Biosynthetic potential of the global ocean microbiome

Nature, Год журнала: 2022, Номер 607(7917), С. 111 - 118

Опубликована: Июнь 22, 2022

Natural microbial communities are phylogenetically and metabolically diverse. In addition to underexplored organismal groups1, this diversity encompasses a rich discovery potential for ecologically biotechnologically relevant enzymes biochemical compounds2,3. However, studying identify genomic pathways the synthesis of such compounds4 assigning them their respective hosts remains challenging. The biosynthetic microorganisms in open ocean largely uncharted owing limitations analysis genome-resolved data at global scale. Here we investigated novelty gene clusters by integrating around 10,000 genomes from cultivated single cells with more than 25,000 newly reconstructed draft 1,000 seawater samples. These efforts revealed approximately 40,000 putative mostly new clusters, several which were found previously unsuspected phylogenetic groups. Among these groups, identified lineage ('Candidatus Eudoremicrobiaceae') that belongs an uncultivated bacterial phylum includes some most biosynthetically diverse environment. From these, characterized phospeptin pythonamide pathways, revealing cases unusual bioactive compound structure enzymology, respectively. Together, research demonstrates how microbiomics-driven strategies can enable investigation undescribed natural products groups environments.

Язык: Английский

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Metagenomics: An Effective Approach for Exploring Microbial Diversity and Functions

Foods, Год журнала: 2023, Номер 12(11), С. 2140 - 2140

Опубликована: Май 25, 2023

Various fields have been identified in the "omics" era, such as genomics, proteomics, transcriptomics, metabolomics, phenomics, and metagenomics. Among these, metagenomics has enabled a significant increase discoveries related to microbial world. Newly discovered microbiomes different ecologies provide meaningful information on diversity functions of microorganisms Earth. Therefore, results metagenomic studies new microbe-based applications human health, agriculture, food industry, among others. This review summarizes fundamental procedures recent advances bioinformatic tools. It also explores up-to-date study, plant research, environmental sciences, other fields. Finally, is powerful tool for studying world, it still numerous that are currently hidden awaiting discovery. this discusses future perspectives

Язык: Английский

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Advanced Methods for Natural Products Discovery: Bioactivity Screening, Dereplication, Metabolomics Profiling, Genomic Sequencing, Databases and Informatic Tools, and Structure Elucidation

Marine Drugs, Год журнала: 2023, Номер 21(5), С. 308 - 308

Опубликована: Май 19, 2023

Natural Products (NP) are essential for the discovery of novel drugs and products numerous biotechnological applications. The NP process is expensive time-consuming, having as major hurdles dereplication (early identification known compounds) structure elucidation, particularly determination absolute configuration metabolites with stereogenic centers. This review comprehensively focuses on recent technological instrumental advances, highlighting development methods that alleviate these obstacles, paving way accelerating towards Herein, we emphasize most innovative high-throughput tools advancing bioactivity screening, chemical analysis, dereplication, metabolite profiling, metabolomics, genome sequencing and/or genomics approaches, databases, bioinformatics, chemoinformatics, three-dimensional elucidation.

Язык: Английский

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Recent advances in plastic degradation – From microbial consortia-based methods to data sciences and computational biology driven approaches

Journal of Hazardous Materials, Год журнала: 2021, Номер 426, С. 128086 - 128086

Опубликована: Дек. 15, 2021

Язык: Английский

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Artificial intelligence challenges for predicting the impact of mutations on protein stability

Current Opinion in Structural Biology, Год журнала: 2021, Номер 72, С. 161 - 168

Опубликована: Дек. 15, 2021

Язык: Английский

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Marine drugs: Biology, pipelines, current and future prospects for production

Biotechnology Advances, Год журнала: 2021, Номер 54, С. 107871 - 107871

Опубликована: Ноя. 19, 2021

Язык: Английский

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Biodegradation of poly(ethylene terephthalate): Mechanistic insights, advances, and future innovative strategies

Chemical Engineering Journal, Год журнала: 2022, Номер 457, С. 141230 - 141230

Опубликована: Дек. 28, 2022

Язык: Английский

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Green catalysis for chemical transformation: The need for the sustainable development

Current Research in Green and Sustainable Chemistry, Год журнала: 2021, Номер 5, С. 100248 - 100248

Опубликована: Дек. 29, 2021

The worldwide concern for the sustainable future along with advancement in green products biotechnological routes has enhanced utilization of bio-catalysis also called as catalyst industrial domains. developments chemistry are intrinsically connected mostly to bio-catalyst due its key synthesis from renewable sources. Green potential catalyse different chemical reaction and therefore being an essential alternative environmentally unsafe mechanisms. In this context, purpose review is present brief introduction, importance bio-catalytic techniques perspective, mainly far-reaching applications. development metagenomics computational tools demonstrated developed fast growth leading progression novel enzymes properties future. However, it requires comprehensive study commercial supply, approach will fundamentally play role transformation broad industries including pharmaceutical, agriculture, healthcare industry next few decades. For all these reasons, aim significance integration enzymatic approaches challenges prominence a way forward direction.

Язык: Английский

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The plastisphere microbiome in alpine soils alters the microbial genetic potential for plastic degradation and biogeochemical cycling

Journal of Hazardous Materials, Год журнала: 2022, Номер 441, С. 129941 - 129941

Опубликована: Сен. 14, 2022

Plastic is exceedingly abundant in soils, but little known about its ecological consequences for soil microbiome functioning. Here we report the impacts of polyethylene and biodegradable Ecovio BI-OPL plastic films buried alpine soils 5 months on genetic potential using shotgun metagenomics. The was more affected by than polyethylene. Fungi, α- β-Proteobacteria dominated films. showed signs degradation after incubation, whereas did not. Genes involved cellular processes signaling (intracellular trafficking, secretion, vesicular transport), as well metabolism (carbohydrate, lipid secondary metabolism), were enriched plastisphere. Several α/β-hydrolase gene families (cutinase_like, polyesterase-lipase-cutinase, carboxylesterase), which encode enzymes essential to degradation, carbohydrate-active genes lignin murein increased Enriched nitrogen fixation organic N synthesis decreased nitrification altered biogeochemical cycling, leading higher ammonium concentrations depletion nitrite nitrate soil. Our results indicate that plastics affect functions suggest plastisphere has an untapped microbial biodegradation.

Язык: Английский

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Accelerating Biocatalysis Discovery with Machine Learning: A Paradigm Shift in Enzyme Engineering, Discovery, and Design

ACS Catalysis, Год журнала: 2023, Номер 13(21), С. 14454 - 14469

Опубликована: Окт. 26, 2023

Emerging computational tools promise to revolutionize protein engineering for biocatalytic applications and accelerate the development timelines previously needed optimize an enzyme its more efficient variant. For over a decade, benefits of predictive algorithms have helped scientists engineers navigate complexity functional sequence space. More recently, spurred by dramatic advances in underlying tools, faster, cheaper, accurate identification, characterization, has catapulted terms such as artificial intelligence machine learning must-have vocabulary field. This Perspective aims showcase current status pharmaceutical industry also discuss celebrate innovative approaches science highlighting their potential selected recent developments offering thoughts on future opportunities biocatalysis. It critically assesses technology's limitations, unanswered questions, unmet challenges.

Язык: Английский

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