Comprehensive Identification of Antibiotic Resistance Genes in Plant Microbiomes

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Abstract Summary

It is known that plants have antibiotic resistance genes, which suggests that plants are exposed to antibiotics. Various microorganisms are found in soil including among those closely associated with plant roots. However, their ability to produce antibiotics has not been examined. We analyzed plant associated metagenomes for the presence of antibiotic resistance genes as a proxy for antibiotic production. We compared the usefulness of two antibiotic resistance databases for identifying the highest number of antibiotic resistance genes in the metagenomics samples. The first database, FARME DB, predominantly originates from environmental samples while the second database, CARD, originates from clinical isolates. Plant-associated metagenome reads were downloaded from the Joint Genome Institute and the program DIAMOND was used to align reads with either of the two databases. A higher number of reads were found to align with the FARME DB. Further examination of hits indicated enrichment for genes coding for β-lactam antibiotics in plant microbiomes. Finally, among genes encoding for aminoglycoside resistance, the most represented genes encode for transporters responsible for pumping out the antibiotic. This high representation of transporters to the detriment of aminoglycoside modifying enzymes suggests a large number of aminoglycoside producing bacteria are present in the plant microbiome.

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