What happens if healthy Westerners consume a diet that shares key characteristics with non-industrialized dietary patterns? What happens to the gut microbiome? What happens to risk markers of cardiometabolic health? This is precisely what the team led by Prof. Jens Walter, a leading scientist at APC Microbiome Ireland, University College Cork, tested, publishing their groundbreaking findings in Cell1.
The modern diet crisis
In Western societies, non-communicable diseases like obesity, diabetes, cancer, cardiovascular disease, and neurodegenerative conditions are on the rise. A significant contributor to this trend is the industrialized diet, which is characterized by processed foods and insufficient dietary fiber. To understand the potential benefits of transitioning to a non-industrialized diet, it is essential to first examine the impact of industrialized diets on the gut microbiota and overall health.
While an industrialized diet is efficient for feeding large populations, it often comes at the cost of quality and nutrition. Ultra-processed foods, such as sugary cereals, snack bars, fizzy drinks, instant noodles, and microwave meals, are emblematic of the industrialized diet. These foods are high in added sugar and saturated fat, calorie-dense, and have a high glycemic index. They cause frequent insulin spikes and overeating, paving the way for diabetes, obesity, and heart diseases. Furthermore, the food is stripped of its natural structure, destroying the dietary fiber that is essential for a healthy gut microbiome2.
An industrialized diet disrupts the gut microbiome through several mechanisms:
- Fiber Deficiency: Without sufficient fiber, gut bacteria lose their primary energy source, shifting metabolism from carbohydrate fermentation (from fiber) to proteolytic fermentation (from protein), which generates harmful metabolites.
- Additives: Ingredients like emulsifiers damage the gut’s protective mucus layer, triggering inflammation.
- Saturated Fats: Excess intake of these fats lead to increased production of bile acids, which certain gut bacteria transform into harmful substances that may increase the risk of cancer.
These changes result in disrupted gut metabolism and pathological interactions at the intestinal lining, leading to inflammation – a hallmark of chronic diseases. Prof. Walter summarizes, “If you live an industrialized lifestyle, and eat a Western diet, you are predisposed to chronic diseases even if currently healthy. This provides the rationale for attempts to restore gut microbiome health”.
Restoring the gut microbiome
To restore the gut microbiome, the research team developed a “Non-Industrialized Microbiome Restore diet” (NiMe™), inspired by previous research from the group on the dietary patterns and gut microbiome in rural Papua New Guinea. The NiMe™ focuses on counteracting the disruptions caused by industrialized diets (characterized as low fiber, high-calorie density, and a high glycemic index) by targeting microbiome restoration. The diet is adapted to Canadian ingredients and emphasizes fiber-rich (22 g per 1 000 kcal) whole-plant foods. It is low in saturated fat and animal protein (limited to salmon, chicken, and pork) and excludes dairy, beef, and wheat.
Thirty healthy Canadian participants followed the NIMe™ diet for three weeks, with meals tailored to their individual calorie needs. Additionally, they received a dose of Limosilactobacillus reuteri, a bacterium detected regularly in rural Papua New Guinean microbiomes but largely absent in industrialized populations. Researchers monitored changes in gut microbiome, plasma metabolome and markers linked to chronic disease risk.
Fiber, gut transit, and the microbiome
By doubling their intake of dietary fiber, participants experienced softer stools and more frequent bowel movements. “The diet was well-tolerated overall, but it did increase flatulence and abdominal discomfort in some individuals. Several participants dropped out of the study because they experienced too much discomfort from fibre fermentation” noted Prof. Walter. The NiMeTM diet increased persistence and survival of the Limosilactobacillus reuteri, but the species disappeared just two weeks after participants stopped taking it in all but one participant.
Interestingly, microbiota diversity (often seen as a hallmark of gut health) actually decreased. Prof. Walter explained, “This was likely due to the enhanced fibre fermentation making the gut environment more acidic, which inhibits certain sensitive bacteria. But the diet still increased beneficial bacteria while reducing inflammatory ones, which is a win”.
It also restored functional aspects of the gut microbiome. For bacteria to ferment and utilise nutrients, they require a specific set of instruments called enzymes. The NiMeTM diet boosted enzymes for fiber digestion while reducing those involved in breaking down the protective mucus layer in the gut. The diet also lowered gut pH, which was linked to higher levels of short-chain fatty acids (SCFAs), the beneficial molecules produced by the gut bacteria, and a drop in branched-chain fatty acids (BCFAs), which are associated with harmful protein fermentation. In the blood, the diet led to an increase in beneficial metabolites produced by gut bacteria.
Consequence of these gut microbiota changes on human health?
“Participants lost weight despite consuming their calculated caloric requirements, which really surprised us initially. However, it is actually what you would expect, as nutrients are less accessible in high-fibre whole plant foods than in highly processed foods”, explained Prof. Walter.
The research team observed a significant drop in numerous markers (molecules found in the blood) associated with non-communicable diseases:
- Cholesterol: levels dropped, particularly “bad cholesterol”, lowering the risk of cardiovascular disease.
- Blood Glucose: Blood sugar levels decreased, likely reducing diabetes risk.
- Inflammation: Markers of both systematic (in the blood) and intestinal inflammation decreased.
Using advanced statistical tools, the researchers identified specific features of the gut microbiome that responded to the diet and their role in conditions related to metabolism and immunity. Most improvements were heavily influenced by the microbiome’s response to the NiMeTM diet. “The diet consistently impacted participants in a positive way, even if their microbiomes changed differently “, said Prof. Walter.
Takeaways and next steps
The NiMeTM diet confirmed that dietary interventions can meaningfully improve health. However, the benefits were short-lived, once participants switched back to eating their usual diets, their gut microbiomes reverted to their original state.
Prof. Walter highlighted the broader implications: “The work highlights the importance of considering how the industrialization of diet has impacted our microbiome and health.” He added “the findings can guide dietary recommendations and pave the way for the development of therapeutic and nutritional strategies”.
To help the public benefit from the diet developed in this research, Dr. Anissa Armet from the University of Alberta, a registered dietitian who designed the diet and one of the lead authors of the study, has made the recipes used in the study publicly available, ensuring the NiMe™ diet is accessible to everyone.
References:
- Li, F., Armet, A.M., Korpela, K., Liu, J., Margain Quevedo, R., Asnicar, F., Seethaler, B., Rusnak, T.B.S., Cole, J.L., Zhang, Z., Zhao, S., Wang, X., Gagnon, A., Deehan, E.C., Mota, J.F., Bakal, J.A., Greiner, R., Knights, D., Segata, N., Bischoff, S.C., Mereu, L., Haqq, A.M., Field, C.J., Li, L., Prado, C.M., & Walter, J. Cardiometabolic benefits of a non-industrialized-type diet are linked to gut microbiota modulation. Cell 188, 1–22 (2025). https://doi.org/10.1016/j.cell.2024.12.034
- Whelan, K., Bancil, A.S., Lindsay, J.O. et al. Ultra-processed foods and food additives in gut health and disease. Nat Rev Gastroenterol Hepatol 21, 406–427 (2024). https://doi.org/10.1038/s41575-024-00893-5