Integrated molecular approaches for fermented food microbiome research
Open accessAbstract
Molecular technologies, including high-throughput sequencing, have expanded our perception of the microbial world. Unprecedented insights into the composition and function of microbial communities have generated large interest, with numerous landmark studies published in recent years relating the important roles of microbiomes and the environment-especially diet and nutrition-in human, animal, and global health. As such, food microbiomes represent an important cross-over between the environment and host. This is especially true of fermented food microbiomes, which actively introduce microbial metabolites and, to a lesser extent, live microbes into the human gut. Here, we discuss the history of fermented foods, and examine how molecular approaches have advanced research of these fermented foods over the past decade. We highlight how various molecular approaches have helped us to understand the ways in which microbes shape the qualities of these products, and we summarize the impacts of consuming fermented foods on the gut. Finally, we explore how advances in bioinformatics could be leveraged to enhance our understanding of fermented foods. This review highlights how integrated molecular approaches are changing our understanding of the microbial communities associated with food fermentation, the creation of unique food products, and their influences on the human microbiome and health.
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Shotgun metagenomics is the sole approach able to comprehensively survey the microbial composition of a sample and unearth its genomic potential along with the reconstruction of genomes of multiple strains.
“While cultivation has extended to high-throughput settings, 14 shotgun metagenomics is the sole approach able to comprehensively survey the microbial composition of a sample and unearth its genomic potential 12,15 along with the reconstruction of genomes of multiple strains. 16,17”
From Unexplored microbial diversity from 2,500 food metagenomes and links with the human microbiome. (2024) · cites this paper as [17]
The Introduction’s “High-throughput sequencing approaches” section says shotgun metagenomics provides a microbiome functional profile and that long-read methods can recover strain-resolved genomes. It does not call shotgun metagenomics the sole approach, and it cautions that strain-level analysis is often limited to dominant species and that separating mixtures of strains remains challenging. Page numbers were not available in our copy. (LLM, conf=0.88)
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Fermented Milk and Dairy Products
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Unexplored microbial diversity from 2,500 food metagenomes and links with the human microbiome.
Carlino, N., Blanco-Míguez, A., Punčochář, M., Mengoni, C., Pinto, F., Tatti, A., Manghi, P., Armanini, F., Avagliano, M., Barcenilla, C., et al. (2024) · Cell · doi:10.1016/j.cell.2024.07.039 · Cited by 146 · see citing works
“16,17 47 Comprehensive investigations of the overlap between food and human microbiomes at a population-scale and strain-level resolution are thus required.”
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Self-citation
- Authors
- Walsh, A. M., Leech, J., Huttenhower, C., Delhomme-Nguyen, H., Crispie, F., Chervaux, C., & Cotter, P. D.
- Affiliations
- Broad Institute (US)
- Teagasc - The Irish Agriculture and Food Development Authority (IE)
- Danone (France) (FR)
- Corresponding author
- Cotter, Paul D
- Venue
- FEMS Microbiology Reviews
- Publisher
- Oxford University Press (OUP)
- Published
- 2023-02-01
- Volume
- 47
- Issue
- 2
- ISSN
- 0168-6445 (ISSN-L)
- 1574-6976
- PMC
- PMC10002906
- OpenAlex
- W4318926642
- Cited by
- 56
- References
- 145
- Citations by year
- 2026: 23 · 2025: 18 · 2024: 14 · 2023: 1
- FWCI
- 1.29
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- FEMS Microbiology Reviews (publishedVersion, cc-by-nc)
- PubMed Central (publishedVersion, cc-by-nc)
- PubMed (publishedVersion)
- T-Stór (Teagasc) (submittedVersion, cc-by-nc-sa)
- Funders
- Horizon 2020 (818368)
- Science Foundation Ireland (SFI/12/RC/2273P1, SFI/12/RC/2273P2)
- Department of Agriculture, Food and the Marine (16/RC/3835)
- Topics
- Life Sciences › Agricultural and Biological Sciences › Food Science › Probiotics and Fermented Foods
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Life Sciences › Agricultural and Biological Sciences › Food Science › Fermentation and Sensory Analysis
- Keywords
- fermented foods, food microbiome, gut microbiota, microbial communities, microbial metabolites, bioinformatics, human health, diet and nutrition
- MeSH terms
- Fermented Foods, Animals, Diet, Fermentation, Humans, High-Throughput Nucleotide Sequencing, Microbiota
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