Complete Genome Sequence of Weissella confusa LM1 and Comparative Genomic Analysis

Abstract

The genus Weissella is attracting an increasing amount of attention because of its multiple functions and probiotic potential. In particular, the species Weissella confusa is known to have great potential in industrial applications and exhibits numerous biological functions. However, the knowledge on this bacterium in insects is not investigated. Here, we isolated and identified W. confusa as the dominant lactic acid bacteria in the gut of the migratory locust. We named this strain W. confusa LM1, which is the first genome of an insect-derived W. confusa strain with one complete chromosome and one complete plasmid. Among all W. confusa strains, W. confusa LM1 had the largest genome. Its genome was the closest to that of W. confusa 1001271B_151109_G12, a strain from human feces. Our results provided accurate evolutionary relationships of known Weissella species and W. confusa strains. Based on genomic analysis, the pan-genome of W. confusa is in an open state. Most strains of W. confusa had the unique genes, indicating that these strains can adapt to different ecological niches and organisms. However, the variation of strain-specific genes did represent significant correlations with their hosts and ecological niches. These strains were predicted to have low potential to produce secondary metabolites. Furthermore, no antibiotic resistance genes were identified. At the same time, virulence factors associated with toxin production and secretion system were not found, indicating that W. confusa strains were not sufficient to perform virulence. Our study facilitated the discovery of the functions of W. confusa LM1 in locust biology and their potential application to locust management.

Complete Genome Sequence of Weissella cibaria NH9449 and Comprehensive Comparative-Genomic Analysis: Genomic Diversity and Versatility Trait Revealed

“…W. cibaria (101), W. confusa (88), and W. jogaejeotgali (83) are the three species that encode most CAZyme genes in their genomes. Our identification results are consistent with those of a previous study ( Yuan et al, 2021 ), which found that W. confusa and W. cibaria metabolize carbohydrates and could be beneficial in several applications. These findings could also imply that most Weissella species, and especially W. cibaria and W. confusa , specialize in carbohydrate metabolism, which helps control mass degradation in the fermentation process.…”

“…However, W. cibaria was not the only species whose pan-genome showed a tendency to be closed. In a previous report ( Yuan et al, 2021 ), the pan-genome of 39 W. confusa strains was also open but in this study, when we analyzed 77 strains of W. confusa , the pan-genome status tended to be closed. In addition, we observed that the core genome sizes of W. cibaria strains seemed to be stable after sequencing around 50 genomes including ≈ 1,200 genes ( Supplementary Figure 5B ).…”

“…Several research works have focused on the potential of phenotypic and genotypic traits of Weissella spp. ( Panthee et al, 2019 ; Shin et al, 2020 ; Yeong et al, 2020 ; Yuan et al, 2021 ). In particular W. cibaria , this species is a key member of the genus and exhibits a variety of traits and abilities.…”

Lactiplantibacillus plantarum from Unexplored Tunisian Ecological Niches: Antimicrobial Potential, Probiotic and Food Applications

“…Indeed, some very recent research has looked into the probiotic potential of LAB obtained from insect guts [64,75,76]. A complete genome sequence of Weissella confusa LM1, found in the gut of the migratory locust, indicated the ability to adapt to different ecological niches [77]. While there are studies on microbiological communities (including LAB) in grasshoppers (Locusta migratoria migratorioides) sold for human consumption [78], to our knowledge, this is the first report studying the probiotic potentialities of locust-derived LAB.…”

The Weissella and Periweissella genera: up-to-date taxonomy, ecology, safety, biotechnological, and probiotic potential

“…Culture-independent approaches including PCR-DGGE and next-generation sequencing approaches such as metagenetics and metagenomics have allowed the detection of weissellas in various ecological niches ( Table 2 ). Whole-genome sequencing is another approach that is being widely used to identify and characterize weissellas (Benomar et al, 2011 ; Kim et al, 2011 ; Amari et al, 2012 ; Lee J. H. et al, 2012 ; Figueiredo et al, 2014a , b , 2015 ; Tanizawa et al, 2014 ; Malik et al, 2016 ; Heng et al, 2017 ; Ku et al, 2017 ; Li et al, 2017 ; Du et al, 2018 ; Garcia-Cancino et al, 2019 ; Kwak et al, 2019 ; Panthee et al, 2019 ; Lin et al, 2020 ; Månberger et al, 2020 ; Baugh et al, 2021 ; Contente et al, 2021 ; Jang et al, 2021 ; Patrone et al, 2021 ; Yuan et al, 2021 ; Apostolakos et al, 2022 ; Fanelli et al, 2022 ; Fukuda and Nolasco-Hipolito, 2022 ; Surachat et al, 2022 ; Teixeira et al, 2022 ).…”