The Dogma Project
Food Microbes & Human Health
DOGMA investigates how high-diversity fermented foods influence the gut microbiome, metabolic health, and microbial resilience in Western populations.
Background and Motivations
In recent decades, traditional fermentation practices have been progressively replaced by industrial processes based on selected microbial strains.
This transition has drastically reduced the microbial diversity naturally present in fermented foods and contributed to a lower intake of live microbes in the diet of Western populations.
At the same time, changes in lifestyle and environment have been associated with a progressive loss of microbial diversity in the gut microbiome of Western individuals.
A growing body of evidence shows that this reduced microbial biodiversity—especially when compared with rural or traditional communities—is linked to the global rise of chronic diseases such as:
- obesity
- type 2 diabetes
- metabolic disorders
- chronic inflammatory conditions
These trends suggest a strong connection between industrialized dietary patterns, reduced microbial exposure, and declining gut microbiome health.
Hypothesis
DOGMA is based on a central hypothesis:
The reduced intake of live and diverse microbes in Western diets has contributed to the decline of gut microbial diversity and to the increase in chronic diseases.
The project aims to determine whether consuming fermented foods with high microbial diversity can modulate disrupted Western gut microbiomes and help restore microbial biodiversity.
The final goal is to understand if and how fermented foods can serve as a tool to rebuild gut microbial resilience and counteract the negative effects of modern dietary habits.
Objectives
In recent decades, traditional fermentation practices have been progressively replaced by industrial processes based on selected microbial strains.
DOGMA adopts an integrated approach combining:
- metagenomics,
- synthetic communities,
- in vitro gastrointestinal models,
- and an in vivo clinical trial.
Through this multidisciplinary workflow, the project aims to:
1) Identify the role of high-diversity fermented foods in shaping the gut microbiome
- Determine whether microbes from fermented foods can transfer to the human gut.
- Characterize which microbial functions they may contribute to.
2) Assess how fermented food microbes can modulate human health
Evaluate their potential to support metabolic and inflammatory health.
Understand to what extent fermented foods can restore gut microbial diversity in Western populations.
Work Packages
WP1 — Human Gut and Fermented Food Metagenomics
Main activities:
- Study of co-occurrence patterns to understand functional interactions and potential health benefits
- Collection and sequencing of fermented food samples
- Analysis of human gut microbiomes from non-Westernized populations in Africa and South America
- Mapping of microbial diversity and identification of potential microbe transfer between foods and the gut
WP2 — In vitro Testing in the mSHIME Gastrointestinal Simulator
Main activities:
- Development of synthetic microbial communities derived from non-Western fermented foods
- Optimization for the production of beneficial metabolites
- Gastrointestinal simulation using mSHIME to evaluate:
– restoration potential
– the modulation of dysbiotic microbiomes
– functional metabolic responses
WP3 — In Vivo Fermented Food Testing (Human Clinical Trial)
Main activities:
- Clinical trial in individuals with metabolic syndrome
- Dietary intervention enriched with fermented foods containing high microbial diversity
- Evaluation of:
– gut microbiome changes
– metabolomic responses
-metabolic and intestinal health biomarkers - Identification of fermented foods capable of enhancing microbial diversity and improving metabolic health
Expected Outcomes
DOGMA will:
- Clarify the contribution of dietary microbes to gut microbiome resilience
- Determine their role in functional recovery following dysbiosis
- Provide a mechanistic framework to design evidence-based nutritional strategies
- Support interventions aimed at counteracting the progressive loss of gut microbial diversity in Western populations
In the long term, DOGMA aims to guide scientific understanding and policy decisions on how fermented foods can contribute to public health.
