Welcome to the Centre for Microbiome Research at the Translational Research Institute, where cutting-edge technology meets world-class expertise.
Our dedicated PC2-certified laboratory is fully equipped to support a wide range of microbiome and molecular biology research, providing access to advanced tools like the BD FACSAria Fusion and Cytek Aurora CS fluorescence-activated cell sorter housed in an anaerobic chamber for high-precision sorting of even the most challenging microorganisms.
With our Leica white-light laser confocal microscope, PromethION (Oxford Nanopore Technologies) sequencing platform, and access to the Illumina NovaSeq 6000, we offer unparalleled resources for everything from high-resolution imaging to next-generation sequencing. Additionally, our in-house high-performance computing resources – including over 1,000 cores and 8 nodes – ensure we can handle substantial data loads and provide rapid analysis for your research needs.
Whether you’re exploring microbial communities or tackling complex molecular biology questions, the Centre for Microbiome Research has the facilities, expertise, and state-of-the-art technologies to help advance your studies. Let us support your work with the unique microbiological services you need to push the boundaries of discovery. Click the links below for more information.
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.
The Centre for Microbiome Research Flow Cytometry facility is equipped with state-of-the-art instrumentation operated by dedicated staff. Our Senior Flow Cytometry Scientist, Dr Allison McInnes, has a PhD in Biological Oceanography with training and research focused on microbial ecology and biogeochemistry. Allison has over 10 years’ experience in flow cytometry and cell sorting. She is a leader in microbial flow cytometry and is keen to assist in helping to resolve your flow cytometry related microbiology needs.
Instrumentation
BD FACSAria Fusion (SORP)
CMR Flow Cytometry facility staff operate the BD FACSAria Fusion. This SORP instrument is customised with Small Particle detector (resolution between 100-150nm for biological particles) for finding and isolation of components of the microbiological community.
- 3 laser (3 pinhole, 405nm, 488nm, 640nm)
- 4 scatter channels (SPO, SSC-v, SSC-b, FSC) 12 fluorescent channels (5 violet, 5 blue, 2 red)
- 2-way, 4-way and plate sorting into variety of collection tubes (5 mL polypropylene, 10 mL and 15 mL and 50 mL tubes) and 96- and 384- well plates.
- Index sorting for full fluorescent identification of sorted particle.
- Sample chamber and sort chamber can be temperature controlled to maintain optimal temperature for sample and product.
- Housed in a biosafety cabinet to allow sorting of human cells, human cell lines, virally-transduced cells and samples with potential RG2 members.
Cytek Aurora CS
CMR Flow Cytometry facility staff operate the Cytek Aurora CS. This full spectrum cytometer is housed in a custom anaerobic chamber for full atmosphere control during sample preparation, sorting and post-processing.
- 5 lasers (355nm, 405nm, 488nm, 561nm and 640nm).
- 67 parameters instrument (FSC, SSC-B, SSC-V and 64 fluorescence channels).
- Fluorescence data is measured over a dynamic 6 decades of data.
- 2-way, 4-way, 6-way and plate sorting into variety of collection tubes (5 mL polypropylene, 10 mL and 15 mL and 50 mL tubes) and 96- and 384- well plates.
- Index sorting for full fluorescent identification of sorted particle.
- Sample chamber can be temperature controlled to maintain optimal temperature for sample and product.
Services
High-throughput (anaerobic) cultivation platform
The Centre for Microbiome Research is uniquely equipped with a BD FACS Aria Fusion outfitted and optimised for anaerobic sorting of microbes. The small particle detector (the first in the world on the BD Fusion) allows discrimination of microbes from the noise making the use of DNA dyes unnecessary, enhancing post-sort viability. The sorter is run using nitrogen gas instead of compressed air to ensure anaerobic conditions are maintained inside the machine. The sort chamber is flooded with nitrogen gas to ensure cell deposition is in a low oxygen environment (<0.1%). Capable of sorting 96 or 384 individual cells onto solid or liquid media enables large numbers of single cells to be obtained. We have had success isolating fastidious anaerobes from feacal samples.
Single cell sorting
Single Amplified Genomes (SAGs) and mini-metagenomes can be obtained from targeted sorting of select populations from complex mixed assemblages. These methods allow for deeper sequencing of community components of interest. Selection can be made through fluorescent antibody labelling, functional dyes (DNA, activity, ROS), fixation free fluorescence in situ hybridisation, or based on size or autofluorescence. Further extraction, amplification and sequencing can also be done through our sister facilities.
Small particle sorting (plasmid, virus, and EVs)
The small particle option fitted to the FACS Aria Fusion allows resolution of very small biological particles based on scatter alone (100-150nm based on refractive index). This is necessary for EVs and other small particles which may not have DNA cargo. For particles containing DNA a fluorescent DNA dye can be added to resolve even smaller particles. We have successfully isolated 9kb plasmids and virus-like particles. These particles can be sorted individually or into a bulk sort for futher investigation.
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.