New insights into hologenomics research in wild vertebrates
In a new technical paper just published in Methods in Ecology and Evolution, researchers highlight the potential of hologenomics to deepen our understanding of biological systems from a host-microbiota perspective. However, at the same time the team warns that various challenges in fieldwork, laboratory protocols, and bioinformatics must be addressed to enhance the quality and comparability of hologenomic data.
An Earth-wide initiative
The Earth Hologenomics Initiative analysed a comprehensive set of 2,025 samples sourced from 151 wild diverse vertebrate species and aimed to scrutinise the multiple steps involved in generating hologenomic data. The findings, which reveal novel insights into laboratory quality metrics and their relationship to genomic data, underscore the importance of rigorous methodologies in obtaining reliable results.
“Selecting the methodology is essential for the unbiased detection of microbial diversity and for enhancing the comparability and reproducibility of research findings. This paper marks a significant milestone for our initiative, as standardising and optimising methods is one of our primary goals. We hope our study will serve as a valuable resource for the research community to guide future studies’ technical decision-making.” Says postdoc, and lead author of this article, Carlotta Pietroni.
Challenging bats and birds
Among the significant revelations, the study found that faecal samples are far superior to anal and cloacal swabs for studying intestinal microbiomes using genome-resolved metagenomics. This has important implications for future research methodologies, suggesting that sample type can greatly influence data quality.
Additionally, the researchers discovered notable differences in microbial DNA fractions among various animal groups. Birds and bats exhibited lower microbial DNA fractions and greater sample variability compared to amphibians, reptiles, and non-flying mammals. This variability could pose challenges for comparative studies across taxa, highlighting the need for careful consideration of sample types in future hologenomic research.
“Finding such an unreliable microbial signal in birds and bats is very interesting, and suggests that either A) birds/bats don’t rely on their microbes as much as other vertebrates, or B) there are still technical challenges yet to be solved to unlock these microbial communities.” postdoc, and senior author of this article Raphael Eisenhofer adds.
Robust hologenomic data
The team has put forth recommendations to streamline the generation of robust hologenomic data, advocating for standardised practices to improve data quality and efficiency in studying wild vertebrates. By addressing these methodological challenges, the researchers hope to advance the field and unlock further insights into the complex interactions between hosts and their microbial communities.
As the field of hologenomics continues to evolve, this study serves as a critical stepping stone, paving the way for future investigations that could unravel fundamental biological questions and enhance our understanding of ecosystem dynamics.
Read the open access published paper in Methods in Ecology and Evolution.
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Postdoc Raphael Eisenhofer