eggNOG-mapper v2: Functional Annotation, Orthology Assignments, and Domain Prediction at the Metagenomic Scale

Molecular Biology and Evolution, Journal Year: 2021, Volume and Issue: 38(12), P. 5825 - 5829

Published: Sept. 30, 2021

Even though automated functional annotation of genes represents a fundamental step in most genomic and metagenomic workflows, it remains challenging at large scales. Here, we describe major upgrade to eggNOG-mapper, tool for based on precomputed orthology assignments, now optimized vast (meta)genomic data sets. Improvements version 2 include full update both the genomes databases those from eggNOG v5, as well several efficiency enhancements new features. Most notably, eggNOG-mapper v2 allows for: 1) de novo gene prediction raw contigs, 2) built-in pairwise prediction, 3) fast protein domain discovery, 4) GFF decoration. is available standalone or an online service http://eggnog-mapper.embl.de.

Language: Английский

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Life and death in the soil microbiome: how ecological processes influence biogeochemistry

Nature Reviews Microbiology, Journal Year: 2022, Volume and Issue: 20(7), P. 415 - 430

Published: Feb. 28, 2022

Language: Английский

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CheckM2: a rapid, scalable and accurate tool for assessing microbial genome quality using machine learning

Nature Methods, Journal Year: 2023, Volume and Issue: 20(8), P. 1203 - 1212

Published: July 27, 2023

Language: Английский

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eggNOG-mapper v2: Functional Annotation, Orthology Assignments, and Domain Prediction at the Metagenomic Scale

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2021, Volume and Issue: unknown

Published: June 3, 2021

Abstract Even though automated functional annotation of genes represents a fundamental step in most genomic and metagenomic workflows, it remains challenging at large scales. Here, we describe major upgrade to eggNOG-mapper, tool for based on precomputed orthology assignments, now optimized vast (meta)genomic data sets. Improvements version 2 include full update both the genomes databases those from eggNOG v5, as well several efficiency enhancements new features. Most notably, eggNOG-mapper v2 allows: (i) de novo gene prediction raw contigs, (ii) built-in pairwise prediction, (iii) fast protein domain discovery, (iv) GFF decoration. is available standalone or an online service http://eggnog-mapper.embl.de .

Language: Английский

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dbCAN3: automated carbohydrate-active enzyme and substrate annotation

Nucleic Acids Research, Journal Year: 2023, Volume and Issue: 51(W1), P. W115 - W121

Published: May 1, 2023

Carbohydrate active enzymes (CAZymes) are made by various organisms for complex carbohydrate metabolism. Genome mining of CAZymes has become a routine data analysis in (meta-)genome projects, owing to the importance bioenergy, microbiome, nutrition, agriculture, and global carbon recycling. In 2012, dbCAN was provided as an online web server automated CAZyme annotation. dbCAN2 (https://bcb.unl.edu/dbCAN2) further developed 2018 meta combine multiple tools improved also included CGC-Finder, tool identifying gene clusters (CGCs) (meta-)genomes. We have updated dbCAN3 with following new functions components: (i) dbCAN-sub profile Hidden Markov Model database (HMMdb) substrate prediction at subfamily level; (ii) searching against experimentally characterized polysaccharide utilization loci (PULs) known glycan substates dbCAN-PUL CGC (iii) majority voting method consider all predicted from (iv) browsing visualization results on website. summary, not only inherits dbCAN2, but integrates three methods prediction.

Language: Английский

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METABOLIC: high-throughput profiling of microbial genomes for functional traits, metabolism, biogeochemistry, and community-scale functional networks

Microbiome, Journal Year: 2022, Volume and Issue: 10(1)

Published: Feb. 16, 2022

Advances in microbiome science are being driven large part due to our ability study and infer microbial ecology from genomes reconstructed mixed communities using metagenomics single-cell genomics. Such omics-based techniques allow us read genomic blueprints of microorganisms, decipher their functional capacities activities, reconstruct roles biogeochemical processes. Currently available tools for analyses data can annotate depict metabolic functions some extent; however, no standardized approaches currently the comprehensive characterization predictions, metabolite exchanges, interactions, contributions cycling.

Language: Английский

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Deep sea sediments associated with cold seeps are a subsurface reservoir of viral diversity

The ISME Journal, Journal Year: 2021, Volume and Issue: 15(8), P. 2366 - 2378

Published: March 1, 2021

Abstract In marine ecosystems, viruses exert control on the composition and metabolism of microbial communities, influencing overall biogeochemical cycling. Deep sea sediments associated with cold seeps are known to host taxonomically diverse but little is about infecting these microorganisms. Here, we probed metagenomes from seven geographically across global oceans assess viral diversity, virus–host interaction, virus-encoded auxiliary metabolic genes (AMGs). Gene-sharing network comparisons inhabiting other ecosystems reveal that seep harbour considerable unexplored diversity. Most display high degrees endemism fluid flux being one main drivers community composition. silico predictions linked 14.2% populations many belonging poorly understood candidate bacterial archaeal phyla. Lysis was predicted be a predominant lifestyle based lineage-specific virus/host abundance ratios. Metabolic prokaryotic genomes AMGs suggest influence hydrocarbon biodegradation at seeps, as well carbon, sulfur nitrogen cycling via virus-induced mortality and/or augmentation. Overall, findings diversity biogeography indicate how may manipulate ecology biogeochemistry.

Language: Английский

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Integrating cultivation and metagenomics for a multi-kingdom view of skin microbiome diversity and functions

Nature Microbiology, Journal Year: 2021, Volume and Issue: 7(1), P. 169 - 179

Published: Dec. 24, 2021

Language: Английский

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Non-syntrophic methanogenic hydrocarbon degradation by an archaeal species

Nature, Journal Year: 2021, Volume and Issue: 601(7892), P. 257 - 262

Published: Dec. 22, 2021

Language: Английский

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Wildfire-dependent changes in soil microbiome diversity and function

Nature Microbiology, Journal Year: 2022, Volume and Issue: 7(9), P. 1419 - 1430

Published: Aug. 25, 2022

Abstract Forest soil microbiomes have crucial roles in carbon storage, biogeochemical cycling and rhizosphere processes. Wildfire season length, the frequency size of severe fires increased owing to climate change. Fires affect ecosystem recovery modify microbially mediated To study wildfire-dependent changes microbiomes, we characterized functional shifts microbiota (bacteria, fungi viruses) across burn severity gradients (low, moderate high severity) 1 yr post fire coniferous forests Colorado Wyoming, USA. We found severity-dependent increases Actinobacteria encoding genes for heat resistance, fast growth, pyrogenic utilization that might enhance post-fire survival. report led loss ectomycorrhizal less tolerant microbial taxa. Viruses remained active soils probably influenced biogeochemistry via turnover biomass ecosystem-relevant auxiliary metabolic genes. Our genome-resolved analyses link taxonomy functions reveal complexity microbiome activity.

Language: Английский

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