Study quantifies functional recovery limitations of whole metagenome sequencing depth in oral microbiome of Nigerian youths (microbiomejournal.biomedcentral.com)

• At 10% of study sequencing depth, 30% of estimated microbiome functional repertoire detectable; at full depth, only 60% recovered.
• Low-prevalence functions disproportionately lost at shallow depths; annotation strategy trades off breadth vs specificity.
• Depth-to-function mapping framework provided to guide WMS study design and batch effect control.

"A new study analyzing oral-rinse whole metagenome shotgun data from 671 Nigerian youths (ages 9-18) on two Illumina platforms reveals that increasing sequencing depth does not proportionally improve functional recovery. At 10% depth, 30% of functions were detected; at full depth, only 60% were recovered. Annotation strategy choice traded off breadth against specificity. Low-prevalence functions were disproportionately lost at shallow depths. The authors provide a depth-to-function mapping framework to guide study design."