Ancient microbes in traditional fermented foods may unlock next-gen probiotics

Researchers examining nine Ethiopian fermented foods and beverages propose that foreign microbial communities may be cultivated to develop next-generation probiotics. Darwin Bioprospecting Excellence identified strains in foods rich in lactic acid species and environmental microorganisms, with dominant and undetected bacterial strains.

“The main difference between the microbial composition of traditionally fermented foods and that of industrial ones is biodiversity,” Manuel Porcar Miralles, founder and CEO of the biotechnology company, tells Nutrition Insight. “Yogurt has two microorganisms, for example.”

“Cheeses may have more, but the number and variety of microorganisms from traditional food is typically higher than from processed food. Additionally, there are many fermented products unknown to Westerners. In Ethiopia, for example, there are many fermented beverages made from cereals, local plants, spices, or honey.”

He explains that diversity is a microbial “treasure” selected by cultural knowledge over thousands of years.

Commercialization hurdles 

Ethiopian food, such as injera, and beverages, such as tella and tej, contain a higher microbial diversity. Although the nutritional and health benefits of such foods are widely acknowledged, Darwin researchers stress that scientific understanding of their microbial composition has been lacking.

Manuel Porcar Miralles, founder and CEO of Darwin Bioprospecting Excellence.This gap prevents the scientific validation of health benefits and thus prevents standardized and scalable biosolutions.

However, we ask Miralles a crucial question: How might the health benefits of fermented products change if they are commercialized beyond their local context?

He explains that, generally, a beneficial microorganism will still be beneficial regardless of which human population consumes it.

“But it is true that actual human populations can diverge a lot on their gut content, basically because of diet and lifestyle. Including microorganisms from exotic sources may hypothetically ‘spark’ the diversity of your microbiome.”

Next-gen probiotics 

Darwin collaborated with academics to conduct one of the most thorough microbial analyses of Ethiopian food, published in Frontiers in Microbiology. They used culturomic and metataxonomic techniques to analyze kotcho, injera, datta, tej, tella, cheka, kinito, borde, and shamita. 

Researchers used culturomic and metataxonomic techniques to analyze microbial composition (Image credit: Darwin).The paper suggests that some bacterial species found during fermentation may boost the safety and nutritional quality of fermented foods while enhancing any probiotic property. 

“Most traditional fermentation practices involve spontaneous processes in which raw materials are fermented at ambient temperatures, often uncovered, allowing exposure to environmental microorganisms,” reads the paper.

Miralles adds: “In the case of environmental microorganisms, such as the Ethiopian soil and river samples we are currently analyzing in our laboratories, the amount of uncommon taxa is particularly striking.”

“At Darwin, we are used to sampling many different locations, and exotic samples, like the ones we have analyzed from Ethiopia, tend to be rich in lactic acid species that are rare in Europe.” These species were especially abundant in drinks, cheka and tella, and foods such as injera.

The researchers also call for more comprehensive sampling from various regions and producers, as the study identified microorganisms from only one sample of each fermented product.

According to Miralles, these microbial communities remained so understudied despite their dietary importance as local cuisine is not commonly known outside Ethiopia.

“If you look for the microbiome of any type of French cheese, you’ll end up with dozens of scientific publications describing that in detail. If you do the same thing with Ethiopia’s tej or injera, you will hardly find any consistent information.” 

“The microbial diversity of the world’s cuisine has been and still is very poorly studied to date,” he adds.

Changing climates

With microbial growth and traditional practices relying on environmental conditions for safe and successful ferments, Miralles discusses the importance of preserving the microorganisms and culinary techniques.

“Not unlike cheese, sourdough, or kefir communities, the microbiomes we have found in Ethiopian fermented foods and beverages are the result of adaptation,” says Miralles. “They originally come from natural environments (plants, soil, human skin) but have been selected as a ‘microbial tribe’ that performs a metabolic, yet gastronomic procedure.”

Fermented beverages (A) Borde, (B) Cheka, (C) Kinito, (D) Shamita, (E) Tej, and (F) Tella; food condiment (G) Datta; and foods (H) Kotcho and (I) Injera are analyzed in this study (Image credit: Frontiers in Microbiology).“These microorganisms are very robust and they may be used, either alone or in combination, as a source of fermented products of all kinds. A changing climate would, in principle, not affect them directly, but the plants they live on or they ferment are, of course, very sensitive to the dramatic climatic changes we are living through today.”

“If those plants are lost, so would be the microorganisms and the culinary techniques used to combine plants and microorganisms,” Miralles cautions. By keeping exotic bacteria in microbial collections, we can save traditional foods, ancient culinary techniques, and their microorganisms from extinction.”

Power of fermentation 

In other fermentation news, Corbion and five global partners joined the Ferment4Health project, which aims to explore how fermented foods and postbiotics can enhance gut health and lower chronic low-grade inflammation, a key factor in many lifestyle-related diseases.

According to a recent study, using optimal fermentation conditions for pulses improved their antioxidant and antidiabetic properties while increasing their soluble protein content.

A systematic review claiming to be the first to analyze the effects of fermented foods on irritable bowel syndrome suggested probiotic fermented milk may help people suffering from the gastrointestinal disorder.