Clustering of Pan- and Core-genome of Lactobacillus provides Novel Evolutionary Insights for Differentiation.

BACKGROUND: Bacterial taxonomy aims to classify bacteria based on true evolutionary events and relies on a polyphasic approach that includes phenotypic, genotypic and chemotaxonomic analyses. Until now, complete genomes are largely ignored in taxonomy. The genus Lactobacillus consists of 173 species and many genomes are available to study taxonomy and evolutionary events. RESULTS: We analyzed and clustered 98 completely sequenced genomes of the genus Lactobacillus and 234 draft genomes of 5 different Lactobacillus species, i.e. L. reuteri, L. delbrueckii, L. plantarum, L. rhamnosus and L. helveticus. The core-genome of the genus Lactobacillus contains 266 genes and the pan-genome 20'800 genes. Clustering of the Lactobacillus pan- and core-genome resulted in two highly similar trees. This shows that evolutionary history is traceable in the core-genome and that clustering of the core-genome is sufficient to explore relationships. Clustering of core- and pan-genomes at species' level resulted in similar trees as well. Detailed analyses of the core-genomes showed that the functional class "genetic information processing" is conserved in the core-genome but that "signaling and cellular processes" is not. The latter class encodes functions that are involved in environmental interactions. Evolution of lactobacilli seems therefore directed by the environment. The type species L. delbrueckii was analyzed in detail and its pan-genome based tree contained two major clades whose members contained different genes yet identical functions. In addition, evidence for horizontal gene transfer between strains of L. delbrueckii, L. plantarum, and L. rhamnosus, and between species of the genus Lactobacillus is presented. Our data provide evidence for evolution of some lactobacilli according to a parapatric-like model for species differentiation. CONCLUSIONS: Core-genome trees are useful to detect evolutionary relationships in lactobacilli and might be useful in taxonomic analyses. Lactobacillus' evolution is directed by the environment and HGT.

Draft Genome Sequences of 43 Lactobacillus Strains from the Species L. curvatus, L. fermentum, L. paracasei, L. plantarum, L. rhamnosus, and L. sakei, Isolated from Food Products.

The genome sequences of 43 Lactobacillus strains from the species L. curvatus, L. fermentum, L. paracasei, L. plantarum, L. rhamnosus, and L. sakei were determined using Illumina MiSeq.

Complete and Assembled Genome Sequence of Lactobacillus plantarum RI-113 Isolated from Salami.

We present here the complete genome sequence of Lactobacillus plantarum RI-113, a strain isolated from salami, which was determined using single-molecule real-time sequencing.

Complete and Assembled Genome Sequence of Vagococcus teuberi DSM 21459T, a Novel Species Isolated from Fermented Cow Milk in Mali.

The genome of Vagococcus teuberi DSM 21459T, a strain isolated from Malian fermented milk, was sequenced using single-molecule real-time sequencing. The genome of V. teuberi DSM 21459T is the first sequenced genome of this novel species and the second genome among the genus Vagococcus.

High-throughput screening assays for antibacterial and antifungal activities of Lactobacillus species.

We describe high-throughput screening techniques to rapidly detect either antimicrobial activity, using an agar-well diffusion assay in microtiter plates, or antifungal activity using an agar-spot assay in 24-well plates. 504 Lactobacillus isolates were screened with minimal laboratory equipment and screening rates of 2000-5000 individual antimicrobial interactions.