New gene markers for classification and quantification of Faecalibacterium spp. in the human gut

Abstract

<p><em>Faecalibacterium prausnitzii</em> is a promising biomarker of a healthy human microbiota. However, previous studies reported the heterogeneity of this species and found the presence of several distinct groups at the species level among <em>F. prausnitzii</em> strains. Our recent study revealed that methods previously developed for quantification of <em>F. prausnitzii</em> were not specific to the species level because of the heterogeneity within the <em>F. prausnitzii</em> species and the application of 16S rRNA gene, which is an invalid genetic marker for the species. Therefore, previously available data failed to provide information on different groups, which limits our understanding of the importance of this organism for host health. Here, we propose an alternative gene marker for quantification of <em>F. prausnitzii</em>-related taxa. A total of nine group-specific primer pairs were designed by targeting <em>rpoA</em> gene sequences. The newly developed <em>rpoA</em>-based qPCR successfully quantified targeted groups. Application of the developed qPCR assay in six healthy adults revealed marked differences in abundance and prevalence among the different targeted groups in stool samples. The developed assay will facilitate detailed understanding of the impact of <em>Faecalibacterium</em> populations at the group level on human health and to understand the links between depletion of specific groups in <em>Faecalibacterium</em> and different human disorders.<br></p>