A5088893810- Genomics and Phylogenetic Studies
- Microbial Community Ecology and Physiology
- Probiotics and Fermented Foods
- Distributed and Parallel Computing Systems
- Diabetes Treatment and Management
- Plant Pathogens and Fungal Diseases
- RNA and protein synthesis mechanisms
- Amino Acid Enzymes and Metabolism
- Gut microbiota and health
- Plant Pathogenic Bacteria Studies
- Protist diversity and phylogeny
- Legume Nitrogen Fixing Symbiosis
- Bacteriophages and microbial interactions
- Microbial Metabolism and Applications
- CRISPR and Genetic Engineering
- Mycobacterium research and diagnosis
- Identification and Quantification in Food
The University of Queensland
2018-2024
Ecogenomics (Japan)
2018-2024
The GTDB Toolkit (GTDB-Tk) provides objective taxonomic assignments for bacterial and archaeal genomes based on the Genome Taxonomy Database (GTDB). GTDB-Tk is computationally efficient able to classify thousands of draft in parallel. Here we demonstrate accuracy by evaluating its performance a phylogenetically diverse set 10,156 metagenome-assembled genomes.
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...
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...
Abstract The Genome Taxonomy Database (GTDB) is a taxonomic framework that defines prokaryotic taxa as monophyletic groups in concatenated protein reference trees according to systematic criteria. This has resulted substantial number of changes existing classifications (https://gtdb.ecogenomic.org). In the case union taxa, GTDB names were applied based on priority publication. division or change rank led formation new Latin above genus only made publicly available via website without...
Abstract We recently introduced the Genome Taxonomy Database (GTDB), a phylogenetically consistent, genome-based taxonomy providing rank normalized classifications for nearly 150,000 genomes from domain to genus. However, 40% of used infer GTDB reference tree lack species name, reflecting large number in public repositories without complete taxonomic assignments. Here we address this limitation by proposing 24,706 clusters which encompass all publicly available bacterial and archaeal when...
Abstract 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...
Abstract An increasing wealth of genomic data from cultured and uncultured microorganisms provides the opportunity to develop a systematic taxonomy based on evolutionary relationships. Here we propose standardized archaeal taxonomy, as part Genome Taxonomy Database (GTDB), derived 122 concatenated protein phylogeny that resolves polyphyletic groups normalizes ranks relative divergence (RED). The resulting is stable under range phylogenetic variables, including marker genes, inference...
The Genome Taxonomy Database (GTDB) provides a species to domain classification of publicly available genomes based on average nucleotide identity (ANI) (for species) and concatenated gene phylogeny normalized by evolutionary rates genus phylum), which has been widely adopted the scientific community. Here, we use UNClutterer (GUNC) software identify putatively contaminated in GTDB release 07-RS207. We found that GUNC reported 35,723 as contaminated, comprising 11.25 % 317,542 To assess...
Abstract Candidatus Patescibacteria is a diverse bacterial phylum that notable for members with ultrasmall cell size, reduced genomes, limited metabolic capabilities, and dependence on other prokaryotic hosts. Despite the prevalence of name Ca. in scientific literature, it not officially recognized under International Code Nomenclature Prokaryotes lacks nomenclatural type. Here, we rectify this situation by describing two closely related circular metagenome-assembled genomes proposing one...
Microbial taxonomy and nomenclature have been challenged by methodological advances in high-throughput sequencing high-performance computing. While appears to adapt rapidly has benefited enormously from the availability of whole-genome sequences, still struggles embrace these changes. Here, we present two independent initiatives that resulted transitions taxonomic practices microbiology a phenotypic single gene-driven framework genome-based driven framework. The first initiative, Genome...
Abstract Genomes are fundamental to understanding microbial ecology and evolution. The emergence of high-throughput, long-read DNA sequencing has enabled recovery genomes from environmental samples at scale. However, expanding the genome catalogue soils sediments been challenging due enormous complexity these environments. Here, we performed deep, Nanopore 154 soil sediment collected across Denmark through an optimised bioinformatics pipeline, recovered 15,314 novel species, including 4,757...
Abstract Candidatus Patescibacteria is a diverse bacterial phylum that notable for members with ultrasmall cell size, reduced genomes, limited metabolic capabilities and dependence on other prokaryotic hosts. Despite the prevalence of name Ca. in scientific literature, it not officially recognized under International Code Nomenclature Prokaryotes (ICNP) lacks nomenclatural type. Here, we rectify this situation by describing two closely related circular metagenome-assembled genomes (MAGs)...
Abstract The Genome Taxonomy Database (GTDB) is a taxonomic framework that defines prokaryotic taxa as monophyletic groups in concatenated protein reference trees according to systematic criteria. This has resulted substantial number of changes existing classifications (https://gtdb.ecogenomic.org). In the case union taxa, names were applied based on priority publication. division or change rank led formation new Latin above genus only made publicly available via GTDB website without...