The Australian Microbiome Initiative

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Introduction

Australia is a vast continent that comprises a varied range of terrestrial environments with rich coastal and marine regions. These ecological systems are supported by communities of microbes that, despite being invisible to the naked eye, are the hidden force behind many events impacting both the environment and living organisms.

Microbes are fundamental to human and ecosystem health. They underpin the majority of processes on Earth from mediating global biogeochemical cycling to being responsible for diseases and their treatment.

Two seeding established Bioplatforms Australia framework data initiatives have generated and maintained valuable resources for the investigation of microbial communities in both terrestrial (soil; Biomes of Australian Soil Environments BASE) and marine (pelagic and coastal; Marine Microbes MM) environments. These initiatives comprised over 40 organisational partners. This nationally inclusive consortium approach has facilitated the development of two highly aligned efforts with impactful deliveries both in terms of data resource and analysis abilities.

The Australian Microbiome Initiative builds upon the success of these two consortiums, in creating a global aligned Australian network that will strengthen this critical continental resource and significantly enhance the value of each effort to support national research efforts in defining the primary drivers in environment productivity, monitoring the health of our environment and driving conservation.

The Australian Microbiome Initiative is generating a resource consisting of reference genomic dataset of microbial community composition with extensive contextual metadata augmented by reference genomes of abundant microbes.

For further information, please visit the initiative webpage

Aims

The consortium objectives are to:

  • Sustain the establishment of the genomic resource by maintaining and growing the sampling effort of the consortium whilst strengthening the standardisation of the associated contextual data.
  • Extend and diversify the initiative’s resource with the inclusion of broader available dataset of value from confluent programs/studies established outside of the umbrella of the Australian Microbiome consortium. This will expand the consortium network to other national and international collaborators.
  • Innovate by driving functionalisation of the resource to respond to the needs of end users. Provide access to the data that will cater for a broad range of end users including, but not limited to management consultants; government departments such as the Dept. of the Environment and Energy or Dept. of Agriculture and Water Resources; law enforcement agencies; research and development corporations such as the Fisheries RDC; and the gas and mining industry.

Uses of the resource being built would include research/academic users as well as those with more applied questions such as biosecurity or productivity management. In addition, it provides a valuable resource for training purposes.

Experimental setup, methods

Methods from the legacy initiatives Marine Microbes and BASE can be found here

The Australian Microbiome consortium

The Australian Microbiome Initiative is an Australian wide collaboration founded on two established Bioplatforms Australia framework data initiatives: Marine Microbes (MM) and Biomes of Australian Soil Environments (BASE). The consortium involves researchers from more than 40 institutions supported by the following core partners:

Project contacts

Bioplatforms Australia promotes data sharing and collaborative interactions are encouraged to advance scientific discovery and maximise the value to the community from this Australian Government (NCRIS)-funded dataset. As such, the consortium would like to extend an invitation to collaborate.

Data from the Initiative is made available to members of the consortium upon generation. Following a period of mediated access, where access to the data will be limited to members of the consortium and other approved parties, the data will be made available publicly.

Should you wish to access the data during this mediated period, please email with your name, affiliation, specific data for which access is being requested and a brief outline of the intended data use. This information will be assessed by Bioplatforms Australia and the consortium, and you will be contacted to discuss collaborative access.

Publications / Conference presentations

The Australian Microbiome has a strong interest in seeing that the data and capability produced by the initiative is actively communicated to and used by the wider community both scientific and general.

All consortium members have agreed to the communications policy set at the inception of the program.

Data policy and access

All consortium members have agreed to the data policy set at the inception of the program.

The data is publicly available. To access the consortium data, for administrative purposes and to enable us to assess the utility of the database, its frequency and type of utilisation, we require registration.

Open Science Framework page (consortium members only)

Access on the OSF page

Acknowledging the consortium

When using Australian Microbiome Initiative data, please acknowledge the Consortium and Bioplatforms Australia support using the following wording:

We would like to acknowledge the contribution of the Marine Microbes (MM) and Biomes of Australian Soil Environments (BASE) projects, through the Australian Microbiome Initiative in the generation of data used in this publication. The Australian Microbiome Initiative is supported by funding from Bioplatforms Australia and the Integrated Marine Observing System (IMOS) through the Australian Government's National Collaborative Research Infrastructure Strategy (NCRIS), the Director of National Parks with BHP, and the CSIRO.

All communications (scientific or general publications and presentations) that arise from the consortium’s work must appropriately acknowledge the input of all relevant contributions. The publications should specify the collaborative nature of the project, and authorship is expected to include all those contributing significantly to the work.