Bifidobacterium canis sp. nov., a novel member of the Bifidobacterium pseudolongum phylogenetic group isolated from faeces of a dog (Canis lupus f. familiaris)

Abstract

A fructose-6-phosphate phosphoketolase-positive strain (GSD1FST) was isolated from a faecal sample of a 3 weeks old German Shepherd dog. The closest related taxa to isolate GSD1FST based on results from the EZBioCloud database were Bifidobacterium animalis subsp. animalis ATCC 25527T, Bifidobacterium animalis subsp. lactis DSM 10140T and Bifidobacterium anseris LMG 30189T, belonging to the Bifidobacterium pseudolongum phylogenetic group. The resulting 16S rRNA gene identities (compared length of 1454 nucleotides) towards these taxa were 97.30, 97.23 and 97.09 %, respectively. The pairwise similarities of strain GSD1FST using argS, atpA, fusA, hsp60, pyrG, rpsC, thrS and xfp gene fragments to all valid representatives of the B. pseudolongum phylogenetic group were in the concatenated range of 83.08–88.34 %. Phylogenomic analysis based on whole-genome methods such as average nucleotide identity revealed that bifidobacterial strain GSD1FST exhibits close phylogenetic relatedness (88.17 %) to Bifidobacetrium cuniculi LMG 10738T. Genotypic characteristics and phylogenetic analyses based on nine molecular markers, as well as genomic and comparative phenotypic analyses, clearly proved that the evaluated strain should be considered as representing a novel species within the B. pseudolongum phylogenetic group named as Bifidobacterium canis sp. nov. (GSD1FST=DSM 105923T=LMG 30345T=CCM 8806T).

Decoding the Genomic Variability among Members of the Bifidobacterium dentium Species

“…These microorganisms were classified as Gram-positive, nonspore-forming, and nonmotile bacteria that belong to the phylum Actinobacteria [4]. To date, 88 different bifidobacterial (sub)species were classified, mostly isolated from the gastrointestinal tract of numerous animals, the human gut and oral cavity, and insect hindgut [5][6][7][8][9][10][11][12][13][14][15][16][17][18][19].…”

The bifidobacterial distribution in the microbiome of captive primates reflects parvorder and feed specialization of the host

“…A similar statistically significant trend was found in colony forming units cultivated on WPS-MUP medium intended for bifidobacteria that reached 8.91 ± 1.38 log CFU g -1 in the NWM compared to 7.02 ± 0.93 log CFU g -1 in the OWM (t (50) = 5.87, p = 3.50e-07). In case of FS with lower numbers of bifidobacteria and the presence of clostridia, this medium was not sufficiently selective also allowing the growth of clostridia 51 , 52 . Consequently, a notably greater statistically significant difference was detected between primate parvorders on more selective WSP-NORF medium with bifidobacterial counts of 8.57 ± 2.13 log CFU g -1 for the NWM and 4.32 ± 2.04 log CFU g -1 for the OWM (Z = 5.17, p = 2.38e-07).…”

Exploring the Ecology of Bifidobacteria and Their Genetic Adaptation to the Mammalian Gut

“…They represent nonmotile, anaerobic, nonsporulating, saccharolytic bacteria with a bifid or multiple-branching rod morphology. Currently, the genus Bifidobacterium comprises 94 taxa, representing 82 species and 12 subspecies [4][5][6][7][8][9][10][11][12] (Table 1). In recent years, the phylogeny of the Bifidobacterium genus has been explored using different methods based on the sequencing of the 16S rRNA gene, by means of a multilocus approach, or the sequencing of several housekeeping genes (i.e., clpC, dnaJ, rpoC, xpf, dnaB, and purF) [13,14].…”

“…Bifidobacteria also naturally occur in the gastrointestinal tract (GIT) of animals, such as nonhuman mammals, insects, and birds [5][6][7][8][9][10][11], while they have also been isolated from human blood [51], sewage [42], the oral cavity [55], and fermented milk [15]. In this context, it has been demonstrated that the ability of bifidobacteria to adapt to specific environments is species-dependent [4].…”