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Integrated genome based evaluation of safety and probiotic characteristics of Lactiplantibacillus plantarum YW11 isolated from Tibetan kefir

The comparative genomic analysis of Lactiplantibacillus plantarum YW11 (L. plantarum YW11) isolated from Tibetan kefir involves comparison of the complete genome sequences of the isolated strain with other closely related L. plantarum strains. This type of analysis can be used to identify the geneti...

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Autores principales: Aziz, Tariq, Naveed, Muhammad, Jabeen, Khizra, Shabbir, Muhammad Aqib, Sarwar, Abid, Zhennai, Yang, Alharbi, Metab, Alshammari, Abdulrahman, Alasmari, Abdullah F.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10158936/
https://www.ncbi.nlm.nih.gov/pubmed/37152722
http://dx.doi.org/10.3389/fmicb.2023.1157615
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author Aziz, Tariq
Naveed, Muhammad
Jabeen, Khizra
Shabbir, Muhammad Aqib
Sarwar, Abid
Zhennai, Yang
Alharbi, Metab
Alshammari, Abdulrahman
Alasmari, Abdullah F.
author_facet Aziz, Tariq
Naveed, Muhammad
Jabeen, Khizra
Shabbir, Muhammad Aqib
Sarwar, Abid
Zhennai, Yang
Alharbi, Metab
Alshammari, Abdulrahman
Alasmari, Abdullah F.
author_sort Aziz, Tariq
collection PubMed
description The comparative genomic analysis of Lactiplantibacillus plantarum YW11 (L. plantarum YW11) isolated from Tibetan kefir involves comparison of the complete genome sequences of the isolated strain with other closely related L. plantarum strains. This type of analysis can be used to identify the genetic diversity among strains and to explore the genetic characteristics of the YW11 strain. The genome of L. plantarum YW11 was found to be composed of a circular single chromosome of 4,597,470 bp with a G + C content of 43.2%. A total of 4,278 open reading frames (ORFs) were identified in the genome and the coding density was found to be 87.8%. A comparative genomic analysis was conducted using two other L. plantarum strains, L. plantarum C11 and L. plantarum LMG21703. Genomic comparison revealed that L. plantarum YW11 shared 72.7 and 75.2% of gene content with L. plantarum C11 and L. plantarum LMG21703, respectively. Most of the genes shared between the three L. plantarum strains were involved in carbohydrate metabolism, energy production and conversion, amino acid metabolism, and transcription. In this analysis, 10 previously sequenced entire genomes of the species were compared using an in-silico technique to discover genomic divergence in genes linked with carbohydrate intake and their potential adaptations to distinct human intestinal environments. The subspecies pan-genome was open, which correlated with its extraordinary capacity to colonize several environments. Phylogenetic analysis revealed that the novel genomes were homogenously grouped among subspecies of l Lactiplantibacillus. L. plantarum was resistant to cefoxitin, erythromycin, and metronidazole, inhibited pathogens including Listeria monocytogenes, Clostridium difficile, Vibrio cholera, and others, and had excellent aerotolerance, which is useful for industrial operations. The comparative genomic analysis of L. plantarum YW11 isolated from Tibetan kefir can provide insights into the genetic characteristics of the strain, which can be used to further understand its role in the production of kefir.
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spelling pubmed-101589362023-05-05 Integrated genome based evaluation of safety and probiotic characteristics of Lactiplantibacillus plantarum YW11 isolated from Tibetan kefir Aziz, Tariq Naveed, Muhammad Jabeen, Khizra Shabbir, Muhammad Aqib Sarwar, Abid Zhennai, Yang Alharbi, Metab Alshammari, Abdulrahman Alasmari, Abdullah F. Front Microbiol Microbiology The comparative genomic analysis of Lactiplantibacillus plantarum YW11 (L. plantarum YW11) isolated from Tibetan kefir involves comparison of the complete genome sequences of the isolated strain with other closely related L. plantarum strains. This type of analysis can be used to identify the genetic diversity among strains and to explore the genetic characteristics of the YW11 strain. The genome of L. plantarum YW11 was found to be composed of a circular single chromosome of 4,597,470 bp with a G + C content of 43.2%. A total of 4,278 open reading frames (ORFs) were identified in the genome and the coding density was found to be 87.8%. A comparative genomic analysis was conducted using two other L. plantarum strains, L. plantarum C11 and L. plantarum LMG21703. Genomic comparison revealed that L. plantarum YW11 shared 72.7 and 75.2% of gene content with L. plantarum C11 and L. plantarum LMG21703, respectively. Most of the genes shared between the three L. plantarum strains were involved in carbohydrate metabolism, energy production and conversion, amino acid metabolism, and transcription. In this analysis, 10 previously sequenced entire genomes of the species were compared using an in-silico technique to discover genomic divergence in genes linked with carbohydrate intake and their potential adaptations to distinct human intestinal environments. The subspecies pan-genome was open, which correlated with its extraordinary capacity to colonize several environments. Phylogenetic analysis revealed that the novel genomes were homogenously grouped among subspecies of l Lactiplantibacillus. L. plantarum was resistant to cefoxitin, erythromycin, and metronidazole, inhibited pathogens including Listeria monocytogenes, Clostridium difficile, Vibrio cholera, and others, and had excellent aerotolerance, which is useful for industrial operations. The comparative genomic analysis of L. plantarum YW11 isolated from Tibetan kefir can provide insights into the genetic characteristics of the strain, which can be used to further understand its role in the production of kefir. Frontiers Media S.A. 2023-04-20 /pmc/articles/PMC10158936/ /pubmed/37152722 http://dx.doi.org/10.3389/fmicb.2023.1157615 Text en Copyright © 2023 Aziz, Naveed, Jabeen, Shabbir, Sarwar, Zhennai, Alharbi, Alshammari and Alasmari. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Microbiology
Aziz, Tariq
Naveed, Muhammad
Jabeen, Khizra
Shabbir, Muhammad Aqib
Sarwar, Abid
Zhennai, Yang
Alharbi, Metab
Alshammari, Abdulrahman
Alasmari, Abdullah F.
Integrated genome based evaluation of safety and probiotic characteristics of Lactiplantibacillus plantarum YW11 isolated from Tibetan kefir
title Integrated genome based evaluation of safety and probiotic characteristics of Lactiplantibacillus plantarum YW11 isolated from Tibetan kefir
title_full Integrated genome based evaluation of safety and probiotic characteristics of Lactiplantibacillus plantarum YW11 isolated from Tibetan kefir
title_fullStr Integrated genome based evaluation of safety and probiotic characteristics of Lactiplantibacillus plantarum YW11 isolated from Tibetan kefir
title_full_unstemmed Integrated genome based evaluation of safety and probiotic characteristics of Lactiplantibacillus plantarum YW11 isolated from Tibetan kefir
title_short Integrated genome based evaluation of safety and probiotic characteristics of Lactiplantibacillus plantarum YW11 isolated from Tibetan kefir
title_sort integrated genome based evaluation of safety and probiotic characteristics of lactiplantibacillus plantarum yw11 isolated from tibetan kefir
topic Microbiology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10158936/
https://www.ncbi.nlm.nih.gov/pubmed/37152722
http://dx.doi.org/10.3389/fmicb.2023.1157615
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