Coprococcus intestinalis sp. nov., Parabacteroides caecihominis sp. nov., and “Akkermansia massiliensis” B2-R-115 with High Probiotic Potential from the Human Gut Microbiome

Three novel bacterial strains obtained from human fecal samples were characterized for their taxonomic classification and probiotic potential. The strains included one Gram-stain-positive (B2-R-112^T) and two Gram-stain-negative (TA-V-105^T and B2-R-115) strains; all were anaerobic and non-motile. Phylogenetic analysis based on 16S rRNA gene sequences placed them within the genera Coprococcus, Parabacteroides, and Akkermansia. Specifically, B2-R-112^T showed 97.7% sequence similarity to Coprococcus catus L8^T, TA-V-105^T showed 97.8% to Parabacteroides goldsteinii DSM 19448^T, and B2-R-115 exhibited 99.6% sequence similarity to "Akkermansia massiliensis" Marseille P6666^T. The genome sizes were 3,311,086 bp, 7,396,255 bp, and 3,288,486 bp, with G + C contents of 43.9%, 43.2%, and 57.8%, respectively. All strains demonstrated strong survival at pH 2.0–3.0 and robust bile salt tolerance (0.3% w/v oxgall) after 4 h, maintaining high viability in simulated gastric (pH 2.5, 4 h) and intestinal (pH 8.0, 6 h) fluids. They also exhibited significant antioxidant, antidiabetic, and anti-inflammatory activities. In silico DNA–DNA hybridization (dDDH) and average nucleotide identity (ANI) analyses, using thresholds of ≥ 70% and ≥ 95%, respectively, supported the classification of strain B2-R-112^T and strain TA-V-105^T as novel species. Based on these phenotypic, genomic, and phylogenetic analyses, we propose the classification of these potential probiotic strains as novel species: Coprococcus intestinalis sp. nov. (type strain B2-R-112^T = KCTC 25419^T = CGMCC 1.17967^T and Parabacteroides caecihominis) sp. nov. (type strain TA-V-105^T = KCTC 25451^T = CGMCC 1.17989^T.