Characterizing a Novel Toxin in Interbacterial Competition Among B. fragilis

Bacteroides fragilis is a gram-negative intestinal commensal that comprises up to 1% of total gut bacteria. While often considered harmless, this microbe remains a leading cause of anaerobic sepsis and abdominopelvic infections. The rise of antimicrobial resistance (AMR) in B. fragilis clinical isolates has complicated treatment of these infections. In particular, a distinct clade of B. fragilis strains (clade II) that represent 10% of B. fragilis from human clinical isolates were found to harbor cfiA, a genomically encoded metallo-β-lactamase. Carbapenem resistance in these strains is concerning not only due to the lack of available treatment options but also the risk of transmission to other microbes. Recent studies have also identified differences in average nucleotide identity between clade II and clade I—the remaining 90% of B. fragilis. This suggests that these clades might actually represent two different species, and thus, biology of clade II cannot simply be assumed from clade I. As all B. fragilis niche acquisition studies to date have utilized clade I strains, the mechanisms by which a clade II strain comes to dominate and persist within the colonic niche remain unknown. Previous microbiome studies in adults have revealed predominance of a single B. fragilis strain within an individual microbiota. Interestingly, no studies have identified a single host to harbor both clade I and clade II simultaneously, suggesting that intraspecific competition between clade I and clade II may influence niche establishment and strain dominance. Further studies are thus necessary to identify factors unique to clade II biology, as long-term colonization by these strains may engender a reservoir for carbapenem resistance within the host. Recent work has identified Bcf1 as a novel secreted toxin that is utilized by clade II in the context of interbacterial competition against clade I. This method of antagonism is dependent on an interaction with Bat1—a confirmed functional target of Bcf1 and a putative TonB-dependent transporter. Orthologs of Bcf1 can be found throughout Bacteroides spp., suggesting that this may be a novel family of toxins. However, the mechanism of Bcf1 activity remains unknown and all functional studies to date have only been conducted in vitro. The proposed studies will provide mechanistic insight into Bcf1 function (Aim 1) and its role in interbacterial competition in vivo (Aim 2). Aim 1 will test the hypothesis that Bcf1 binds to Bat1 and blocks translocation of an unidentified nutrient through Bat1 via a form of nutritional competition. Aim 2 will leverage various animal models to test the hypothesis that Bcf-mediated competition allows clade II to dominate its niche and achieve long-term colonization. These studies will enable us to consider functional links between interbacterial competition and high-level drug resistance from an ecologic perspective. Understanding the inherent differences in intraspecies biology and strain-level competition dynamics may inform the development of microbiome-targeted therapies to prevent colonization of pathogenic B. fragilis strains or translate to future consideration of AMR risk during clinical treatment of B. fragilis infections. Project Number: 1F30AI197460-01 | Fiscal Year: 2026 | NIH Institute/Center: National Institute of Allergy and Infectious Diseases (NIAID) | Principal Investigator: Jesse Pak | Institution: WASHINGTON UNIVERSITY, SAINT LOUIS, MO | Award Amount: $36,673 | Activity Code: F30 | Study Section: Special Emphasis Panel[ZRG1 F07A-W (20)] View on NIH RePORTER: https://reporter.nih.gov/project-details/1F30AI19746001