PSV-14 Genome Centric Approaches to Understand Antimicrobial Resistance in the Rumen Microbiome

Abstract Global meat and milk demands are projected to increase by 50% by the year 2050, making a highly efficient cattle industry a top priority. Widespread use of antibiotics over the last 70 years has led to increases in antibiotic resistance genes (ARGs) in microbial populations, posing health risks to animal and human populations. Thus, a thorough understanding of where antibiotic resistance genes reside in microbial ecosystems surrounding livestock is paramount in developing strategies to mitigate transfer of antibiotic resistance. Recent advances in metagenome sequencing have made it possible to predict microbial genomes from shotgun metagenome datasets. However, genomes binned from metagenome data are often smaller than genomes from pure cultures, omitting genetic information that is not part of the core genome e.g. antibiotic resistance. This study uses a new linked-read metagenome sequencing approach, partitioning long fragments of DNA (>40Kbp) into millions of droplets which are individually barcoded giving each strand a unique index, improving metagenome assembly and increasing access to genetic information pertaining to antibiotic resistance. Rumen samples from four animals which received daily antibiotics in feed as well as antibiotic injections were pooled for linked-read metagenome sequencing. Additionally, soil samples from the animal pen were collected from three locations and pooled for analysis. Linked-read sequencing reads were assembled using MEGAHIT and ATHENA assemblers (N50 > 2702bp, 578,838 contigs >1000bp). Metagenome assembled genomes (MAGs) were binned using MetaBAT2, yielding 341 genome bins. Of these, 144 bins were of intermediate to high quality (>70% completeness, < 10% contamination), 79 genomes from rumen and 65 from soil samples, respectively. Genomes were scanned for ARGs (ABRicate), revealing 12 genomes containing ARGs, 5 from rumen, 7 from soil. MAGs possessed genes conferring resistance to penicillin, macrolide, nitroimidazole, aminoglycoside, and tetracycline class antibiotics, helping uncover information about where ARGs are sequestered in their respective environments. USDA is an equal opportunity provider and employer.