Details zur Publikation

Kategorie Textpublikation
Referenztyp Zeitschriften
DOI 10.1186/s42523-023-00267-3
Lizenz creative commons licence
Titel (primär) The AnimalAssociatedMetagenomeDB reveals a bias towards livestock and developed countries and blind spots in functional-potential studies of animal-associated microbiomes
Autor Avila Santos, A.P.; Kabiru Nata’ala, M.; Kasmanas, J.C.; Bartholomäus, A.; Keller-Costa, T.; Jurburg, S.D.; Tal, T.; Camarinha-Silva, A.; Saraiva, J.P.; de Carvalho, A.C.P.L.F.; Stadler, P.F.; Sipoli Sanches, D.; Nunes da Rocha, U.
Quelle Animal Microbiome
Erscheinungsjahr 2023
Department BIOTOX; UMB; iDiv
Band/Volume 5
Seite von art. 48
Sprache englisch
Topic T7 Bioeconomy
T9 Healthy Planet
Keywords Metagenome; Animal-Associated Microbiomes; Microbial Ecology; Metadata; Database; FAIR principles
Abstract 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/.
dauerhafte UFZ-Verlinkung https://www.ufz.de/index.php?en=20939&ufzPublicationIdentifier=28022
Avila Santos, A.P., Kabiru Nata’ala, M., Kasmanas, J.C., Bartholomäus, A., Keller-Costa, T., Jurburg, S.D., Tal, T., Camarinha-Silva, A., Saraiva, J.P., de Carvalho, A.C.P.L.F., Stadler, P.F., Sipoli Sanches, D., Nunes da Rocha, U. (2023):
The AnimalAssociatedMetagenomeDB reveals a bias towards livestock and developed countries and blind spots in functional-potential studies of animal-associated microbiomes
Animal Microbiome 5 , art. 48 10.1186/s42523-023-00267-3