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Complete genome sequencing and comparative genomic analysis of Lactobacillus acidophilus C5 as a potential canine probiotics

Lactobacillus acidophilus is a gram-positive, microaerophilic, and acidophilic bacterial species. L. acidophilus strains in the gastrointestinal tracts of humans and other animals have been profiled, but strains found in the canine gut have not been studied yet. Our study helps in understanding the...

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Autores principales: Son, Seungwoo, Lee, Raham, Park, Seung-Moon, Lee, Sung Ho, Lee, Hak-Kyo, Kim, Yangseon, Shin, Donghyun
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Korean Society of Animal Sciences and Technology 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8672248/
https://www.ncbi.nlm.nih.gov/pubmed/34957454
http://dx.doi.org/10.5187/jast.2021.e126
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author Son, Seungwoo
Lee, Raham
Park, Seung-Moon
Lee, Sung Ho
Lee, Hak-Kyo
Kim, Yangseon
Shin, Donghyun
author_facet Son, Seungwoo
Lee, Raham
Park, Seung-Moon
Lee, Sung Ho
Lee, Hak-Kyo
Kim, Yangseon
Shin, Donghyun
author_sort Son, Seungwoo
collection PubMed
description Lactobacillus acidophilus is a gram-positive, microaerophilic, and acidophilic bacterial species. L. acidophilus strains in the gastrointestinal tracts of humans and other animals have been profiled, but strains found in the canine gut have not been studied yet. Our study helps in understanding the genetic features of the L. acidophilus C5 strain found in the canine gut, determining its adaptive features evolved to survive in the canine gut environment, and in elucidating its probiotic functions. To examine the canine L. acidophilus C5 genome, we isolated the C5 strain from a Korean dog and sequenced it using PacBio SMRT sequencing technology. A comparative genomic approach was used to assess genetic relationships between C5 and six other strains and study the distinguishing features related to different hosts. We found that most genes in the C5 strain were related to carbohydrate transport and metabolism. The pan-genome of seven L. acidophilus strains contained 2,254 gene families, and the core genome contained 1,726 gene families. The phylogenetic tree of the core genes in the canine L. acidophilus C5 strain was very close to that of two strains (DSM20079 and NCFM) from humans. We identified 30 evolutionarily accelerated genes in the L. acidophilus C5 strain in the ratio of non-synonymous to synonymous substitutions (dN/dS) analysis. Five of these thirty genes were associated with carbohydrate transport and metabolism. This study provides insights into genetic features and adaptations of the L. acidophilus C5 strain to survive the canine intestinal environment. It also suggests that the evolution of the L. acidophilus genome is closely related to the host’s evolutionary adaptation process.
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spelling pubmed-86722482021-12-23 Complete genome sequencing and comparative genomic analysis of Lactobacillus acidophilus C5 as a potential canine probiotics Son, Seungwoo Lee, Raham Park, Seung-Moon Lee, Sung Ho Lee, Hak-Kyo Kim, Yangseon Shin, Donghyun J Anim Sci Technol Research Article Lactobacillus acidophilus is a gram-positive, microaerophilic, and acidophilic bacterial species. L. acidophilus strains in the gastrointestinal tracts of humans and other animals have been profiled, but strains found in the canine gut have not been studied yet. Our study helps in understanding the genetic features of the L. acidophilus C5 strain found in the canine gut, determining its adaptive features evolved to survive in the canine gut environment, and in elucidating its probiotic functions. To examine the canine L. acidophilus C5 genome, we isolated the C5 strain from a Korean dog and sequenced it using PacBio SMRT sequencing technology. A comparative genomic approach was used to assess genetic relationships between C5 and six other strains and study the distinguishing features related to different hosts. We found that most genes in the C5 strain were related to carbohydrate transport and metabolism. The pan-genome of seven L. acidophilus strains contained 2,254 gene families, and the core genome contained 1,726 gene families. The phylogenetic tree of the core genes in the canine L. acidophilus C5 strain was very close to that of two strains (DSM20079 and NCFM) from humans. We identified 30 evolutionarily accelerated genes in the L. acidophilus C5 strain in the ratio of non-synonymous to synonymous substitutions (dN/dS) analysis. Five of these thirty genes were associated with carbohydrate transport and metabolism. This study provides insights into genetic features and adaptations of the L. acidophilus C5 strain to survive the canine intestinal environment. It also suggests that the evolution of the L. acidophilus genome is closely related to the host’s evolutionary adaptation process. Korean Society of Animal Sciences and Technology 2021-11 2021-11-30 /pmc/articles/PMC8672248/ /pubmed/34957454 http://dx.doi.org/10.5187/jast.2021.e126 Text en © Copyright 2021 Korean Society of Animal Science and Technology https://creativecommons.org/licenses/by-nc/4.0/This is an Open-Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
Son, Seungwoo
Lee, Raham
Park, Seung-Moon
Lee, Sung Ho
Lee, Hak-Kyo
Kim, Yangseon
Shin, Donghyun
Complete genome sequencing and comparative genomic analysis of Lactobacillus acidophilus C5 as a potential canine probiotics
title Complete genome sequencing and comparative genomic analysis of Lactobacillus acidophilus C5 as a potential canine probiotics
title_full Complete genome sequencing and comparative genomic analysis of Lactobacillus acidophilus C5 as a potential canine probiotics
title_fullStr Complete genome sequencing and comparative genomic analysis of Lactobacillus acidophilus C5 as a potential canine probiotics
title_full_unstemmed Complete genome sequencing and comparative genomic analysis of Lactobacillus acidophilus C5 as a potential canine probiotics
title_short Complete genome sequencing and comparative genomic analysis of Lactobacillus acidophilus C5 as a potential canine probiotics
title_sort complete genome sequencing and comparative genomic analysis of lactobacillus acidophilus c5 as a potential canine probiotics
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8672248/
https://www.ncbi.nlm.nih.gov/pubmed/34957454
http://dx.doi.org/10.5187/jast.2021.e126
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