title: Identification of lactic acid bacteria within the consortium of a kefir grain by sequencing 16S rDNA variable regions.
abstract: The microflora of a kefir grain was identified using a polymerase chain reaction-based strategy combined with 16S rRNA gene sequencing. DNA was extracted from the kefir grain and amplified in its 16S rDNA V1 and V2 regions. To guarantee a good representation of the overall lactic acid bacteria populations, DNA amplification was performed separately with primers specific either to the dominant or to the less abundant bacterial groups. The amplified fragments were cloned in Escherichia coli and then sequenced. Sequences of the V1 region were gathered into 5 groups of similarity and identified by aligning with the sequences of a public library. The V1 region allowed the identification of Lactobacillus kefiranofaciens, L. kefir, L. parakefir, and Lactococcus lactis but was inappropriate for the identification of leuconostocs at species level. Among 16S rDNA variable regions, the V2 region showed the highest variability between Leuconostoc species. Nevertheless, even in the V2 region, differences were too tenuous for effective identification of L. mesenteroides. The methodology described here allowed detection of the dominant species within each targeted microbial group.
authors.affiliation: Département Qualité des Productions Agricoles, Centre Wallon de Recherches Agronomiques (CRA-W), 24 Chaussée de Namur, B-5030 Gembloux, Belgium.
authors.forename: Véronique
authors.initials: V
authors.lastname: Ninane
authors.forename: Radegonde
authors.initials: R
authors.lastname: Mukandayambaje
authors.forename: Gilbert
authors.initials: G
authors.lastname: Berben
mesh_terms: D000595:Amino Acid Sequence; D001483:Base Sequence; D002623:Chemistry Techniques, Analytical / Q000379:methods*; D003001:Cloning, Molecular; D043302:Cultured Milk Products / Q000378:metabolism*; D004247:DNA / Q000378:metabolism; D017931:DNA Primers / Q000737:chemistry; D004275:DNA, Ribosomal / Q000235:genetics*; D005504:Food Analysis / Q000379:methods*; D005506:Food Contamination; D019344:Lactic Acid / Q000378:metabolism*; D008969:Molecular Sequence Data; D015203:Reproducibility of Results; D012689:Sequence Homology, Nucleic Acid; D045249:Sphingobacterium / Q000378:metabolism
chemical_list: D017931:DNA Primers; D004275:DNA, Ribosomal; D019344:Lactic Acid; D004247:DNA