Phenotypic and phylogenetic diversity of plant origin lactic acid bacteria
Naoto Tanaka1, Hideaki Sugawara2, Sanae Okada1
1
NODAI Culture Collection Center, Tokyo University of Agriculture, 1-1-1 Sakuragaoka,
Setagaya-ku, Tokyo 156-8502, Japan
2
Laboratory of Research and Development of Biological Databases, Center for Information
Biology and DNA Data Bank of Japan, National Institute of genetics, 1111 Yata, Mishima
Shizuoka, 411-8540, Japan
We have isolated approximately 2,600 strains of lactic acid bacteria from various plant origin
materials, such as fermented food. In addition, their phenotypic and genotypic data have
been accumulated. Phenotypic data for isolates are derived mainly from litmus milk, nitrate
reduction, and growth tests including carbon assimilation, pH, and temperature tests.
Genotypic data include 16S rRNA and recA gene data of isolates. In this study, we
comprehensively evaluated and characterized the diversity of plant origin lactic acid bacteria
with a data integration system, InforBIO software (http://wdcm.nig.ac.jp/inforbio/).
Isolates were assigned to 13 genera on the basis of 16S rRNA gene sequences. To research
the phylogenetic diversity in isolates, 16S rRNA gene sequences of isolates were clustered
by using the blastclust program (threshold, similarity > 99.6% and coverage > 80%), and then
480 clusters were constructed. The largest cluster constructed was composed of 600
isolates, belonging to Lactobacillus plantarum phylogenetic group. Other large clusters were
composed of Lactobacillus casei group (280 isolates), Leuconostoc mesenteroides group
(130 isolates), Pediococcus pentosaceus group (130 isolates), and Lactobacillus fermentum
group (130 isolates). Phenotypic diversity in each group was evaluated by Shannon's
entropy and primary component analysis (PCA) with phenotypic data of isolates.
Interestingly, L. plantarum and P. pentosaceus groups were more diverse in various tests
than other groups, and the results of PCA seemed to indicate that the phenotypic diversity
was correlated with several traits in each phylogenetic group, such as acid and alkali
tolerance abilities in L. plantarum group. Diversity of such a trait might be an important
feature for the characterization of the phylogenetic group and species.