ADDAGMA: A database for domestic animal gut microbiome atlas
Animal gut microbiomes play important roles in the health, diseases, and production of animal hosts. The volume of animal gut metagenomic data, including both 16S amplicon and metagenomic sequencing data, has been increasing exponentially in recent years, making it increasingly difficult for researc...
| Main Authors: | , , , , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2022-01-01
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| Series: | Computational and Structural Biotechnology Journal |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S200103702200040X |
| _version_ | 1797978196005617664 |
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| author | Yueren Xu Bingbing Lei Qingfeng Zhang Yunjiao Lei Cunyuan Li Xiaoyue Li Rui Yao Ruirui Hu Kaiping Liu Yue Wang Yuying Cui Limin Wang Jihong Dai Lei Li Wei Ni Ping Zhou Ze-Xian Liu Shengwei Hu |
| author_facet | Yueren Xu Bingbing Lei Qingfeng Zhang Yunjiao Lei Cunyuan Li Xiaoyue Li Rui Yao Ruirui Hu Kaiping Liu Yue Wang Yuying Cui Limin Wang Jihong Dai Lei Li Wei Ni Ping Zhou Ze-Xian Liu Shengwei Hu |
| author_sort | Yueren Xu |
| collection | DOAJ |
| description | Animal gut microbiomes play important roles in the health, diseases, and production of animal hosts. The volume of animal gut metagenomic data, including both 16S amplicon and metagenomic sequencing data, has been increasing exponentially in recent years, making it increasingly difficult for researchers to query, retrieve, and reanalyze experimental data and explore new hypotheses. We designed a database called the domestic animal gut microbiome atlas (ADDAGMA) to house all publicly available, high-throughput sequencing data for the gut microbiome in domestic animals. ADDAGMA enhances the availability and accessibility of the rapidly growing body of metagenomic data. We annotated microbial and metadata from four domestic animals (cattle, horse, pig, and chicken) from 356 published papers to construct a comprehensive database that is equipped with browse and search functions, enabling users to make customized, complicated, biologically relevant queries. Users can quickly and accurately obtain experimental information on sample types, conditions, and sequencing platforms, and experimental results including microbial relative abundances, microbial taxon-associated host phenotype, and P-values for gut microbes of interest. The current version of ADDAGMA includes 290,422 quantification events (changes in abundance) for 3215 microbial taxa associated with 48 phenotypes. ADDAGMA presently covers gut microbiota sequencing data from pig, cattle, horse, and chicken, but will be expanded to include other domestic animals. ADDAGMA is freely available at (http://addagma.omicsbio.info/). |
| first_indexed | 2024-04-11T05:20:10Z |
| format | Article |
| id | doaj.art-08bcaa0e2e394b8593338f28783974b7 |
| institution | Directory Open Access Journal |
| issn | 2001-0370 |
| language | English |
| last_indexed | 2024-04-11T05:20:10Z |
| publishDate | 2022-01-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Computational and Structural Biotechnology Journal |
| spelling | doaj.art-08bcaa0e2e394b8593338f28783974b72022-12-24T04:51:26ZengElsevierComputational and Structural Biotechnology Journal2001-03702022-01-0120891898ADDAGMA: A database for domestic animal gut microbiome atlasYueren Xu0Bingbing Lei1Qingfeng Zhang2Yunjiao Lei3Cunyuan Li4Xiaoyue Li5Rui Yao6Ruirui Hu7Kaiping Liu8Yue Wang9Yuying Cui10Limin Wang11Jihong Dai12Lei Li13Wei Ni14Ping Zhou15Ze-Xian Liu16Shengwei Hu17College of Life Sciences, Shihezi University, Shihezi, Xinjiang 832003, ChinaCollege of Life Sciences, Shihezi University, Shihezi, Xinjiang 832003, ChinaState Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, ChinaCollege of Life Sciences, Shihezi University, Shihezi, Xinjiang 832003, ChinaCollege of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang 832003, ChinaCollege of Life Sciences, Shihezi University, Shihezi, Xinjiang 832003, ChinaCollege of Life Sciences, Shihezi University, Shihezi, Xinjiang 832003, ChinaCollege of Life Sciences, Shihezi University, Shihezi, Xinjiang 832003, ChinaCollege of Life Sciences, Shihezi University, Shihezi, Xinjiang 832003, ChinaCollege of Life Sciences, Shihezi University, Shihezi, Xinjiang 832003, ChinaCollege of Life Sciences, Shihezi University, Shihezi, Xinjiang 832003, ChinaState Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, Xinjiang 832003, ChinaCollege of Life Sciences, Shihezi University, Shihezi, Xinjiang 832003, ChinaCollege of Life Sciences, Shihezi University, Shihezi, Xinjiang 832003, ChinaCollege of Life Sciences, Shihezi University, Shihezi, Xinjiang 832003, ChinaState Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, Xinjiang 832003, China; Corresponding authors.State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China; Corresponding authors.College of Life Sciences, Shihezi University, Shihezi, Xinjiang 832003, China; Corresponding authors.Animal gut microbiomes play important roles in the health, diseases, and production of animal hosts. The volume of animal gut metagenomic data, including both 16S amplicon and metagenomic sequencing data, has been increasing exponentially in recent years, making it increasingly difficult for researchers to query, retrieve, and reanalyze experimental data and explore new hypotheses. We designed a database called the domestic animal gut microbiome atlas (ADDAGMA) to house all publicly available, high-throughput sequencing data for the gut microbiome in domestic animals. ADDAGMA enhances the availability and accessibility of the rapidly growing body of metagenomic data. We annotated microbial and metadata from four domestic animals (cattle, horse, pig, and chicken) from 356 published papers to construct a comprehensive database that is equipped with browse and search functions, enabling users to make customized, complicated, biologically relevant queries. Users can quickly and accurately obtain experimental information on sample types, conditions, and sequencing platforms, and experimental results including microbial relative abundances, microbial taxon-associated host phenotype, and P-values for gut microbes of interest. The current version of ADDAGMA includes 290,422 quantification events (changes in abundance) for 3215 microbial taxa associated with 48 phenotypes. ADDAGMA presently covers gut microbiota sequencing data from pig, cattle, horse, and chicken, but will be expanded to include other domestic animals. ADDAGMA is freely available at (http://addagma.omicsbio.info/).http://www.sciencedirect.com/science/article/pii/S200103702200040XGut microbiotaMetagenomicsDomestic animalsPhenotypesDatabase |
| spellingShingle | Yueren Xu Bingbing Lei Qingfeng Zhang Yunjiao Lei Cunyuan Li Xiaoyue Li Rui Yao Ruirui Hu Kaiping Liu Yue Wang Yuying Cui Limin Wang Jihong Dai Lei Li Wei Ni Ping Zhou Ze-Xian Liu Shengwei Hu ADDAGMA: A database for domestic animal gut microbiome atlas Computational and Structural Biotechnology Journal Gut microbiota Metagenomics Domestic animals Phenotypes Database |
| title | ADDAGMA: A database for domestic animal gut microbiome atlas |
| title_full | ADDAGMA: A database for domestic animal gut microbiome atlas |
| title_fullStr | ADDAGMA: A database for domestic animal gut microbiome atlas |
| title_full_unstemmed | ADDAGMA: A database for domestic animal gut microbiome atlas |
| title_short | ADDAGMA: A database for domestic animal gut microbiome atlas |
| title_sort | addagma a database for domestic animal gut microbiome atlas |
| topic | Gut microbiota Metagenomics Domestic animals Phenotypes Database |
| url | http://www.sciencedirect.com/science/article/pii/S200103702200040X |
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