Hologenomic data generation and analysis in wild vertebrates

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dc.contributor.authorPietroni, C.
dc.contributor.authorGaun, N.
dc.contributor.authorLeonard, A.
dc.contributor.authorLauritsen, J.
dc.contributor.authorMartin-Bideguren, G.
dc.contributor.authorOdriozola, I.
dc.contributor.authorAizpurua, O.
dc.contributor.authorAlberdi, A.
dc.contributor.authorEisenhofer, R.
dc.date.issued2024
dc.description.abstract1. Hologenomics, the joint analysis of host genomes and microbial metagenomes, has the potential to address fundamental biological questions from a systemic host-microbiota perspective. However, multiple fieldwork, laboratory and bioinformatic steps challenge quality, representativeness and comparability of hologenomic data. 2. Leveraging the first 2025 samples sourced from 151 wild vertebrate species analysed in the Earth Hologenome Initiative, we scrutinise hologenomic data generation steps, including laboratory and bioinformatic procedures. Comparisons across taxa and sample types provide novel insights into the relationships between laboratory quality metrics and derived data, the variation of host, prokaryotic and non-prokaryotic fractions of shotgun data, and the relationship between data quality and quantity with genome and metagenome reconstruction. 3. Our results show that faecal samples are significantly better than anal and cloacal swabs to study intestinal microbiomes using genome-resolved metagenomics. We also report that birds and bats both have substantially lower microbial DNA fractions and a higher degree of sample-to- sample variability compared to amphibians, reptiles and non-flying mammals. 4. Based on these data, we provide suggestions to the field for robustly and efficiently generating hologenomic data from wild vertebrates.
dc.description.statementofresponsibilityCarlotta Pietroni, Nanna Gaun, Aoife Leonard, Jonas Lauritsen, Garazi Martin-Bideguren, IƱaki Odriozola, Ostaizka Aizpurua, Antton Alberdi, Raphael Eisenhofer
dc.identifier.citationMethods in Ecology and Evolution, 2024; 16(1):97-107
dc.identifier.doi10.1111/2041-210X.14456
dc.identifier.issn2041-210X
dc.identifier.issn2041-210X
dc.identifier.urihttps://hdl.handle.net/2440/146618
dc.language.isoen
dc.publisherWiley
dc.rightsĀ© 2024 The Author(s). Methods in Ecology and Evolution published by John Wiley & Sons Ltd on behalf of British Ecological Society. This is an open access article under the terms of the Creative Commons Attribution-NonCommercial License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited and is not used for commercial purposes.
dc.source.urihttps://doi.org/10.1111/2041-210x.14456
dc.subjectbioinformatics; ecological genetics; laboratory methods; microbial ecology; molecular biology; molecular methods; population genetics
dc.titleHologenomic data generation and analysis in wild vertebrates
dc.typeJournal article
pubs.publication-statusPublished

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