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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...
Autores principales: | , , , , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Research Network of Computational and Structural Biotechnology
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8858777/ https://www.ncbi.nlm.nih.gov/pubmed/35222847 http://dx.doi.org/10.1016/j.csbj.2022.02.003 |
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author | Xu, Yueren Lei, Bingbing Zhang, Qingfeng Lei, Yunjiao Li, Cunyuan Li, Xiaoyue Yao, Rui Hu, Ruirui Liu, Kaiping Wang, Yue Cui, Yuying Wang, Limin Dai, Jihong Li, Lei Ni, Wei Zhou, Ping Liu, Ze-Xian Hu, Shengwei |
author_facet | Xu, Yueren Lei, Bingbing Zhang, Qingfeng Lei, Yunjiao Li, Cunyuan Li, Xiaoyue Yao, Rui Hu, Ruirui Liu, Kaiping Wang, Yue Cui, Yuying Wang, Limin Dai, Jihong Li, Lei Ni, Wei Zhou, Ping Liu, Ze-Xian Hu, Shengwei |
author_sort | Xu, Yueren |
collection | PubMed |
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/). |
format | Online Article Text |
id | pubmed-8858777 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Research Network of Computational and Structural Biotechnology |
record_format | MEDLINE/PubMed |
spelling | pubmed-88587772022-02-25 ADDAGMA: A database for domestic animal gut microbiome atlas Xu, Yueren Lei, Bingbing Zhang, Qingfeng Lei, Yunjiao Li, Cunyuan Li, Xiaoyue Yao, Rui Hu, Ruirui Liu, Kaiping Wang, Yue Cui, Yuying Wang, Limin Dai, Jihong Li, Lei Ni, Wei Zhou, Ping Liu, Ze-Xian Hu, Shengwei Comput Struct Biotechnol J Research Article 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/). Research Network of Computational and Structural Biotechnology 2022-02-10 /pmc/articles/PMC8858777/ /pubmed/35222847 http://dx.doi.org/10.1016/j.csbj.2022.02.003 Text en © 2022 The Authors https://creativecommons.org/licenses/by-nc-nd/4.0/This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/). |
spellingShingle | Research Article Xu, Yueren Lei, Bingbing Zhang, Qingfeng Lei, Yunjiao Li, Cunyuan Li, Xiaoyue Yao, Rui Hu, Ruirui Liu, Kaiping Wang, Yue Cui, Yuying Wang, Limin Dai, Jihong Li, Lei Ni, Wei Zhou, Ping Liu, Ze-Xian Hu, Shengwei ADDAGMA: A database for domestic animal gut microbiome atlas |
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 | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8858777/ https://www.ncbi.nlm.nih.gov/pubmed/35222847 http://dx.doi.org/10.1016/j.csbj.2022.02.003 |
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