Genes, Vol. 11, Pages 1380: Metagenomic Information Recovery from Human Stool Samples Is Influenced by Sequencing Depth and Profiling Method

Genes, Vol. 11, Pages 1380: Metagenomic Information Recovery from Human Stool Samples Is Influenced by Sequencing Depth and Profiling Method Genes doi: 10.3390/genes11111380 Authors: Tasha M. Santiago-Rodriguez Aaron Garoutte Emmase Adams Waleed Nasser Matthew C. Ross Alex La Reau Zachariah Henseler Tonya Ward Dan Knights Joseph F. Petrosino Emily B. Hollister Sequencing of the 16S rRNA gene (16S) has long been a go-to method for microbiome characterization due to its accessibility and lower cost compared to shotgun metagenomic sequencing (SMS). However, 16S sequencing rarely provides species-level resolution and cannot provide direct assessment of other taxa (e.g., viruses and fungi) or functional gene content. Shallow shotgun metagenomic sequencing (SSMS) has emerged as an approach to bridge the gap between 16S sequencing and deep metagenomic sequencing. SSMS is cost-competitive with 16S sequencing, while also providing species-level resolution and functional gene content insights. In the present study, we evaluated the effects of sequencing depth on marker gene-mapping- and alignment-based annotation of bacteria in healthy human stool samples. The number of identified taxa decreased with lower sequencing depths, particularly with the marker gene-mapping-based approach. Other annotations, including viruses and pathways, also showed a depth-dependent effect on feature recovery. These results refine the understanding of the suitability and shortcom...
Source: Genes - Category: Genetics & Stem Cells Authors: Tags: Article Source Type: research
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