Amplicon Target Choice, Not Sequencing Depth, Determines Whether Cutibacterium acnes Subspecies and Types Can Be Measured: A Re-Analysis of Three Public Acne Cohorts

The anaerobe Cutibacterium acnes has long been reported to participate in the pathogenesis of acne. The species comprises three subspecies, and subspecies acnes has four types designated IA1, IA2, IB, and IC, whose reported clinical associations differ. Amplicon surveys of the 16S ribosomal RNA gene nevertheless report broadly similar abundance of the genus Cutibacterium in affected and unaffected skin, and whether this reflects the skin or the limits of the marker has not been quantified for each unit. Genome assemblies of Cutibacterium were retrieved, comprising 2236 of C. acnes and 71 of C. granulosum, and units were assigned by eight-locus multilocus sequence typing. The full-length 16S gene and the V1–V3, V3–V4, and V4 regions were extracted, the extent to which each resolves the six units was measured, and three published cohorts were re-analyzed. In each short region, a single identical sequence spanned all six units in 96% to 98% of assemblies. Subspecies defendens and elongatum were detected in 94% of their assemblies by full-length 16S, whereas the four types within subspecies acnes fell below 5%. A 16S survey, therefore, did not separate the types within subspecies acnes in these assemblies, and where bacterial load differs, a genus of reagent origin may be reported as a biomarker. In the typing cohort, acne skin carried less subspecies defendens and more type IA2, whereas in the shotgun cohort, only type IA1 differed after puberty; whether IA2 rather than IA1 distinguishes acne skin, therefore, remains to be established.