ADDAGMA: A database for domestic animal gut microbiome atlas

Xu, Yuwen; Lei, Bingbing; 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, Zexian; Hu, Shengwei

doi:10.1016/j.csbj.2022.02.003

Cited by 12 publications

(10 citation statements)

References 41 publications

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“…The interactive interface of AMDB is convenient for searching by taxa of interest, taxonomic profiles of the samples, and summary of included projects. Another comprehensive database, ADDAGMA (abbreviated from A Database for Domestic Animal Gut Microbiome Atlas), is a publicly available database for domestic animal gut microbiome equipped with browsing and query-based searching for annotated microbial and metadata from major four domestic animals (cattle, chicken, horse, and pig) along with 48 relevant phenotypes 111 . Databases of these volumes are quite useful for capturing the variation in the animal gut microbiome and their association with host phenotypes.…”

Section: Microbiome Databasesmentioning

confidence: 99%

Big Data for a Small World: A Review on Databases and Resources for Studying Microbiomes

et al. 2023

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Microorganisms are ubiquitous in nature and form complex community networks to survive in various environments. This community structure depends on numerous factors like nutrient availability, abiotic factors like temperature and pH as well as microbial composition. Categorising accessible biomes according to their habitats would help in understanding the complexity of the environment-specific communities. Owing to the recent improvements in sequencing facilities, researchers have started to explore diverse microbiomes rapidly and attempts have been made to study microbial crosstalk. However, different metagenomics sampling, preprocessing, and annotation methods make it difficult to compare multiple studies and hinder the recycling of data. Huge datasets originating from these experiments demand systematic computational methods to extract biological information beyond microbial compositions. Further exploration of microbial co-occurring patterns across the biomes could help us in designing cross-biome experiments. In this review, we catalogue databases with system-specific microbiomes, discussing publicly available common databases as well as specialised databases for a range of microbiomes. If the new datasets generated in the future could maintain at least biome-specific annotation, then researchers could use those contemporary tools for relevant and bias-free analysis of complex metagenomics data.

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Section: Microbiome Databasesmentioning

confidence: 99%

Big Data for a Small World: A Review on Databases and Resources for Studying Microbiomes

et al. 2023

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“…Following this procedur narrowed our focus to genetic variants previously associated with growth traits in ho In the outcomes of the host-microbiome association, SNPs were annotated u Equcab2.0 (Ensembl release 94). Concurrence with horse growth-associated taxa determined using the ADDAGMA database [25]. A plot of the genomic arrangements created using a phenogram [26].…”

Section: Gut Microbial Composition and α Diversitymentioning

confidence: 99%

Exploring the Influence of Growth-Associated Host Genetics on the Initial Gut Microbiota in Horses

Lee

Kang

Kim

et al. 2023

Genes

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The influences of diet and environmental factors on gut microbial profiles have been widely acknowledged; however, the specific roles of host genetics remain uncertain. To unravel host genetic effects, we raised 47 Jeju crossbred (Jeju × Thoroughbred) foals that exhibited higher genetic diversity. Foals were raised under identical environmental conditions and diets. Microbial composition revealed that Firmicutes, Bacteroidetes, and Spirochaetes were the predominant phyla. We identified 31 host–microbiome associations by utilizing 47,668 single nucleotide polymorphisms (SNPs) and 734 taxa with quantitative trait locus (QTL) information related to horse growth. The taxa involved in 31 host–microbiome associations were functionally linked to carbohydrate metabolism, energy metabolic processes, short-chain fatty acid (SCFA) production, and lactic acid production. Abundances of these taxa were affected by specific SNP genotypes. Most growth-associated SNPs are found between genes. The rs69057439 and rs69127732 SNPs are located within the introns of the VWA8 and MFSD6 genes, respectively. These genes are known to affect energy balance and metabolism. These discoveries emphasize the significant effect of host SNPs on the development of the intestinal microbiome during the initial phases of life and provide insights into the influence of gut microbial composition on horse growth.

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“…Metagenomics is an expanding field of study, and the number of metagenomes in public databases has grown exponentially [ 1 ]. While genomic studies consider a specific organism’s genetic material, metagenomic studies consider the genetic material of entire communities of organisms [ 2 , 3 ].…”

Section: Introductionmentioning

confidence: 99%

“…As the number of publicly available metagenomic studies continues to grow, developing centralized resources and curated metadata is essential to improving the findability and reusability of these data. While several such resources exist for environmental [ 1 , 14 , 15 ] and human-associated metadata [ 16 – 19 ], animal-associated metagenomes have received less attention. Searching and reusing samples can be difficult due to incomplete or poor-quality metadata accompanying the metagenome data [ 14 – 16 , 20 – 22 ].…”

Section: Introductionmentioning

confidence: 99%

The AnimalAssociatedMetagenomeDB reveals a bias towards livestock and developed countries and blind spots in functional-potential studies of animal-associated microbiomes

Avila Santos,

Kabiru Nata’ala,

Kasmanas

et al. 2023

anim microbiome

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Background Metagenomic data can shed light on animal-microbiome relationships and the functional potential of these communities. Over the past years, the generation of metagenomics data has increased exponentially, and so has the availability and reusability of data present in public repositories. However, identifying which datasets and associated metadata are available is not straightforward. We created the Animal-Associated Metagenome Metadata Database (AnimalAssociatedMetagenomeDB - AAMDB) to facilitate the identification and reuse of publicly available non-human, animal-associated metagenomic data, and metadata. Further, we used the AAMDB to (i) annotate common and scientific names of the species; (ii) determine the fraction of vertebrates and invertebrates; (iii) study their biogeography; and (iv) specify whether the animals were wild, pets, livestock or used for medical research. Results We manually selected metagenomes associated with non-human animals from SRA and MG-RAST. Next, we standardized and curated 51 metadata attributes (e.g., host, compartment, geographic coordinates, and country). The AAMDB version 1.0 contains 10,885 metagenomes associated with 165 different species from 65 different countries. From the collected metagenomes, 51.1% were recovered from animals associated with medical research or grown for human consumption (i.e., mice, rats, cattle, pigs, and poultry). Further, we observed an over-representation of animals collected in temperate regions (89.2%) and a lower representation of samples from the polar zones, with only 11 samples in total. The most common genus among invertebrate animals was Trichocerca (rotifers). Conclusion Our work may guide host species selection in novel animal-associated metagenome research, especially in biodiversity and conservation studies. The data available in our database will allow scientists to perform meta-analyses and test new hypotheses (e.g., host-specificity, strain heterogeneity, and biogeography of animal-associated metagenomes), leveraging existing data. The AAMDB WebApp is a user-friendly interface that is publicly available at https://webapp.ufz.de/aamdb/.

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ADDAGMA: A database for domestic animal gut microbiome atlas

Cited by 12 publications

References 41 publications

Big Data for a Small World: A Review on Databases and Resources for Studying Microbiomes

Big Data for a Small World: A Review on Databases and Resources for Studying Microbiomes

Exploring the Influence of Growth-Associated Host Genetics on the Initial Gut Microbiota in Horses

The AnimalAssociatedMetagenomeDB reveals a bias towards livestock and developed countries and blind spots in functional-potential studies of animal-associated microbiomes

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