Hologenomic data generation and analysis in wild vertebrates
Abstract 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 co...
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| Format: | Article |
| Language: | English |
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Wiley
2025-01-01
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| Series: | Methods in Ecology and Evolution |
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| Online Access: | https://doi.org/10.1111/2041-210X.14456 |
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| author | Carlotta Pietroni Nanna Gaun Aoife Leonard Jonas Lauritsen Garazi Martin‐Bideguren Iñaki Odriozola Ostaizka Aizpurua Antton Alberdi Raphael Eisenhofer |
| author_facet | Carlotta Pietroni Nanna Gaun Aoife Leonard Jonas Lauritsen Garazi Martin‐Bideguren Iñaki Odriozola Ostaizka Aizpurua Antton Alberdi Raphael Eisenhofer |
| author_sort | Carlotta Pietroni |
| collection | DOAJ |
| description | Abstract 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. 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. 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. Based on these data, we provide suggestions to the field for robustly and efficiently generating hologenomic data from wild vertebrates. |
| format | Article |
| id | doaj-art-9815a0af3ecf4dd0bd389645bf5b628d |
| institution | DOAJ |
| issn | 2041-210X |
| language | English |
| publishDate | 2025-01-01 |
| publisher | Wiley |
| record_format | Article |
| series | Methods in Ecology and Evolution |
| spelling | doaj-art-9815a0af3ecf4dd0bd389645bf5b628d2025-08-20T02:44:47ZengWileyMethods in Ecology and Evolution2041-210X2025-01-011619710710.1111/2041-210X.14456Hologenomic data generation and analysis in wild vertebratesCarlotta Pietroni0Nanna Gaun1Aoife Leonard2Jonas Lauritsen3Garazi Martin‐Bideguren4Iñaki Odriozola5Ostaizka Aizpurua6Antton Alberdi7Raphael Eisenhofer8Centre for Evolutionary Hologenomics (CEH), Globe Institute University of Copenhagen Copenhagen DenmarkCentre for Evolutionary Hologenomics (CEH), Globe Institute University of Copenhagen Copenhagen DenmarkCentre for Evolutionary Hologenomics (CEH), Globe Institute University of Copenhagen Copenhagen DenmarkCentre for Evolutionary Hologenomics (CEH), Globe Institute University of Copenhagen Copenhagen DenmarkCentre for Evolutionary Hologenomics (CEH), Globe Institute University of Copenhagen Copenhagen DenmarkCentre for Evolutionary Hologenomics (CEH), Globe Institute University of Copenhagen Copenhagen DenmarkCentre for Evolutionary Hologenomics (CEH), Globe Institute University of Copenhagen Copenhagen DenmarkCentre for Evolutionary Hologenomics (CEH), Globe Institute University of Copenhagen Copenhagen DenmarkCentre for Evolutionary Hologenomics (CEH), Globe Institute University of Copenhagen Copenhagen DenmarkAbstract 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. 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. 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. Based on these data, we provide suggestions to the field for robustly and efficiently generating hologenomic data from wild vertebrates.https://doi.org/10.1111/2041-210X.14456bioinformaticsecological geneticslaboratory methodsmicrobial ecologymolecular biologymolecular methods |
| spellingShingle | Carlotta Pietroni Nanna Gaun Aoife Leonard Jonas Lauritsen Garazi Martin‐Bideguren Iñaki Odriozola Ostaizka Aizpurua Antton Alberdi Raphael Eisenhofer Hologenomic data generation and analysis in wild vertebrates Methods in Ecology and Evolution bioinformatics ecological genetics laboratory methods microbial ecology molecular biology molecular methods |
| title | Hologenomic data generation and analysis in wild vertebrates |
| title_full | Hologenomic data generation and analysis in wild vertebrates |
| title_fullStr | Hologenomic data generation and analysis in wild vertebrates |
| title_full_unstemmed | Hologenomic data generation and analysis in wild vertebrates |
| title_short | Hologenomic data generation and analysis in wild vertebrates |
| title_sort | hologenomic data generation and analysis in wild vertebrates |
| topic | bioinformatics ecological genetics laboratory methods microbial ecology molecular biology molecular methods |
| url | https://doi.org/10.1111/2041-210X.14456 |
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