In silico comparative genomics analysis of Lactiplantibacillus plantarum DW12, a potential gamma-aminobutyric acid (GABA)-producing strain

Surachat, Komwit; Deachamag, Panchalika; Kantachote, Duangporn; Wonglapsuwan, Monwadee; Jeenkeawpiam, Kongpop; Chukamnerd, Arnon

doi:10.1016/j.micres.2021.126833

Cited by 17 publications

(12 citation statements)

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“…This analysis clarified the frequency of bacteriocin-encoding genes in Weissella spp. We found that only a few bacterial strains in the genus encode ribosomally synthesized antibacterial peptides, while LAB in other genera encode a larger diversity of bacteriocin-encoding genes: for example, Pediococcus ( Jiang et al, 2020 ; Surachat et al, 2021b ), Lactobacillus ( Kaskoniene et al, 2017 ; Surachat et al, 2021a ), and Enterococcus ( Nes et al, 2007 ; Lopez-Cuellar et al, 2016 ). Even though bacteriocins are a crucial biological tool for inhibiting pathogens and other microorganisms, most Weissella spp.…”

Section: Resultsmentioning

confidence: 96%

“…The assembly process was then performed by Unicycler v0.4.7 ( Wick et al, 2017 ) using both the short-read and long-read sequences. We then scanned for a small plasmid that could be absent from the assembly as described previously ( Surachat et al, 2021a , b ). Briefly, we mapped short-read sequences to draft assembly and extracted all unmapped reads to perform de novo assembly with spades v3.12 ( Bankevich et al, 2012 ).…”

Section: Methodsmentioning

confidence: 99%

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

et al. 2022

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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.

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Section: Resultsmentioning

confidence: 96%

Section: Methodsmentioning

confidence: 99%

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

et al. 2022

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“…These values are similar and within the normal range reported in the literature for most of the P. acidilactici and Lpb. paraplantarum strains [ 53 , 54 , 55 , 56 , 57 ]. Other characteristics of these genomes are summarized in Table 4 .…”

Section: Resultsmentioning

confidence: 99%

Lactiplantibacillus paraplantarum BPF2 and Pediococcus acidilactici ST6, Two Bacteriocinogenic Isolated Strains from Andalusian Spontaneous Fermented Sausages

García-López

Teso-Pérez

Martín‐Platero

et al. 2023

Foods

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Traditional spontaneously fermented foods are well known for their sensory and safety properties, which is mainly due to their indigenous microflora. Within this group of food, Mediterranean dry-cured sausages stand out as a significant source of lactic-acid bacterial strains (LAB) with biotechnological properties, such as their antimicrobial activity. The aim of this study was to investigate the biodiversity of antagonistic LAB strains from different Andalusian traditional sausages, such as salchichón and chorizo. First, a screening was carried out focusing on the antimicrobial activity against foodborne pathogens, such as Listeria monocytogenes, Escherichia coli, Clostridium perfringens, and Staphylococcus aureus, selecting two strains due to their higher antibiosis properties, both in agar and liquid media. These bacteria were identified as Lactiplantibacillus paraplantarum BPF2 and Pediococcus acidilactici ST6. In addition, genomic studies confirmed the presence of certain structural genes related to the production of bacteriocins. Finally, the culture supernatants of both strains were purified and analyzed by LC-MS/MS, obtaining the relative molecular mass and the amino acid sequence and identifying the peptides as the bacteriocins Pediocin-PA and Leucocin K. In conclusion, genomes and antimicrobial substances of P. acidilactici ST6, a Pediocin-PA producer, and Lpb. paraplantarum BPF2, a Leucocin K producer, isolated from Andalusian salchichón and chorizo, respectively, are presented in this work. Although further studies are required, these strains could be used alone or in combination as starters or protective cultures for the food industry.

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“…Further investigation, conducted by Surachat et al indicates that L. plantarum is a key GABA-producing species in nature since almost all strains encoded the GAD operon in their genome [83].…”

Section: Gaba Function and Metabolismmentioning

confidence: 99%

Biosynthesis of Gamma-Aminobutyric Acid (GABA) by Lactiplantibacillus plantarum in Fermented Food Production

Iorizzo,

Paventi,

Di Martino

2023

CIMB

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In recent decades, given the important role of gamma-aminobutyric acid (GABA) in human health, scientists have paid great attention to the enrichment of this chemical compound in food using various methods, including microbial fermentation. Moreover, GABA or GABA-rich products have been successfully commercialized as food additives or functional dietary supplements. Several microorganisms can produce GABA, including bacteria, fungi, and yeasts. Among GABA-producing microorganisms, lactic acid bacteria (LAB) are commonly used in the production of many fermented foods. Lactiplantibacillus plantarum (formerly Lactobacillus plantarum) is a LAB species that has a long history of natural occurrence and safe use in a wide variety of fermented foods and beverages. Within this species, some strains possess not only good pro-technological properties but also the ability to produce various bioactive compounds, including GABA. The present review aims, after a preliminary excursus on the function and biosynthesis of GABA, to provide an overview of the current uses of microorganisms and, in particular, of L. plantarum in the production of GABA, with a detailed focus on fermented foods. The results of the studies reported in this review highlight that the selection of new probiotic strains of L. plantarum with the ability to synthesize GABA may offer concrete opportunities for the design of new functional foods.

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In silico comparative genomics analysis of Lactiplantibacillus plantarum DW12, a potential gamma-aminobutyric acid (GABA)-producing strain

Cited by 17 publications

References 78 publications

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

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

Lactiplantibacillus paraplantarum BPF2 and Pediococcus acidilactici ST6, Two Bacteriocinogenic Isolated Strains from Andalusian Spontaneous Fermented Sausages

Biosynthesis of Gamma-Aminobutyric Acid (GABA) by Lactiplantibacillus plantarum in Fermented Food Production

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