin DM, Galindo-Villegas J. Selective Manipulation of the Gut Microbiota Improves Immune Status in Vertebrates. Front Immunol 2015; 6:512. [PMID: 26500650 PMCID: PMC4598590 DOI: 10.3389/fimmu.2015.00512] [Citation(s) in RCA: 86] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Accepted: 09/20/2015] [Indexed: 12/12/2022] Open
Abstract
All animals develop in association with complex microbial communities. It is now well established that commensal microbiota is essential for the correct functionality of each organ in the host. Particularly, the commensal gastro-intestinal microbiota (CGIM) is a key factor for development, immunity and nutrient conversion, rendering them bio-available for various uses. Thus, nutritional inputs generate a positive loop in maintaining host health and are essential in shaping the composition of the CGIM communities. Probiotics, which are live exogenous microorganisms, selectively provided to the host, are a promising concept for manipulating the microbiota and thus for increasing the host health status. Nevertheless, most mechanisms induced by probiotics to fortify the immune system are still a matter of debate. Alternatively, prebiotics, which are non-digestible food ingredients, can favor the growth of specific target groups of CGIM. Several metabolites are produced by the CGIM, one of the most important are the short-chain fatty acids (SCFAs), which emerge from the fermentation of complex carbohydrates. SCFAs have been recognized as key players in triggering beneficial effects elicited by simple diffusion and by specific receptors present, thus, far only in epithelial cells of higher vertebrates at different gastro-intestinal locations. However, both strategies have shown to provide resistance against pathogens during periods of high stress. In fish, knowledge about the action of pro- and prebiotics and SCFAs is still limited. Thus, in this review, we briefly summarize the mechanisms described on this topic for higher vertebrates and discuss why many of them may operate in the fish gut representing a model for different mucosal tissues
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Affiliation(s)
| | - Peter De Schryver
- Laboratory of Aquaculture & Artemia Reference Center, Ghent University , Ghent , Belgium
| | - Peter Bossier
- Laboratory of Aquaculture & Artemia Reference Center, Ghent University , Ghent , Belgium
| | | | - Victoriano Mulero
- Department of Cell Biology and Histology, Faculty of Biology, Instituto Murciano de Investigación Biosanitaria Virgen de la Arrixaca, University of Murcia , Murcia , Spain
| | - Delbert Monroe Gatlin
- Department of Wildlife and Fisheries Sciences, College of Agriculture and Life Sciences, Texas A&M University , College Station, TX , USA
| | - Jorge Galindo-Villegas
- Department of Cell Biology and Histology, Faculty of Biology, Instituto Murciano de Investigación Biosanitaria Virgen de la Arrixaca, University of Murcia , Murcia , Spain
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419
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Taxis TM, Wolff S, Gregg SJ, Minton NO, Zhang C, Dai J, Schnabel RD, Taylor JF, Kerley MS, Pires JC, Lamberson WR, Conant GC. The players may change but the game remains: network analyses of ruminal microbiomes suggest taxonomic differences mask functional similarity. Nucleic Acids Res 2015; 43:9600-12. [PMID: 26420832 PMCID: PMC4787786 DOI: 10.1093/nar/gkv973] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 09/15/2015] [Indexed: 01/29/2023] Open
Abstract
By mapping translated metagenomic reads to a microbial metabolic network, we show that ruminal ecosystems that are rather dissimilar in their taxonomy can be considerably more similar at the metabolic network level. Using a new network bi-partition approach for linking the microbial network to a bovine metabolic network, we observe that these ruminal metabolic networks exhibit properties consistent with distinct metabolic communities producing similar outputs from common inputs. For instance, the closer in network space that a microbial reaction is to a reaction found in the host, the lower will be the variability of its enzyme copy number across hosts. Similarly, these microbial enzymes that are nearby to host nodes are also higher in copy number than are more distant enzymes. Collectively, these results demonstrate a widely expected pattern that, to our knowledge, has not been explicitly demonstrated in microbial communities: namely that there can exist different community metabolic networks that have the same metabolic inputs and outputs but differ in their internal structure.
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Affiliation(s)
- Tasia M Taxis
- Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Sara Wolff
- Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Sarah J Gregg
- Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Nicholas O Minton
- Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Chiqian Zhang
- Department of Civil & Environmental Engineering, University of Missouri, Columbia, MO 65211, USA
| | - Jingjing Dai
- Department of Civil & Environmental Engineering, University of Missouri, Columbia, MO 65211, USA
| | - Robert D Schnabel
- Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA Informatics Institute, University of Missouri, Columbia, MO 65211, USA
| | - Jeremy F Taylor
- Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Monty S Kerley
- Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA
| | - J Chris Pires
- Informatics Institute, University of Missouri, Columbia, MO 65211, USA Division of Biological Sciences, University of Missouri, Columbia, MO 65211, USA
| | - William R Lamberson
- Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Gavin C Conant
- Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA Informatics Institute, University of Missouri, Columbia, MO 65211, USA
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420
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Greshake B, Zehr S, Dal Grande F, Meiser A, Schmitt I, Ebersberger I. Potential and pitfalls of eukaryotic metagenome skimming: a test case for lichens. Mol Ecol Resour 2015; 16:511-23. [PMID: 26345272 DOI: 10.1111/1755-0998.12463] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Revised: 07/28/2015] [Accepted: 08/22/2015] [Indexed: 11/30/2022]
Abstract
Whole-genome shotgun sequencing of multispecies communities using only a single library layout is commonly used to assess taxonomic and functional diversity of microbial assemblages. Here, we investigate to what extent such metagenome skimming approaches are applicable for in-depth genomic characterizations of eukaryotic communities, for example lichens. We address how to best assemble a particular eukaryotic metagenome skimming data, what pitfalls can occur, and what genome quality can be expected from these data. To facilitate a project-specific benchmarking, we introduce the concept of twin sets, simulated data resembling the outcome of a particular metagenome sequencing study. We show that the quality of genome reconstructions depends essentially on assembler choice. Individual tools, including the metagenome assemblers Omega and MetaVelvet, are surprisingly sensitive to low and uneven coverages. In combination with the routine of assembly parameter choice to optimize the assembly N50 size, these tools can preclude an entire genome from the assembly. In contrast, MIRA, an all-purpose overlap assembler, and SPAdes, a multisized de Bruijn graph assembler, facilitate a comprehensive view on the individual genomes across a wide range of coverage ratios. Testing assemblers on a real-world metagenome skimming data from the lichen Lasallia pustulata demonstrates the applicability of twin sets for guiding method selection. Furthermore, it reveals that the assembly outcome for the photobiont Trebouxia sp. falls behind the a priori expectation given the simulations. Although the underlying reasons remain still unclear, this highlights that further studies on this organism require special attention during sequence data generation and downstream analysis.
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Affiliation(s)
- Bastian Greshake
- Institute of Cell Biology and Neuroscience, Goethe University Frankfurt, Max-von-Laue Str. 13, D-60438, Frankfurt, Germany
| | - Simonida Zehr
- Institute of Cell Biology and Neuroscience, Goethe University Frankfurt, Max-von-Laue Str. 13, D-60438, Frankfurt, Germany
| | - Francesco Dal Grande
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberg Anlage 25, D-60325, Frankfurt, Germany
| | - Anjuli Meiser
- Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Max-von-Laue Str. 13, D-60438, Frankfurt, Germany
| | - Imke Schmitt
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberg Anlage 25, D-60325, Frankfurt, Germany.,Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Max-von-Laue Str. 13, D-60438, Frankfurt, Germany
| | - Ingo Ebersberger
- Institute of Cell Biology and Neuroscience, Goethe University Frankfurt, Max-von-Laue Str. 13, D-60438, Frankfurt, Germany
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421
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Kolmeder CA, Ritari J, Verdam FJ, Muth T, Keskitalo S, Varjosalo M, Fuentes S, Greve JW, Buurman WA, Reichl U, Rapp E, Martens L, Palva A, Salonen A, Rensen SS, de Vos WM. Colonic metaproteomic signatures of active bacteria and the host in obesity. Proteomics 2015; 15:3544-52. [DOI: 10.1002/pmic.201500049] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 07/03/2015] [Accepted: 07/24/2015] [Indexed: 11/10/2022]
Affiliation(s)
- Carolin A. Kolmeder
- Department of Veterinary Biosciences; University of Helsinki; Helsinki Finland
| | - Jarmo Ritari
- Department of Veterinary Biosciences; University of Helsinki; Helsinki Finland
| | - Froukje J. Verdam
- Department of General Surgery; NUTRIM School of Nutrition and Translational Research in Metabolism; Maastricht University Medical Center; Maastricht The Netherlands
| | - Thilo Muth
- Max Planck Institute for Dynamics of Complex Technical Systems; Bioprocess Engineering; Magdeburg Germany
| | - Salla Keskitalo
- Institute of Biotechnology; University of Helsinki; Helsinki Finland
| | - Markku Varjosalo
- Institute of Biotechnology; University of Helsinki; Helsinki Finland
| | - Susana Fuentes
- Laboratory of Microbiology; Wageningen University; Wageningen The Netherlands
| | - Jan Willem Greve
- Department of General Surgery; NUTRIM School of Nutrition and Translational Research in Metabolism; Maastricht University Medical Center; Maastricht The Netherlands
| | - Wim A. Buurman
- Department of General Surgery; NUTRIM School of Nutrition and Translational Research in Metabolism; Maastricht University Medical Center; Maastricht The Netherlands
| | - Udo Reichl
- Max Planck Institute for Dynamics of Complex Technical Systems; Bioprocess Engineering; Magdeburg Germany
- Chair of Bioprocess Engineering; Otto-von-Guericke University; Magdeburg Germany
| | - Erdmann Rapp
- Max Planck Institute for Dynamics of Complex Technical Systems; Bioprocess Engineering; Magdeburg Germany
| | - Lennart Martens
- Department of Biochemistry; Ghent University; Ghent Belgium
- VIB Medical Biotechnology Center; Department of Medical Protein Research; Ghent Belgium
| | - Airi Palva
- Department of Veterinary Biosciences; University of Helsinki; Helsinki Finland
| | - Anne Salonen
- Department of Bacteriology and Immunology; Immunobiology Research Program; University of Helsinki; Helsinki Finland
| | - Sander S. Rensen
- Department of General Surgery; NUTRIM School of Nutrition and Translational Research in Metabolism; Maastricht University Medical Center; Maastricht The Netherlands
| | - Willem M. de Vos
- Department of Veterinary Biosciences; University of Helsinki; Helsinki Finland
- Laboratory of Microbiology; Wageningen University; Wageningen The Netherlands
- Department of Bacteriology and Immunology; Immunobiology Research Program; University of Helsinki; Helsinki Finland
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422
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Thomas V, Clark J, Doré J. Fecal microbiota analysis: an overview of sample collection methods and sequencing strategies. Future Microbiol 2015; 10:1485-504. [PMID: 26347019 DOI: 10.2217/fmb.15.87] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Despite huge interest, there are still no universally accepted standards to conduct clinical studies in the field of gut microbiota analysis. Stool material is frequently used as a proxy of gut microbiota, but many different protocols can be used for collection and DNA extraction. Whereas 16S rRNA encoding gene amplification and sequencing has been widely used to study the composition of bacterial populations, it is now being challenged by the random, shotgun approach that brings far more information, although at a higher cost. In this review we give an overview of existing methods and important points to consider when conducting gut microbiota studies, with the objective to provide recommendations to those who would like to conduct such research.
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Affiliation(s)
- Vincent Thomas
- Enterome Biosciences, 94-96 Avenue Ledru Rollin, 75011 Paris, France
| | - James Clark
- Enterome Biosciences, 94-96 Avenue Ledru Rollin, 75011 Paris, France
| | - Joël Doré
- INRA, MetaGenoPolis & Micalis Research Units 1319 & 1367, Jouy-en-Josas, France
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423
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May A, Brandt BW, El-Kebir M, Klau GW, Zaura E, Crielaard W, Heringa J, Abeln S. metaModules identifies key functional subnetworks in microbiome-related disease. Bioinformatics 2015; 32:1678-85. [PMID: 26342232 DOI: 10.1093/bioinformatics/btv526] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Accepted: 09/02/2015] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION The human microbiome plays a key role in health and disease. Thanks to comparative metatranscriptomics, the cellular functions that are deregulated by the microbiome in disease can now be computationally explored. Unlike gene-centric approaches, pathway-based methods provide a systemic view of such functions; however, they typically consider each pathway in isolation and in its entirety. They can therefore overlook the key differences that (i) span multiple pathways, (ii) contain bidirectionally deregulated components, (iii) are confined to a pathway region. To capture these properties, computational methods that reach beyond the scope of predefined pathways are needed. RESULTS By integrating an existing module discovery algorithm into comparative metatranscriptomic analysis, we developed metaModules, a novel computational framework for automated identification of the key functional differences between health- and disease-associated communities. Using this framework, we recovered significantly deregulated subnetworks that were indeed recognized to be involved in two well-studied, microbiome-mediated oral diseases, such as butanoate production in periodontal disease and metabolism of sugar alcohols in dental caries. More importantly, our results indicate that our method can be used for hypothesis generation based on automated discovery of novel, disease-related functional subnetworks, which would otherwise require extensive and laborious manual assessment. AVAILABILITY AND IMPLEMENTATION metaModules is available at https://bitbucket.org/alimay/metamodules/ CONTACT a.may@vu.nl or s.abeln@vu.nl SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Ali May
- Centre for Integrative Bioinformatics VU (IBIVU), VU University Amsterdam, Amsterdam, The Netherlands, Department of Preventive Dentistry, Academic Centre for Dentistry Amsterdam (ACTA), University of Amsterdam and VU University Amsterdam, Amsterdam, The Netherlands, Amsterdam Institute for Molecules Medicines and Systems (AIMMS), VU University Amsterdam, Amsterdam, The Netherlands
| | - Bernd W Brandt
- Department of Preventive Dentistry, Academic Centre for Dentistry Amsterdam (ACTA), University of Amsterdam and VU University Amsterdam, Amsterdam, The Netherlands
| | - Mohammed El-Kebir
- Centre for Integrative Bioinformatics VU (IBIVU), VU University Amsterdam, Amsterdam, The Netherlands, Department of Computer Science and Center for Computational Molecular Biology, Brown University, Providence, USA and Life Sciences, Centre for Mathematics and Computer Science (CWI), Amsterdam, The Netherlands
| | - Gunnar W Klau
- Centre for Integrative Bioinformatics VU (IBIVU), VU University Amsterdam, Amsterdam, The Netherlands, Amsterdam Institute for Molecules Medicines and Systems (AIMMS), VU University Amsterdam, Amsterdam, The Netherlands, Life Sciences, Centre for Mathematics and Computer Science (CWI), Amsterdam, The Netherlands
| | - Egija Zaura
- Department of Preventive Dentistry, Academic Centre for Dentistry Amsterdam (ACTA), University of Amsterdam and VU University Amsterdam, Amsterdam, The Netherlands
| | - Wim Crielaard
- Department of Preventive Dentistry, Academic Centre for Dentistry Amsterdam (ACTA), University of Amsterdam and VU University Amsterdam, Amsterdam, The Netherlands
| | - Jaap Heringa
- Centre for Integrative Bioinformatics VU (IBIVU), VU University Amsterdam, Amsterdam, The Netherlands, Amsterdam Institute for Molecules Medicines and Systems (AIMMS), VU University Amsterdam, Amsterdam, The Netherlands
| | - Sanne Abeln
- Centre for Integrative Bioinformatics VU (IBIVU), VU University Amsterdam, Amsterdam, The Netherlands, Amsterdam Institute for Molecules Medicines and Systems (AIMMS), VU University Amsterdam, Amsterdam, The Netherlands
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424
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Rogers GB. The human microbiome: opportunities and challenges for clinical care. Intern Med J 2015; 45:889-98. [DOI: 10.1111/imj.12650] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Accepted: 11/19/2014] [Indexed: 12/11/2022]
Affiliation(s)
- G. B. Rogers
- Microbiome Research; South Australian Health and Medical Research Institute Infection and Immunity Theme; School of Medicine; Flinders University; Adelaide South Australia Australia
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425
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Bao G, Wang M, Doak TG, Ye Y. Strand-specific community RNA-seq reveals prevalent and dynamic antisense transcription in human gut microbiota. Front Microbiol 2015; 6:896. [PMID: 26388849 PMCID: PMC4555090 DOI: 10.3389/fmicb.2015.00896] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Accepted: 08/17/2015] [Indexed: 01/17/2023] Open
Abstract
Metagenomics and other meta-omics approaches (including metatranscriptomics) provide insights into the composition and function of microbial communities living in different environments or animal hosts. Metatranscriptomics research provides an unprecedented opportunity to examine gene regulation for many microbial species simultaneously, and more importantly, for the majority that are unculturable microbial species, in their natural environments (or hosts). Current analyses of metatranscriptomic datasets focus on the detection of gene expression levels and the study of the relationship between changes of gene expression and changes of environment. As a demonstration of utilizing metatranscriptomics beyond these common analyses, we developed a computational and statistical procedure to analyze the antisense transcripts in strand-specific metatranscriptomic datasets. Antisense RNAs encoded on the DNA strand opposite a gene’s CDS have the potential to form extensive base-pairing interactions with the corresponding sense RNA, and can have important regulatory functions. Most studies of antisense RNAs in bacteria are rather recent, are mostly based on transcriptome analysis, and have been applied mainly to single bacterial species. Application of our approaches to human gut-associated metatranscriptomic datasets allowed us to survey antisense transcription for a large number of bacterial species associated with human beings. The ratio of protein coding genes with antisense transcription ranges from 0 to 35.8% (median = 10.0%) among 47 species. Our results show that antisense transcription is dynamic, varying between human individuals. Functional enrichment analysis revealed a preference of certain gene functions for antisense transcription, and transposase genes are among the most prominent ones (but we also observed antisense transcription in bacterial house-keeping genes).
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Affiliation(s)
- Guanhui Bao
- School of Informatics and Computing, Indiana University Bloomington, IN, USA
| | - Mingjie Wang
- School of Informatics and Computing, Indiana University Bloomington, IN, USA
| | - Thomas G Doak
- Department of Biology, Indiana University Bloomington, IN, USA ; National Center for Genome Analysis Support, Indiana University Bloomington, IN, USA
| | - Yuzhen Ye
- School of Informatics and Computing, Indiana University Bloomington, IN, USA
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426
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Ye Y, Tang H. Utilizing de Bruijn graph of metagenome assembly for metatranscriptome analysis. Bioinformatics 2015; 32:1001-8. [PMID: 26319390 PMCID: PMC4896364 DOI: 10.1093/bioinformatics/btv510] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Accepted: 08/24/2015] [Indexed: 11/26/2022] Open
Abstract
Motivation: Metagenomics research has accelerated the studies of microbial organisms, providing insights into the composition and potential functionality of various microbial communities. Metatranscriptomics (studies of the transcripts from a mixture of microbial species) and other meta-omics approaches hold even greater promise for providing additional insights into functional and regulatory characteristics of the microbial communities. Current metatranscriptomics projects are often carried out without matched metagenomic datasets (of the same microbial communities). For the projects that produce both metatranscriptomic and metagenomic datasets, their analyses are often not integrated. Metagenome assemblies are far from perfect, partially explaining why metagenome assemblies are not used for the analysis of metatranscriptomic datasets. Results: Here, we report a reads mapping algorithm for mapping of short reads onto a de Bruijn graph of assemblies. A hash table of junction k-mers (k-mers spanning branching structures in the de Bruijn graph) is used to facilitate fast mapping of reads to the graph. We developed an application of this mapping algorithm: a reference-based approach to metatranscriptome assembly using graphs of metagenome assembly as the reference. Our results show that this new approach (called TAG) helps to assemble substantially more transcripts that otherwise would have been missed or truncated because of the fragmented nature of the reference metagenome. Availability and implementation: TAG was implemented in C++ and has been tested extensively on the Linux platform. It is available for download as open source at http://omics.informatics.indiana.edu/TAG. Contact:yye@indiana.edu
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Affiliation(s)
- Yuzhen Ye
- School of Informatics and Computing, Indiana University, Bloomington, IN 47405, USA
| | - Haixu Tang
- School of Informatics and Computing, Indiana University, Bloomington, IN 47405, USA
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427
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Castro-Nallar E, Bendall ML, Pérez-Losada M, Sabuncyan S, Severance EG, Dickerson FB, Schroeder JR, Yolken RH, Crandall KA. Composition, taxonomy and functional diversity of the oropharynx microbiome in individuals with schizophrenia and controls. PeerJ 2015; 3:e1140. [PMID: 26336637 PMCID: PMC4556144 DOI: 10.7717/peerj.1140] [Citation(s) in RCA: 172] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Accepted: 07/10/2015] [Indexed: 12/13/2022] Open
Abstract
The role of the human microbiome in schizophrenia remains largely unexplored. The microbiome has been shown to alter brain development and modulate behavior and cognition in animals through gut-brain connections, and research in humans suggests that it may be a modulating factor in many disorders. This study reports findings from a shotgun metagenomic analysis of the oropharyngeal microbiome in 16 individuals with schizophrenia and 16 controls. High-level differences were evident at both the phylum and genus levels, with Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria dominating both schizophrenia patients and controls, and Ascomycota being more abundant in schizophrenia patients than controls. Controls were richer in species but less even in their distributions, i.e., dominated by fewer species, as opposed to schizophrenia patients. Lactic acid bacteria were relatively more abundant in schizophrenia, including species of Lactobacilli and Bifidobacterium, which have been shown to modulate chronic inflammation. We also found Eubacterium halii, a lactate-utilizing species. Functionally, the microbiome of schizophrenia patients was characterized by an increased number of metabolic pathways related to metabolite transport systems including siderophores, glutamate, and vitamin B12. In contrast, carbohydrate and lipid pathways and energy metabolism were abundant in controls. These findings suggest that the oropharyngeal microbiome in individuals with schizophrenia is significantly different compared to controls, and that particular microbial species and metabolic pathways differentiate both groups. Confirmation of these findings in larger and more diverse samples, e.g., gut microbiome, will contribute to elucidating potential links between schizophrenia and the human microbiota.
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Affiliation(s)
- Eduardo Castro-Nallar
- Computational Biology Institute, George Washington University , Ashburn, VA , USA ; Center for Bioinformatics and Integrative Biology, Universidad Andrés Bello, Facultad de Ciencias Biológicas , Santiago , Chile
| | - Matthew L Bendall
- Computational Biology Institute, George Washington University , Ashburn, VA , USA
| | - Marcos Pérez-Losada
- Computational Biology Institute, George Washington University , Ashburn, VA , USA ; CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto , Vairão , USA ; Division of Emergency Medicine, Children's National Medical Center , Washington, D.C. , USA
| | - Sarven Sabuncyan
- Stanley Neurovirology Laboratory, Johns Hopkins School of Medicine , Baltimore, MD , USA
| | - Emily G Severance
- Stanley Neurovirology Laboratory, Johns Hopkins School of Medicine , Baltimore, MD , USA
| | | | | | - Robert H Yolken
- Stanley Neurovirology Laboratory, Johns Hopkins School of Medicine , Baltimore, MD , USA
| | - Keith A Crandall
- Computational Biology Institute, George Washington University , Ashburn, VA , USA
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428
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Hammer TJ, Dickerson JC, Fierer N. Evidence-based recommendations on storing and handling specimens for analyses of insect microbiota. PeerJ 2015; 3:e1190. [PMID: 26311208 PMCID: PMC4548535 DOI: 10.7717/peerj.1190] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Accepted: 07/24/2015] [Indexed: 11/20/2022] Open
Abstract
Research on insect microbiota has greatly expanded over the past decade, along with a growing appreciation of the microbial contributions to insect ecology and evolution. Many of these studies use DNA sequencing to characterize the diversity and composition of insect-associated microbial communities. The choice of strategies used for specimen collection, storage, and handling could introduce biases in molecular assessments of insect microbiota, but such potential influences have not been systematically evaluated. Likewise, although it is common practice to surface sterilize insects prior to DNA extraction, it is not known if this time-consuming step has any effect on microbial community analyses. To resolve these methodological unknowns, we conducted an experiment wherein replicate individual insects of four species were stored intact for two months using five different methods—freezing, ethanol, dimethyl sulfoxide (DMSO), cetrimonium bromide (CTAB), and room-temperature storage without preservative—and then subjected to whole-specimen 16S rRNA gene sequencing to assess whether the structure of the insect-associated bacterial communities was impacted by these different storage strategies. Overall, different insect species harbored markedly distinct bacterial communities, a pattern that was highly robust to the method used to store samples. Storage method had little to no effect on assessments of microbiota composition, and the magnitude of the effect differed among the insect species examined. No single method emerged as “best,” i.e., one consistently having the highest similarity in community structure to control specimens, which were not stored prior to homogenization and DNA sequencing. We also found that surface sterilization did not change bacterial community structure as compared to unsterilized insects, presumably due to the vastly greater microbial biomass inside the insect body relative to its surface. We therefore recommend that researchers can use any of the methods tested here, and base their choice according to practical considerations such as prior use, cost, and availability in the field, although we still advise that all samples within a study be handled in an identical manner when possible. We also suggest that, in large-scale molecular studies of hundreds of insect specimens, surface sterilization may not be worth the time and effort involved. This information should help researchers design sampling strategies and will facilitate cross-comparisons and meta-analyses of microbial community data obtained from insect specimens preserved in different ways.
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Affiliation(s)
- Tobin J Hammer
- Department of Ecology and Evolutionary Biology, University of Colorado at Boulder , Boulder, CO , United States ; Cooperative Institute for Research in Environmental Sciences, University of Colorado at Boulder , Boulder, CO , United States
| | - Jacob C Dickerson
- Department of Ecology and Evolutionary Biology, University of Colorado at Boulder , Boulder, CO , United States
| | - Noah Fierer
- Department of Ecology and Evolutionary Biology, University of Colorado at Boulder , Boulder, CO , United States ; Cooperative Institute for Research in Environmental Sciences, University of Colorado at Boulder , Boulder, CO , United States
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429
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Castro-Nallar E, Shen Y, Freishtat RJ, Pérez-Losada M, Manimaran S, Liu G, Johnson WE, Crandall KA. Integrating microbial and host transcriptomics to characterize asthma-associated microbial communities. BMC Med Genomics 2015; 8:50. [PMID: 26277095 PMCID: PMC4537781 DOI: 10.1186/s12920-015-0121-1] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Accepted: 07/13/2015] [Indexed: 12/21/2022] Open
Abstract
Background The relationships between infections in early life and asthma are not completely understood. Likewise, the clinical relevance of microbial communities present in the respiratory tract is only partially known. A number of microbiome studies analyzing respiratory tract samples have found increased proportions of gamma-Proteobacteria including Haemophilus influenzae, Moraxella catarrhalis, and Firmicutes such as Streptococcus pneumoniae. The aim of this study was to present a new approach that combines RNA microbial identification with host gene expression to characterize and validate metagenomic taxonomic profiling in individuals with asthma. Methods Using whole metagenomic shotgun RNA sequencing, we characterized and compared the microbial communities of individuals, children and adolescents, with asthma and controls. The resulting data were analyzed by partitioning human and microbial reads. Microbial reads were then used to characterize the microbial diversity of each patient, and potential differences between asthmatic and healthy groups. Human reads were used to assess the expression of known genes involved in the host immune response to specific pathogens and detect potential differences between those with asthma and controls. Results Microbial communities in the nasal cavities of children differed significantly between asthmatics and controls. After read count normalization, some bacterial species were significantly overrepresented in asthma patients (Wald test, p-value < 0.05), including Escherichia coli and Psychrobacter. Among these, Moraxella catarrhalis exhibited ~14-fold over abundance in asthmatics versus controls. Differential host gene expression analysis confirms that the presence of Moraxella catarrhalis is associated to a specific M. catarrhalis core gene signature expressed by the host. Conclusions For the first time, we show the power of combining RNA taxonomic profiling and host gene expression signatures for microbial identification. Our approach not only identifies microbes from metagenomic data, but also adds support to these inferences by determining if the host is mounting a response against specific infectious agents. In particular, we show that M. catarrhalis is abundant in asthma patients but not in controls, and that its presence is associated with a specific host gene expression signature. Electronic supplementary material The online version of this article (doi:10.1186/s12920-015-0121-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Eduardo Castro-Nallar
- Computational Biology Institute, George Washington University, Ashburn, VA, 20147, USA. .,Universidad Andrés Bello, Center for Bioinformatics and Integrative Biology, Facultad de Ciencias Biológicas, Av. República 239, Santiago, 8370146, Chile.
| | - Ying Shen
- Division of Computational Biomedicine, Boston University School of Medicine, Boston, MA, 02118, USA.
| | - Robert J Freishtat
- Division of Emergency Medicine, Children's National Medical Center, Washington, DC, 20010, USA.
| | - Marcos Pérez-Losada
- Computational Biology Institute, George Washington University, Ashburn, VA, 20147, USA. .,Division of Emergency Medicine, Children's National Medical Center, Washington, DC, 20010, USA. .,CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Vairão, 4485-661, Portugal.
| | - Solaiappan Manimaran
- Division of Computational Biomedicine, Boston University School of Medicine, Boston, MA, 02118, USA.
| | - Gang Liu
- Division of Computational Biomedicine, Boston University School of Medicine, Boston, MA, 02118, USA.
| | - W Evan Johnson
- Division of Computational Biomedicine, Boston University School of Medicine, Boston, MA, 02118, USA.
| | - Keith A Crandall
- Computational Biology Institute, George Washington University, Ashburn, VA, 20147, USA.
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Pozuelo M, Panda S, Santiago A, Mendez S, Accarino A, Santos J, Guarner F, Azpiroz F, Manichanh C. Reduction of butyrate- and methane-producing microorganisms in patients with Irritable Bowel Syndrome. Sci Rep 2015; 5:12693. [PMID: 26239401 PMCID: PMC4523847 DOI: 10.1038/srep12693] [Citation(s) in RCA: 225] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Accepted: 07/03/2015] [Indexed: 12/19/2022] Open
Abstract
The pathophysiology of irritable bowel syndrome (IBS) remains unclear. Here we investigated the microbiome of a large cohort of patients to identify specific signatures for IBS subtypes. We examined the microbiome of 113 patients with IBS and 66 healthy controls. A subset of these participants provided two samples one month apart. We analyzed a total of 273 fecal samples, generating more than 20 million 16S rRNA sequences. In patients with IBS, a significantly lower microbial diversity was associated with a lower relative abundance of butyrate-producing bacteria (P = 0.002; q < 0.06), in particular in patients with IBS-D and IBS-M. IBS patients who did not receive any treatment harboured a lower abundance of Methanobacteria compared to healthy controls (P = 0.005; q = 0.05). Furthermore, significant correlations were observed between several bacterial taxa and sensation of flatulence and abdominal pain (P < 0.05). Altogether, our findings showed that IBS-M and IBS-D patients are characterized by a reduction of butyrate producing bacteria, known to improve intestinal barrier function, and a reduction of methane producing microorganisms a major mechanism of hydrogen disposal in the human colon, which could explain excess of abdominal gas in IBS.
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Affiliation(s)
- Marta Pozuelo
- Digestive System Research Unit, Vall d'Hebron Research Institute, Passeig Vall d'Hebron 119-129, Barcelona 08035, Spain
| | - Suchita Panda
- Digestive System Research Unit, Vall d'Hebron Research Institute, Passeig Vall d'Hebron 119-129, Barcelona 08035, Spain
| | - Alba Santiago
- Digestive System Research Unit, Vall d'Hebron Research Institute, Passeig Vall d'Hebron 119-129, Barcelona 08035, Spain
| | - Sara Mendez
- Digestive Unit, University Hospital Vall d'Hebron, Passeig Vall d'Hebron 119-129, Barcelona 08035, Spain
| | - Anna Accarino
- 1] Digestive Unit, University Hospital Vall d'Hebron, Passeig Vall d'Hebron 119-129, Barcelona 08035, Spain [2] Centro de Investigacion Biomedica en Red en el Área tematica de Enfermedades Heptaticas y Digestivas, CIBERehd, Instituto de Salud Carlos III, Madrid, Spain
| | - Javier Santos
- 1] Digestive System Research Unit, Vall d'Hebron Research Institute, Passeig Vall d'Hebron 119-129, Barcelona 08035, Spain [2] Digestive Unit, University Hospital Vall d'Hebron, Passeig Vall d'Hebron 119-129, Barcelona 08035, Spain [3] Centro de Investigacion Biomedica en Red en el Área tematica de Enfermedades Heptaticas y Digestivas, CIBERehd, Instituto de Salud Carlos III, Madrid, Spain
| | - Francisco Guarner
- 1] Digestive System Research Unit, Vall d'Hebron Research Institute, Passeig Vall d'Hebron 119-129, Barcelona 08035, Spain [2] Digestive Unit, University Hospital Vall d'Hebron, Passeig Vall d'Hebron 119-129, Barcelona 08035, Spain [3] Centro de Investigacion Biomedica en Red en el Área tematica de Enfermedades Heptaticas y Digestivas, CIBERehd, Instituto de Salud Carlos III, Madrid, Spain
| | - Fernando Azpiroz
- 1] Digestive System Research Unit, Vall d'Hebron Research Institute, Passeig Vall d'Hebron 119-129, Barcelona 08035, Spain [2] Digestive Unit, University Hospital Vall d'Hebron, Passeig Vall d'Hebron 119-129, Barcelona 08035, Spain [3] Centro de Investigacion Biomedica en Red en el Área tematica de Enfermedades Heptaticas y Digestivas, CIBERehd, Instituto de Salud Carlos III, Madrid, Spain
| | - Chaysavanh Manichanh
- 1] Digestive System Research Unit, Vall d'Hebron Research Institute, Passeig Vall d'Hebron 119-129, Barcelona 08035, Spain [2] Centro de Investigacion Biomedica en Red en el Área tematica de Enfermedades Heptaticas y Digestivas, CIBERehd, Instituto de Salud Carlos III, Madrid, Spain
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Rodrigues Hoffmann A, Proctor LM, Surette MG, Suchodolski JS. The Microbiome: The Trillions of Microorganisms That Maintain Health and Cause Disease in Humans and Companion Animals. Vet Pathol 2015. [PMID: 26220947 DOI: 10.1177/0300985815595517] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The microbiome is the complex collection of microorganisms, their genes, and their metabolites, colonizing the human and animal mucosal surfaces, digestive tract, and skin. It is now well known that the microbiome interacts with its host, assisting in digestion and detoxification, supporting immunity, protecting against pathogens, and maintaining health. Studies published to date have demonstrated that healthy individuals are often colonized with different microbiomes than those with disease involving various organ systems. This review covers a brief history of the development of the microbiome field, the main objectives of the Human Microbiome Project, and the most common microbiomes inhabiting the human respiratory tract, companion animal digestive tract, and skin in humans and companion animals. The main changes in the microbiomes in patients with pulmonary, gastrointestinal, and cutaneous lesions are described.
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Affiliation(s)
- A Rodrigues Hoffmann
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA
| | - L M Proctor
- National Human Genome Research Institute, National Institute of Health, Bethesda, MD, USA
| | - M G Surette
- Department of Medicine, Department of Biochemistry and Biomedical Sciences, Faculty of Health Sciences, Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, ON, Canada
| | - J S Suchodolski
- Department of Small Animal Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA
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432
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Reck M, Tomasch J, Deng Z, Jarek M, Husemann P, Wagner-Döbler I. Stool metatranscriptomics: A technical guideline for mRNA stabilisation and isolation. BMC Genomics 2015; 16:494. [PMID: 26140923 PMCID: PMC4490624 DOI: 10.1186/s12864-015-1694-y] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2014] [Accepted: 06/11/2015] [Indexed: 02/08/2023] Open
Abstract
Background The complex microbiome of the gut has an enormous impact on human health. Analysis of the transcriptional activity of microorganisms through mRNA sequencing (metatranscriptomics) opens a completely new window into their activity in vivo, but it is highly challenging due to numerous technical and bioinformatical obstacles. Here we present an optimized pipeline for extraction of high quality mRNA from stool samples. Results Comparison of three commercially available RNA extraction kits with the method of Zoetendal revealed that the Powermicrobiome Kit (MoBio) performed best with respect to RNA yield and purity. Next, the influence of the stabilization reagent during sample storage for up to 15 days was studied. RIN analysis and qRT-PCR of spiked-in and indigenous genes revealed that RNA Later preserved mRNA integrity most efficiently, while samples conserved in RNA Protect showed substantial mRNA decay. Using the optimized pipeline developed here, recovery rates for spiked-in E.coli cells expressing fluorescing proteins were 8.7-9.7 % for SuperfolderGFP and 14.7-17.8 % for mCherry. The mRNA of stabilized stool samples as well as of snap-frozen controls was sequenced with Illumina Hiseq, yielding on average 74 million reads per sample. PCoA analysis, taxonomic classification using Kraken and functional classification using bwa showed that the transcriptomes of samples conserved in RNA Later were unchanged for up to 6 days even at room temperature, while RNA Protect was inefficient for storage durations exceeding 24 h. However, our data indicate that RNA Later introduces a bias which is then maintained throughout storage, while RNA Protect conserved samples are initially more similar to the snap frozen controls. RNA Later conserved samples had a reduced abundance of e.g. Prevotellaceae transcripts and were depleted for e.g. COG category “Carbohydrate transport and metabolism”. Conclusion Since the overall similarity between all stool transcriptional profiles studied here was >0.92, these differences are unlikely to affect global comparisons, but should be taken into account when rare but critically important members of the stool microbiome are being studied. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1694-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Michael Reck
- Research Group Microbial Communication, Helmholtz Centre for Infection Research, Braunschweig, Germany.
| | - Jürgen Tomasch
- Research Group Microbial Communication, Helmholtz Centre for Infection Research, Braunschweig, Germany.
| | - Zhiluo Deng
- Research Group Microbial Communication, Helmholtz Centre for Infection Research, Braunschweig, Germany.
| | - Michael Jarek
- Research Group Genome Analysis, Helmholtz Centre for Infection Research, Braunschweig, Germany.
| | - Peter Husemann
- Research Group Genome Analysis, Helmholtz Centre for Infection Research, Braunschweig, Germany.
| | - Irene Wagner-Döbler
- Research Group Microbial Communication, Helmholtz Centre for Infection Research, Braunschweig, Germany.
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433
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Duran-Pinedo AE, Frias-Lopez J. Beyond microbial community composition: functional activities of the oral microbiome in health and disease. Microbes Infect 2015; 17:505-516. [PMID: 25862077 DOI: 10.1016/j.micinf.2015.03.014doi|] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Revised: 03/23/2015] [Accepted: 03/26/2015] [Indexed: 05/25/2023]
Abstract
The oral microbiome plays a relevant role in the health status of the host and is a key element in a variety of oral and non-oral diseases. Despite advances in our knowledge of changes in microbial composition associated with different health conditions the functional aspects of the oral microbiome that lead to dysbiosis remain for the most part unknown. In this review, we discuss the progress made towards understanding the functional role of the oral microbiome in health and disease and how novel technologies are expanding our knowledge on this subject.
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Affiliation(s)
- Ana E Duran-Pinedo
- Department of Microbiology, The Forsyth Institute, 245 First Street, Cambridge, MA 02142, USA
| | - Jorge Frias-Lopez
- Department of Microbiology, The Forsyth Institute, 245 First Street, Cambridge, MA 02142, USA; Department of Oral Medicine, Infection, and Immunity, Harvard School of Dental Medicine, 188 Longwood Ave, Boston, MA 02115, USA.
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434
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Brooks B, Mueller RS, Young JC, Morowitz MJ, Hettich RL, Banfield JF. Strain-resolved microbial community proteomics reveals simultaneous aerobic and anaerobic function during gastrointestinal tract colonization of a preterm infant. Front Microbiol 2015; 6:654. [PMID: 26191049 PMCID: PMC4487087 DOI: 10.3389/fmicb.2015.00654] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Accepted: 06/15/2015] [Indexed: 12/31/2022] Open
Abstract
While there has been growing interest in the gut microbiome in recent years, it remains unclear whether closely related species and strains have similar or distinct functional roles and if organisms capable of both aerobic and anaerobic growth do so simultaneously. To investigate these questions, we implemented a high-throughput mass spectrometry-based proteomics approach to identify proteins in fecal samples collected on days of life 13-21 from an infant born at 28 weeks gestation. No prior studies have coupled strain-resolved community metagenomics to proteomics for such a purpose. Sequences were manually curated to resolve the genomes of two strains of Citrobacter that were present during the later stage of colonization. Proteome extracts from fecal samples were processed via a nano-2D-LC-MS/MS and peptides were identified based on information predicted from the genome sequences for the dominant organisms, Serratia and the two Citrobacter strains. These organisms are facultative anaerobes, and proteomic information indicates the utilization of both aerobic and anaerobic metabolisms throughout the time series. This may indicate growth in distinct niches within the gastrointestinal tract. We uncovered differences in the physiology of coexisting Citrobacter strains, including differences in motility and chemotaxis functions. Additionally, for both Citrobacter strains we resolved a community-essential role in vitamin metabolism and a predominant role in propionate production. Finally, in this case study we detected differences between genome abundance and activity levels for the dominant populations. This underlines the value in layering proteomic information over genetic potential.
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Affiliation(s)
- Brandon Brooks
- Department of Earth and Planetary Sciences, University of California, BerkeleyBerkeley, CA, USA
| | - Ryan S. Mueller
- Department of Earth and Planetary Sciences, University of California, BerkeleyBerkeley, CA, USA
- Department of Microbiology, Oregon State UniversityCorvallis, OR, USA
| | - Jacque C. Young
- Department of Genome Sciences and Technology, The University of Tennessee, KnoxvilleKnoxville, TN, USA
- Chemical Sciences Division, Oak Ridge National LaboratoryOak Ridge, TN, USA
| | - Michael J. Morowitz
- Department of Surgery, University of Pittsburgh School of MedicinePittsburgh, PA, USA
| | - Robert L. Hettich
- Department of Genome Sciences and Technology, The University of Tennessee, KnoxvilleKnoxville, TN, USA
- Chemical Sciences Division, Oak Ridge National LaboratoryOak Ridge, TN, USA
| | - Jillian F. Banfield
- Department of Earth and Planetary Sciences, University of California, BerkeleyBerkeley, CA, USA
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435
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Duran-Pinedo AE, Frias-Lopez J. Beyond microbial community composition: functional activities of the oral microbiome in health and disease. Microbes Infect 2015; 17:505-16. [PMID: 25862077 PMCID: PMC4495649 DOI: 10.1016/j.micinf.2015.03.014] [Citation(s) in RCA: 110] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Revised: 03/23/2015] [Accepted: 03/26/2015] [Indexed: 01/05/2023]
Abstract
The oral microbiome plays a relevant role in the health status of the host and is a key element in a variety of oral and non-oral diseases. Despite advances in our knowledge of changes in microbial composition associated with different health conditions the functional aspects of the oral microbiome that lead to dysbiosis remain for the most part unknown. In this review, we discuss the progress made towards understanding the functional role of the oral microbiome in health and disease and how novel technologies are expanding our knowledge on this subject.
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Affiliation(s)
- Ana E Duran-Pinedo
- Department of Microbiology, The Forsyth Institute, 245 First Street, Cambridge, MA 02142, USA
| | - Jorge Frias-Lopez
- Department of Microbiology, The Forsyth Institute, 245 First Street, Cambridge, MA 02142, USA; Department of Oral Medicine, Infection, and Immunity, Harvard School of Dental Medicine, 188 Longwood Ave, Boston, MA 02115, USA.
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436
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Pérez-Losada M, Castro-Nallar E, Bendall ML, Freishtat RJ, Crandall KA. Dual Transcriptomic Profiling of Host and Microbiota during Health and Disease in Pediatric Asthma. PLoS One 2015; 10:e0131819. [PMID: 26125632 PMCID: PMC4488395 DOI: 10.1371/journal.pone.0131819] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Accepted: 06/07/2015] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND High-throughput sequencing (HTS) analysis of microbial communities from the respiratory airways has heavily relied on the 16S rRNA gene. Given the intrinsic limitations of this approach, airway microbiome research has focused on assessing bacterial composition during health and disease, and its variation in relation to clinical and environmental factors, or other microbiomes. Consequently, very little effort has been dedicated to describing the functional characteristics of the airway microbiota and even less to explore the microbe-host interactions. Here we present a simultaneous assessment of microbiome and host functional diversity and host-microbe interactions from the same RNA-seq experiment, while accounting for variation in clinical metadata. METHODS Transcriptomic (host) and metatranscriptomic (microbiota) sequences from the nasal epithelium of 8 asthmatics and 6 healthy controls were separated in silico and mapped to available human and NCBI-NR protein reference databases. Human genes differentially expressed in asthmatics and controls were then used to infer upstream regulators involved in immune and inflammatory responses. Concomitantly, microbial genes were mapped to metabolic databases (COG, SEED, and KEGG) to infer microbial functions differentially expressed in asthmatics and controls. Finally, multivariate analysis was applied to find associations between microbiome characteristics and host upstream regulators while accounting for clinical variation. RESULTS AND DISCUSSION Our study showed significant differences in the metabolism of microbiomes from asthmatic and non-asthmatic children for up to 25% of the functional properties tested. Enrichment analysis of 499 differentially expressed host genes for inflammatory and immune responses revealed 43 upstream regulators differentially activated in asthma. Microbial adhesion (virulence) and Proteobacteria abundance were significantly associated with variation in the expression of the upstream regulator IL1A; suggesting that microbiome characteristics modulate host inflammatory and immune systems during asthma.
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Affiliation(s)
- Marcos Pérez-Losada
- Computational Biology Institute, George Washington University, Ashburn, Virginia, United States of America
- Division of Emergency Medicine, Children’s National Medical Center, Washington, DC, United States of America
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Vairão, Portugal
| | - Eduardo Castro-Nallar
- Computational Biology Institute, George Washington University, Ashburn, Virginia, United States of America
- Universidad Andrés Bello, Center for Bioinformatics and Integrative Biology, Facultad de Ciencias Biológicas, Santiago, Chile
| | - Matthew L. Bendall
- Computational Biology Institute, George Washington University, Ashburn, Virginia, United States of America
| | - Robert J. Freishtat
- Division of Emergency Medicine, Children’s National Medical Center, Washington, DC, United States of America
| | - Keith A. Crandall
- Computational Biology Institute, George Washington University, Ashburn, Virginia, United States of America
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437
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The Integrative Human Microbiome Project: dynamic analysis of microbiome-host omics profiles during periods of human health and disease. Cell Host Microbe 2015; 16:276-89. [PMID: 25211071 PMCID: PMC5109542 DOI: 10.1016/j.chom.2014.08.014] [Citation(s) in RCA: 323] [Impact Index Per Article: 35.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Much has been learned about the diversity and distribution of human-associated microbial communities, but we still know little about the biology of the microbiome, how it interacts with the host, and how the host responds to its resident microbiota. The Integrative Human Microbiome Project (iHMP, http://hmp2.org), the second phase of the NIH Human Microbiome Project, will study these interactions by analyzing microbiome and host activities in longitudinal studies of disease-specific cohorts and by creating integrated data sets of microbiome and host functional properties. These data sets will serve as experimental test beds to evaluate new models, methods, and analyses on the interactions of host and microbiome. Here we describe the three models of microbiome-associated human conditions, on the dynamics of preterm birth, inflammatory bowel disease, and type 2 diabetes, and their underlying hypotheses, as well as the multi-omic data types to be collected, integrated, and distributed through public repositories as a community resource.
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438
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Bikel S, Valdez-Lara A, Cornejo-Granados F, Rico K, Canizales-Quinteros S, Soberón X, Del Pozo-Yauner L, Ochoa-Leyva A. Combining metagenomics, metatranscriptomics and viromics to explore novel microbial interactions: towards a systems-level understanding of human microbiome. Comput Struct Biotechnol J 2015; 13:390-401. [PMID: 26137199 PMCID: PMC4484546 DOI: 10.1016/j.csbj.2015.06.001] [Citation(s) in RCA: 132] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Revised: 06/01/2015] [Accepted: 06/04/2015] [Indexed: 02/07/2023] Open
Abstract
The advances in experimental methods and the development of high performance bioinformatic tools have substantially improved our understanding of microbial communities associated with human niches. Many studies have documented that changes in microbial abundance and composition of the human microbiome is associated with human health and diseased state. The majority of research on human microbiome is typically focused in the analysis of one level of biological information, i.e., metagenomics or metatranscriptomics. In this review, we describe some of the different experimental and bioinformatic strategies applied to analyze the 16S rRNA gene profiling and shotgun sequencing data of the human microbiome. We also discuss how some of the recent insights in the combination of metagenomics, metatranscriptomics and viromics can provide more detailed description on the interactions between microorganisms and viruses in oral and gut microbiomes. Recent studies on viromics have begun to gain importance due to the potential involvement of viruses in microbial dysbiosis. In addition, metatranscriptomic combined with metagenomic analysis have shown that a substantial fraction of microbial transcripts can be differentially regulated relative to their microbial genomic abundances. Thus, understanding the molecular interactions in the microbiome using the combination of metagenomics, metatranscriptomics and viromics is one of the main challenges towards a system level understanding of human microbiome.
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Affiliation(s)
- Shirley Bikel
- Unidad de Genómica de Poblaciones Aplicada la Salud, Facultad de Química, UNAM, Instituto Nacional de Medicina Genómica (INMEGEN), México, D.F. 14610, Mexico ; Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de Mexico, Avenida Universidad 2001, Cuernavaca C.P. 62210, Mexico
| | - Alejandra Valdez-Lara
- Unidad de Genómica de Poblaciones Aplicada la Salud, Facultad de Química, UNAM, Instituto Nacional de Medicina Genómica (INMEGEN), México, D.F. 14610, Mexico ; Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de Mexico, Avenida Universidad 2001, Cuernavaca C.P. 62210, Mexico
| | - Fernanda Cornejo-Granados
- Unidad de Genómica de Poblaciones Aplicada la Salud, Facultad de Química, UNAM, Instituto Nacional de Medicina Genómica (INMEGEN), México, D.F. 14610, Mexico ; Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de Mexico, Avenida Universidad 2001, Cuernavaca C.P. 62210, Mexico
| | - Karina Rico
- Unidad de Genómica de Poblaciones Aplicada la Salud, Facultad de Química, UNAM, Instituto Nacional de Medicina Genómica (INMEGEN), México, D.F. 14610, Mexico
| | - Samuel Canizales-Quinteros
- Unidad de Genómica de Poblaciones Aplicada la Salud, Facultad de Química, UNAM, Instituto Nacional de Medicina Genómica (INMEGEN), México, D.F. 14610, Mexico
| | - Xavier Soberón
- Instituto Nacional de Medicina Genómica (INMEGEN), México, D.F., Mexico
| | | | - Adrián Ochoa-Leyva
- Unidad de Genómica de Poblaciones Aplicada la Salud, Facultad de Química, UNAM, Instituto Nacional de Medicina Genómica (INMEGEN), México, D.F. 14610, Mexico ; Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de Mexico, Avenida Universidad 2001, Cuernavaca C.P. 62210, Mexico
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439
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Sequencing and beyond: integrating molecular 'omics' for microbial community profiling. Nat Rev Microbiol 2015; 13:360-72. [PMID: 25915636 DOI: 10.1038/nrmicro3451] [Citation(s) in RCA: 406] [Impact Index Per Article: 45.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
High-throughput DNA sequencing has proven invaluable for investigating diverse environmental and host-associated microbial communities. In this Review, we discuss emerging strategies for microbial community analysis that complement and expand traditional metagenomic profiling. These include novel DNA sequencing strategies for identifying strain-level microbial variation and community temporal dynamics; measuring multiple 'omic' data types that better capture community functional activity, such as transcriptomics, proteomics and metabolomics; and combining multiple forms of omic data in an integrated framework. We highlight studies in which the 'multi-omics' approach has led to improved mechanistic models of microbial community structure and function.
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440
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Voigt AY, Costea PI, Kultima JR, Li SS, Zeller G, Sunagawa S, Bork P. Temporal and technical variability of human gut metagenomes. Genome Biol 2015; 16:73. [PMID: 25888008 PMCID: PMC4416267 DOI: 10.1186/s13059-015-0639-8] [Citation(s) in RCA: 97] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 03/19/2015] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Metagenomics has become a prominent approach for exploring the role of the gut microbiota in human health. However, the temporal variability of the healthy gut microbiome has not yet been studied in depth using metagenomics and little is known about the effects of different sampling and preservation approaches. We performed metagenomic analysis on fecal samples from seven subjects collected over a period of up to two years to investigate temporal variability and assess preservation-induced variation, specifically, fresh frozen compared to RNALater. We also monitored short-term disturbances caused by antibiotic treatment and bowel cleansing in one subject. RESULTS We find that the human gut microbiome is temporally stable and highly personalized at both taxonomic and functional levels. Over multiple time points, samples from the same subject clustered together, even in the context of a large dataset of 888 European and American fecal metagenomes. One exception was observed in an antibiotic intervention case where, more than one year after the treatment, samples did not resemble the pre-treatment state. Clustering was not affected by the preservation method. No species differed significantly in abundance, and only 0.36% of gene families were differentially abundant between preservation methods. CONCLUSIONS Technical variability is small compared to the temporal variability of an unperturbed gut microbiome, which in turn is much smaller than the observed between-subject variability. Thus, short-term preservation of fecal samples in RNALater is an appropriate and cost-effective alternative to freezing of fecal samples for metagenomic studies.
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Affiliation(s)
- Anita Y Voigt
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117, Heidelberg, Germany. .,Department of Applied Tumor Biology, Institute of Pathology, University Hospital Heidelberg, 69120, Heidelberg, Germany. .,Molecular Medicine Partnership Unit (MMPU), University of Heidelberg and European Molecular Biology Laboratory, 69120, Heidelberg, Germany.
| | - Paul I Costea
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117, Heidelberg, Germany.
| | - Jens Roat Kultima
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117, Heidelberg, Germany.
| | - Simone S Li
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117, Heidelberg, Germany. .,School of Biotechnology and Biomolecular Sciences, University of New South Wales, 2052, Sydney, Australia.
| | - Georg Zeller
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117, Heidelberg, Germany.
| | - Shinichi Sunagawa
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117, Heidelberg, Germany.
| | - Peer Bork
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117, Heidelberg, Germany. .,Molecular Medicine Partnership Unit (MMPU), University of Heidelberg and European Molecular Biology Laboratory, 69120, Heidelberg, Germany. .,Max Delbrück Centre for Molecular Medicine, 13125, Berlin, Germany.
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441
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No difference in small bowel microbiota between patients with irritable bowel syndrome and healthy controls. Sci Rep 2015; 5:8508. [PMID: 25687743 PMCID: PMC4330528 DOI: 10.1038/srep08508] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Accepted: 01/22/2015] [Indexed: 12/17/2022] Open
Abstract
Several studies have indicated that colonic microbiota may exhibit important differences between patients with irritable bowel syndrome (IBS) and healthy controls. Less is known about the microbiota of the small bowel. We used massive parallel sequencing to explore the composition of small bowel mucosa-associated microbiota in patients with IBS and healthy controls. We analysed capsule biopsies from the jejunum of 35 patients (26 females) with IBS aged 18-(36)-57 years and 16 healthy volunteers (11 females) aged 20-(32)-48 years. Sequences were analysed based on taxonomic classification. The phyla with the highest total abundance across all samples were: Firmicutes (43%), Proteobacteria (23%), Bacteroidetes (15%), Actinobacteria (9.3%) and Fusobacteria (7.0%). The most abundant genera were: Streptococcus (19%), Veillonella (13%), Prevotella (12%), Rothia (6.4%), Haemophilus (5.7%), Actinobacillus (5.5%), Escherichia (4.6%) and Fusobacterium (4.3%). We found no difference among major phyla or genera between patients with IBS and controls. We identified a cluster of samples in the small bowel microbiota dominated by Prevotella, which may represent a common enterotype of the upper small intestine. The remaining samples formed a gradient, dominated by Streptococcus at one end and Escherichia at the other.
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442
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Transcriptional regulation and adaptation to a high-fiber environment in Bacillus subtilis HH2 isolated from feces of the giant panda. PLoS One 2015; 10:e0116935. [PMID: 25658435 PMCID: PMC4319723 DOI: 10.1371/journal.pone.0116935] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2014] [Accepted: 12/16/2014] [Indexed: 02/07/2023] Open
Abstract
In the giant panda, adaptation to a high-fiber environment is a first step for the adequate functioning of intestinal bacteria, as the high cellulose content of the gut due to the panda's vegetarian appetite results in a harsh environment. As an excellent producer of several enzymes and vitamins, Bacillus subtilis imparts various advantages to animals. In our previous study, we determined that several strains of B. subtilis isolated from pandas exhibited good cellulose decomposition ability, and we hypothesized that this bacterial species can survive in and adapt well to a high-fiber environment. To evaluate this hypothesis, we employed RNA-Seq technology to analyze the differentially expressed genes of the selected strain B. subtilis HH2, which demonstrates significant cellulose hydrolysis of different carbon sources (cellulose and glucose). In addition, we used bioinformatics software and resources to analyze the functions and pathways of differentially expressed genes. Interestingly, comparison of the cellulose and glucose groups revealed that the up-regulated genes were involved in amino acid and lipid metabolism or transmembrane transport, both of which are involved in cellulose utilization. Conversely, the down-regulated genes were involved in non-essential functions for bacterial life, such as toxin and bacteriocin secretion, possibly to conserve energy for environmental adaptation. The results indicate that B. subtilis HH2 triggered a series of adaptive mechanisms at the transcriptional level, which suggests that this bacterium could act as a probiotic for pandas fed a high-fiber diet, despite the fact that cellulose is not a very suitable carbon source for this bacterial species. In this study, we present a model to understand the dynamic organization of and interactions between various functional and regulatory networks for unicellular organisms in a high-fiber environment.
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443
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Wang WL, Xu SY, Ren ZG, Tao L, Jiang JW, Zheng SS. Application of metagenomics in the human gut microbiome. World J Gastroenterol 2015; 21:803-814. [PMID: 25624713 PMCID: PMC4299332 DOI: 10.3748/wjg.v21.i3.803] [Citation(s) in RCA: 214] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Revised: 09/30/2014] [Accepted: 11/11/2014] [Indexed: 02/06/2023] Open
Abstract
There are more than 1000 microbial species living in the complex human intestine. The gut microbial community plays an important role in protecting the host against pathogenic microbes, modulating immunity, regulating metabolic processes, and is even regarded as an endocrine organ. However, traditional culture methods are very limited for identifying microbes. With the application of molecular biologic technology in the field of the intestinal microbiome, especially metagenomic sequencing of the next-generation sequencing technology, progress has been made in the study of the human intestinal microbiome. Metagenomics can be used to study intestinal microbiome diversity and dysbiosis, as well as its relationship to health and disease. Moreover, functional metagenomics can identify novel functional genes, microbial pathways, antibiotic resistance genes, functional dysbiosis of the intestinal microbiome, and determine interactions and co-evolution between microbiota and host, though there are still some limitations. Metatranscriptomics, metaproteomics and metabolomics represent enormous complements to the understanding of the human gut microbiome. This review aims to demonstrate that metagenomics can be a powerful tool in studying the human gut microbiome with encouraging prospects. The limitations of metagenomics to be overcome are also discussed. Metatranscriptomics, metaproteomics and metabolomics in relation to the study of the human gut microbiome are also briefly discussed.
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444
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Caballero S, Pamer EG. Microbiota-mediated inflammation and antimicrobial defense in the intestine. Annu Rev Immunol 2015; 33:227-56. [PMID: 25581310 DOI: 10.1146/annurev-immunol-032713-120238] [Citation(s) in RCA: 186] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The diverse microbial populations constituting the intestinal microbiota promote immune development and differentiation, but because of their complex metabolic requirements and the consequent difficulty culturing them, they remained, until recently, largely uncharacterized and mysterious. In the last decade, deep nucleic acid sequencing platforms, new computational and bioinformatics tools, and full-genome characterization of several hundred commensal bacterial species facilitated studies of the microbiota and revealed that differences in microbiota composition can be associated with inflammatory, metabolic, and infectious diseases, that each human is colonized by a distinct bacterial flora, and that the microbiota can be manipulated to reduce and even cure some diseases. Different bacterial species induce distinct immune cell populations that can play pro- and anti-inflammatory roles, and thus the composition of the microbiota determines, in part, the level of resistance to infection and susceptibility to inflammatory diseases. This review summarizes recent work characterizing commensal microbes that contribute to the antimicrobial defense/inflammation axis.
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Affiliation(s)
- Silvia Caballero
- Immunology Program, Sloan Kettering Institute, Infectious Diseases Service, Memorial Sloan Kettering Cancer Center, New York, NY 10065;
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445
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Salazar N, Arboleya S, Valdés L, Stanton C, Ross P, Ruiz L, Gueimonde M, de Los Reyes-Gavilán CG. The human intestinal microbiome at extreme ages of life. Dietary intervention as a way to counteract alterations. Front Genet 2014; 5:406. [PMID: 25484891 PMCID: PMC4240173 DOI: 10.3389/fgene.2014.00406] [Citation(s) in RCA: 101] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Accepted: 11/02/2014] [Indexed: 12/21/2022] Open
Abstract
The intestinal microbiome is defined as the assembly of genomes from microorganisms inhabiting the gut. This microbial ecosystem regulates important functions of the host and its correct composition and functionality is essential for a “healthy status.” Metagenomic studies have highlighted variations of the intestinal microbiota as a function of age and diet. Colonization of the infant gut starts at birth and is influenced by feeding habits (formula vs. breast-feeding), birth mode and antibiotic exposure. The intestinal microbiota of full-term vaginally delivered breast-fed infants is considered the gold-standard, representing the reference for studies of alterations in other pediatric populations. At 2–3 years of age, the intestinal microbiota reaches a composition similar to adults, remaining without noticeable variations until senescence, when microbial instability and changes reappear. Here we summarize the current knowledge on intestinal microbiota alterations at extreme stages of life and tools for designing differentiated nutritional strategies by the use of probiotics, prebiotics and specific nutrients in order to restore a balanced microbiota and to improve immune and nutritional status.
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Affiliation(s)
- Nuria Salazar
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias - Consejo Superior de Investigaciones Científicas Villaviciosa, Spain
| | - Silvia Arboleya
- Alimentary Pharmabiotic Centre, Teagasc, Food Research Centre Moorepark Fermoy, Ireland
| | - Lorena Valdés
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias - Consejo Superior de Investigaciones Científicas Villaviciosa, Spain
| | - Catherine Stanton
- Alimentary Pharmabiotic Centre, Teagasc, Food Research Centre Moorepark Fermoy, Ireland
| | - Paul Ross
- Alimentary Pharmabiotic Centre, University College Cork Cork, Ireland
| | - Lorena Ruiz
- Alimentary Pharmabiotic Centre, University College Cork Cork, Ireland
| | - Miguel Gueimonde
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias - Consejo Superior de Investigaciones Científicas Villaviciosa, Spain
| | - Clara G de Los Reyes-Gavilán
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias - Consejo Superior de Investigaciones Científicas Villaviciosa, Spain
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446
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Joice R, Yasuda K, Shafquat A, Morgan XC, Huttenhower C. Determining microbial products and identifying molecular targets in the human microbiome. Cell Metab 2014; 20:731-741. [PMID: 25440055 PMCID: PMC4254638 DOI: 10.1016/j.cmet.2014.10.003] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Human-associated microbes are the source of many bioactive microbial products (proteins and metabolites) that play key functions both in human host pathways and in microbe-microbe interactions. Culture-independent studies now provide an accelerated means of exploring novel bioactives in the human microbiome; however, intriguingly, a substantial fraction of the microbial metagenome cannot be mapped to annotated genes or isolate genomes and is thus of unknown function. Meta'omic approaches, including metagenomic sequencing, metatranscriptomics, metabolomics, and integration of multiple assay types, represent an opportunity to efficiently explore this large pool of potential therapeutics. In combination with appropriate follow-up validation, high-throughput culture-independent assays can be combined with computational approaches to identify and characterize novel and biologically interesting microbial products. Here we briefly review the state of microbial product identification and characterization and discuss possible next steps to catalog and leverage the large uncharted fraction of the microbial metagenome.
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Affiliation(s)
- Regina Joice
- Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Koji Yasuda
- Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Afrah Shafquat
- Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Xochitl C Morgan
- Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | - Curtis Huttenhower
- Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
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447
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Thermophilic microbial cellulose decomposition and methanogenesis pathways recharacterized by metatranscriptomic and metagenomic analysis. Sci Rep 2014; 4:6708. [PMID: 25330991 PMCID: PMC4204047 DOI: 10.1038/srep06708] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Accepted: 10/02/2014] [Indexed: 02/01/2023] Open
Abstract
The metatranscriptomic recharacterization in the present study captured microbial enzymes at the unprecedented scale of 40,000 active genes belonged to 2,269 KEGG functions were identified. The novel information obtained herein revealed interesting patterns and provides an initial transcriptional insight into the thermophilic cellulose methanization process. Synergistic beta-sugar consumption by Thermotogales is crucial for cellulose hydrolysis in the thermophilic cellulose-degrading consortium because the primary cellulose degraders Clostridiales showed metabolic incompetence in subsequent beta-sugar pathways. Additionally, comparable transcription of putative Sus-like polysaccharide utilization loci (PULs) was observed in an unclassified order of Bacteroidetes suggesting the importance of PULs mechanism for polysaccharides breakdown in thermophilic systems. Despite the abundance of acetate as a fermentation product, the acetate-utilizing Methanosarcinales were less prevalent by 60% than the hydrogenotrophic Methanobacteriales. Whereas the aceticlastic methanogenesis pathway was markedly more active in terms of transcriptional activities in key genes, indicating that the less dominant Methanosarcinales are more active than their hydrogenotrophic counterparts in methane metabolism. These findings suggest that the minority of aceticlastic methanogens are not necessarily associated with repressed metabolism, in a pattern that was commonly observed in the cellulose-based methanization consortium, and thus challenge the causal likelihood proposed by previous studies.
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448
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Huttenhower C, Kostic AD, Xavier RJ. Inflammatory bowel disease as a model for translating the microbiome. Immunity 2014; 40:843-54. [PMID: 24950204 DOI: 10.1016/j.immuni.2014.05.013] [Citation(s) in RCA: 234] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Indexed: 02/06/2023]
Abstract
The inflammatory bowel diseases (IBDs) are among the most closely studied chronic inflammatory disorders that involve environmental, host genetic, and commensal microbial factors. This combination of features has made IBD both an appropriate and a high-priority platform for translatable research in host-microbiome interactions. Decades of epidemiology have identified environmental risk factors, although most mechanisms of action remain unexplained. The genetic architecture of IBD has been carefully dissected in multiple large populations, identifying several responsible host epithelial and immune pathways but without yet a complete systems-level explanation. Most recently, the commensal gut microbiota have been found to be both ecologically and functionally perturbed during the disease, but with as-yet-unexplained heterogeneity among IBD subtypes and individual patients. IBD thus represents perhaps the most comprehensive current model for understanding the human microbiome's role in complex inflammatory disease. Here, we review the influences of the microbiota on IBD and its potential for translational medicine.
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Affiliation(s)
- Curtis Huttenhower
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA; Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA.
| | - Aleksandar D Kostic
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA; Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Ramnik J Xavier
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Gastrointestinal Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA.
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