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Genome Biol Evol. 2016 Apr 25;8(4):1197-207. doi: 10.1093/gbe/evw070.

Extensive Mobilome-Driven Genome Diversification in Mouse Gut-Associated Bacteroides vulgatus mpk.

Author information

1
Interfacultary Institute for Microbiology and Infection Medicine, Department for Medical Microbiology and Hygiene, University of Tübingen, Tübingen, Germany.
2
Algorithms in Bioinformatics, ZBIT Center for Bioinformatics, University of Tübingen, Tübingen, Germany.
3
Algorithms in Bioinformatics, ZBIT Center for Bioinformatics, University of Tübingen, Tübingen, Germany julia-stefanie.frick@med.uni-tuebingen.de daniel.huson@uni-tuebingen.de.
4
Interfacultary Institute for Microbiology and Infection Medicine, Department for Medical Microbiology and Hygiene, University of Tübingen, Tübingen, Germany julia-stefanie.frick@med.uni-tuebingen.de daniel.huson@uni-tuebingen.de.

Abstract

Like many other Bacteroides species, Bacteroides vulgatus strain mpk, a mouse fecal isolate which was shown to promote intestinal homeostasis, utilizes a variety of mobile elements for genome evolution. Based on sequences collected by Pacific Biosciences SMRT sequencing technology, we discuss the challenges of assembling and studying a bacterial genome of high plasticity. Additionally, we conducted comparative genomics comparing this commensal strain with the B. vulgatus type strain ATCC 8482 as well as multiple other Bacteroides and Parabacteroides strains to reveal the most important differences and identify the unique features of B. vulgatus mpk. The genome of B. vulgatus mpk harbors a large and diverse set of mobile element proteins compared with other sequenced Bacteroides strains. We found evidence of a number of different horizontal gene transfer events and a genome landscape that has been extensively altered by different mobilization events. A CRISPR/Cas system could be identified that provides a possible mechanism for preventing the integration of invading external DNA. We propose that the high genome plasticity and the introduced genome instabilities of B. vulgatus mpk arising from the various mobilization events might play an important role not only in its adaptation to the challenging intestinal environment in general, but also in its ability to interact with the gut microbiota.

KEYWORDS:

Bacteroides vulgatus; CRISPR/Cas; genome plasticity; horizontal gene transfer; mobile elements

PMID:
27071651
PMCID:
PMC4860699
DOI:
10.1093/gbe/evw070
[Indexed for MEDLINE]
Free PMC Article

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