UC Davis

Environmental resistance genes in a microbial community influence the taxonomic persistence and subsequently the functional capacity of a microbial population. Understanding factors influencing the retention and dissemination of environmental resistance genes will elucidate avenues of treatment and mitigation of resistant microbes. Two data sets (one metagenomic set of 18 samples, and one whole genome sequencing set of 201 isolates) were analyzed for environmental resistance genes in the context of taxonomic and functional relationships. The bioinformatic analyses of these previously-generated datasets also highlights the importance of the adoption of FAIR data practices in microbial genomics to enable the continued development of reproducible and robust analyses answering important questions with real-world relevance. Methods Sequencing data from previously-generated metagenomic and whole genome sequencing projects were analyzed for environmental resistance genes in the context of environmental variables. Metagenomic data from samples of the residential built environment of backyard poultry (BYP) owners were analyzed for the presence and taxonomic origin of antimicrobial resistance (AMR) genes. Additionally, this data set was also analyzed to determine any significant correlations between AMR genes and genetically encoded elements that may have implications for future potential therapeutic solutions, such as antimicrobial peptide genes, bacteriophage lysins, and bacterio-phage encoded auxiliary genes. Bacterial isolates collected from spacecraft-associated hardware in the Spacecraft Assembly Facility (SAF) at NASA’s Jet Propulsion Laboratory (JPL) were analyzed for genes implicated in the increased likelihood of microbial survival in harsh conditions. The evaluation of these environmental resistance genes is a critical and novel approach to understanding the risk of forward contamination to extraterrestrial environments. Metagenomic analysis of BYP-associated built environments revealed ubiquitous AMR presence and significant relationships between AMR genes and other genomic features with clear differences between homes that administered antibiotics to their BYP flocks and homes that did not. WGS analysis of NASA JPL bacterial isolates revealed the presence of resistance genes in all isolates, with fluctuations in frequency between taxonomic groups and between NASA missions. These studies elucidate the ecological relationships surrounding environmental resistance gene retention and reveal associations with taxonomic and functional components that with further research may lead to measures preventing the retention and dissemination of environmental resistance genes.