GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy

Nucleic Acids Research, Год журнала: 2021, Номер 50(D1), С. D785 - D794

Опубликована: Сен. 8, 2021

Abstract The Genome Taxonomy Database (GTDB; https://gtdb.ecogenomic.org) provides a phylogenetically consistent and rank normalized genome-based taxonomy for prokaryotic genomes sourced from the NCBI Assembly database. GTDB R06-RS202 spans 254 090 bacterial 4316 archaeal genomes, 270% increase since introduction of in November, 2017. These are organized into 45 555 2339 species clusters which is 200% integration June, 2019. Here, we explore diversity perspective highlight importance metagenome-assembled expanding available genomic representation. We also discuss improvements to website allow tracking taxonomic changes, easy assessment genome assembly quality, identification assembled type material or used as representatives. Methodological updates policy changes made inception then described along with procedure update GTDB. conclude discussion on use average nucleotide identities pragmatic approach delineating species.

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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A genomic surveillance framework and genotyping tool for Klebsiella pneumoniae and its related species complex

Nature Communications, Год журнала: 2021, Номер 12(1)

Опубликована: Июль 7, 2021

Abstract Klebsiella pneumoniae is a leading cause of antimicrobial-resistant (AMR) healthcare-associated infections, neonatal sepsis and community-acquired liver abscess, associated with chronic intestinal diseases. Its diversity complex population structure pose challenges for analysis interpretation K. genome data. Here we introduce Kleborate, tool analysing genomes its species complex, which consolidates interrogation key features proven clinical importance. Kleborate provides framework to support genomic surveillance epidemiology in research, public health settings. To demonstrate utility apply analyse publicly available genomes, including isolates from pan-European study carbapenemase-producing , highlighting global trends AMR virulence as examples what could be achieved by applying this within more systematic efforts. We also the application detect type gut metagenomes.

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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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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Polypolish: Short-read polishing of long-read bacterial genome assemblies

PLoS Computational Biology, Год журнала: 2022, Номер 18(1), С. e1009802 - e1009802

Опубликована: Янв. 24, 2022

Long-read-only bacterial genome assemblies usually contain residual errors, most commonly homopolymer-length errors. Short-read polishing tools can use short reads to fix these but rely on short-read alignment which is unreliable in repeat regions. Errors such regions are therefore challenging and often remain after polishing. Here we introduce Polypolish, a new polisher uses all-per-read alignments repair errors sequences that other polishers cannot. Polypolish performed well benchmarking tests using both simulated real reads, it almost never introduced during The best results were achieved by combination with polishers.

Язык: Английский

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Trycycler: consensus long-read assemblies for bacterial genomes

Genome biology, Год журнала: 2021, Номер 22(1)

Опубликована: Сен. 14, 2021

Abstract While long-read sequencing allows for the complete assembly of bacterial genomes, assemblies contain a variety errors. Here, we present Trycycler, tool which produces consensus from multiple input same genome. Benchmarking showed that Trycycler contained fewer errors than constructed with single tool. Post-assembly polishing further reduced and Trycycler+polishing were most accurate genomes in our study. As requires manual intervention, its output is not deterministic. However, demonstrated users converge on similar are consistently more those produced by automated tools.

Язык: Английский

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Effect of host genetics on the gut microbiome in 7,738 participants of the Dutch Microbiome Project

Nature Genetics, Год журнала: 2022, Номер 54(2), С. 143 - 151

Опубликована: Фев. 1, 2022

Язык: Английский

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Combined effects of host genetics and diet on human gut microbiota and incident disease in a single population cohort

Nature Genetics, Год журнала: 2022, Номер 54(2), С. 134 - 142

Опубликована: Фев. 1, 2022

Язык: Английский

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Roseobacters in a Sea of Poly- and Paraphyly: Whole Genome-Based Taxonomy of the Family Rhodobacteraceae and the Proposal for the Split of the “Roseobacter Clade” Into a Novel Family, Roseobacteraceae fam. nov.

Frontiers in Microbiology, Год журнала: 2021, Номер 12

Опубликована: Июнь 25, 2021

The family Rhodobacteraceae consists of alphaproteobacteria that are metabolically, phenotypically, and ecologically diverse. It includes the roseobacter clade, an informal designation, representing one most abundant groups marine bacteria. rapid pace discovery novel roseobacters in last three decades meant best practice for taxonomic classification, a polyphasic approach utilizing phenotypic, genotypic, phylogenetic characteristics, was not always followed. Early efforts classification relied heavily on 16S rRNA gene sequence similarity resulted numerous inconsistencies, with several poly- paraphyletic genera within this family. Next-generation sequencing technologies have allowed whole-genome sequences to be obtained type strains, making revision their taxonomy possible. In study, we performed genotypic analyses combined meta-analysis phenotypic data review classifications 331 strains (under 119 genera) Representatives clade only different environmental adaptions from other isolates but were also found distinct based genomic, phylogenetic, silico -predicted data. As such, propose move group bacteria into new family, Roseobacteraceae fam. nov. total, reclassifications 327 species 128 genera, suggesting misidentification is more problematic at genus than level. By resolving inconsistencies established set coherent criteria whole-genome-based will help guide future prevent propagation errors.

Язык: Английский

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