Extensive mobilome-driven genome diversification in mouse gut-associated Bacteroides vulgatus mpk

Abstract

Likemany other Bacteroides species, Bacteroides vulgatus strain mpk, amouse 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 genomeof 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 themost 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 beenextensively altered by differentmobilization events. ACRISPR/Cas system couldbe identified that provides apossiblemechanism 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 variousmobilization eventsmight 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.