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.