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.
", "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": "10.1093/femsre/fuaa015", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-27T16:19:04Z", "type": "Journal Article", "created": "2020-05-20", "title": "The food-gut axis: lactic acid bacteria and their link to food, the gut microbiome and human health", "description": "ABSTRACTLactic acid bacteria (LAB) are present in foods, the environment and the animal gut, although fermented foods (FFs) are recognized as the primary niche of LAB activity. Several LAB strains have been studied for their health-promoting properties and are employed as probiotics. FFs are recognized for their potential beneficial effects, which we review in this article. They are also an important source of LAB, which are ingested daily upon FF consumption. In this review, we describe the diversity of LAB and their occurrence in food as well as the gut microbiome. We discuss the opportunities to study LAB diversity and functional properties by considering the availability of both genomic and metagenomic data in public repositories, as well as the different latest computational tools for data analysis. In addition, we discuss the role of LAB as potential probiotics by reporting the prevalence of key genomic features in public genomes and by surveying the outcomes of LAB use in clinical trials involving human subjects. Finally, we highlight the need for further studies aimed at improving our knowledge of the link between LAB-fermented foods and the human gut from the perspective of health promotion.
", "keywords": ["0301 basic medicine", "2. Zero hunger", "0303 health sciences", "human microbiome", "Review Article", "Gastrointestinal Microbiome", "3. Good health", "lactic acid bacteria", "03 medical and health sciences", "probiotics", "Health", "Lactobacillales", "food microbiome; human microbiome; lactic acid bacteria; probiotics", "food microbiome", "Food Microbiology", "Humans"]}, "links": [{"href": "https://www.iris.unina.it/bitstream/11588/811718/2/FEMSMicroRev%2c2020_LABfoodgut.pdf"}, {"href": "http://academic.oup.com/femsre/article-pdf/44/4/454/37084083/fuaa015.pdf"}, {"href": "https://doi.org/10.1093/femsre/fuaa015"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/FEMS%20Microbiology%20Reviews", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1093/femsre/fuaa015", "name": "item", "description": "10.1093/femsre/fuaa015", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1093/femsre/fuaa015"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-06-18T00:00:00Z"}}, {"id": "10.3389/fmicb.2022.813480", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-27T16:21:37Z", "type": "Journal Article", "created": "2022-03-01", "title": "Metatranscriptomic analyses unravel dynamic changes in the microbial and metabolic transcriptional profiles in artisanal Austrian hard-cheeses during ripening", "description": "Vorarlberger Bergk\uffc3\uffa4se (VB) is an artisanal Austrian washed-rind hard cheese produced from alpine cows\uffe2\uff80\uff99 raw milk without the addition of ripening cultures. Ripening time is a key factor in VB, as it strongly influences the microbial communities present in the cheeses and the organoleptic properties of the product. In this study, the microbial and metabolic transcriptional profiles in VB rinds at different ripening times were investigated. VB products before (30\uffe2\uff80\uff89days of ripening) and after (90\uffe2\uff80\uff89days of ripening) selling were selected, RNA was extracted and subjected to shotgun metatranscriptomic sequencing. The analysis revealed some of the previously described abundant bacterial taxa of Brevibacterium, Corynebacterium, Halomonas, Psychrobacter, and Staphylococcus to be highly active in VB rinds. Additionally, the investigation of most important metabolic pathways in cheese ripening clearly showed differences in the gene transcription profiles and the active microbiota between the two ripening points investigated. At 30\uffe2\uff80\uff89days of ripening, metabolic events related with the degradation of residual lactose, lactate, citrate, proteolysis, and lipolysis were significantly more transcribed and mainly associated with Staphylococcus. On the other hand, genes involved in the degradation of smaller compounds derived from previous metabolism (i.e., metabolism of free amino acids and fatty acids) were significantly more expressed in VB rinds with 90 of ripening, and mainly associated with Brevibacterium and Corynebacterium. These latter metabolic activities are responsible of the generation of compounds, such as methanethiol and 2,3-butanediol, that are very important for the flavor and aroma characteristics of cheeses. This study shows the dynamic changes in the gene transcriptional profiles associated with energy substrates metabolism and the generation of organoleptic compounds during VB ripening and uncovers bacterial taxa as key drivers of the ripening process. These taxa might be the target for future studies toward an accelerated cheese ripening and the enhancement of its organoleptic properties.
", "keywords": ["2. Zero hunger", "0301 basic medicine", "0303 health sciences", "791", "metatranscriptomics", "organoleptic compounds", "cheese ripening", "DegreeDisciplines::Life Sciences::Animal Sciences", "microbial dynamics", "Microbiology", "QR1-502", "differential gene transcription", "03 medical and health sciences", "metabolic pathways", "Bacteria; Identification; Quality; Communities; Microflora; Alignment; Pathways; Products; Genes; Acid", "DegreeDisciplines::Life Sciences::Food Science::Food Microbiology"]}, "links": [{"href": "https://doi.org/10.3389/fmicb.2022.813480"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Frontiers%20in%20Microbiology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.3389/fmicb.2022.813480", "name": "item", "description": "10.3389/fmicb.2022.813480", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3389/fmicb.2022.813480"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-03-01T00:00:00Z"}}, {"id": "10.1038/s41538-021-00087-2", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-27T16:18:22Z", "type": "Journal Article", "created": "2020-09-12", "title": "Microbiome-based environmental monitoring of a dairy processing facility highlights the challenges associated with low microbial-load samples.", "description": "AbstractFood processing environments can harbor microorganisms responsible for food spoilage or foodborne disease. Efficient and accurate identification of microorganisms throughout the food chain can allow the identification of sources of contamination and the timely implementation of control measures. Currently, microbial monitoring of the food chain relies heavily on culture-based techniques. These assays are determined on the microbes expected to be present in the environment, and thus do not cater for unexpected contaminants. Many culture-based assays are also unable to distinguish between undesirable taxa and closely related harmless species. Furthermore, even when multiple culture-based approaches are used in parallel, it is still not possible to comprehensively characterize the entire microbiology of a food-chain sample.
High throughput DNA sequencing represents a potential means through which microbial monitoring of the food chain can be enhanced. While sequencing platforms, such as the Illumina MiSeq, NextSeq and NovaSeq, are most typically found in research or commercial sequencing laboratories, newer portable platforms, such as the Oxford Nanopore Technologies (ONT) MinION, offer the potential for rapid analysis of food chain microbiomes. In this study, having initially assessed the ability of rapid MinION-based sequencing to discriminate between different microbes within a simple mock metagenomic mixture of related food spoilage, spore-forming microorganisms. Subsequently, we proceeded to compare the performance of both ONT and Illumina sequencing for environmental monitoring of an active food processing facility.
Overall, ONT MinION sequencing provided accurate classification to species level, which was comparable to Illumina-derived outputs. However, while the MinION-based approach provided a means of easy library preparations and portability, the high concentrations of DNA needed to run the rapid sequencing protocols was a limiting factor, requiring the random amplification of template DNA in order to generate sufficient material for analysis.
", "keywords": ["0301 basic medicine", "2. Zero hunger", "03 medical and health sciences", "Nutrition. Foods and food supply", "13. Climate action", "0206 medical engineering", "TX341-641", "Metagenomics", "02 engineering and technology", "Food microbiology", "TP368-456", "Food processing and manufacture", "Article"]}, "links": [{"href": "https://www.nature.com/articles/s41538-021-00087-2.pdf"}, {"href": "https://doi.org/10.1038/s41538-021-00087-2"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/npj%20Science%20of%20Food", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1038/s41538-021-00087-2", "name": "item", "description": "10.1038/s41538-021-00087-2", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1038/s41538-021-00087-2"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-09-11T00:00:00Z"}}, {"id": "10.1128/aem.01081-21", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-27T16:19:54Z", "type": "Journal Article", "created": "2021-09-01", "title": "Seasonality and geography have a greater influence than the use of chlorine-based cleaning agents on the microbiota of bulk tank raw milk.", "description": "The microbiota of raw milk is affected by many factors that can control or promote the introduction of undesirable microorganisms. Chlorine-based cleaning agents have been commonly used due to their effectiveness in controlling undesirable microorganisms, but they have been associated with the formation of chlorine residues that are detrimental to product quality and may impact consumer health.
", "keywords": ["0301 basic medicine", "2. Zero hunger", "0303 health sciences", "Geography", "Microbiota", "Dairy", "Dairying", "03 medical and health sciences", "Milk", "Food Microbiology", "Animals", "Equipment Contamination", "DNA sequencing", "Metagenomics", "Seasons", "Chlorine", "Ireland", "Disinfectants"]}, "links": [{"href": "https://journals.asm.org/doi/pdf/10.1128/AEM.01081-21"}, {"href": "https://doi.org/10.1128/aem.01081-21"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Applied%20and%20Environmental%20Microbiology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1128/aem.01081-21", "name": "item", "description": "10.1128/aem.01081-21", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1128/aem.01081-21"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-10-28T00:00:00Z"}}, {"id": "10.1371/journal.pone.0199127", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-27T16:20:15Z", "type": "Journal Article", "created": "2018-06-20", "title": "Fungal communities associated with almond throughout crop development: Implications for aflatoxin biocontrol management in California", "description": "Interactions between pathogenic and nonpathogenic fungal species in the tree canopy are complex and can determine if disease will manifest in the plant and in other organisms such as honey bees. Seasonal dynamics of fungi were studied in an almond orchard in California where experimental release of the atoxigenic biopesticide Aspergillus flavus AF36 to displace toxigenic Aspergillus strains has been conducted for five years. The presence of the vegetative compatibility group (VCG) YV36, to which AF36 belongs, in the blossoms, and the honey bees that attend these blossoms, was assessed. In blossoms, A. flavus frequencies ranged from 0 to 4.5%, depending on the year of study. Frequencies of honey bees carrying A. flavus ranged from 6.5 to 10%. Only one A. flavus isolate recovered from a blossom in 2016 belonged to YV36, while members of the VCG were not detected contaminating honey bees. Exposure of pollinator honey bees to AF36 was detected to be very low. The density of several Aspergillus species was found to increase during almond hull split and throughout the final stages of maturation; this also occurred in pistachio orchards during the maturation period. Additionally, we found that AF36 effectively limited almond aflatoxin contamination in laboratory assays. This study provides knowledge and understanding of the seasonal dynamics of Aspergillus fungi and will help design aflatoxin management strategies for almond. The evidence of the low levels of VCG YV36 encountered on almond blossoms and bees during pollination and AF36's effectiveness in limiting aflatoxin contamination in almond provided additional support for the registration of AF36 with USEPA to use in almond in California.", "keywords": ["honey bees", "Crop and Pasture Production", "Crops", " Agricultural", "0301 basic medicine", "aflatoxins", "570", "General Science & Technology", "Science", "Veterinary and Food Sciences", "Crops", "Food Contamination", "Flowers", "Microbiology", "630", "California", "Trees", "03 medical and health sciences", "aspergillus flavus", "Aflatoxins", "Species Specificity", "Animals", "Nuts", "california", "Pest Control", " Biological", "Pollination", "2. Zero hunger", "Agricultural", "Q", "R", "almonds", "Feeding Behavior", "Biological Sciences", "Bees", "Biological", "Prunus dulcis", "Emerging Infectious Diseases", "Infectious Diseases", "Pistacia", "Food Microbiology", "Medicine", "Pest Control", "Research Article", "Aspergillus flavus", "Mycobiome"]}, "links": [{"href": "https://escholarship.org/content/qt84b3j5md/qt84b3j5md.pdf"}, {"href": "https://doi.org/10.1371/journal.pone.0199127"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/PLOS%20ONE", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1371/journal.pone.0199127", "name": "item", "description": "10.1371/journal.pone.0199127", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1371/journal.pone.0199127"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2018-06-20T00:00:00Z"}}, {"id": "10568/96134", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-27T16:26:05Z", "type": "Journal Article", "created": "2018-06-20", "title": "Fungal communities associated with almond throughout crop development: Implications for aflatoxin biocontrol management in California", "description": "Interactions between pathogenic and nonpathogenic fungal species in the tree canopy are complex and can determine if disease will manifest in the plant and in other organisms such as honey bees. Seasonal dynamics of fungi were studied in an almond orchard in California where experimental release of the atoxigenic biopesticide Aspergillus flavus AF36 to displace toxigenic Aspergillus strains has been conducted for five years. The presence of the vegetative compatibility group (VCG) YV36, to which AF36 belongs, in the blossoms, and the honey bees that attend these blossoms, was assessed. In blossoms, A. flavus frequencies ranged from 0 to 4.5%, depending on the year of study. Frequencies of honey bees carrying A. flavus ranged from 6.5 to 10%. Only one A. flavus isolate recovered from a blossom in 2016 belonged to YV36, while members of the VCG were not detected contaminating honey bees. Exposure of pollinator honey bees to AF36 was detected to be very low. The density of several Aspergillus species was found to increase during almond hull split and throughout the final stages of maturation; this also occurred in pistachio orchards during the maturation period. Additionally, we found that AF36 effectively limited almond aflatoxin contamination in laboratory assays. This study provides knowledge and understanding of the seasonal dynamics of Aspergillus fungi and will help design aflatoxin management strategies for almond. The evidence of the low levels of VCG YV36 encountered on almond blossoms and bees during pollination and AF36's effectiveness in limiting aflatoxin contamination in almond provided additional support for the registration of AF36 with USEPA to use in almond in California.", "keywords": ["honey bees", "Crop and Pasture Production", "Crops", " Agricultural", "0301 basic medicine", "aflatoxins", "570", "General Science & Technology", "Science", "Veterinary and Food Sciences", "Crops", "Food Contamination", "Flowers", "Microbiology", "630", "California", "Trees", "03 medical and health sciences", "aspergillus flavus", "Aflatoxins", "Species Specificity", "Animals", "Nuts", "california", "Pest Control", " Biological", "Pollination", "2. 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