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

Molecular Biology and Evolution, Год журнала: 2021, Номер 38(12), С. 5825 - 5829

Опубликована: Сен. 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.

Язык: Английский

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Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3

eLife, Год журнала: 2021, Номер 10

Опубликована: Май 4, 2021

Culture-independent analyses of microbial communities have progressed dramatically in the last decade, particularly due to advances methods for biological profiling via shotgun metagenomics. Opportunities improvement continue accelerate, with greater access multi-omics, reference genomes, and strain-level diversity. To leverage these, we present bioBakery 3, a set integrated, improved taxonomic, strain-level, functional, phylogenetic metagenomes newly developed build on largest sequences now available. Compared current alternatives, MetaPhlAn 3 increases accuracy taxonomic profiling, HUMAnN improves that functional potential activity. These detected novel disease-microbiome links applications CRC (1262 metagenomes) IBD (1635 817 metatranscriptomes). Strain-level an additional 4077 StrainPhlAn PanPhlAn unraveled structure common gut microbe Ruminococcus bromii , previously described by only 15 isolate genomes. With open-source implementations cloud-deployable reproducible workflows, platform can help researchers deepen resolution, scale, multi-omic community studies.

Язык: Английский

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GTDB-Tk v2: memory friendly classification with the genome taxonomy database

Bioinformatics, Год журнала: 2022, Номер 38(23), С. 5315 - 5316

Опубликована: Окт. 11, 2022

Abstract Summary The Genome Taxonomy Database (GTDB) and associated taxonomic classification toolkit (GTDB-Tk) have been widely adopted by the microbiology community. However, growing size of GTDB bacterial reference tree has resulted in GTDB-Tk requiring substantial amounts memory (∼320 GB) which limits its adoption ease use. Here, we present an update to that uses a divide-and-conquer approach where user genomes are initially placed into with family-level representatives followed placement appropriate class-level subtree comprising species representatives. This substantially reduces requirements while having minimal impact on classification. Availability implementation is implemented Python licenced under GNU General Public Licence v3.0. Source code documentation available at: https://github.com/ecogenomics/gtdbtk. Supplementary information data at Bioinformatics online.

Язык: Английский

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Extending and improving metagenomic taxonomic profiling with uncharacterized species using MetaPhlAn 4

Nature Biotechnology, Год журнала: 2023, Номер 41(11), С. 1633 - 1644

Опубликована: Фев. 23, 2023

Abstract Metagenomic assembly enables new organism discovery from microbial communities, but it can only capture few abundant organisms most metagenomes. Here we present MetaPhlAn 4, which integrates information metagenome assemblies and isolate genomes for more comprehensive metagenomic taxonomic profiling. From a curated collection of 1.01 M prokaryotic reference metagenome-assembled genomes, define unique marker genes 26,970 species-level genome bins, 4,992 them taxonomically unidentified at the species level. 4 explains ~20% reads in international human gut microbiomes >40% less-characterized environments such as rumen microbiome proves accurate than available alternatives on synthetic evaluations while also reliably quantifying with no cultured isolates. Application method to >24,500 metagenomes highlights previously undetected be strong biomarkers host conditions lifestyles mouse shows that even uncharacterized genetically profiled resolution single strains.

Язык: Английский

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Enlightening the taxonomy darkness of human gut microbiomes with a cultured biobank

Microbiome, Год журнала: 2021, Номер 9(1)

Опубликована: Май 21, 2021

Abstract Background In gut microbiome studies, the cultured microbial resource plays essential roles, such as helping to unravel functions and host-microbe interactions. Although several major studies have been performed elucidate human microbiota, up 70% of Unified Human Gastrointestinal Genome species not date. Large-scale isolation identification well availability public are imperative for further characterizing functions. Results this study, we constructed a Gut Microbial Biobank (hGMB; homepage: hgmb.nmdc.cn ) through cultivation 10,558 isolates from 31 sample mixtures 239 fresh fecal samples healthy Chinese volunteers, deposited 1170 strains representing 400 different in culture collections International Depository Authority long-term preservation access worldwide. Following rules Code Nomenclature Prokaryotes, 102 new were characterized denominated, while 28 genera 3 families proposed. hGMB represented over 80% common dominant global 16S rRNA gene amplicon data ( n = 11,647) 24 “most-wanted” “medium priority” taxa proposed by Microbiome Project. We total sequenced 115 genomes novel 13 previously known species. Further silico analysis revealed that newly 22 uncultured (UHGG) contributed representatives potentially “dark taxa” had discovered UHGG. The nonredundant catalogs generated covered 50% functionally genes (KEGG orthologs) largest approximately 10% “most wanted” unknown proteins FUnkFams database. Conclusions A publicly accessible (hGMB) was established contained represents expands resources genomic repository adding species, genera, families, microbes.

Язык: Английский

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The Gut Virome Database Reveals Age-Dependent Patterns of Virome Diversity in the Human Gut

Cell Host & Microbe, Год журнала: 2020, Номер 28(5), С. 724 - 740.e8

Опубликована: Авг. 24, 2020

Язык: Английский

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Assessment of global health risk of antibiotic resistance genes

Nature Communications, Год журнала: 2022, Номер 13(1)

Опубликована: Март 23, 2022

Antibiotic resistance genes (ARGs) have accelerated microbial threats to human health in the last decade. Many can confer resistance, but evaluating relative risks of ARGs is complex. Factors such as abundance, propensity for lateral transmission and ability be expressed pathogens are all important. Here, an analysis at metagenomic level from various habitats (6 types habitats, 4572 samples) detects 2561 that collectively conferred 24 classes antibiotics. We quantitatively evaluate risk humans, defined will confound clinical treatment pathogens, these by integrating accessibility, mobility, pathogenicity availability. Our results demonstrate 23.78% pose a risk, especially those which multidrug resistance. also calculate antibiotic samples four main with machine learning, successfully map global marine over 75% accuracy. novel method surveilling help manage one most important animal health.

Язык: Английский

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Massive expansion of human gut bacteriophage diversity

Cell, Год журнала: 2021, Номер 184(4), С. 1098 - 1109.e9

Опубликована: Фев. 1, 2021

Bacteriophages drive evolutionary change in bacterial communities by creating gene flow networks that fuel ecological adaptions. However, the extent of viral diversity and its prevalence human gut remains largely unknown. Here, we introduce Gut Phage Database, a collection ∼142,000 non-redundant genomes (>10 kb) obtained mining dataset 28,060 globally distributed metagenomes 2,898 reference cultured bacteria. Host assignment revealed is highest Firmicutes phyla ∼36% clusters (VCs) are not restricted to single species, across phylogenetically distinct species. Epidemiological analysis uncovered 280 VCs found at least 5 continents highly prevalent phage clade with features reminiscent p-crAssphage. This high-quality, large-scale catalog will improve future virome studies enable bacteriophages.

Язык: Английский

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Prevotella diversity, niches and interactions with the human host

Nature Reviews Microbiology, Год журнала: 2021, Номер 19(9), С. 585 - 599

Опубликована: Май 28, 2021

Язык: Английский

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Role and Mechanism of Gut Microbiota in Human Disease

Frontiers in Cellular and Infection Microbiology, Год журнала: 2021, Номер 11

Опубликована: Март 17, 2021

The human gut microbiome is a huge microbial community that plays an irreplaceable role in life. With the further development of research, influence intestinal flora on diseases has been gradually excavated. Gut microbiota (GM) dysbiosis adverse health effects body will lead to variety chronic diseases. underlying mechanisms GM are incredibly complicated. This review focuses regulation and mechanism neurodegenerative diseases, cardiovascular metabolic gastrointestinal thus providing potential target for prevention treatment disease.

Язык: Английский

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