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<p>Three novel bacterial strains obtained from human fecal samples were characterized for their taxonomic classification and probiotic potential.&#xa0;The strains included one Gram-stain-positive (B2-R-112<sup>T</sup>) and&#xa0;two Gram-stain-negative (TA-V-105<sup>T</sup> and B2-R-115) strains; all were anaerobic and non-motile. Phylogenetic analysis based on 16S rRNA gene sequences placed&#xa0;them within&#xa0;the genera <i>Coprococcus</i>, <i>Parabacteroides</i>, and <i>Akkermansia</i>. Specifically, B2-R-112<sup>T</sup> showed 97.7% sequence similarity to <i>Coprococcus catus</i> L8<sup>T</sup>,&#xa0;TA-V-105<sup>T</sup> showed 97.8%&#xa0;to <i>Parabacteroides goldsteinii</i> DSM 19448<sup>T</sup>, and B2-R-115 exhibited 99.6% sequence similarity&#xa0;to "<i>Akkermansia&#xa0;massiliensis</i>" Marseille P6666<sup>T</sup>.&#xa0;The genome sizes were 3,311,086&#xa0;bp, 7,396,255&#xa0;bp, and 3,288,486&#xa0;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&#xa0;tolerance (0.3% w/v oxgall) after 4&#xa0;h, maintaining high viability in simulated gastric (pH 2.5, 4&#xa0;h) and intestinal (pH 8.0, 6&#xa0;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&#xa0;thresholds of ≥ 70% and ≥ 95%, respectively, supported the classification of strain B2-R-112<sup>T</sup> and strain&#xa0;TA-V-105<sup>T</sup> as novel species. Based on&#xa0;these phenotypic, genomic, and phylogenetic analyses, we propose&#xa0;the classification of these potential probiotic strains as novel species: <i>Coprococcus intestinalis</i> sp. nov. (type strain B2-R-112<sup>T</sup> = KCTC 25419<sup>T</sup> = CGMCC 1.17967<sup>T</sup> and <i>Parabacteroides caecihominis</i>) sp. nov. (type strain&#xa0;TA-V-105<sup>T</sup> = KCTC 25451<sup>T</sup> = CGMCC 1.17989<sup>T</sup>.</p>

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

  • 期刊论文

  • 发表日期：

    2025年9月20日

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  • Md Shamsuzzaman,
  • Ram Hari Dahal,
  • Yoon-Jung Choi,
  • Shukho Kim,
  • Jungmin Kim

摘要

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-112T) and two Gram-stain-negative (TA-V-105T 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-112T showed 97.7% sequence similarity to Coprococcus catus L8T, TA-V-105T showed 97.8% to Parabacteroides goldsteinii DSM 19448T, and B2-R-115 exhibited 99.6% sequence similarity to "Akkermansia massiliensis" Marseille P6666T. 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-112T and strain TA-V-105T 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-112T = KCTC 25419T = CGMCC 1.17967T and Parabacteroides caecihominis) sp. nov. (type strain TA-V-105T = KCTC 25451T = CGMCC 1.17989T.