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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. The explosive growth in taxonomic metagenome profiling methods over the past years has created a need for systematic comparisons using relevant performance criteria. The Open-community Profiling Assessment too...

    Authors: Fernando Meyer, Andreas Bremges, Peter Belmann, Stefan Janssen, Alice C. McHardy and David Koslicki
    Citation: Genome Biology 2019 20:51
    Content type: Software Published on:

  3. Gut microbiota from individuals in rural, non-industrialized societies differ from those in individuals from industrialized societies. Here, we use 16S rRNA sequencing to survey the gut bacteria of seven non-i...

    Authors: Matthew E. B. Hansen, Meagan A. Rubel, Aubrey G. Bailey, Alessia Ranciaro, Simon R. Thompson, Michael C. Campbell, William Beggs, Jaanki R. Dave, Gaonyadiwe G. Mokone, Sununguko Wata Mpoloka, Thomas Nyambo, Christian Abnet, Stephen J. Chanock, Frederic D. Bushman and Sarah A. Tishkoff
    Citation: Genome Biology 2019 20:16
    Content type: Research Published on:

  4. False-positive identifications are a significant problem in metagenomics classification. We present KrakenUniq, a novel metagenomics classifier that combines the fast k-mer-based classification of Kraken with an ...

    Authors: F. P. Breitwieser, D. N. Baker and S. L. Salzberg
    Citation: Genome Biology 2018 19:198
    Content type: Software Published on:

    The Protocol to this article has been published in Nature Protocols 2022 17:s41596-022-00738-y

  5. Lung cancer is the leading cancer diagnosis worldwide and the number one cause of cancer deaths. Exposure to cigarette smoke, the primary risk factor in lung cancer, reduces epithelial barrier integrity and in...

    Authors: K. Leigh Greathouse, James R. White, Ashely J. Vargas, Valery V. Bliskovsky, Jessica A. Beck, Natalia von Muhlinen, Eric C. Polley, Elise D. Bowman, Mohammed A. Khan, Ana I. Robles, Tomer Cooks, Bríd M. Ryan, Noah Padgett, Amiran H. Dzutsev, Giorgio Trinchieri, Marbin A. Pineda…
    Citation: Genome Biology 2018 19:123
    Content type: Research Published on:

    The Author Correction to this article has been published in Genome Biology 2020 21:41

  6. The gut microbiome, a key constituent of the colonic environment, has been implicated as an important modulator of human health. The eukaryotic epigenome is postulated to respond to environmental stimuli throu...

    Authors: Yufeng Qin, John D. Roberts, Sara A. Grimm, Fred B. Lih, Leesa J. Deterding, Ruifang Li, Kaliopi Chrysovergis and Paul A. Wade
    Citation: Genome Biology 2018 19:7
    Content type: Research Published on:

  7. One of the main challenges in metagenomics is the identification of microorganisms in clinical and environmental samples. While an extensive and heterogeneous set of computational tools is available to classif...

    Authors: Alexa B. R. McIntyre, Rachid Ounit, Ebrahim Afshinnekoo, Robert J. Prill, Elizabeth Hénaff, Noah Alexander, Samuel S. Minot, David Danko, Jonathan Foox, Sofia Ahsanuddin, Scott Tighe, Nur A. Hasan, Poorani Subramanian, Kelly Moffat, Shawn Levy, Stefano Lonardi…
    Citation: Genome Biology 2017 18:182
    Content type: Research Published on:

    The Correction to this article has been published in Genome Biology 2019 20:72

  8. 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...

    Authors: 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…
    Citation: Genome Biology 2017 18:142
    Content type: Research Published on:

    The Correction to this article has been published in Genome Biology 2017 18:214

  9. 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...

    Authors: 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
    Citation: Genome Biology 2017 18:130
    Content type: Research Published on:

  10. 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...

    Authors: 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
    Citation: Genome Biology 2017 18:70
    Content type: Research Published on:

  11. 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...

    Authors: 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…
    Citation: Genome Biology 2017 18:8
    Content type: Research Published on:

  12. 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...

    Authors: 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
    Citation: Genome Biology 2016 17:260
    Content type: Software Published on:

  13. 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...

    Authors: Ola Brynildsrud, Jon Bohlin, Lonneke Scheffer and Vegard Eldholm
    Citation: Genome Biology 2016 17:238
    Content type: Software Published on:

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

  14. 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...

    Authors: Justine Debelius, Se Jin Song, Yoshiki Vazquez-Baeza, Zhenjiang Zech Xu, Antonio Gonzalez and Rob Knight
    Citation: Genome Biology 2016 17:217
    Content type: Review Published on:

  15. 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-...

    Authors: 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
    Citation: Genome Biology 2016 17:189
    Content type: Research Published on:

  16. 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...

    Authors: 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
    Citation: Genome Biology 2016 17:163
    Content type: Research Published on:

  17. 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...

    Authors: 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
    Citation: Genome Biology 2016 17:121
    Content type: Method Published on:

  18. 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...

    Authors: 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…
    Citation: Genome Biology 2016 17:111
    Content type: Software Published on:

  19. 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.

    Authors: David Zeevi, Tal Korem and Eran Segal
    Citation: Genome Biology 2016 17:50
    Content type: Meeting Report Published on: