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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. Parkinson’s disease (PD) is a systemic disease clinically defined by the degeneration of dopaminergic neurons in the brain. While alterations in the gut microbiome composition have been reported in PD, their f...

    Authors: Federico Baldini, Johannes Hertel, Estelle Sandt, Cyrille C. Thinnes, Lorieza Neuberger-Castillo, Lukas Pavelka, Fay Betsou, Rejko Krüger and Ines Thiele
    Citation: BMC Biology 2020 18:62
    Content type: Research article Published on:

  2. Many microbial agents have been implicated as contributors to cancer genesis and development, and the search to identify and characterize new cancer-related organisms is ongoing. Modern developments in methodo...

    Authors: Sumeed Syed Manzoor, Annemiek Doedens and Michael B. Burns
    Citation: Genome Biology 2020 21:131
    Content type: Review Published on:

  3. There is an increasing demand for accurate and fast metagenome classifiers that can not only identify bacteria, but all members of a microbial community. We used a recently developed concept in read mapping to...

    Authors: Vanessa R. Marcelino, Philip T. L. C. Clausen, Jan P. Buchmann, Michelle Wille, Jonathan R. Iredell, Wieland Meyer, Ole Lund, Tania C. Sorrell and Edward C. Holmes
    Citation: Genome Biology 2020 21:103
    Content type: Software Published on:

  4. Metagenomics studies leverage genomic reference databases to generate discoveries in basic science and translational research. However, current microbial studies use disparate reference databases that lack con...

    Authors: Caitlin Loeffler, Aaron Karlsberg, Lana S. Martin, Eleazar Eskin, David Koslicki and Serghei Mangul
    Citation: BMC Biology 2020 18:37
    Content type: Comment Published on:

    The Correction to this article has been published in BMC Biology 2020 18:92

  5. The soil environment is responsible for sustaining most terrestrial plant life, yet we know surprisingly little about the important functions carried out by diverse microbial communities in soil. Soil microbes...

    Authors: Yi Zhou, David R. Coventry, Vadakattu V. S. R. Gupta, David Fuentes, Andrew Merchant, Brent N. Kaiser, Jishun Li, Yanli Wei, Huan Liu, Yayu Wang, Shuheng Gan and Matthew D. Denton
    Citation: Genome Biology 2020 21:89
    Content type: Research Published on:

  6. How intestinal epithelial cells interact with the microbiota and how this is regulated at the gene expression level are critical questions. Smarcad1 is a conserved chromatin remodeling factor with a poorly und...

    Authors: Juri Kazakevych, Jérémy Denizot, Anke Liebert, Mariana Portovedo, Mia Mosavie, Payal Jain, Claudia Stellato, Claire Fraser, Renan Oliveira Corrêa, Marina Célestine, Raphaël Mattiuz, Hanneke Okkenhaug, J. Ross Miller, Marco Aurélio Ramirez Vinolo, Marc Veldhoen and Patrick Varga-Weisz
    Citation: Genome Biology 2020 21:64
    Content type: Research Published on:

  7. Microbial populations exhibit functional changes in response to different ambient environments. Although whole metagenome sequencing promises enough raw data to study those changes, existing tools are limited ...

    Authors: Sumaiya Nazeen, Yun William Yu and Bonnie Berger
    Citation: Genome Biology 2020 21:47
    Content type: Method Published on:

  8. Chickens are a highly important source of protein for a large proportion of the human population. The caecal microbiota plays a crucial role in chicken nutrition through the production of short-chain fatty aci...

    Authors: Laura Glendinning, Robert D. Stewart, Mark J. Pallen, Kellie A. Watson and Mick Watson
    Citation: Genome Biology 2020 21:34
    Content type: Research Published on:

    The Author Correction to this article has been published in Genome Biology 2021 22:60

  9. Host-associated microbiomes, the microorganisms occurring inside and on host surfaces, influence evolutionary, immunological, and ecological processes. Interactions between host and microbiome affect metabolis...

    Authors: Douglas C. Woodhams, Molly C. Bletz, C. Guilherme Becker, Hayden A. Bender, Daniel Buitrago-Rosas, Hannah Diebboll, Roger Huynh, Patrick J. Kearns, Jordan Kueneman, Emmi Kurosawa, Brandon C. LaBumbard, Casandra Lyons, Kerry McNally, Klaus Schliep, Nachiket Shankar, Amanda G. Tokash-Peters…
    Citation: Genome Biology 2020 21:23
    Content type: Research Published on:

  10. Resistance to enteric pathogens is a complex trait at the crossroads of multiple biological processes. We have previously shown in the Drosophila Genetic Reference Panel (DGRP) that resistance to infection is hig...

    Authors: Michael V. Frochaux, Maroun Bou Sleiman, Vincent Gardeux, Riccardo Dainese, Brian Hollis, Maria Litovchenko, Virginie S. Braman, Tommaso Andreani, Dani Osman and Bart Deplancke
    Citation: Genome Biology 2020 21:6
    Content type: Research Published on:

  11. RNA splicing is a key post-transcriptional mechanism that generates protein diversity and contributes to the fine-tuning of gene expression, which may facilitate adaptation to environmental challenges. Here, w...

    Authors: Maroun Bou Sleiman, Michael Vincent Frochaux, Tommaso Andreani, Dani Osman, Roderic Guigo and Bart Deplancke
    Citation: Genome Biology 2020 21:4
    Content type: Research Published on:

  12. Viruses of Archaea and Bacteria are among the most abundant and diverse biological entities on Earth. Unraveling their biodiversity has been challenging due to methodological limitations. Recent advances in cultu...

    Authors: F. H. Coutinho, R. A. Edwards and F. Rodríguez-Valera
    Citation: BMC Biology 2019 17:109
    Content type: Research article Published on:

  13. Humans have coevolved with microbial communities to establish a mutually advantageous relationship that is still poorly characterized and can provide a better understanding of the human microbiome. Comparative...

    Authors: Serena Manara, Francesco Asnicar, Francesco Beghini, Davide Bazzani, Fabio Cumbo, Moreno Zolfo, Eleonora Nigro, Nicolai Karcher, Paolo Manghi, Marisa Isabell Metzger, Edoardo Pasolli and Nicola Segata
    Citation: Genome Biology 2019 20:299
    Content type: Research Published on:

  14. Untangling the complex variations of microbiome associated with large-scale host phenotypes or environment types challenges the currently available analytic methods. Here, we present tmap, an integrative framewor...

    Authors: Tianhua Liao, Yuchen Wei, Mingjing Luo, Guo-Ping Zhao and Haokui Zhou
    Citation: Genome Biology 2019 20:293
    Content type: Method Published on:

  15. Although it is assumed that contamination in bacterial whole-genome sequencing causes errors, the influences of contamination on clustering analyses, such as single-nucleotide polymorphism discovery, phylogene...

    Authors: Arthur W. Pightling, James B. Pettengill, Yu Wang, Hugh Rand and Errol Strain
    Citation: Genome Biology 2019 20:286
    Content type: Short Report Published on:

  16. The early-life microbiota exerts a profound and lifelong impact on host health. Longitudinal studies in humans have been informative but are mostly based on the analysis of fecal samples and cannot shed direct...

    Authors: Hongbin Liu, Xiangfang Zeng, Guolong Zhang, Chengli Hou, Ning Li, Haitao Yu, Lijun Shang, Xiaoya Zhang, Paolo Trevisi, Feiyun Yang, Zuohua Liu and Shiyan Qiao
    Citation: BMC Biology 2019 17:106
    Content type: Research article Published on:

  17. High-throughput DNA sequencing enables large-scale metagenomic analyses of complex biological systems. Such analyses are not restricted to present-day samples and can also be applied to molecular data from arc...

    Authors: Ron Hübler, Felix M. Key, Christina Warinner, Kirsten I. Bos, Johannes Krause and Alexander Herbig
    Citation: Genome Biology 2019 20:280
    Content type: Method Published on:

  18. Management of blood cholesterol is a major focus of efforts to prevent cardiovascular diseases. The objective of this study was to investigate how the gut microbiota affects host cholesterol homeostasis at the...

    Authors: Tiphaine Le Roy, Emelyne Lécuyer, Benoit Chassaing, Moez Rhimi, Marie Lhomme, Samira Boudebbouze, Farid Ichou, Júlia Haro Barceló, Thierry Huby, Maryse Guerin, Philippe Giral, Emmanuelle Maguin, Nathalie Kapel, Philippe Gérard, Karine Clément and Philippe Lesnik
    Citation: BMC Biology 2019 17:94
    Content type: Research article Published on:

  19. Recent metagenomic analyses have revealed dysbiosis of the gut microbiota of ulcerative colitis (UC) patients. However, the impacts of this dysbiosis are not fully understood, particularly at the strain level.

    Authors: Jun Seishima, Noriho Iida, Kazuya Kitamura, Masahiro Yutani, Ziyu Wang, Akihiro Seki, Taro Yamashita, Yoshio Sakai, Masao Honda, Tatsuya Yamashita, Takashi Kagaya, Yukihiro Shirota, Yukako Fujinaga, Eishiro Mizukoshi and Shuichi Kaneko
    Citation: Genome Biology 2019 20:252
    Content type: Research Published on:

  20. The human upper respiratory tract (URT) offers a variety of niches for microbial colonization. Local microbial communities are shaped by the different characteristics of the specific location within the URT, b...

    Authors: Christina Kumpitsch, Kaisa Koskinen, Veronika Schöpf and Christine Moissl-Eichinger
    Citation: BMC Biology 2019 17:87
    Content type: Review Published on:

  21. The MinHash algorithm has proven effective for rapidly estimating the resemblance of two genomes or metagenomes. However, this method cannot reliably estimate the containment of a genome within a metagenome. H...

    Authors: Brian D. Ondov, Gabriel J. Starrett, Anna Sappington, Aleksandra Kostic, Sergey Koren, Christopher B. Buck and Adam M. Phillippy
    Citation: Genome Biology 2019 20:232
    Content type: Method Published on:

  22. The ocean microbiome represents one of the largest microbiomes and produces nearly half of the primary energy on the planet through photosynthesis or chemosynthesis. Using recent advances in marine genomics, w...

    Authors: Yan Wang, Qiang Shi, Pengshuo Yang, Chengxin Zhang, S. M. Mortuza, Zhidong Xue, Kang Ning and Yang Zhang
    Citation: Genome Biology 2019 20:229
    Content type: Research Published on:

  23. Hispanics living in the USA may have unrecognized potential birthplace and lifestyle influences on the gut microbiome. We report a cross-sectional analysis of 1674 participants from four centers of the Hispani...

    Authors: Robert C. Kaplan, Zheng Wang, Mykhaylo Usyk, Daniela Sotres-Alvarez, Martha L. Daviglus, Neil Schneiderman, Gregory A. Talavera, Marc D. Gellman, Bharat Thyagarajan, Jee-Young Moon, Yoshiki Vázquez-Baeza, Daniel McDonald, Jessica S. Williams-Nguyen, Michael C. Wu, Kari E. North, Justin Shaffer…
    Citation: Genome Biology 2019 20:219
    Content type: Research Published on:

    The Author Correction to this article has been published in Genome Biology 2020 21:50

  24. As metagenomic studies move to increasing numbers of samples, communities like the human gut may benefit more from the assembly of abundant microbes in many samples, rather than the exhaustive assembly of fewe...

    Authors: Jon G. Sanders, Sergey Nurk, Rodolfo A. Salido, Jeremiah Minich, Zhenjiang Z. Xu, Qiyun Zhu, Cameron Martino, Marcus Fedarko, Timothy D. Arthur, Feng Chen, Brigid S. Boland, Greg C. Humphrey, Caitriona Brennan, Karenina Sanders, James Gaffney, Kristen Jepsen…
    Citation: Genome Biology 2019 20:226
    Content type: Method Published on:

  25. The human gut harbors a complex ecosystem of microorganisms, including bacteria and viruses. With the rise of next-generation sequencing technologies, we have seen a quantum leap in the study of human-gut-inha...

    Authors: Sanzhima Garmaeva, Trishla Sinha, Alexander Kurilshikov, Jingyuan Fu, Cisca Wijmenga and Alexandra Zhernakova
    Citation: BMC Biology 2019 17:84
    Content type: Review Published on:

  27. Soils are a key component of agricultural productivity, and soil microbiota determine the availability of many essential plant nutrients. Agricultural domestication of soils, that is, the conversion of previou...

    Authors: Joseph Edwards, Christian Santos-Medellín, Bao Nguyen, John Kilmer, Zachary Liechty, Esteban Veliz, Jiadong Ni, Gregory Phillips and Venkatesan Sundaresan
    Citation: Genome Biology 2019 20:221
    Content type: Research Published on:

  28. Current-day metagenomics analyses increasingly involve de novo taxonomic classification of long DNA sequences and metagenome-assembled genomes. Here, we show that the conventional best-hit approach often leads...

    Authors: F. A. Bastiaan von Meijenfeldt, Ksenia Arkhipova, Diego D. Cambuy, Felipe H. Coutinho and Bas E. Dutilh
    Citation: Genome Biology 2019 20:217
    Content type: Method Published on:

  30. Comparative data from non-human primates provide insight into the processes that shaped the evolution of the human gut microbiome and highlight microbiome traits that differentiate humans from other primates. ...

    Authors: Katherine R. Amato, Elizabeth K. Mallott, Daniel McDonald, Nathaniel J. Dominy, Tony Goldberg, Joanna E. Lambert, Larissa Swedell, Jessica L. Metcalf, Andres Gomez, Gillian A. O. Britton, Rebecca M. Stumpf, Steven R. Leigh and Rob Knight
    Citation: Genome Biology 2019 20:201
    Content type: Research Published on:

  31. The selection pressure exercised by antibiotic drugs is an important consideration for the wise stewardship of antimicrobial treatment programs. Treatment decisions are currently based on crude assumptions, an...

    Authors: Matthias Willmann, Maria J. G. T. Vehreschild, Lena M. Biehl, Wichard Vogel, Daniela Dörfel, Axel Hamprecht, Harald Seifert, Ingo B. Autenrieth and Silke Peter
    Citation: BMC Biology 2019 17:76
    Content type: Research article Published on:

  34. 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
    Content type: Method Published on:

  35. 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
    Content type: Research Published on:

  37. 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
    Content type: Research article Published on:

  38. We develop a metagenomic data analysis pipeline, MicroPro, that takes into account all reads from known and unknown microbial organisms and associates viruses with complex diseases. We utilize MicroPro to anal...

    Authors: Zifan Zhu, Jie Ren, Sonia Michail and Fengzhu Sun
    Citation: Genome Biology 2019 20:154
    Content type: Software Published on:

    The Correction to this article has been published in Genome Biology 2019 20:214

  39. 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
    Content type: Method Published on:

  42. 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
    Content type: Comment Published on:

  43. 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
    Content type: Research article Published on:

  44. 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
    Content type: Research article Published on:

  46. 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
    Content type: Short Report Published on:

  47. 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
    Content type: Research article Published on: