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Gut. 2017 Jun;66(6):1039-1048. doi: 10.1136/gutjnl-2015-310746. Epub 2016 Feb 3.

Fungal microbiota dysbiosis in IBD.

Author information

1
Sorbonne University-UPMC Univ Paris 06, INSERM ERL 1157, Avenir Team Gut Microbiota and Immunity, UMR 7203, Saint-Antoine Hospital, AP-HP, UPMC Univ Paris 06, Paris, France.
2
Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France.
3
Department of Gastroenterology, Saint Antoine Hospital, Paris, France.
4
Inflammation-Immunopathology-Biotherapy Department (DHU i2B), Paris, France.
5
Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, USA.
6
ILTOO Pharma, iPEPS ICM, Hôpital Pitié Salpêtrière, Paris, France.
7
Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy.
8
Division of Infectious Diseases, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA.
9
Massachusetts Technology and Analytics, Brookline, Massachusetts, USA.

Abstract

OBJECTIVE:

The bacterial intestinal microbiota plays major roles in human physiology and IBDs. Although some data suggest a role of the fungal microbiota in IBD pathogenesis, the available data are scarce. The aim of our study was to characterise the faecal fungal microbiota in patients with IBD.

DESIGN:

Bacterial and fungal composition of the faecal microbiota of 235 patients with IBD and 38 healthy subjects (HS) was determined using 16S and ITS2 sequencing, respectively. The obtained sequences were analysed using the Qiime pipeline to assess composition and diversity. Bacterial and fungal taxa associated with clinical parameters were identified using multivariate association with linear models. Correlation between bacterial and fungal microbiota was investigated using Spearman's test and distance correlation.

RESULTS:

We observed that fungal microbiota is skewed in IBD, with an increased Basidiomycota/Ascomycota ratio, a decreased proportion of Saccharomyces cerevisiae and an increased proportion of Candida albicans compared with HS. We also identified disease-specific alterations in diversity, indicating that a Crohn's disease-specific gut environment may favour fungi at the expense of bacteria. The concomitant analysis of bacterial and fungal microbiota showed a dense and homogenous correlation network in HS but a dramatically unbalanced network in IBD, suggesting the existence of disease-specific inter-kingdom alterations.

CONCLUSIONS:

Besides bacterial dysbiosis, our study identifies a distinct fungal microbiota dysbiosis in IBD characterised by alterations in biodiversity and composition. Moreover, we unravel here disease-specific inter-kingdom network alterations in IBD, suggesting that, beyond bacteria, fungi might also play a role in IBD pathogenesis.

KEYWORDS:

INFLAMMATORY BOWEL DISEASE

PMID:
26843508
PMCID:
PMC5532459
DOI:
10.1136/gutjnl-2015-310746
[Indexed for MEDLINE]
Free PMC Article

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