Integrated 16S rRNA and metagenomic sequencing reveals the distribution of key antibiotic resistance genes in duck gut microbiota
The duck gut microbiota is essential for host health and is considered a potential reservoir for antibiotic resistance genes (ARGs). However, research on ARGs in the duck gut microbiota is limited. This study collected 120 intestinal content samples from five segments (duodenum, jejunum, ileum, cecu...
Saved in:
| Main Authors: | , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Elsevier
2025-07-01
|
| Series: | Poultry Science |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S0032579125004481 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1849689641920233472 |
|---|---|
| author | Hongbo Zeng Hua Yang Zixian Fu Lingyan Ma Lizhi Lu Tao Zeng Yingping Xiao Wentao Lyu |
| author_facet | Hongbo Zeng Hua Yang Zixian Fu Lingyan Ma Lizhi Lu Tao Zeng Yingping Xiao Wentao Lyu |
| author_sort | Hongbo Zeng |
| collection | DOAJ |
| description | The duck gut microbiota is essential for host health and is considered a potential reservoir for antibiotic resistance genes (ARGs). However, research on ARGs in the duck gut microbiota is limited. This study collected 120 intestinal content samples from five segments (duodenum, jejunum, ileum, cecum, and colorectum) of ducks raised under two rearing conditions (with or without an open-air swimming pool). We compiled a comprehensive inventory of microbial genes in the duck gut and conducted an analysis of microbial composition and function across all intestinal segments using 16S rRNA gene sequencing combined with metagenomics. The findings revealed that Firmicutes were the most prevalent microbes in all intestinal segments. In the foregut (duodenum, jejunum, and ileum), microbial functions were mainly related to genetic information processing such as transcription, translation, replication, and glycosynthesis/gluconeogenesis. Conversely, in the hindgut (cecum and colorectum), microbial functions were primarily associated with the biosynthesis of secondary metabolites and various metabolic pathways. The analysis of ARGs indicated a higher relative abundance of ARGs in the cecum and colorectum (P < 0.05) of ducks in the presence of an open-air swimming pool compared to the absence of one. Furthermore, through co-occurrence network analysis, we identified Bacteroides, Roseburia, Ruminococcus, and Blautia as potential hosts of ARGs such as tetQ, tet32, tet37, vanR, vanG, and acrB in the hindgut. This study provides new insights into the complex relationship between ARGs and the microbial community in duck intestines, laying a theoretical groundwork for understanding the transmission dynamics of ARGs in these ecosystems. |
| format | Article |
| id | doaj-art-00ecdf38a3d34977ad9744c68ac42db7 |
| institution | DOAJ |
| issn | 0032-5791 |
| language | English |
| publishDate | 2025-07-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Poultry Science |
| spelling | doaj-art-00ecdf38a3d34977ad9744c68ac42db72025-08-20T03:21:32ZengElsevierPoultry Science0032-57912025-07-01104710520610.1016/j.psj.2025.105206Integrated 16S rRNA and metagenomic sequencing reveals the distribution of key antibiotic resistance genes in duck gut microbiotaHongbo Zeng0Hua Yang1Zixian Fu2Lingyan Ma3Lizhi Lu4Tao Zeng5Yingping Xiao6Wentao Lyu7State Key Laboratory for Quality and Safety of Agro-Products, Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, ChinaState Key Laboratory for Quality and Safety of Agro-Products, Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, ChinaCollege of Animal Science, Zhejiang A&F University, Hangzhou, ChinaState Key Laboratory for Quality and Safety of Agro-Products, Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, ChinaState Key Laboratory for Quality and Safety of Agro-Products, Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, ChinaState Key Laboratory for Quality and Safety of Agro-Products, Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, ChinaState Key Laboratory for Quality and Safety of Agro-Products, Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, ChinaState Key Laboratory for Quality and Safety of Agro-Products, Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China; Corresponding author.The duck gut microbiota is essential for host health and is considered a potential reservoir for antibiotic resistance genes (ARGs). However, research on ARGs in the duck gut microbiota is limited. This study collected 120 intestinal content samples from five segments (duodenum, jejunum, ileum, cecum, and colorectum) of ducks raised under two rearing conditions (with or without an open-air swimming pool). We compiled a comprehensive inventory of microbial genes in the duck gut and conducted an analysis of microbial composition and function across all intestinal segments using 16S rRNA gene sequencing combined with metagenomics. The findings revealed that Firmicutes were the most prevalent microbes in all intestinal segments. In the foregut (duodenum, jejunum, and ileum), microbial functions were mainly related to genetic information processing such as transcription, translation, replication, and glycosynthesis/gluconeogenesis. Conversely, in the hindgut (cecum and colorectum), microbial functions were primarily associated with the biosynthesis of secondary metabolites and various metabolic pathways. The analysis of ARGs indicated a higher relative abundance of ARGs in the cecum and colorectum (P < 0.05) of ducks in the presence of an open-air swimming pool compared to the absence of one. Furthermore, through co-occurrence network analysis, we identified Bacteroides, Roseburia, Ruminococcus, and Blautia as potential hosts of ARGs such as tetQ, tet32, tet37, vanR, vanG, and acrB in the hindgut. This study provides new insights into the complex relationship between ARGs and the microbial community in duck intestines, laying a theoretical groundwork for understanding the transmission dynamics of ARGs in these ecosystems.http://www.sciencedirect.com/science/article/pii/S0032579125004481Antibiotic resistance gene16S rRNA gene sequencingMetagenomic analysisGut microbiotaDuck |
| spellingShingle | Hongbo Zeng Hua Yang Zixian Fu Lingyan Ma Lizhi Lu Tao Zeng Yingping Xiao Wentao Lyu Integrated 16S rRNA and metagenomic sequencing reveals the distribution of key antibiotic resistance genes in duck gut microbiota Poultry Science Antibiotic resistance gene 16S rRNA gene sequencing Metagenomic analysis Gut microbiota Duck |
| title | Integrated 16S rRNA and metagenomic sequencing reveals the distribution of key antibiotic resistance genes in duck gut microbiota |
| title_full | Integrated 16S rRNA and metagenomic sequencing reveals the distribution of key antibiotic resistance genes in duck gut microbiota |
| title_fullStr | Integrated 16S rRNA and metagenomic sequencing reveals the distribution of key antibiotic resistance genes in duck gut microbiota |
| title_full_unstemmed | Integrated 16S rRNA and metagenomic sequencing reveals the distribution of key antibiotic resistance genes in duck gut microbiota |
| title_short | Integrated 16S rRNA and metagenomic sequencing reveals the distribution of key antibiotic resistance genes in duck gut microbiota |
| title_sort | integrated 16s rrna and metagenomic sequencing reveals the distribution of key antibiotic resistance genes in duck gut microbiota |
| topic | Antibiotic resistance gene 16S rRNA gene sequencing Metagenomic analysis Gut microbiota Duck |
| url | http://www.sciencedirect.com/science/article/pii/S0032579125004481 |
| work_keys_str_mv | AT hongbozeng integrated16srrnaandmetagenomicsequencingrevealsthedistributionofkeyantibioticresistancegenesinduckgutmicrobiota AT huayang integrated16srrnaandmetagenomicsequencingrevealsthedistributionofkeyantibioticresistancegenesinduckgutmicrobiota AT zixianfu integrated16srrnaandmetagenomicsequencingrevealsthedistributionofkeyantibioticresistancegenesinduckgutmicrobiota AT lingyanma integrated16srrnaandmetagenomicsequencingrevealsthedistributionofkeyantibioticresistancegenesinduckgutmicrobiota AT lizhilu integrated16srrnaandmetagenomicsequencingrevealsthedistributionofkeyantibioticresistancegenesinduckgutmicrobiota AT taozeng integrated16srrnaandmetagenomicsequencingrevealsthedistributionofkeyantibioticresistancegenesinduckgutmicrobiota AT yingpingxiao integrated16srrnaandmetagenomicsequencingrevealsthedistributionofkeyantibioticresistancegenesinduckgutmicrobiota AT wentaolyu integrated16srrnaandmetagenomicsequencingrevealsthedistributionofkeyantibioticresistancegenesinduckgutmicrobiota |