Assessment of beneficial effects and identification of host adaptation-associated genes of Ligilactobacillus salivarius isolated from badgers
Abstract Background Ligilactobacillus salivarius has been frequently isolated from the gut microbiota of humans and domesticated animals and has been studied as a candidate probiotic. Badger (Meles meles) is known as a “generalist” species that consumes complex foods and exhibits tolerance and resis...
| Main Authors: | , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BMC
2023-09-01
|
| Series: | BMC Genomics |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12864-023-09623-8 |
| _version_ | 1797453785324322816 |
|---|---|
| author | Yu Wang Xiaomeng Xu Huan Chen Fang Yang Bo Xu Kun Wang Qianwen Liu Guixin Liang Ruiqi Zhang Xin’an Jiao Yunzeng Zhang |
| author_facet | Yu Wang Xiaomeng Xu Huan Chen Fang Yang Bo Xu Kun Wang Qianwen Liu Guixin Liang Ruiqi Zhang Xin’an Jiao Yunzeng Zhang |
| author_sort | Yu Wang |
| collection | DOAJ |
| description | Abstract Background Ligilactobacillus salivarius has been frequently isolated from the gut microbiota of humans and domesticated animals and has been studied as a candidate probiotic. Badger (Meles meles) is known as a “generalist” species that consumes complex foods and exhibits tolerance and resistance to certain pathogens, which can be partly attributed to the beneficial microbes such as L. salivarius in the gut microbiota. However, our understanding of the beneficial traits and genomic features of badger-originated L. salivarius remains elusive. Results In this study, nine L. salivarius strains were isolated from wild badgers' feces, one of which exhibited good probiotic properties. Complete genomes of the nine L. salivarius strains were generated, and comparative genomic analysis was performed with the publicly available complete genomes of L. salivarius obtained from humans and domesticated animals. The strains originating from badgers harbored a larger genome, a higher number of protein-coding sequences, and functionally annotated genes than those originating from humans and chickens. The pan-genome phylogenetic tree demonstrated that the strains originating from badgers formed a separate clade, and totally 412 gene families (12.6% of the total gene families in the pan-genome) were identified as genes gained by the last common ancestor of the badger group. The badger group harbored significantly more gene families responsible for the degradation of complex carbohydrate substrates and production of polysaccharides than strains from other hosts; many of these were acquired by gene gain events. Conclusions A candidate probiotic and nine L. salivarius complete genomes were obtained from the badgers’ gut microbiome, and several beneficial genes were identified to be specifically present in the badger-originated strains that were gained in the evolution. Our study provides novel insights into the adaptation of L. salivarius to the intestinal habitat of wild badgers and provides valuable strain and genome resources for the development of L. salivarius as a probiotic. |
| first_indexed | 2024-03-09T15:26:54Z |
| format | Article |
| id | doaj.art-030e6ba1e5d1499aab09f742ea4afa19 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-03-09T15:26:54Z |
| publishDate | 2023-09-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-030e6ba1e5d1499aab09f742ea4afa192023-11-26T12:25:47ZengBMCBMC Genomics1471-21642023-09-0124111610.1186/s12864-023-09623-8Assessment of beneficial effects and identification of host adaptation-associated genes of Ligilactobacillus salivarius isolated from badgersYu Wang0Xiaomeng Xu1Huan Chen2Fang Yang3Bo Xu4Kun Wang5Qianwen Liu6Guixin Liang7Ruiqi Zhang8Xin’an Jiao9Yunzeng Zhang10Jiangsu Co‐Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou UniversityJiangsu Co‐Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou UniversityJiangsu Co‐Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou UniversityJiangsu Co‐Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou UniversityJiangsu Co‐Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou UniversityJiangsu Co‐Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou UniversityJiangsu Co‐Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou UniversityJiangsu Co‐Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou UniversityJiangsu Co‐Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou UniversityJiangsu Co‐Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou UniversityJiangsu Co‐Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou UniversityAbstract Background Ligilactobacillus salivarius has been frequently isolated from the gut microbiota of humans and domesticated animals and has been studied as a candidate probiotic. Badger (Meles meles) is known as a “generalist” species that consumes complex foods and exhibits tolerance and resistance to certain pathogens, which can be partly attributed to the beneficial microbes such as L. salivarius in the gut microbiota. However, our understanding of the beneficial traits and genomic features of badger-originated L. salivarius remains elusive. Results In this study, nine L. salivarius strains were isolated from wild badgers' feces, one of which exhibited good probiotic properties. Complete genomes of the nine L. salivarius strains were generated, and comparative genomic analysis was performed with the publicly available complete genomes of L. salivarius obtained from humans and domesticated animals. The strains originating from badgers harbored a larger genome, a higher number of protein-coding sequences, and functionally annotated genes than those originating from humans and chickens. The pan-genome phylogenetic tree demonstrated that the strains originating from badgers formed a separate clade, and totally 412 gene families (12.6% of the total gene families in the pan-genome) were identified as genes gained by the last common ancestor of the badger group. The badger group harbored significantly more gene families responsible for the degradation of complex carbohydrate substrates and production of polysaccharides than strains from other hosts; many of these were acquired by gene gain events. Conclusions A candidate probiotic and nine L. salivarius complete genomes were obtained from the badgers’ gut microbiome, and several beneficial genes were identified to be specifically present in the badger-originated strains that were gained in the evolution. Our study provides novel insights into the adaptation of L. salivarius to the intestinal habitat of wild badgers and provides valuable strain and genome resources for the development of L. salivarius as a probiotic.https://doi.org/10.1186/s12864-023-09623-8Ligilactobacillus salivariusBadgerHost adaptationBeneficial effectsComplete genome |
| spellingShingle | Yu Wang Xiaomeng Xu Huan Chen Fang Yang Bo Xu Kun Wang Qianwen Liu Guixin Liang Ruiqi Zhang Xin’an Jiao Yunzeng Zhang Assessment of beneficial effects and identification of host adaptation-associated genes of Ligilactobacillus salivarius isolated from badgers BMC Genomics Ligilactobacillus salivarius Badger Host adaptation Beneficial effects Complete genome |
| title | Assessment of beneficial effects and identification of host adaptation-associated genes of Ligilactobacillus salivarius isolated from badgers |
| title_full | Assessment of beneficial effects and identification of host adaptation-associated genes of Ligilactobacillus salivarius isolated from badgers |
| title_fullStr | Assessment of beneficial effects and identification of host adaptation-associated genes of Ligilactobacillus salivarius isolated from badgers |
| title_full_unstemmed | Assessment of beneficial effects and identification of host adaptation-associated genes of Ligilactobacillus salivarius isolated from badgers |
| title_short | Assessment of beneficial effects and identification of host adaptation-associated genes of Ligilactobacillus salivarius isolated from badgers |
| title_sort | assessment of beneficial effects and identification of host adaptation associated genes of ligilactobacillus salivarius isolated from badgers |
| topic | Ligilactobacillus salivarius Badger Host adaptation Beneficial effects Complete genome |
| url | https://doi.org/10.1186/s12864-023-09623-8 |
| work_keys_str_mv | AT yuwang assessmentofbeneficialeffectsandidentificationofhostadaptationassociatedgenesofligilactobacillussalivariusisolatedfrombadgers AT xiaomengxu assessmentofbeneficialeffectsandidentificationofhostadaptationassociatedgenesofligilactobacillussalivariusisolatedfrombadgers AT huanchen assessmentofbeneficialeffectsandidentificationofhostadaptationassociatedgenesofligilactobacillussalivariusisolatedfrombadgers AT fangyang assessmentofbeneficialeffectsandidentificationofhostadaptationassociatedgenesofligilactobacillussalivariusisolatedfrombadgers AT boxu assessmentofbeneficialeffectsandidentificationofhostadaptationassociatedgenesofligilactobacillussalivariusisolatedfrombadgers AT kunwang assessmentofbeneficialeffectsandidentificationofhostadaptationassociatedgenesofligilactobacillussalivariusisolatedfrombadgers AT qianwenliu assessmentofbeneficialeffectsandidentificationofhostadaptationassociatedgenesofligilactobacillussalivariusisolatedfrombadgers AT guixinliang assessmentofbeneficialeffectsandidentificationofhostadaptationassociatedgenesofligilactobacillussalivariusisolatedfrombadgers AT ruiqizhang assessmentofbeneficialeffectsandidentificationofhostadaptationassociatedgenesofligilactobacillussalivariusisolatedfrombadgers AT xinanjiao assessmentofbeneficialeffectsandidentificationofhostadaptationassociatedgenesofligilactobacillussalivariusisolatedfrombadgers AT yunzengzhang assessmentofbeneficialeffectsandidentificationofhostadaptationassociatedgenesofligilactobacillussalivariusisolatedfrombadgers |