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Microbiomes and Metagenomics

Genome Biology Collection

microbiomes and metagenomicsAll plants and animals live in close association with a complex community of microbial species. The microbiome can influence host immune and endocrine systems, as well as digestion and metabolism. In this collection, Genome Biology highlights advances in the study of microbial communities, with a focus on the human microbiome and its implications in health and disease. Technological advances for microbiome studies are also included.

  1. Research

    Quantitative metagenomics reveals unique gut microbiome biomarkers in ankylosing spondylitis

    The assessment and characterization of the gut microbiome has become a focus of research in the area of human autoimmune diseases. Ankylosing spondylitis is an inflammatory autoimmune disease and evidence show...

    Chengping Wen, Zhijun Zheng, Tiejuan Shao, Lin Liu, Zhijun Xie, Emmanuelle Le Chatelier, Zhixing He, Wendi Zhong, Yongsheng Fan, Linshuang Zhang, Haichang Li, Chunyan Wu, Changfeng Hu, Qian Xu, Jia Zhou, Shunfeng Cai…

    Genome Biology 2017 18:142

    Published on: 27 July 2017

  2. Research

    Methicillin-resistant Staphylococcus aureus emerged long before the introduction of methicillin into clinical practice

    The spread of drug-resistant bacterial pathogens poses a major threat to global health. It is widely recognised that the widespread use of antibiotics has generated selective pressures that have driven the eme...

    Catriona P. Harkins, Bruno Pichon, Michel Doumith, Julian Parkhill, Henrik Westh, Alexander Tomasz, Herminia de Lencastre, Stephen D. Bentley, Angela M. Kearns and Matthew T. G. Holden

    Genome Biology 2017 18:130

    Published on: 20 July 2017

  3. Research

    Relationships between gut microbiota, plasma metabolites, and metabolic syndrome traits in the METSIM cohort

    The gut microbiome is a complex and metabolically active community that directly influences host phenotypes. In this study, we profile gut microbiota using 16S rRNA gene sequencing in 531 well-phenotyped Finni...

    Elin Org, Yuna Blum, Silva Kasela, Margarete Mehrabian, Johanna Kuusisto, Antti J. Kangas, Pasi Soininen, Zeneng Wang, Mika Ala-Korpela, Stanley L. Hazen, Markku Laakso and Aldons J. Lusis

    Genome Biology 2017 18:70

    Published on: 13 April 2017

  4. Research

    Gut microbial degradation of organophosphate insecticides-induces glucose intolerance via gluconeogenesis

    Organophosphates are the most frequently and largely applied insecticide in the world due to their biodegradable nature. Gut microbes were shown to degrade organophosphates and cause intestinal dysfunction. Th...

    Ganesan Velmurugan, Tharmarajan Ramprasath, Krishnan Swaminathan, Gilles Mithieux, Jeyaprakash Rajendhran, Mani Dhivakar, Ayothi Parthasarathy, D.D. Venkatesh Babu, Leishman John Thumburaj, Allen J. Freddy, Vasudevan Dinakaran, Shanavas Syed Mohamed Puhari, Balakrishnan Rekha, Yacob Jenifer Christy, Sivakumar Anusha, Ganesan Divya…

    Genome Biology 2017 18:8

    Published on: 24 January 2017

  5. Software

    IMP: a pipeline for reproducible reference-independent integrated metagenomic and metatranscriptomic analyses

    Existing workflows for the analysis of multi-omic microbiome datasets are lab-specific and often result in sub-optimal data usage. Here we present IMP, a reproducible and modular pipeline for the integrated an...

    Shaman Narayanasamy, Yohan Jarosz, Emilie E. L. Muller, Anna Heintz-Buschart, Malte Herold, Anne Kaysen, Cédric C. Laczny, Nicolás Pinel, Patrick May and Paul Wilmes

    Genome Biology 2016 17:260

    Published on: 16 December 2016

  6. Software

    Rapid scoring of genes in microbial pan-genome-wide association studies with Scoary

    Genome-wide association studies (GWAS) have become indispensable in human medicine and genomics, but very few have been carried out on bacteria. Here we introduce Scoary, an ultra-fast, easy-to-use, and widely...

    Ola Brynildsrud, Jon Bohlin, Lonneke Scheffer and Vegard Eldholm

    Genome Biology 2016 17:238

    Published on: 25 November 2016

    The Erratum to this article has been published in Genome Biology 2016 17:262

  7. Review

    Tiny microbes, enormous impacts: what matters in gut microbiome studies?

    Many factors affect the microbiomes of humans, mice, and other mammals, but substantial challenges remain in determining which of these factors are of practical importance. Considering the relative effect size...

    Justine Debelius, Se Jin Song, Yoshiki Vazquez-Baeza, Zhenjiang Zech Xu, Antonio Gonzalez and Rob Knight

    Genome Biology 2016 17:217

    Published on: 19 October 2016

  8. Research

    Heritable components of the human fecal microbiome are associated with visceral fat

    Variation in the human fecal microbiota has previously been associated with body mass index (BMI). Although obesity is a global health burden, the accumulation of abdominal visceral fat is the specific cardio-...

    Michelle Beaumont, Julia K. Goodrich, Matthew A. Jackson, Idil Yet, Emily R. Davenport, Sara Vieira-Silva, Justine Debelius, Tess Pallister, Massimo Mangino, Jeroen Raes, Rob Knight, Andrew G. Clark, Ruth E. Ley, Tim D. Spector and Jordana T. Bell

    Genome Biology 2016 17:189

    Published on: 26 September 2016

  9. Research

    Characterizing human lung tissue microbiota and its relationship to epidemiological and clinical features

    The human lung tissue microbiota remains largely uncharacterized, although a number of studies based on airway samples suggest the existence of a viable human lung microbiota. Here we characterized the taxonom...

    Guoqin Yu, Mitchell H. Gail, Dario Consonni, Michele Carugno, Michael Humphrys, Angela C. Pesatori, Neil E. Caporaso, James J. Goedert, Jacques Ravel and Maria Teresa Landi

    Genome Biology 2016 17:163

    Published on: 28 July 2016

  10. Method

    MDSINE: Microbial Dynamical Systems INference Engine for microbiome time-series analyses

    Predicting dynamics of host-microbial ecosystems is crucial for the rational design of bacteriotherapies. We present MDSINE, a suite of algorithms for inferring dynamical systems models from microbiome time-se...

    Vanni Bucci, Belinda Tzen, Ning Li, Matt Simmons, Takeshi Tanoue, Elijah Bogart, Luxue Deng, Vladimir Yeliseyev, Mary L. Delaney, Qing Liu, Bernat Olle, Richard R. Stein, Kenya Honda, Lynn Bry and Georg K. Gerber

    Genome Biology 2016 17:121

    Published on: 3 June 2016

  11. Software

    Taxonomer: an interactive metagenomics analysis portal for universal pathogen detection and host mRNA expression profiling

    High-throughput sequencing enables unbiased profiling of microbial communities, universal pathogen detection, and host response to infectious diseases. However, computation times and algorithmic inaccuracies h...

    Steven Flygare, Keith Simmon, Chase Miller, Yi Qiao, Brett Kennedy, Tonya Di Sera, Erin H. Graf, Keith D. Tardif, Aurélie Kapusta, Shawn Rynearson, Chris Stockmann, Krista Queen, Suxiang Tong, Karl V. Voelkerding, Anne Blaschke, Carrie L. Byington…

    Genome Biology 2016 17:111

    Published on: 26 May 2016

  12. Meeting Report

    Talking about cross-talk: the immune system and the microbiome

    A report on the first EMBO conference entitled “Next Gen Immunology—From Host Genome to the Microbiome: Immunity in the Genomic Era”, held at the Weizmann Institute of Science, Israel, 14–16 February, 2016.

    David Zeevi, Tal Korem and Eran Segal

    Genome Biology 2016 17:50

    Published on: 17 March 2016