Analysis of Twelve Genomes of the Bacterium from Brown-throated Sloths (), the First from a Non-human Host

is a Gram-negative bacterium found in various animals, including humans, where it has been associated with various infections. Knowledge of the basic biology of is essential to understand the evolutionary strategies of niche adaptation and how this organism contributes to infectious diseases; however, genomic data about is very limited, especially from non-human hosts. In this work, we sequenced 12 genomes isolated from healthy free-living brown-throated sloths () in the Parque Estadual das Fontes do Ipiranga (São Paulo, Brazil), and compared them with genomes from isolates of human origin, in order to gain insights into genomic diversity, phylogeny, and host specialization of this species. Phylogenetic analysis revealed that these strains are structured according to host. Despite the fact that sloth isolates were sampled from a single geographic location, the intra-sloth diversity was divided into three clusters, with differences of more than 1,000 single nucleotide polymorphisms between them, suggesting the circulation of various lineages in sloths. Genes involved in mobilome and defense mechanisms against mobile genetic elements were the main source of gene content variation between isolates from different hosts. Sloth-specific genome features include an IncN2 plasmid, a phage sequence, and a CRISPR-Cas system. The broad diversity of defense elements in (14 systems) may prevent further mobile element flow and explain the low amount of mobile genetic elements in genomes. Gene content variation may be important for the adaptation of to different host niches. This study furthers our understanding of diversity, host adaptation, and evolution of , by presenting and analyzing the first genomes of non-human isolates.