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

Abstract

<b>Background:</b> 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 <i>Bacteroides</i> species, the most prevalent anaerobic bacteria in the lower intestinal tract. Microbes of the genus <i>Bacteroides</i> make up ~25% of the total gut microbiome. <i>Bacteroides fragilis</i> comprises only 2% of the total <i>Bacteroides</i> in the gut, yet causes of >70% of <i>Bacteroides</i> 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. <b>Results:</b> Clustered regularly interspaced short palindromic repeats (CRISPR) elements in all strains of <i>B. fragilis</i> (<i>n</i> = 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 <i>cas1</i> 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 <i>cas</i> genes present in most of the isolates; these CRISPRs were found immediately upstream of a <i>hipA/hipB</i> 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 <i>B. fragilis</i> did not have Type IIC CRISPR-Cas systems and had atypical Type IIIB CRISPR-Cas systems that were lacking adjacent <i>cas</i> genes. <b>Conclusions:</b> This is the first systematic report of CRISPR-Cas systems in a wide range of <i>B. fragilis</i> strains from a variety of sources. There are four apparent CRISPR-Cas systems in <i>B. fragilis</i>-three systems have adjacent <i>cas</i> genes. Understanding CRISPR/Cas function in <i>B. fragilis</i> 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 <i>B. fragilis</i> be viewed a separate subgroup.