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

Four strains, representing two novel <i>Bifidobacterium</i> 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 <i>Bifidobacterium aquikefiri</i> LMG 28769^T. 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 <i>B. aquikefiri</i> LMG 28769^T 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 <i>Bifidobacterium fermentum</i> sp. nov. and <i>Bifidobacterium aquikefiricola</i> sp. nov. for these novel species within the <i>Bifidobacterium</i> genus. The proposed type strain <i>B. fermentum</i> WK012_4_13^T (= LMG 33104^T = DSM 116073^T; 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 <i>B. aquikefiricola</i> WK041_4_12^T (= LMG 33105^T = DSM 116074^T; GenBank accession number GCF_041080795.1) has a genome size of 2.36 Mbp and a G+C content of 53.94 mol%. <i>B. fermentum</i> cells are Gram-positive staining, non-motile, non-spore-forming, fructose-6-phosphate phosphoketolase (F6PPK)-positive, catalase- and oxidase-negative and bacillary club shaped. <i>B. aquikefiricola</i> cells are Gram-positive staining, non-motile, non-spore-forming, F6PPK-positive, catalase- and oxidase-negative and square rod shaped.