{"type": "FeatureCollection", "features": [{"id": "10.1038/s41467-020-16438-8", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-27T16:18:21Z", "type": "Journal Article", "created": "2020-05-25", "title": "Large-scale genome-wide analysis links lactic acid bacteria from food with the gut microbiome", "description": "Abstract<p>Lactic acid bacteria (LAB) are fundamental in the production of fermented foods and several strains are regarded as probiotics. Large quantities of live LAB are consumed within fermented foods, but it is not yet known to what extent the LAB we ingest become members of the gut microbiome. By analysis of 9445 metagenomes from human samples, we demonstrate that the prevalence and abundance of LAB species in stool samples is generally low and linked to age, lifestyle, and geography, with Streptococcus thermophilus and Lactococcus lactis being most prevalent. Moreover, we identify genome-based differences between food and gut microbes by considering 666 metagenome-assembled genomes (MAGs) newly reconstructed from fermented food microbiomes along with 154,723 human MAGs and 193,078 reference genomes. Our large-scale genome-wide analysis demonstrates that closely related LAB strains occur in both food and gut environments and provides unprecedented evidence that fermented foods can be indeed regarded as a possible source of LAB for the gut microbiome.</p>", "keywords": ["Primates", "0301 basic medicine", "2. Zero hunger", "0303 health sciences", "Science", "Probiotics", "Q", "gut microbiome", "Article", "Gastrointestinal Microbiome", "lactic acid bacteria", "Lactococcus lactis", "03 medical and health sciences", "Lactobacillales", "Databases", " Genetic", "Food Microbiology", "Animals", "Humans", "Metagenome", "Streptococcus thermophilus", "Fermented Foods", "[PHYS.ASTR] Physics [physics]/Astrophysics [astro-ph]", "Life Style", "genome analysis"]}, "links": [{"href": "https://iris.unitn.it/bitstream/11572/269813/1/s41467-020-16438-8.pdf"}, {"href": "https://www.iris.unina.it/bitstream/11588/811717/2/NatComm%2c2020_LABfoodgut.pdf"}, {"href": "https://www.nature.com/articles/s41467-020-16438-8.pdf"}, {"href": "https://doi.org/10.1038/s41467-020-16438-8"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Nature%20Communications", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1038/s41467-020-16438-8", "name": "item", "description": "10.1038/s41467-020-16438-8", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1038/s41467-020-16438-8"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-05-25T00:00:00Z"}}, {"id": "10.1080/1040841x.2022.2132850", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-27T16:18:57Z", "type": "Journal Article", "created": "2022-10-26", "title": "Bioinformatic approaches for studying the microbiome of fermented food", "description": "High-throughput DNA sequencing-based approaches continue to revolutionise our understanding of microbial ecosystems, including those associated with fermented foods. Metagenomic and metatranscriptomic approaches are state-of-the-art biological profiling methods and are employed to investigate a wide variety of characteristics of microbial communities, such as taxonomic membership, gene content and the range and level at which these genes are expressed. Individual groups and consortia of researchers are utilising these approaches to produce increasingly large and complex datasets, representing vast populations of microorganisms. There is a corresponding requirement for the development and application of appropriate bioinformatic tools and pipelines to interpret this data. This review critically analyses the tools and pipelines that have been used or that could be applied to the analysis of metagenomic and metatranscriptomic data from fermented foods. In addition, we critically analyse a number of studies of fermented foods in which these tools have previously been applied, to highlight the insights that these approaches can provide.", "keywords": ["2. 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