Profiling of Pharmaceutical Sludge Microbiome, Resistome and Secondary Metabolites Using Metagenomics

Indian Journal of Microbiology, Год журнала: 2024, Номер unknown

Опубликована: Авг. 16, 2024

Язык: Английский

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Metagenomic insights into microalgae-bacterium-virus interactions and viral functions in phycosphere facing environmental fluctuations

Water Research, Год журнала: 2024, Номер 268, С. 122676 - 122676

Опубликована: Окт. 22, 2024

Язык: Английский

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Biosynthetic gene cluster synteny: Orthologous polyketide synthases in Hypogymnia physodes, Hypogymnia tubulosa, and Parmelia sulcata

MicrobiologyOpen, Год журнала: 2023, Номер 12(5)

Опубликована: Окт. 1, 2023

Lichens are symbiotic associations consisting of a photobiont (algae or cyanobacteria) and mycobiont (fungus), which together generate variety unique secondary metabolites. To access this biosynthetic potential for biotechnological applications, deeper insights into the pathways corresponding gene clusters necessary. Here, we provide comparative view three lichen mycobionts derived from Hypogymnia physodes, tubulosa, Parmelia sulcata. In addition, present high-quality PacBio metagenome sulcata, extracted bin containing 214 clusters. Most in these genomes were associated with T1PKSs, followed by NRPSs terpenes. This study focused on related to polyketide synthesis. Based ketosynthase homology, identified nine highly syntenic all species. Among four belonging nonreducing PKSs, two putatively linked substances orsellinic acid (orcinol depsides depsidones, e.g., lecanoric acid, physodic lobaric acid), one compounds methylated forms (beta orcinol depsides, atranorin), melanins. Five orthologs species reducing PKSs. Our contributes sorting dereplicating vast PKS diversity found lichenized fungi. High-quality sequences common foundation further exploration applications molecular evolution substances.

Язык: Английский

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MetaKSSD Enables Rapid and Online Metagenomic Taxonomic Profiling and Profile Searching

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Июнь 25, 2024

Abstract The rapid increase in genomes and metagenomic data presents major scalability efficiency challenges for current profilers. In response, we introduce MetaKSSD, which redefines reference taxonomic marker database (MarkerDB) construction profiling using sketch operations, offering improvements by orders of magnitude. MetaKSSD encompasses 85,202 species its MarkerDB just 0.17GB storage profiles 10GB within seconds, utilizing only 0.5GB memory. Extensive benchmarking experiments demonstrated that is among the top-performing profilers across various metrics. a microbiome-phenotype association study, identified significantly more effective associations than MetaPhlAn4. We profiled 382,016 runs conducted extensive sample clustering analyses, suggested potential yet-to-be-discovered niches. Additionally, developed functionality instantaneous searching large-scale profiles. client-server architecture allows swift transmission metagenome sketches over network enables real-time online analysis, facilitating use non-expert users.

Язык: Английский

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

Journal of Hazardous Materials, Год журнала: 2024, Номер 479, С. 135669 - 135669

Опубликована: Авг. 27, 2024

Язык: Английский

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