Using Homology-Based Methods and Functional Similarity to Identify Antibiotic Resistance in a Natural Environment

Abstract

Antibiotics are the crux of modern medicine, and antibiotic resistance (AbR) is a challenge to overcome. It has long been known that antibiotic production by soil microbiota is a natural process. Antibiotics such as streptomycin and penicillin come from common soil microorganisms. AbR is said to spread readily and rapidly through the environment, but its natural occurrence is poorly constrained. In studies analyzing natural AbR across a variety of habitats, researchers have found resistance in agricultural fields, human and animal feces, soils, deep caves, prehistoric ice cores, marine habitats, and reclaimed wastewater. Permafrost soils represent a pristine (human-unimpacted) environment capable of serving as a model system for natural AbR. I compared a functionality-based approach to a traditional identity-based approach to identify AbR sequences in permafrost microbial community genomes. The functionality-based approach yielded better quality results overall, and identified sequences more likely to be mappable to molecular pathways with the KEGG database.