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Gut Relations: Fermented foods are tightly linked to the gut microbiome

Fermented foods can be a primary source of potentially probiotic lactic acid bacteria (LAB) for the human gut, as is shown in a new international study published in Nature Communications

The majority of fermented foods contain thousands of live LAB that are ingested when we consume yogurt, cheese, kefir, etc. Some of these LAB have probiotic properties and, thus, many fermented foods are believed to be naturally healthy as a result.

How many of these bacteria reach the gut? And how many become part of the microbiome, the large community of microorganisms, in the gut?

Researchers at the University of Naples Federico II (Italy) in collaboration with the University of Trento (Italy), Teagasc (Ireland) and the APC Microbiome Ireland SFI Research Centre (Ireland) have analyzed the genetic information from LAB strains (genomes) found in fermented foods and in human faeces to answer these questions.

LAB are among the best studied microorganisms across the globe. They are used in the production of numerous fermented foods including yogurt, cheese, kefir, bakery products, fermented meats or fermented vegetables. Fermentation processes have been studied for over a century, but the practice of fermenting food as a strategy for the preservation of milk, meat and vegetables has been used for millennia. The role of LAB is to transform raw materials, to produce molecules that preserve the food and to contribute to the key characteristics, such as taste of the food. In other words, there would be no yogurt or cheese without the activity of these important microorganisms.

Several strains of LAB are also well known probiotics, the most common belonging to the genus Lactobacillus. Probiotics are of considerable interest as supplements for various purposes but also for their potential to add to the value and health promoting properties of certain foods.

Using state-of-the-art computational analysis tools, LAB genomes were reconstructed from about 300 foods and nearly 10,000 human faecal samples from different continents, looking at the distribution of LAB in humans based on geographical origin, age and lifestyle.  LAB were found in relatively low abundance in the human faeces and their prevalence depended on age, lifestyle and geography. The LAB most frequently found in the human faeces were Streptococcus thermophilus and Lactococcus lactis, which are commonly found in yogurt and cheese.

The DNA sequences of about 3,000 LAB genomes were also compared; and analysis revealed a high level of similarity of LAB from food with those of LAB from the human gut. This new finding suggests that consuming foods rich in LAB can enrich our intestines with these potentially probiotic microorganisms.

“Fermented foods are the principal ecological niche for LAB in nature.  Our results support the hypothesis that food is the major source of LAB for the gut microbiome.  This research also offers hints and methodologies to implement novel strategies for tracing the life of probiotics and other LAB from foods and/or supplements all the way to the human body” said Professor Danilo Ercolini, senior author of the study. “This research opens new horizons for studies on potentially health promoting foods”, concluded Ercolini.

The study was carried out as part of the MASTER project (Microbiome Applications for Sustainable Food Systems through Technologies and Enterprise; www.master-h2020.eu). Professor Paul Cotter, co-author and leader of the MASTER project explained: “MASTER is one of the largest EU-funded grants for food microbiome studies in Horizon 2020 and we expect this to be one the first of many ground-breaking studies that will result”.



E. Pasolli et al., 2020. Large-scale genome-wide analysis links lactic acid bacteria from food with the gut microbiome. Nature Communications. https://doi.org/10.1038/s41467-020-16438-8

For further information please contact Professor Paul Cotter (paul.cotter@teagasc.ie) [Ireland], Prof Danilo Ercolini (danilo.ercolini@unina.it; skype danilo.ercolini) [Italy] or Dr Catherine Buckley, Communications Manager, APC Microbiome Ireland (c.buckley@ucc.ie; mobile +353 (0) 86 8554744)