Metagenomic analysis of the microbial community in kefir grains

Ufuk Nalbantoglu, Atilla Cakar, Haluk Dogan, Neslihan Abaci, Duran Ustek, Khalid Sayood, Handan Can

Research output: Contribution to journalArticle

46 Citations (Scopus)

Abstract

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 ~1.6Gbp of data assembled into 6151 contigs with a total length of ~24Mbp. Species identification mapped 88.16% and 93.81% of the reads rendering 4Mpb 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.

Original languageEnglish (US)
Pages (from-to)42-51
Number of pages10
JournalFood Microbiology
Volume41
DOIs
StatePublished - Aug 1 2014

Fingerprint

kefir
Metagenomics
Lactobacillus
microbial communities
Firearms
Lactobacillus helveticus
Genome
Lactobacillus buchneri
genome
Probiotics
rendering
bacterial communities
probiotics
data analysis
ribosomal RNA
Kefir
methodology

Keywords

  • Kefir
  • Metagenomics
  • Microbial diversity
  • Pyrosequencing
  • Whole genome sequencing

ASJC Scopus subject areas

  • Food Science
  • Microbiology

Cite this

Nalbantoglu, U., Cakar, A., Dogan, H., Abaci, N., Ustek, D., Sayood, K., & Can, H. (2014). Metagenomic analysis of the microbial community in kefir grains. Food Microbiology, 41, 42-51. https://doi.org/10.1016/j.fm.2014.01.014

Metagenomic analysis of the microbial community in kefir grains. / Nalbantoglu, Ufuk; Cakar, Atilla; Dogan, Haluk; Abaci, Neslihan; Ustek, Duran; Sayood, Khalid; Can, Handan.

In: Food Microbiology, Vol. 41, 01.08.2014, p. 42-51.

Research output: Contribution to journalArticle

Nalbantoglu, U, Cakar, A, Dogan, H, Abaci, N, Ustek, D, Sayood, K & Can, H 2014, 'Metagenomic analysis of the microbial community in kefir grains', Food Microbiology, vol. 41, pp. 42-51. https://doi.org/10.1016/j.fm.2014.01.014
Nalbantoglu, Ufuk ; Cakar, Atilla ; Dogan, Haluk ; Abaci, Neslihan ; Ustek, Duran ; Sayood, Khalid ; Can, Handan. / Metagenomic analysis of the microbial community in kefir grains. In: Food Microbiology. 2014 ; Vol. 41. pp. 42-51.
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