title: Extensive Mobilome-Driven Genome Diversification in Mouse Gut-Associated Bacteroides vulgatus mpk.
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.
authors.affiliation: Interfacultary Institute for Microbiology and Infection Medicine, Department for Medical Microbiology and Hygiene, University of Tübingen, Tübingen, Germany.
authors.forename: Anna
authors.initials: A
authors.lastname: Lange
authors.affiliation: Algorithms in Bioinformatics, ZBIT Center for Bioinformatics, University of Tübingen, Tübingen, Germany.
authors.forename: Sina
authors.initials: S
authors.lastname: Beier
authors.affiliation: Interfacultary Institute for Microbiology and Infection Medicine, Department for Medical Microbiology and Hygiene, University of Tübingen, Tübingen, Germany.
authors.forename: Alex
authors.initials: A
authors.lastname: Steimle
authors.affiliation: Interfacultary Institute for Microbiology and Infection Medicine, Department for Medical Microbiology and Hygiene, University of Tübingen, Tübingen, Germany.
authors.forename: Ingo B
authors.initials: IB
authors.lastname: Autenrieth
authors.affiliation: Algorithms in Bioinformatics, ZBIT Center for Bioinformatics, University of Tübingen, Tübingen, Germany julia-stefanie.frick@med.uni-tuebingen.de daniel.huson@uni-tuebingen.de.
authors.forename: Daniel H
authors.initials: DH
authors.lastname: Huson
authors.affiliation: 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.
authors.forename: Julia-Stefanie
authors.initials: JS
authors.lastname: Frick
mesh_terms: D000818:Animals; D001439:Bacteroides / Q000235:genetics*; D001483:Base Sequence; D064113:CRISPR-Cas Systems; D004269:DNA, Bacterial / Q000235:genetics; D019143:Evolution, Molecular; D022761:Gene Transfer, Horizontal; D016680:Genome, Bacterial; D007422:Intestines / Q000382:microbiology; D051379:Mice / Q000382:microbiology*; D010802:Phylogeny
chemical_list: D004269:DNA, Bacterial
keywords: Bacteroides vulgatus; CRISPR/Cas; genome plasticity; horizontal gene transfer; mobile elements