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.

Probiotic Potential and Safety Assessment of Type Strains of Weissella and Periweissella Species

“…Considering both the probiotic and safety assessments of the six type strains, it can be concluded that P. beninensis LMG 25373 T is a safe potential probiotic strain. This strain in a previous study ( 2 ) showed the widest consumption of carbon sources. Indeed, among the six type strains tested, P. beninensis LMG 25373 T was the only one capable of using d -galactose (indeed, it was found to harbor the galA gene, encoding α-galactosidase [EC 3.2.1.22] [KAK10_01740], which hydrolyzes α-1,6-galactoside linkages found in sugars such as raffinose, melibiose, and stachyose and branched polysaccharides like galactomannans and galactoglucomannans), α- d -lactose, lactulose, d -melibiose, β-methyl- d -galactoside, d -raffinose, sucrose, pyruvic acid methyl ester, and UMP ( 2 ).…”

“…The EPS production influences the biochemical properties of the cell, including hydrophobicity and surface charge; EPS stabilizes microbial biofilm, enhancing bacterial adhesion and aggregation and increasing the tolerance to environmental stress ( 45 ). The consumption of sucrose and raffinose by P. beninensis LMG 25373 T was previously demonstrated ( 2 ), and only this strain was able to produce EPS in MRS agar supplemented with sucrose.…”

“…We performed a homology-based analysis to verify the presence of genes putatively involved with the functional and probiotic capacities of Weissella and Periweissella type strains, whose genomes were recently sequenced and reported by Fanelli et al ( 2 ); the analysis was based on the genetic screening previously performed by Turpin et al ( 19 ). The set of genes evaluated include those involved in bile salt tolerance, pH survival, biogenic amine synthesis, riboflavin synthesis, folate synthesis, and starch metabolism.…”

“…The ability of the P. beninensis type strain to metabolize nondigestible sugars, such as oligosaccharides of the raffinose family and galactomannans, is a feature common to several probiotic bacteria ( 2 ). Recently, the potential of raffinose as a prebiotic, i.e., a dietary fiber component that cannot be digested by the human gastrointestinal tract but can be selectively fermented by bacteria in the gastrointestinal tract, has been highlighted.…”

“…The genus Weissella comprises a group of lactic acid bacteria (LAB), which have received increased attention in the last decade mainly for their biotechnological and probiotic potential ( 1 – 3 ). The taxonomy of this genus, which belongs to the phylum Firmicutes , order Lactobacillales , and the family Lactobacillaceae , was recently updated by Fanelli et al ( 2 ), who, based on a comprehensive phylogenomic analysis, clustered the 21 Weissella species described to date into six species groups. Furthermore, Bello et al ( 4 ) recently revised the taxonomy of the family Leuconostocaceae merged with the Lactobacillaceae ( 5 ) by phylogenomic and comparative genomic analysis.…”