Rethinking Faecalibacterium: Taxonomic Advances and Biomarkers of a Healthy Gut Microbiota
Faecalibacterium prausnitzii has long been regarded as the most major butyrate producer in the human gut and one of the most important anti-inflammatory microbes in the human gut. Significantly reduced cell numbers of the species have been reported in patients with several disorders, including Crohn’s disease, ulcerative colitis, colorectal cancers, and type 2 diabetes, mainly based on qPCR and meta-16S rRNA gene sequencing. Consequently, this organism has been proposed as a promising biomarker of a healthy gut microbiota. During the last decade, however, several studies revealed considerable genomic heterogeneity within the species. We therefore re-evaluated the taxonomic position of F. prausnitzii strains using the genomes deposited as “F. prasunitzii” in public database. Average nucleotide identity (ANI) analysis revealed that these strains were divided into 8 species-level taxonomic groups based on the 94% ANI threshold. These groups were subsequently reclassified, and the genus currently contains 10 validated species of human origin. Core-gene phylogenetic tree agreed with the ANI value-based classification. In contrast, 2 of the 8 ANI-based taxonomic groups were divided into multiple clusters in 16S rRNA gene-based phylogenetic tree, which was mainly due to intragenomic heterogeneity (<99% similarities) among 16S rRNA gene copies within individual strains. Because of this intragenomic heterogeneity, previously reported “F. prausnitzii” -specific primers for qPCR were not specific to F. prausnitzii. These findings suggested that part of the accumulated knowledge regarding F. prausnitzii may have been based on biased results and that the 16S rRNA gene is not an appropriate marker for the classification and quantification of Faecalibacterium spp. We therefore developed a rpoA-based qPCR assay for species-level quantification of Faecalibacterium spp. Application of this assay identified F. taiwanense and F. longum as the most prevalent and abundant Faecalibacterium species in healthy Japanese adults, followed by F. duncaniae and F. prausnitzii. rpoA-based sequencing analysis agreed with the findings and further identified a yet-to-be-classified species (designated Group 11) as one of the abundant species. We are currently characterizing species level distributions of Faecalibacterium in patients with several diseases to identify the species that play key roles in host health.
List of articles related to our Faecalibacterium study:
1. Tanno H, Maeno S, Salminen S, Gueimonde M, Endo A. 16S rRNA gene sequence diversity in Faecalibacterium prausnitzii-complex taxa has marked impacts on quantitative analysis. FEMS Microbiol Ecol. 2022 Feb 10;98(1):fiac004.
2. Sakamoto M, Sakurai N, Tanno H, Iino T, Ohkuma M, Endo A. Genome-based, phenotypic and chemotaxonomic classification of Faecalibacterium strains: proposal of three novel species Faecalibacterium duncaniae sp. nov., Faecalibacterium hattorii sp. nov. and Faecalibacterium gallinarum sp. nov. Int J Syst Evol Microbiol. 2022 Apr;72(4).
3. Tanno H, Chatel JM, Martin R, Mariat D, Sakamoto M, Yamazaki M, Salminen S, Gueimonde M, Endo A. New gene markers for classification and quantification of Faecalibacterium spp. in the human gut. FEMS Microbiol Ecol. 2023 Apr 7;99(5):fiad035.
4. Sakamoto M, Sakurai N, Tanno H, Iino T, Ohkuma M, Endo A. Faecalibacterium hominis Liu et al. 2023 is a later heterotypic synonym of Faecalibacterium duncaniae Sakamoto et al. 2022. Int J Syst Evol Microbiol. 2023 Aug;73(8).
5. Hirasaki M, Kadowaki R, Xuan AAL, Harata G, Miyazawa K, Maeno S, Gueimonde M, Endo A. Species-level quantification of Faecalibacterium spp. in faeces of healthy Japanese adults. J Med Microbiol. 2025 May;74(5):002019.
6. Ang A, Robert V, Hisatomi A, Hirasaki M, Maeno S, Ohkuma M, Sakamoto M, Chatel JM, Endo A. Faecalibacterium langellae sp. nov. isolated from human faeces. Int J Syst Evol Microbiol. 2025 Jun;75(6).
7. Ang A, Mitsuyama E, Kaneko H, Odamaki T, Endo A. Species level composition of Faecalibacterium spp. in the gut of Japanese adults revealed by rpoA-based sequencing analysis. FEMS Microbiol Ecol. 2026 May 21;102(6):fiag049.
Short bio
Deputy Director of Center for Global Initiatives, Tokyo University of Agriculture, Japan (since 2025)
Professor at Department of Nutritional Science and Food Safety, Faculty of Applied Bioscience, Tokyo University of Agriculture, Japan (since 2022)
PhD in Fermentation Science Tokyo University of Agriculture (2005)
Laboratory of the speaker
Department of Nutritional Science and Food Safety, Faculty of Applied Bioscience, Tokyo University of Agriculture
Invited by
Jean-Marc Chatel
