Comparative phylobiomic analysis of the bacterial community of water kefir by 16S rRNA gene amplicon sequencing and ARDRA analysis
Article first published online: 29 JAN 2013
© 2013 The Society for Applied Microbiology
Journal of Applied Microbiology
Volume 114, Issue 4, pages 1082–1091, April 2013
How to Cite
Gulitz, A., Stadie, J., Ehrmann, M.A., Ludwig, W. and Vogel, R.F. (2013), Comparative phylobiomic analysis of the bacterial community of water kefir by 16S rRNA gene amplicon sequencing and ARDRA analysis. Journal of Applied Microbiology, 114: 1082–1091. doi: 10.1111/jam.12124
- Issue published online: 18 MAR 2013
- Article first published online: 29 JAN 2013
- Accepted manuscript online: 5 JAN 2013 02:40AM EST
- Manuscript Accepted: 23 DEC 2012
- Manuscript Revised: 20 DEC 2012
- Manuscript Received: 8 NOV 2012
- German Ministry of Economics and Technology
- WiFö (Wissenschaftsförderung der Deutschen Brauwirtschaft, Berlin, Germany). Grant Number: AiF 16454
- DFG (Deutsche Forschungsgemeinschaft). Grant Number: Lu 421/7-1
- 16S rRNA gene amplicon sequencing;
- microbiota of water kefir;
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 16S rDNA amplicon sequencing and ARDRA. The microbiota consisted of different proportions of the genera Lactobacillus (Lact.), Leuconostoc (Leuc.), Acetobacter (Acet.) and Gluconobacter. Surprisingly, varying but consistently high numbers of sequences representing members of the genus Bifidobacterium (Bif.) were found in all kefirs. Whereas part of the bifidobacterial sequences could be assigned to Bifidobacterium 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 Bif. psychraerophilum. A Bifidobacterium-specific ARDRA analysis reflected the abundance of the novel Bifidobacterium species by revealing its unique MboI restriction profile. Attempts to isolate the bifidobacteria were successful for Bif. psychraerophilum only.
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.