Speaking at the IPA World Congress + Probiota 2026, Dr. Simone Guglielmetti, professor of food microbiology at the University of Milano-Bicocca, presented data that identified how a microbe-rich diet can alter gut microbiome composition, improve bowel regularity, enhance immune responses and reduce the presence of oral bacteria in the gut.
“This work supports the idea that dietary guidelines may eventually include recommendations not only on what we eat but also on the amount of viable microbes we consume—through fermented foods, raw foods or even probiotics,” he said.
How dietary microbes impact chronic disease risk
Modern lifestyles are known to reduce microbial exposure. In industrialized societies, factors such as high sanitation, widespread medication use and dietary changes can contribute to gut microbiome dysbiosis, which is associated with non-communicable diseases and infection susceptibility.
Food is a major source of microbes entering the body, Dr. Guglielmetti explained, with dietary microbes coming from sources like fermented foods and raw foods like vegetables carrying soil microbes.
Higher microbial intake is associated with better health, with some research suggesting that consuming 2 billion viable microbes per day is linked to lower cardiovascular disease risk, lower chronic kidney disease risk and reduced fatigue and depression. However, as Dr. Guglielmetti explained, most evidence so far is correlational, not causal.
Live food microbes influence gut health, immunity and microbial balance
Dr. Guglielmetti’s research team recently designed an intervention crossover human trial, in which participants followed a microbe-enriched diet (more yogurt, dairy, raw vegetables) and a low-microbial diet (washing vegetables with disinfectant, cooking foods).
The study recruited participants from the metropolitan area around Milan, which, as Dr. Guglielmetti noted, is one of the most industrialized and polluted regions in Europe. They aimed to determine whether differences in dietary microbial exposure could influence the gut microbiome, immune system activity, bowel habits and other host-related physiological parameters.
The researchers collected fecal, blood and saliva samples, and conducted multiple omics analyses. Participants also completed detailed daily food diaries before and during each intervention.
Findings showed that nutrient intake did not differ significantly between the two diets, which confirmed that the interventions primarily affected microbial exposure rather than macronutrient composition, Dr. Guglielmetti said.
Early data assessment indicated that the low-microbial diet shifted gut microbial metabolism toward proteolytic activity, indicating increased protein fermentation rather than carbohydrate metabolism.
In a typical healthy gut environment, many microbes prefer to ferment carbohydrates; however, a proteolytic metabolism means that gut microbes start breaking down proteins and amino acids instead of carbohydrates, producing metabolites associated with less favorable gut conditions.
Participants following the low-microbial diet also showed reduced bowel regularity and more reactive immune systems.
In contrast, the microbe-rich diet altered the abundance of several microbial taxa in the gut, in particular, dairy starter bacteria (such as Streptococcus thermophilus) increased, reflecting the higher intake of fermented dairy foods.
“Overall, 59 microbial taxa were significantly altered,” Dr. Guglielmetti explained, adding that surprisingly, increasing dietary microbial intake led to a reduction in gut microbial richness, while richness increased during the low-microbial diet.
“We also observed increases in Akkermansia and Faecalibacterium during the low-microbial diet—both taxa commonly associated with beneficial health effects,” Dr. Guglielmetti said.
Furthermore, researchers found that the amount of oral microbes detected in the gut decreased during the microbe-rich diet.
Several oral microbes detected in participants’ gut samples—including Streptococcus species and Rothia—have previously been linked to cardiovascular disease and gastrointestinal inflammation, Dr. Guglielmetti said.
He noted that the findings suggest that increasing the intake of viable microbes through food may help limit oral-to-gut bacterial translocation, also known as ectopic colonization. The results could be particularly relevant for individuals taking proton pump inhibitors, who are known to have higher levels of oral bacteria in the gut and an increased risk of non-communicable diseases, Dr. Guglielmetti added.
According to Dr. Guglielmetti, the findings demonstrate that microbes naturally present in food are biologically relevant dietary components and may prompt a broader reconsideration of how dietary recommendations are defined.
“These findings suggest that we may need to rethink dietary patterns, not only in terms of nutrients, vitamins and minerals, but also by considering the intake of viable microbes,” he told NutraIngredients.
“Developing something like a recommended daily intake of live microbes will not be easy, but this study may represent one of the first steps in that direction.”
