Novel Insights Into the Phylogeny and Biotechnological Potential of Weissella Species

Abstract

In this study, the genomes of the Weissella (W.) beninensis, W. diestrammenae, W. fabalis, W. fabaria, W. ghanensis, and W. uvarum type strains were sequenced and analyzed. Moreover, the ability of these strains to metabolize 95 carbohydrates was investigated, and the genetic determinants of such capability were searched within the sequenced genomes. 16S rRNA gene and genome-based-phylogeny of all the Weissella species described to date allowed a reassessment of the Weissella genus species groups. As a result, six distinct species groups within the genus, namely, W. beninensis, W. kandleri, W. confusa, W. halotolerans, W. oryzae, and W. paramesenteroides species groups, could be described. Phenotypic analyses provided further knowledge about the ability of the W. beninensis, W. ghanensis, W. fabaria, W. fabalis, W. uvarum, and W. diestrammenae type strains to metabolize certain carbohydrates and confirmed the interspecific diversity of the analyzed strains. Moreover, in many cases, the carbohydrate metabolism pathway and phylogenomic species group clustering overlapped. The novel insights provided in our study significantly improved the knowledge about the Weissella genus and allowed us to identify features that define the role of the analyzed type strains in fermentative processes and their biotechnological potential.

Keywords: Weissella spp.; carbohydrate metabolism; genomics; phylogenomics; trehalose.

Figure 1

16S rRNA gene-based phylogeny of Weissella species. Phylogeny was performed using the neighbor-joining method; phylogenetic robustness was inferred by a bootstrapping procedure from 500 replications to obtain the confidence value for the aligned sequence dataset. Bifidobacterium bifidum ATCC 29521^T was used as an outgroup. The tree was drawn to scale, with branch lengths measured in the number of substitutions per site. Scaled circles are representative of bootstrap values.

Figure 2

Genome-based phylogeny of Weissella species. The tree was inferred by using the maximum likelihood method RAxML with progressive refinements. Bifidobacterium bifidum ATCC 29521^T was used as an outgroup. The tree is drawn to scale. Support values are represented by scaled circles at each node.

Figure 3

Comparative analysis of CAZymes in Weissella species. The heatmap was manually constructed based on CAZymes count in each species and visualized with the average linkage as a clustering method and the Euclidean distance measurement method, providing the resulting dendrogram.

Figure 4

Comparative analysis of carbohydrate metabolism in Weissella species. The heatmap was manually constructed based on the number of proteins associated with each KEGG pathway in each genome and visualized with the average linkage as a clustering method and the Euclidean distance measurement method, providing the resulting dendrogram.

Figure 5

Comparative analysis of SEED subsystem features in Weissella species. Genes annotated by RAST were assigned to functional categories and grouped into subsystems. Colored bars indicate the number of genes assigned to each category.

Figure 6

Trehalose operon in Weissella species. Genomic organization of the putative trehalose operon in the Weissella species. Gene clustering is represented by the arrows superposed on the black horizontal line. Gene and intergenic spaces are not drawn in scale. Lactococcus lactis subsp. lactis Il1403 (GenBank accession no. NC_002662): glmM, phosphoglucosamine mutase; treR, trehalose operon repressor; IIA, PTS glucose transporter subunit IIA; EIIc, PTS transporter subunit EIIC; pmgB, beta-phosphoglucomutase; α/βH, alpha/beta hydrolase; gH, glycosyl-hydrolase; polysaccharide biosynthesis C-terminal domain-containing protein flip, flippase; gT, glycosyltransferase; ppT, polysaccharide pyruvyl transferase family protein; EpsG, EpsG family protein; sT, sugar transferase; rbfABCD, rhamnose operon; dTMPk, dTMP kinase, LicD, LicD family protein.