Genomic Insight into <i>Pediococcus acidilactici</i> HN9, a Potential Probiotic Strain Isolated from the Traditional Thai-Style Fermented Beef Nhang
<i>Pediococcus acidilactici</i> HN9 is a beneficial lactic acid bacterium isolated from Nhang, a traditional Thai-style fermented beef. In this study, the molecular properties of <i>P. acidilactici</i> HN9 were characterized to provide insights into its potential probiotic ac...
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MDPI AG
2020-12-01
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| Series: | Microorganisms |
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| Online Access: | https://www.mdpi.com/2076-2607/9/1/50 |
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| author | Komwit Surachat Duangporn Kantachote Panchalika Deachamag Monwadee Wonglapsuwan |
| author_facet | Komwit Surachat Duangporn Kantachote Panchalika Deachamag Monwadee Wonglapsuwan |
| author_sort | Komwit Surachat |
| collection | DOAJ |
| description | <i>Pediococcus acidilactici</i> HN9 is a beneficial lactic acid bacterium isolated from Nhang, a traditional Thai-style fermented beef. In this study, the molecular properties of <i>P. acidilactici</i> HN9 were characterized to provide insights into its potential probiotic activity. Specifically, this work sought to report the complete genome of <i>P. acidilactici</i> HN9 and perform a comparative genome analysis with other bacterial strains belonging to the genus <i>Pediococcus</i>. Genomic features of HN9 were compared with those of all other bacterial <i>Pediococcus</i> 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 <i>Pediococcus</i> species. Two CRISPR regions were identified in <i>P. acidilactici</i> HN9, including type II-A CRISPR/CRISPR-associated (Cas). This study provides an in-depth analysis on <i>P. acidilactici</i> HN9, facilitating a better understanding of its adaptability to different environments and its mechanism to maintain genome stability over time. |
| first_indexed | 2024-03-10T13:44:33Z |
| format | Article |
| id | doaj.art-691d88e4a23e40d29e865ceaceeb52df |
| institution | Directory Open Access Journal |
| issn | 2076-2607 |
| language | English |
| last_indexed | 2024-03-10T13:44:33Z |
| publishDate | 2020-12-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Microorganisms |
| spelling | doaj.art-691d88e4a23e40d29e865ceaceeb52df2023-11-21T02:44:33ZengMDPI AGMicroorganisms2076-26072020-12-01915010.3390/microorganisms9010050Genomic Insight into <i>Pediococcus acidilactici</i> HN9, a Potential Probiotic Strain Isolated from the Traditional Thai-Style Fermented Beef NhangKomwit Surachat0Duangporn Kantachote1Panchalika Deachamag2Monwadee Wonglapsuwan3Division of Computational Science, Faculty of Science, Prince of Songkla University, Hatyai, Songkhla 90110, ThailandDivision of Biological Science, Faculty of Science, Prince of Songkla University, Hatyai, Songkhla 90110, ThailandDivision of Biological Science, Faculty of Science, Prince of Songkla University, Hatyai, Songkhla 90110, ThailandDivision of Biological Science, Faculty of Science, Prince of Songkla University, Hatyai, Songkhla 90110, Thailand<i>Pediococcus acidilactici</i> HN9 is a beneficial lactic acid bacterium isolated from Nhang, a traditional Thai-style fermented beef. In this study, the molecular properties of <i>P. acidilactici</i> HN9 were characterized to provide insights into its potential probiotic activity. Specifically, this work sought to report the complete genome of <i>P. acidilactici</i> HN9 and perform a comparative genome analysis with other bacterial strains belonging to the genus <i>Pediococcus</i>. Genomic features of HN9 were compared with those of all other bacterial <i>Pediococcus</i> 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 <i>Pediococcus</i> species. Two CRISPR regions were identified in <i>P. acidilactici</i> HN9, including type II-A CRISPR/CRISPR-associated (Cas). This study provides an in-depth analysis on <i>P. acidilactici</i> HN9, facilitating a better understanding of its adaptability to different environments and its mechanism to maintain genome stability over time.https://www.mdpi.com/2076-2607/9/1/50beneficial lactic acid bacteriapediococci<i>Pediococcus acidilactici</i>comparative genome analysisfermented food |
| spellingShingle | Komwit Surachat Duangporn Kantachote Panchalika Deachamag Monwadee Wonglapsuwan Genomic Insight into <i>Pediococcus acidilactici</i> HN9, a Potential Probiotic Strain Isolated from the Traditional Thai-Style Fermented Beef Nhang Microorganisms beneficial lactic acid bacteria pediococci <i>Pediococcus acidilactici</i> comparative genome analysis fermented food |
| title | Genomic Insight into <i>Pediococcus acidilactici</i> HN9, a Potential Probiotic Strain Isolated from the Traditional Thai-Style Fermented Beef Nhang |
| title_full | Genomic Insight into <i>Pediococcus acidilactici</i> HN9, a Potential Probiotic Strain Isolated from the Traditional Thai-Style Fermented Beef Nhang |
| title_fullStr | Genomic Insight into <i>Pediococcus acidilactici</i> HN9, a Potential Probiotic Strain Isolated from the Traditional Thai-Style Fermented Beef Nhang |
| title_full_unstemmed | Genomic Insight into <i>Pediococcus acidilactici</i> HN9, a Potential Probiotic Strain Isolated from the Traditional Thai-Style Fermented Beef Nhang |
| title_short | Genomic Insight into <i>Pediococcus acidilactici</i> HN9, a Potential Probiotic Strain Isolated from the Traditional Thai-Style Fermented Beef Nhang |
| title_sort | genomic insight into i pediococcus acidilactici i hn9 a potential probiotic strain isolated from the traditional thai style fermented beef nhang |
| topic | beneficial lactic acid bacteria pediococci <i>Pediococcus acidilactici</i> comparative genome analysis fermented food |
| url | https://www.mdpi.com/2076-2607/9/1/50 |
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