A study recently published in Cell has revealed a fascinating connection between the microbes in our food and those residing in the human microbiome. The research, led by Nicola Segata from the University of Trento, presents the largest-ever catalog of microorganisms found in various food types, from fermented products like cheese and sauerkraut to fresh produce. This study has profound implications for understanding how diet affects human health by influencing the gut microbiome.
Microbes in food and the human microbiome
The relationship between the microbes in our food and those in our microbiome has long been suspected, but until now, it has remained largely unexplored. According to the study, approximately 3% of the microbes in the adult gut microbiome can be traced directly to the food we consume. This number jumps to 8% in children and over 50% in newborns, suggesting that food plays a particularly significant role in shaping the microbiome early in life.
Interestingly, the study found that specific strains of bacteria found in fermented foods, like Lacticaseibacillus paracasei from cheese, can be directly transmitted from food to the gut, where they may colonize and potentially impact health. This discovery builds upon the understanding that the human microbiome is shaped not only by person-to-person microbial transmission but also by diet, a theory that opens up new avenues for research into the health effects of different foods.
The study and its findings
The researchers analyzed over 2,500 food metagenomes—genetic material from a wide range of foods, including fermented dairy products, meat, vegetables, and fruits. They discovered a microbial diversity that was previously unknown. Specifically, they identified more than 10,000 metagenome-assembled genomes (MAGs), with 320 representing species that had never been described before. These included both prokaryotic (bacteria) and eukaryotic (fungi) organisms, offering a glimpse into the vast microbial biodiversity present in the foods we eat.
What is particularly intriguing about the study is the overlap between these food microbes and those found in human microbiomes. About 1,409 species found in food were also detected in human microbiomes, accounting for an average of 3% of the adult gut microbiome. The overlap was more significant in newborns, where food-associated species constituted 56% of the gut microbiome, likely due to exposure to microbes in breast milk and dairy products1.
This discovery challenges the conventional view that the human microbiome is predominantly shaped by environmental factors like hygiene and direct microbial transmission between individuals. The findings suggest that diet plays a more central role in shaping the microbiome than previously thought.
Implications of the study
The implications of this research are vast, not just for understanding the microbiome but also for food science and public health. Since certain microbes in food can colonize the gut, they may offer new ways to improve gut health through diet. For instance, incorporating fermented foods rich in beneficial microbes like Lacticaseibacillus could enhance gut health and improve immunity, digestion, and even mental well-being, given the gut-brain axis.
This study also provides a foundation for the development of functional foods designed to modulate the microbiome. Functional foods—those that have been enhanced with added health benefits—could be tailored to deliver specific microbes that have been shown to promote gut health. This could be particularly useful in managing conditions like irritable bowel syndrome (IBS) or obesity, both of which are linked to imbalances in the gut microbiome.
In addition, the presence of yet-to-be-characterized species in our food suggests there may be untapped potential for discovering new probiotics or other health-promoting microbes. As microbiologist Benjamin Wolfe from Tufts University noted, mining these unknown microbes could lead to novel food products with enhanced health properties.
Challenging existing theories about the human microbiome
This study also challenges existing theories about the microbiome and diet. Previous research largely focused on how diet influences the microbiome by providing nutrients that promote or inhibit the growth of certain microbes. However, the idea that the microbes in the food itself can become part of the human microbiome is relatively new. This research suggests that food-to-gut microbial transmission plays a more significant role than previously understood.
The findings also support the notion that humans have coevolved with their diets, with certain food-associated microbes becoming integral to our biology. The discovery that over half of newborns’ gut microbiomes consist of food-associated microbes underscores the importance of early dietary exposures in shaping lifelong health.
The study’s findings represent a significant leap forward in our understanding of the human microbiome and its relationship with diet. By demonstrating that microbes present in food can directly influence the composition of the human microbiome, the research opens the door to new approaches in nutrition, food science, and health interventions.
References
- Carlino, Niccolò, Aitor Blanco-Míguez, Michal Punčochář, Claudia Mengoni, Federica Pinto, Alessia Tatti, Paolo Manghi et al. “Unexplored Microbial Diversity from 2,500 Food Metagenomes and Links with the Human Microbiome.” Cell, (2024). Accessed September 16, 2024. https://doi.org/10.1016/j.cell.2024.07.039. ↩︎
