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Antonie van Leeuwenhoek

, Volume 112, Issue 12, pp 1785–1800 | Cite as

Genetic marker-based multi-locus sequence analysis for classification, genotyping, and phylogenetics of the family Bifidobacteriaceae as an alternative approach to phylogenomics

  • Chahrazed Mekadim
  • Věra Bunešová
  • Eva Vlková
  • Zuzana Hroncová
  • Jiří KillerEmail author
Original Paper

Abstract

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.

Keywords

Bifidobacteria Scardovia Identification Housekeeping genes 

Notes

Acknowledgements

This study was supported by Project Excellence [Grant No. CZ.02.1.01/0.0/0.0/15_003/0000460], the Czech National Agency for Agricultural Research [Projects Nos. QJ1610248 and QJ1510338], and an internal university grant application [Grant No. CIGA 20182018].

Author’s contribution

JK, CM are conceived and designed experiments. CM, VB, EV, ZH, JK are performed the experiments. JK, VB, EV, CM are analysed the data. VB, EV, ZH are contributed reagents/materials/analysis tools. JK, CM are wrote the manuscript.

Compliance with ethical standards

Conflict of interest

The authors declare that they no conflict of interest.

Supplementary material

10482_2019_1307_MOESM1_ESM.pptx (1.8 mb)
Supplementary material 1 (PPTX 1847 kb)
10482_2019_1307_MOESM2_ESM.xlsx (32 kb)
Supplementary material 2 (XLSX 31 kb)
10482_2019_1307_MOESM3_ESM.xls (116 kb)
Supplementary material 3 (XLS 115 kb)

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© Springer Nature Switzerland AG 2019

Authors and Affiliations

  1. 1.Institute of Animal Physiology and Genetics of the Czech Academy of SciencesKrčCzech Republic
  2. 2.Department of Microbiology, Nutrition and Dietetics, Food and Natural Resources, Faculty of AgrobiologyCzech University of Life SciencesSuchdolCzech Republic

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