Three previously unidentified Gram‐positive anaerobic coccoid bacteria, strains KhD‐2 ^T , KHD 4 ^T , and Kh‐D5 ^T , isolated from a vaginal swab, were characterized using the taxonogenomics concept. The phylogenic analysis, phenotypic characteristics, and genotypic data presented in this report attest that these three bacteria are distinct from previously known bacterial species with standing in nomenclature and represent three new Peptoniphilus species. Strain KhD‐2 ^T is most closely related to Peptoniphilus sp. DNF 00840 and Peptoniphilus harei (99.7% and 98.2% identity, respectively); strain KHD 4 ^T to Peptoniphilus lacrimalis (96%) and strain Kh‐D5 ^T to Peptoniphilus coxii (97.2%). Strains KhD‐2 ^T , KHD 4 ^T , and Kh‐D5 ^T DNA G+C contents are, respectively, 34.23%, 31.87%, and 49.38%; their major fatty acid was C _16:0 (41.6%, 32.0%, and 36.4%, respectively). We propose that strains KhD‐2 ^T (= CSUR P0125 = DSM 101742), KHD 4 ^T (= CSUR P0110 = CECT 9308), and Kh‐D5 ^T (= CSUR P2271 = DSM 101839) be the type strains of the new species for which the names Peptoniphilus vaginalis sp. nov. , Peptoniphilus raoultii sp. nov., and Peptoniphilu pacaensis sp. nov., are proposed, respectively.

Strain Marseille‐P2341 ^T , a nonmotile, nonspore‐forming, Gram‐stain‐positive anaerobic coccus, was isolated in the vaginal specimen of a patient with bacterial vaginosis using culturomics. Its growth occurred at temperatures ranging from 25 to 42°C, with pH between 6.5 and 8.5, and at NaCl concentrations lower than 5%. The major fatty acids were C _18:1n9 (27.7%) and C _16:0 (24.4%). Its genome is 1,671,491 bp long with 49.48 mol% of G+C content. It is composed of 1,501 genes: 1,446 were protein‐coding genes and 55 were RNA s. Strain Marseille‐P2341 ^T shared 97.3% of 16S rRNA gene sequence similarity with Murdochiella asaccharolytica , the phylogenetically closest species. These results enabled the classification of strain Marseille‐P2341 ^T as a new species of the genus Murdochiella for which we proposed the name Murdochiella vaginalis sp. nov. The type strain is strain Marseille‐P2341 ^T (= DSM 102237, = CSUR P2341).

A Gram-stain-positive anaerobic rod-shaped bacterium, designated strain Marseille-P3275^T, was isolated using culturomics from the vaginal discharge of healthy French woman. Marseille-P3275^T was non-motile and did not form spores. Cells had neither catalase nor oxidase activity. The major fatty acids were C_16 : 0 (29 %), C_18:1ω9 (18 %), and iso-C_15 : 0 (17 %). The genomic DNA G+C content was 50.64 mol%. The phylogenetic analysis based on 16S rRNA gene sequence indicated that Marseille-P3275^T was related to members of the family Propionibacteriaceae (between 90.32–92.92 % sequence similarity) with formation of a clade with the monospecific genus Propionimicrobium (type species Propionimicrobium lymphophilum ). On the basis of these phylogenetic and phenotypic differences, Marseille-P3275^T was classified in a novel genus, Vaginimicrobium, as Vaginimicrobium propionicum gen. nov., sp. nov. The type strain is Marseille-P3275^T (=CSUR P3275^T=CECT 9677^T).

Fecal microbiome culturomics of a cancer patient treated with immune checkpoint inhibitors led to the identification of a Gram-negative, rod-shaped, obligate anaerobic, non-motile, non-spore-forming bacterium, designated strain kh20^T, which was phylogenetically assigned to the genus Alistipes. Strain kh20^T demonstrated a 98.61% 16S rRNA sequence similarity with A.shahii WAL 8301^T. The bacteria cells generated catalase but no oxidase. Iso-C_15:0 (26.6%), anteiso-C_15:0 (19.9%), and iso-C_17:0 (17.2%) were the major cellular fatty acids identified in its composition. The G+C content of its genome was 57.2%. Strain kh20^T showed significantly low values for DNA-DNA Hybridation (DDH ≤ 33.70%) and Average Nucleotide Identity (ANI ≤ 86.35%) compared with other Alistipes species. Based on these findings, we concluded that strain kh20^T represented a novel bacterium, and we proposed the name Alistipes montrealensis sp. nov. (CECT 30384 and CSUR Q6005).

Strain KD21^T, isolated from the fecal sample of a healthy female volunteer, is a strictly anaerobic, non-motile, Gram-staining-positive, saccharolytic small rod, that does not produce spores. Strain KD21^T was able to grow in the range of temperature 28–37°C (optimum, 37 °C), pH 6.0–8.0 (optimum, pH 7.0), and with 0–5.0 g/L NaCl (optimum, 0 g/L NaCl). Bacteria cells reduced nitrates to nitrites. Its major fatty acids were C_18:1ω9c, C_16:0, C_18:0 and summed in feature 8 (C_18:1ω7c and/or C_18:1ω6c). 16S rRNA gene phylogenetic analysis revealed that KD21^T is a member of the genus Tractidigestivibacter and is distinct from any species with validly published names. The sequence showed 98.48% similarity with T. scatoligenes SK9K4^T. The DNA G + C content of strain KD21^T was 62.6 mol%. The DNA-DNA hybridization and OrthoANI values between strain KD21^T and T. scatoligenes SK9K4^T were were 40.2% and 90.2%, respectively. Differences in phenotypic, phylogenetic, chemotaxonomic, and genomic characteristics indicated that strain KD21^T represents a novel species within the genus Tractidigestivibacter. The name Tractidigestivibacter montrealensis sp. nov. is proposed and the type strain is KD21^T ( = CSUR Q8103^T = DSM 115111^T).

Background: Bacterial vaginosis is a very common vaginal disorder, with a gynaeco-obstetrical impact, but remains poorly understood. Current antibiotic treatment most often fails. Our objective was to exhaustively map the bacterial community present in bacterial vaginosis and normal flora, using not only a molecular approach but also a highly efficient culture approach, culturomics. Vaginal bacterial diversity was evaluated using both strategies for 24 Caucasian French women, including 7 cases of bacterial vaginosis, and 10 rural Senegalese women, including 5 cases of bacterial vaginosis. An additional 16 specimens (three cases of bacterial vaginosis and 13 normal flora) obtained during the follow-up visits of five French women with bacterial vaginosis were analysed using metagenomics.Results: The combination of culturomics and metagenomics reveals the richness and diversity of vaginal microbiota. Our data demonstrated that compared to healthy women, those with bacterial vaginosis present a shift in vaginal flora. The microbiota of the bacterial vaginosis group can be easily distinguished from that of healthy group by their increased bacterial diversity, abundance of Bacteroidales and Leptotrichiaeceae, and depletion of Proteobacteria and Lactobacillaceae species. In addition, a complex of 10 genera was associated with bacterial vaginosis: Gardnerella, Atopobium, Snethia, Aerococcus, Prevotella, Gemella, Facklamia, Porphyromonas, Mycoplasma, and Urinacoccus. Overall, the microbial population detected in bacterial vaginosis flora was largely similar to the bacterial communities found in gut microbiota. The two approaches showed a diverse vaginal microbiota that was largely non-overlapping, with only 146 common species. Furthermore, culturomics extends the repertoire of human-associated bacteria with the isolation of 27 new bacterial species.Conclusions: This study provides the most representative topology of the vaginal microbiota of normal flora and bacterial vaginosis and suggests the transplantation of gut microbiota into the vagina during bacterial vaginosis. Several sets of clinically relevant anaerobic bacteria and new species were also isolated from the human vagina, confirming that some previously “uncultivated” species may be cultivated using an appropriate strategy. Exhaustive characterisation of vaginal microbiota will enable a better understanding and management of bacterial vaginosis. Obtaining isolates will allow us to explore the bacterial interactions of the vaginal microbiota and will serve as a basis for the potential development of bacteriotherapy to prevent or treat vaginal dysbiosis.