Biosynthetic gene cluster profiling predicts the positive association between antagonism and phylogeny in Bacillus

Nature Communications, Journal Year: 2022, Volume and Issue: 13(1)

Published: Feb. 23, 2022

Understanding the driving forces and intrinsic mechanisms of microbial competition is a fundamental question in ecology. Despite well-established negative correlation between exploitation phylogenetic distance, process interference that exemplified by antagonism remains controversial. Here, we studied genus Bacillus, commonly recognized producer multifarious antibiotics, to explore role patterns biosynthetic gene clusters (BGCs) mediating relationship phylogeny. Comparative genomic analysis revealed positive association BGC distance distance. Antagonistic tests demonstrated inhibition phenotype positively correlated with both predicted especially for antagonistic strains possessing abundant BGCs. Mutant-based verification showed was dependent on BGCs specifically harbored strain. These findings highlight BGC-phylogeny coherence regulates congeneric which deepens our understanding force mechanism interactions.

Language: Английский

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A review on mechanisms and prospects of endophytic bacteria in biocontrol of plant pathogenic fungi and their plant growth-promoting activities

Heliyon, Journal Year: 2024, Volume and Issue: 10(11), P. e31573 - e31573

Published: May 23, 2024

Endophytic bacteria, living inside plants, are competent plant colonizers, capable of enhancing immune responses in plants and establishing a mutual relationship with them. bacteria have been described as being used to control phytopathogenic fungi while exhibiting growth-promoting activity. Here, we discussed the mechanisms actions discovered some major groups beneficial endophytic such Bacillus, Paenibacillus, Pseudomonas. Most studied strains these genera were isolated from rhizosphere soils, more extensive study is needed. It essential understand underlying biocontrol develop an effective screening approach for selecting potential bacteria. We suggested strategy based on mechanistic phenomena. This review will help screen sustainable agriculture.

Language: Английский

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Research advances in the identification of regulatory mechanisms of surfactin production by Bacillus: a review

Microbial Cell Factories, Journal Year: 2024, Volume and Issue: 23(1)

Published: April 2, 2024

Abstract Surfactin is a cyclic hexalipopeptide compound, nonribosomal synthesized by representatives of the Bacillus subtilis species complex which includes B. group and its closely related species, such as subsp subtilis, spizizenii, inaquosorum , atrophaeus, amyloliquefaciens, velezensis (Steinke mSystems 6: e00057, 2021) It functions biosurfactant signaling molecule has antibacterial, antiviral, antitumor, plant disease resistance properties. The lipopeptides play an important role in agriculture, oil recovery, cosmetics, food processing pharmaceuticals, but natural yield surfactin low. This paper reviews regulatory pathways mechanisms that affect synthesis release, highlighting genes involved transcription srfAA-AD operon. several ways to enhance production, governing expression regulation transport, removal competitive pathways, optimization media, fermentation conditions were commented. review will provide theoretical platform for systematic genetic modification high-yielding strains surfactin. Graphical

Language: Английский

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Bacillus velezensis RC218 and emerging biocontrol agents against Fusarium graminearum and Fusarium poae in barley: in vitro, greenhouse and field conditions

International Journal of Food Microbiology, Journal Year: 2024, Volume and Issue: 413, P. 110580 - 110580

Published: Jan. 20, 2024

Language: Английский

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Adaptive laboratory evolution reveals regulators involved in repressing biofilm development as key players in Bacillus subtilis root colonization

mSystems, Journal Year: 2024, Volume and Issue: 9(2)

Published: Jan. 11, 2024

Root-associated microorganisms play an important role in plant health, such as growth-promoting rhizobacteria (PGPR) from the

Language: Английский

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Bacillus spp. as Bio-factories for Antifungal Secondary Metabolites: Innovation Beyond Whole Organism Formulations

Microbial Ecology, Journal Year: 2022, Volume and Issue: 86(1), P. 1 - 24

Published: May 23, 2022

Language: Английский

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Plant-associated Bacillus mobilizes its secondary metabolites upon perception of the siderophore pyochelin produced by a Pseudomonas competitor

The ISME Journal, Journal Year: 2022, Volume and Issue: 17(2), P. 263 - 275

Published: Nov. 10, 2022

Bacillus velezensis is considered as model species for plant-associated bacilli providing benefits to its host such protection against phytopathogens. This mainly due the potential secrete a wide range of secondary metabolites with specific and complementary bioactivities. metabolite arsenal has been quite well defined genetically chemically but much remains be explored regarding how it expressed under natural conditions notably can modulated upon interspecies interactions in competitive rhizosphere niche. Here, we show that B. mobilize substantial part metabolome perception Pseudomonas, soil-dwelling competitor. response reflects multimodal defensive strategy includes polyketides bacteriocin amylocyclicin, broad antibiotic activity, surfactin lipopeptides, contributing biofilm formation enhanced motility. Furthermore, identified Pseudomonas siderophore pyochelin an info-chemical, which triggers this via mechanism independent iron stress. We hypothesize relies on chelator sensing accurately identify competitors, illustrating new facet siderophore-mediated beyond concept competition piracy. phenomenon may thus represent component microbial conversations driving behavior members community.

Language: Английский

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Evolutionary investigations of the biosynthetic diversity in the skin microbiome using lsaBGC

Microbial Genomics, Journal Year: 2023, Volume and Issue: 9(4)

Published: April 28, 2023

Bacterial secondary metabolites, synthesized by enzymes encoded in biosynthetic gene clusters (BGCs), can underlie microbiome homeostasis and serve as commercialized products, which have historically been mined from a select group of taxa. While evolutionary approaches proven beneficial for prioritizing BGCs experimental characterization efforts to uncover new natural dedicated bioinformatics tools designed comparative analysis within focal taxa are limited. We thus developed l ineage s pecific nalysis ( lsa BGC; https://github.com/Kalan-Lab/lsaBGC ) aid exploration microdiversity trends across homologous groupings BGCs, cluster families (GCFs), any bacterial interest. BGC enables rapid direct identification GCFs genomes, calculates statistics conservation genes, builds framework allow base resolution mining novel variants through metagenomic exploration. Through application the suite four genera commonly found skin microbiomes, we insights into evolution diversity their BGCs. show that virulence-associated carotenoid staphyloxanthin Staphylococcus aureus is ubiquitous genus . one GCF encoding biosynthesis showcases evidence plasmid-mediated horizontal transfer (HGT) between species, another appears be transmitted vertically amongst sub-clade skin-associated Further, latter GCF, well conserved S. , has lost most epidermidis common species on human also regarded commensal. identify thousands single-nucleotide (SNVs) Corynebacterium tuberculostearicum sp. complex, narrow, multi-species clade features prevalent healthy microbiomes. Although SNVs were approximately 10 times likely correspond synonymous changes when located top five percentile sites, identified defied this trend predicted amino acid functionally key enzymatic domains. Ultimately, beyond supporting investigations provides important functionalities discovery or directed modification products.

Language: Английский

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BGCFlow: systematic pangenome workflow for the analysis of biosynthetic gene clusters across large genomic datasets

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

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Pangenome mining of the Streptomyces genus redefines species’ biosynthetic potential

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

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