Microbiome Research
From bed-side to bench and back again
The microbiome plays a crucial role in health and disease and can determine the fate and efficiency of therapeutics. To understand the interaction between the microbiome and the host and the ability to modulate the microbiome will open new avenues for personalized precision medicine.
Microbiome Research
From bed-side to bench and back again
The microbiome plays a crucial role in health and disease and can determine the fate and efficiency of therapeutics. To understand the interaction between the microbiome and the host and the ability to modulate the microbiome will open new avenues for personalized precision medicine.
Technologies and Services
Within the last 20 years, a strong interaction between diseases, therapeutics and the human gut microbiome has crystallized whereby several acute and chronic diseases can cause or can be caused by disturbances of the gut microbiome, known as dysbiosis. Also drugs can cause dysbiosis or being modified by the microbiome. We enable a deeper understanding of the role of the human gut microbiome in disease conditions to identify predictive or diagnostic biomarker and therapeutic targets.
We provide a full range of microbiome research services, translating clinical problems into actionable research questions using clinical data and biosamples. Our offerings include biomarker identification, bacterial strain isolation, and a unique patient-derived microbiome modulation platform. Supported by extensive biological and technological methodologies, our customizable research lifecycle delivers results for clinical interventions. Outcomes can lead to licensable products or specialized services, with opportunities for publication and conference presentations. Partner with us for innovative microbiome research solutions.
Services in this research area are centered around the understanding of microbiome composition and function and the effects of alterations of microbiomes on the host. There is no restriction to disease areas. All our services are highly customizable and can be offered as a end-to-end study execution or ad-hoc support by conducting certain services.
CBioMe
Microbiome Research Platform
Observing the dynamic of the microbiome in health and disease is a crucial source of information. We are experienced in microbiome-related studies, clinical and in-vitro.
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OmiXScope
Data Science
High-throughput data sets harbor a cornucopia of information but also come with their own challenges. We can help you navigate through all stages of your project, from study design and sample size calculation, to data analysis, visualization and interpretation.
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IntestiScope
Gut Barrier Model
The gut barrier facilitates an intricate balancing act between supply and protection and is a crucial part of the microbiome gut-health axis. Learn about our gut permeability models and our longstanding experience with gut permeability markers in the clinical setting.
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ProBioScope
Probiotic Strain Characterization Pipeline
Probiotic microorganisms have unique abilities to strengthen the gut barrier, inhibit pathogen growth or modulate the immune response. With our diverse panel of tests, we can highlight the strengths of your strains and help you develop a clinically relevent product.
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ImmuneScope
Innate Immune Model
We speciallize in the innate immune system with a strong focus on neutrophil function and acellular immunity as potential biomarker for infection risk.
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Service Catalogue
| Service Category | Service Description | Typical Application | Maturity level | Example Targets and Reference Publications |
|---|---|---|---|---|
| Clinical cohorts | End-to-end clinical study support for microbiome research, including remote workflows with informed consent, prospective cohort setup, quality-controlled sample collection, in-house biobanking, wet-lab analyses, data analysis and interpretation. | Access to clinical cohorts and biosamples, including prospective study conduct for research questions in the gut microbiome field. | L3 – L4 | https://pubmed.ncbi.nlm.nih.gov/41406626/ https://pubmed.ncbi.nlm.nih.gov/41637999/ https://pubmed.ncbi.nlm.nih.gov/39599756/ |
| Gut permeability studies (clinical/ in vivo) | Clinical gut permeability assessment using validated biomarker panels in stool, urine and plasma, supported by experience across established markers and access to biobanked samples for testing novel biomarkers. | Validated assays for gut permeability biomarkers in serum, plasma, stool and urine samples, suitable for endpoint assessment in clinical studies and group comparisons in cohort studies. | L3 | Examples include zonulin, calprotectin, sCD14, lipopolysaccharide-binding protein and diamine oxidase; the panel can be extended depending on the study question. Can be combined with multiplex chromogenic or fluorescent immunohistochemistry. |
| Mircobiome data analysis pipeline | Specialized analysis of clinical microbiome datasets, including longitudinal and parallel-group study designs. Integration and visualization of clinical, microbiome sequencing and metabolomics data using multi-omics systems biology approaches. | As a standalone service or as part of a clinical study, our standardized yet customizable pipeline supports industry and academic partners from study design and sample-size calculation through data analysis, visualization and interpretation. | L3 | https://pubmed.ncbi.nlm.nih.gov/39599626/ https://pubmed.ncbi.nlm.nih.gov/41406626/ https://pubmed.ncbi.nlm.nih.gov/41561025/ |
| In vitro gut microbiome model | The proprietary MyBioScope platform is a quality-controlled, bioreactor-based gut microbiome model that maintains anaerobic conditions throughout the experiment. The setup can be tailored to each project, including study population, culture time, feeding mode and endpoints. Standard endpoints include pH, optical density, total and viable cell count, 16S rRNA gene sequencing for community profiling, and targeted or untargeted metabolomics. | In vitro testing of drugs and interventions in complete human microbiomes. | L3 | https://link.springer.com/article/10.1186/s40643-026-01044-1 |
| Gut barrier model | Cell-culture model for gut barrier research using transwell cultures to assess how different substances affect barrier integrity and to generate mechanistic insights into gut barrier dysfunction. | Mechanistic readouts include protein expression, cytokine production and tight-junction visualization. Transepithelial electrical resistance is used to monitor monolayer development and assess the effects of pathogens, probiotics or other substances on cell-cell contacts. | L2 | https://onlinelibrary.wiley.com/doi/10.1002/ueg2.70262 |
| Innate immune fuction assays | CBmed offers ex vivo models based on freshly isolated neutrophils from volunteers or patients, covering key neutrophil functions and measurements in clinical samples. Core readouts include reactive oxygen species production, phagocytosis and cytokine production, with additional assays such as NET formation and migration available on request. We have also developed AGRA, an acellular marker of innate immune response. | These assays can serve as clinical study endpoints or stratification parameters in intervention studies, particularly in settings where infection risk and immune dysfunction are clinically relevant. | L2 | https://pubmed.ncbi.nlm.nih.gov/38505257/ https://pubmed.ncbi.nlm.nih.gov/35220689/ https://pubmed.ncbi.nlm.nih.gov/37364519/ Patent: https://www.cbmed.at/agra/ |
| Probiotic strain characterization pipeline | A-to-Z probiotic strain services, from strain characterization and selection to clinical safety, efficacy and validation studies. Additional tests are available on request. | Strain isolation, strain characterization and targeted functional testing to demonstrate pathogen inhibition and immune-modulating potential. | L3 |
Exploratory
(RUO)
Feasibility
Discovery
Hypothesis
Fit-for-
purpose
Define use
Decision support
Internally
Validated
SOP
QC strategy
reproducibility
Clinically
Aligned
Trial-ready
audit-support
Approaching precision medicine along the microbiome-gut-health axis.