Multi-omics illuminates the functional significance of previously unknown species in a full-scale landfill leachate treatment plant DOI
Tianyi Chen,

Chunfang Deng,

S. Li

et al.

Journal of Hazardous Materials, Journal Year: 2024, Volume and Issue: 479, P. 135669 - 135669

Published: Aug. 27, 2024

Language: Английский

The antiSMASH database version 4: additional genomes and BGCs, new sequence-based searches and more DOI Creative Commons
Kai Blin, Simon J. Shaw, Marnix H. Medema

et al.

Nucleic Acids Research, Journal Year: 2023, Volume and Issue: 52(D1), P. D586 - D589

Published: Oct. 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/.

Language: Английский

Citations

58

Nanopore sequencing: flourishing in its teenage years DOI
Tianyuan Zhang, Hanzhou Li, Mian Jiang

et al.

Journal of genetics and genomics/Journal of Genetics and Genomics, Journal Year: 2024, Volume and Issue: unknown

Published: Sept. 1, 2024

Language: Английский

Citations

20

Pangenome mining of the Streptomyces genus redefines species’ biosynthetic potential DOI Creative Commons
Omkar S. Mohite, Tue Sparholt Jørgensen, Thomas Booth

et al.

Genome biology, Journal Year: 2025, Volume and Issue: 26(1)

Published: Jan. 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.

Language: Английский

Citations

3

BGCFlow: systematic pangenome workflow for the analysis of biosynthetic gene clusters across large genomic datasets DOI Creative Commons
Matin Nuhamunada, Omkar S. Mohite, Patrick V. Phaneuf

et al.

Nucleic Acids Research, Journal Year: 2024, Volume and Issue: 52(10), P. 5478 - 5495

Published: April 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.

Language: Английский

Citations

11

A treasure trove of 1034 actinomycete genomes DOI Creative Commons
Tue Sparholt Jørgensen, Omkar S. Mohite, Eva Baggesgaard Sterndorff

et al.

Nucleic Acids Research, Journal Year: 2024, Volume and Issue: 52(13), P. 7487 - 7503

Published: June 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.

Language: Английский

Citations

10

Biosynthetic potential of uncultured anammox community bacteria revealed through multi-omics analysis DOI
Yicheng Wang, Huimin Fu, Yu Shen

et al.

Bioresource Technology, Journal Year: 2024, Volume and Issue: 401, P. 130740 - 130740

Published: April 25, 2024

Language: Английский

Citations

7

Long-Read Metagenomics of Marine Microbes Reveals Diversely Expressed Secondary Metabolites DOI Creative Commons
Ranran Huang, Yafei Wang,

Daixi Liu

et al.

Microbiology Spectrum, Journal Year: 2023, Volume and Issue: 11(4)

Published: July 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

Language: Английский

Citations

14

Pangenome mining of theStreptomycesgenus redefines their biosynthetic potential DOI Creative Commons
Omkar S. Mohite, Tue Sparholt Jørgensen, Thomas Booth

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Feb. 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.

Language: Английский

Citations

5

Exploring the secrets of marine microorganisms: Unveiling secondary metabolites through metagenomics DOI Creative Commons
S. Wang,

Xinyan Li,

Weiqin Yang

et al.

Microbial Biotechnology, Journal Year: 2024, Volume and Issue: 17(8)

Published: July 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.

Language: Английский

Citations

5

Multi-omics in Crohn's disease: New insights from inside DOI Creative Commons

Chenlu Mu,

Qianjing Zhao,

Qing Zhao

et al.

Computational and Structural Biotechnology Journal, Journal Year: 2023, Volume and Issue: 21, P. 3054 - 3072

Published: Jan. 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.

Language: Английский

Citations

10