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Comparative phylobiomic analysis of the bacterial community of water kefir by 16 S r RNA gene amplicon sequencing and ARDRA analysis
Author(s) -
Gulitz A.,
Stadie J.,
Ehrmann M.A.,
Ludwig W.,
Vogel R.F.
Publication year - 2013
Publication title -
journal of applied microbiology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.889
H-Index - 156
eISSN - 1365-2672
pISSN - 1364-5072
DOI - 10.1111/jam.12124
Subject(s) - biology , leuconostoc , bifidobacterium , 16s ribosomal rna , amplicon , metagenomics , amplified ribosomal dna restriction analysis , lactobacillus , bacteroides , ribosomal rna , sequence analysis , microbiology and biotechnology , genetics , phylogenetics , gene , bacteria , ribosomal dna , polymerase chain reaction
Aims The aim of this study was to analyse the bacterial microbiota of water kefir using culture‐independent methods. Methods and Results We compared four water kefirs of different origins using 16 S rDNA amplicon sequencing and ARDRA . The microbiota consisted of different proportions of the genera L actobacillus ( L act .), L euconostoc ( L euc .), A cetobacter ( A cet .) and G luconobacter . Surprisingly, varying but consistently high numbers of sequences representing members of the genus B ifidobacterium ( B if .) were found in all kefirs. Whereas part of the bifidobacterial sequences could be assigned to B ifidobacterium psychraerophilum , a majority of sequences identical to each other could not be assigned to any known species. A nearly full‐length sequence of the latter exhibited a beyond‐species similarity (96·4%) with the sequence from the closest relative species B if. psychraerophilum . A B ifidobacterium ‐specific ARDRA analysis reflected the abundance of the novel B ifidobacterium species by revealing its unique M bo I restriction profile. Attempts to isolate the bifidobacteria were successful for B if. psychraerophilum only. Conclusions The complexity of the water kefir microbiota has been underestimated in previously studies. The occurrence of bifidobacteria as part of the consortium is novel. Significance and Impact of the Study These data give new insights into the understanding of the complexity of food fermentations and underline the need for approaches detecting noncultivable organisms.