Bifidobacterium fermentum sp. nov. and Bifidobacterium aquikefiricola sp. nov., isolated from water kefir

• Published in: International journal of systematic and evolutionary microbiology Vol. 74; no. 10
• Main Authors: Breselge, Samuel, Bellassi, Paolo, Barcenilla, Coral, Álvarez-Ordóñez, Avelino, Morelli, Lorenzo, Cotter, Paul D
• Format: Journal Article
• Language: English
• Published: England 24.10.2024
• Subjects: Bacterial Typing Techniques; Base Composition; Bifidobacterium - classification; Bifidobacterium - genetics; Bifidobacterium - isolation & purification; DNA, Bacterial - genetics; Fatty Acids - analysis; Genome, Bacterial; Kefir - microbiology; Nucleic Acid Hybridization; Phylogeny; RNA, Ribosomal, 16S - genetics; Sequence Analysis, DNA; Bifidobacterium; water kefir; metagenomics; polyphasic taxonomy
• ISSN: 1466-5034
• DOI: 10.1099/ijsem.0.006549

Four strains, representing two novel species, were isolated from water kefir, a fermented beverage. 16S rRNA gene analysis suggested that the novel species share high identities (98.82-98.89%) with LMG 28769 . Complete genomes were assembled with a short- and long-read hybrid sequencing approach. In agreement with the 16S rRNA gene analysis, phylogenetics with 117 marker genes places the novel species closest to LMG 28769 as well. The isolates have average nucleotide identity (ANI) scores ranging from 81.46 to 84.84% and digital DNA-DNA hybridization (dDDH) scores from 23.9 to 38.5% with the closest related species, as well as ANI scores between the proposed new species of 80.50%, indicating that the isolates represent two novel species. Matrix-assisted laser desorption/ionization-time of flight chemotaxonomic analysis supported the gene-based taxonomic placement. We propose the names sp. nov. and sp. nov. for these novel species within the genus. The proposed type strain WK012_4_13 (= LMG 33104 = DSM 116073 ; GenBank accession number GCF_041080835.1) has a genome size of 2.43 Mbp, with a G+C content of 56.00 mol%. The proposed type strain for WK041_4_12 (= LMG 33105 = DSM 116074 ; GenBank accession number GCF_041080795.1) has a genome size of 2.36 Mbp and a G+C content of 53.94 mol%. cells are Gram-positive staining, non-motile, non-spore-forming, fructose-6-phosphate phosphoketolase (F6PPK)-positive, catalase- and oxidase-negative and bacillary club shaped. cells are Gram-positive staining, non-motile, non-spore-forming, F6PPK-positive, catalase- and oxidase-negative and square rod shaped.