Advances in genomics and safety studies of <italic>Weissella confusa </italic>

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Weissella confusa is an important species of lactic acid bacteria in the fermentation industry, primarily presents in fresh fruits, vegetables and fermented products. Nowadays, W. confusa is often used to improve the textural properties of food products in the food industry because it is rich in extracellular polysaccharides. W. confusa is resistant to bile salts and exhibits bacteriostatic effects; in addition, it can colonise the intestines of animals and humans, thereby fulfilling probiotic functions. However, previous studies have reported that W. confusa is possibly pathogenic on animals and humans, although case reports are rare. It also showed resistance to some antibiotics, especially vancomycin. The safety of this strain is still unclear and it is not included in the list of QPS (Qualified Presumption of Safety) by the EFSA (European Food Safety Authority) for the time being. With the completion of the first whole-genome sequence of W. confusa , LBAE C39-2, genome research on this species is emerging. Presently, complete genome sequences are available for 34 W. confusa . The genome sizes are between 1.44 and 2.38 Mb and the GC contents are between 43.90% and 45.08%. In this review, we first summarise the taxonomic profile and identification methods of W. confusa at the genomic level, emphasising its high similarity to W. cibaria at the phenotypic and phylogenetic levels. The identification methods include housekeeping genes, amplified fragment length polymorphism (AFTP) and specific gene clusters. Then, the important functional genes of the W. confusa genome are introduced, such as gtf genes and ftf genes, which have a close relationship to the characteristics of extracellular polysaccharides. Subsequently, heterologous expression of functional genes has also been shown through several previous studies, and bacterial plasmids play a crucial role in this process. Furthermore, some functional genes associated with the production of bacteriocin and amino acids were also found in W. confusa . We describe the current status of safety assessment for W. confusa , animal tests and in vitro toxicological experiments with further analysis of virulence and antibiotic resistance genes, which confirmed that some strains of W. confusa are nontoxic. Finally, this review summarises the current research on the genomics of W. confusa . More attention must be paid to identify more accurate specific marker genes for interspecific identification and phylogenetic analysis of evolutionary differences among W. confusa strains. In the future, genetic engineering technology, such as heterologous gene expression, should be used to improve the fermentation efficiency of W. confusa in industrial applications. On the basis of current studies on the safety of W. confusa , corresponding MIC-specific breakpoints of this species need to be designated. Further research should be established to identify additional virulence factors and resistance genes to lay a theoretical foundation for the application of W. confusa .