The Microbiome in Precision Medicine: The Way Forward Original paper

March 18, 2025

  • Microbiome Signatures Definition: A Conceptual Advancement for Translational Microbiome Science
    Microbiome Signatures Definition: A Conceptual Advancement for Translational Microbiome Science

    Microbiome signatures are reproducible ecological and functional patterns—encompassing traits, interactions, and metabolic functions—that reflect microbial adaptation to specific host or environmental states. Beyond taxonomy, they capture conserved features like metal metabolism or immune modulation, enabling systems-level diagnosis and intervention in health and disease.

  • Microbiome-Targeted Interventions (MBTIs)
    Microbiome-Targeted Interventions (MBTIs)

    Microbiome Targeted Interventions (MBTIs) are cutting-edge treatments that utilize information from Microbiome Signatures to modulate the microbiome, revolutionizing medicine with unparalleled precision and impact.

Last Updated: 2024

Microbiome Signatures identifies and validates condition-specific microbiome shifts and interventions to accelerate clinical translation. Our multidisciplinary team supports clinicians, researchers, and innovators in turning microbiome science into actionable medicine.

Karen Pendergrass

Karen Pendergrass is a microbiome researcher specializing in microbiome-targeted interventions (MBTIs). She systematically analyzes scientific literature to identify microbial patterns, develop hypotheses, and validate interventions. As the founder of the Microbiome Signatures Database, she bridges microbiome research with clinical practice. In 2012, based on her own investigative research, she became the first documented case of FMT for Celiac Disease—four years before the first published case study.

Overview

Joseph F. Petrosino’s editorial highlights the microbiome’s pivotal role in precision medicine, emphasizing its potential to advance personalized diagnostics and therapeutic strategies. The integration of microbiome signatures with other ‘omics’ data, such as genomics and metabolomics, offers a comprehensive understanding of disease mechanisms and tailored treatments. Petrosino draws parallels between microbiome signature research and genomics, with both fields leveraging next-generation sequencing technologies to uncover associations that can be exploited for clinical interventions.

Precision Microbiome Interventions

A notable advancement discussed is the precision editing of the microbiome to treat inflammatory diseases. For instance, Zhu et al. demonstrated how targeting molybdenum-cofactor-dependent pathways with tungstate suppressed Enterobacteriaceae overgrowth in colitis models, restoring microbial diversity and reducing inflammation.[1] This targeted approach exemplifies the potential of microbiome-targeted interventions (MBTIs) to effectively manage dysbiosis without disrupting beneficial microbial communities.

Future Directions

Petrosino advocates for the routine integration of microbiome data with clinical and multi-omics datasets to enhance diagnostic precision, treatment customization, and early disease detection. He envisions a future where microbiome profiling becomes standard practice in clinical trials and patient care, facilitating the stratification of patients for personalized interventions. Furthermore, the editorial calls for banking samples from large cohort studies to enable future integrative analyses, maximizing the clinical potential of microbiome research.

Conclusion

In conclusion, Petrosino establishes the microbiome as a cornerstone of precision medicine, emphasizing the need for continued innovation and translational efforts to unlock its full potential in clinical practice.

FAQs

What role does the microbiome play in precision medicine?

The microbiome contributes to precision medicine by providing unique microbial signatures and metabolic pathways that influence disease phenotypes, treatment responses, and immune modulation. Integrating microbiome data with genomics and other ‘omics’ can personalize diagnostics and therapies.

What are some examples of microbiome-driven advancements in immunotherapy?

Studies have shown that certain gut bacteria, such as Faecalibacterium and Bifidobacterium, are linked to better responses to PD-1/PD-L1 checkpoint inhibitors in cancer treatment. These microbes enhance immune activation and T-cell infiltration, offering predictive biomarkers for therapy success.

How might microbiome profiling be integrated into routine clinical practice?

Routine microbiome sampling, alongside genomic and clinical data, could become a standard in primary care to detect early disease markers, stratify patients for specific treatments, and inform personalized therapeutic strategies.

We aim to assist in suggesting microbiome-targeted interventions based on the genomic and clinical data that informed the microbiome signatures.

 

 

Microbiome-Targeted Interventions (MBTIs)

Microbiome Targeted Interventions (MBTIs) are cutting-edge treatments that utilize information from Microbiome Signatures to modulate the microbiome, revolutionizing medicine with unparalleled precision and impact.

References

  1. Precision editing of the gut microbiota ameliorates colitis.. Zhu W, Winter MG, Byndloss MX, Spiga L, Duerkop BA, Hughes ER, Buttner L, de Lima RE, Behrendt CL, Lopez CA, et al.. (Nature. January 11, 2018.)

Zhu W, Winter MG, Byndloss MX, Spiga L, Duerkop BA, Hughes ER, Buttner L, de Lima RE, Behrendt CL, Lopez CA, et al.

Precision editing of the gut microbiota ameliorates colitis.

Nature. January 11, 2018.

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