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Translating the microbiome: health and disease

 Guest editor: Curtis Huttenhower

The era of metagenomics for the characterisation of microbiota has led to a surge in surprising associations of the human microbiome with disease states. However, much remains unknown about what defines a normal microbiome and how perturbation predisposes to disease. To capture the advances in this emerging area, Genome Medicine is pleased to present a special issue focused on Translating the microbiome: health and disease.

This collection of articles has not been sponsored and articles have undergone the journal’s standard peer-review process. The Guest editor declares no competing interests.

  1. Research

    Microbiomic differences in tumor and paired-normal tissue in head and neck squamous cell carcinomas

    While the role of the gut microbiome in inflammation and colorectal cancers has received much recent attention, there are few data to support an association between the oral microbiome and head and neck squamo...

    Hannah Wang, Pauline Funchain, Gurkan Bebek, Jessica Altemus, Huan Zhang, Farshad Niazi, Charissa Peterson, Walter T. Lee, Brian B. Burkey and Charis Eng

    Genome Medicine 2017 9:14

    Published on: 7 February 2017

  2. Research

    Potential contribution of the uterine microbiome in the development of endometrial cancer

    Endometrial cancer studies have led to a number of well-defined but mechanistically unconnected genetic and environmental risk factors. One of the emerging modulators between environmental triggers and genetic...

    Marina R. S. Walther-António, Jun Chen, Francesco Multinu, Alexis Hokenstad, Tammy J. Distad, E. Heidi Cheek, Gary L. Keeney, Douglas J. Creedon, Heidi Nelson, Andrea Mariani and Nicholas Chia

    Genome Medicine 2016 8:122

    Published on: 25 November 2016

  3. Research

    Altered gut microbiota in female mice with persistent low body weights following removal of post-weaning chronic dietary restriction

    Nutritional interventions often fail to prevent growth failure in childhood and adolescent malnutrition and the mechanisms remain unclear. Recent studies revealed altered microbiota in malnourished children an...

    Jun Chen, Yoshitaka Toyomasu, Yujiro Hayashi, David R. Linden, Joseph H. Szurszewski, Heidi Nelson, Gianrico Farrugia, Purna C. Kashyap, Nicholas Chia and Tamas Ordog

    Genome Medicine 2016 8:103

    Published on: 3 October 2016

  4. Research

    The early infant gut microbiome varies in association with a maternal high-fat diet

    Emerging evidence suggests that the in utero environment is not sterile as once presumed. Work in the mouse demonstrated transmission of commensal bacteria from mother to fetus during gestation, though it is uncl...

    Derrick M. Chu, Kathleen M. Antony, Jun Ma, Amanda L. Prince, Lori Showalter, Michelle Moller and Kjersti M. Aagaard

    Genome Medicine 2016 8:77

    Published on: 9 August 2016

  5. Research

    Dysbiosis, inflammation, and response to treatment: a longitudinal study of pediatric subjects with newly diagnosed inflammatory bowel disease

    Gut microbiome dysbiosis has been demonstrated in subjects with newly diagnosed and chronic inflammatory bowel disease (IBD). In this study we sought to explore longitudinal changes in dysbiosis and ascertain ...

    Kelly A. Shaw, Madeline Bertha, Tatyana Hofmekler, Pankaj Chopra, Tommi Vatanen, Abhiram Srivatsa, Jarod Prince, Archana Kumar, Cary Sauer, Michael E. Zwick, Glen A. Satten, Aleksandar D. Kostic, Jennifer G. Mulle, Ramnik J. Xavier and Subra Kugathasan

    Genome Medicine 2016 8:75

    Published on: 13 July 2016

  6. Research

    Capturing the diversity of the human gut microbiota through culture-enriched molecular profiling

    The human gut microbiota has been implicated in most aspects of health and disease; however, most of the bacteria in this community are considered unculturable, so studies have relied on molecular-based method...

    Jennifer T. Lau, Fiona J. Whelan, Isiri Herath, Christine H. Lee, Stephen M. Collins, Premysl Bercik and Michael G. Surette

    Genome Medicine 2016 8:72

    Published on: 1 July 2016

  7. Research

    Roux-en-Y gastric bypass surgery of morbidly obese patients induces swift and persistent changes of the individual gut microbiota

    Roux-en-Y gastric bypass (RYGB) is an effective means to achieve sustained weight loss for morbidly obese individuals. Besides rapid weight reduction, patients achieve major improvements of insulin sensitivity...

    Albert Palleja, Alireza Kashani, Kristine H. Allin, Trine Nielsen, Chenchen Zhang, Yin Li, Thorsten Brach, Suisha Liang, Qiang Feng, Nils Bruun Jørgensen, Kirstine N. Bojsen-Møller, Carsten Dirksen, Kristoffer S. Burgdorf, Jens J. Holst, Sten Madsbad, Jun Wang…

    Genome Medicine 2016 8:67

    Published on: 15 June 2016

  8. METHOD

    An adaptive association test for microbiome data

    There is increasing interest in investigating how the compositions of microbial communities are associated with human health and disease. Although existing methods have identified many associations, a proper c...

    Chong Wu, Jun Chen, Junghi Kim and Wei Pan

    Genome Medicine 2016 8:56

    Published on: 19 May 2016

  9. Research

    Alterations in fecal microbiota composition by probiotic supplementation in healthy adults: a systematic review of randomized controlled trials

    The effects of probiotic supplementation on fecal microbiota composition in healthy adults have not been well established. We aimed to provide a systematic review of the potential evidence for an effect of pro...

    Nadja B. Kristensen, Thomas Bryrup, Kristine H. Allin, Trine Nielsen, Tue H. Hansen and Oluf Pedersen

    Genome Medicine 2016 8:52

    Published on: 10 May 2016

  10. Research

    Pretreatment gut microbiome predicts chemotherapy-related bloodstream infection

    Bacteremia, or bloodstream infection (BSI), is a leading cause of death among patients with certain types of cancer. A previous study reported that intestinal domination, defined as occupation of at least 30 %...

    Emmanuel Montassier, Gabriel A. Al-Ghalith, Tonya Ward, Stephane Corvec, Thomas Gastinne, Gilles Potel, Philippe Moreau, Marie France de la Cochetiere, Eric Batard and Dan Knights

    Genome Medicine 2016 8:49

    Published on: 28 April 2016

    The Erratum to this article has been published in Genome Medicine 2016 8:61

  11. Research

    Antibiotic perturbation of the murine gut microbiome enhances the adiposity, insulin resistance, and liver disease associated with high-fat diet

    Obesity, type 2 diabetes, and non-alcoholic fatty liver disease (NAFLD) are serious health concerns, especially in Western populations. Antibiotic exposure and high-fat diet (HFD) are important and modifiable ...

    Douglas Mahana, Chad M. Trent, Zachary D. Kurtz, Nicholas A. Bokulich, Thomas Battaglia, Jennifer Chung, Christian L. Müller, Huilin Li, Richard A. Bonneau and Martin J. Blaser

    Genome Medicine 2016 8:48

    Published on: 27 April 2016

  12. Review

    The healthy human microbiome

    Humans are virtually identical in their genetic makeup, yet the small differences in our DNA give rise to tremendous phenotypic diversity across the human population. By contrast, the metagenome of the human m...

    Jason Lloyd-Price, Galeb Abu-Ali and Curtis Huttenhower

    Genome Medicine 2016 8:51

    Published on: 27 April 2016

  13. Research

    The influence of a short-term gluten-free diet on the human gut microbiome

    A gluten-free diet (GFD) is the most commonly adopted special diet worldwide. It is an effective treatment for coeliac disease and is also often followed by individuals to alleviate gastrointestinal complaints...

    Marc Jan Bonder, Ettje F. Tigchelaar, Xianghang Cai, Gosia Trynka, Maria C. Cenit, Barbara Hrdlickova, Huanzi Zhong, Tommi Vatanen, Dirk Gevers, Cisca Wijmenga, Yang Wang and Alexandra Zhernakova

    Genome Medicine 2016 8:45

    Published on: 21 April 2016

  14. Research

    Ultra-deep and quantitative saliva proteome reveals dynamics of the oral microbiome

    The oral cavity is home to one of the most diverse microbial communities of the human body and a major entry portal for pathogens. Its homeostasis is maintained by saliva, which fulfills key functions includin...

    Niklas Grassl, Nils Alexander Kulak, Garwin Pichler, Philipp Emanuel Geyer, Jette Jung, Sören Schubert, Pavel Sinitcyn, Juergen Cox and Matthias Mann

    Genome Medicine 2016 8:44

    Published on: 21 April 2016

  15. Research

    An expansion of rare lineage intestinal microbes characterizes rheumatoid arthritis

    The adaptive immune response in rheumatoid arthritis (RA) is influenced by an interaction between host genetics and environment, particularly the host microbiome. Association of the gut microbiota with various...

    Jun Chen, Kerry Wright, John M. Davis, Patricio Jeraldo, Eric V. Marietta, Joseph Murray, Heidi Nelson, Eric L. Matteson and Veena Taneja

    Genome Medicine 2016 8:43

    Published on: 21 April 2016

  16. Review

    Impact of the gut microbiota on inflammation, obesity, and metabolic disease

    The human gut harbors more than 100 trillion microbial cells, which have an essential role in human metabolic regulation via their symbiotic interactions with the host. Altered gut microbial ecosystems have be...

    Claire L. Boulangé, Ana Luisa Neves, Julien Chilloux, Jeremy K. Nicholson and Marc-Emmanuel Dumas

    Genome Medicine 2016 8:42

    Published on: 20 April 2016

  17. Review

    Microbiome mediation of infections in the cancer setting

    Infections encountered in the cancer setting may arise from intensive cancer treatments or may result from the cancer itself, leading to risk of infections through immune compromise, disruption of anatomic bar...

    Ying Taur and Eric G. Pamer

    Genome Medicine 2016 8:40

    Published on: 18 April 2016

  18. Comment

    Mood by microbe: towards clinical translation

    There is a growing realization that the gut–brain axis plays a key role in maintaining brain health and the stress response. Recently, the gut microbiota has emerged as a master regulator of this axis. Thus, o...

    Timothy G. Dinan and John F. Cryan

    Genome Medicine 2016 8:36

    Published on: 6 April 2016

  19. Comment

    Translating the vaginal microbiome: gaps and challenges

    Management, manipulation, and restoration of a robust vaginal microbiota has the potential to vastly improve women’s health and disease prevention. However, a systems level understanding of how the vaginal mic...

    Jacques Ravel and Rebecca M. Brotman

    Genome Medicine 2016 8:35

    Published on: 1 April 2016

  20. Research

    Signatures of early frailty in the gut microbiota

    Frailty is arguably the biggest problem associated with population ageing, and associates with gut microbiome composition in elderly and care-dependent individuals. Here we characterize frailty associations wi...

    Matthew A. Jackson, Ian B. Jeffery, Michelle Beaumont, Jordana T. Bell, Andrew G. Clark, Ruth E. Ley, Paul W. O’Toole, Tim D. Spector and Claire J. Steves

    Genome Medicine 2016 8:8

    Published on: 29 January 2016

    The Erratum to this article has been published in Genome Medicine 2016 8:21

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