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Antibiotic resistance genes across a wide variety of metagenomes
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Journal Article
Antibiotic resistance genes across a wide variety of metagenomes
2016
Overview
The distribution of potential clinically relevant antibiotic resistance (AR) genes across soil, water, animal, plant and human microbiomes is not well understood. We aimed to investigate if there were differences in the distribution and relative abundances of resistance genes across a variety of ecological niches. All sequence reads (human, animal, water, soil, plant and insect metagenomes) from the MG-RAST database were downloaded and assembled into a local sequence database. We show that there are many reservoirs of the basic form of resistance genes e.g. bla
TEM, but the human and mammalian gut microbiomes contain the widest diversity of clinically relevant resistance genes using metagenomic analysis. The human microbiomes contained a high relative abundance of resistance genes, while the relative abundances varied greatly in the marine and soil metagenomes, when datasets with greater than one million genes were compared. While these results reflect a bias in the distribution of AR genes across the metagenomes, we note this interpretation with caution. Metagenomics analysis includes limits in terms of detection and identification of AR genes in complex and diverse microbiome population. Therefore, if we do not detect the AR gene is it in fact not there or just below the limits of our techniques?
Distribution and relative abundances of antibiotic resistance genes across the world from the ocean to the human gut and everywhere in between.
Graphical Abstract Figure.
Distribution and relative abundances of antibiotic resistance genes across the world from the ocean to the human gut and everywhere in between.
Publisher
Oxford University Press
