RSB Directors Seminar: The Australian Microbiome database and applications to Australian microbial ecology

The Australian Microbiome (AM) initiative is a collaborative network of researchers, centrally administered and supported primarily by CSIRO, Director of National Parks, Bioplatforms Australia and the Integrated Marine Observing System (IMOS), providing publically available data characterizing Australia’s environmental microbial diversity. The AM produces both amplicon sequences (bacteria, archaea, eukaryote and fungal targets) and shotgun metagenomes, primarily from soil and marine environments.  The AM currently comprises data from 7723 samples.  Every sample is accompanied by rich sample specific metadata describing its physical and chemical composition, as well as its geolocation and regional descriptors.  Methods used to collect samples, perform wet lab analyses and downstream bioinformatic analyses are standardised.  Sequence and sample specific metadata is available via the AM data portal ( ), as both raw sequences data and curated sequence abundance tables, as well as from international nucleotide archives.  Data produced by the AM is also available for direct export to and analysis by the Galaxy Australia server.

AM was formed by aligning the previous Marine Metagenome (MM) and Biomes of Australian Soil Environments (BASE) projects into a single Australian microbial diversity resource.  Soil data comprise samples from two depths per site, covering the breadth of Australian soil heterogeneity, as determined by soil chemical and physical maps and overlying plant community data.  Soil samples also include limited samples from Antarctica.  Marine data includes depth profiles and relatively high temporal resolution time series data from IMOS national reference stations, as well as samples from around the Australian coastline, from both pelagic and near shore sites.

The AM is currently expanding to include greater temporal and spatial coverage with an expected 3500 samples sequenced with amplicons and 400 metagenomes in the next 3 years.  AM will also continue to improve secondary data types and accessibility.

Applications of data produced by AM will be described.

Andrew is a microbial ecologist interested in all facets of microbial interaction with the environment and how microbial diversity maintains ecosystem health and function.  His research has included investigation of microbial diversity/function relationships, microbial biogeography and microbial symbioses in soils, marine and freshwater systems using molecular and biogeochemical tools.

Andrew is a senior research scientist at CSIRO, based in Hobart, where he is involved in the Australian Microbiome projects (  Andrew completed his PhD at UTAS and completed a postdoctoral fellowship at the Max Planck Institute for Marine Microbiology in Germany, before returning to CSIRO in Canberra, and eventually returning to Hobart.