Over the past decade the field of metagenomics has enabled substantial advancement in the knowledge of microbial ecology, evolution, and diversity.
This study helps define a balance between cost and required sequencing depth to acquire meaningful results. We found a depth of D0.5 was suitable to describe the microbiome and resistome of cattle fecal samples. However, the number of reads being assigned to ARGs as well as to microbial taxa increased significantly with increasing depth. A comparative analysis of the relative abundance of reads aligning to different phyla and antimicrobial classes indicated that the relative proportions of read assignments remained fairly constant regardless of depth. Metagenomic DNA was sequenced to various depths, D1, D0.5 and D0.25, with average sample read counts of 117, 59 and 26 million, respectively.
Metagenomic sequencing was conducted on eight composite fecal samples originating from four beef cattle feedlots. In the present study, we compared the ability of varying sequencing depths to generate meaningful information about the taxonomic structure and prevalence of antimicrobial resistance genes (ARGs) in the bovine fecal microbial community.
Developments in high-throughput next generation sequencing (NGS) technology have rapidly advanced the understanding of overall microbial ecology as well as occurrence and diversity of specific genes within diverse environments.
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