{"type": "FeatureCollection", "features": [{"id": "10.1080/1040841x.2022.2132850", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-09-22T16:17:29Z", "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. Zero hunger", "0301 basic medicine", "metatranscriptomics", "Microbiota", "0206 medical engineering", "high-throughput sequencing", "Computational Biology", "High-Throughput Nucleotide Sequencing", "bioinformatics", "02 engineering and technology", "fermented foods", "03 medical and health sciences", "Metagenome", "Metagenomics", "Fermented Foods"]}, "links": [{"href": "https://www.tandfonline.com/doi/pdf/10.1080/1040841X.2022.2132850"}, {"href": "https://doi.org/10.1080/1040841x.2022.2132850"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Critical%20Reviews%20in%20Microbiology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1080/1040841x.2022.2132850", "name": "item", "description": "10.1080/1040841x.2022.2132850", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1080/1040841x.2022.2132850"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-10-26T00:00:00Z"}}, {"id": "10.1093/femsec/fiaa119", "type": "Feature", "geometry": null, "properties": {"updated": "2026-09-22T16:17:33Z", "type": "Journal Article", "created": "2020-06-14", "title": "Microbiome approaches provide the key to biologically control postharvest pathogens and storability of fruits and vegetables", "description": "ABSTRACT                <p>Microbes play an important role in plants and interact closely with their host starting from sprouting seeds, continuing during growth and after harvest. The discovery of their importance for plant and postharvest health initiated a biotechnological development of various antagonistic bacteria and fungi for disease control. Nevertheless, their application often showed inconsistent effects. Recently, high-throughput sequencing-based techniques including advanced microscopy reveal fruits and vegetables as holobionts. At harvest, all fruits and vegetables harbor a highly abundant and specific microbiota including beneficial, pathogenic and spoilage microorganisms. Especially, a high microbial diversity and resilient microbial networks were shown to be linked to fruit and vegetable health, while diseased products showed severe dysbiosis. Field and postharvest handling of fruits and vegetables was shown to affect the indigenous microbiome and therefore has a substantial impact on the storability of fruits and vegetables. Microbiome tracking can be implemented as a new tool to evaluate and assess all postharvest processes and contribute to fruit and vegetable health. Here, we summarize current research advancements in the emerging field of postharvest microbiomes and elaborate its importance. The generated knowledge provides profound insights into postharvest microbiome dynamics and sets a new basis for targeted, microbiome-driven and sustainable control strategies.</p", "keywords": ["0301 basic medicine", "2. Zero hunger", "Fruit microbiome", "0303 health sciences", "High-throughput sequencing", "Bacteria", "Microbiota", "Fungi", "Biocontrol", "15. Life on land", "Biopreservation", "Postharvest decay", "03 medical and health sciences", "Fruit", "Vegetables", "biocontrol", " biopreservation", " postharvest decay", " high-throughput sequencing", " fruit microbiome"]}, "links": [{"href": "http://academic.oup.com/femsec/article-pdf/96/7/fiaa119/33453502/fiaa119.pdf"}, {"href": "https://doi.org/10.1093/femsec/fiaa119"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/FEMS%20Microbiology%20Ecology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1093/femsec/fiaa119", "name": "item", "description": "10.1093/femsec/fiaa119", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1093/femsec/fiaa119"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-06-16T00:00:00Z"}}, {"id": "10.1146/annurev-food-052720-010751", "type": "Feature", "geometry": null, "properties": {"updated": "2026-09-22T16:18:13Z", "type": "Journal Article", "created": "2021-10-22", "title": "Next-generation food research: Use of meta-omic approaches for characterizing microbial communities along the food chain", "description": "<p> Microorganisms exist along the food chain and impact the quality and safety of foods in both positive and negative ways. Identifying and understanding the behavior of these microbial communities enable the implementation of preventative or corrective measures in public health and food industry settings. Current culture-dependent microbial analyses are time-consuming and target only specific subsets of microbes. However, the greater use of culture-independent meta-omic approaches has the potential to facilitate a thorough characterization of the microbial communities along the food chain. Indeed, these methods have shown potential in contributing to outbreak investigation, ensuring food authenticity, assessing the spread ofantimicrobial resistance, tracking microbial dynamics during fermentation and processing, and uncovering the factors along the food chain that impact food quality and safety. This review examines the community-based approaches, and particularly the application of sequencing-based meta-omics strategies, for characterizing microbial communities along the food chain. </p>", "keywords": ["0301 basic medicine", "2. Zero hunger", "0303 health sciences", "High-throughput sequencing", "Food Chain", "Food microbiome", "Microbiota", "high-throughput sequencing", "Meta-omic approaches", "food processing environment", "3. Good health", "meta-omic approaches", "03 medical and health sciences", "food-processing environment", "food microbiome; food-processing environment; high-throughput sequencing; meta-omic approaches; Fermentation; Food Industry; Food Chain; Microbiota", "food microbiome", "Fermentation", "Food Industry", "Food-processing environment"]}, "links": [{"href": "https://www.annualreviews.org/doi/pdf/10.1146/annurev-food-052720-010751"}, {"href": "https://doi.org/10.1146/annurev-food-052720-010751"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Annual%20Review%20of%20Food%20Science%20and%20Technology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1146/annurev-food-052720-010751", "name": "item", "description": "10.1146/annurev-food-052720-010751", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1146/annurev-food-052720-010751"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-03-25T00:00:00Z"}}, {"id": "10.3390/agriculture11050445", "type": "Feature", "geometry": null, "properties": {"updated": "2026-09-22T16:19:16Z", "type": "Journal Article", "created": "2021-05-17", "title": "Changes in Bacterial and Fungal Soil Communities in Long-Term Organic Cropping Systems", "description": "<p>Long-term organic farming aims to reduce synthetic fertilizer and pesticide use in order to sustainably produce and improve soil quality. To do this, there is a need for more information about the soil microbial community, which plays a key role in a sustainable agriculture. In this paper, we assessed the long-term effects of two organic and one conventional cropping systems on the soil microbial community structure using high-throughput sequencing analysis, as well as the link between these communities and the changes in the soil properties and crop yield. The results showed that the crop yield was similar among the three cropping systems. The microbial community changed according to cropping system. Organic cultivation with manure compost and compost tea (Org_C) showed a change in the bacterial community associated with an improved soil carbon and nutrient content. A linear discriminant analysis effect size showed different bacteria and fungi as key microorganisms for each of the three different cropping systems, for conventional systems (Conv), different microorganisms such as Nesterenkonia, Galbibacter, Gramella, Limnobacter, Pseudoalteromonas, Pantoe, and Sporobolomyces were associated with pesticides, while for Org_C and organic cultivation with manure (Org_M), other types of microorganisms were associated with organic amendments with different functions, which, in some cases, reduce soil borne pathogens. However, further investigations such as functional approaches or network analyses are need to better understand the mechanisms behind this behavior.</p>", "keywords": ["2. Zero hunger", "compost", "High-throughput sequencing", "Organic farming", "Agriculture (General)", "high-throughput sequencing", "Microbial community structure", "Compost", "04 agricultural and veterinary sciences", "sheep manure", "crop yield", "15. Life on land", "Gen\u00e9tica", "S1-972", "12. Responsible consumption", "agricultural_sciences_agronomy", "3107.01 Producci\u00f3n de Cultivos", "microbial community structure", "organic farming", "soil properties", "5102.01 Agricultura", "0401 agriculture", " forestry", " and fisheries", "Crop yield", "Soil properties", "Sheep manure"]}, "links": [{"href": "http://www.mdpi.com/2077-0472/11/5/445/pdf"}, {"href": "https://www.mdpi.com/2077-0472/11/5/445/pdf"}, {"href": "https://doi.org/10.3390/agriculture11050445"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Agriculture", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.3390/agriculture11050445", "name": "item", "description": "10.3390/agriculture11050445", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3390/agriculture11050445"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-04-14T00:00:00Z"}}, {"id": "10.3390/agronomy10101535", "type": "Feature", "geometry": null, "properties": {"updated": "2026-09-22T16:19:17Z", "type": "Journal Article", "created": "2020-10-09", "title": "Temporal and Cultivar-Specific Effects on Potato Root and Soil Fungal Diversity", "description": "<?xml version='1.0' encoding='UTF-8'?><article><p>The soil fungal community plays an important role in determining plant growth and health. In this study, we investigated the fungal diversity and community composition in the roots and soil of 21 potato (Solanum tuberosum L.) cultivars using high-throughput sequencing at three different time points across the growing season. In soil and roots, the fungal richness and relative abundance of pathogens and saprotrophs were mainly affected by sampling time. While sampling time affected fungal composition in soil, root fungal communities were also significantly affected by cultivar. The cultivar had the strongest effect on diversity of pathogens and abundance of particular pathogen species. Our results demonstrate changes in soil and root fungal communities of potato over the growing season, as well as highlighting the importance of potato cultivar on root fungal communities and abundance of pathogens.</p></article>", "keywords": ["0301 basic medicine", "2. Zero hunger", "0303 health sciences", "agroecosystems", "S", "high-throughput sequencing", "fungal guild", "<i>Solanum tuberosum</i>", "Agriculture", "15. Life on land", "fungal diversity", "03 medical and health sciences", "potato cultivars", "host specificity", "Solanum tuberosum"]}, "links": [{"href": "http://www.mdpi.com/2073-4395/10/10/1535/pdf"}, {"href": "https://www.mdpi.com/2073-4395/10/10/1535/pdf"}, {"href": "https://doi.org/10.3390/agronomy10101535"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Agronomy", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.3390/agronomy10101535", "name": "item", "description": "10.3390/agronomy10101535", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3390/agronomy10101535"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-10-09T00:00:00Z"}}, {"id": "10.5281/zenodo.4476976", "type": "Feature", "geometry": null, "properties": {"updated": "2026-09-22T16:21:03Z", "type": "Journal Article", "created": "2020-10-09", "title": "Temporal and Cultivar-Specific Effects on Potato Root and Soil Fungal Diversity", "description": "<?xml version='1.0' encoding='UTF-8'?><article><p>The soil fungal community plays an important role in determining plant growth and health. In this study, we investigated the fungal diversity and community composition in the roots and soil of 21 potato (Solanum tuberosum L.) cultivars using high-throughput sequencing at three different time points across the growing season. In soil and roots, the fungal richness and relative abundance of pathogens and saprotrophs were mainly affected by sampling time. While sampling time affected fungal composition in soil, root fungal communities were also significantly affected by cultivar. The cultivar had the strongest effect on diversity of pathogens and abundance of particular pathogen species. Our results demonstrate changes in soil and root fungal communities of potato over the growing season, as well as highlighting the importance of potato cultivar on root fungal communities and abundance of pathogens.</p></article>", "keywords": ["2. Zero hunger", "0301 basic medicine", "0303 health sciences", "agroecosystems", "S", "high-throughput sequencing", "fungal guild", "<i>Solanum tuberosum</i>", "Agriculture", "15. Life on land", "fungal diversity", "03 medical and health sciences", "potato cultivars", "host specificity", "Solanum tuberosum"]}, "links": [{"href": "http://www.mdpi.com/2073-4395/10/10/1535/pdf"}, {"href": "https://www.mdpi.com/2073-4395/10/10/1535/pdf"}, {"href": "https://doi.org/10.5281/zenodo.4476976"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Agronomy", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.5281/zenodo.4476976", "name": "item", "description": "10.5281/zenodo.4476976", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.5281/zenodo.4476976"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-10-09T00:00:00Z"}}, {"id": "2263/80147", "type": "Feature", "geometry": null, "properties": {"updated": "2026-09-22T16:22:41Z", "type": "Journal Article", "created": "2020-06-14", "title": "Microbiome approaches provide the key to biologically control postharvest pathogens and storability of fruits and vegetables", "description": "ABSTRACT                <p>Microbes play an important role in plants and interact closely with their host starting from sprouting seeds, continuing during growth and after harvest. The discovery of their importance for plant and postharvest health initiated a biotechnological development of various antagonistic bacteria and fungi for disease control. Nevertheless, their application often showed inconsistent effects. Recently, high-throughput sequencing-based techniques including advanced microscopy reveal fruits and vegetables as holobionts. At harvest, all fruits and vegetables harbor a highly abundant and specific microbiota including beneficial, pathogenic and spoilage microorganisms. Especially, a high microbial diversity and resilient microbial networks were shown to be linked to fruit and vegetable health, while diseased products showed severe dysbiosis. Field and postharvest handling of fruits and vegetables was shown to affect the indigenous microbiome and therefore has a substantial impact on the storability of fruits and vegetables. Microbiome tracking can be implemented as a new tool to evaluate and assess all postharvest processes and contribute to fruit and vegetable health. Here, we summarize current research advancements in the emerging field of postharvest microbiomes and elaborate its importance. The generated knowledge provides profound insights into postharvest microbiome dynamics and sets a new basis for targeted, microbiome-driven and sustainable control strategies.</p", "keywords": ["0301 basic medicine", "2. Zero hunger", "Fruit microbiome", "0303 health sciences", "High-throughput sequencing", "Bacteria", "Microbiota", "Fungi", "Biocontrol", "15. Life on land", "Biopreservation", "Postharvest decay", "03 medical and health sciences", "Fruit", "Vegetables"]}, "links": [{"href": "http://academic.oup.com/femsec/article-pdf/96/7/fiaa119/33453502/fiaa119.pdf"}, {"href": "https://doi.org/2263/80147"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/FEMS%20Microbiology%20Ecology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "2263/80147", "name": "item", "description": "2263/80147", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/2263/80147"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-06-16T00:00:00Z"}}, {"id": "3091904565", "type": "Feature", "geometry": null, "properties": {"updated": "2026-09-22T16:23:01Z", "type": "Journal Article", "created": "2020-10-09", "title": "Temporal and Cultivar-Specific Effects on Potato Root and Soil Fungal Diversity", "description": "<?xml version='1.0' encoding='UTF-8'?><article><p>The soil fungal community plays an important role in determining plant growth and health. In this study, we investigated the fungal diversity and community composition in the roots and soil of 21 potato (Solanum tuberosum L.) cultivars using high-throughput sequencing at three different time points across the growing season. In soil and roots, the fungal richness and relative abundance of pathogens and saprotrophs were mainly affected by sampling time. While sampling time affected fungal composition in soil, root fungal communities were also significantly affected by cultivar. The cultivar had the strongest effect on diversity of pathogens and abundance of particular pathogen species. Our results demonstrate changes in soil and root fungal communities of potato over the growing season, as well as highlighting the importance of potato cultivar on root fungal communities and abundance of pathogens.</p></article>", "keywords": ["2. Zero hunger", "0301 basic medicine", "0303 health sciences", "agroecosystems", "S", "high-throughput sequencing", "fungal guild", "<i>Solanum tuberosum</i>", "Agriculture", "15. Life on land", "fungal diversity", "03 medical and health sciences", "potato cultivars", "host specificity", "Solanum tuberosum"]}, "links": [{"href": "http://www.mdpi.com/2073-4395/10/10/1535/pdf"}, {"href": "https://www.mdpi.com/2073-4395/10/10/1535/pdf"}, {"href": "https://doi.org/3091904565"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Agronomy", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "3091904565", "name": "item", "description": "3091904565", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/3091904565"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-10-09T00:00:00Z"}}], "links": [{"rel": "self", "type": "application/geo+json", "title": "This document as GeoJSON", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items?keywords=high-throughput+sequencing&f=json", "hreflang": "en-US"}, {"rel": "alternate", "type": "text/html", "title": "This document as HTML", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items?keywords=high-throughput+sequencing&f=html", "hreflang": "en-US"}, {"rel": "collection", "type": "application/json", "title": "Collection URL", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main", "hreflang": "en-US"}, {"type": "application/geo+json", "rel": "first", "title": "items (first)", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items?keywords=high-throughput+sequencing&", "hreflang": "en-US"}, {"rel": "last", "type": "application/geo+json", "title": "items (last)", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items?keywords=high-throughput+sequencing&offset=8", "hreflang": "en-US"}], "numberMatched": 8, "numberReturned": 8, "distributedFeatures": [], "timeStamp": "2026-09-23T02:46:46.945185Z"}