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

Abstract

Lactic acid bacteria (LAB) in the genus Weissella spp. contain traits in their genome that confer versatility. In particular, Weissella cibaria encodes several beneficial genes that are useful in biotechnological applications. The complete genome of W. cibaria NH9449 was sequenced and an in silico comparative analysis was performed to gain insight into the genomic diversity among members of the genus Weissella. A total of 219 Weissella genomes were used in a bioinformatics analysis of pan-genomes, phylogenetics, self-defense mechanisms, virulence factors, antimicrobial resistance, and carbohydrate-active enzymes. These investigations showed that the strain NH9449 encodes several restriction-modification-related genes and a CRISPR-Cas region in its genome. The identification of carbohydrate-active enzyme-encoding genes indicated that this strain could be beneficial in biotechnological applications. The comparative genomic analysis reveals the very high genomic diversity in this genus, and some marked differences in genetic variation and genes among Weissella species. The calculated average amino acid identity (AAI) and phylogenetic analysis of core and accessory genes shows the possible existence of three new species in this genus. These new genomic insights into Weissella species and their biological functions could be useful in the food industry and other applications.

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 ).…”

Probiotic Insights from the Genomic Exploration of Lacticaseibacillus paracasei Strains Isolated from Fermented Palm Sap

“…Out of these, 12,259 genomes (1639 of which are complete) belong to the Lactobacillaceae family [ 14 ]. Previous studies have used whole-genome sequencing (WGS) technologies and bioinformatics to investigate the safety and potential benefits of probiotics used in food fermentation, such as fermented pork sausages [ 20 , 21 ], fermented milk [ 22 , 23 ], and fermented congee [ 24 ]. These studies conducted an in silico safety assessment using the complete nucleotide sequence of the bacterial genome to confirm safety and unveil traits derived from the predicted genes.…”