16S rRNA gene sequence diversity in Faecalibacterium prausnitzii-complex taxa has marked impacts on quantitative analysis

Faecalibacterium prausnitzii has been suggested as a biomarker of a healthy microbiota in human adults. Here, we report a taxonomic study of F. prausnitzii using genomic information and evaluation of the quantitative real-time PCR (qPCR) assay by focusing on specific primers to quantify its population. Average nucleotide identity values revealed that strains deposited as F. prausnitzii in a public database were separated into eight genomogroups with significant differences at the species level. A total of six of the 10 primer pairs used in the previous studies for qPCR of F. prausnitzii contained sequence mismatches to 16S rRNA gene sequences of the tested strains with markedly different levels by in silico analysis. In vitro primer evaluation by qPCR generally agreed with the in silico analysis, and markedly reduced amount of DNA was recorded by qPCR in combination with the primer pairs containing sequence mismatches. The present study demonstrated that a part of the accumulated knowledge on F. prausnitzii is maybe based on biased results.