Genetic marker-based multi-locus sequence analysis for classification, genotyping, and phylogenetics of the family Bifidobacteriaceae as an alternative approach to phylogenomics
Bifidobacteria are widely known for their probiotic potential; however, little is known regarding the ecological significance and potential probiotic effects of the phylogenetically related ‘scardovial’ genera ( Aeriscardovia , Alloscardovia , Bombiscardovia , Galliscardovia , Neoscardovia , Parasca...
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Published in | Antonie van Leeuwenhoek Vol. 112; no. 12; pp. 1785 - 1800 |
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Main Authors | , , , , |
Format | Journal Article |
Language | English |
Published |
Cham
Springer International Publishing
01.12.2019
Springer Nature B.V |
Subjects | |
Online Access | Get full text |
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Summary: | Bifidobacteria are widely known for their probiotic potential; however, little is known regarding the ecological significance and potential probiotic effects of the phylogenetically related ‘scardovial’ genera (
Aeriscardovia
,
Alloscardovia
,
Bombiscardovia
,
Galliscardovia
,
Neoscardovia
,
Parascardovia
,
Pseudoscardovia
and
Scardovia
) and
Gardnerella
classified with bifidobacteria within the
Bifidobacteriaceae
family. Accurate classification and genotyping of bacteria using certain housekeeping genes is possible, whilst current phylogenomic analyses allow for extremely precise classification. Studies of applicable genetic markers may provide results comparable to those obtained from phylogenomic analyses of the family
Bifidobacteriaceae.
Segments of the
glyS
(624 nucleotides),
pheS
(555 nucleotides),
rpsA
(630 nucleotides), and
rpsB
(432 nucleotides) genes and their concatenated sequence were explored. The mean
glyS
,
pheS
,
rpsB
and
rpsA
gene sequence similarities calculated for
Bifidobacterium
taxa were 84.8, 85.2, 90.2 and 86.8%, respectively. Interestingly, the average value of the Average Nucleotide Identity among 67 type strains of the family
Bifidobacteriaceae
(84.70%) calculated based on values published recently was in agreement with the average pairwise similarity (84.6%) among 75 type strains of
Bifidobacteriaceae
family computed in this study using the concatenated sequences of four gene fragments. Similar to phylogenomic analyses, several gene sequence and phylogenetic analyses revealed that concatenated gene regions allow for classification of
Bifidobacteriaceae
strains into particular phylogenetic clusters and groups. Phylogeny reconstructed from the concatenated sequences assisted in defining two novel phylogenetic groups, the
Bifidobacterium psychraerophilum
group consisting of
B. psychraerophilum
,
Bifidobacterium crudilactis
and
Bifidobacterium aquikefiri
species and the
Bifidobacterium bombi
group consisting of
B. bombi
,
Bifidobacterium bohemicum
and
Bifidobacterium commune
. |
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Bibliography: | ObjectType-Article-2 SourceType-Scholarly Journals-1 ObjectType-Undefined-1 ObjectType-Feature-3 content type line 23 |
ISSN: | 0003-6072 1572-9699 |
DOI: | 10.1007/s10482-019-01307-2 |