Lactic acid bacteria in fermented foods can be transferred to the human gut

Fermented foods are a known source of lactic acid bacteria. A high-throughput sequencing analysis of food and human metagenomes proves that fermented foods are a source of lactic acid bacteria for the gut microbiome, and that abundance is shaped by both age and lifestyle.

Lactic acid bacteria (LAB) have long been used for the production of fermented foods. These bacteria, which are also commensal members of the human microbiome, are known for improving lactose digestion and have been regarded as safe when ingested in cheese and yogurt.

More interestingly, some LAB present in fermented foods may contribute to human health in a manner similar to probiotics. That is, the notion that fermented food microorganisms have probiotic features is supported, as many of the species found in fermented foods are either identical to or share physiological traits with species that play a role in improving gut health. Whether the LAB we usually ingest within fermented foods become members of the gut microbiome (measured with stool samples), however, is not yet known.

A new genome-wide analysis led by Dr. Danilo Ercolini from University of Naples Federico II (Italy) proves that the LAB found in the human gut resemble the ones typically found in fermented foods and beverages, with some patterns shared within global populations.

The analysis considered around 303 publicly available and new food metagenomes, corresponding to a wide range of fermented foods and beverages including cheese, yogurt and milk kefir, among others. While some bacteria grouped together in human and food genomes, the reconstruction of previously underexplored microbial genomes from food sources allowed for the disentangling of lactobacilli found in food that did not overlap with human lactobacilli, and they require further characterization. A strain-level analysis of 9445 human metagenomes from public datasets, including multiple body sites, was performed to provide a comparison.

LAB species occurred with variable prevalence and generally low abundance in the human gut, with Streptococcus thermophilus and Lactococcus lactis being the most abundant (31.2% and 16.3%, respectively). Continuous consumption of these bacteria through diet (mainly dairy products) might explain these findings, suggesting that it could be worth exploring their potential as probiotics. On the other hand, a broad range of Lactobacillus species of food origin were detected at lower prevalence, suggesting that they were unlikely to be long-term gut commensals.

The authors also stratified 9445 publicly available human metagenomes according to host conditions such as body site, age, westernized lifestyle and continent. It turned out that age, lifestyle—intended as consumption of fermented foods that vary geographically and culturally— and geographical origin were the factors that most affected the abundance of LAB in human microbiomes.

For instance, LAB abundance tended to increase from childhood to adulthood, which may be due to the increased consumption of fermented foods such as yogurt and cheese. As for geography, food-related LAB were most abundant in westernized populations. By contrast, China and non-westernized cohorts harbored Leuconostoc and Weissella from the microbiota of fermented vegetables and cereal-based fermented foods, while showing a very low abundance of S. thermophilus and L. lactis. That reflected these populations’ lower consumption of dairy products.

A comparative analysis of the DNA sequences of 2859 LAB genomes showed a high level of similarity of LAB from fermented foods with those of LAB from the human gut. This noteworthy finding suggests that consuming foods rich in LAB may enrich the gut with potentially probiotic microorganisms, acknowledges Ercolini in an article in

The lack of health-related metadata from the human cohorts under consideration did not provide any clues about how LAB in stool samples were related to health.

On the whole, the analysis provides an idea of which LAB occur in the human gut. Human metagenomes also allowed for the reconstruction of LAB genomes of human origin that were not previously available, and that in itself is a step forward in the field. These findings highlight that fermented foods are a valuable source of viable LAB that can be transferred to the human gut. Last but not least, it seems that the stool detection of LAB could be used as an indicator of fermented food and probiotics consumption.


Marco ML, Heeney D, Binda S, et al. Health benefits of fermented foods: microbiota and beyond. Curr Opin Biotechnol. 2017; 44:94-102. doi: 10.1016/j.copbio.2016.11.010.

Pasolli E, De Filippis F, Mauriello IE, et al. Large-scale genome-wide analysis links lactic acid bacteria from food with the gut microbiome. Nat Commun. 2020; 11:2610. doi: 10.1038/s41467-020-16438-8.