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Microorganisms
Volume 8
Issue 11
10.3390/microorganisms8111663
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Article

Ecological Structuring of Temperate Bacteriophages in the Inflammatory Bowel Disease-Affected Gut

by
Hiroki Nishiyama
1,
Hisashi Endo
1,
Romain Blanc-Mathieu
2 and
Hiroyuki Ogata
1,*
1
Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji 611-0011, Japan
2
Laboratoire de Physiologie Cellulaire & Végétale, CEA, CNRS, INRA, IRIG, Université Grenoble Alpes, 38000 Grenoble, France
*
Author to whom correspondence should be addressed.
Microorganisms 2020, 8(11), 1663; https://doi.org/10.3390/microorganisms8111663
Received: 30 September 2020 / Revised: 23 October 2020 / Accepted: 23 October 2020 / Published: 27 October 2020
(This article belongs to the Section Gut Microbiota)
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Abstract

The aim of this study was to elucidate the ecological structure of the human gut temperate bacteriophage community and its role in inflammatory bowel disease (IBD). Temperate bacteriophages make up a large proportion of the human gut microbiota and are likely to play a role in IBD pathogenesis. However, many of these bacteriophages await characterization in reference databases. Therefore, we conducted a large-scale reconstruction of temperate bacteriophage and bacterial genomes from the whole-metagenome sequence data generated by the IBD Multi’omics Database project. By associating phages with their hosts via genome comparisons, we found that temperate bacteriophages infect a phylogenetically wide range of bacteria. The majority of variance in bacteriophage community composition was explained by variation among individuals, but differences in the abundance of temperate bacteriophages were identified between IBD and non-IBD patients. Of note, in active ulcerative colitis patients, temperate bacteriophages infecting Bacteroides uniformis and Bacteroides thetaiotaomicron—two species experimentally proven to be beneficial to gut homeostasis—were over-represented, whereas their hosts were under-represented in comparison with non-IBD patients. Supporting the mounting evidence that gut viral community plays a vital role in IBD, our results show potential association between temperate bacteriophages and IBD pathogenesis. View Full-Text
Keywords: temperate bacteriophage; inflammatory bowel disease; ulcerative colitis; Crohn’s disease; gut microbiota temperate bacteriophage; inflammatory bowel disease; ulcerative colitis; Crohn’s disease; gut microbiota
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MDPI and ACS Style

Nishiyama, H.; Endo, H.; Blanc-Mathieu, R.; Ogata, H. Ecological Structuring of Temperate Bacteriophages in the Inflammatory Bowel Disease-Affected Gut. Microorganisms 2020, 8, 1663. https://doi.org/10.3390/microorganisms8111663

AMA Style

Nishiyama H, Endo H, Blanc-Mathieu R, Ogata H. Ecological Structuring of Temperate Bacteriophages in the Inflammatory Bowel Disease-Affected Gut. Microorganisms. 2020; 8(11):1663. https://doi.org/10.3390/microorganisms8111663

Chicago/Turabian Style

Nishiyama, Hiroki, Hisashi Endo, Romain Blanc-Mathieu, and Hiroyuki Ogata. 2020. "Ecological Structuring of Temperate Bacteriophages in the Inflammatory Bowel Disease-Affected Gut" Microorganisms 8, no. 11: 1663. https://doi.org/10.3390/microorganisms8111663

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