Ruminant microbiome data are skewed and unFAIR, undermining their usefulness for improving sustainable production

Abstract

The ruminant microbiome plays a key role in the health, feed utilization and environmental impact of ruminant production systems. Microbiome research provides insights to reduce the environmental footprint and improve meat and milk production from ruminants. However, the microbiome composition depends on the ruminant species, habitat and diet, highlighting the importance of having a good representation of ruminant microbiomes in their local environment to translate research findings into beneficial approaches. This information is currently lacking. In this study, we explored the metadata of microbiome studies from farmed ruminants to determine global representativeness and summarized information according to ruminant species, geographic location, body site, and host information. We accessed data from the International Nucleotide Sequence Database Collaboration through the National Center for Biotechnology Information database. We recovered 47,628 sample metadata with cattle accounting for over two-thirds of the samples. In contrast, goats with a worldwide population similar to cattle were markedly underrepresented, making up less than 4% of the total samples. Most samples originated in Western Europe, North America, Australasia and China but countries with large ruminant populations in South America, Africa, Asia, and Eastern Europe were underrepresented. Microbiomes from the gastrointestinal tract were the most frequently studied comprising about 87% of all samples. Additionally, the number of samples from other body sites such as the respiratory tract, milk, skin, reproductive tract, and fetal tissue, has markedly increased over the past decade. More than 40% of the samples lacked basic information and many were retrieved from generic taxonomic classifications where the ruminant species was manually recovered. The lack of information on diet, production system, age, or breed limits the reusability of the data for reanalysis and follow-up studies. Taxonomic assignment of the ruminant host and a minimum set of metadata attributes using accepted ontologies adapted to host-associated microbiomes are prerequisites for this. Public repositories are encouraged to require this information. The results from this survey highlight the need to encourage studies of the ruminant microbiome from underrepresented ruminant species and underrepresented countries worldwide.