Microbial Shift and Realignment Process (MSRP)

Overview

The Microbial Shift and Realignment Process (MSRP) is the proprietary framework used to construct every microbiome signature in the Microbiome Signatures Database. It is designed to overcome the complexity, inconsistency, and heterogeneity of microbiome research by applying a structured, evidence-weighted approach to microbial pattern recognition and clinical translation. Rather than merely cataloging taxonomic associations, the MSRP defines coherent, condition-specific patterns of dysbiosis by aligning microbial shifts with mechanistic plausibility, interventional reversibility, and reproducibility across study types. The result is a microbiome signature that not only reflects disease-associated trends, but also serves as a targetable framework for microbiome-guided clinical interventions.

Core Components

Systematic Literature Retrieval and Screening

Studies are identified using domain-specific queries across databases such as PubMed, Scopus, and Google Scholar. Search strategies integrate MeSH terms, taxonomic keywords, and study design filters (e.g., human, murine, in vitro) to ensure comprehensive inclusion of both disease- and microbiome-specific data. Screening prioritizes taxonomic resolution, sample type consistency, and reproducibility of findings across cohorts.

Manual Data Extraction and Taxonomic Harmonization

Microbial abundance data are manually extracted and mapped to standardized taxonomies (e.g., NCBI, GTDB) to ensure species-level precision. Synonyms are merged, and naming inconsistencies are corrected. Each taxon is categorized as enriched, depleted, or inconclusive, and is tagged at the most granular level reported.

Pattern Recognition and Inclusion Criteria

Only taxa that meet one or more of the following criteria are included in the signature:

Statistically significant abundance shifts in ≥2 independent studies.

High effect size in large or methodologically rigorous studies.

Mechanistic relevance via functional, immunologic, or metabolic pathways.

Each taxon is annotated with metadata: directionality of shift, sample type, taxonomic resolution, and DOI-linked references.

Designation of Major Microbial Associations (MMAs)

A subset of taxa are classified as Major Microbial Associations (MMAs) based on their potential causal, modulatory, or pathophysiological role. MMA selection prioritizes taxa with known virulence or metabolic factors, immune/hormonal modulatory effects, or associations with metal ions and xenobiotics relevant to the disease’s etiology.

Bidirectional Validation Using MBTIs

Where possible, microbiome-targeted interventions (MBTIs) are used to validate the signature. An MBTI must reverse the identified microbial shifts and improve clinical outcomes in relevant models. This dual validation reinforces both the signature’s integrity and the intervention’s legitimacy.

Continuous Refinement and Transparency

Every signature developed through the MSRP is version-controlled and accompanied by a last-updated date and methodological notes. Updates incorporate new evidence, taxonomic reclassifications, and evolving intervention data. All included studies are traceable through linked source tables and summaries on the signature page.

Why MSRP Matters

Traditional microbiome research often struggles to move from association to actionable insight, leaving clinicians without clear guidance. The Microbial Shift and Realignment Process (MSRP) bridges this gap by distilling noisy, heterogeneous data into structured, reproducible patterns of dysbiosis. It aligns microbial shifts with plausible therapeutic targets and validates those patterns using interventions that demonstrably reverse dysbiosis and improve clinical outcomes. Rather than offering yet another list of microbes, MSRP provides clinicians with a targetable, evidence-aligned framework designed to inform and guide real-world decision-making in microbiome-based care.

FAQ