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Home / Equine Research Bank / Sci Data / A database of animal metagenomes.
Scientific data2022; 9(1); 312; doi: 10.1038/s41597-022-01444-w

A database of animal metagenomes.

Abstract: With the rapid development of high-throughput sequencing technology, the amount of metagenomic data (including both 16S and whole-genome sequencing data) in public repositories is increasing exponentially. However, owing to the large and decentralized nature of the data, it is still difficult for users to mine, compare, and analyze the data. The animal metagenome database (AnimalMetagenome DB) integrates metagenomic sequencing data with host information, making it easier for users to find data of interest. The AnimalMetagenome DB is designed to contain all public metagenomic data from animals, and the data are divided into domestic and wild animal categories. Users can browse, search, and download animal metagenomic data of interest based on different attributes of the metadata such as animal species, sample site, study purpose, and DNA extraction method. The AnimalMetagenome DB version 1.0 includes metadata for 82,097 metagenomes from 4 domestic animals (pigs, bovines, horses, and sheep) and 540 wild animals. These metagenomes cover 15 years of experiments, 73 countries, 1,044 studies, 63,214 amplicon sequencing data, and 10,672 whole genome sequencing data. All data in the database are hosted and available in figshare https://doi.org/10.6084/m9.figshare.19728619 .
© 2022. The Author(s).
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Publication Date: 2022-06-16 PubMed ID: 35710683PubMed Central: PMC9203544DOI: 10.1038/s41597-022-01444-wGoogle Scholar: Lookup
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Summary

This research summary has been generated with artificial intelligence and may contain errors and omissions. Refer to the original study to confirm details provided. Submit correction.

The study presents an Animal Metagenome Database (AnimalMetagenome DB), which collates and organises public data on metagenomes from various animal species, making it easier for users to find, analyze, and compare pertinent data.

Database Development and Purpose

  • The study discusses the creation of the AnimalMetagenome DB in response to the rapid accumulation of metagenomic data in public repositories, propelled by advancements in high-throughput sequencing technology.
  • This data, which includes both 16S and whole-genome sequencing data, was previously challenging to mine, compare, and analyze due to its significant volume and decentralization.
  • The AnimalMetagenome DB serves to consolidate this data, coupling metagenomic sequencing data and host information. This integrated approach simplifies the process of finding data of interest.

Database Structure and Categories

  • The AnimalMetagenome DB is designed to include all public metagenomic data derived from animals; essentially acting as a complete repository for this type of information.
  • The collected data is divided into two primary categories: domestic animals and wild animals. This categorization further aids in the search and identification of specific data.
  • Users can browse, search, and download the metagenomic data that interests them based on various metadata attributes such as animal species, sample site, study purpose, and the DNA extraction method used.

Data Content in Version 1.0 of the Database

  • Version 1.0 of the AnimalMetagenome DB contained metadata for 82,097 metagenomes. This information stretched across four domestic animals (pigs, bovines, horses, and sheep) and 540 wild animals.
  • These metagenomes covered 15 years of experimentation and span 73 countries, with contributions from 1,044 separate studies.
  • The database is comprised of 63,214 amplicon sequencing data and 10,672 whole genome sequencing data.
  • All data within the AnimalMetagenome DB are hosted and readily available for access on figshare, a web-based platform for the sharing and preservation of research outputs.

Cite This Article

APA
Hu R, Yao R, Li L, Xu Y, Lei B, Tang G, Liang H, Lei Y, Li C, Li X, Liu K, Wang L, Zhang Y, Wang Y, Cui Y, Dai J, Ni W, Zhou P, Yu B, Hu S. (2022). A database of animal metagenomes. Sci Data, 9(1), 312. https://doi.org/10.1038/s41597-022-01444-w

Publication

Scientific data
ISSN: 2052-4463
NlmUniqueID: 101640192
Country: England
Language: English
Volume: 9
Issue: 1
Pages: 312
PII: 312

Researcher Affiliations

Hu, Ruirui
  • State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, Xinjiang, China.
  • College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China.
Yao, Rui
  • College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China.
Li, Lei
  • College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China.
Xu, Yueren
  • College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China.
Lei, Bingbing
  • College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China.
Tang, Guohao
  • College of Information Science and Technology, Shihezi University, Shihezi, Xinjiang, 832003, China.
Liang, Haowei
  • College of Information Science and Technology, Shihezi University, Shihezi, Xinjiang, 832003, China.
Lei, Yunjiao
  • College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China.
Li, Cunyuan
  • College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China.
  • College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang, 832003, China.
Li, Xiaoyue
  • College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China.
Liu, Kaiping
  • College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China.
Wang, Limin
  • State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, Xinjiang, China.
Zhang, Yunfeng
  • State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, Xinjiang, China.
Wang, Yue
  • College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China.
Cui, Yuying
  • College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China.
Dai, Jihong
  • College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China.
Ni, Wei
  • College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China.
Zhou, Ping
  • State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, Xinjiang, China. zhpxqf@163.com.
Yu, Baohua
  • College of Information Science and Technology, Shihezi University, Shihezi, Xinjiang, 832003, China. 1498322833@qq.com.
Hu, Shengwei
  • State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, Xinjiang, China. hushengwei@163.com.
  • College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China. hushengwei@163.com.

MeSH Terms

  • Animals
  • Cattle
  • Databases, Factual
  • High-Throughput Nucleotide Sequencing
  • Horses
  • Metadata
  • Metagenome
  • Metagenomics
  • Sheep
  • Swine

Conflict of Interest Statement

The authors declare no competing interests.

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Citations

This article has been cited 1 times.
  1. Suminda GGD, Ghosh M, Son YO. The Innovative Informatics Approaches of High-Throughput Technologies in Livestock: Spearheading the Sustainability and Resiliency of Agrigenomics Research.. Life (Basel) 2022 Nov 15;12(11).
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