Microbiome and Gut-Brain Axis
1 JAX AI-Integrated Gut Microbiome Diagnostic
Principal Investigator:: Jackson Laboratory and Duke University collaborators
Institution:: JAX / Duke University (USA)
Contact/URL:: https://www.jax.org/news-and-insights/2025/july/gut-microbiome-may-predict-invisible-chronic-fatigue-syndrome-and-long-covid
Funder:: Institutional / NIH
Status:: Published July 2025
Phase:: Diagnostic development (AI-driven)
Cohort:: 249 individuals
Mechanism/Focus:: Applied an AI platform to stool, blood, and routine lab data to identify disease-specific biomarkers. Achieved 90% accuracy in distinguishing ME/CFS from healthy controls using microbiome and metabolite features.
Primary Outcomes:: 90% diagnostic accuracy; multimodal data (stool + blood + labs) outperforms any single data type
Estimated Completion:: Published
Document Relevance:: Ch. 11 (gut microbiome), Ch. 20 (biomarker research), Ch. 25 (translational findings)
The 90% accuracy is the highest reported for any ME/CFS biomarker panel to date, though it awaits independent validation in a blinded, multi-site cohort (2025a). The multimodal approach (combining stool microbiome with blood and clinical data) may explain the performance gain over single-modality studies. This directly informs the diagnostic algorithm discussed in Ch. 20.
2 Gut Microbial Composition Differences in CFS
Principal Investigator:: Multiple groups
Institution:: Multi-centre
Contact/URL:: https://doi.org/10.1038/s41598-025-16438-y
Status:: Published 2025
Phase:: Observational (case-control)
Cohort:: CFS patients versus healthy controls
Mechanism/Focus:: 16S rRNA sequencing of gut microbiota. Found reduced microbial diversity, depletion of anti-inflammatory taxa (Faecalibacterium prausnitzii, Bifidobacterium), and enrichment of pro-inflammatory Clostridium species in ME/CFS.
Primary Outcomes:: Significant between-group differences in gut microbial composition
Estimated Completion:: Published
Publication Medium:: Scientific Reports
Document Relevance:: Ch. 11 (gut microbiome), Ch. 7 (immune dysfunction—gut-mediated inflammation)
The depletion of F. prausnitzii (a major butyrate producer) is particularly notable because butyrate maintains intestinal barrier integrity. Its loss could contribute to the intestinal permeability (“leaky gut”) reported in ME/CFS, creating a pathway from microbiome dysbiosis to systemic immune activation (2025b).