Insights from metagenomics on microbial biosynthesis of vitamins B and K2 in chicken gut microbiota
IntroductionThe chicken gut microbiome plays a pivotal role in nutrient absorption and overall health, contributing to the biosynthesis of essential vitamins. However, the biosynthesis of vitamins B and K2 by the whole gut microbiome, as well as their abundances across different gut regions, remains...
Saved in:
| Main Authors: | , , , , , , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Frontiers Media S.A.
2025-08-01
|
| Series: | Frontiers in Veterinary Science |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/articles/10.3389/fvets.2025.1646825/full |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1849765489879810048 |
|---|---|
| author | Hai-Long Yu Hai-Long Yu Xin-Wen Hou Ji-Xin Zhao Guo-Hua Liu Jin-Xin Meng Jin-Xin Meng Yong-Jie Wei Yanan Cai Jian Liu Kai-Meng Shang Hong-Bo Ni Rui Liu He Ma Fu-Long Nan Xiao-Xuan Zhang Bei-Ni Chen Xing Yang |
| author_facet | Hai-Long Yu Hai-Long Yu Xin-Wen Hou Ji-Xin Zhao Guo-Hua Liu Jin-Xin Meng Jin-Xin Meng Yong-Jie Wei Yanan Cai Jian Liu Kai-Meng Shang Hong-Bo Ni Rui Liu He Ma Fu-Long Nan Xiao-Xuan Zhang Bei-Ni Chen Xing Yang |
| author_sort | Hai-Long Yu |
| collection | DOAJ |
| description | IntroductionThe chicken gut microbiome plays a pivotal role in nutrient absorption and overall health, contributing to the biosynthesis of essential vitamins. However, the biosynthesis of vitamins B and K2 by the whole gut microbiome, as well as their abundances across different gut regions, remains largely unknown.MethodsWe employed both metagenomic sequencing and culture-based techniques, collecting a total of 25,825 genomes (25,764 metagenome-assembled genomes and 61 isolated genomes). After quality assessment and average nucleotide identity (ANI), 13,734 genomes were retained for downstream analysis.ResultsWhole-genome clustering analysis identified 2,675 species-level genome bins (SGBs), predominantly from the phyla Bacillota, Bacteroidota, Pseudomonadota, and Actinomycetota. A gene catalog comprising 9.69 million genes revealed that 195,517 genes are involved in the biosynthesis of vitamins B and K2, exhibiting significant regional variation. The large intestine exhibited greater species richness and evenness compared to the small intestine. From the 13,734 genomes, we discovered 3,063 high-quality ones capable of synthesizing at least one vitamin. Genomic analysis revealed that a mere 8.2% of genomes were capable of producing five or more vitamins, while almost half were limited to synthesizing just one. Comparative genomics of cobalamin (B12) biosynthesis highlighted the predominance of the anaerobic pathway. Additionally, changes in microbial abundance were observed, such as increased abundance of the genera Phocaeicola and Faecalibacterium during bacterial infections, and Limisoma during parasitic infections.DiscussionThis study provides detailed metagenomic insights into the capacity of chicken gut microbiome for vitamins B and K2 biosynthesis, revealing significant regional and taxonomic variations. These results suggest a collaborative microbial effort in vitamin biosynthesis, with potential implications for optimizing poultry health and nutrition through targeted microbial interventions. |
| format | Article |
| id | doaj-art-6c05f2a7e711459f9c81d8df92b7ebca |
| institution | DOAJ |
| issn | 2297-1769 |
| language | English |
| publishDate | 2025-08-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Veterinary Science |
| spelling | doaj-art-6c05f2a7e711459f9c81d8df92b7ebca2025-08-20T03:04:50ZengFrontiers Media S.A.Frontiers in Veterinary Science2297-17692025-08-011210.3389/fvets.2025.16468251646825Insights from metagenomics on microbial biosynthesis of vitamins B and K2 in chicken gut microbiotaHai-Long Yu0Hai-Long Yu1Xin-Wen Hou2Ji-Xin Zhao3Guo-Hua Liu4Jin-Xin Meng5Jin-Xin Meng6Yong-Jie Wei7Yanan Cai8Jian Liu9Kai-Meng Shang10Hong-Bo Ni11Rui Liu12He Ma13Fu-Long Nan14Xiao-Xuan Zhang15Bei-Ni Chen16Xing Yang17Department of Medical Microbiology and Immunology, School of Basic Medicine, Dali University, Dali, Yunnan Province, ChinaCollege of Veterinary Medicine, Jilin Agricultural University, Changchun, Jilin Province, ChinaCollege of Veterinary Medicine, Qingdao Agricultural University, Qingdao, Shandong Province, ChinaCollege of Veterinary Medicine, Qingdao Agricultural University, Qingdao, Shandong Province, ChinaResearch Center for Parasites and Vectors, College of Veterinary Medicine, Hunan Agricultural University, Changsha, ChinaCollege of Veterinary Medicine, Qingdao Agricultural University, Qingdao, Shandong Province, ChinaDepartment of Veterinary Medicine, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, ChinaCollege of Veterinary Medicine, Qingdao Agricultural University, Qingdao, Shandong Province, ChinaCollege of Veterinary Medicine, Jilin Agricultural University, Changchun, Jilin Province, ChinaCollege of Veterinary Medicine, Qingdao Agricultural University, Qingdao, Shandong Province, ChinaCollege of Veterinary Medicine, Qingdao Agricultural University, Qingdao, Shandong Province, ChinaCollege of Veterinary Medicine, Qingdao Agricultural University, Qingdao, Shandong Province, ChinaCollege of Veterinary Medicine, Qingdao Agricultural University, Qingdao, Shandong Province, ChinaCollege of Veterinary Medicine, Qingdao Agricultural University, Qingdao, Shandong Province, ChinaCollege of Veterinary Medicine, Qingdao Agricultural University, Qingdao, Shandong Province, ChinaCollege of Veterinary Medicine, Qingdao Agricultural University, Qingdao, Shandong Province, ChinaCollege of Veterinary Medicine, Jilin Agricultural University, Changchun, Jilin Province, ChinaDepartment of Medical Microbiology and Immunology, School of Basic Medicine, Dali University, Dali, Yunnan Province, ChinaIntroductionThe chicken gut microbiome plays a pivotal role in nutrient absorption and overall health, contributing to the biosynthesis of essential vitamins. However, the biosynthesis of vitamins B and K2 by the whole gut microbiome, as well as their abundances across different gut regions, remains largely unknown.MethodsWe employed both metagenomic sequencing and culture-based techniques, collecting a total of 25,825 genomes (25,764 metagenome-assembled genomes and 61 isolated genomes). After quality assessment and average nucleotide identity (ANI), 13,734 genomes were retained for downstream analysis.ResultsWhole-genome clustering analysis identified 2,675 species-level genome bins (SGBs), predominantly from the phyla Bacillota, Bacteroidota, Pseudomonadota, and Actinomycetota. A gene catalog comprising 9.69 million genes revealed that 195,517 genes are involved in the biosynthesis of vitamins B and K2, exhibiting significant regional variation. The large intestine exhibited greater species richness and evenness compared to the small intestine. From the 13,734 genomes, we discovered 3,063 high-quality ones capable of synthesizing at least one vitamin. Genomic analysis revealed that a mere 8.2% of genomes were capable of producing five or more vitamins, while almost half were limited to synthesizing just one. Comparative genomics of cobalamin (B12) biosynthesis highlighted the predominance of the anaerobic pathway. Additionally, changes in microbial abundance were observed, such as increased abundance of the genera Phocaeicola and Faecalibacterium during bacterial infections, and Limisoma during parasitic infections.DiscussionThis study provides detailed metagenomic insights into the capacity of chicken gut microbiome for vitamins B and K2 biosynthesis, revealing significant regional and taxonomic variations. These results suggest a collaborative microbial effort in vitamin biosynthesis, with potential implications for optimizing poultry health and nutrition through targeted microbial interventions.https://www.frontiersin.org/articles/10.3389/fvets.2025.1646825/fullvitamins B and K2chicken gut microbiomemetagenomic analysiscobalaminpathogen infection |
| spellingShingle | Hai-Long Yu Hai-Long Yu Xin-Wen Hou Ji-Xin Zhao Guo-Hua Liu Jin-Xin Meng Jin-Xin Meng Yong-Jie Wei Yanan Cai Jian Liu Kai-Meng Shang Hong-Bo Ni Rui Liu He Ma Fu-Long Nan Xiao-Xuan Zhang Bei-Ni Chen Xing Yang Insights from metagenomics on microbial biosynthesis of vitamins B and K2 in chicken gut microbiota Frontiers in Veterinary Science vitamins B and K2 chicken gut microbiome metagenomic analysis cobalamin pathogen infection |
| title | Insights from metagenomics on microbial biosynthesis of vitamins B and K2 in chicken gut microbiota |
| title_full | Insights from metagenomics on microbial biosynthesis of vitamins B and K2 in chicken gut microbiota |
| title_fullStr | Insights from metagenomics on microbial biosynthesis of vitamins B and K2 in chicken gut microbiota |
| title_full_unstemmed | Insights from metagenomics on microbial biosynthesis of vitamins B and K2 in chicken gut microbiota |
| title_short | Insights from metagenomics on microbial biosynthesis of vitamins B and K2 in chicken gut microbiota |
| title_sort | insights from metagenomics on microbial biosynthesis of vitamins b and k2 in chicken gut microbiota |
| topic | vitamins B and K2 chicken gut microbiome metagenomic analysis cobalamin pathogen infection |
| url | https://www.frontiersin.org/articles/10.3389/fvets.2025.1646825/full |
| work_keys_str_mv | AT hailongyu insightsfrommetagenomicsonmicrobialbiosynthesisofvitaminsbandk2inchickengutmicrobiota AT hailongyu insightsfrommetagenomicsonmicrobialbiosynthesisofvitaminsbandk2inchickengutmicrobiota AT xinwenhou insightsfrommetagenomicsonmicrobialbiosynthesisofvitaminsbandk2inchickengutmicrobiota AT jixinzhao insightsfrommetagenomicsonmicrobialbiosynthesisofvitaminsbandk2inchickengutmicrobiota AT guohualiu insightsfrommetagenomicsonmicrobialbiosynthesisofvitaminsbandk2inchickengutmicrobiota AT jinxinmeng insightsfrommetagenomicsonmicrobialbiosynthesisofvitaminsbandk2inchickengutmicrobiota AT jinxinmeng insightsfrommetagenomicsonmicrobialbiosynthesisofvitaminsbandk2inchickengutmicrobiota AT yongjiewei insightsfrommetagenomicsonmicrobialbiosynthesisofvitaminsbandk2inchickengutmicrobiota AT yanancai insightsfrommetagenomicsonmicrobialbiosynthesisofvitaminsbandk2inchickengutmicrobiota AT jianliu insightsfrommetagenomicsonmicrobialbiosynthesisofvitaminsbandk2inchickengutmicrobiota AT kaimengshang insightsfrommetagenomicsonmicrobialbiosynthesisofvitaminsbandk2inchickengutmicrobiota AT hongboni insightsfrommetagenomicsonmicrobialbiosynthesisofvitaminsbandk2inchickengutmicrobiota AT ruiliu insightsfrommetagenomicsonmicrobialbiosynthesisofvitaminsbandk2inchickengutmicrobiota AT hema insightsfrommetagenomicsonmicrobialbiosynthesisofvitaminsbandk2inchickengutmicrobiota AT fulongnan insightsfrommetagenomicsonmicrobialbiosynthesisofvitaminsbandk2inchickengutmicrobiota AT xiaoxuanzhang insightsfrommetagenomicsonmicrobialbiosynthesisofvitaminsbandk2inchickengutmicrobiota AT beinichen insightsfrommetagenomicsonmicrobialbiosynthesisofvitaminsbandk2inchickengutmicrobiota AT xingyang insightsfrommetagenomicsonmicrobialbiosynthesisofvitaminsbandk2inchickengutmicrobiota |