Executive Summary

Microbiomes play a critical role in everything from fighting infections to managing chronic diseases—and hold immense potential to improve both human and environmental health. But despite rapid scientific advances, microbiome research is still unevenly applied and rarely integrated into clinical care, public health or policy. 

By bringing together researchers, clinicians, industry and regulators, ASM-H can help turn microbiome discoveries into real-world solutions—improving medicine, shaping regulation and advancing public health on a broad scale.

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Problem

Microbiome research has grown exponentially, but its clinical, regulatory and societal integration lags behind. Key challenges include:

• Lack of standardized clinical guidelines and regulatory pathways.
• Limited access to validated microbiome-based diagnostics and therapies.
• Siloed research across human, animal, environmental and One Health domains.
• Underuse of microbiome insights in antimicrobial stewardship, chronic disease, oncology and health equity.
• Insufficient integration of AI/ML for data interpretation and clinical decision-making.
• Exclusion of the virome and mycobiome from standard microbiome research frameworks.
• Lack of actionable pathways for personalized interventions, including nutrition.

Scientific Approach: A Systems-Level Microbiome Strategy

ASM Health proposes a coordinated initiative to accelerate the transition from microbiome discovery to clinical and public health action. This strategy spans diagnostics, therapeutics, stewardship, policy and equity—powered by cross-sector collaboration and advanced analytics.

• Standards and Clinical Guidelines
  • Develop consensus standards for microbiome sampling, interpretation and quality control.
  • Align with retulatory and accreditation agencies.
  • Publish frameworks through ASM journals to guide clinical and laboratory practice.
• Translational Research and Therapeutics
  • Advance microbiome-informed therapies for metabolic, autoimmune, cancer, neurodegenerative and infectious diseases.
  • Support validation of microbiome interventions, including synbiotics and microbiome-modulating drugs.
  • Promote multi-omics integration (genomics, metabolomics, microbiome) to refine clinical applications.
• Diagnostics Innovation Pipeline
  • Accelerate development of microbiome-based diagnostics using pathogen-agnostic and functional approaches.
  • Leverage microbiome signatures in blood, stool or tissue for early cancer detection, prognosis and therapy response prediction.
  • Integrate AI/ML to identify clinically relevant microbial patterns across the bacteriome, virome and mycobiome.
  • Establish shared clinical validation hubs through ASM-H infrastructure.
• Microbiome-Informed Stewardship
  • Leverage microbiome data to optimize antimicrobial use via colonization resistance and dysbiosis tracking.
  • Pilot stewardship tools that incorporate host-microbiome interactions and resistance gene surveillance.
• One Health & Environmental Surveillance
  • Monitor microbial ecosystems across humans, animals and environments.
  • Link microbiome dynamics to AMR, zoonoses and environmental risk factors.
  • Collaborate with One Health platforms to build interoperable sequencing and metadata pipelines.
• Equity and Population Health Metrics
  • Define microbial health indicators tied to geography, socioeconomic status and environmental exposure.
  • Embed microbiome metrics into public health surveillance systems.
  • Address disparities by supporting data from underrepresented regions and populations.
• Personalized Nutrition and Lifestyle Interventions
  • Use microbiome profiles to guide individualized dietary recommendations.
  • Integrate nutrition data with host-microbe interactions for chronic disease prevention.
  • Partner with precision nutrition platforms and clinical researchers to validate interventions.
• Training and Community Building
  • Develop certification programs in clinical microbiome science, AI applications and data ethics.
  • Host global convenings to connect researchers, clinicians and public health leaders.
  • Cultivate a global network of microbiome advocates through ASM-H engagement.

Strategic Vision for ASM Health

ASM Health will serve as a neutral convening body and implementation partner to:

• Provide a neutral platform to align standards, trials and infrastructure.
• Leverage existing ASM networks, journals and convenings.
• Catalyze multi-sector collaboration across diagnostics, stewardship, nutrition and public health.
• Lead global discussions on clinical microbiome integration.

How We Will Execute

ASM Health will deliver the Microbiome to Medicine agenda through a science-first, consortium-driven model focused on standardization, clinical validation, regulatory alignment and equitable scale-up:

• Set Priorities and Roadmaps: identify gaps across diagnostics, therapeutics, stewardship, One Health surveillance and personalized nutrition. Maintain roadmaps tied to pilots and validation.
• Standardization and Clinical Use: publish clinical use playbooks and standards for microbiome sampling, interpretation, reporting, host-microbiome interaction testing, resistance monitoring and multi-omics integration. Leverage ASM journals and convenings to disseminate frameworks and best practices.
• Regulation and Reimbursement Alignment: convert registry and pilot outputs into a Global Playbook Series (clinical validation, quality, ethics, coverage). Convene targeted roundtables to align on minimum datasets, quality control and post-market monitoring and coverage pathways.
• Secure Funding and Partnerships: run a Funding Radar to scout for federal, philanthropic and private sector opportunities to support multisite trials, registry cells and LMIC adaptations.
• Knowledge Dissemination: translate pilot outputs into white papers, benchmarking notes and peer-reviewed publications. Publish “State of Microbiome Integration” reports with metrics on diagnostic adoption, stewardship impact and equity progress.
• Data and Standards Infrastructure: enable federated sharing across sites and biobanks and operate an innovation sandbox for algorithmic biomarker prediction and resistance forecasting (AI-guided matching).
• Convene and Build Consensus: use ASM’s neutral convening power to align academia, industry, regulators and payers on endpoints, metadata, interpretation and responsible use. Leverage exemplars from global microbiome initiatives and One Health platforms.
• Consulting and Advisory Services: offer neutral advisory on protocol design, endpoints, IRB/ethics, reimbursement evidence under COI guardrails.
• Engage Industry: facilitate scientific matchmaking and validation via the Trial Network and Registry. Use tiered participation for in-kind support and early-career funding.
• Measure Impact: track funding wins, validation milestones, multisite reproducibility, workforce trained, publications/playbooks, regulatory/payer acceptance, diagnostic adoption and patient outcomes.

Impact

Short-Term

• Consensus microbiome testing protocols and reporting standards.
• Accelerated clinical validation of microbiome-informed tools.
• Expanded recognition of the virome and mycobiome in diagnostic design.

Mid-Term

• Integration of microbiome metrics into public health and clinical decision-making.
• Demonstrated benefit of AI-powered interpretation in routine microbiome diagnostics.
• Uptake of personalized microbiome-based interventions, including nutrition and lifestyle.

Long-Term

• Widespread clinical adoption of microbiome-informed diagnostics, therapies and prevention models.
• Global frameworks recognizing microbiome relevance across reimbursement and regulation.
• Cultural shift toward treating the microbiome as a cornerstone of precision and preventive medicine.

Call to Action

The microbiome holds transformative potential for diagnostics, therapeutics and prevention—but realizing that potential requires standards, collaboration and leadership.

ASM Health calls on partners across science, medicine and policy to:

• Co-develop clinical and regulatory standards.
• Validate AI-integrated microbiome diagnostics.
• Launch pilots linking microbial insights to therapy, stewardship and nutrition.
• Build global capacity and equity in microbiome science.

Together, we can embed the microbiome into the future of personalized, preventive and planetary health.

Interested in Joining Us?

Be among the first to shape ASM-H initiatives—if you’re driving cutting-edge microbiome research or product innovation, reach out to us for early access.