Introduction
The study of microbial communities across host species and environments
(hereafter the ‘microbiome’) is a major focus of research in the field
of molecular ecology. As such, Molecular Ecology andMolecular Ecology Resources regularly publish papers and special
issues in the field. Molecular Ecology is at the forefront of
examining the importance of microbiomes across ecosystems, from
increasing our understanding of host-pathogen (e.g., Bergner et al.,
2020; Wille et al., 2018) and host-symbiont interactions (e.g., Rubin et
al., 2019) to investigating the impact of climate and other
environmental factors on microbial populations (e.g., Santos-Júnior et
al., 2022; Wu et al., 2022). Complementing these efforts,Molecular Ecology Resource s publishes significant methodological
advances that continue to shape the field (e.g., Harrison et al., 2020;
Schnell et al., 2015; Stothart et al., 2021). Based on our collective
experience as subject editors at Molecular Ecology andMolecular Ecology Resources , here we discuss some of the best
practices and advances for analysing microbiomes, from study design to
data analysis, and highlight anticipated future directions in the field.
With this article we hope to inspire and encourage researchers to obtain
more robust insights from microbiome data, which will enable the field
to advance and tackle the new horizons enabled by recent advances in
technology.