Our Services

The Centre for Microbiome Research at the Translational Research Institute has a dedicated PC2-certified laboratory, fully equipped for molecular biology – with an in-house white-light laser confocal microscope (Leica), a PromethION (Oxford Nanopore Technologies), and access to a NovaSeq 6000 (Illumina). The Centre also has a specialised BD FACSAria Fusion fluorescence activated cell sorter enclosed in an anaerobic chamber, invaluable for studying microorganisms that have so far managed to evade cultivation. CMR also houses its own high-performance computing resources consisting of >1,000 cores and 8 nodes, able to support substantial quantities of data. Together, the unique resources at CMR enable us to develop and provide specific microbiological services for all your research needs.

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Sequencing

Advancements in high-throughput next-generation sequencing (NGS) technologies have revolutionised genomic research and can largely replace single gene approaches. NGS enables paralleled sequencing of short and long fragments of DNA that are then pieced together into a continuous genomic sequence. This method is a high-throughput, low-cost option to sequence whole genomes. Sequencing is available for both eukaryotic and prokaryotic samples. Sequence data processing and analysis are covered in our bioinformatics services.

Long read sequencing

Long-read sequencing technologies directly sequence single molecules of DNA, thus improving de novo assembly, mapping certainty, and identification of transcript isoforms and structural variants. We are one of the only certified service labs in Australia to offer a long-read DNA sequencing service on the Oxford Nanopore Technologies PromethION 24. This technology provides improved efficiency and accuracy over existing DNA sequencing applications, including:

  • Direct sequencing of native DNA and RNA with capacity for real time analysis
  • No restrictions on read length, capable of high-throughput sequencing of ultra-long reads
  • Ability to sequence up to 24 flow cells at a time, and generate up to 200Gbp of data per flow cell.

Short read sequencing

Short-read sequencing technologies offer the opportunity to simultaneously sequence all DNA or RNA in a sample. Using the Illumina NovaSeq 6000 platform, we can provide high-throughput genome, exome, or transcriptome sequencing with high accuracy.

Flow cytometry

Fluorescence activated cell sorting is a powerful tool commonly used in mammalian studies to isolate cells of interest. We use FACS for isolation of target cells from different complex matrices, these sorted cells are suitable for sequencing (including single cell sequencing) or culture. Microbial samples pose unique challenges and require specialised instrumentation and processing. Our BD FACS Aria Fusion is uniquely configured to target microbial populations. Equipped with small particle detector it is capable of clearly resolving beads < 100 nm. It is configured to be capable of hypoxic sorting, housed in BSCII for processing PC2 samples.

Additionally, our dedicated operator with expertise in environmental microbiology can help with project design and development of new assays to target populations of interest.
Samples we have experience sorting from include:

  • Coral mucus
  • Coral tissue
  • Sea water
  • Soil / sediment
  • Faecal

Single cell genomics

Single cell isolation and sequencing allows in depth investigation into the true heterogeneity of a sample. Individual cellular differences can have profound effects on their functioning in an environment. We have combined our FACS and sequencing capabilities into a high throughput single cell genomics pipeline. Using this method, we are able to sort out individual cells from various microbial communities, extract and amplify their DNA, and sequence each cell individually. This method gives high quality genome recovery that is ideal for creating reference genomes for your samples of interest, as well as targeting rare species with low coverage in metagenomic sequence data.

Amplifying and sequencing single cell targets requires meticulous attention to detail. Our instrumentation is maintained to the highest standards and controls are collected throughout the pipeline. Lysis and amplification are carried using state of the art Perkin Elmer Flex Drop IQ in a sterile laminar flow cabinet to minimize risk of contamination.

Confocal microscopy

Confocal microscopy is an optical imaging technique for increasing the resolution and contrast of a micrograph. Our Leica STELLARIS 5 white light confocal microscope is capable of:

  • Visualising more fluorophore combinations than any other confocal platform
  • Fluoresence lifetime imaging
  • Two-dimensional imaging
  • Reconstructing three-dimensional structures by combining multiple two-dimensional images at different depths (optical sectioning)

These capabilities allow exploration of microbial habitats and the observation of microorganisms in situ with an unprecedented accuracy.

Figure right: Fluorescent image of a coal thin section. Symbionium are visible in the top R due to their bright autofluorescence, and their complex nuclei are highlighted with DAPI staining. FISH probes allow localisation of microbial communities in the coral tissue.

Bioinformatics

CMR offers range of bioinformatic and statistical analysis services for both amplicon and whole metagenome sequencing data, with particular experience in environmental ecology and the human microbiome.
Our powerful, high performance computing resources include 8 servers with 128 CPU cores and 1 Tb ram each, and one specialised server with 96 CPU cores and a nVidia GPU. We also use specialised in-house software to achieve the most robust, high quality analyses in the metagenomics field.

Our bioinformatics services include:

  • Metagenome-assembled genome (MAG) recovery
  • Taxonomic reconstruction
  • Functional profiling
  • Transcriptome and metatranscriptome analysis

CMR facilities were established with funding from QUT and the Ian Potter Foundation.