Whole metagenome sequencing of cecum microbiomes in Ethiopian indigenous chickens from two different altitudes reveals antibiotic resistance genes
We analyzed the whole genomes of cecum microbiomes of Ethiopian indigenous chickens from two distinct geographical zones: Afar (AF) district (Dulecha, 730 m above sea level) and Amhara (AM) district (Menz Gera Midir, 3300 m). Through metagenomic analysis we found that microbial populations were main...
| Autores principales: | , , , , , , , , , |
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| Formato: | Journal Article |
| Lenguaje: | Inglés |
| Publicado: |
Elsevier
2020
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| Materias: | |
| Acceso en línea: | https://hdl.handle.net/10568/106282 |
| _version_ | 1855529467725742080 |
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| author | Kumar, H. Park, W. Dajeong Lim Srikanth, K. Jun-Mo Kim Xin-Zheng Jia Han Jianlin Hanotte, Olivier H. Park, Jong-Eun Oyola, Samuel O. |
| author_browse | Dajeong Lim Han Jianlin Hanotte, Olivier H. Jun-Mo Kim Kumar, H. Oyola, Samuel O. Park, Jong-Eun Park, W. Srikanth, K. Xin-Zheng Jia |
| author_facet | Kumar, H. Park, W. Dajeong Lim Srikanth, K. Jun-Mo Kim Xin-Zheng Jia Han Jianlin Hanotte, Olivier H. Park, Jong-Eun Oyola, Samuel O. |
| author_sort | Kumar, H. |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | We analyzed the whole genomes of cecum microbiomes of Ethiopian indigenous chickens from two distinct geographical zones: Afar (AF) district (Dulecha, 730 m above sea level) and Amhara (AM) district (Menz Gera Midir, 3300 m). Through metagenomic analysis we found that microbial populations were mainly dominated by Bacteroidetes and Firmicutes. We identified 2210 common genes in the two groups. LEfSe showed that the distribution of Coprobacter, Geobacter, Cronobacter, Alloprevotella, and Dysgonomonas were more abundant in AF than AM. Analyses using KEGG, eggNOG, and CAZy databases indicated that the pathways of metabolism, genetic information processing, environmental information processing, and cellular process were significantly enriched. Functional abundance was found to be associated with the nutrient absorption and microbial localization of indigenous chickens. We also investigated antibiotic resistant genes and found antibiotics like LSM, cephalosporin, and tetracycline were significantly more abundant in AF than AM. |
| format | Journal Article |
| id | CGSpace106282 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2020 |
| publishDateRange | 2020 |
| publishDateSort | 2020 |
| publisher | Elsevier |
| publisherStr | Elsevier |
| record_format | dspace |
| spelling | CGSpace1062822024-01-17T12:58:34Z Whole metagenome sequencing of cecum microbiomes in Ethiopian indigenous chickens from two different altitudes reveals antibiotic resistance genes Kumar, H. Park, W. Dajeong Lim Srikanth, K. Jun-Mo Kim Xin-Zheng Jia Han Jianlin Hanotte, Olivier H. Park, Jong-Eun Oyola, Samuel O. indigenous breeds chickens resistance to antibiotics genes research We analyzed the whole genomes of cecum microbiomes of Ethiopian indigenous chickens from two distinct geographical zones: Afar (AF) district (Dulecha, 730 m above sea level) and Amhara (AM) district (Menz Gera Midir, 3300 m). Through metagenomic analysis we found that microbial populations were mainly dominated by Bacteroidetes and Firmicutes. We identified 2210 common genes in the two groups. LEfSe showed that the distribution of Coprobacter, Geobacter, Cronobacter, Alloprevotella, and Dysgonomonas were more abundant in AF than AM. Analyses using KEGG, eggNOG, and CAZy databases indicated that the pathways of metabolism, genetic information processing, environmental information processing, and cellular process were significantly enriched. Functional abundance was found to be associated with the nutrient absorption and microbial localization of indigenous chickens. We also investigated antibiotic resistant genes and found antibiotics like LSM, cephalosporin, and tetracycline were significantly more abundant in AF than AM. 2020-03 2019-12-20T10:47:36Z 2019-12-20T10:47:36Z Journal Article https://hdl.handle.net/10568/106282 en Limited Access Elsevier Kumar, H., Park, W., Dajeong Lim, Srikanth, K., Jun-Mo Kim, Xin-Zheng Jia, Jian-Lin Han, Hanotte, O., Park, J.-E. and Oyola, S.O. 2020. Whole metagenome sequencing of cecum microbiomes in Ethiopian indigenous chickens from two different altitudes reveals antibiotic resistance genes. Genomics 112(2):1988-1999. |
| spellingShingle | indigenous breeds chickens resistance to antibiotics genes research Kumar, H. Park, W. Dajeong Lim Srikanth, K. Jun-Mo Kim Xin-Zheng Jia Han Jianlin Hanotte, Olivier H. Park, Jong-Eun Oyola, Samuel O. Whole metagenome sequencing of cecum microbiomes in Ethiopian indigenous chickens from two different altitudes reveals antibiotic resistance genes |
| title | Whole metagenome sequencing of cecum microbiomes in Ethiopian indigenous chickens from two different altitudes reveals antibiotic resistance genes |
| title_full | Whole metagenome sequencing of cecum microbiomes in Ethiopian indigenous chickens from two different altitudes reveals antibiotic resistance genes |
| title_fullStr | Whole metagenome sequencing of cecum microbiomes in Ethiopian indigenous chickens from two different altitudes reveals antibiotic resistance genes |
| title_full_unstemmed | Whole metagenome sequencing of cecum microbiomes in Ethiopian indigenous chickens from two different altitudes reveals antibiotic resistance genes |
| title_short | Whole metagenome sequencing of cecum microbiomes in Ethiopian indigenous chickens from two different altitudes reveals antibiotic resistance genes |
| title_sort | whole metagenome sequencing of cecum microbiomes in ethiopian indigenous chickens from two different altitudes reveals antibiotic resistance genes |
| topic | indigenous breeds chickens resistance to antibiotics genes research |
| url | https://hdl.handle.net/10568/106282 |
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