Commentary: The microbial dependence continuum: Towards a comparative physiology approach to understand host reliance on microbes

Williams, Claire E.; Fontaine, Samantha S.

doi:10.1016/j.cbpa.2024.111690

Comparative Biochemistry and Physiology Part A: Molecular &

2024

DOI: 10.1016/j.cbpa.2024.111690

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Commentary: The microbial dependence continuum: Towards a comparative physiology approach to understand host reliance on microbes

Claire E. Williams,

Samantha S. Fontaine

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Hologenomic data generation and analysis in wild vertebrates

Pietroni,

Gaun,

Leonard

et al. 2024

Methods Ecol Evol

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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.

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Hologenomic data generation and analysis in wild vertebrates

Pietroni,

Gaun,

Leonard

et al. 2024

Methods Ecol Evol

View full text Add to dashboard Cite

show abstract

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Commentary: The microbial dependence continuum: Towards a comparative physiology approach to understand host reliance on microbes

Cited by 1 publication

References 66 publications

Hologenomic data generation and analysis in wild vertebrates

Hologenomic data generation and analysis in wild vertebrates

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