Metagenomic analysis of the microbial community in kefir grains

Kefir grains as a probiotic have been subject to microbial community identification using culture-dependent and independent methods that target specific strains in the community, or that are based on limited 16S rRNA analysis. We performed whole genome shotgun pyrosequencing using two Turkish Kefir...

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Bibliographic Details
Published in:Food microbiology 2014-08, Vol.41, p.42-51
Main Authors: Nalbantoglu, Ufuk, Cakar, Atilla, Dogan, Haluk, Abaci, Neslihan, Ustek, Duran, Sayood, Khalid, Can, Handan
Format: Article
Language:English
Subjects:
Animals
Biological and medical sciences
Cattle
Cultured Milk Products - microbiology
Food industries
Food microbiology
Fundamental and applied biological sciences. Psychology
Kefir
Lactobacillaceae - classification
Lactobacillaceae - genetics
Lactobacillaceae - isolation & purification
Lactobacillaceae - metabolism
Metagenomics
Microbial diversity
Molecular Sequence Data
Phylogeny
Pyrosequencing
Sequence Analysis, DNA
Whole genome sequencing
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Summary:Kefir grains as a probiotic have been subject to microbial community identification using culture-dependent and independent methods that target specific strains in the community, or that are based on limited 16S rRNA analysis. We performed whole genome shotgun pyrosequencing using two Turkish Kefir grains. Sequencing generated 3,682,455 high quality reads for a total of ∼1.6 Gbp of data assembled into 6151 contigs with a total length of ∼24 Mbp. Species identification mapped 88.16% and 93.81% of the reads rendering 4 Mpb of assembly that did not show any homology to known bacterial sequences. Identified communities in the two grains showed high concordance where Lactobacillus was the most abundant genus with a mapped abundance of 99.42% and 99.79%. This genus was dominantly represented by three species Lactobacillus kefiranofaciens, Lactobacillus buchneri and Lactobacillus helveticus with a total mapped abundance of 97.63% and 98.74%. We compared and verified our findings with 16S pyrosequencing and model based 16S data analysis. Our results suggest that microbial community profiling using whole genome shotgun data is feasible, can identify novel species data, and has the potential to generate a more accurate and detailed assessment of the underlying bacterial community, especially for low abundance species. •Two Turkish kefir grains were pyrosequenced using Whole Genome Shotgun (WGS).•WGS results were compared with 16S based species identification.•WGS provided a higher resolution and more accurate assessment of the microflora.•Both samples were dominantly made up of the genus Lactobacillus.•4 Mbp of novel species sequence data was generated.
ISSN:0740-0020
1095-9998
DOI:10.1016/j.fm.2014.01.014