The NiMe Diet Story
Village in New Britain, Papua New Guinea. Photo by: Jens Walter, 2019.
The chronic disease crisis and its causes
Living in a modern, industrialized society certainly has advantages: infant mortality is low and life expectancy is high; sanitation and antibiotics prevent and fight infections; and modern industrialized food systems provide reliable access to food, including plenty of delectable delights.
Nevertheless, this abundance comes with a cost. The prevalence of several non-communicable chronic diseases – obesity, type 2 diabetes, heart disease, inflammatory bowel diseases, certain cancers (e.g., colorectal), and other immune-mediated diseases – has risen substantially. Although these diseases are quite different in their manifestations, they share inflammation as a common pathophysiological mechanism.
What is causing the rise in chronic diseases? It is not entirely clear. But what is clear is that it is not primarily genetics, as human genes have not changed enough over the last two centuries. It is, therefore, more likely that lifestyle-induced changes in industrialized societies are the key contributors. Central to this is a diet that has changed substantially due to industrialization and extensive food processing, which differs significantly from what humans consumed over the course of evolution.
Although food processing led to many advancements in food safety and security (like pasteurization and preservation techniques such as canning and freezing), the industrialization of food production resulted in a general reduction in the nutritional value of food. Many modern foods are energy-dense and oversupply fat and refined carbohydrates. So-called “ultra-processed” foods now make up the bulk of the diet in places like Canada, the USA, and the United Kingdom. Such foods are low in dietary fibre, have a high glycemic index (cause higher blood sugar spikes), and are designed to be highly palatable, leading to overeating, hyperglycemia, and systemic inflammation. Epidemiological evidence indicates that the foods that make up the “Western” diet are linked to the substantial rise in chronic diseases. Recent research has also established that such a diet has adverse effects on our gut microbiome.
The role of the microbiome in human health
The human gut microbiome, a complex community of bacteria, fungi, viruses, and other microbes that reside in our intestinal tract, plays an important role in human health and the prevention of chronic disease. Our relationship with the microbiome can be described as a “symbiosis”, meaning it is mutually beneficial. We provide gut microbes with a home and food to eat and, in turn, the microbiome helps us fight infections, develop our immune system, and extract nutrients from our diet. Microbial metabolism produces hundreds of intermediates and products (metabolites) that are absorbed in the digestive system and circulated throughout the body. They influence and regulate bodily functions, including metabolism, immunity, and can even affect our mood. Production of these microbial metabolites is influenced by the nutrients we provide our microbes. In other words, our diet has a profound effect on the metabolic output of the gut microbiome and, consequently, our health.
It is important to consider that this symbiotic relationship with the gut microbiome evolved over millions of years under environmental and nutritional conditions that are substantially different from those in modern industrialized societies. This made scientists hypothesize that a disruption of human-microbiome symbiosis through industrialized lifestyle is one of the factors that led to the sudden rise in chronic diseases.
How does industrialization alter the gut microbiome? What are the consequences?
There is now convincing evidence that industrialization alters both gut microbiome composition and metabolic function. We can draw these conclusions by comparing gut microbiomes of non-industrialized human populations, such as Hadza hunter-gatherers in Tanzania and South American Amerindians, to those in industrialized settings. It is likely a combination of factors related to industrialization that alters our microbiome: antibiotics, sanitation, refined diets, and some modern clinical practices (like cesarean sections).
When it comes to functional attributes of the gut microbiome, diet is a central tenant. For example, without sufficient dietary fibre, the gut microbiome is essentially starved. This leads to reduced production of beneficial metabolites from fibre fermentation and increased degradation of the intestine’s protective mucus layer. Artificial ingredients of processed foods like emulsifiers (added to enhance mouthfeel and prevent liquids from separating) further damage the mucus layer. Overall, this breakdown of the protective barrier in the gut causes inflammation, linking industrialized diets and resulting changes to the gut microbiome with increased chronic disease risk.
Some microbial taxa have disappeared entirely from the industrialized microbiome, and microbiome diversity has dropped. Pro-inflammatory microbial taxa that benefit from saturated animal fat (e.g., a bacterium called Bilophila) have increased, while fibre fermentation and its beneficial metabolites (e.g., short-chain fatty acids) have reduced. The enzymatic capacity of the gut microbiome for degrading plant carbohydrates is diminished, while mucus-degrading bacteria and enzymes are enriched. Several of these effects can be observed across generations of immigrants, meaning that if individuals from non-industrialized societies immigrate to an industrialized country, their microbiome is altered in parallel with the extent to which their lifestyle changes (or how long they have lived in an industrialized country).
Scientifically, it is very difficult to establish if such microbiome changes in humans do, in fact, cause the chronic pathologies with which they are associated. However, such work can be performed in animal models of human chronic diseases. There is ample research in animals confirming that perturbations of the gut microbiome that model the impact of industrialization, like Western-style diets, cause metabolic and immunological pathologies reminiscent of human chronic diseases.
Overall, mounting evidence suggests that lifestyle-induced adverse effects on the gut microbiome contribute to chronic disease risk.
The case for microbiome restoration
The research described above provides a strong rationale – supported by epidemiology, anthropology, and mechanistic animal model research – to restore the gut microbiome to redress adverse effects of industrialization. However, there are also voices that question such a need. After all, industrialization has made us live longer and, based on key societal health indicators, healthier overall. So, why try and restore the gut microbiome?
It is important to consider that the main benefits of industrialization are the prevention of infections and malnutrition through sanitation, antibiotics, and reliable access to food. These are very good things, and no one wants to get rid of them. However, it is equally important to understand the unintended, negative side effects. We have traded the reduced burden of infectious diseases with higher rates of chronic diseases. In addition, the incentive of food companies is to sell as much food as possible. Ultra-processed foods are designed to make us eat more by taking advantage of our own biology – reward systems in our brains favour food products high in fat and sugar because they evolved in an environment of food scarcity. Even non-industrialized populations, like Hadza hunter-gatherers, prefer to eat honey and meat when they are available over fibre-rich tubers that are more readily accessible.
Therefore, the idea is to explore how we can maintain the benefits of industrialization while avoiding its negative side effects – to get the best of both worlds! We can attempt to administer and reestablish beneficial microbes that have been lost, while still preventing pathogens from spreading. We can also try to make our food supply healthier and more microbiome friendly without jeopardizing food security.
Lessons from Papua New Guinea
Since Jens Walter was a child, he was fascinated by Papua New Guinea, with its more than 800 languages and remote valleys almost untouched by the modern world until 1930. The country is located on an island north of Australia and shares a border with Indonesia. Being unaffected by industrialization and maintaining an ancient system of subsistence agriculture, the traditional diet in rural Papua New Guinea is rich in unprocessed, whole-plant foods grown in personal gardens and sold in markets. On a trip to Papua New Guinea in 2019, Jens observed these gardens and markets for the first time, and began to understand how the non-industrialized diet could positively affect the microbiome and be harnessed to benefit health.
Local gardens growing food close to Goroka, Eastern Highlands province, Papua New Guinea. Photo by: Jens Walter, 2019.
Local market in New Britain, Papua New Guinea. Photo by: Jens Walter, 2019.
In collaboration with scientists from the Papua New Guinea Institute of Medical Research (PNGIMR), Jens’ team discovered that the gut microbiomes of rural Papua New Guineans were more diverse than their industrialized counterparts, enriched in bacteria that thrive from dietary fibre (Prevotella) or originate from fermented foods (lactobacilli). There were also lower levels of pro-inflammatory bacteria linked to the consumption of saturated animal fat (Bilophila and Alistipes). These findings echo those of other studies that have shown that the industrialized lifestyle, particularly modern diet, leads to tractable changes in the gut microbiome.
In recent decades, however, many areas in Papua New Guinea have undergone a rapid transition to urbanization, marked by a shift from traditional, locally-sourced diets to ultra-processed foods and beverages. Although these changes have increased life expectancy and reduced levels of malnutrition, they led to a rapid increase in chronic diseases like type 2 diabetes. These developments recapitulate the detrimental side effects of industrialization on human health that have been observed in many parts of the world and reiterate the need for countermeasures.
