AHMB Facility · Centre for Microbiome Research, QUT
Bacterial Isolation & Cultivation Service
A high-throughput, fee-for-service platform operated by expert microbiologists at QUT, Brisbane, Australia. The platform delivers authenticated bacterial isolates and comprehensive genomic and phenotypic characterisation data from human-derived samples under an ISO 20387-aligned quality management system.
Platform Overview
A fee-for-service bacterial isolation and characterisation platform
The AHMB High-Throughput Cultivation Platform is a fee-for-service bacterial isolation and cultivation service that provides academic and commercial partners with access to standardised, high-throughput bacterial isolation and characterisation workflows underpinning the Australian Human Microbiome Biobank collection.
The platform enables research groups to obtain authenticated, fully characterised bacterial isolates from their own samples, without the need to establish or maintain specialised in-house cultivation infrastructure.
Our primary area of expertise is the human microbiome, with established bacterial isolation protocols spanning major anatomical sites, including the gastrointestinal tract, oral cavity, skin, vaginal microbiome and biopsy-derived tissues.
In addition, the platform supports microbial isolation from non-human sample types, including environmental and animal-derived matrices, subject to feasibility assessment.
The platform is operated by specialist microbiologists within the Centre for Microbiome Research (CMR) at Queensland University of Technology (QUT), and is housed in a purpose-built facility at the Translational Research Institute (TRI), Brisbane.
All activities are conducted in accordance with documented standard operating procedures within a rigorous quality management system, ensuring traceability, reproducibility, and scientific integrity throughout the service workflow.
Pre-submission consultations are strongly encouraged. We invite researchers to contact the platform team prior to initiating a formal service request to discuss sample matrix, target organism groups, experimental design considerations and expected deliverables. Our scientific team will assess protocol suitability and provide a tailored fee estimate prior to any commitment.
Technical Capabilities
Integrated bacterial isolation, genomic sequencing and characterisation capabilities
The High-Throughput Cultivation Platform consolidates high-throughput bacterial isolation with state-of-the-art whole genome sequencing infrastructure, providing a comprehensive suite of microbial characterisation services within a single dedicated facility.
High-Throughput Bacterial Isolation
The platform delivers scalable, high-throughput bacterial isolation workflows designed to support the processing of large sample cohorts in parallel. Selective and non-selective culture media are specifically formulated and optimised for defined sample matrices and target taxonomic groups, with atmospheric conditions tightly controlled to reflect the physiological requirements of target organisms. Experimental design consultation is available through our in-house scientific team prior to sample submission.
Aerobic, Microaerophilic & Anaerobic Culture
Our purpose-built culture facility supports the isolation of oxygen-sensitive and fastidious microorganisms, including key members of the gut microbiome that are challenging to cultivate under standard laboratory conditions. Our custom-built anaerobic chambers house advanced automation systems, including the PIXL colony-picking robot (Singer Instruments) enabling high-throughput bacterial isolation and cultivation. This integrated infrastructure provides the capability to recover and culture a broad diversity of microbiome associated taxa.
Illumina Short-Read Whole Genome Sequencing
Illumina short-read whole genome sequencing (WGS) is included as a standard component of all bacterial isolate characterisation workflows. This platform generates high accuracy sequencing data suitable for strain level taxonomic assignment, comparative genomic analyses, antimicrobial resistance (AMR) gene profiling, mobile genetic element identification and comprehensive functional annotation of each isolated strain.
Oxford Nanopore Long-Read Sequencing
Oxford Nanopore long-read sequencing is available in-house as an optional add-on to the standard Illumina WGS workflow. This approach enables complete or near-complete genome assemblies, improved resolution of repetitive genomic regions, detection of structural variation and enhanced characterisation of plasmids and mobile genetic elements that are not readily resolved using short-read sequencing alone.
Cryopreservation & Biobanking
All isolated strains are cryopreserved under validated conditions to ensure long-term viability and phenotypic stability. Multiple cryopreservation stocks can be produced for each isolate, comprising working stocks for immediate experimental use and master stocks archived under monitored long-term storage conditions. Client target strains are prepared and delivered in accordance with the terms of the service agreement.
Data Reporting & Documentation
All service outputs are accompanied by a comprehensive data report documenting isolation success metrics, taxonomic identification outcomes, whole genome sequencing data, growth and phenotypic characteristics, and quality control results. Reports are provided in agreed formats aligned with project and data integration requirement. Each strain is supplied with a Certificate of Analysis (CoA) and Product Information Sheet (PIS), detailing culture conditions, media composition, atmospheric requirements, and handling and storage specifications.
Compatible Sample Types
Supported sample matrices
The platform's primary area of expertise is the isolation and characterisation of bacteria from human-derived samples, with validated protocols spanning all major human microbiome niches. Non-human sample types are also supported, including environmental, animal-derived and other complex matrices, subject to an initial feasibility assessment. Researchers working with non-standard sample types are encouraged to contact the platform team prior to submission to assess suitability and determine any required adaptations to established isolation workflows.
Faecal & Intestinal Samples
The platform's primary area of technical specialisation. Established and validated protocols achieve broad spectrum recovery of the intestinal microbiota, including obligate anaerobes and oxygen sensitive taxa that require strictly controlled atmospheric conditions for viable isolation and culture.
Oral Swabs & Salivary Samples
Isolation of the oral microbiota from buccal mucosal swabs, saliva and dental plaque. Protocols accommodate the substantial phylogenetic diversity of the oral cavity, encompassing aerobic, facultatively anaerobic and microaerophilic taxa across supragingival and subgingival niches.
Cutaneous Swabs & Skin Microbiome Samples
Isolation of cutaneous microbiota from swab samples collected at any body site. Applicable to dermatological research programs, wound microbiology investigations and skin microbiome studies encompassing both healthy reference cohorts and disease affected populations.
Vaginal & Reproductive Tract Samples
Targeted isolation of vaginal and reproductive tract microbiota, including Lactobacillus dominant communities and associated taxa. Applicable to studies of reproductive health, bacterial vaginosis pathogenesis and microbiome associated obstetric and gynaecological outcomes.
Biopsy & Surgically-Derived Tissue Specimens
Bacterial isolation from endoscopic biopsy material and surgically derived tissue specimens. The platform has established workflows for processing low biomass samples, with capacity to adapt isolation strategies to address the specific analytical challenges presented by tissue associated and mucosal microbial communities.
Other Human-Derived & Non-Human Matrices
The platform accommodates additional human-derived samples including urinary tract, respiratory tract, nasal and ocular specimens, as well as non-human sample types such as environmental, animal derived, soil and water matrices. All non-standard sample types are subject to an initial feasibility assessment; our team is experienced in developing adapted isolation strategies for novel and methodologically challenging matrices.
Non-standard and complex sample types welcomed
We actively collaborate with researchers addressing methodologically challenging sample types or research questions requiring bespoke isolation strategies. Our team has extensive experience adapting bacterial isolation workflows for novel matrices—both human-derived and non-human—in partnership with academic, clinical and industry stakeholders.
Enquiries regarding sample types not described above are welcomed. All human samples submitted to the platform must be accompanied by documentation of valid institutional ethics approval and evidence of informed participant consent appropriate to the intended use.
For non-human sample types, investigators should engage with the platform team at the earliest opportunity to confirm any applicable regulatory, biosafety or import/export requirements prior to submission.
Comprehensive guidance on sample collection, including containers, preservation conditions and transport requirements, is provided to all clients at the time of engagement.
Service Workflow
From sample submission to authenticated strain delivery
The bacterial isolation and cultivation service is managed end-to-end by our specialist scientific team. The following describes the standard workflow from initial scientific consultation through to delivery of quality released isolates, associated genomic data and supporting documentation.
Feasibility Assessment & Scientific Consultation
Investigators are encouraged to contact the platform team prior to formal submission to discuss research objectives, sample types, target organism groups and desired deliverables. Our team conducts an initial feasibility assessment, advises on protocol suitability and experimental design and issues a tailored fee estimate prior to any commitment. This consultation is provided at no charge and is strongly recommended for novel or complex sample types.
Service Agreement Execution
Upon confirmation of project scope, a formal Service Agreement is executed specifying the work to be performed, deliverables, project timelines, fee structure and provisions relating to intellectual property, data ownership and publication rights. Where institutional or commercial contracting requirements apply, QUT's Office of Research Services team is engaged to support agreement finalisation.
Sample Submission
Clients submit samples directly to the AHMB facility at TRI, Brisbane, in accordance with platform specific sample handling and transport protocols provided at the time of engagement. Detailed written guidance is provided covering collection containers, preservation conditions, temperature requirements and regulatory shipping documentation (including for international submissions) to ensure sample integrity is maintained throughout transit.
Isolation & Phenotypic Characterisation
Samples are processed according to validated isolation protocols selected or adapted for the specific sample type and target organisms. Cultivation is performed under aerobic, microaerophilic and/or obligate anaerobic conditions as indicated by the target community. Formal progress updates are communicated to clients at defined project milestones throughout the isolation and characterisation phase.
Genomic Identification & Quality Control Program
All isolates undergo taxonomic identity confirmation by whole genome sequencing prior to release. The quality control program encompasses purity assessment, viability confirmation and identity verification against curated reference databases. Isolates failing pre-defined quality thresholds are excluded from client deliverables and flagged with explanatory detail in the project data report.
Delivery of Authenticated Strains, Data Report & Documentation
Clients receive cryopreserved, quality released bacterial isolates accompanied by a comprehensive project data report, a Certificate of Analysis (CoA) and a Product Information Sheet (PIS) for each authenticated strain. Target strains are prepared and delivered to the client in accordance with the terms of the service agreement.
Frequently Asked Questions
Common questions about the bacterial isolation service
The platform accepts a wide range of human-derived samples including faecal and intestinal samples, oral swabs and saliva, cutaneous swabs, vaginal and reproductive tract samples and biopsy or surgically-derived tissue specimens. Non-human sample types including environmental, animal-derived, soil and water matrices are also supported subject to an initial feasibility assessment.
Yes. Illumina short-read whole genome sequencing (WGS) is included as a standard component of all bacterial isolate characterisation workflows. Oxford Nanopore long-read sequencing is available as an optional add-on for complete or near-complete genome assemblies.
Yes. The platform's purpose-built culture facility supports the isolation of oxygen-sensitive and fastidious microorganisms, including obligate anaerobes. Custom-built anaerobic chambers house advanced automation systems, enabling high-throughput isolation of a broad diversity of microbiome associated taxa.
A pre-submission consultation is strongly encouraged before formal sample submission. Contact the platform team to discuss your sample matrix, target organisms and experimental design. Following a feasibility assessment and execution of a Service Agreement, detailed guidance on sample collection, containers, preservation conditions and transport requirements will be provided.
Clients receive cryopreserved, quality-released bacterial isolates accompanied by a comprehensive project data report, a Certificate of Analysis (CoA) and a Product Information Sheet (PIS) for each authenticated strain. Reports include isolation success metrics, taxonomic identification outcomes, whole genome sequencing data and quality control results.
Yes. The High-Throughput Cultivation Platform operates on a fee-for-service basis, serving both academic and commercial partners. A tailored fee estimate is provided following an initial feasibility consultation, which is offered at no charge.
Enquire about the bacterial isolation service
Contact our scientific team to discuss your research objectives, sample matrix, and how the High-Throughput Cultivation Platform can support your microbiome research program or product development pipeline.
Australian Human Microbiome Biobank · Centre for Microbiome Research, QUT