Lawhon, S. D. | bioRxiv Science

bioRxiv2026

Description of canine- and feline-derived strains of the bile acid-converting bacterium Peptacetobacter hiranonis: P. hiranonis subsp. deconjugans subsp. nov. and P. hiranonis subsp. nondeconjugans subsp. nov.

The bile acid-converting Peptacetobacter hiranonis is a Gram-positive, anaerobic, potentially spore-forming bacterium. It was first isolated from human feces and was subsequently shown to convert bile acids (BA) in both in vitro and in vivo experiments. The conversion of BA relies on the presence of the 7alpha-dehydroxylation multi-step pathway, encoded by the BA-inducible (bai) operon, harbored by P. hiranonis. In companion animals, P. hiranonis has been characterized as a biomarker for intestinal health, with its loss associated with dysbiosis. However, characterization of P. hiranonis cultured from companion animals is limited. An in-depth characterization of P. hiranonis was published by Chen et al. recently, including the proposal of a new species, Peptacetobacter hominis. We have sequenced the whole genome of both canine- and feline-derived strains of P. hiranonis, characterized these strains biochemically, and assessed their in vitro BA-converting ability as well as their antimicrobial resistance profiles. The strains described here can convert primary into secondary BAs and are whole-genome inhibited by low concentrations of amoxicillin-clavulanate, cefepime, ceftriaxone, chloramphenicol, ciprofloxacin, clindamycin, and metronidazole. Based on whole genome analysis, we propose dividing P. hiranonis into two host-adapted subspecies: P. hiranonis subsp. deconjugans and P. hiranonis subsp. nondeconjugans, based on their genomic differences and divergent ability to deconjugate BAs; a function that appears widely distributed among P. hiranonis strains cultured from dogs, but absent from those cultured from cats. Taken together, our results confirmed the BA conversion ability of P. hiranonis cultured from dogs and cats and reveal host-associated genomic and functional differences within the species.

microbiology↗

bioRxiv2020

High-resolution genomic comparisons within Salmonella enterica serotypes derived from beef feedlot cattle: parsing the roles of cattle source, pen, animal, sample type and production period

Salmonella enterica is a major foodborne pathogen, and contaminated beef products have been identified as the primary source of Salmonella-related outbreaks. Pathogenicity and antibiotic resistance of Salmonella are highly serotype- and subpopulation-specific, which makes it essential to understand high-resolution Salmonella population dynamics in cattle. Time of year, source of cattle, pen, and sample type(i.e., feces, hide or lymph nodes) have previously been identified as important factors influencing the serotype distribution of Salmonella (e.g., Anatum, Lubbock, Cerro, Montevideo, Kentucky, Newport, and Norwich) that were isolated from a longitudinal sampling design in a research feedlot. In this study, we performed high-resolution genomic comparisons of Salmonella isolates within each serotype using both single-nucleotide polymorphism (SNP)-based maximum likelihood phylogeny and hierarchical clustering of core-genome multi-locus sequence typing. The importance of the aforementioned features on clonal Salmonella expansion was further explored using a supervised machine learning algorithm. In addition, we identified and compared the resistance genes, plasmids, and pathogenicity island profiles of the isolates within each sub-population. Our findings indicate that clonal expansion of Salmonella strains in cattle was mainly influenced by the randomization of block and pen, as well as the origin/source of the cattle; that is, regardless of sampling time and sample type (i.e., feces, lymph node or hide). Further research is needed concerning the role of the feedlot pen environment prior to cattle placement to better understand carry-over contributions of existing strains of Salmonella and their bacteriophages. ImportanceSalmonella serotypes isolated from outbreaks in humans can also be found in beef cattle and feedlots. Virulence factors and antibiotic resistance are among the primary defense mechanisms of Salmonella, and are often associated with clonal expansion. This makes understanding the subpopulation dynamics of Salmonella in cattle critical for effective mitigation. There remains a gap in the literature concerning subpopulation dynamics within Salmonella serotypes in feedlot cattle from the beginning of feeding up until slaughter. Here, we explore Salmonella population dynamics within each serotype using core genome phylogeny and hierarchical classifications. We used machine-learning to quantitatively parse the relative importance of both hierarchical and longitudinal clustering among cattle host samples. Our results reveal that Salmonella populations in cattle are highly clonal over a 6-month study period, and that clonal dissemination of Salmonella in cattle is mainly influenced spatially by experimental block and pen, as well by the geographical origin of the cattle.

microbiology↗