NEW YORK – An international research team has assembled the metagenomes of more than 2,500 food sources, detecting microbes important for food production, flavor, and quality, as well as some that overlap with the human gut microbiome.
"[W]ith traditional cultivation-based approaches, it is difficult to scale the investigation to cover the current large diversity of food and to unravel all members of the complex microbial communities present on foods," Nicola Segata, a researcher affiliated with the University of Trento, the European Institute of Oncology in Italy, and King's College London, said in an email, noting that "[m]etagenomic approaches with advanced computational analysis can overcome these limitations."
As they reported in Cell on Thursday, Segata and his colleagues in Italy, the UK, and elsewhere generated 1,950 new metagenomic sequences, combining them with more than 580 published food metagenomes in an open access microbiome sequence data collection dubbed the curatedFoodMetagenomicData (cFMD) resource. Together, the metagenomes represented foods ranging from dairy to fermented meat, fermented drinks, fermented seeds, and non-fermented fish and meat.
"In this work, we developed and described cFMD, a resource resulting from the collection of thousands of newly sequenced and publicly available food metagenomes with standardized metadata and data products," the study's authors explained.
The team tapped into the metagenomic data to put together nearly 10,900 metagenome-assembled genome sequences, representing 1,036 prokaryotic species and more than 100 eukaryotic species — a set that encompassed 320 taxa not described in the past.
In the process, the authors saw "significant microbial diversity within and between food categories" when they delved into the species-level genome sets they found. While microbiome variation was particularly pronounced in dairy products, the microbial features found in fermented beverages tended to be more uniform.
Likewise, the team's analyses suggested that foods originating from specific locations may be more microbiologically similar to one another than to similar food types coming from other sites.
The investigators subsequently compared the food microbial sequence data against metagenomic sequences from the curatedMetagenomicData collection that spanned some 19,833 human gut or oral microbiomes from individuals tested in 39 countries.
From those analyses, they estimated that some 3 percent of microbes in the human gut microbiome came from food sources, on average, particularly when it came to certain microbial species and strains. That fraction jumped to 56 percent, on average, for the infant gut microbiome, based on available metagenomic microbiome data for 2,892 infants in the curatedMetagenomicData set.
"[B]y integrating the many thousands of available gut metagenomes that we previously cataloged, we were able to estimate with higher accuracy the extent of the potential overlap between food and human microbiomes," Segata explained, noting that the team's ongoing research is now aimed at untangling the foods with the most pronounced effects on microbiomes in the human gut and beyond, including food microbes with health effects.
"In the future, we want to explore the diversity of these food microbiomes with respect to different foods, cultures, lifestyles, and populations," co-senior author Paul Cotter, a researcher affiliated with the Teagasc Food Research Centre and University College Cork, said in a statement.