{"type": "FeatureCollection", "features": [{"id": "10.1016/j.ijfoodmicro.2021.109043", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-27T16:16:50Z", "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": "10.1038/s41598-023-49194-y", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-27T16:18:27Z", "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<p>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.</p", "keywords": ["0301 basic medicine", "Bacillus", "Gene", "Agricultural and Biological Sciences", "https://purl.org/becyt/ford/1.6", "Phylogeny", "GC-content", "2. Zero hunger", "0303 health sciences", "Genome", "Acinetobacter", "soil bacteria", "Q", "Probiotics and Prebiotics", "R", "Life Sciences", "Anti-Bacterial Agents", "3. Good health", "Ribosomal RNA", "Medicine", "Microbial genetics", "metagenomics assembly", "Biotechnology", "Bacteriocin", "Science", ".", "Synteny", "Microbiology", "Article", "Applied microbiology", "Lipopeptides", "03 medical and health sciences", "Biochemistry", " Genetics and Molecular Biology", "Genetics", "Escherichia coli", "RNA Sequencing Data Analysis", "https://purl.org/becyt/ford/1", "Molecular Biology", "Biology", "genetic engineering", "Bacteria", "Secondary metabolites", "In silico", "bacterial genomes", "Whole genome sequencing", "FOS: Biological sciences", "Microbial Enzymes and Biotechnological Applications", "Antibacterial activity", "Genome", " Bacterial", "Food Science", "Phylogenetic tree"]}, "links": [{"href": "https://www.nature.com/articles/s41598-023-49194-y.pdf"}, {"href": "https://doi.org/10.1038/s41598-023-49194-y"}, {"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/s41598-023-49194-y", "name": "item", "description": "10.1038/s41598-023-49194-y", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1038/s41598-023-49194-y"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2023-12-13T00:00:00Z"}}, {"id": "10.1099/mgen.0.000363", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-27T16:19:11Z", "type": "Journal Article", "created": "2020-04-02", "title": "Analysis of the biodegradative and adaptive potential of the novel polychlorinated biphenyl degrader Rhodococcus sp. WAY2 revealed by its complete genome sequence", "description": "<p>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.</p>", "keywords": ["0301 basic medicine", "0303 health sciences", "PCB", "Whole Genome Sequencing", "AlkB Enzymes", "Rhodococcus; biodegradation; PAH; PCB; hydrocarbons; complete genome", "High-Throughput Nucleotide Sequencing", "PAH", "Naphthalenes", "Xylenes", "Biolog\u00eda y Biomedicina / Biolog\u00eda", "biodegradation", "Polychlorinated Biphenyls", "Hydrocarbons", "Complete genome", "03 medical and health sciences", "Biodegradation", " Environmental", "RNA", " Ribosomal", " 16S", "Biodegradation", "Cluster Analysis", "Rhodococcus", "Phylogeny", "Research Article"]}, "links": [{"href": "https://doi.org/10.1099/mgen.0.000363"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Microbial%20Genomics", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1099/mgen.0.000363", "name": "item", "description": "10.1099/mgen.0.000363", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1099/mgen.0.000363"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-04-01T00:00:00Z"}}, {"id": "10.1186/s12864-019-5692-3", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-27T16:20:04Z", "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": "10.1534/g3.119.400716", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-27T16:20:22Z", "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                <p>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.</p", "keywords": ["2. Zero hunger", "Whole Genome Sequencing", "complete genomes", "Virulence Factors", "Antinematodal Agents", "virulence factors", "bacillus firmus", "biological control", "Bacillus", "bioinformatics", "Genomics", "QH426-470", "Genome Report", "3. Good health", "Bacterial Proteins", "Drug Resistance", " Bacterial", "Genetics", "BACILLUS FIRMUS", " COMPLETE GENOMES", " BIOINFORMATICS", " BIOLOGICAL CONTROL", " NEMATICIDAL ACTIVITY", " VIRULENCE FACTORS", "Bacillus firmus", "nematicidal activity", "Genome", " Bacterial"]}, "links": [{"href": "http://academic.oup.com/g3journal/article-pdf/10/3/881/38825647/g3journal0881.pdf"}, {"href": "https://doi.org/10.1534/g3.119.400716"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/G3%20Genes%7CGenomes%7CGenetics", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1534/g3.119.400716", "name": "item", "description": "10.1534/g3.119.400716", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1534/g3.119.400716"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-03-01T00:00:00Z"}}, {"id": "10.23725/vb9p-yq49", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-27T16:21:22Z", "type": "Dataset", "title": "NWD479271.freeze5.v1.vcf.gz.csi", "description": "TOPMed: NWD479271.freeze5.v1.vcf.gz.csi <br>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.2021.662144", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-27T16:21:37Z", "type": "Journal Article", "created": "2021-07-05", "title": "Whole resistome analysis in Campylobacter jejuni and Campylobacter coli genomes available in public repositories", "description": "<p>Campylobacter spp. are the most frequent agent of human gastroenteritis worldwide, and the spread of multidrug-resistant strains makes the clinical treatment difficult. The current study presents the resistome analysis of 39,798 Campylobacter jejuni and 11,920 Campylobacter coli genomes available in public repositories. Determinants of resistance to \uffce\uffb2-lactams (Be) and tetracyclines (Te) were the most frequent for both species, with resistance to quinolones (Qu) as the third most important on C. jejuni and to aminoglycosides (Am) on C. coli. Moreover, resistance to Te, Qu, and Am was frequently found in co-occurrence with resistance to other antibiotic families. Geographical differences on clonal complexes distribution were found for C. jejuni and on resistome genotypes for both C. jejuni and C. coli species. Attending to the resistome patterns by isolation source, three main clusters of genomes were found on C. jejuni genomes at antimicrobial resistance gene level. The first cluster was formed by genomes from human, food production animals (e.g., sheep, cow, and chicken), and food (e.g., dairy products) isolates. The higher incidence of tet(O), associated with tetracycline resistance, and the gyrA (T86I) single-nucleotide polymorphism (SNP), associated with quinolone resistance, among genomes from this cluster could be due to the intense use of these antibiotics in veterinary and human clinical settings. Similarly, a high incidence of tet(O) genes of C. coli genomes from pig, cow, and turkey was found. Moreover, the cluster based on resistome patterns formed by C. jejuni and C. coli genomes of human, turkey, and chicken origin is in agreement with previous observations reporting chicken or poultry-related environments as the main source of human campylobacteriosis infections. Most clonal complexes (CCs) associated with chicken host specialization (e.g., ST-354, ST-573, ST-464, and ST-446) were the CCs with the highest prevalence of determinants of resistance to Be, Qu, and Te. Finally, a clear trend toward an increase in the occurrence of Te and Qu resistance determinants on C. jejuni, linked to the spread of the co-occurrence of the blaOXA\uffe2\uff80\uff9361 and tet(O)-tet(O/W/O) genes and the gyrA (T86I) SNP, was found from 2001 to date in Europe.</p>", "keywords": ["2. Zero hunger", "0301 basic medicine", "whole genome sequencing", "0303 health sciences", "livestock and human sources", "Host specialization", "Campylobacter coli", "Gen\u00e9tica", "Microbiology", "QR1-502", "Resistome", "Livestock and human sources", "3. Good health", "Campylobacter jejuni", "03 medical and health sciences", "Whole genome sequencing", "host specialization", "14. Life underwater", "resistome"], "contacts": [{"organization": "Jos\u00e9 F. Cobo-D\u00edaz, Paloma Gonz\u00e1lez del R\u00edo, Avelino \u00c1lvarez-Ord\u00f3\u00f1ez, Avelino \u00c1lvarez-Ord\u00f3\u00f1ez,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.3389/fmicb.2021.662144"}, {"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.2021.662144", "name": "item", "description": "10.3389/fmicb.2021.662144", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3389/fmicb.2021.662144"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-07-05T00:00:00Z"}}, {"id": "2999294732", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-27T16:27:22Z", "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                <p>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.</p", "keywords": ["2. Zero hunger", "Whole Genome Sequencing", "complete genomes", "Virulence Factors", "Antinematodal Agents", "virulence factors", "bacillus firmus", "biological control", "Bacillus", "bioinformatics", "Genomics", "QH426-470", "Genome Report", "3. Good health", "Bacterial Proteins", "Drug Resistance", " Bacterial", "Genetics", "BACILLUS FIRMUS", " COMPLETE GENOMES", " BIOINFORMATICS", " BIOLOGICAL CONTROL", " NEMATICIDAL ACTIVITY", " VIRULENCE FACTORS", "Bacillus firmus", "nematicidal activity", "Genome", " Bacterial"]}, "links": [{"href": "http://academic.oup.com/g3journal/article-pdf/10/3/881/38825647/g3journal0881.pdf"}, {"href": "https://doi.org/2999294732"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/G3%20Genes%7CGenomes%7CGenetics", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "2999294732", "name": "item", "description": "2999294732", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/2999294732"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-03-01T00:00:00Z"}}, {"id": "11336/226991", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-27T16:26:12Z", "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<p>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.</p", "keywords": ["0301 basic medicine", "Bacteriocin", "Science", "Bacillus", ".", "Gene", "Synteny", "Microbiology", "Article", "Agricultural and Biological Sciences", "Lipopeptides", "03 medical and health sciences", "https://purl.org/becyt/ford/1.6", "Biochemistry", " Genetics and Molecular Biology", "Genetics", "Escherichia coli", "RNA Sequencing Data Analysis", "https://purl.org/becyt/ford/1", "Molecular Biology", "Biology", "Phylogeny", "GC-content", "2. Zero hunger", "0303 health sciences", "Genome", "Acinetobacter", "Bacteria", "Secondary metabolites", "Q", "Probiotics and Prebiotics", "In silico", "R", "Life Sciences", "Anti-Bacterial Agents", "3. Good health", "Ribosomal RNA", "Whole genome sequencing", "FOS: Biological sciences", "Medicine", "Microbial Enzymes and Biotechnological Applications", "Antibacterial activity", "Genome", " Bacterial", "metagenomics assembly", "Biotechnology", "Food Science", "Phylogenetic tree"]}, "links": [{"href": "https://www.nature.com/articles/s41598-023-49194-y.pdf"}, {"href": "https://doi.org/11336/226991"}, {"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": "11336/226991", "name": "item", "description": "11336/226991", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/11336/226991"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2023-12-13T00:00:00Z"}}, {"id": "11104/0309544", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-07-27T16:26:09Z", "type": "Journal Article", "created": "2020-04-02", "title": "Analysis of the biodegradative and adaptive potential of the novel polychlorinated biphenyl degrader Rhodococcus sp. WAY2 revealed by its complete genome sequence", "description": "<p>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.</p", "keywords": ["0301 basic medicine", "0303 health sciences", "PCB", "Whole Genome Sequencing", "AlkB Enzymes", "High-Throughput Nucleotide Sequencing", "PAH", "Naphthalenes", "Xylenes", "Biolog\u00eda y Biomedicina / Biolog\u00eda", "biodegradation", "Polychlorinated Biphenyls", "Hydrocarbons", "Complete genome", "03 medical and health sciences", "Biodegradation", " Environmental", "RNA", " Ribosomal", " 16S", "Biodegradation", "Cluster Analysis", "Rhodococcus", "Phylogeny", "Research Article"]}, "links": [{"href": "https://doi.org/11104/0309544"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Microbial%20Genomics", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "11104/0309544", "name": "item", "description": "11104/0309544", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/11104/0309544"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-04-01T00:00:00Z"}}, {"id": "50|userclaim___::85c2e6974a364f4a96fdee6d82a5dd41", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-27T16:28:25Z", "type": "Other", "title": "Unraveling the genome of Bacillus velezensis MEP218, a strain producing fengycin homologs with broad antibacterial activity: comprehensive comparative genome analysis", "keywords": ["Bacteriocin", "Gene", "Synteny", "Microbiology", "Agricultural and Biological Sciences", "Biochemistry", " Genetics and Molecular Biology", "Genetics", "Escherichia coli", "RNA Sequencing Data Analysis", "Molecular Biology", "Biology", "GC-content", "Genome", "Acinetobacter", "Bacteria", "Probiotics and Prebiotics", "In silico", "Life Sciences", "Ribosomal RNA", "Whole genome sequencing", "FOS: Biological sciences", "Microbial Enzymes and Biotechnological Applications", "metagenomics assembly", "Biotechnology", "Food Science", "Phylogenetic tree"], "contacts": [{"organization": "Mariano Pistorio, Mar\u00eda Julia Estrella, Edgardo Jofr\u00e9, Gonzalo Torres Tejerizo, Bruno Contreras-Moreira, Daniela Medeot, Anal\u00eda Sannazzaro, Medeot, Daniela, Daniela B. Medeot, Sannazzaro, Anal\u00eda, Anal\u00eda In\u00e9s Sannazzaro, Estrella, Maria Julia, Mar\u00eda Julia Estrella, Torres Tejerizo, Gonzalo, Gonzalo Torres Tejerizo, Contreras\u2011Moreira, Bruno, Bruno Contreras\u2010Moreira, Pistorio, Mariano, Mariano Pistorio, Jofr\u00e9, Edgardo, Edgardo Jofr\u00e9,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/50|userclaim___::85c2e6974a364f4a96fdee6d82a5dd41"}, {"rel": "self", "type": "application/geo+json", "title": "50|userclaim___::85c2e6974a364f4a96fdee6d82a5dd41", "name": "item", "description": "50|userclaim___::85c2e6974a364f4a96fdee6d82a5dd41", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/50|userclaim___::85c2e6974a364f4a96fdee6d82a5dd41"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2023-12-13T00:00:00Z"}}, {"id": "85c2e6974a364f4a96fdee6d82a5dd41", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-27T16:29:24Z", "type": "Other", "title": "Unraveling the genome of Bacillus velezensis MEP218, a strain producing fengycin homologs with broad antibacterial activity: comprehensive comparative genome analysis", "keywords": ["Bacteriocin", "Gene", "Synteny", "Microbiology", "Agricultural and Biological Sciences", "Biochemistry", " Genetics and Molecular Biology", "Genetics", "Escherichia coli", "RNA Sequencing Data Analysis", "Molecular Biology", "Biology", "GC-content", "Genome", "Acinetobacter", "Bacteria", "Probiotics and Prebiotics", "In silico", "Life Sciences", "Ribosomal RNA", "Whole genome sequencing", "FOS: Biological sciences", "Microbial Enzymes and Biotechnological Applications", "metagenomics assembly", "Biotechnology", "Food Science", "Phylogenetic tree"], "contacts": [{"organization": "Mariano Pistorio, Mar\u00eda Julia Estrella, Edgardo Jofr\u00e9, Gonzalo Torres Tejerizo, Bruno Contreras-Moreira, Daniela Medeot, Anal\u00eda Sannazzaro, Medeot, Daniela, Daniela B. Medeot, Sannazzaro, Anal\u00eda, Anal\u00eda In\u00e9s Sannazzaro, Estrella, Maria Julia, Mar\u00eda Julia Estrella, Torres Tejerizo, Gonzalo, Gonzalo Torres Tejerizo, Contreras\u2011Moreira, Bruno, Bruno Contreras\u2010Moreira, Pistorio, Mariano, Mariano Pistorio, Jofr\u00e9, Edgardo, Edgardo Jofr\u00e9,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/85c2e6974a364f4a96fdee6d82a5dd41"}, {"rel": "self", "type": "application/geo+json", "title": "85c2e6974a364f4a96fdee6d82a5dd41", "name": "item", "description": "85c2e6974a364f4a96fdee6d82a5dd41", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/85c2e6974a364f4a96fdee6d82a5dd41"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2023-12-13T00:00:00Z"}}, {"id": "PMC7056983", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-27T16:30:27Z", "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                <p>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.</p", "keywords": ["2. Zero hunger", "Whole Genome Sequencing", "complete genomes", "Virulence Factors", "Antinematodal Agents", "virulence factors", "bacillus firmus", "biological control", "Bacillus", "bioinformatics", "Genomics", "QH426-470", "Genome Report", "3. Good health", "Bacterial Proteins", "Drug Resistance", " Bacterial", "Genetics", "Bacillus firmus", "nematicidal activity", "Genome", " Bacterial"]}, "links": [{"href": "http://academic.oup.com/g3journal/article-pdf/10/3/881/38825647/g3journal0881.pdf"}, {"href": "https://doi.org/PMC7056983"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/G3%20Genes%7CGenomes%7CGenetics", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "PMC7056983", "name": "item", "description": "PMC7056983", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/PMC7056983"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-03-01T00:00:00Z"}}], "links": [{"rel": "self", "type": "application/geo+json", "title": "This document as GeoJSON", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items?keywords=Whole+genome+sequencing&f=json", "hreflang": "en-US"}, {"rel": "alternate", "type": "text/html", "title": "This document as HTML", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items?keywords=Whole+genome+sequencing&f=html", "hreflang": "en-US"}, {"rel": "collection", "type": "application/json", "title": "Collection URL", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main", "hreflang": "en-US"}, {"type": "application/geo+json", "rel": "first", "title": "items (first)", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items?keywords=Whole+genome+sequencing&", "hreflang": "en-US"}, {"rel": "last", "type": "application/geo+json", "title": "items (last)", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items?keywords=Whole+genome+sequencing&offset=13", "hreflang": "en-US"}], "numberMatched": 13, "numberReturned": 13, "distributedFeatures": [], "timeStamp": "2026-07-28T07:07:15.768371Z"}