Genomic Insight into Pediococcus acidilactici HN9, a Potential Probiotic Strain Isolated from the Traditional Thai-Style Fermented Beef Nhang

Abstract

Pediococcus acidilactici HN9 is a beneficial lactic acid bacterium isolated from Nhang, a traditional Thai-style fermented beef. In this study, the molecular properties of P. acidilactici HN9 were characterized to provide insights into its potential probiotic activity. Specifically, this work sought to report the complete genome of P. acidilactici HN9 and perform a comparative genome analysis with other bacterial strains belonging to the genus Pediococcus. Genomic features of HN9 were compared with those of all other bacterial Pediococcus strains to examine the adaptation, evolutionary relationships, and diversity within this genus. Additionally, several bioinformatic approaches were used to investigate phylogenetic relationships, genome stability, virulence factors, bacteriocin production, and antimicrobial resistance genes of the HN9 strain, as well as to ensure its safety as a potential starter culture in food applications. A 2,034,522 bp circular chromosome and two circular plasmids, designated pHN9-1 (42,239-bp) and pHN9-2 (30,711-bp), were detected, and used for pan-genome analysis, as well as for identification of bacteriocin-encoding genes in 129 strains belonging to all Pediococcus species. Two CRISPR regions were identified in P. acidilactici HN9, including type II-A CRISPR/CRISPR-associated (Cas). This study provides an in-depth analysis on P. acidilactici HN9, facilitating a better understanding of its adaptability to different environments and its mechanism to maintain genome stability over time.

Bacteriocinogenic lactic acid bacteria in the traditional cereal-based beverage Boza: a genomic and functional approach

“…The P. acidilactici ST31BZ genome showed similar values of size, GC content, number of predicted proteins and ribosomal operons as other P. acidilactici strains 10,12 . Detected CRISPR systems are similar to previously described in P. acidilactici HN9 13 . A small plasmid-encoded bacteriocin (~ 9 kb) was detected, such as found in pSMB74 14 and pCP289 15 .…”

“…2a). The pST31BZ-1 plasmid was similar to pHN9-1 (BLASTn, Identity: 98.19%; Coverage: 58%), a 42,239 bp plasmid found in P. acidilactici HN9 isolated from the Traditional Thai-Style Fermented Beef Nhang (Surachat et al, 2021). No antibiotic resistance genes were predicted using ARIBA in the genome or plasmids of strain ST31BZ, however, we were able to predict the following resistance genes using the KEGG GhostKoala automatic annotation pipeline: Lantibiotic tranporter system (NisE/F/G), Lincosamide and streptogramin A resistance (Lsa), Beta lactamase class A (PenP), Cationic antimicrobial P. acidilactici ST31BZ genome presented genes coding for several sugar transporters such as sucrose, maltose/glucose and cellobiose, and is likely able to degrade them all to lactate and acetate.…”

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

“…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.…”

“…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 ).…”

Pan-genomic and comparative analysis of Pediococcus pentosaceus focused on the in silico assessment of pediocin-like bacteriocins

“…Also, the bacteriocin enterolysin is detected in many strains of this analysis and is known to degrade bacterial cell walls and be produced by bacteria of genera Enterococcus , Lactobacillus , Streptococcus , and Pediococcus , showing potential for inhibition of enterococci, pediococci, lactococci, and lactobacilli [60] . This bacteriocin belongs to class III, which are thermostable peptides with a broad inhibitory spectrum [61] .…”