AUTHOR=Tajkarimi Mehrdad , Wexler Hannah M. 

TITLE=CRISPR-Cas Systems in Bacteroides fragilis, an Important Pathobiont in the Human Gut Microbiome

JOURNAL=Frontiers in Microbiology

VOLUME=Volume 8 - 2017

YEAR=2017

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2017.02234

DOI=10.3389/fmicb.2017.02234

ISSN=1664-302X

ABSTRACT=Background: While CRISPR-Cas systems have been identified in bacteria from a wide variety of ecological niches, there are no studies to describe CRISPR-Cas elements in Bacteroides species, the most prevalent anaerobic bacteria in the lower intestinal tract.  Bacteroides make up ~25% of the total gut microbiome.  B. fragilis comprises only 2% of the total Bacteroides in the gut, yet causes >70% of Bacteroides infections.  The factors causing it to transition from benign resident of the gut microbiome to virulent pathogen are not well understood, but a combination of horizontal gene transfer (HGT) of virulence genes and differential transcription of endogenous genes are clearly involved.  The CRISPR-Cas system is a multi-functional system described in prokaryotes that may be involved in control both of HGT and of gene regulation.  
Results: CRISPR elements in all strains of B. fragilis (n=109) with publically available genomes were identified.   Three different CRISPR-Cas types, corresponding to Type IB, Type IIIB and Type IIC, were identified.  Thirty-five strains had two CRISPR-Cas types, and three strains included all three CRISPR-Cas types in their respective genomes.  The cas1 gene in the Type IIIB system encoded a reverse-transcriptase/Cas1 fusion protein rarely found in prokaryotes.  We identified a short CRISPR (3 DR) with no associated cas genes; these CRISPRs were found immediately upstream of a hipA/hipB operon implicated in other bacteria in formation of persister cells.   Also, blood isolates of B. fragilis did not have Type IIC CRISPR-Cas systems and had atypical Type IIIB CRISPR-Cas systems that were lacking adjacent cas genes.   
Conclusions:  This is the first systematic report of CRISPR-Cas systems in a wide range of B. fragilis strains from a variety of sources.  There are four apparent CRISPR-Cas systems in B. fragilis—three systems have adjacent cas genes.   Understanding CRISPR/Cas function in B. fragilis will elucidate their role in gene expression, DNA repair and ability to survive exposure to antibiotics.  Also, based on their unique CRISPR-Cas arrays, their phylogenetic clustering and their virulence potential, we are proposing that blood isolates of B. fragilis be viewed a separate subgroup.