Scientists map food microbes and their gut microbiome impact

Could the hidden microbial diversity in everyday foods be quietly influencing your gut health, and even transmitting directly to your microbiome?

Study: Unexplored microbial diversity from 2,500 food metagenomes and links with the human microbiome. 

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By Vijay Kumar Malesu

Reviewed by Susha Cheriyedath, M.Sc.

Sep 1 2024

In a recent study published in the journal Cell, a group of researchers explored the diversity of food microbiomes and their influence on the human microbiome by creating the open-access curatedFoodMetagenomicData (cFMD) resource.

Background 

Microorganisms play a crucial role in food science, improving preservation methods and enhancing food quality, safety, and health benefits through fermentation. However, much of the microbial diversity in foods remains unexplored. Shotgun metagenomics has advanced the understanding of these communities, but further research is necessary to fully uncover their diversity and impact on human health.

About the study 

The present study acquired 1,950 newly sequenced and 583 publicly available food metagenomes globally from 50 countries across five continents, with most samples from Asia, Europe, and North America. For each sample, 27 metadata fields were collected, including sample-related, food-related, and technical characteristics. These fields were standardized based on previous work and expanded with input from food microbiologists. The samples were classified by composition and production into categories, types, and subtypes, with an additional classification of fermented and non-fermented groups.

Deoxyribonucleic Acid (DNA) isolation and sequencing followed a protocol designed to maximize microbial DNA recovery from low-biomass samples. After sequencing, raw reads were pre-processed to remove low-quality reads and contaminations, resulting in a total of 2,512 food metagenomes. Metagenome-assembled genomes (MAGs) were generated through a series of steps, including quality control, metagenomic assembly, and binning, leading to the identification of 5,136 high-quality prokaryotic MAGs and 787 eukaryotic MAGs. These MAGs were clustered into 1,036 prokaryotic and 108 eukaryotic species-level genome bins (SGBs), including 320 previously undescribed taxa.

The MAGs were integrated into the expanded MetaRefSGB and ChocoPhlAn resources, contributing to known and unknown species genome bins (SGBs). A comprehensive phylogenetic tree of life was constructed using representative genomes, and taxonomic and functional profiles were generated for further analysis.

Study results

The study investigated the microbial populations present in food by acquiring and metagenomically sequencing 1,950 food microbiomes through the Microbiome Applications for Sustainable Food Systems through Technologies and EnteRprise (MASTER EU) Consortium. These were combined with 583 publicly available samples, resulting in 2,533 metagenomes from 59 datasets across 50 countries. The addition of the MASTER samples significantly increased the number of food metagenomes and sequencing depth, allowing for comprehensive multi-level metagenomic profiles. Metadata was organized into 27 fields covering sample, food-related, and technical information, with hierarchical food categorization based on food type, production approach (fermented/non-fermented), and specific food features. The study included diverse food categories, from dairy and fermented beverages to less characterized categories like fermented seeds and non-fermented fish.

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The study generated 27,123 MAGs, which were filtered to result in 10,112 high- or medium-quality prokaryotic MAGs.  These were integrated with over 1 million genomic sequences and clustered into 1,036 SGBs specific to food. The study further expanded the genomic diversity of typical food-associated bacterial species, with a significant portion of MAGs derived from dairy sources. However, non-dairy samples also contributed notably to the genomic diversity, with species like Lactiplantibacillus plantarum and Bacillus subtilis being prevalent in fermented foods.

Half of the food SGBs contained at least one reference genome and were taxonomically assigned at the species level. This reflects the high representation of dairy products among the most reconstructed species. However, a significant portion of the study focused on unknown SGBs (uSGBs), which represented a considerable portion of the microbial diversity in food and were found across various food categories. These uSGBs represented a considerable portion of the microbial diversity in food and were found across various food categories. The study also identified food-specific microbial signatures and highlighted the potential for using these signatures in food traceability and authentication.

Furthermore, the study explored the overlap between food and human microbiomes, revealing that certain food-associated bacteria are prevalent colonizers of the human microbiome, particularly in infants. The study conducted strain-level analysis to identify potential transmission patterns between food and human microbiomes, with species like Lactobacillus paracasei and Streptococcus gallolyticus showing evidence of strain overlap. The investigation also extended to fungal taxa, with Saccharomyces cerevisiae being the most abundant eukaryote in the food metagenomes, further emphasizing the complexity and diversity of food microbiomes.

Conclusions

To summarize, the study developed cFMD, a comprehensive resource combining newly sequenced and publicly available food metagenomes with standardized metadata. This expanded the characterization of food microbiomes, adding 10,899 MAGs and identifying 320 new species. Integrating these data with over 20,000 human metagenomes revealed a 3% overlap in microbial species between food and adult human microbiomes, with a higher overlap (56%) in infants. The study also highlights the potential for food-to-human microbiome transmission, emphasizing the significance of these overlaps and the complex interactions between food and human microbiomes.

Journal reference:

• Carlino, NiccolòAlvarez-Ordóñez, Avelino et al. Unexplored microbial diversity from 2,500 food metagenomes and links with the human microbiome, Cell (2024), DOI- https://doi.org/10.1016/j.cell.2024.07.039, https://www.cell.com/cell/fulltext/S0092-8674(24)00833-X

Written by

Vijay Kumar Malesu

Vijay holds a Ph.D. in Biotechnology and possesses a deep passion for microbiology. His academic journey has allowed him to delve deeper into understanding the intricate world of microorganisms. Through his research and studies, he has gained expertise in various aspects of microbiology, which includes microbial genetics, microbial physiology, and microbial ecology. Vijay has six years of scientific research experience at renowned research institutes such as the Indian Council for Agricultural Research and KIIT University. He has worked on diverse projects in microbiology, biopolymers, and drug delivery. His contributions to these areas have provided him with a comprehensive understanding of the subject matter and the ability to tackle complex research challenges.