This document summarises microbiome analysis tools and methodologies (i.e. either targeted (amplicon analysis) or random shotgun (metagenomics) approaches), how the Australian life science research community currently undertakes this work as well as common data-, software- or compute-related infrastructure challenges faced by that community when using current approaches (information obtained through consultation with a ‘Special Interest Group’ (SIG) of researchers undertaking microbiome analysis across Australia). Also included is a high level description of key components of an envisaged shared infrastructure for Australia, which, when implemented, would enable Australian researchers from a wide range of institutions to perform microbiome analysis work who would otherwise be unable to do so because of the reported data-, software- or compute-related roadblocks. This document has incorporated feedback from the Microbiome Analysis SIG, other Australian researchers undertaking microbiome analysis, international groups undertaking similar work (e.g. the National Microbiome Data Collaborative (NMDC) in the USA), and numerous Australian research IT infrastructure partners. Implementation of some of the infrastructure outlined in this roadmap document began in 2021, and will continue through 2021-22.