Understanding the precise mechanism of action (MOA) of probiotics is critical in the development of live biotherapeutic products (LBPs) with reproducible efficacy. As probiotics exert complex and pleiotropic effects on host physiology—ranging from immune modulation and metabolic regulation to gut barrier maintenance—isolating the molecular pathways and biomarkers behind these effects requires robust and high-resolution analytical tools.
At Creative Biolabs, our metabolomic and transcriptomic MOA study service combines high-throughput multi-omics technologies to decode the intricate molecular networks governing probiotic–host and probiotic–microbiota interactions. By profiling host gene expression and metabolic shifts under probiotic influence, this integrative service provides invaluable insight into the functional efficacy and molecular signatures of probiotic candidates.
Why Omics-Based MOA Profiling is Essential in Probiotic R&D
Addressing the Industry Need for Functional Validation
The surge in probiotic innovation, especially within pharmaceutical-grade LBPs, has prompted a shift from traditional viability and colonization assessments toward functional and mechanistic validation. Regulatory agencies increasingly require detailed molecular-level evidence supporting the rationale behind strain selection and downstream applications. Multi-omics profiling has emerged as the gold standard in this context.
Transcriptomics enables the evaluation of global gene expression changes in host cells, epithelial tissues, or co-culture models upon probiotic exposure. In parallel, metabolomics captures shifts in small-molecule metabolites that reflect functional consequences of microbial activity, including SCFA production, bile acid transformation, and neurotransmitter biosynthesis.
Unique Advantages of Integrated Omics Analysis
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Mechanistic Depth: Simultaneous profiling of mRNA and metabolite signatures offers holistic insights into both upstream regulatory pathways and downstream phenotypic effects.
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Host- and Microbe-Responsive: Detects molecular changes in host and microbial systems, allowing dissection of direct and indirect MOAs.
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Biomarker Discovery: Facilitates identification of predictive markers for efficacy, stability, or colonization dynamics.
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Strain-Specific MOA Differentiation: Supports head-to-head comparison of probiotic strains or engineered constructs based on molecular outcomes.
Creative Biolabs supports clients in leveraging these advantages through validated, customizable pipelines and deep scientific expertise in microbiome-host interaction research.
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Integrated Omics Capabilities at Creative Biolabs
Our Metabolomic and Transcriptomic MOA Study Service is powered by advanced platforms and expert-designed pipelines, ensuring high-quality data generation, interpretation, and integration.
Transcriptomic Profiling
We offer full-spectrum RNA-Seq-based transcriptome analysis, tailored for host cell lines (e.g., intestinal epithelial, macrophage), animal models, or probiotic monocultures under co-culture conditions. Key features include:
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Strand-specific RNA-seq with rRNA depletion or polyA selection
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Detection of differential gene expression (DGE) and pathway enrichment
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Support for dual RNA-Seq for host–microbiota simultaneous analysis
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Coverage of cytokine signaling, barrier integrity genes, metabolic pathways, and immune response regulators
Metabolomic Profiling
Creative Biolabs deploys untargeted and targeted metabolomics platforms, including:
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LC-MS/MS and GC-MS for global metabolic profiling
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SCFA, bile acid, amino acid, and neurotransmitter quantification
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Metabolite fingerprinting of cell culture supernatants, fecal extracts, serum, and urine
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Isotopic labeling support for metabolic flux analysis
Data Integration and Pathway Reconstruction
We employ systems biology pipelines to merge transcriptomic and metabolomic datasets, enabling:
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Multi-omics network mapping
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Identification of causative regulatory cascades
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Visualization of probiotic-induced systemic shifts
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Custom reports tailored to regulatory submission or publication
Our comprehensive approach empowers clients to move beyond descriptive analytics and derive actionable mechanistic hypotheses.
Metabolomic and Transcriptomic MOA Analysis Workflow
Our optimized workflow ensures reproducibility, scalability, and scientific rigor across all immunomodulation assays. The standard pipeline is as follows:
All workflows are customizable to meet specific research questions and regulatory standards.
Detailed Deliverables to Support Your Research Pipeline
Clients working with Creative Biolabs can expect an end-to-end analytical package that enables strategic decision-making and regulatory compliance. Deliverables include:
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Transcriptomic Report: DGE tables, pathway enrichment analysis, volcano plots, heatmaps
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Metabolomic Report: Quantified metabolite tables, PCA plots, metabolic pathway diagrams
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Integrated Pathway Analysis: Mechanistic network diagrams linking genes and metabolites
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Raw & Processed Data Files: FASTQ, count matrices, metabolite abundance tables, normalization scripts
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Consultation Support: One-on-one data interpretation and next-step advisory session
We also support regulatory data formatting and IND-enabling documentation for clients in translational development stages.
Applications Across Probiotic Development Stages
The Metabolomic and Transcriptomic MOA Study Service is applicable across multiple R&D phases and experimental models:
Strain Screening and Ranking
By profiling gene expression and metabolite output in host cells exposed to candidate strains, researchers can rank probiotic efficacy based on immune modulation, metabolic regulation, or epithelial barrier enhancement.
Mechanism Validation in Co-culture or Organoid Models
Combined omics readouts from gut organoids, Caco-2 cells, or macrophage-organoid co-cultures enable precise mechanistic attribution of probiotic action in intestinal environments.
In Vivo Efficacy Correlation
In mouse or gnotobiotic models, multi-omics profiling aligns changes in transcriptome and metabolome with physiological parameters such as SCFA levels, intestinal permeability, or systemic inflammation.
Biomarker Discovery for MOA and Colonization
Integrated datasets uncover biomarkers predictive of probiotic colonization, persistence, and functional outcomes—supporting rational formulation and dosing strategies.
Related Mechanistic Study Services from Creative Biolabs
Explore additional solutions to complement your MOA profiling efforts:
With decades of experience in microbiome-host interaction analysis and live biotherapeutic development, Creative Biolabs offers unparalleled scientific depth and technical precision in MOA profiling. Our metabolomic and transcriptomic service platform delivers reliable, integrative, and actionable insights to accelerate probiotic R&D pipelines. Contact us or Request a Quote today and let's define the true mechanism of your probiotic strain.
FAQs
What is the benefit of integrating metabolomics and transcriptomics in probiotic MOA studies?
Combining metabolomics and transcriptomics offers a systems-level view, linking gene expression with downstream metabolic changes, helping researchers uncover precise functional mechanisms and identify actionable biomarkers related to probiotic-host and probiotic-microbiota interactions.
Can this service be used to compare different probiotic strains for functional screening?
Yes, our platform enables direct comparison of transcriptomic and metabolic responses to multiple strains, supporting evidence-based selection based on immunomodulation, metabolic output, or barrier-supporting gene expression profiles in host models.
What types of samples are compatible with this MOA analysis platform?
We support a wide range of samples, including epithelial cell lines, co-culture supernatants, gut organoids, animal tissues, feces, and serum, offering flexibility across in vitro, ex vivo, and in vivo models. Fill out the sample submission form.
Other Resources
References
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Zmora, Niv, et al. "Personalized gut mucosal colonization resistance to empiric probiotics is associated with unique host and microbiome features." Cell 174.6 (2018): 1388-1405. https://doi.org/10.1016/j.cell.2018.08.041
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Qin, Ming, et al. "Integrated transcriptome and metabolomics analysis reveals that probiotics and tea polyphenols synergetically regulate Lipid metabolism in laying hens." Agriculture 14.11 (2024): 2072. https://doi.org/10.3390/agriculture14112072
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Liu, Xinyue, et al. "Transcriptomics and metabolomics reveal the adaption of Akkermansia muciniphila to high mucin by regulating energy homeostasis." Scientific Reports 11.1 (2021): 9073. https://doi.org/10.1038/s41598-021-88397-z
