Journal of Hazardous Materials, Год журнала: 2024, Номер 479, С. 135669 - 135669
Опубликована: Авг. 27, 2024
Язык: Английский
Nucleic Acids Research, Год журнала: 2023, Номер 52(D1), С. D586 - D589
Опубликована: Окт. 30, 2023
Abstract Many microorganisms produce natural products that are frequently used in the development of medicines and crop protection agents. Genome mining has evolved into a prominent method to access this potential. antiSMASH is most popular tool for task. Here we present version 4 database, providing biosynthetic gene clusters detected by 7.1 publicly available, dereplicated, high-quality microbial genomes via an interactive graphical user interface. In 4, database contains 231 534 high quality BGC regions from 592 archaeal, 35 726 bacterial 236 fungal available at https://antismash-db.secondarymetabolites.org/.
Язык: Английский
Процитировано
56
Journal of genetics and genomics/Journal of Genetics and Genomics, Год журнала: 2024, Номер unknown
Опубликована: Сен. 1, 2024
Язык: Английский
Процитировано
20
Genome biology, Год журнала: 2025, Номер 26(1)
Опубликована: Янв. 14, 2025
Background Streptomyces is a highly diverse genus known for the production of secondary or specialized metabolites with wide range applications in medical and agricultural industries. Several thousand complete nearly genome sequences are now available, affording opportunity to deeply investigate biosynthetic potential within these organisms advance natural product discovery initiatives. Results We perform pangenome analysis on 2371 genomes, including approximately 1200 assemblies. Employing data-driven approach based similarities, was classified into 7 primary 42 Mash-clusters, forming basis comprehensive mining. A refined workflow grouping gene clusters (BGCs) redefines their diversity across different Mash-clusters. This also reassigns 2729 BGC families only 440 families, reduction caused by inaccuracies boundary detections. When genomic location BGCs included analysis, conserved structure, synteny, among becomes apparent species synteny suggests that vertical inheritance major factor diversification BGCs. Conclusions Our dataset at scale thousands genomes refines predictions using Mash-clusters as analysis. The observed conservation order BGCs’ locations shows vertically inherited. presented in-depth pave way large-scale investigations enhance our understanding genus.
Язык: Английский
Процитировано
3
Nucleic Acids Research, Год журнала: 2024, Номер 52(10), С. 5478 - 5495
Опубликована: Апрель 30, 2024
Abstract Genome mining is revolutionizing natural products discovery efforts. The rapid increase in available genomes demands comprehensive computational platforms to effectively extract biosynthetic knowledge encoded across bacterial pangenomes. Here, we present BGCFlow, a novel systematic workflow integrating analytics for large-scale genome of BGCFlow incorporates several and tools grouped into five common stages analysis such as: (i) data selection, (ii) functional annotation, (iii) phylogenetic analysis, (iv) mining, (v) comparative analysis. Furthermore, provides easy configuration different projects, parallel distribution, scheduled job monitoring, an interactive database visualize tables, exploratory Jupyter Notebooks, customized reports. demonstrate the application by investigating distribution various gene clusters detected 42 Saccharopolyspora genus, known produce industrially important secondary/specialized metabolites. BGCFlow-guided predicted more accurate dereplication BGCs guided targeted selected RiPPs. scalable, interoperable, adaptable, re-entrant, reproducible nature will provide effective way from ever-growing genomic datasets biotechnologically relevant species.
Язык: Английский
Процитировано
11
Nucleic Acids Research, Год журнала: 2024, Номер 52(13), С. 7487 - 7503
Опубликована: Июнь 22, 2024
Abstract Filamentous Actinobacteria, recently renamed Actinomycetia, are the most prolific source of microbial bioactive natural products. Studies on biosynthetic gene clusters benefit from or require chromosome-level assemblies. Here, we provide DNA sequences >1000 isolates: 881 complete genomes and 153 near-complete genomes, representing 28 genera 389 species, including 244 likely novel species. All filamentous isolates class Actinomycetia NBC culture collection. The largest genus is Streptomyces with 886 742 We use this data to show that analysis can bring biological understanding not previously derived more fragmented less systematic datasets. document central structured location core genes distal specialized metabolite duplicate linear chromosome, analyze content length terminal inverted repeats which characteristic for Streptomyces. then diversity trans-AT polyketide synthase clusters, encodes machinery a biotechnologically highly interesting compound class. These insights have both ecological biotechnological implications in importance high quality genomic resources complex role synteny plays biology.
Язык: Английский
Процитировано
10
Microbiology Spectrum, Год журнала: 2023, Номер 11(4)
Опубликована: Июль 6, 2023
Microbial secondary metabolites play crucial roles in microbial competition, communication, resource acquisition, antibiotic production, and a variety of other biotechnological processes. The retrieval full-length BGC (biosynthetic gene cluster) sequences from uncultivated bacteria is difficult due to the technical constraints short-read sequencing, making it impossible determine diversity. Using long-read sequencing genome mining, 339 mainly BGCs were recovered this study, illuminating wide range lineages discovered seawater Aoshan Bay, Yellow Sea, China. Many extremely diverse bacterial phyla such as
Язык: Английский
Процитировано
14
Bioresource Technology, Год журнала: 2024, Номер 401, С. 130740 - 130740
Опубликована: Апрель 25, 2024
Язык: Английский
Процитировано
6
bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown
Опубликована: Фев. 22, 2024
Abstract Background Streptomyces is a highly diverse genus known for the production of secondary or specialized metabolites with wide range applications in medical and agricultural industries. Several thousand complete nearly-complete genome sequences are now available, affording opportunity to deeply investigate biosynthetic potential within these organisms advance natural product discovery initiatives. Result We performed pangenome analysis on 2,371 genomes, including approximately 1,200 assemblies. Employing data-driven approach based similarities, was classified into 7 primary 42 MASH-clusters, forming basis comprehensive mining. A refined workflow grouping gene clusters (BGCs) redefined their diversity across different MASH-clusters. This also reassigned 2,729 BGC families only 440 families, reduction caused by inaccuracies boundary detections. When genomic location BGCs included analysis, conserved structure (synteny) among becomes apparent species synteny suggests that vertical inheritance major factor acquisition new BGCs. Conclusion Our dataset at scale thousands genomes predictions using MASH-clusters as analysis. The observed conservation order BGCs’ locations showed vertically inherited. presented in-depth pave way large-scale investigations enhance our understanding genus.
Язык: Английский
Процитировано
5
Microbial Biotechnology, Год журнала: 2024, Номер 17(8)
Опубликована: Июль 29, 2024
Abstract Marine microorganisms are increasingly recognized as primary producers of marine secondary metabolites, drawing growing research interest. Many these organisms unculturable, posing challenges for study. Metagenomic techniques enable on unculturable microorganisms, identifying various biosynthetic gene clusters (BGCs) related to microbial thereby unveiling their secrets. This review comprehensively analyses metagenomic methods used in discovering highlighting tools commonly employed BGC identification, and discussing the potential this field. It emphasizes key role metagenomics particularly sponges tunicates. The also explores current limitations studying metabolites through metagenomics, noting how long‐read sequencing technologies evolution computational biology offer more possibilities discovery. Furthermore, development synthetic allows experimental validation computationally identified BGCs, showcasing vast mining metabolites.
Язык: Английский
Процитировано
5
Computational and Structural Biotechnology Journal, Год журнала: 2023, Номер 21, С. 3054 - 3072
Опубликована: Янв. 1, 2023
Crohn's disease (CD) is an inflammatory bowel (IBD) with complex clinical manifestations such as chronic diarrhea, weight loss and hematochezia. Despite the increasing incidence worldwide, cure of CD remains extremely difficult. The rapid development high-throughput sequencing technology integrated-omics analyses in recent years has provided a new means for exploring pathogenesis, mining biomarkers designing targeted personalized therapeutics CD. Host genomics epigenomics unveil heredity-related mechanisms susceptible individuals, while microbiome metabolomics map host-microbe interactions patients. Proteomics shows great potential searching promising biomarkers. Nonetheless, single omics cannot holistically connect heterogeneity pathological behavior rise multi-omics analysis integrates genetic/epigenetic profiles protein/microbial metabolite functionality, providing hope comprehensive in-depth exploration Herein, we emphasized different features applications discussed current research limitations This review will update deepen our understanding from integration broad spectra provide evidence individualized therapeutics.
Язык: Английский
Процитировано
10