Species level composition of <i>Faecalibacterium</i> spp. in the gut of Japanese adults revealed by <i>rpoA</i> -based sequencing analysis

Faecalibacterium is a predominant genus in the human gut that potentially supports intestinal and systemic health. Recent genomic studies revealed heterogeneity within the genus, leading to the recognition of additional species beyond the type species, Faecalibacterium prausnitzii. Despite its biological importance, the species-level distribution and ecological diversity of Faecalibacterium spp. remains poorly characterized, partly due to methodological constraints. Here, we developed a rpoA-based primer set specific to the Faecalibacterium genus and applied on fecal samples from 580 healthy Japanese adults for species-level profiling with next-generation sequencing. Our results revealed clear distinctions in species-level population, as well as inter-individual variations influenced by host characteristics and dietary factors. The majority of Faecalibacterium composition consisted of F. longum, F. taiwanense, F. duncaniae, F. prausnitzii, and a yet-to-be-classified species (Group 11). Notably, F. prausnitzii was neither the most prevalent nor the most abundant species. Besides that, host driven differences such as body mass index revealed negative association between relative abundance of F. duncaniae and Group 11. Additionally, Group 11 displayed lower relative abundance in lower caloric intake group. Overall, these findings highlight environment- and host-dependent shifts in Faecalibacterium populations, revealing species-specific ecological adaptations and potential physiological roles in human health.