Segatella intestinalis sp. nov., and Parabacteroides caeci sp. nov., novel potential probiotics from the human gut microbiome

Abstract

Two bacterial strains, B2-R-102^T and W1-Q-101^T, were isolated from the feces of a healthy Korean individual. These strains were Gram-stain negative, anaerobic, and non-motile, growing optimally between 20 and 40 °C and at pH 5.5–8.0. Importantly, they survived at pH 2.0 and tolerated 0.3% bile salts and pepsin after a 4 h exposure. The strains demonstrated in vitro antioxidant activity, inhibiting DPPH radicals by 48.12 ± 1.45 and 70.80 ± 12.8%, respectively. Furthermore, they inhibited α-amylase activity by 46.52 ± 4.42 to 60.84 ± 2.20%, compared to 74.82 ± 0.76% inhibition by sitagliptin. In vitro, anti-inflammatory assays revealed 57.77 ± 3.15 to 62.39 ± 2.23% inhibition of albumin protein denaturation, comparable to aspirin 72 ± 2.39% inhibition. The abundant cellular fatty acids were C_15:0, C_16:0, iso-C_15:0, C_18:1ω9c_, anteiso-C_15:0 and iso-C_17:0 3-OH. Neither strain exhibited haemolytic activity, and genomic analysis revealed no acquired antibiotic resistance or virulence genes. Phylogenetic analysis showed that B2-R-102^T and W1-Q-101^T belonged to the genera Segatella and Parabacteroides, with 96.9 and 97.7% 16S rRNA gene sequence similarities to Segatella copri CB7^T and Parabacteroides goldsteinii DSM 19448^T, respectively. Furthermore, biosynthetic gene cluster analysis revealed the potential for antimicrobial thiopeptides, lanthipeptides, and non-ribosomal peptides (NRPs). In silico average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values were below the thresholds to distinguish novel species. Based on phenotypic, genomic, and phylogenetic analysis, we propose the names Segatella intestinalis sp. nov. (type strain B2-R-102^T = CGMCC 1.17963^T = KCTC 25417^T) and Parabacteroides caeci sp. nov. (type strain W1-Q-101^T = KCTC 25456^T = CGMCC 1.17991^T).