The study of microbiomes across organisms and environments has become a
prominent focus in molecular ecology. This perspective article explores
methodological advancements, common challenges 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.