Molecular ecology of microbiomes in the wild: Common pitfalls, methodological advances and future directions

Nicholas M Fountain-Jones; Tatiana Giraud; Lucie Zinger; Holly Bik; Simon Creer; Elin Videvall

doi:10.1111/mec.17223

Molecular ecology of microbiomes in the wild: Common pitfalls, methodological advances and future directions

Mol Ecol. 2024 Jan;33(2):e17223. doi: 10.1111/mec.17223. Epub 2023 Nov 28.

Authors

Nicholas M Fountain-Jones¹, Tatiana Giraud², Lucie Zinger^{3

4}, Holly Bik⁵, Simon Creer⁶, Elin Videvall^{7

8

9}

Affiliations

¹ School of Natural Sciences, University of Tasmania, Hobart, Tasmania, Australia.
² Laboratoire Ecologie Systématique et Evolution, UMR 8079, Bâtiment 680, Université Paris-Saclay, CNRS, AgroParisTech, Gif-sur-Yvette, France.
³ Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, PSL Université Paris, Paris, France.
⁴ Laboratoire Evolution et Diversité Biologique (EDB), UMR5174, CNRS, Institut de Recherche pour le Développement (IRD), Université Toulouse 3 Paul Sabatier, Toulouse, France.
⁵ Department of Marine Sciences and Institute of Bioinformatics, University of Georgia, Athens, Georgia, USA.
⁶ School of Environmental and Natural Sciences, Bangor University, Bangor, UK.
⁷ Department of Ecology, Evolution and Organismal Biology, Brown University, Providence, Rhode Island, USA.
⁸ Institute at Brown for Environment and Society, Brown University, Providence, Rhode Island, USA.
⁹ Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden.

PMID: 38014746
DOI: 10.1111/mec.17223

Abstract

The study of microbiomes across organisms and environments has become a prominent focus in molecular ecology. This perspective article explores common challenges, methodological advancements, and future directions in the field. Key research areas include understanding the drivers of microbiome community assembly, linking microbiome composition to host genetics, exploring microbial functions, transience and spatial partitioning, and disentangling non-bacterial components of the microbiome. Methodological advancements, such as quantifying absolute abundances, sequencing complete genomes, and utilizing novel statistical approaches, are also useful tools for understanding complex microbial diversity patterns. Our aims are to encourage robust practices in microbiome studies and inspire researchers to explore the next frontier of this rapidly changing field.

Keywords: bioinformatics; eDNA; host-parasite interactions; microbial communities; statistics.

MeSH terms

Bacteria*
Ecology
Microbiota* / genetics