Despite many individuals sharing the same bacterial species, very few share the same specific strains, making it essential that gut health focused interventions are personalized to the individual, according to Prof. Nicola Segata, of University of Trento, Italy.
“Our microbiomes are incredibly unique, meaning its hard to think about a one-size-fits-all solution that can modify the microbiomes of all individuals,” he said.
Speaking to NutraIngredients ahead of his presentation at the next IPC (International Scientific Conference on Probiotics, Prebiotics, Gut Microbiota and Health) conference in Kraków, Poland (June 22-24, 2027), he said more large-scale and long term research is needed to connect microbiome sequencing results with nutrition recommendations.
Pioneer in microbiome sequencing
With his training in computer science and a Ph.D in AI, Prof. Segata has played a key role in developing computational methods that allow researchers to discover which microorganisms are present in a microbiome, what they are capable of doing, and how those communities differ between populations and disease states.
His work includes MetaPhlAn, a widely used method for profiling the taxonomic composition of microbial communities from metagenomic sequencing data.
Most recently, he has worked with researchers at the personalized nutrition platform Zoe to conduct a series of large-scale microbiome mapping studies which he believes go a long way to improving our ability to deliver personalized recommendations.
Their primary study, published in Nature, utilized deep shotgun metagenomic sequencing on a core cohort of over 34,000 U.S. and U.K. participants (users of the Zoe platform) to rank more than 100 species of gut bacteria based on how they connect to markers of inflammation, blood sugar, heart health and body fat.
The ranking has been made available for research scientists across the world as “a reliable and repeatable measure of microbiome health”.
The research explicitly showed how diets rich in diverse plants, complex fibers, and polyphenols directly feed and multiply the 50 ‘good’ microbes. Conversely, highly processed foods encourage the proliferation of the 50 ‘bad’ microbes, which are heavily linked to visceral body fat, inflammation, and heart disease risk.
The research team has now sequenced the microbiome data of 250,000 participants, said Prof. Segata. By shifting from lab research to a large community cohort, he said it is possible to start building an important picture of links between diet and gut bacteria.
“This is powerful research because we can start to identify the strains associated with specific foods,” said Prof. Segata. “For example, we know the bacteria stimulated by coffee, so we can tell from the gut microbiome whether the person drinks coffee with 95% accuracy.”
The challenge, he noted, is that this same data is needed for all nutritional components and many more bacteria.
“We aren’t close but we do have all the tools we need,” he added.
Data holding back AI’s impact
Given MetaPhlAn uses machine learning to help classify and profile microbial communities from sequencing data, Prof. Segata noted that AI has already been fundamental in this field. Yet, there is ‘clearly’ potential for it to do much more, he said.
“The potential, however, of AI in this field is linked with the data availability and the amount of data we can process. Most of the AI systems we are excited about outside the science world have been enabled by AI plus a huge availability of data.”
He added: “In microbiome science, we are not necessarily at that point in terms of the amount of data for all the tasks that we imagine AI can be revolutionizing.”
One and done testing
Discussing services on the market which utilize questionnaires alongside gut microbiome testing to offer nutrition, lifestyle and supplementation advice, he highlighted the importance of context and follow-up testing.
“The microbiome needs to be contextualized by age, sex, BMI, drugs you are taking, diseases you may have etc” he said. “And we need to be careful about the message that you can do one test and know everything you should know about diet for the next 10 years.”
Highlighting the importance of regular testing, he noted that the population of one strain already present in the gut will vary throughout the day, depending on the meals eaten.
“If you eat a fiber which a particular strain feeds on then the population of that strain will increase postprandially, but changes to the specific strains present in the gut require long-term changes.”
The 20th International Scientific Conference on Probiotics, Prebiotics, Postbiotics and Gut Microbes (IPC 2027) is now open for abstract submissions.
The event will take place from June 22–24, 2027, in Kraków, Poland, bringing together world-leading researchers, clinicians and industry experts to explore the latest advances in probiotics, microbiome science and biotics innovation.
To find out more and register your interest, visit the IPC website here.
