A model screening pipeline for bile acid converting anti-Clostridioides difficile bacteria reveals unique biotherapeutic potential of Peptacetobacter hiranonis

Abstract

Clostridioides difficile is an antibiotic-resistant bacterium that causes serious, toxin-mediated enteric disease in humans and animals. Gut dysbiosis and resultant alterations in the intestinal bile acid profile play an important role in the pathogenesis of C. difficile infection (CDI). Restoration of the gut microbiota and re-establishment of bacterial bile acid metabolism using fecal microbiota transplantation (FMT) has been established as a promising strategy against this disease, although this method has several limitations. Thus, a more defined and precise microbiota-based approach using bacteria that biotransform primary bile acids into secondary bile acids could effectively overcome these limitations and control CDI. Therefore, a screening pipeline was developed to isolate bile acid converting bacteria from fecal samples. Dogs were selected as a model CDI-resistant microbiota donor for this pipeline, which yielded a novel Peptacetobacter hiranonis strain that possesses unique anti-C. difficile properties, and both bile acid deconjugation and 7-α dehydroxylating activities to perform bile acid conversion. The screening pipeline included a set of in vitro tests along with a precision in vivo gut colonization and bile acid conversion test using altered Schadler flora (ASF) colonized mice. In addition, this pipeline also provided essential information on the growth requirements for screening and cultivating the candidate bacterium, its survival in a CDI predisposing environment, and potential pathogenicity. The model pipeline documented here yielded multiple bile acid converting bacteria, including a P. hiranonis isolate with unique anti-C. difficile biotherapeutic potential, which can be further tested in subsequent preclinical and human clinical trials.

Strain-dependent induction of primary bile acid 7-dehydroxylation by cholic acid

“…The C. scindens ATCC 35704 and VPI 12708 strains show rapid transformation to DCA while E. muris DSM 28560 has more limited activity [19,20,27]. Other known 7-DH-ing strains such as Clostridium hylemonae and Peptacetobacter hiranonis have been reported as harboring weak and strong activity, respectively [28] and a new strain of P. hiranonis recently isolated from dog faeces displayed in vitro 7-DH-ion at around 30% conversion of CA to DCA [29]. Notably, in vitro 7-DH-ion of other primary BAs has been reported to be minor (CDCA) or non-existent (MCAs and UDCA) [20,22,30].…”

Correlation between Peptacetobacter hiranonis, the baiCD Gene, and Secondary Bile Acids in Dogs

“…In dogs, P. hiranonis is described as a biomarker for gastrointestinal functionality and is closely linked to maintaining balanced gastrointestinal health [17]. P. hiranonis occupies a pivotal role in the conversion of primary to secondary fUBA and is described as the main species with this ability within the canine and feline gastrointestinal microbiome [18][19][20][21]. This conversion involves a multi-step biochemical pathway encoded by the bai operon.…”

Strain-dependent induction of primary bile acid 7-dehydroxylation by cholic acid

“…The C. scindens ATCC 35704 and VPI 12708 strains show almost complete transformation to DCA while E. muris DSM 28560 has more limited activity 19,20,26 . Other known 7-DH-ing strains such as Clostridium hylemonae and Peptacetobacter hiranonis have been reported as harbouring weak and strong activity, respectively 27 and a new strain of P. hiranonis recently isolated from dog faeces displayed in vitro 7-DH-ion at around 30% conversion of CA to DCA 28 . Notably, in vitro 7-DH-ion of other primary BAs has been reported to be minor (CDCA) or non-existent (MCAs and UDCA) 20,23,29 .…”