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Clinical insights into the human microbiome

Guest editor: Dr Omry Koren

The human microbiome is responsible for a host of functions that influence the body in both health and disease. Its roles are being thoroughly explored in several fields of research, highlighting the strong interdependence between the microbiota and humans. There is growing consensus that the microbiome is a major player in the immune system, and also determines the control of the body at multiple levels. A number of diseases and immune reactions are now believed to be closely linked to how the microbial balance changes throughout a person’s life.

In this article collection we explore the most recent and exciting findings on how the microbiome shapes our body responses and affects treatment.

Examples of featured topics include the gut brain axis, the role of microbiome in treatment outcomes, immune response and microbiome diversity and the effect of antibiotics in children.

If you have any presubmission queries about this article collection, please email us at

  1. Research article

    Exposure to bacterial products lipopolysaccharide and flagellin and hepatocellular carcinoma: a nested case-control study

    Leakage of bacterial products across the gut barrier may play a role in liver diseases which often precede the development of liver cancer. However, human studies, particularly from prospective settings, are l...

    Veronika Fedirko, Hao Quang Tran, Andrew T. Gewirtz, Magdalena Stepien, Antonia Trichopoulou, Krasimira Aleksandrova, Anja Olsen, Anne Tjønneland, Kim Overvad, Franck Carbonnel, Marie-Christine Boutron-Ruault, Gianluca Severi, Tilman Kühn, Rudolf Kaaks, Heiner Boeing, Christina Bamia…

    BMC Medicine 2017 15:72

    Published on: 4 April 2017

  2. Commentary

    Ethical issues in microbiome research and medicine

    The human microbiome is the collection of bacteria, viruses, and fungi that live on and in the human organism’s skin, mucosa, and intestinal tract. Re-examining commonly accepted ethical standards from the per...

    Rosamond Rhodes

    BMC Medicine 2016 14:156

    Published on: 12 October 2016

  3. Research article

    Long-term effects on luminal and mucosal microbiota and commonly acquired taxa in faecal microbiota transplantation for recurrent Clostridium difficile infection

    Faecal microbiota transplantation (FMT) is an effective treatment for recurrent Clostridium difficile infection (rCDI). It restores the disrupted intestinal microbiota and subsequently suppresses C. difficile. Th...

    Jonna Jalanka, Eero Mattila, Hanne Jouhten, Jorn Hartman, Willem M. de Vos, Perttu Arkkila and Reetta Satokari

    BMC Medicine 2016 14:155

    Published on: 11 October 2016

  4. Research article

    Oral, frozen fecal microbiota transplant (FMT) capsules for recurrent Clostridium difficile infection

    Fecal microbiota transplantation (FMT) has been shown to be safe and effective in treating refractory or relapsing C. difficile infection (CDI), but its use has been limited by practical barriers. We recently rep...

    Ilan Youngster, Jasmin Mahabamunuge, Hannah K. Systrom, Jenny Sauk, Hamed Khalili, Joanne Levin, Jess L. Kaplan and Elizabeth L. Hohmann

    BMC Medicine 2016 14:134

    Published on: 9 September 2016

  5. Opinion

    Antibiotic use during pregnancy: how bad is it?

    Our microbial companions (the “microbiota”) are extremely important for the preservation of human health. Although changes in bacterial communities (dysbiosis) are commonly associated with disease, such change...

    Amir A. Kuperman and Omry Koren

    BMC Medicine 2016 14:91

    Published on: 17 June 2016

  6. Minireview

    The gut microbiome in human immunodeficiency virus infection

    HIV/AIDS causes severe dysfunction of the immune system through CD4+ T cell depletion, leading to dysregulation of both the adaptive and innate immune arms. A primary target for viral infection is the gastroin...

    Gili Zilberman-Schapira, Niv Zmora, Shlomik Itav, Stavros Bashiardes, Hila Elinav and Eran Elinav

    BMC Medicine 2016 14:83

    Published on: 3 June 2016

  7. Commentary

    Probiotics and microbiota composition

    Accumulated evidence, corroborated by a new systematic review by Kristensen et al. (Genome Med 8:52, 2016), suggests that probiotics do not significantly impact the fecal microbiota composition of healthy subj...

    Mary Ellen Sanders

    BMC Medicine 2016 14:82

    Published on: 2 June 2016

  8. Commentary

    Policing of gut microbiota by the adaptive immune system

    The intestinal microbiota is a large and diverse microbial community that inhabits the intestine, containing about 100 trillion bacteria of 500-1000 distinct species that, collectively, provide benefits to the...

    Laurent Dollé, Hao Q. Tran, Lucie Etienne-Mesmin and Benoit Chassaing

    BMC Medicine 2016 14:27

    Published on: 12 February 2016