Strains belonging to the
Weissella genus are frequently recovered from spontaneously fermented foods. Their functional, microbial-modulating, and probiotic traits enhance not only the sensorial properties but also the nutritional value, beneficial effects, and safety of fermented products. Sporadic cases of opportunistic pathogenicity and
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Strains belonging to the
Weissella genus are frequently recovered from spontaneously fermented foods. Their functional, microbial-modulating, and probiotic traits enhance not only the sensorial properties but also the nutritional value, beneficial effects, and safety of fermented products. Sporadic cases of opportunistic pathogenicity and antibiotic resistance have deprived safety status from all
Weissella species, which thus remain understudied. Our study increased the number of available high-quality and taxonomically accurate
W. paramesenteroides genomes by 25% (9 genomes reported, leading to a total of 36 genomes). We conducted a phylogenetic and comparative genomic analysis of the most dominant
Weissella species (
W. cibaria,
W. paramesenteroides,
W. viridescens,
W. soli,
W. koreensis,
W. hellenica and
W. thailadensis). The phylogenetic tree corroborated species assignment but also revealed phylogenetic diversity within the
Weissella species, which is likely related to the adaptation of
Weissella in different niches. Using robust alignment criteria, we showed the overall absence of resistance and virulence genes in
Weissella spp., except for one
W. cibaria isolate carrying
blaTEM-181. Enrichment analysis showed the association of
Weissella species several CAZymes, which are essential for biotechnological applications. Additionally, the combination of CAZyme metabolites with probiotics can potentially lead to beneficial effects for hosts, such as the inhibition of inflammatory processes and the reduction of cholesterol levels. Bacteriocins and mobile genetic elements MGEs (
Inc11 plasmid and
ISS1N insertion sequence) were less abundant, however
W. thailadensis and
W. viridescens showed significant association with specific bacteriocin-encoding genes. Lastly, an analysis of phenotypic traits underlined the need to carefully evaluate
W. cibaria strains before use as food additives and suggested the possibility of employing
W. paramesenteroides and
W. hellenica in the fermentation process of vegetable products. More studies providing high-resolution characterization of
Weissella strains from various sources are necessary to elucidate the safety of
Weissella spp. and exploit their beneficial characteristics.
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