{"type": "FeatureCollection", "features": [{"id": "10.1007/s10123-021-00215-8", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:14:50Z", "type": "Journal Article", "created": "2021-10-23", "title": "Novel methods of microbiome analysis in the food industry", "description": "The study of the food microbiome has gained considerable interest in recent years, mainly due to the wide range of applications that can be derived from the analysis of metagenomes. Among these applications, it is worth mentioning the possibility of using metagenomic analyses to determine food authenticity, to assess the microbiological safety of foods thanks to the detection and tracking of pathogens, antibiotic resistance genes and other undesirable traits, as well to identify the microorganisms responsible for food processing defects. Metataxonomics and metagenomics are currently the gold standard methodologies to explore the full potential of metagenomes in the food industry. However, there are still a number of challenges that must be solved in order to implement these methods routinely in food chain monitoring, and for the regulatory agencies to take them into account in their opinions. These challenges include the difficulties of analysing foods and food-related environments with a low microbial load, the lack of validated bioinformatics pipelines adapted to food microbiomes and the difficulty of assessing the viability of the detected microorganisms. This review summarizes the methods of microbiome analysis that have been used, so far, in foods and food-related environments, with a specific focus on those involving Next-Generation Sequencing technologies.", "keywords": ["2. Zero hunger", "0301 basic medicine", "Food metagenome", "0303 health sciences", "Food microbiome", "3309 Tecnolog\u00eda de Los Alimentos", "Tecnolog\u00eda de los alimentos", "Metataxonomics", "Microbiota", "3309.90 Microbiolog\u00eda de Alimentos", "Drug Resistance", " Microbial", "Resistome", "03 medical and health sciences", "Food Industry", "Metagenome", "Metagenomics"]}, "links": [{"href": "https://link.springer.com/content/pdf/10.1007/s10123-021-00215-8.pdf"}, {"href": "https://doi.org/10.1007/s10123-021-00215-8"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/International%20Microbiology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007/s10123-021-00215-8", "name": "item", "description": "10.1007/s10123-021-00215-8", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s10123-021-00215-8"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-10-23T00:00:00Z"}}, {"id": "10.1016/j.cub.2020.09.063", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:16:02Z", "type": "Journal Article", "created": "2020-10-15", "title": "Newly explored\u00a0Faecalibacterium\u00a0diversity is connected to age, lifestyle, geography, and disease.", "description": "Faecalibacterium is prevalent in the human gut and a promising microbe for the development of next-generation probiotics (NGPs) or biotherapeutics. Analyzing reference Faecalibacterium genomes and almost 3,000 Faecalibacterium-like metagenome-assembled genomes (MAGs) reconstructed from 7,907 human and 203 non-human primate gut metagenomes, we identified the presence of 22 different Faecalibacterium-like species-level genome bins (SGBs), some further divided in different strains according to the subject geographical origin. Twelve SGBs are globally spread in the human gut and show different genomic potential in the utilization of complex polysaccharides, suggesting that higher SGB diversity may be related with increased utilization of plant-based foods. Moreover, up to 11 different species may co-occur in the same subject, with lower diversity in Western populations, as well as intestinal inflammatory states and obesity. The newly explored Faecalibacterium diversity will be able to support the choice of strains suitable as NGPs, guided by the consideration of the differences existing in their functional potential.", "keywords": ["Adult", "0301 basic medicine", "pangenome", "Adolescent", "gut microbiome", "Datasets as Topic", "General Biochemistry", " Genetics and Molecular Biology", "Innovation action", "Feces", "03 medical and health sciences", "Animals", "Humans", "biotherapeutics", "European Commission", "Child", "Life Style", "Faecalibacterium", "Aged", "Aurora Universities Network", "Horizon 2020", "0303 health sciences", "EC", "Geography", "Faecalibacterium prausnitzii", "H2020", "Age Factors", "Infant", "Middle Aged", "Gastrointestinal Microbiome", "Faecalibacterium prausnitzii", " gut microbiome", " strain diversity", " pangenome", " novel probiotics", " biotherapeutics", "Child", " Preschool", "novel probiotics", "Dysbiosis", "Macaca", "Metagenome", "strain diversity", "Metagenomics", "General Agricultural and Biological Sciences"]}, "links": [{"href": "https://www.iris.unina.it/bitstream/11588/819607/1/PIIS0960982220314330.pdf"}, {"href": "https://doi.org/10.1016/j.cub.2020.09.063"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Current%20Biology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.cub.2020.09.063", "name": "item", "description": "10.1016/j.cub.2020.09.063", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.cub.2020.09.063"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-12-01T00:00:00Z"}}, {"id": "10.1007/s11274-011-0809-0", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:15:17Z", "type": "Journal Article", "created": "2011-06-15", "title": "Soil Bacterial Community Composition And Diversity Respond To Cultivation In Karst Ecosystems", "description": "Soil microorganisms play vital roles in recovering and maintaining the health of ecosystems, particularly in fragile Karst ecosystems that are easily degraded after cultivation. We investigated the composition and diversity of soil bacterial communities, based on RFLP and 16S rDNA sequencing, in a cropland, a naturally revegetated land with former cultivation disturbance and a primeval forest in the subtropical Karst of southwest China. Our results illustrated that Proteobacteria accounted for 44.8% of the 600 tested clones, making it the most dominant phylum observed. This phylum was followed by Acidobacteria and Planctomycetes for the three Karst soils analyzed. Compared with the primeval forest soil, the proportions of Proteobacteria were decreased by 30.2 and 37.9%, while Acidobacteria increased by 93.9 and 87.9%, and the Shannon-Wiener diversity indices and the physicochemical parameters declined in the cropland and the revegetated land, respectively. Among the three soils, the proportion of dominant bacterial phyla and the diversity indices in the revegetated land were similar to the cropland, implying the bacterial community in the cropland was relatively stable, and the after-effects of cultivation were difficult to eliminate. However, similar distributions of the four Proteobacteria subphyla were observed between the revegetated land and the primeval forest soil. Furthermore, the proportion of Rhizobiales belonging to \u03b1-Proteobacteria was sharply decreased with cultivation compared to the primeval forest soil, while a small cluster of Rhizobiales recurred with vegetation recovery. These results indicated that although the subphyla of the dominant bacterial phylum had some positive responses to 20\u00a0years of vegetation recovery, it is a slow process. Our results suggest that priority should be given to conserve the primeval forest and inoculation of functional microorganisms on the basis of vegetation recovery may be more effective for the restoration of Karst ecosystems after cultivation.", "keywords": ["2. Zero hunger", "0301 basic medicine", "China", "0303 health sciences", "Bacteria", "Agriculture", "Biodiversity", "15. Life on land", "Trees", "RNA", " Bacterial", "Soil", "03 medical and health sciences", "RNA", " Ribosomal", " 16S", "Metagenome", "Ecosystem", "Phylogeny", "Polymorphism", " Restriction Fragment Length", "Soil Microbiology"], "contacts": [{"organization": "Xiangbi Chen, Ya-wei Wei, Wenxue Wei, Jinshui Wu, Yirong Su, Xunyang He,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.1007/s11274-011-0809-0"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/World%20Journal%20of%20Microbiology%20and%20Biotechnology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007/s11274-011-0809-0", "name": "item", "description": "10.1007/s11274-011-0809-0", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s11274-011-0809-0"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2011-06-15T00:00:00Z"}}, {"id": "10.1007/s13225-024-00533-y", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:15:24Z", "type": "Journal Article", "created": "2024-02-26", "title": "Class-wide genomic tendency throughout specific extremes in black fungi", "description": "Open AccessPeer reviewed", "keywords": ["570", "Black Fungi", "Plant Biology", "Mycology & Parasitology", "Evolutionary biology", "Microbiology", "Genetics", "Black fungi \u00b7 Stress resistance \u00b7 Comparative genomics \u00b7 Extreme environments", "14. Life underwater", "Plant biology", "2. Zero hunger", "Evolutionary Biology", "Black fungi", "Comparative genomics", "Human Genome", "500", "Extreme environments", "Biological Sciences", "15. Life on land", "3. Good health", "Health Disparities", "13. Climate action", "8. Economic growth", "Stress resistance", "Settore BIO/19 - MICROBIOLOGIA GENERALE", "Biotechnology"]}, "links": [{"href": "https://iris.unitn.it/bitstream/11572/450837/1/FUDI_Coleine%20et%20al%20v2..pdf"}, {"href": "https://iris.unitn.it/bitstream/11572/450837/3/s13225-024-00533-y.pdf"}, {"href": "https://escholarship.org/content/qt86f967px/qt86f967px.pdf"}, {"href": "https://doi.org/10.1007/s13225-024-00533-y"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Fungal%20Diversity", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007/s13225-024-00533-y", "name": "item", "description": "10.1007/s13225-024-00533-y", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s13225-024-00533-y"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2024-02-26T00:00:00Z"}}, {"id": "10.1016/j.ijfoodmicro.2021.109043", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:16:37Z", "type": "Journal Article", "created": "2021-01-08", "title": "Unraveling the emergence and population diversity of Listeria monocytogenes in a newly built meat facility through whole genome sequencing", "description": "The food processing environments of a newly opened meat processing facility were sampled in ten visits carried out during its first 1.5\u00a0years of activity and analyzed for the presence of Listeria monocytogenes. A total of 18 L. monocytogenes isolates were obtained from 229 samples, and their genomes were sequenced to perform comparative genomic analyses. An increase in the frequency of isolation of L. monocytogenes and in the diversity of sequence types (STs) detected was observed along time. Although the strains isolated belonged to six different STs (ST8, ST9, ST14, ST37, ST121 and ST155), ST9 was the most abundant (8 out of 18 strains). Low (0 and 2) single nucleotide polymorphism (SNP) distances were found between two pairs of ST9 strains isolated in both cases 3\u00a0months apart from the same processing room (Lm-1267 and Lm-1705, with a 2 SNPs distance in the core genome; Lm-1265 and Lm-1706, with a 0 SNPs distance), which suggests that these strains may be persistent L. monocytogenes strains in the food processing environment. Most strains showed an in silico attenuated virulence potential either through the truncation of InlA (in 67% of the isolates) or the absence of other virulence factors involved in cell adhesion or invasion. Twelve of the eighteen L. monocytogenes isolates contained a plasmid, which ranged in size from 4 to 87 Kb and harbored stress survival, in addition to heavy metals and biocides resistance determinants. Identical or highly similar plasmids were identified for various sets of L. monocytogenes ST9 isolates, which suggests the clonal expansion and persistence of plasmid-containing ST9 strains in the processing environments of the meat facility. Finally, the analysis of the L. monocytogenes genomes available in the NCBI database, and their associated metadata, evidenced that strains from ST9 are more frequently reported in Europe, linked to foods, particularly to meat and pork products, and less represented among clinical isolates than other L. monocytogenes STs. It also showed that the ST9 strains here isolated were more closely related to the European isolates, which clustered together and separated from ST9 North American isolates.", "keywords": ["0301 basic medicine", "Meat", "Food Handling", "Swine", "Virulence Factors", "Tecnolog\u00eda de los alimentos", "Food processing environment", "Persistence", "03 medical and health sciences", "Manufacturing and Industrial Facilities", "Floors and Floorcoverings", "Animals", "2. Zero hunger", "0303 health sciences", "Virulence", "Whole Genome Sequencing", "Genetic Variation", "Gen\u00e9tica", "Listeria monocytogenes", "Europe", "Genes", " Bacterial", "Whole genome sequencing", "Food Microbiology", "Equipment Contamination", "Disinfectants", "Plasmids"]}, "links": [{"href": "https://doi.org/10.1016/j.ijfoodmicro.2021.109043"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/International%20Journal%20of%20Food%20Microbiology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.ijfoodmicro.2021.109043", "name": "item", "description": "10.1016/j.ijfoodmicro.2021.109043", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.ijfoodmicro.2021.109043"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-02-01T00:00:00Z"}}, {"id": "10.1016/j.scitotenv.2024.170290", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:17:00Z", "type": "Journal Article", "created": "2024-01-19", "title": "Metagenomics untangles potential adaptations of Antarctic endolithic bacteria at the fringe of habitability", "description": "Survival and growth strategies of Antarctic endolithic microbes residing in Earth's driest and coldest desert remain virtually unknown. From 109 endolithic microbiomes, 4539 metagenome-assembled genomes were generated, 49.3\u00a0% of which were novel candidate bacterial species. We present evidence that trace gas oxidation and atmospheric chemosynthesis may be the prevalent strategies supporting metabolic activity and persistence of these ecosystems at the fringe of life and the limits of habitability.", "keywords": ["570", "Bacteria", "Microbiota", "Habitability", "500", "Antarctic Regions", "Astronomical Sciences", "15. Life on land", "Extremophiles", "13. Climate action", "Physical Sciences", "Antarctica", "Metagenome", "Metagenomics", "14. Life underwater", "Adaptation", "MAGs", "Settore BIO/19 - MICROBIOLOGIA GENERALE", "Environmental Sciences"]}, "links": [{"href": "https://openpub.fmach.it/bitstream/10449/83880/5/2024%20STE%20Albanese.pdf"}, {"href": "https://doi.org/10.1016/j.scitotenv.2024.170290"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Science%20of%20The%20Total%20Environment", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.scitotenv.2024.170290", "name": "item", "description": "10.1016/j.scitotenv.2024.170290", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.scitotenv.2024.170290"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2024-03-01T00:00:00Z"}}, {"id": "10.1016/j.jhazmat.2024.134885", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:16:45Z", "type": "Journal Article", "created": "2024-06-12", "title": "Anthropogenic pollution may enhance natural transformation in water, favouring the spread of antibiotic resistance genes", "description": "Aquatic ecosystems are crucial in the antimicrobial resistance cycle. While intracellular DNA has been extensively studied to understand human activity's impact on antimicrobial resistance gene (ARG) dissemination, extracellular DNA is frequently overlooked. This study examines the effect of anthropogenic water pollution on microbial community diversity, the resistome, and ARG dissemination. We analyzed intracellular and extracellular DNA from wastewater treatment plant effluents and lake surface water by shotgun sequencing. We also conducted experiments to evaluate anthropogenic pollution's effect on transforming extracellular DNA (using Gfp-plasmids carrying ARGs) within a natural microbial community. Chemical analysis showed treated wastewater had higher anthropogenic pollution-related parameters than lake water. The richness of microbial community, antimicrobial resistome, and high-risk ARGs was greater in treated wastewaters than in lake waters both for intracellular and extracellular DNA. Except for the high-risk ARGs, richness was significantly higher in intracellular than in extracellular DNA. Several ARGs were associated with mobile genetic elements and located on plasmids. Furthermore, Gfp-plasmid transformation within a natural microbial community was enhanced by anthropogenic pollution levels. Our findings underscore anthropogenic pollution's pivotal role in shaping microbial communities and their antimicrobial resistome. Additionally, it may facilitate ARG dissemination through extracellular DNA plasmid uptake.", "keywords": ["Bacteria", "Antibiotic resistance", "Microbiota", "Water Pollution", "Metagenome assembled genomes", "Drug Resistance", " Microbial", "Horizontal gene transfer", "Wastewater", "extracellular DNA; antibiotic resistance; metagenome assembled genomes; transformation; horizontal gene transfer", "Transformation", "Anti-Bacterial Agents", "Lakes", "Extracellular DNA", "Genes", " Bacterial", "Drug Resistance", " Bacterial", "Water Microbiology", "Plasmids"]}, "links": [{"href": "https://air.unimi.it/bitstream/2434/1115155/2/Sivalingam%20et%20al%202024.pdf"}, {"href": "https://doi.org/10.1016/j.jhazmat.2024.134885"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Journal%20of%20Hazardous%20Materials", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.jhazmat.2024.134885", "name": "item", "description": "10.1016/j.jhazmat.2024.134885", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.jhazmat.2024.134885"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2024-08-01T00:00:00Z"}}, {"id": "10.1016/j.mec.2020.e00126", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:16:48Z", "type": "Journal Article", "created": "2020-03-19", "title": "Synthetic control of plasmid replication enables target- and self-curing of vectors and expedites genome engineering of Pseudomonas putida", "description": "Genome engineering of non-conventional microorganisms calls for the development of dedicated synthetic biology tools. Pseudomonas putida is a Gram-negative, non-pathogenic soil bacterium widely used for metabolic engineering owing to its versatile metabolism and high levels of tolerance to different types of stress. Genome editing of P. putida largely relies on homologous recombination events, assisted by helper plasmid-based expression of genes encoding DNA modifying enzymes. Plasmid curing from selected isolates is the most tedious and time-consuming step of this procedure, and implementing commonly used methods to this end in P. putida (e.g. temperature-sensitive replicons) is often impractical. To tackle this issue, we have developed a toolbox for both target- and self-curing of plasmid DNA in Pseudomonas species. Our method enables plasmid-curing in a simple cultivation step by combining in vivo digestion of vectors by the I-SceI homing nuclease with synthetic control of plasmid replication, triggered by the addition of a cheap chemical inducer (3-methylbenzoate) to the medium. The system displays an efficiency of vector curing >90% and the screening of plasmid-free clones is greatly facilitated by the use of fluorescent markers that can be selected according to the application intended. Furthermore, quick genome engineering of P. putida using self-curing plasmids is demonstrated through genome reduction of the platform strain EM42 by eliminating all genes encoding \u03b2-lactamases, the catabolic ben gene cluster, and the pyoverdine synthesis machinery. Physiological characterization of the resulting streamlined strain, P. putida SEM10, revealed advantageous features that could be exploited for metabolic engineering.", "keywords": ["Genome engineering", "0301 basic medicine", "0303 health sciences", "Pseudomonas putida", "QH301-705.5", "Plasmid curing", "3. Good health", "03 medical and health sciences", "Special issue on Non-conventional microbes edited by Ian Wheeldon and Aindrila Mukhopadhyay", "Biology (General)", "Metabolic engineering", "Synthetic biology", "TP248.13-248.65", "Biotechnology"]}, "links": [{"href": "https://doi.org/10.1016/j.mec.2020.e00126"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Metabolic%20Engineering%20Communications", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.mec.2020.e00126", "name": "item", "description": "10.1016/j.mec.2020.e00126", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.mec.2020.e00126"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-06-01T00:00:00Z"}}, {"id": "10.1016/j.xgen.2024.100639", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:17:31Z", "type": "Journal Article", "created": "2024-08-30", "title": "ONCOLINER: A new solution for monitoring, improving, and harmonizing somatic variant calling across genomic oncology centers", "description": "The characterization of somatic genomic variation associated with the biology of tumors is fundamental for cancer research and personalized medicine, as it guides the reliability and impact of cancer studies and genomic-based decisions in clinical oncology. However, the quality and scope of tumor genome analysis across cancer research centers and hospitals are currently highly heterogeneous, limiting the consistency of tumor diagnoses across hospitals and the possibilities of data sharing and data integration across studies. With the aim of providing users with actionable and personalized recommendations for the overall enhancement and harmonization of somatic variant identification across research and clinical environments, we have developed ONCOLINER. Using specifically designed mosaic and tumorized genomes for the analysis of recall and precision across somatic SNVs, insertions or deletions (indels), and structural variants (SVs), we demonstrate that ONCOLINER is capable of improving and harmonizing genome analysis across three state-of-the-art variant discovery pipelines in genomic oncology.", "keywords": ["330", "Bioinformatics", "Genome", " Human", "610", "Genomics", "Medical Oncology", "Somatic variant calling", "Polymorphism", " Single Nucleotide", "Article", "Benchmarking", "Oncology", "INDEL Mutation", "\u00c0rees tem\u00e0tiques de la UPC::Inform\u00e0tica::Aplicacions de la inform\u00e0tica::Bioinform\u00e0tica", "Neoplasms", "Cancer genomics", "Humans", "Benchmarking data", "Precision Medicine", "Software"]}, "links": [{"href": "https://doi.org/10.1016/j.xgen.2024.100639"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Cell%20Genomics", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.xgen.2024.100639", "name": "item", "description": "10.1016/j.xgen.2024.100639", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.xgen.2024.100639"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2024-09-01T00:00:00Z"}}, {"id": "10.1128/aem.03393-12", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:19:30Z", "type": "Journal Article", "created": "2012-12-16", "title": "Functional Gene Differences In Soil Microbial Communities From Conventional, Low-Input, And Organic Farmlands", "description": "ABSTRACT

Various agriculture management practices may have distinct influences on soil microbial communities and their ecological functions. In this study, we utilized GeoChip, a high-throughput microarray-based technique containing approximately 28,000 probes for genes involved in nitrogen (N)/carbon (C)/sulfur (S)/phosphorus (P) cycles and other processes, to evaluate the potential functions of soil microbial communities under conventional (CT), low-input (LI), and organic (ORG) management systems at an agricultural research site in Michigan. Compared to CT, a high diversity of functional genes was observed in LI. The functional gene diversity in ORG did not differ significantly from that of either CT or LI. Abundances of genes encoding enzymes involved in C/N/P/S cycles were generally lower in CT than in LI or ORG, with the exceptions of genes in pathways for lignin degradation, methane generation/oxidation, and assimilatory N reduction, which all remained unchanged. Canonical correlation analysis showed that selected soil (bulk density, pH, cation exchange capacity, total C, C/N ratio, NO 3 \uffe2\uff88\uff92 , NH 4 + , available phosphorus content, and available potassium content) and crop (seed and whole biomass) variables could explain 69.5% of the variation of soil microbial community composition. Also, significant correlations were observed between NO 3 \uffe2\uff88\uff92 concentration and denitrification genes, NH 4 + concentration and ammonification genes, and N 2 O flux and denitrification genes, indicating a close linkage between soil N availability or process and associated functional genes.

", "keywords": ["2. Zero hunger", "Michigan", "Nitrogen", "Agriculture", "Phosphorus", "04 agricultural and veterinary sciences", "15. Life on land", "Microarray Analysis", "Biota", "Carbon", "Soil", "Genes", " Bacterial", "Metagenome", "0401 agriculture", " forestry", " and fisheries", "Metabolic Networks and Pathways", "Soil Microbiology", "Sulfur"]}, "links": [{"href": "https://doi.org/10.1128/aem.03393-12"}, {"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.03393-12", "name": "item", "description": "10.1128/aem.03393-12", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1128/aem.03393-12"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2013-02-15T00:00:00Z"}}, {"id": "10.1038/nature02053", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:17:54Z", "type": "Journal Article", "created": "2003-10-22", "title": "Genome-Scale Approaches To Resolving Incongruence In Molecular Phylogenies", "description": "One of the most pervasive challenges in molecular phylogenetics is the incongruence between phylogenies obtained using different data sets, such as individual genes. To systematically investigate the degree of incongruence, and potential methods for resolving it, we screened the genome sequences of eight yeast species and selected 106 widely distributed orthologous genes for phylogenetic analyses, singly and by concatenation. Our results suggest that data sets consisting of single or a small number of concatenated genes have a significant probability of supporting conflicting topologies. By contrast, analyses of the entire data set of concatenated genes yielded a single, fully resolved species tree with maximum support. Comparable results were obtained with a concatenation of a minimum of 20 genes; substantially more genes than commonly used but a small fraction of any genome. These results have important implications for resolving branches of the tree of life.", "keywords": ["0301 basic medicine", "Saccharomyces", "0303 health sciences", "03 medical and health sciences", "Genes", " Fungal", "Regression Analysis", "Reproducibility of Results", "Genomics", "Genome", " Fungal", "Phylogeny"]}, "links": [{"href": "https://doi.org/10.1038/nature02053"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Nature", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1038/nature02053", "name": "item", "description": "10.1038/nature02053", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1038/nature02053"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2003-10-01T00:00:00Z"}}, {"id": "10.1038/s41467-019-14197-9", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:17:57Z", "type": "Journal Article", "created": "2020-01-24", "title": "High-quality genome sequence of white lupin provides insight into soil exploration and seed quality", "description": "Abstract

White lupin (Lupinus albus L.) is an annual crop cultivated for its protein-rich seeds. It is adapted to poor soils due to the production of cluster roots, which are made of dozens of determinate lateral roots that drastically improve soil exploration and nutrient acquisition (mostly phosphate). Using long-read sequencing technologies, we provide a high-quality genome sequence of a cultivated accession of white lupin (2n\uffe2\uff80\uff89=\uffe2\uff80\uff8950, 451\uffe2\uff80\uff89Mb), as well as de novo assemblies of a landrace and a wild relative. We describe a modern accession displaying increased soil exploration capacity through early establishment of lateral and cluster roots. We also show how seed quality may have been impacted by domestication in term of protein profiles and alkaloid content. The availability of a high-quality genome assembly together with companion genomic and transcriptomic resources will enable the development of modern breeding strategies to increase and stabilize white lupin yield.

", "keywords": ["Repetitive Sequences", " Nucleic Acid/genetics", "0301 basic medicine", "[SDV]Life Sciences [q-bio]", "Plant Roots/genetics", "Gene Dosage", "Plant Science", "Crop", "Alkaloids/chemistry", "Plant Roots", "Gene", "Repetitive Sequences", "630", "Agricultural and Biological Sciences", "Domestication", "Soil", "Models", "Symbiotic Nitrogen Fixation in Legumes", "Gene Duplication", "[SDV.BV] Life Sciences [q-bio]/Vegetal Biology", "http://aims.fao.org/aos/agrovoc/c_3224", "Plant Proteins/metabolism", "Plant Proteins", "2. Zero hunger", "0303 health sciences", "Genome", "Q", "http://aims.fao.org/aos/agrovoc/c_27583", "Life Sciences", "Transcriptome/genetics", "http://aims.fao.org/aos/agrovoc/c_92382", "Polymorphism", " Single Nucleotide/genetics", "Lupinus", "[SDV] Life Sciences [q-bio]", "Protein Crop", "Seeds", "http://aims.fao.org/aos/agrovoc/c_5956", "White (mutation)", "Single Nucleotide/genetics", "Sequence Analysis", "Genome", " Plant", "expression des g\u00e8nes", "http://aims.fao.org/aos/agrovoc/c_4464", "Synteny/genetics", "Evolution", "Lupin Seeds", "Science", "Centromere", "Lupinus/genetics", "Polymorphism", " Single Nucleotide", "Article", "g\u00e9nomique", "Evolution", " Molecular", "Evolution and Nutritional Properties of Lupin Seeds", "physiologie v\u00e9g\u00e9tale", "03 medical and health sciences", "Alkaloids", "Genetic", "Nucleic Acid/genetics", "Seeds/physiology", "Centromere/genetics", "Genetics", "[SDV.BV]Life Sciences [q-bio]/Vegetal Biology", "Polymorphism", "Biology", "Ecology", " Evolution", " Behavior and Systematics", "Repetitive Sequences", " Nucleic Acid", "Sequence assembly", "http://aims.fao.org/aos/agrovoc/c_25189", "Ecotype", "Models", " Genetic", "g\u00e9nome", "Botany", "Molecular", "Genetic Variation", "Molecular Sequence Annotation", "Plant", "DNA", "Sequence Analysis", " DNA", "s\u00e9quence nucl\u00e9otidique", "15. Life on land", "http://aims.fao.org/aos/agrovoc/c_27527", "Agronomy", "Plant Leaves", "Evolution and Ecology of Endophyte-Grass Symbiosis", "Lupinus albus", "FOS: Biological sciences", "Genomic Structural Variation", "Plant Leaves/metabolism", "Gene expression", "Transcriptome", "am\u00e9lioration des plantes"]}, "links": [{"href": "https://www.nature.com/articles/s41467-019-14197-9.pdf"}, {"href": "https://doi.org/10.1038/s41467-019-14197-9"}, {"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/s41467-019-14197-9", "name": "item", "description": "10.1038/s41467-019-14197-9", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1038/s41467-019-14197-9"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-01-24T00:00:00Z"}}, {"id": "10.1038/s41467-020-16438-8", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:17:57Z", "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

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": "10.1038/s41586-023-05791-5", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:18:00Z", "type": "Journal Article", "created": "2023-03-08", "title": "The giant diploid faba genome unlocks variation in a global protein crop", "description": "Abstract

Increasing the proportion of locally produced plant protein in currently meat-rich diets could substantially reduce greenhouse gas emissions and loss of biodiversity1. However, plant protein production is hampered by the lack of a cool-season legume equivalent to soybean in agronomic value2. Faba bean (Vicia fabaL.) has a high yield potential and is well suited for cultivation in temperate regions, but genomic resources are scarce. Here, we report a high-quality chromosome-scale assembly of the faba bean genome and show that it has expanded to a massive 13\uffe2\uff80\uff89Gb in size through an imbalance between the rates of amplification and elimination of retrotransposons and satellite repeats. Genes and recombination events are evenly dispersed across chromosomes and the gene space is remarkably compact considering the genome size, although with substantial copy number variation driven by tandem duplication. Demonstrating practical application of the genome sequence, we develop a targeted genotyping assay and use high-resolution genome-wide association analysis to dissect the genetic basis of seed size and hilum colour. The resources presented constitute a genomics-based breeding platform for faba bean, enabling breeders and geneticists to accelerate the\uffc2\uffa0improvement of sustainable protein production across the\uffc2\uffa0Mediterranean, subtropical and northern temperate agroecological zones.The increasing emergence of multi-resistant bacteria in healthcare settings, in the community and in the environment represents a major health threat worldwide. In 2016, we started a pilot project to investigate antimicrobial resistance in surface water. Bacteria were enriched, cultivated on selective chromogenic media and species identification was carried out by MALDI-TOF analysis. From a river in southern Austria a methicillin resistant Staphylococcus aureus (MRSA) was isolated. Whole genome sequence analysis identified the isolate as ST8, spa type t008, SCCmecIV, PVL and ACME positive, which are main features of CA-MRSA USA300. Whole genome based cgMLST of the water isolate and comparison to 18 clinical MRSA USA300 isolates from the Austrian national reference laboratory for coagulase positive staphylococci originating from 2004, 2005 and 2016 and sequences of 146 USA300 isolates arbitrarily retrieved from the Sequence Read Archive revealed a close relatedness to a clinical isolate from Austria. The presence of a CA-MRSA USA300 isolate in an aquatic environment might pose a public health risk by serving as a potential source of infection or a source for emergence of new pathogenic MRSA clones.

", "keywords": ["Methicillin-Resistant Staphylococcus aureus", "0301 basic medicine", "METHICILLIN-RESISTANT", "GENES", "TRANSMISSION", "Article", "Applied microbiology", "EMERGENCE", "03 medical and health sciences", "106005 Bioinformatik", "SDG 3 - Good Health and Well-being", "Rivers", "Sequence Homology", " Nucleic Acid", "Infectious-disease epidemiology", "ENVIRONMENT", "0303 health sciences", "ANTIMICROBIAL RESISTANCE", "RESISTANT STAPHYLOCOCCUS-AUREUS", "ANTIBIOTIC-RESISTANCE", "EVOLUTION", "3. Good health", "Community-Acquired Infections", "SDG 3 \u2013 Gesundheit und Wohlergehen", "Austria", "VIRULENCE", "Bacterial infection", "106005 Bioinformatics", "Genome", " Bacterial"]}, "links": [{"href": "https://www.nature.com/articles/s41598-018-27781-8.pdf"}, {"href": "https://doi.org/10.1038/s41598-018-27781-8"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Scientific%20Reports", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1038/s41598-018-27781-8", "name": "item", "description": "10.1038/s41598-018-27781-8", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1038/s41598-018-27781-8"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2018-06-21T00:00:00Z"}}, {"id": "10.1038/s41598-020-58025-3", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:18:01Z", "type": "Journal Article", "created": "2020-01-28", "title": "Building de novo reference genome assemblies of complex eukaryotic microorganisms from single nuclei", "description": "Abstract

The advent of novel sequencing techniques has unraveled a tremendous diversity on Earth. Genomic data allow us to understand ecology and function of organisms that we would not otherwise know existed. However, major methodological challenges remain, in particular for multicellular organisms with large genomes. Arbuscular mycorrhizal (AM) fungi are important plant symbionts with cryptic and complex multicellular life cycles, thus representing a suitable model system for method development. Here, we report a novel method for large scale, unbiased nuclear sorting, sequencing, and de novo assembling of AM fungal genomes. After comparative analyses of three assembly workflows we discuss how sequence data from single nuclei can best be used for different downstream analyses such as phylogenomics and comparative genomics of single nuclei. Based on analysis of completeness, we conclude that comprehensive de novo genome assemblies can be produced from six to seven nuclei. The method is highly applicable for a broad range of taxa, and will greatly improve our ability to study multicellular eukaryotes with complex life cycles.

", "keywords": ["0301 basic medicine", "Evolutionary Biology", "0303 health sciences", "Genome", "Fungi", "Computational Biology", "Eukaryota", "Genomics", "Article", "Workflow", "Evolutionsbiologi", "03 medical and health sciences", "13. Climate action", "Algorithms"]}, "links": [{"href": "https://www.nature.com/articles/s41598-020-58025-3.pdf"}, {"href": "https://doi.org/10.1038/s41598-020-58025-3"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Scientific%20Reports", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1038/s41598-020-58025-3", "name": "item", "description": "10.1038/s41598-020-58025-3", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1038/s41598-020-58025-3"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-01-28T00:00:00Z"}}, {"id": "10.1038/s41598-023-49194-y", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:18:02Z", "type": "Journal Article", "created": "2023-12-13", "title": "Unraveling the genome of Bacillus velezensis MEP218, a strain producing fengycin homologs with broad antibacterial activity: comprehensive comparative genome analysis", "description": "Abstract

Bacillus sp. MEP218, a soil bacterium with high potential as a source of bioactive molecules, produces mostly C16\uffe2\uff80\uff93C17 fengycin and other cyclic lipopeptides (CLP) when growing under previously optimized culture conditions. This work addressed the elucidation of the genome sequence of MEP218 and its taxonomic classification. The genome comprises 3,944,892\uffc2\uffa0bp, with a total of 3474 coding sequences and a G\uffe2\uff80\uff89+\uffe2\uff80\uff89C content of 46.59%. Our phylogenetic analysis to determine the taxonomic position demonstrated that the assignment of the MEP218 strain to Bacillus velezensis species provides insights into its evolutionary context and potential functional attributes. The in silico genome analysis revealed eleven gene clusters involved in the synthesis of secondary metabolites, including non-ribosomal CLP (fengycins and surfactin), polyketides, terpenes, and bacteriocins. Furthermore, genes encoding phytase, involved in the release of phytic phosphate for plant and animal nutrition, or other enzymes such as cellulase, xylanase, and alpha 1\uffe2\uff80\uff934 glucanase were detected. In vitro antagonistic assays against Salmonella typhimurium, Acinetobacter baumanii, Escherichia coli, among others, demonstrated a broad spectrum of C16\uffe2\uff80\uff93C17 fengycin produced by MEP218. MEP218 genome sequence analysis expanded our understanding of the diversity and genetic relationships within the Bacillus genus and updated the Bacillus databases with its unique trait to produce antibacterial fengycins and its potential as a resource of biotechnologically useful enzymes. The climate-active gas isoprene (2-methyl-1,3-butadiene) is released to the atmosphere in huge quantities, almost equaling that of methane, yet we know little about the biological cycling of isoprene in the environment. Although bacteria capable of growth on isoprene as the sole source of carbon and energy have previously been isolated from soils and sediments, no microbiological studies have targeted the major source of isoprene and examined the phyllosphere of isoprene-emitting trees for the presence of degraders of this abundant carbon source. Here, we identified isoprene-degrading bacteria in poplar tree-derived microcosms by DNA stable isotope probing. The genomes of isoprene-degrading taxa were reconstructed, putative isoprene metabolic genes were identified, and isoprene-related gene transcription was analyzed by shotgun metagenomics and metatranscriptomics. Gram-positive bacteria of the genus Rhodococcus proved to be the dominant isoprene degraders, as previously found in soil. However, a wider diversity of isoprene utilizers was also revealed, notably Variovorax , a genus not previously associated with this trait. This finding was confirmed by expression of the isoprene monooxygenase from Variovorax in a heterologous host. A Variovorax strain that could grow on isoprene as the sole carbon and energy source was isolated. Analysis of its genome confirmed that it contained isoprene metabolic genes with an identical layout and high similarity to those identified by DNA-stable isotope probing and metagenomics. This study provides evidence of a wide diversity of isoprene-degrading bacteria in the isoprene-emitting tree phyllosphere and greatly enhances our understanding of the biodegradation of this important metabolite and climate-active gas.

", "keywords": ["DNA", " Bacterial", "0301 basic medicine", "2. Zero hunger", "570", "0303 health sciences", "QH301 Biology", "Biological Sciences", "15. Life on land", "Mixed Function Oxygenases", "Comamonadaceae", "03 medical and health sciences", "Biodegradation", " Environmental", "Hemiterpenes", "Populus", "13. Climate action", "Butadienes", "Rhodococcus", "Metagenomics", "Genome", " Bacterial", "Phylogeny", "Soil Microbiology"]}, "links": [{"href": "https://ueaeprints.uea.ac.uk/id/eprint/69197/1/Published_manuscript.pdf"}, {"href": "https://pnas.org/doi/pdf/10.1073/pnas.1812668115"}, {"href": "https://repository.essex.ac.uk/23631/1/1812668115.full.pdf"}, {"href": "https://doi.org/10.1073/pnas.1812668115"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Proceedings%20of%20the%20National%20Academy%20of%20Sciences", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1073/pnas.1812668115", "name": "item", "description": "10.1073/pnas.1812668115", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1073/pnas.1812668115"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2018-11-29T00:00:00Z"}}, {"id": "10.3390/microorganisms9020426", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:21:25Z", "type": "Journal Article", "created": "2021-02-19", "title": "Identification of Beneficial Microbial Consortia and Bioactive Compounds with Potential as Plant Biostimulants for a Sustainable Agriculture", "description": "

A growing body of evidence demonstrates the potential of various microbes to enhance plant productivity in cropping systems although their successful field application may be impaired by several biotic and abiotic constraints. In the present work, we aimed at developing multifunctional synthetic microbial consortia to be used in combination with suitable bioactive compounds for improving crop yield and quality. Plant growth-promoting microorganisms (PGPMs) with different functional attributes were identified by a bottom-up approach. A comprehensive literature survey on PGPMs associated with maize, wheat, potato and tomato, and on commercial formulations, was conducted by examining peer-reviewed scientific publications and results from relevant European projects. Metagenome fragment recruitments on genomes of potential PGPMs represented in databases were also performed to help identify plant growth-promoting (PGP) strains. Following evidence of their ability to coexist, isolated PGPMs were synthetically assembled into three different microbial consortia. Additionally, the effects of bioactive compounds on the growth of individually PGPMs were tested in starvation conditions. The different combination products based on microbial and non-microbial biostimulants (BS) appear worth considering for greenhouse and open field trials to select those potentially adoptable in sustainable agriculture.

", "keywords": ["0301 basic medicine", "QH301-705.5", "delivery method", "Plant growth-promoting microorganisms", "SIMBA; sustainable agriculture; plant growth-promoting microorganisms; microbial consortia; metagenome fragment recruitments; delivery methods; in vitro compatibility; bioactive compounds", "630", "Bioactive compounds", "Article", "660.6", "12. Responsible consumption", "03 medical and health sciences", "plant growth-promoting microorganisms", "Delivery methods", "microbial consortia", "plant growth-promoting microorganism", "Biology (General)", "Metagenome fragment recruitments", "bioactive compound", "2. Zero hunger", "0303 health sciences", "bioactive compounds", "660", "in vitro compatibility", "Sustainable agriculture", "metagenome fragment recruitment", "ta4111", "SIMBA", "3. Good health", "sustainable agriculture", "Microbial consortia", "metagenome fragment recruitments", "delivery methods", "In vitro compatibility"]}, "links": [{"href": "http://www.mdpi.com/2076-2607/9/2/426/pdf"}, {"href": "https://www.mdpi.com/2076-2607/9/2/426/pdf"}, {"href": "https://doi.org/10.3390/microorganisms9020426"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Microorganisms", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.3390/microorganisms9020426", "name": "item", "description": "10.3390/microorganisms9020426", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3390/microorganisms9020426"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-02-19T00:00:00Z"}}, {"id": "10.1080/1040841x.2022.2132850", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:18:31Z", "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/bioinformatics/btz584", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:18:37Z", "type": "Journal Article", "created": "2019-08-19", "title": "MOOMIN - Mathematical explOration of 'Omics data on a MetabolIc Network", "description": "Abstract Motivation

Analysis of differential expression of genes is often performed to understand how the metabolic activity of an organism is impacted by a perturbation. However, because the system of metabolic regulation is complex and all changes are not directly reflected in the expression levels, interpreting these data can be difficult.

Results

In this work, we present a new algorithm and computational tool that uses a genome-scale metabolic reconstruction to infer metabolic changes from differential expression data. Using the framework of constraint-based analysis, our method produces a qualitative hypothesis of a change in metabolic activity. In other words, each reaction of the network is inferred to have increased, decreased, or remained unchanged in flux. In contrast to similar previous approaches, our method does not require a biological objective function and does not assign on/off activity states to genes. An implementation is provided and it is available online. We apply the method to three published datasets to show that it successfully accomplishes its two main goals: confirming or rejecting metabolic changes suggested by differentially expressed genes based on how well they fit in as parts of a coordinated metabolic change, as well as inferring changes in reactions whose genes did not undergo differential expression.

Availability and implementation

github.com/htpusa/moomin.

Supplementary information

Supplementary data are available at Bioinformatics online.

", "keywords": ["0301 basic medicine", "570", "[SDV.BIBS] Life Sciences [q-bio]/Quantitative Methods [q-bio.QM]", "Metabolic networks; omics data", "Genome", "[INFO.INFO-DS]Computer Science [cs]/Data Structures and Algorithms [cs.DS]", "0206 medical engineering", "610", "Computational Biology", "[INFO.INFO-DS] Computer Science [cs]/Data Structures and Algorithms [cs.DS]", "02 engineering and technology", "[SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM]", "Original Papers", "Models", " Biological", "03 medical and health sciences", "[INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM]", "Algorithms", "Metabolic Networks and Pathways", "[INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM]"]}, "links": [{"href": "https://iris.uniroma1.it/bitstream/11573/1321358/5/Pusa_MOOMIN_2020.pdf"}, {"href": "https://academic.oup.com/bioinformatics/article-pdf/36/2/514/48991611/btz584.pdf"}, {"href": "https://doi.org/10.1093/bioinformatics/btz584"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Bioinformatics", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1093/bioinformatics/btz584", "name": "item", "description": "10.1093/bioinformatics/btz584", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1093/bioinformatics/btz584"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-08-22T00:00:00Z"}}, {"id": "10.1093/pcp/pcae113", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:18:41Z", "type": "Journal Article", "created": "2024-11-06", "title": "Population Genomics Reveals Demographic History and Climate Adaptation in Japanese Arabidopsis halleri", "description": "Abstract

Climate oscillations in the Quaternary forced species to major latitudinal or altitudinal range shifts. It has been suggested that adaptation concomitant with range shifts plays key roles in species responses during climate oscillations, but the role of selection for local adaptation to climatic changes remains largely unexplored. Here, we investigated population structure, demographic history and signatures of climate-driven selection based on genome-wide polymorphism data of 141 Japanese Arabidopsis halleri individuals, with European ones as outgroups. Coalescent-based analyses suggested a genetic differentiation between Japanese subpopulations since the Last Glacial Period (LGP), which would have contributed to shaping the current pattern of population structure. Population demographic analysis revealed the population size fluctuations in the LGP, which were particularly prominent since the subpopulations started to diverge (\uffe2\uff88\uffbc50, 000 years ago). The ecological niche modeling predicted the geographic or distribution range shifts from southern coastal regions to northern coastal and mountainous areas, possibly in association with the population size fluctuations. Through genome-wide association analyses of bioclimatic variables and selection scans, we investigated whether climate-associated loci are enriched in the extreme tails of selection scans, and demonstrated the prevailing signatures of selection, particularly toward a warmer climate in southern subpopulations and a drier environment in northern subpopulations, which may have taken place during or after the LGP. Our study highlights the importance of integrating climate associations, selection scans and population demographic analyses for identifying genomic signatures of population-specific adaptation, which would also help us predict the evolutionary responses to future climate changes.The complete genome sequence of Rhodococcus sp. WAY2 (WAY2) consists of a circular chromosome, three linear replicons and a small circular plasmid. The linear replicons contain typical actinobacterial invertron-type telomeres with the central CGTXCGC motif. Comparative phylogenetic analysis of the 16S rRNA gene along with phylogenomic analysis based on the genome-to-genome blast distance phylogeny (GBDP) algorithm and digital DNA\uffe2\uff80\uff93DNA hybridization (dDDH) with other Rhodococcus type strains resulted in a clear differentiation of WAY2, which is likely a new species. The genome of WAY2 contains five distinct clusters of bph, etb and nah genes, putatively involved in the degradation of several aromatic compounds. These clusters are distributed throughout the linear plasmids. The high sequence homology of the ring-hydroxylating subunits of these systems with other known enzymes has allowed us to model the range of aromatic substrates they could degrade. Further functional characterization revealed that WAY2 was able to grow with biphenyl, naphthalene and xylene as sole carbon and energy sources, and could oxidize multiple aromatic compounds, including ethylbenzene, phenanthrene, dibenzofuran and toluene. In addition, WAY2 was able to co-metabolize 23 polychlorinated biphenyl congeners, consistent with the five different ring-hydroxylating systems encoded by its genome. WAY2 could also use n-alkanes of various chain-lengths as a sole carbon source, probably due to the presence of alkB and ladA gene copies, which are only found in its chromosome. These results show that WAY2 has a potential to be used for the biodegradation of multiple organic compounds.Environmental factors relating to soil pH are widely known to be important in structuring soil bacterial communities, yet the relationship between taxonomic community composition and functional diversity remains to be determined. Here, we analyze geographically distributed soils spanning a wide pH gradient and assess the functional gene capacity within those communities using whole genome metagenomics. Low pH soils consistently had fewer taxa (lower alpha and gamma diversity), but only marginal reductions in functional alpha diversity and equivalent functional gamma diversity. However, coherent changes in the relative abundances of annotated genes between pH classes were identified; with functional profiles clustering according to pH independent of geography. Differences in gene abundances were found to reflect survival and nutrient acquisition strategies, with organic-rich acidic soils harboring a greater abundance of cation efflux pumps, C and N direct fixation systems and fermentation pathways indicative of anaerobiosis. Conversely, high pH soils possessed more direct transporter-mediated mechanisms for organic C and N substrate acquisition. These findings show that bacterial functional versatility may not be constrained by taxonomy, and we further identify the range of physiological adaptations required to exist in soils of varying nutrient availability and edaphic conditions.By developing a high-density murine immunophenotyping platform compatible with high-throughput genetic screening, we have established profound contributions of genetics and structure to immune variation. Specifically, high-throughput phenotyping of 530 knockout mouse lines identified 140 monogenic \uffe2\uff80\uff9chits\uffe2\uff80\uff9d (>25%), most of which had never hitherto been implicated in immunology. Furthermore, they were conspicuously enriched in genes for which humans show poor tolerance to loss-of-function. The immunophenotyping platform also exposed dense correlation networks linking immune parameters with one another and with specific physiologic traits. By limiting the freedom of individual immune parameters, such linkages impose genetically regulated \uffe2\uff80\uff9cimmunological structures\uffe2\uff80\uff9d, whose integrity was found to be associated with immunocompetence. Hence, our findings provide an expanded genetic resource and structural perspective for understanding and monitoring immune variation in health and disease.Bacteria of Lactobacillus sp. are very useful to humans. However, the biology and genomic diversity of their (bacterio)phage enemies remains understudied. Knowledge on Lactobacillus phage diversity should broaden to develop efficient phage control strategies. To this end, organic waste samples were screened for phages against two wine-related Lactobacillus plantarum strains. Isolates were shotgun sequenced and compared against the phage database and each other by phylogenetics and comparative genomics. The new isolates had only three distant relatives from the database, but displayed a high overall degree of genomic similarity amongst them. The latter allowed for the use of one isolate as a representative to conduct transmission electron microscopy and structural protein sequencing, and to study phage adsorption and growth kinetics. The microscopy and proteomics tests confirmed the observed diversity of the new isolates and supported their classification to the family Siphoviridae and the proposal of the new phage genus \uffe2\uff80\uff9cSilenusvirus\uffe2\uff80\uff9d.

", "keywords": ["0301 basic medicine", "0303 health sciences", "FRAMESHIFT", "Denmark", "BACTERIOPHAGES", "PROTEIN", "Wine", "Genome", " Viral", "Viral Plaque Assay", "SEQUENCE", "CLASSIFICATION", "Article", "12. Responsible consumption", "Microscopy", " Electron", "Waste Disposal Facilities", "03 medical and health sciences", "Bacteriolysis", "Species Specificity", "DNA", " Viral", "Bacteriophages", "Adsorption", "Phylogeny", "Lactobacillus plantarum"]}, "links": [{"href": "https://www.biorxiv.org/content/10.1101/728261v1.full.pdf"}, {"href": "https://doi.org/10.1101/728261"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Scientific%20Reports", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1101/728261", "name": "item", "description": "10.1101/728261", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1101/728261"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-08-07T00:00:00Z"}}, {"id": "10.1105/tpc.20.00318", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:18:49Z", "type": "Journal Article", "created": "2020-10-10", "title": "ARADEEPOPSIS, an Automated Workflow for Top-View Plant Phenomics using Semantic Segmentation of Leaf States", "description": "Linking plant phenotype to genotype is a common goal to both plant breeders and geneticists. However, collecting phenotypic data for large numbers of plants remain a bottleneck. Plant phenotyping is mostly image based and therefore requires rapid and robust extraction of phenotypic measurements from image data. However, because segmentation tools usually rely on color information, they are sensitive to background or plant color deviations. We have developed a versatile, fully open-source pipeline to extract phenotypic measurements from plant images in an unsupervised manner. ARADEEPOPSIS (https://github.com/Gregor-Mendel-Institute/aradeepopsis) uses semantic segmentation of top-view images to classify leaf tissue into three categories: healthy, anthocyanin rich, and senescent. This makes it particularly powerful at quantitative phenotyping of different developmental stages, mutants with aberrant leaf color and/or phenotype, and plants growing in stressful conditions. On a panel of 210 natural Arabidopsis (Arabidopsis thaliana) accessions, we were able to not only accurately segment images of phenotypically diverse genotypes but also to identify known loci related to anthocyanin production and early necrosis in genome-wide association analyses. Our pipeline accurately processed images of diverse origin, quality, and background composition, and of a distantly related Brassicaceae. ARADEEPOPSIS is deployable on most operating systems and high-performance computing environments and can be used independently of bioinformatics expertise and resources.", "keywords": ["0301 basic medicine", "0303 health sciences", "Genotype", "Large-Scale Biology Articles", "Arabidopsis", "Computational Biology", "Semantics", "Workflow", "Plant Leaves", "03 medical and health sciences", "Phenotype", "Image Processing", " Computer-Assisted", "Phenomics", "Software", "Genome-Wide Association Study"]}, "links": [{"href": "https://doi.org/10.1105/tpc.20.00318"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/The%20Plant%20Cell", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1105/tpc.20.00318", "name": "item", "description": "10.1105/tpc.20.00318", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1105/tpc.20.00318"}, {"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": "10.1109/isit.2019.8849847", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:18:50Z", "type": "Journal Article", "created": "2019-09-26", "title": "Some Enumeration Problems in the Duplication-Loss Model of Genome Rearrangement", "description": "Open AccessTandem-duplication-random-loss (TDRL) is an important genome rearrangement operation studied in evolutionary biology. This paper investigates some of the formal properties of TDRL operations on the symmetric group (the space of permutations over an $ n $-set). In particular, the cardinality of `balls' of radius one in the TDRL metric, as well as the cardinality of the maximum intersection of two such balls, are determined. The corresponding problems for the so-called mirror (or palindromic) TDRL rearrangement operations are also solved. The results represent an initial step in the study of error correction and reconstruction problems in this context and are of potential interest in DNA-based data storage applications.", "keywords": ["genome rearrangement", "sequence reconstruction", "Genomics (q-bio.GN)", "FOS: Computer and information sciences", "Discrete Mathematics (cs.DM)", "DNA storage", "Computer Science - Information Theory", "Information Theory (cs.IT)", "0102 computer and information sciences", "02 engineering and technology", "permutation", "Quantitative Biology - Quantitative Methods", "01 natural sciences", "05A05", " 68R05", " 92B99", " 92D20", " 94B25", "error-correcting code", "FOS: Biological sciences", "0202 electrical engineering", " electronic engineering", " information engineering", "Tandem-duplication-random-loss", "Quantitative Biology - Genomics", "Quantitative Methods (q-bio.QM)", "Computer Science - Discrete Mathematics"], "contacts": [{"organization": "Kova\u010devi\u0107, Mladen, Brdar, Sanja, Crnojevi\u0107, Vladimir,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.1109/isit.2019.8849847"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/2019%20IEEE%20International%20Symposium%20on%20Information%20Theory%20%28ISIT%29", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1109/isit.2019.8849847", "name": "item", "description": "10.1109/isit.2019.8849847", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1109/isit.2019.8849847"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-07-01T00:00:00Z"}}, {"id": "10.1111/1462-2920.13842", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:18:53Z", "type": "Journal Article", "created": "2017-06-27", "title": "Identification and characterisation of isoprene-degrading bacteria in an estuarine environment", "description": "Summary

Approximately one\uffe2\uff80\uff90third of volatile organic compounds (VOCs) emitted to the atmosphere consists of isoprene, originating from the terrestrial and marine biosphere, with a profound effect on atmospheric chemistry. However, isoprene provides an abundant and largely unexplored source of carbon and energy for microbes. The potential for isoprene degradation in marine and estuarine samples from the Colne Estuary, UK, was investigated using DNA\uffe2\uff80\uff90Stable Isotope Probing (DNA\uffe2\uff80\uff90SIP). Analysis at two timepoints showed the development of communities dominated by Actinobacteria including members of the genera Mycobacterium, Rhodococcus, Microbacterium and Gordonia. Representative isolates, capable of growth on isoprene as sole carbon and energy source, were obtained from marine and estuarine locations, and isoprene\uffe2\uff80\uff90degrading strains of Gordonia and Mycobacterium were characterised physiologically and their genomes were sequenced. Genes predicted to be required for isoprene metabolism, including four\uffe2\uff80\uff90component isoprene monooxygenases (IsoMO), were identified and compared with previously characterised examples. Transcriptional and activity assays of strains growing on isoprene or alternative carbon sources showed that growth on isoprene is an inducible trait requiring a specific IsoMO. This study is the first to identify active isoprene degraders in estuarine and marine environments using DNA\uffe2\uff80\uff90SIP and to characterise marine isoprene\uffe2\uff80\uff90degrading bacteria at the physiological and molecular level.

", "keywords": ["0301 basic medicine", "570", "Volatile Organic Compounds", "0303 health sciences", "550", "Base Sequence", "610", "QR Microbiology", "Sequence Analysis", " DNA", "Environment", "6. Clean water", "Mixed Function Oxygenases", "Mycobacterium", "03 medical and health sciences", "Hemiterpenes", "13. Climate action", "Pentanes", "Butadienes", "Rhodococcus", "14. Life underwater", "Gordonia Bacterium", "Research Articles", "Genome", " Bacterial", "GE Environmental Sciences"]}, "links": [{"href": "https://ueaeprints.uea.ac.uk/id/eprint/63998/4/Published_manuscript.pdf"}, {"href": "http://onlinelibrary.wiley.com/wol1/doi/10.1111/1462-2920.13842/fullpdf"}, {"href": "https://doi.org/10.1111/1462-2920.13842"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Environmental%20Microbiology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1111/1462-2920.13842", "name": "item", "description": "10.1111/1462-2920.13842", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/1462-2920.13842"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2017-07-21T00:00:00Z"}}, {"id": "10.1111/1574-6941.12384", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:18:54Z", "type": "Journal Article", "created": "2014-07-21", "title": "Impact Of Long-Term N, P, K, And Npk Fertilization On The Composition And Potential Functions Of The Bacterial Community In Grassland Soil", "description": "Soil abiotic and biotic interactions govern important ecosystem processes. However, the mechanisms behind these interactions are complex, and the links between specific environmental factors, microbial community structures, and functions are not well understood. Here, we applied DNA shotgun metagenomic techniques to investigate the effect of inorganic fertilizers N, P, K, and NPK on the bacterial community composition and potential functions in grassland soils in a 54-year experiment. Differences in total and available nutrients were found in the treatment soils; interestingly, Al, As, Mg, and Mn contents were variable in N, P, K, and NPK treatments. Bacterial community compositions shifted and Actinobacteria were overrepresented under the four fertilization treatments compared to the control. Redundancy analysis of the soil parameters and the bacterial community profiles showed that Mg, total N, Cd, and Al were linked to community variation. Using correlation analysis, Acidobacteria, Bacteroidetes, and Verrucomicrobia were linked similarly to soil parameters, and Actinobacteria and Proteobacteria were linked separately to different suites of parameters. Surprisingly, we found no fertilizers effect on microbial functional profiles which supports functional redundancy as a mechanism for stabilization of functions during changes in microbial composition. We suggest that functional profiles are more resistant to environmental changes than community compositions in the grassland ecosystem.", "keywords": ["0301 basic medicine", "sandy loam", "Nitrogen", "verrucomicrobia", "microbial communities", "nitrogen", "diversity", "Phosphates", "Soil", "03 medical and health sciences", "Fertilizers", "Soil Microbiology", "2. Zero hunger", "metagenomics", "0303 health sciences", "Bacteria", "national", "15. Life on land", "Grassland", "13. Climate action", "genome size", "ammonia-oxidizing bacteria", "Potassium", "Metagenomics", "ecosystems", "management"]}, "links": [{"href": "https://doi.org/10.1111/1574-6941.12384"}, {"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": "10.1111/1574-6941.12384", "name": "item", "description": "10.1111/1574-6941.12384", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/1574-6941.12384"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2014-08-21T00:00:00Z"}}, {"id": "10.1128/msystems.00562-19", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:19:31Z", "type": "Journal Article", "created": "2020-01-13", "title": "Transcriptomic Response of Nitrosomonas europaea Transitioned from Ammonia- to Oxygen-Limited Steady-State Growth", "description": "

Nitrification is a ubiquitous microbially mediated process in the environment and an essential process in engineered systems such as wastewater and drinking water treatment plants. However, nitrification also contributes to fertilizer loss from agricultural environments, increasing the eutrophication of downstream aquatic ecosystems, and produces the greenhouse gas nitrous oxide. As ammonia-oxidizing bacteria are the most dominant ammonia-oxidizing microbes in fertilized agricultural soils, understanding their responses to a variety of environmental conditions is essential for curbing the negative environmental effects of nitrification. Notably, oxygen limitation has been reported to significantly increase nitric oxide and nitrous oxide production during nitrification. Here, we investigate the physiology of the best-characterized ammonia-oxidizing bacterium, Nitrosomonas europaea , growing under oxygen-limited conditions. Selective logging and forest conversion to oil palm agriculture are rapidly altering tropical forests. However, functional responses of the soil microbiome to these land\uffe2\uff80\uff90use changes are poorly understood. Using 16S rRNA gene and shotgun metagenomic sequencing, we compared composition and functional attributes of soil biota between unlogged, once\uffe2\uff80\uff90logged and twice\uffe2\uff80\uff90logged rainforest, and areas converted to oil palm plantations in Sabah, Borneo. Although there was no significant effect of logging history, we found a significant difference between the taxonomic and functional composition of both primary and logged forests and oil palm. Oil palm had greater abundances of genes associated with DNA, RNA, protein metabolism and other core metabolic functions, but conversely, lower abundance of genes associated with secondary metabolism and cell\uffe2\uff80\uff93cell interactions, indicating less importance of antagonism or mutualism in the more oligotrophic oil palm environment. Overall, these results show a striking difference in taxonomic composition and functional gene diversity of soil microorganisms between oil palm and forest, but no significant difference between primary forest and forest areas with differing logging history. This reinforces the view that logged forest retains most features and functions of the original soil community. However, networks based on strong correlations between taxonomy and functions showed that network complexity is unexpectedly increased due to both logging and oil palm agriculture, which suggests a pervasive effect of both land\uffe2\uff80\uff90use changes on the interaction of soil microbes.

", "keywords": ["0301 basic medicine", "Conservation of Natural Resources", "0303 health sciences", "Bacteria", "Microbiota", "Agriculture", "Forestry", "Biodiversity", "Arecaceae", "Forests", "15. Life on land", "03 medical and health sciences", "Borneo", "international", "RNA", " Ribosomal", " 16S", "Metagenome", "Soil Microbiology"]}, "links": [{"href": "https://doi.org/10.1111/mec.13620"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Molecular%20Ecology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1111/mec.13620", "name": "item", "description": "10.1111/mec.13620", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/mec.13620"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2016-04-20T00:00:00Z"}}, {"id": "10.1111/pce.14205", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:19:26Z", "type": "Journal Article", "created": "2021-10-30", "title": "Root dynamic growth strategies in response to salinity", "description": "Abstract

Increasing soil salinization largely impacts crop yield worldwide. To deal with salinity stress, plants exhibit an array of responses, including root system architecture remodelling. Here, we review recent progress in physiological, developmental and cellular mechanisms of root growth responses to salinity. Most recent research in modulation of root branching, root tropisms, as well as in root cell wall modifications under salinity stress, is discussed in the context of the contribution of these responses to overall plant performance. We highlight the power of natural variation approaches revealing novel potential pathways responsible for differences in root salt stress responses. Together, these new findings promote our understanding of how salt shapes the root phenotype, which may provide potential avenues for engineering crops with better yield and survival in saline soils.White lupin is an old crop with renewed interest due to its seed high protein content and high nutritional value. Despite a long domestication history in the Mediterranean basin, modern breeding efforts have been fairly scarce. Recent sequencing of its genome has provided tools for further description of genetic resources but detailed characterization of genomic diversity is still missing. Here, we report the genome sequencing of 39 accessions that were used to establish a white lupin pangenome. We defined 32\uffe2\uff80\uff89068 core genes that are present in all individuals and 14\uffe2\uff80\uff89822 that are absent in some and may represent a gene pool for breeding for improved productivity, grain quality, and stress adaptation. We used this new pangenome resource to identify candidate genes for alkaloid synthesis, a key grain quality trait. The white lupin pangenome provides a novel genetic resource to better understand how domestication has shaped the genomic variability within this crop. Thus, this pangenome resource is an important step towards the effective and efficient genetic improvement of white lupin to help meet the rapidly growing demand for plant protein sources for human and animal consumption.

", "keywords": ["0301 basic medicine", "white lupin", "pangenome", "[SDV.BIO]Life Sciences [q-bio]/Biotechnology", "http://aims.fao.org/aos/agrovoc/c_49985", "630", "diversit\u00e9 g\u00e9n\u00e9tique (comme ressource)", "Domestication", "domestication", "03 medical and health sciences", "ressource g\u00e9n\u00e9tique v\u00e9g\u00e9tale", "[SDV.BV]Life Sciences [q-bio]/Vegetal Biology", "[SDV.BV] Life Sciences [q-bio]/Vegetal Biology", "http://aims.fao.org/aos/agrovoc/c_37418", "http://aims.fao.org/aos/agrovoc/c_37419", "http://aims.fao.org/aos/agrovoc/c_3224", "http://aims.fao.org/aos/agrovoc/c_33952", "Research Articles", "ressource g\u00e9n\u00e9tique animale", "2. Zero hunger", "0303 health sciences", "g\u00e9nome", "phytog\u00e9n\u00e9tique", "http://aims.fao.org/aos/agrovoc/c_27583", "Chromosome Mapping", "600", "s\u00e9quence nucl\u00e9otidique", "15. Life on land", "variation g\u00e9n\u00e9tique", "plant diversity", "[SDV.BIO] Life Sciences [q-bio]/Biotechnology", "Lupinus", "Plant Breeding", "http://aims.fao.org/aos/agrovoc/c_15975", "Genome", " Plant"]}, "links": [{"href": "https://onlinelibrary.wiley.com/doi/pdf/10.1111/pbi.13678"}, {"href": "https://doi.org/10.1111/pbi.13678"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Plant%20Biotechnology%20Journal", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1111/pbi.13678", "name": "item", "description": "10.1111/pbi.13678", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/pbi.13678"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-06-22T00:00:00Z"}}, {"id": "10.1111/tpj.15544", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:19:28Z", "type": "Journal Article", "created": "2021-10-20", "title": "Constitutively enhanced genome integrity maintenance and direct stress mitigation characterize transcriptome of extreme stress\u2010adapted Arabidopsis halleri", "description": "SUMMARY

Heavy metal\uffe2\uff80\uff90rich toxic soils and ordinary soils are both natural habitats of Arabidopsis halleri, a diploid perennial and obligate outcrosser in the sister clade of the genetic model plant Arabidopsis thaliana. The molecular divergence underlying survival in sharply contrasting environments is unknown. Here we comparatively address metal physiology and transcriptomes of A. halleri originating from the most highly heavy metal\uffe2\uff80\uff90contaminated soil in Europe, Ponte Nossa, Italy (Noss), and from non\uffe2\uff80\uff90metalliferous (NM) soils. Plants from Noss exhibit enhanced hypertolerance and attenuated accumulation of cadmium (Cd), and their transcriptomic Cd responsiveness is decreased, compared to plants of NM soil origin. Among the condition\uffe2\uff80\uff90independent transcriptome characteristics of Noss, the most highly overrepresented functional class of \uffe2\uff80\uff98meiotic cell cycle\uffe2\uff80\uff99 comprises 21 transcripts with elevated abundance in vegetative tissues, in particular Argonaute 9 (AGO9) and the synaptonemal complex transverse filament protein\uffe2\uff80\uff90encoding ZYP1a/b. Increased AGO9 transcript levels in Noss are accompanied by decreased long terminal repeat retrotransposon expression. Similar to Noss, plants from other highly metalliferous sites in Poland and Germany share elevated somatic AGO9 transcript levels in comparison to plants originating from NM soils in their respective geographic regions. Transcript levels of Iron\uffe2\uff80\uff90Regulated Transporter 1 (IRT1) are very low and transcript levels of Heavy Metal ATPase 2 (HMA2) are strongly elevated in Noss, which can account for its altered Cd handling. We conclude that in plants adapted to the most extreme abiotic stress, broadly enhanced functions comprise genes with likely roles in somatic genome integrity maintenance, accompanied by few alterations in stress\uffe2\uff80\uff90specific functional networks. The activated sludge process is the most widely applied biotechnology and is one of the best ecosystems to address microbial ecological principles. Yet, the cultivation of core bacteria and the exploration of their physiology and ecology are limited. In this study, the core and novel bacterial taxon C. huifangae was cultivated and characterized. This study revealed that C. huifangae functioned as an important module hub in the activated sludge microbiome, and it potentially plays an important role in municipal wastewater treatment plants.

", "keywords": ["0301 basic medicine", "activated sludge microbiome", "DATABASE", "DIVERSITY", "nitrogen and phosphorus removal", "GENOME ANNOTATION", "POLYPHOSPHATE-ACCUMULATING ORGANISMS", "12. Responsible consumption", "ACTIVATED-SLUDGE", "03 medical and health sciences", "SEARCH", "RNA", " Ribosomal", " 16S", "11. Sustainability", "microbial network", "Phylogeny", "WWTP", "0303 health sciences", "IDENTIFICATION", "Sewage", "Microbiota", "Betaproteobacteria", "core taxa", "15. Life on land", "6. Clean water", "COMMUNITY", "RNA", " Bacterial", "Casimicrobium huifangae", "13. Climate action", "Earth and Environmental Sciences", "BIOLOGICAL PHOSPHORUS REMOVAL", "municipal wastewater treatment plant", "CARBON SOURCE"]}, "links": [{"href": "https://journals.asm.org/doi/pdf/10.1128/AEM.02209-19"}, {"href": "https://doi.org/10.1128/aem.02209-19"}, {"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.02209-19", "name": "item", "description": "10.1128/aem.02209-19", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1128/aem.02209-19"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-02-03T00:00:00Z"}}, {"id": "10.1128/mBio.00799-17", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:19:31Z", "type": "Journal Article", "created": "2017-03-19", "title": "Bacterial Physiological Adaptations to Contrasting Edaphic Conditions Identified Using Landscape Scale Metagenomics", "description": "Abstract

Environmental factors relating to soil pH are widely known to be important in structuring soil bacterial communities, yet the relationship between taxonomic community composition and functional diversity remains to be determined. Here, we analyze geographically distributed soils spanning a wide pH gradient and assess the functional gene capacity within those communities using whole genome metagenomics. Low pH soils consistently had fewer taxa (lower alpha and gamma diversity), but only marginal reductions in functional alpha diversity and equivalent functional gamma diversity. However, coherent changes in the relative abundances of annotated genes between pH classes were identified; with functional profiles clustering according to pH independent of geography. Differences in gene abundances were found to reflect survival and nutrient acquisition strategies, with organic-rich acidic soils harboring a greater abundance of cation efflux pumps, C and N direct fixation systems and fermentation pathways indicative of anaerobiosis. Conversely, high pH soils possessed more direct transporter-mediated mechanisms for organic C and N substrate acquisition. These findings show that bacterial functional versatility may not be constrained by taxonomy, and we further identify the range of physiological adaptations required to exist in soils of varying nutrient availability and edaphic conditions.

", "keywords": ["Q Science", "0301 basic medicine", "330", "Supplementary Data", "ecophysiology", "Ecophysiology", "NE/E006353/1", "Bacterial Physiological Phenomena", "Microbiology", "Soil", "03 medical and health sciences", "Virology", "European Commission", "Ecosystem", "Phylogeny", "Soil Microbiology", "2. Zero hunger", "655240", "metagenomics", "0303 health sciences", "Bacteria", "Natural Environment Research Council (NERC)", "Q", "NE/M017125/1", "Biodiversity", "Hydrogen-Ion Concentration", "15. Life on land", "Adaptation", " Physiological", "soil microbiology", "QR1-502", "United Kingdom", "3. Good health", "Soil microbiology", "Metagenomics", "Genome", " Bacterial", "Research Article"]}, "links": [{"href": "https://www.biorxiv.org/content/10.1101/117887v1.full.pdf"}, {"href": "https://journals.asm.org/doi/pdf/10.1128/mBio.00799-17"}, {"href": "https://doi.org/10.1128/mBio.00799-17"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/mBio", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1128/mBio.00799-17", "name": "item", "description": "10.1128/mBio.00799-17", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1128/mBio.00799-17"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2017-03-18T00:00:00Z"}}, {"id": "10.1128/spectrum.01101-23", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:19:31Z", "type": "Journal Article", "created": "2023-09-19", "title": "Bacteriophages limitedly contribute to the antimicrobial resistome of microbial communities in wastewater treatment plants", "description": "ABSTRACT

Bacteriophages are known as players in the transmission of antimicrobial resistance genes (ARGs) by horizontal gene transfer. In this study, we characterized the bacteriophage community and the associated ARGs to estimate the potential for phages to spread ARGs in aquatic ecosystems analyzing the intra- and extracellular DNA isolated from two wastewater treatment plants (WWTPs) by shotgun metagenomics. We compared the phage antimicrobial resistome with the bacterial resistome and investigated the effect of the final disinfection treatment on the phage community and its resistome. Phage community was mainly composed by Siphoviridae and other members of the order Caudovirales . The final disinfection only marginally affected the composition of the phage community, and it was not possible to measure its effect on the antimicrobial resistome. Indeed, only three phage metagenome-assembled genomes (pMAGs) annotated as Siphoviridae , Padoviridae , and Myoviridae were positive for putative ARGs. Among the detected ARGs, i.e., dfr B6, rpo B mutants, and EF-Tu mutants, the first one was not annotated in the bacterial MAGs. Overall, these results demonstrate that bacteriophages limitedly contribute to the whole antimicrobial resistome. However, in order to obtain a comprehensive understanding of the antimicrobial resistome within a microbial community, the role of bacteriophages needs to be investigated.

IMPORTANCE

WWTPs are considered hotspots for the spread of ARGs by horizontal gene transfer. In this study, we evaluated the phage composition and the associated antimicrobial resistome by shotgun metagenomics of samples collected before and after the final disinfection treatment. Only a few bacteriophages carried ARGs. However, since one of the detected genes was not found in the bacterial metagenome-assembled genomes, it is necessary to investigate the phage community in order to gain a comprehensive overview of the antimicrobial resistome. This investigation could help assess the potential threats to human health.

", "keywords": ["metagenomics", "bacteriophages", "11. Sustainability", "Bacteriophages", "metagenomic assembled genomes", "antimicrobial resistance", "antimicrobial resistome", "wastewater treatment plants", "Microbiology", "6. Clean water", "QR1-502", "12. Responsible consumption", "Research Article"]}, "links": [{"href": "https://journals.asm.org/doi/pdf/10.1128/spectrum.01101-23"}, {"href": "https://doi.org/10.1128/spectrum.01101-23"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Microbiology%20Spectrum", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1128/spectrum.01101-23", "name": "item", "description": "10.1128/spectrum.01101-23", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1128/spectrum.01101-23"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2023-10-17T00:00:00Z"}}, {"id": "10.1186/s40168-020-00941-7", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:19:42Z", "type": "Journal Article", "created": "2020-11-19", "title": "Antimicrobial use and production system shape the fecal, environmental, and slurry resistomes of pig farms", "description": "Abstract Background

The global threat of antimicrobial resistance (AMR) is a One Health problem impacted by antimicrobial use (AMU) for human and livestock applications. Extensive Iberian swine production is based on a more sustainable and eco-friendly management system, providing an excellent opportunity to evaluate how sustained differences in AMU impact the resistome, not only in the animals but also on the farm environment. Here, we evaluate the resistome footprint of an extensive pig farming system, maintained for decades, as compared to that of industrialized intensive pig farming by analyzing 105 fecal, environmental and slurry metagenomes from 38 farms.

Results

Our results evidence a significantly higher abundance of antimicrobial resistance genes (ARGs) on intensive farms and a link between AMU and AMR to certain antimicrobial classes. We observed differences in the resistome across sample types, with a higher richness and dispersion of ARGs within environmental samples than on those from feces or slurry. Indeed, a deeper analysis revealed that differences among the three sample types were defined by taxa-ARGs associations. Interestingly, mobilome analyses revealed that the observed AMR differences between intensive and extensive farms could be linked to differences in the abundance of mobile genetic elements (MGEs). Thus, while there were no differences in the abundance of chromosomal-associated ARGs between intensive and extensive herds, a significantly higher abundance of integrons in the environment and plasmids, regardless of the sample type, was detected on intensive farms.

Conclusions

Overall, this study shows how AMU, production system, and sample type influence, mainly through MGEs, the profile and dispersion of ARGs in pig production.

", "keywords": ["0301 basic medicine", "Farms", "Sanidad animal", "Swine", "Antimicrobial resistance", "Microbial ecology", "Sustainable farming", "Cerdos", "Feces", "03 medical and health sciences", "Anti-Infective Agents", "Environmental Microbiology", "Animals", "Mobilome", "Antiinfecciosos", "One health", "2. Zero hunger", "Excrementos", "0303 health sciences", "Research", "QR100-130", "Drug Resistance", " Microbial", "15. Life on land", "Farm environment", "6. Clean water", "Genes", " Bacterial", "Animals", " Domestic", "2401.05 desarrollo Animal", "Metagenome", "Veterinaria"]}, "links": [{"href": "http://link.springer.com/content/pdf/10.1186/s40168-020-00941-7.pdf"}, {"href": "https://doi.org/10.1186/s40168-020-00941-7"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Microbiome", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1186/s40168-020-00941-7", "name": "item", "description": "10.1186/s40168-020-00941-7", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1186/s40168-020-00941-7"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-11-19T00:00:00Z"}}, {"id": "10.1186/s12864-019-5692-3", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:19:41Z", "type": "Journal Article", "created": "2019-05-02", "title": "Expanding the biodiversity of Oenococcus oeni through comparative genomics of apple cider and kombucha strains", "description": "Oenococcus oeni is a lactic acid bacteria species adapted to the low pH, ethanol-rich environments of wine and cider fermentation, where it performs the crucial role of malolactic fermentation. It has a small genome and has lost the mutS-mutL DNA mismatch repair genes, making it a hypermutable and highly specialized species. Two main lineages of strains, named groups A and B, have been described to date, as well as other subgroups correlated to different types of wines or regions. A third group 'C' has also been hypothesized based on sequence analysis, but it remains controversial. In this study we have elucidated the species population structure by sequencing 14 genomes of new strains isolated from cider and kombucha and performing comparative genomics analyses.Sequence-based phylogenetic trees confirmed a population structure of 4 clades: The previously identified A and B, a third group 'C' consisting of the new cider strains and a small subgroup of wine strains previously attributed to group B, and a fourth group 'D' exclusively represented by kombucha strains. A pair of complete genomes from group C and D were compared to the circularized O. oeni PSU-1 strain reference genome and no genomic rearrangements were found. Phylogenetic trees, K-means clustering and pangenome gene clusters evidenced the existence of smaller, specialized subgroups of strains. Using the pangenome, genomic differences in stress resistance and biosynthetic pathways were found to uniquely distinguish the C and D clades.The obtained results, including the additional cider and kombucha strains, firmly established the O. oeni population structure. Group C does not appear as fully domesticated as group A to wine, but showed several unique patterns which may be due to ongoing specialization to the cider environment. Group D was shown to be the most divergent member of O. oeni to date, appearing as the closest to a pre-domestication state of the species.", "keywords": ["0301 basic medicine", "570", "Wine", "QH426-470", "Pan-genome", "Industrial microbiology", "630", "03 medical and health sciences", "Lactic acid bacteria", "Genetics", "[SDV.BV]Life Sciences [q-bio]/Vegetal Biology", "[SDV.BV] Life Sciences [q-bio]/Vegetal Biology", "Oenococcus", "Phylogeny", "2. Zero hunger", "0303 health sciences", "Genome", "Whole Genome Sequencing", "Comparative genomics", "Bacterial", "Phylogenomics", "Kombucha Tea", "Biodiversity", "15. Life on land", "Malus", "Oenococcus oeni", "TP248.13-248.65", "Genome", " Bacterial", "Biotechnology", "Research Article"]}, "links": [{"href": "http://link.springer.com/content/pdf/10.1186/s12864-019-5692-3.pdf"}, {"href": "https://doi.org/10.1186/s12864-019-5692-3"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/BMC%20Genomics", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1186/s12864-019-5692-3", "name": "item", "description": "10.1186/s12864-019-5692-3", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1186/s12864-019-5692-3"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-05-02T00:00:00Z"}}, {"id": "10.1186/s40168-018-0572-7", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:19:41Z", "type": "Journal Article", "created": "2018-10-18", "title": "Consistent responses of soil microbial taxonomic and functional attributes to mercury pollution across China", "description": "The ecological consequences of mercury (Hg) pollution-one of the major pollutants worldwide-on microbial taxonomic and functional attributes remain poorly understood and largely unexplored. Using soils from two typical Hg-impacted regions across China, here, we evaluated the role of Hg pollution in regulating bacterial abundance, diversity, and co-occurrence network. We also investigated the associations between Hg contents and the relative abundance of microbial functional genes by analyzing the soil metagenomes from a subset of those sites.We found that soil Hg largely influenced the taxonomic and functional attributes of microbial communities in the two studied regions. In general, Hg pollution was negatively related to bacterial abundance, but positively related to the diversity of bacteria in two separate regions. We also found some consistent associations between soil Hg contents and the community composition of bacteria. For example, soil total Hg content was positively related to the relative abundance of Firmicutes and Bacteroidetes in both paddy and upland soils. In contrast, the methylmercury (MeHg) concentration was negatively correlated to the relative abundance of Nitrospirae in the two types of soils. Increases in soil Hg pollution correlated with drastic changes in the relative abundance of ecological clusters within the co-occurrence network of bacterial communities for the two regions. Using metagenomic data, we were also able to detect the effect of Hg pollution on multiple functional genes relevant to key soil processes such as element cycles and Hg transformations (e.g., methylation and reduction).Together, our study provides solid evidence that Hg pollution has predictable and significant effects on multiple taxonomic and functional attributes including bacterial abundance, diversity, and the relative abundance of ecological clusters and functional genes. Our results suggest an increase in soil Hg pollution linked to human activities will lead to predictable shifts in the taxonomic and functional attributes in the Hg-impacted areas, with potential implications for sustainable management of agricultural ecosystems and elsewhere.", "keywords": ["0301 basic medicine", "570", "China", "550", "Co-occurrence network", "Firmicutes", "333", "12. Responsible consumption", "Microbial ecology", "Soil", "03 medical and health sciences", "XXXXXX - Unknown", "Soil Pollutants", "Soil Microbiology", "2. Zero hunger", "Bacteroidetes", "Research", "Microbiota", "QR100-130", "Biodiversity", "Mercury", "Methylmercury Compounds", "15. Life on land", "Mercury pollution", "6. Clean water", "13. Climate action", "Soil microbial community", "Metagenome", "Metagenomics", "Functional gene", "Environmental Pollution", "Environmental Monitoring"]}, "links": [{"href": "https://doi.org/10.1186/s40168-018-0572-7"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Microbiome", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1186/s40168-018-0572-7", "name": "item", "description": "10.1186/s40168-018-0572-7", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1186/s40168-018-0572-7"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2018-10-18T00:00:00Z"}}, {"id": "10.1186/s40793-023-00479-9", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:19:42Z", "type": "Journal Article", "created": "2023-03-30", "title": "Abundance, classification and genetic potential of Thaumarchaeota in metagenomes of European agricultural soils: a meta-analysis", "description": "Abstract Background

For a sustainable production of food, research on agricultural soil microbial communities is inevitable. Due to its immense complexity, soil is still some kind of black box. Soil study designs for identifying microbiome members of relevance have various scopes and focus on particular environmental factors. To identify common features of soil microbiomes, data from multiple studies should be compiled and processed. Taxonomic compositions and functional capabilities of microbial communities associated with soils and plants have been identified and characterized in the past few decades. From a fertile Loess\uffe2\uff80\uff93Chernozem-type soil located in Germany, metagenomically assembled genomes (MAGs) classified as members of the phylum Thaumarchaeota/Thermoproteota were obtained. These possibly represent keystone agricultural soil community members encoding functions of relevance for soil fertility and plant health. Their importance for the analyzed microbiomes is corroborated by the fact that they were predicted to contribute to the cycling of nitrogen, feature the genetic potential to fix carbon dioxide and possess genes with predicted functions in plant-growth-promotion (PGP). To expand the knowledge on soil community members belonging to the phylum Thaumarchaeota, we conducted a meta-analysis integrating primary studies on European agricultural soil microbiomes.

Results

Taxonomic classification of the selected soil metagenomes revealed the shared agricultural soil core microbiome of European soils from 19 locations. Metadata reporting was heterogeneous between the different studies. According to the available metadata, we separated the data into 68 treatments. The phylum Thaumarchaeota is part of the core microbiome and represents a major constituent of the archaeal subcommunities in all European agricultural soils. At a higher taxonomic resolution, 2074 genera constituted the core microbiome. We observed that viral genera strongly contribute to variation in taxonomic profiles. By binning of metagenomically assembled contigs, Thaumarchaeota MAGs could be recovered from several European soil metagenomes. Notably, many of them were classified as members of the family Nitrososphaeraceae, highlighting the importance of this family for agricultural soils. The specific Loess-Chernozem Thaumarchaeota MAGs were most abundant in their original soil, but also seem to be of importance in other agricultural soil microbial communities. Metabolic reconstruction of Switzerland_1_MAG_2 revealed its genetic potential i.a. regarding carbon dioxide (CO$$_2$$ 2 ) fixation, ammonia oxidation, exopolysaccharide production and a beneficial effect on plant growth. Similar genetic features were also present in other reconstructed MAGs. Three Nitrososphaeraceae MAGs are all most likely members of a so far unknown genus.

Conclusions

On a broad view, European agricultural soil microbiomes are similarly structured. Differences in community structure were observable, although analysis was complicated by heterogeneity in metadata recording. Our study highlights the need for standardized metadata reporting and the benefits of networking open data. Future soil sequencing studies should also consider high sequencing depths in order to enable reconstruction of genome bins. Intriguingly, the family Nitrososphaeraceae commonly seems to be of importance in agricultural microbiomes.

", "keywords": ["2. Zero hunger", "570", "Soil microbial diversity", "Metagenomically assembled genomes", "Research", "European soil", "Open metagenome data analysis", "15. Life on land", "Microbiology", "Thaumarchaeota", "QR1-502", "Environmental sciences", "Agricultural microbiome", "Soil health", "GE1-350"]}, "links": [{"href": "https://link.springer.com/content/pdf/10.1186/s40793-023-00479-9.pdf"}, {"href": "https://doi.org/10.1186/s40793-023-00479-9"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Environmental%20Microbiome", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1186/s40793-023-00479-9", "name": "item", "description": "10.1186/s40793-023-00479-9", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1186/s40793-023-00479-9"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2023-03-30T00:00:00Z"}}, {"id": "10.1186/s40793-020-00354-x", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:19:42Z", "type": "Report", "created": "2020-03-02", "title": "Impact of process temperature and organic loading rate on cellulolytic / hydrolytic biofilm microbiomes during biomethanation of ryegrass silage revealed by genome-centered metagenomics and metatranscriptomics", "description": "Abstract Background

Anaerobic digestion (AD) of protein-rich grass silage was performed in experimental two-stage two-phase biogas reactor systems at low vs. increased organic loading rates (OLRs) under mesophilic (37\uffe2\uff80\uff89\uffc2\uffb0C) and thermophilic (55\uffe2\uff80\uff89\uffc2\uffb0C) temperatures. To follow the adaptive response of the biomass-attached cellulolytic/hydrolytic biofilms at increasing ammonium/ammonia contents, genome-centered metagenomics and transcriptional profiling based on metagenome assembled genomes (MAGs) were conducted.

Results

In total, 78 bacterial and archaeal MAGs representing the most abundant members of the communities, and featuring defined quality criteria were selected and characterized in detail. Determination of MAG abundances under the tested conditions by mapping of the obtained metagenome sequence reads to the MAGs revealed that MAG abundance profiles were mainly shaped by the temperature but also by the OLR. However, the OLR effect was more pronounced for the mesophilic systems as compared to the thermophilic ones. In contrast, metatranscriptome mapping to MAGs subsequently normalized to MAG abundances showed that under thermophilic conditions, MAGs respond to increased OLRs by shifting their transcriptional activities mainly without adjusting their proliferation rates. This is a clear difference compared to the behavior of the microbiome under mesophilic conditions. Here, the response to increased OLRs involved adjusting of proliferation rates and corresponding transcriptional activities. The analysis led to the identification of MAGs positively responding to increased OLRs. The most outstanding MAGs in this regard, obviously well adapted to higher OLRs and/or associated conditions, were assigned to the order Clostridiales (Acetivibrio sp.) for the mesophilic biofilm and the orders Bacteroidales (Prevotella sp. and an unknown species), Lachnospirales (Herbinix sp. and Kineothrix sp.) and Clostridiales (Clostridium sp.) for the thermophilic biofilm. Genome-based metabolic reconstruction and transcriptional profiling revealed that positively responding MAGs mainly are involved in hydrolysis of grass silage, acidogenesis and / or\uffc2\uffa0acetogenesis.

Conclusions

An integrated -omics approach enabled the identification of new AD biofilm keystone species featuring outstanding performance under stress conditions such as increased OLRs. Genome-based knowledge on the metabolic potential and transcriptional activity of responsive microbiome members will contribute to the development of improved microbiological AD management strategies for biomethanation of renewable biomass.

", "keywords": ["Integrated -omics", "Bioconversion", "0301 basic medicine", "570", "Polyomics", "Integrated-omics", "Biogas", "Microbiology", "7. Clean energy", "03 medical and health sciences", "Anaerobic digestion", "GE1-350", "2. Zero hunger", "0303 health sciences", "Metagenome assembled genomes", "Microbial community structure", "15. Life on land", "QR1-502", "6. Clean water", "3. Good health", "Environmental sciences", "Metagenome assembled genomes", " Integrated -omics", " Polyomics", " Anaerobic digestion", " Biogas", " Bioconversion", " Microbial community structure", " Methane", " Metabolic activity", "13. Climate action", "Metabolic activity", "Methane", "Research Article"]}, "links": [{"href": "http://link.springer.com/content/pdf/10.1186/s40793-020-00354-x.pdf"}, {"href": "https://doi.org/10.1186/s40793-020-00354-x"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Environmental%20Microbiome", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1186/s40793-020-00354-x", "name": "item", "description": "10.1186/s40793-020-00354-x", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1186/s40793-020-00354-x"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-03-02T00:00:00Z"}}, {"id": "10.1534/g3.119.400716", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:19:59Z", "type": "Journal Article", "created": "2020-01-10", "title": "Whole Genome Sequencing and Comparative Genomics of Two Nematicidal Bacillus Strains Reveals a Wide Range of Possible Virulence Factors", "description": "Abstract

Bacillus firmus nematicidal bacterial strains are used to control plant parasitic nematode infestation of crops in agricultural production. Proteases are presumed to be the primary nematode virulence factors in nematicidal B. firmus degrading the nematode cuticle and other organs. We determined and compared the whole genome sequences of two nematicidal strains. Comparative genomics with a particular focus on possible virulence determinants revealed a wider range of possible virulence factors in a B. firmus isolate from a commercial bionematicide and a wild type Bacillus sp. isolate with nematicidal activity. The resulting 4.6 Mb B. firmus I-1582 and 5.3 Mb Bacillus sp. ZZV12-4809 genome assemblies contain respectively 18 and 19 homologs to nematode-virulent proteases, two nematode-virulent chitinase homologs in ZZV12-4809 and 28 and 36 secondary metabolite biosynthetic clusters, projected to encode antibiotics, small peptides, toxins and siderophores. The results of this study point to the genetic capability of B. firmus and related species for nematode virulence through a range of direct and indirect mechanisms.Lactobacillus plantarum is a bacterium with promising applications to the food industry and agriculture and probiotic properties. So far, bacteriophages of this bacterium have been moderately addressed. We examined the diversity of five new L. plantarum phages via whole genome shotgun sequencing and in silico protein predictions. Moreover, we looked into their phylogeny and their potential genomic similarities to other complete phage genome records through extensive nucleotide and protein comparisons. These analyses revealed a high degree of similarity among the five phages, which extended to the vast majority of predicted virion-associated proteins. Based on these, we selected one of the phages as a representative and performed transmission electron microscopy and structural protein sequencing tests. Overall, the results suggested that the five phages belong to the family Myoviridae, they have a long genome of 137.973-141.344 bp, a G/C content of 36,3-36,6% that is quite distinct from their host’s, and, surprisingly, seven to 15 tRNAs. Only an average 41/174 of their predicted genes were assigned a function. The comparative analyses unraveled considerable genetic diversity for the five L. plantarum phages of this study. Hence, the new genus “Semelevirus” was proposed, which comprises exclusively the five phages. This novel lineage of Lactobacillus phages provides further insight into the genetic heterogeneity of phages infecting Lactobacillus sp.. The five new Lactobacillus phages have a potential value for the development of more robust starters through, for example, the selection of mutants insensitive to phage infections. The five phages could also form part of phage cocktails, which producers would apply in different stages of L. plantarum fermentations in order to create a range of organoleptic outputs.

", "keywords": ["0301 basic medicine", "Annotation", "comparative genomics", "Genome", " Viral", "Lactobacillus plantarum", "Microbiology", "Article", "Isolation", "diversity", "03 medical and health sciences", "Microscopy", " Electron", " Transmission", "DNA Packaging", "phage", "Bacteriophages", "Phylogeny", "Viral Structural Proteins", "2. Zero hunger", "Diversity", "Base Composition", "0303 health sciences", "Comparative genomics", "new genus", "Genomics", "Sequence Analysis", " DNA", "QR1-502", "virology", "Phylogenetics", "phylogenetics", "Lactobacillus", "annotation", "Myoviridae", "Phage", "New genus", "isolation", "Lactobacillus plantarum"]}, "links": [{"href": "http://www.mdpi.com/1999-4915/11/7/611/pdf"}, {"href": "https://www.mdpi.com/1999-4915/11/7/611/pdf"}, {"href": "https://doi.org/10.3390/v11070611"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Viruses", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.3390/v11070611", "name": "item", "description": "10.3390/v11070611", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3390/v11070611"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-06-11T00:00:00Z"}}, {"id": "10.3390/microorganisms8010013", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:21:25Z", "type": "Journal Article", "created": "2019-12-20", "title": "Genome Analyses and Genome-Centered Metatranscriptomics of Methanothermobacter wolfeii Strain SIV6, Isolated from a Thermophilic Production-Scale Biogas Fermenter", "description": "

In the thermophilic biogas-producing microbial community, the genus Methanothermobacter was previously described to be frequently abundant. The aim of this study was to establish and analyze the genome sequence of the archaeal strain Methanothermobacter wolfeii SIV6 originating from a thermophilic industrial-scale biogas fermenter and compare it to related reference genomes. The circular chromosome has a size of 1,686,891 bases, featuring a GC content of 48.89%. Comparative analyses considering three completely sequenced Methanothermobacter strains revealed a core genome of 1494 coding sequences and 16 strain specific genes for M. wolfeii SIV6, which include glycosyltransferases and CRISPR/cas associated genes. Moreover, M. wolfeii SIV6 harbors all genes for the hydrogenotrophic methanogenesis pathway and genome-centered metatranscriptomics indicates the high metabolic activity of this strain, with 25.18% of all transcripts per million (TPM) belong to the hydrogenotrophic methanogenesis pathway and 18.02% of these TPM exclusively belonging to the mcr operon. This operon encodes the different subunits of the enzyme methyl-coenzyme M reductase (EC: 2.8.4.1), which catalyzes the final and rate-limiting step during methanogenesis. Finally, fragment recruitment of metagenomic reads from the thermophilic biogas fermenter on the SIV6 genome showed that the strain is abundant (1.2%) within the indigenous microbial community. Detailed analysis of the archaeal isolate M. wolfeii SIV6 indicates its role and function within the microbial community of the thermophilic biogas fermenter, towards a better understanding of the biogas production process and a microbial-based management of this complex process.

", "keywords": ["2. Zero hunger", "0301 basic medicine", "570", "Methanothermobacter wolfeii", "metagenomics", "0303 health sciences", "metatranscriptomics", "thermophilic biogas fermenter", "comparative analyses", "Methanothermobacter wolfeii; thermophilic biogas fermenter; genome mining; comparative analyses; CRISPR/cas; metabolic pathway reconstruction; metagenomics; fragment recruitment; metatranscriptomics", "CRISPR/cas", "metabolic pathway reconstruction", "7. Clean energy", "Article", "03 medical and health sciences", "CRISPR/cas", "genome mining", "8. Economic growth", "Methanothermobacter wolfeii", "fragment recruitment"]}, "links": [{"href": "http://www.mdpi.com/2076-2607/8/1/13/pdf"}, {"href": "https://www.mdpi.com/2076-2607/8/1/13/pdf"}, {"href": "https://doi.org/10.3390/microorganisms8010013"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Microorganisms", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.3390/microorganisms8010013", "name": "item", "description": "10.3390/microorganisms8010013", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3390/microorganisms8010013"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-12-20T00:00:00Z"}}, {"id": "10.23725/vb9p-yq49", "type": "Feature", "geometry": null, "properties": {"license": "unspecified", "updated": "2026-04-04T16:20:58Z", "type": "Dataset", "title": "NWD479271.freeze5.v1.vcf.gz.csi", "description": "TOPMed: NWD479271.freeze5.v1.vcf.gz.csi
File: VCF CSI file", "keywords": ["whole genome sequencing", "topmed"], "contacts": [{"organization": "TOPMed", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.23725/vb9p-yq49"}, {"rel": "self", "type": "application/geo+json", "title": "10.23725/vb9p-yq49", "name": "item", "description": "10.23725/vb9p-yq49", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.23725/vb9p-yq49"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2017-11-30T00:00:00Z"}}, {"id": "10.3389/fmicb.2016.00259", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:21:09Z", "type": "Journal Article", "created": "2016-03-02", "description": "Litter decomposition is an enzymatically-complex process that is mediated by a diverse assemblage of saprophytic microorganisms. It is a globally important biogeochemical process that can be suppressed by anthropogenic N deposition. In a northern hardwood forest ecosystem located in Michigan, USA, 20 years of experimentally increased atmospheric N deposition has reduced forest floor decay and increased soil C storage. Here, we paired extracellular enzyme assays with shotgun metagenomics to assess if anthropogenic N deposition has altered the functional potential of microbial communities inhabiting decaying forest floor. Experimental N deposition significantly reduced the activity of extracellular enzymes mediating plant cell wall decay, which occurred concurrently with changes in the relative abundance of metagenomic functional gene pathways mediating the metabolism of carbohydrates, aromatic compounds, as well as microbial respiration. Moreover, experimental N deposition increased the relative abundance of 50 of the 60 gene pathways, the majority of which were associated with saprotrophic bacteria. Conversely, the relative abundance and composition of fungal genes mediating the metabolism of plant litter was not affected by experimental N deposition. Future rates of atmospheric N deposition have favored saprotrophic soil bacteria, whereas the metabolic potential of saprotrophic fungi appears resilient to this agent of environmental change. Results presented here provide evidence that changes in the functional capacity of saprotrophic soil microorganisms mediate how anthropogenic N deposition increases C storage in soil.", "keywords": ["saprotroph", "2. Zero hunger", "0301 basic medicine", "0303 health sciences", "Climate Change", "C storage", "15. Life on land", "Microbiology", "metagenome", "N deposition", "QR1-502", "03 medical and health sciences", "climate change", "13. Climate action", "Saprotroph", "Metagenome"]}, "links": [{"href": "https://doi.org/10.3389/fmicb.2016.00259"}, {"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.2016.00259", "name": "item", "description": "10.3389/fmicb.2016.00259", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3389/fmicb.2016.00259"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2016-03-02T00:00:00Z"}}, {"id": "10.3389/fmicb.2019.01347", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:21:10Z", "type": "Journal Article", "created": "2019-06-25", "title": "Finding Functional Differences Between Species in a Microbial Community: Case Studies in Wine Fermentation and Kefir Culture", "description": "Microbial life usually takes place in a community where individuals interact, by competition for nutrients, cross-feeding, inhibition by end-products, but also by their spatial distribution. Lactic acid bacteria are prominent members of microbial communities responsible for food fermentations. Their niche in a community depends on their own properties as well as those of the other species. Here, we apply a computational approach, which uses only genomic and metagenomic information and functional annotation of genes, to find properties that distinguish a species from others in the community, as well as to follow individual species in a community. We analyzed isolated and sequenced strains from a kefir community, and metagenomes from wine fermentations. We demonstrate how the distinguishing properties of an organism lead to experimentally testable hypotheses concerning the niche and the interactions with other species. We observe, for example, that L. kefiranofaciens, a dominant organism in kefir, stands out among the Lactobacilli because it potentially has more amino acid auxotrophies. Using metagenomic analysis of industrial wine fermentations we investigate the role of an inoculated L. plantarum in malolactic fermentation. We observed that L. plantarum thrives better on white than on red wine fermentations and has the largest number of phosphotransferase system among the bacteria observed in the wine communities. Also, L. plantarum together with Pantoea, Erwinia, Asaia, Gluconobacter, and Komagataeibacter genera had the highest number of genes involved in biosynthesis of amino acids.", "keywords": ["0301 basic medicine", "metagenomics", "0303 health sciences", "microbial communities", "Microbial communities", "Wine", "Microbiology", "QR1-502", "Computational biology", "lactic acid bacteria", "03 medical and health sciences", "Kefir", "computational biology", "Lactic acid bacteria", "Metagenomics", "Genomes", "wine", "genomes"]}, "links": [{"href": "https://doi.org/10.3389/fmicb.2019.01347"}, {"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.2019.01347", "name": "item", "description": "10.3389/fmicb.2019.01347", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3389/fmicb.2019.01347"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-06-25T00:00:00Z"}}], "links": [{"rel": "self", "type": "application/geo+json", "title": "This document as GeoJSON", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items?keywords=Genome&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=Genome&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=Genome&", "hreflang": "en-US"}, {"rel": "next", "type": "application/geo+json", "title": "items (next)", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items?keywords=Genome&offset=50", "hreflang": "en-US"}], "numberMatched": 108, "numberReturned": 50, "distributedFeatures": [], "timeStamp": "2026-04-05T04:12:54.589137Z"}