Towards sub-species resolution profiling of plant and soil microbiomes

Sequence-based studies to characterise microbial communities remain dominated by platforms that offer ultra-high output of short (100-250 bp), high-quality reads. This is largely because platforms capable of generating much longer, and potentially more informative reads (>10 kb), are prone to high error rates. Recent advances in library preparation and bioinformatics, both internationally and in our lab, make it possible to generate long-high-quality reads that can be used to profile microbial diversity at sub-species-resolution, and enhance the recovery of genomes from metagenomic datasets. Here, we present results from our work with the microbiomes of banana plants and soils and their interactions with Fusarium spp. This novel technology has the potential to revolutionise pathogen diagnostics and our understanding of pathogen-microbiome ecology.