Remarkable genomic diversity among isolates recovered from healthy chickens.

The genus has been extensively studied and it is known to encompass a range of commensal and pathogenic bacteria that primarily inhabit the gastrointestinal tracts of warm-blooded vertebrates. However, the presence of as a model organism and potential pathogen has diverted attention away from commensal strains and other species in the genus. To investigate the diversity of in healthy chickens, we collected fecal samples from antibiotic-free Lohmann Brown layer hens and determined the genome sequences of 100 isolates, 81 of which were indistinguishable at the HC0 level of the Hierarchical Clustering of Core Genome Multi-Locus Sequence Typing scheme. Despite initial selection on CHROMagar Orientation medium, which is considered selective for , phylotyping and core genome single nucleotide polymorphism analysis revealed the presence of at least one representative of all major clades of , except for , and phylogroup B2 and cryptic clade I. The most frequent phylogenomic groups were phylogroups A and B1 and (clades III and IV). We compiled a collection of reference strains isolated from avian sources (predominantly chicken), representing every phylogroup and species, and used it to confirm the phylogeny and diversity of our isolates. Overall, the isolates carried low numbers of the virulence and antibiotic resistance genes typically seen in avian pathogenic . Notably, the clades not recovered are ones that have been most strongly associated with virulence by other studies.