Comparative genomic and phenotypic description of Escherichia ruysiae: a new member of the gut microbiome of the domestic dog

Niokhor Dione Kodjovi D. Mlaga, PhD. Siyi Liang Guillaume Jospin Zara Marfori Nancy Alvarado Elisa Scarsella Ruchita Uttarwar Holly H Ganz ^*

• AnimalBiome, Oakland, United States

In this study, we used culturomic methods to isolate and describe the phenotypic and genomic features of four Escherichia ruysiae isolates found for the first time in the domestic dog, Canis lupus familiaris, and conducted a comparative genomics analysis. Initially identified as Escherichia coli using MALDI-TOF, these recently isolated strains were later confirmed through genomics to belong to a different species. All strains exhibited similar enzymatic activities and resistance to clindamycin, erythromycin, and metronidazole. The pangenome analysis revealed that most missing gene orthologs are related to motility followed by metabolism, including synthetases, reductases, phosphatases, permeases, transferases, and epimerases, as well as structural genes like efflux pumps and transporters. Phylogroup typing using the ClermonTyping method identified two main groups within the E. ruysiae species, Clade III and IV. Typical virulence genes associated with E. coli are absent in these strains. The multiple approaches used in this study expand our understanding of the diverse aspects of the recently described species, E. ruysiae.