title: Metagenomic analysis of the microbial community in kefir grains.
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 ∼1.6 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.
authors.affiliation: Department of Electrical Engineering, University of Nebraska-Lincoln, 68588 Nebraska, USA.
authors.forename: Ufuk
authors.initials: U
authors.lastname: Nalbantoglu
authors.affiliation: Department of Genetics, Institute of Experimental Medical Research, Istanbul University, 34093 Istanbul, Turkey.
authors.forename: Atilla
authors.initials: A
authors.lastname: Cakar
authors.affiliation: Department of Genetics and Bioengineering, Istanbul Bilgi University, 34060 Istanbul, Turkey.
authors.forename: Haluk
authors.initials: H
authors.lastname: Dogan
authors.affiliation: Department of Genetics, Institute of Experimental Medical Research, Istanbul University, 34093 Istanbul, Turkey.
authors.forename: Neslihan
authors.initials: N
authors.lastname: Abaci
authors.affiliation: Department of Genetics, Institute of Experimental Medical Research, Istanbul University, 34093 Istanbul, Turkey.
authors.forename: Duran
authors.initials: D
authors.lastname: Ustek
authors.affiliation: Department of Electrical Engineering, University of Nebraska-Lincoln, 68588 Nebraska, USA.
authors.forename: Khalid
authors.initials: K
authors.lastname: Sayood
authors.affiliation: Department of Genetics and Bioengineering, Istanbul Bilgi University, 34060 Istanbul, Turkey. Electronic address: handan.can@bilgi.edu.tr.
authors.forename: Handan
authors.initials: H
authors.lastname: Can
mesh_terms: D000818:Animals; D002417:Cattle; D043302:Cultured Milk Products / Q000382:microbiology*; D007777:Lactobacillaceae / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification* / Q000378:metabolism; D056186:Metagenomics; D008969:Molecular Sequence Data; D010802:Phylogeny; D017422:Sequence Analysis, DNA
keywords: Kefir; Metagenomics; Microbial diversity; Pyrosequencing; Whole genome sequencing