In this interview, professor Piergiorgio Natali (Mediterranean Task force for Cancer Control) discusses the importance of improving functional foods as a strategy to support health, particularly during aging. In this context, special attention was given to whole tomato as a candidate food source because of its global availability, growing market relevance, and rich content of health-promoting nutrients with well-recognized anti-inflammatory potential.

The research line presented focuses on the development of a physical treatment process applied to the whole tomato, including peels and seeds, in order to obtain a powder with enhanced antioxidant and anti-inflammatory activity. According to the evidence collected so far, this formulation appears capable of inhibiting several biological pathways involved in chronic diseases. Supporting data have been generated across different levels of investigation, including laboratory studies, animal models, and human studies, providing a solid scientific basis for further development.

Tomato also offers an important advantage for clinical research, as the distribution of its major nutrients in the body is already well understood. This makes it possible to identify specific target organs that may benefit from the new formulation, including the liver, testis, and prostate. Beyond its direct biological activity, tomato may also exert beneficial effects on the intestinal microbiome by reducing inflammatory status and improving gut barrier permeability. Altogether, these findings support the potential of a whole-tomato–based functional formulation as an accessible and promising tool for the prevention or modulation of chronic disease-related processes and for the promotion of healthier aging.

The findings, published in Cell Host & Microbe, suggest that targeted dietary strategies could be used to reduce susceptibility to cholera.

Studies have shown that diet influences the gut microbiota and some milk-derived proteins can inhibit cholera toxin activity. However, how specific dietary components affect V. cholerae metabolism and virulence, as well as its interactions with commensal gut bacteria, remains unclear.

Researchers led by Rui Liu at the University of California, Riverside used adult mice to test how different diets affect V. cholerae infection.

Protective diets

The researchers fed mice diets high in carbohydrate, fat, or protein, including protein from casein, soy, or wheat, and then infected the animals with V. cholerae after reducing the mice’s gut microbiota with antibiotics. 

Mice on high-protein diets with casein or wheat protein had much lower levels of V. cholerae colonization compared with mice on high-carbohydrate, high-fat, or soy-protein diets.

V. cholerae in mice fed casein or wheat protein appeared to alter the activity of many genes, reducing some involved in metabolism and virulence. Diets with soy protein did not trigger these changes.

Diet-driven outcomes 

Further experiments revealed that one V. cholerae’s gene, called flrA, is linked to diet-induced changes in metabolism, virulence, and a molecular “weapon” that V. cholerae uses to compete with gut microbes.

Disabling flrA restored bacterial growth and the ability of the bacterium to compete with the resident microbiota, the researchers found.The findings highlight how diet and microbial interactions together may influence the outcome of V. cholerae infection. However, the authors say, “the complexity of actual human diets and microbiota means that the range of potential diet-driven outcomes of V. cholerae colonization or infection is vast and will require much additional study to fully elucidate.”

The findings, published in Scientific Reports, suggest that probiotics protect against obesity and inflammation caused by high sugar intake, supporting their use as a preventive strategy for obesity-related diabetes.

High-sugar diets are known to contribute to a condition known as metabolic syndrome, which can lead to diabetes. An imbalance in gut microbes can contribute to metabolic syndrome by disrupting the gut barrier and increasing inflammation.  Previous research suggests that fruit fibers help support beneficial gut bacteria, and probiotics such as Lactiplantibacillus plantarum dfa1 can reduce inflammation and protect the gut.

Researchers led by Thunnicha Ondee at Chulalongkorn University in Bangkok, Thailand, tested whether combining this probiotic with fiber-rich food could reduce the harmful effects of high-sugar diets.

Protecting the gut

The researchers fed mice two types of high-sugar diets: a high-glucose diet and high-carbohydrate biscuit diet. All mice developed signs of metabolic syndrome, obesity, gut damage, and inflammation.

However, when the probiotic Lactiplantibacillus plantarum dfa1 was added to the diets, it helped protect against these problems. Mice receiving Lactiplantibacillus plantarum dfa1 showed healthier blood sugar levels, less gut damage, and lower inflammation. The probiotic improved the balance of gut bacteria, reducing harmful microbes and increasing beneficial ones, including Lactobacillus, Bacteroides and Akkermansia.

When the mice were given specific metabolites made by probiotic bacteria, damage to gut and liver cells—which is typically caused by bacterial toxins entering the bloodstream—was also reduced. Overall, probiotics appear to help protect both gut and liver cells from the harmful effects of high sugar and bacterial toxins, the researchers say.

Probiotic use

Both the high-glucose diet and the high-carbohydrate biscuit diet caused similar levels of obesity and metabolic syndrome in mice, even though the diets had different amounts of carbs, protein, and fat. 

The fruit fiber in the high-carbohydrate biscuit diet changed gut bacteria more than the high-glucose diet, increasing some types of microbes that help digest plant fiber. However, the fruit fiber didn’t seem to reduce obesity or metabolic syndrome. 

This result suggests that while fiber can improve gut bacteria, the harmful effects of high sugar on gut health outweigh those benefits. However, adding probiotics can help counteract these negative effects, the authors say. “Hence, we encourage the use of probiotics for the prevention of carbohydrate-induced obesity.”

Several studies show that changes in dietary calcium levels influence the composition of the gut microbiota, suggesting variable calcium requirements and roles in the gastrointestinal ecosystem. Moreover, calcium seems to promote the viability of intestinal Lactobacillaceae species. However, this mechanism is still to clarify. 

In the study of Huynh et al., the researchers aimed at evaluating the effects of different concentrations of Ca2+ (0-25mM) on the growth of those two species in various media – rich (MRS) and minimal media (CDM) and minimal media with mucin (mCDM), a protein essential for adhesion and known to bind metal ions. 

Calcium promotes growth of L. Acidophilus and L. Plantarum

The results of the study show that:

• The growth of both species was promoted by the addition of Ca2+, being stronger at lower concentrations for L. acidophilus ATCC 4356. 
• Mucin showed to impact less than Ca2+ on growth, independently on the quantity. In particular, L. acidophilus ATCC 4356 exhibited a similar growth in all Ca2+ conditions and media. Instead, for L. plantarum ATCC 14917, calcium induces the growth in MRS subcultures and, less, in CDM subcultures, but not in the mucin subcultures.
• Mucin seems to act as a significant source of calcium in the mCDM medium, potentially allowing cells to accumulate enough Ca2+ to minimize the impact of its changes on cell growth in CDM.

Calcium’s impact on biofilm formation of L. Acidophilus ATCC 4356 and L. Plantarum ATCC 14917

Along with the cells’ growth, the researchers assessed the biofilm formation under the different calcium concentrations.

• An increase of Ca2+ induced biofilm formation at 24 h and 48 h with the most significant effects from 5 to 25 mM in most subcultures.
• Low Ca2+ (5–10 mM) promoted biofilm formation of L. plantarum ATCC 14917 in all subcultures at 24 h while at 48 h was lowest at 25 mM Ca2+. On the contrary, the total biofilm formation of L. acidophilus ATCC 4356 was highest at 25 mM. 
• At 24 h the cell counts for L. acidophilus ATCC 4356 were slightly higher at 10 and 25 mM Ca2+ compared to 0 mM. Instead, for L. plantarum ATCC 14917 after 24 hours the cell viabilities at 0 mM Ca2+ were highest among the different conditions.
• After 48 h, the biofilms formed with 25 mM Ca2+ declined significantly and the viability of biofilms formed with 0 and 10 mM Ca2+ slightly declined compared to biofilms at 24 h for L. acidophilus ATCC 4356.

Along with the calcium effects, the impact of magnesium ions (0-25mM) on the growth and biofilm formation was investigated. Increasing concentrations showed no effect on biofilm formation of L. acidophilus ATCC 4356 while its supplementation up to 1 mM modestly enhanced the growth of MRS and CDM subcultures and significantly enhanced the growth of mCDM subcultures for both species showing not specificity as for the calcium ions.

Effects of extracellular chelator on growth and biofilm formation in Lactobacillaceae

Calcium ions facilitates aggregation and biofilm formation by binding to cell surface macromolecules. Here, they investigated the effect of EGTA, a synthetic calcium chelator, on biofilm formation in the presence and absence of Ca2+ for Lactobacillaceae species. In particular, EGTA was added to the growth medium to evaluate the bacteria’s ability to compete with the chelator for Ca2+ ions showing that L. plantarum ATCC 14917 has lower Ca2+ requirements in Ca2+-limited medium and/or can more efficiently take up calcium needed for growth than L. acidophilus ATCC 4356. Indeed:

• Despite high concentrations of calcium, EGTA did not induce biofilm formation of L. acidophilus   ATCC 4356. However, it was able to recover its growth kinetics in the presence of excess chelator and at 10 and 25 mM Ca2+.
• EGTA had less impact on L. plantarum ATCC 14917 than L. acidophilus ATCC 4356, but addition of EGTA to 10 and 25 mM Ca2+ resulted in a modest increase in biofilm mass for L. plantarum ATCC 14917.
• When no calcium was added, L. acidophilus ATCC 4356 could still grow in the presence of 50 mM EGTA, not with 80 and 100 mM EGTA. EGTA impacted negatively also the growth of L. plantarum ATCC 14917, although it was not entirely suppressed.

In summary, the biofilm cell counts were reduced for all conditions with added EGTA.
EGTA showed to be more detrimental to the viability of L. acidophilus ATCC 4356 and biofilm cells than L. plantarum ATCC 14917 cells, possibly due to the reduction of the Ca2+ available for interacting with the L. acidophilus ATCC 4356 cell surface.

Microscopy analysis on Lactobacillaceae biofilm formation

Then, the effect of Ca2+ and EGTA on Lactobacillaceae biofilm formation was assessed through microscopy. The results are as follows. 

For L. acidophilus ATCC 4356 :

• the cell-cell aggregation increased with higher Ca2+ concentrations.
• the cells muted from filamentous-like without Ca2+ to bacilloid rods with 25 mM Ca2+. This transformation was reversed by the addition of EGTA.

For L. plantarum ATCC 14917, instead:

• cell density was low for 0 and 25 mM Ca2+, but increased at 10 mM Ca2+.
• The inclusion of EGTA chelator did not influence the apparent cell-cell aggregation (0 and 10 mM Ca2+) nor the cell density (25 mM Ca2+).
• No apparent changes also in morphology, which remain in the form of bacilloid rods under all conditions.

Calcium binding affinity to L. acidophilus ATCC 4356 through biofilm quantitation

Ca2+ seems to facilitate L. acidophilus ATCC 4356 biofilm formation via an extracellular mechanism. To assess that, the biofilm formation was quantified at 48 h in the presence of increasing Ca2+ concentrations. Ca2+ binding affinities for proteins vary widely but tend to be stronger for cytosolic intracellular proteins and weaker for extracellular proteins.
Further work is needed to determine the specific Ca2+-binding site(s) involved in biofilm formation.

Bioinformatic analysis of calcium-binding extracellular proteins in Lactobacillaceae

By using Foldseek analyses for the bioinformatic investigation of extracellular and known or predicted calcium-binding proteins in L. acidophilus and L. plantarum, this study found that L. acidophilus has several potential Ca2+-binding surface proteins compared to L. plantarum. These extracellular proteins are likely to have structural roles in the observed Ca2+-induced biofilm formation of L. acidophilus ATCC 4356. 

This study highlights the distinct and complementary functions of calcium ions in Lactobacillaceae species, L. acidophilus ATCC 4356 and L. plantarum ATCC 14917. Indeed, Ca²⁺ serves as a vital intracellular nutrient, essential for cellular processes and metabolic functions but it also enhances cell-cell interactions, facilitating communication and cooperation among bacterial cells. These dual roles are crucial for the survival and persistence of Lactobacillaceae within the gastrointestinal tract. A deeper understanding of the roles of Ca²⁺ and other metal ions in gut bacteria is essential for understanding how dietary components shape the microbiota and, consequently, impact human health and disease.

The findings, published in Immunity, show that dietary LPS can mimic microbial signals and drive gut immune development, with early-life being a critical window for shaping gut immunity independently of the microbiota.

Scientists have known that the gut’s immune system interacts with a mix of microbes and dietary components. For example, fiber from food is broken down by gut bacteria into short-chain fatty acids that support immune health. Some food contaminants, including LPS, can also trigger immune responses. But whether diet alone can shape gut immunity, especially during early development, remains unclear.

Catherine Mooser at the University of Bern in Switzerland and her colleagues studied how different diets affect the immune system of mice, focusing on a specific type of antibody called IgA, which helps protect the gut.

Food contaminants

The researchers raised germ-free mice on either a high-fat diet, a high-starch diet, or a more complex grain-based chow, all under sterile conditions to study the effects of diet alone, without influence from bacteria. 

Mice fed the simpler diets had fewer and less diverse IgA antibodies compared to those raised on the more complex chow. However, this effect only occurred when the diet was given from birth—switching diets in adulthood did not have the same impact. 

The chow-fed mice, which contains natural contaminants such as LPS, also had more active immune cells in their gut than mice on purified diets. Mice genetically unable to respond to LPS had fewer immune cells regardless of the diet they were fed, confirming that LPS in the chow helps drive immune responses in the gut.

Shaping responses

Adding LPS to a purified diet wasn’t enough to restore normal gut immune activity in mice, but when LPS and a protein were delivered together inside tiny fat-based particles called liposomes, the mice’s gut immune system responded strongly, producing more immune cells and antibodies. 

These results show that dietary LPS, especially when absorbed in lipid-based particles, can mimic microbial signals and drive mucosal immune development, the researchers say.

The findings also highlight how diet, especially LPS in the right form, shapes gut immune responses and may inform future approaches in food and medicine. “These observations are relevant to the debate on reintroduction of safe microbes into industrialized food and the use of microbial systems of pharmaceutical delivery,” the authors say.

The findings, published in Cell Metabolism, suggest that this approach is a promising way to help manage obesity by targeting gut bacteria and metabolism together.

Scientists have been long exploring ways to improve metabolism by targeting gut bacteria. For example, prebiotics such as fiber help good bacteria to grow, but they work differently for everyone. Previous research showed that delivering acetate to the lower gut using a special fiber, called acetylated cellulose (AceCel), may boost metabolism by influencing both the microbiota and the host’s metabolism. 

Building on those findings, researchers led by Tadashi Takeuchi at RIKEN Center for Integrative Medical Sciences in Yokohama, Japan, tested the effects of AceCel, which delivers acetate to the lower intestine, on metabolism and obesity in mice.

Burning fat

The researchers compared AceCel to sodium acetate, which is absorbed earlier during digestion and affects the bloodstream more directly. Unlike sodium acetate, AceCel stayed in the gut and led to higher levels of certain beneficial compounds. It also suppressed weight gain, reduced fat mass, and improved blood sugar levels—without causing muscle loss or reduced appetite. 

AceCel triggered the body to burn more fat and activated genes in the liver and fat tissue that are involved in fat breakdown and energy use, the researchers found. These benefits were specific to AceCel and not seen with other similar compounds.

Further experiments showed that AceCel helps the body switch from burning carbohydrates to burning fat, especially during rest or fasting. It does this by activating genes that promote fat breakdown and reducing sugar absorption in the intestine.

Therapeutic strategy

The beneficial effects of AceCel rely on changes in gut bacteria, the team found. AceCel increased the abundance of helpful bacteria such as Bacteroides caccae and Akkermansia muciniphila, which have been linked to metabolic health. 

When tested in germ-free mice or mice with only specific gut bacteria, AceCel only worked in those with Bacteroides, indicating that its benefits depend on these microbes. The key player appears to be a gut bacterium called Bacteroides thetaiotaomicron, which thrives when acetate is present. 

The authors caution that more research is needed to fully understand how acetate and gut bacteria interact, especially in humans. However, they add, “these findings highlight the potential of AceCel as a prebiotic that regulates carbohydrate metabolism in both bacteria and host, offering promise as a therapeutic strategy for obesity.”

The findings, published in Cell, suggest that dietary interventions can help maintain a healthy gut microbiota.

Previous research has explored ways to restore the microbiota in industrialized regions, for example by combining a diet similar to that of non-industrialized populations with the introduction of beneficial bacteria. This approach has been tested in a Canadian trial to improve gut health and reduce disease risk.

Building upon this work, researchers led by Fuyong Li at the University of Alberta in Edmonton, Canada, gave 30 healthy adults a “restore diet” to see how it affected their gut microbiotas, metabolism and overall health.

Restoring microbiotas

The restore diet focused on plant-based, high-fiber foods while avoiding processed ones, and participants were also given L. reuteri supplements. Although participants reported no serious side effects, by increasing fiber intake, the diet resulted in softer stools and mild gastrointestinal issues in some people. 

Within just two days of L. reuteri supplementation, the bacterium became detectable in the stool of participants, and it was found to survive longer and adapt well to the restore diet. While the diet did reduce gut microbiota diversity, the changes in microbiota composition were specific to each person, and the diet alone explained a small part of these changes. What’s more, restoring certain microbes, such as L. reuteri, proved challenging.

However, the diet did show some positive effects: for example, it increased beneficial bacteria, such as Bifidobacterium and Faecalibacterium, while reducing microbes that have been linked to inflammation.

Disease markers

The restore diet had physiological benefits on the participants, lowering fecal pH and increasing beneficial short-chain fatty acids. These changes were linked to improvements in blood metabolites and cardiometabolic risk markers, such as LDL cholesterol and glucose, the researchers found. 

Machine learning models also showed that changes in the microbiota and blood metabolites could predict the diet’s positive effects on health. However, while microbiota composition could help predict changes in cholesterol and inflammation markers, reductions in glucose levels were highly individualized.

The restore diet might benefit metabolic health and help prevent non-communicable diseases such as diabetes. “The findings suggest that a dietary intervention targeted toward restoring the gut microbiome can improve host-microbiome interactions that likely underpin chronic pathologies, which can guide dietary recommendations and the development of therapeutic and nutritional strategies,” the authors say.

During the Ri.MED Symposium 2024, held recently in Palermo (Italy) Microbiomepost conducted an exclusive interview with Konstantinos Paraskevopoulos (European Food Security Autority, EFSA).

The EFSA expert underscores the importance of microbiome data in assessing the safety of food and feed products across the agri-food chain. EFSA is working to incorporate microbiome information into the risk assessment of chemical compounds in food, recognizing the microbiome’s ubiquitous presence in soil, plants, food products, and living organisms. 

Given that microbiomes can influence food safety at multiple levels, EFSA is actively addressing data gaps and methodological challenges. To this end, the agency has initiated exploratory projects aimed at building a robust framework for microbiome integration in food safety assessments. Collaborative efforts with EU partners are essential to advance knowledge, refine methodologies, and ultimately enhance the precision of EFSA’s risk assessment processes, ensuring safer food systems for Europe.

During the Ri.MED Symposium 2024, held recently in Palermo (Italy) Microbiomepost conducted an exclusive interview with Heather Armstrong, from University of Manitoba and University of Alberta (Canada).

This interview explores the intricate role of dietary fibers in maintaining gut health, focusing on how the microbiome’s ability to process these fibers varies in healthy individuals versus those with autoimmune diseases like inflammatory bowel disease (IBD). 

The research team discovered that while dietary fibers generally support gut health by fostering beneficial microbial activity, certain fibers can have adverse effects in individuals with microbiome imbalances. In IBD patients, for example, specific fibers such as beta-fructans may remain unfermented due to missing fiber-fermenting microbes, leading to inflammation and worsening symptoms. 

This finding suggests that fiber intake should be personalized, especially for those with compromised microbiomes, to avoid potential harm. The team aims to develop predictive tools to assess the impact of different fibers on gut health, providing a foundation for tailored dietary recommendations that support both gut and overall health, particularly in sensitive populations.

During the Ri.MED Symposium 2024, held recently in Palermo (Italy) Microbiomepost conducted an exclusive interview with Hellas Cena, from University of Pavia (Italy).

In this interview, Cena emphasizes the growing importance of nutrition in addressing current global health challenges, including climate change, obesity, malnutrition in aging populations, and the need for improved quality of life. 

The speaker argues for a shift from “one size fits all” dietary guidelines toward personalized nutrition, informed by lifestyle medicine and omics sciences, particularly metagenomics. This approach integrates dietary habits, cultural backgrounds, and geographic factors with insights from microbiome studies, aiming to tailor nutrition to individual needs. 

Emphasizing a diverse, plant-based diet to support gut health, the research highlights how such diets not only improve physical well-being but may also positively influence mental health through the gut-brain connection. Personalized, data-driven nutrition offers a pathway to meet the health demands of an aging population and enhance overall wellness.