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Microbiome Biology

Special Issue

​​​​​​​cauliflower resized © Courtesy of Gary Borisy and reprinted with permission from PNAS.

Guest Editors: Rob Knight, Ruth Ley, Elizabeth Grice, Jeroen Raes

Genome Biology and BMC Biology are pleased to launch the publication of this special issue on Microbiome Biology.

Microbiome research is helping us to understand the pervasive influence of microbial life on ourselves and our living planet.  Recent advances in sequencing, proteomic, and metabolomic technologies, as well as analytical and computational tools, are generating valuable insights into the biology of microbial communities, and their impact on their surroundings and their hosts. Microbiome research has thus integrated the diverse fields of microbiology, genomics, bioinformatics, cell and developmental biology and health and medicine, among others.

This special issue captures some of the progress being made in a field of research that has infiltrated traditional life science domains and changed our perception of organismal biology.

Research, methodology, review and comment articles will be appearing in the collection during the course of the next few months.


  1. Content type: Method

    Reconstructing genomic segments from metagenomics data is a highly complex task. In addition to general challenges, such as repeats and sequencing errors, metagenomic assembly needs to tolerate the uneven dept...

    Authors: Jay Ghurye, Todd Treangen, Marcus Fedarko, W. Judson Hervey IV and Mihai Pop

    Citation: Genome Biology 2019 20:174

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  2. Content type: Research

    Diarrhea is the second leading cause of death in children under 5 years of age. Enhanced understanding of causal pathways, pathogenesis, and sequelae of diarrhea is urgently needed. Although the gut microbiota...

    Authors: Nicholas Rhoades, Tasha Barr, Sara Hendrickson, Kamm Prongay, Andrew Haertel, Leanne Gill, Laura Garzel, Katrine Whiteson, Mark Slifka and Ilhem Messaoudi

    Citation: Genome Biology 2019 20:173

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  3. Content type: Research article

    The planetary sulfur cycle is a complex web of chemical reactions that can be microbial-mediated or can occur spontaneously in the environment, depending on the temperature and pH. Inorganic sulfur compounds c...

    Authors: Charlotte D. Vavourakis, Maliheh Mehrshad, Cherel Balkema, Rutger van Hall, Adrian-Ştefan Andrei, Rohit Ghai, Dimitry Y. Sorokin and Gerard Muyzer

    Citation: BMC Biology 2019 17:69

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  4. Content type: Method

    We describe a method that adds long-read sequencing to a mix of technologies used to assemble a highly complex cattle rumen microbial community, and provide a comparison to short read-based methods. Long-read ...

    Authors: Derek M. Bickhart, Mick Watson, Sergey Koren, Kevin Panke-Buisse, Laura M. Cersosimo, Maximilian O. Press, Curtis P. Van Tassell, Jo Ann S. Van Kessel, Bradd J. Haley, Seon Woo Kim, Cheryl Heiner, Garret Suen, Kiranmayee Bakshy, Ivan Liachko, Shawn T. Sullivan, Phillip R. Myer…

    Citation: Genome Biology 2019 20:153

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  5. Content type: Comment

    Metagenomics allows exploration of aspects of a microbial community that were inaccessible by cultivation-based approaches targeting single microbes. Many new microbial taxa and genes have been discovered usin...

    Authors: Andrew Maltez Thomas and Nicola Segata

    Citation: BMC Biology 2019 17:48

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  6. Content type: Research article

    Use of skin personal care products on a regular basis is nearly ubiquitous, but their effects on molecular and microbial diversity of the skin are unknown. We evaluated the impact of four beauty products (a fa...

    Authors: Amina Bouslimani, Ricardo da Silva, Tomasz Kosciolek, Stefan Janssen, Chris Callewaert, Amnon Amir, Kathleen Dorrestein, Alexey V. Melnik, Livia S. Zaramela, Ji-Nu Kim, Gregory Humphrey, Tara Schwartz, Karenina Sanders, Caitriona Brennan, Tal Luzzatto-Knaan, Gail Ackermann…

    Citation: BMC Biology 2019 17:47

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  7. Content type: Research article

    Environmental resistomes include transferable microbial genes. One important resistome component is resistance to arsenic, a ubiquitous and toxic metalloid that can have negative and chronic consequences for h...

    Authors: Taylor K. Dunivin, Susanna Y. Yeh and Ashley Shade

    Citation: BMC Biology 2019 17:45

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  8. Content type: Short Report

    Whole metagenome shotgun (WMGS) sequencing is a method that provides insights into the genomic composition and arrangement of complex microbial consortia. Here, we report how WMGS coupled with a cultivation ap...

    Authors: Gabriele Andrea Lugli, Christian Milani, Sabrina Duranti, Giulia Alessandri, Francesca Turroni, Leonardo Mancabelli, Danilo Tatoni, Maria Cristina Ossiprandi, Douwe van Sinderen and Marco Ventura

    Citation: Genome Biology 2019 20:96

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  9. Content type: Research article

    Antibiotic resistance is rendering common bacterial infections untreatable. Wildlife can incorporate and disperse antibiotic-resistant bacteria in the environment, such as water systems, which in turn serve as...

    Authors: Vanessa R. Marcelino, Michelle Wille, Aeron C. Hurt, Daniel González-Acuña, Marcel Klaassen, Timothy E. Schlub, John-Sebastian Eden, Mang Shi, Jonathan R. Iredell, Tania C. Sorrell and Edward C. Holmes

    Citation: BMC Biology 2019 17:31

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