Genetic sequence data evidence that human faecal-associated HF183 sequences are on human skin and in urine

Abstract

Aims: The DNA marker HF183 is a partial 16S rRNA gene sequence highly specific to human-associated Bacteroides including Bacteroides dorei. While HF183 is used to assess human faecal contamination in aquatic environments worldwide, little is known about the existence of HF183 and B. dorei in human microbiomes outside of the human gastrointestinal tract and faeces.

Methods and results: Previously published human skin and urine microbiome data sets from five independent human body skin studies, the Human Microbiome Project (HMP) and three independent human urine studies were analysed. The HF183 gene sequence was detected in all skin data sets, with the ratios of positive samples ranging from 0.5% to 36.3%. Popliteal fossa (knee), volar forearm and inguinal (groin) creases were identified as hot spots. HF183 was detected in two of three urine data sets, with ratios of positive samples ranging from 0% to 37.5%. All HF183-containing sequences from these data sets were classified as associated with B. dorei.

Conclusions: HF183 is widespread on human skin and present in urine.

Significance and impact of study: Skin and urine microbiomes could be sources of HF183 to environmental waters. Such non-faecal sources of HF183 might explain low concentrations of HF183 in recreational waters when swimmers are present.

Keywords: Bacteroides dorei; HF183; human faecal contamination; human microbiomes; skin; urine.

FIGURE 1

Phylogenetic relationships of representative HF183 containing sequences from skin microbiome data sets S1–S5, HMP project, urine microbiome data sets U1–U3, together with all B. dorei reference 16S rRNA sequences as well as all Bacteroides genus type stain 16S rRNA sequences archived in RDP database determined by the neighbour‐joining method. Bootstrap values of >50% (obtained with 1000 resamplings) are shown at nodes. Methanosphaera cuniculi type strain DSM 4103 (HE582783) was used as an outgroup. GenBank accession numbers are in parentheses