Whole genome sequences of bacteria isolated from Oil fly (<i>Helaeomyia petrolei</i>) larvae

Larvae from the petroleum oil fly, Helaeomyia petrolei, live in the asphaltene and polyaromatic hydrocarbon rich asphalt seeps of Rancho La Brea, Los Angeles, California. These larvae pass high amounts of viscous asphalt through their digestive system, and their gut microbiota is exposed to these extreme conditions. Environmental stress response mechanisms can co-select for antibiotic resistance, and in the current study we used 16S rRNA and genomic sequencing along with the Comprehensive Antibiotic Resistance Database (CARD) tools to characterize antibiotic resistance profiles from six bacteria previously isolated from the oil fly larval intestinal tract, linking phenotypic and genotypic resistance profiles. The isolates contain a core set of antibiotic resistance determinants along with determinants that are rarely found in these species. Comparing these oil fly isolates to the phenotypic prevalence data generated by the CARD Resistance Gene Identifier revealed sixteen instances where the oil fly bacteria appeared to carry a resistance not seen in related taxa in the database, suggesting a novel suite of resistance families in the oil fly isolates compared to other members of the same taxa. Results highlight the functional duality of genes that code for antibiotic resistance and expand our understanding of the ecological and evolutionary role of antibiotic resistance genes in environmental habitats.