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=8

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=<p><bold>Background:</bold> 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 <italic>Bacteroides</italic> species, the most prevalent anaerobic bacteria in the lower intestinal tract. Microbes of the genus <italic>Bacteroides</italic> make up ~25% of the total gut microbiome. <italic>Bacteroides fragilis</italic> comprises only 2% of the total <italic>Bacteroides</italic> in the gut, yet causes of &gt;70% of <italic>Bacteroides</italic> 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.</p><p><bold>Results:</bold> Clustered regularly interspaced short palindromic repeats (CRISPR) elements in all strains of <italic>B. fragilis</italic> (<italic>n</italic> = 109) with publically available genomes were identified. Three different CRISPR-Cas types, corresponding most closely 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 <italic>cas1</italic> 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 <italic>cas</italic> genes present in most of the isolates; these CRISPRs were found immediately upstream of a <italic>hipA/hipB</italic> operon and we speculate that this element may be involved in regulation of this operon related to formation of persister cells during antimicrobial exposure. Also, blood isolates of <italic>B. fragilis</italic> did not have Type IIC CRISPR-Cas systems and had atypical Type IIIB CRISPR-Cas systems that were lacking adjacent <italic>cas</italic> genes.</p><p><bold>Conclusions:</bold> This is the first systematic report of CRISPR-Cas systems in a wide range of <italic>B. fragilis</italic> strains from a variety of sources. There are four apparent CRISPR-Cas systems in <italic>B. fragilis</italic>—three systems have adjacent <italic>cas</italic> genes. Understanding CRISPR/Cas function in <italic>B. fragilis</italic> 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 <italic>B. fragilis</italic> be viewed a separate subgroup.</p>