Integrating dietary assessment and shotgun metagenomics to characterise diet–gut microbiome associations (GUTDIET-PT): Protocol for a multicentre cross-sectional study
The GUTDIET-PT study is a multicentre cross-sectional protocol aiming to characterise diet–gut microbiome associations in 2,500 healthy Portuguese adults by integrating detailed dietary assessments with shotgun metagenomic sequencing to establish a foundational framework for promoting gut health through tailored nutritional strategies.
Original paper licensed under CC BY 4.0 (https://creativecommons.org/licenses/by/4.0/). This is an AI-generated explanation of a preprint that has not been peer-reviewed. It is not medical advice. Do not make health decisions based on this content. Read full disclaimer
Inside the human gut lives a vast, invisible city of microorganisms, a complex community of bacteria, viruses, and fungi that works tirelessly to keep the body running. These tiny residents help digest food, train the immune system, and produce essential vitamins. For decades, scientists have known that what we eat acts as the primary architect of this internal ecosystem, shaping which microbes thrive and which fade away. While some eating habits, like those rich in plants and whole grains, seem to encourage a diverse and resilient community, others, often heavy in processed foods and sugars, appear to weaken it. Yet, defining exactly what a "healthy" microbiome looks like in a person without disease remains a puzzle. Most research has focused on how these microbes change when someone is already sick, leaving a gap in our understanding of how diet shapes the gut in a state of pure health.
A new study protocol, known as GUTDIET-PT, aims to fill this gap by mapping the relationship between daily eating habits and the gut microbiome in a large group of healthy Portuguese adults. Rather than looking at isolated nutrients like fiber or fat, the researchers are examining entire dietary patterns—how people naturally combine foods over time. They are recruiting 2,500 individuals between the ages of 40 and 74 who are undergoing routine colonoscopy screenings but have no signs of colorectal cancer or other major digestive diseases. By focusing on people who are currently healthy, the team hopes to establish a clear baseline of what a thriving gut looks like before any illness sets in. This approach allows them to see how different ways of eating, from the traditional Mediterranean diet to more modern Western patterns, influence the microscopic life within the gut without the confusion of disease-related changes.
To gather this data, the study combines detailed dietary interviews with advanced genetic sequencing. Participants provide two separate 24-hour accounts of everything they ate and drank, recorded by trained nutritionists who ask about portion sizes, cooking methods, and specific brands. This level of detail helps capture the reality of what people actually consume, rather than relying on memory of what they usually eat. The researchers then analyze these records to identify common dietary patterns, such as adherence to a plant-based diet or a Western-style diet, and calculate how inflammatory each person's diet might be. Alongside these dietary records, participants collect their own stool samples at home. These samples are preserved immediately to protect the genetic material inside, then sent to a laboratory where scientists use a technique called shotgun metagenomics. Unlike older methods that only identify broad groups of bacteria, this technique reads the entire genetic code of every microbe in the sample, revealing not just who is there, but what they are capable of doing.
The study is currently underway, having already enrolled nearly 500 participants since late 2023, with the goal of finishing recruitment by 2029. The researchers expect to publish their findings by the end of 2030. While the full results are still ahead, the design of the study promises to offer a high-resolution map of the connection between food and gut health. By analyzing the genetic potential of the microbiome alongside precise dietary data, the team aims to identify which specific eating habits support a diverse and functional gut community. This work could eventually help doctors and nutritionists move beyond general advice to offer personalized recommendations, suggesting specific dietary changes that might help an individual maintain a healthy gut ecosystem. The ultimate goal is to use this knowledge to prevent disease before it starts, turning the science of the gut microbiome into practical tools for public health.
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