Much research has been done on the human microbiome, but food microbiomes have been neglected. Until now.
In a new paper published in the journal Cell, researchers take a closer look at food microbes. The researchers sequenced food metagenomes (the genetic material of a community of organisms within a sample) to create a “food microbiome” by examining 2,533 samples from 50 different countries.
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The study used Shotgun metagenomics. This technique allows the entire sample to be sequenced at once, without the need for culture. The researchers were able to save a lot of time and learn more about the subjects.
The study included fermented grains, fermented fish, and unfermented animal products.
About half of the 10,899 food-associated microbes found in the study were unknown. The microbes were found in all food categories, but particularly in fermented salmon. The study suggests that these may serve as a topic for further research.
The researchers found greater similarity in metagenomes between similar products. (For example, it is more likely that the metagenome of a fermented beverage will be similar to that of another fermented product than to that of a fermented food.) The microbial diversity of unfermented foods was higher than that found in fermented foods.
The greater variety of dairy products was probably due to their greater range. Most of the diversity of dairy products was observed with cheeses and brines.
What could it do for the food industry?
Food manufacturers could identify harmful microbes by gaining a better understanding of the food microbiome.
The study, for example, did not find many microbes that were clearly pathogenic or harmful to human health. However, they did find a high prevalence of E.hormaechei (which is associated with some infections). The study also identified some microbes that can negatively affect the flavor or preservation of foods.
By providing better knowledge of which microbes can be found in which products, it could help maintain the geographic identity of foods and determine which foods should have geographic markers. Metagenomics, said Nicola Segata, one of the scientists, could be used to verify the geographic origin of products.
This study is important because recent research suggests that we can eat microbes that are part of our microbiome. This means that the microbes in the foods we eat are vitally important to our health.
This study showed that food-associated microbes made up 56 %s of infant microbiomes, but only 3 %s of adult microbiomes. Segata said these 3 %s are not insignificant and could impact how our microbiomes function.
The researchers found that the human microbiome overlapped more with the food microbiome in Westernized populations than in those from non-Westernized cultures (although they acknowledged that sampling bias could be at play).
From: Cell
Unexplored diversity of microbes from food metagenomes: links to the human microbiome
Publication date: August 29, 2024
Doi: https://doi.org/10.1016/j.cell.2024.07.039
Authors: N. Carlino, A, Blanco-Miguez, M. Puncochar, C. Mengoni, F. Pinto, A. atti, P. Manghi F, Armanini, M, Avagliano, C. Barcenilla, S. Breselge, R. Cabrera -Rubio, I. Calvete-Torre, M. Coakley, JF Cobo-Diaz, F. De Filippis, H. Dey, J. Leech, ES Klaassens, S. Knobloch, D. O'Neil, NM Quijada, C. Sabater , S. Skirnisdottir, V. Valentino, , L Walsh, MASTER European Consortium, A. Alvarez-Ordonez, F. Asnicar, G. Fackelmann, V Heidrich, A. Margolles, V. Thor Marteinsson, O. Rota Stabelli, M. Wagner, D. Ercolini, PD Cotter, N. Segata, E. Pasolli
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