Article

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

Seungwoo Son, Raham Lee, Seung-Moon Park, Sung Ho Lee, Hak-Kyo Lee, Yangseon Kim*, Donghyun Shin**
Author Information & Copyright
1Department of Agricultural Convergence Technology, Jeonbuk National University, Jeonju 54896, Korea.
2Department of Animal Biotechnology, College of Agricultural and Life Sciences, Jeonbuk National University, Jeonju 54896, Korea.
3Department of Bioenvironmental Chemistry, College of Agriculture and Life Sciences, Jeonbuk National University, Jeonju 54896, Korea.
4Woogene B&G Co, Ltd., Hwaseong 18630, Korea.
5Center for Industrialization of Agriculture and Livestock Microorganism, Jeongeup 56212, Korea.
**Corresponding Author: Yangseon Kim, Phone: +82-63-270-5931. E-mail: yangseon@cialm.or.kr.
**Corresponding Author: Donghyun Shin, Phone: +82-63-270-5931. E-mail: sdh1214@gmail.com.

© Copyright 2021 Korean Society of Animal Science and Technology. 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.

Received: Aug 20, 2021; Revised: Oct 22, 2021; Accepted: Nov 12, 2021

Published Online: Nov 23, 2021

Abstract

<italic>Lactobacillus acidophilus</italic> is a gram-positive, microaerophilic, and acidophilic bacterial species. <italic>L. acidophilus</italic> 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 <italic>L. acidophilus</italic> 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 <italic>L. acidophilus</italic> 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 <italic>L. acidophilus</italic> 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 <italic>L. acidophilus</italic> C5 strain was very close to that of two strains (DSM20079 and NCFM) from humans. We identified 30 evolutionarily accelerated genes in the <italic>L. acidophilus</italic> C5 strain in the 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 <italic>L. acidophilus</italic> C5 strain to survive the canine intestinal environment. It also suggests that the evolution of the <italic>L. acidophilus</italic> genome is closely related to the host’s evolutionary adaptation process.

Keywords: Lactobacillus acidophilus; Canine; Comparative genomics; Pan-genome analysis; Host adaptation