ArticleBioinformatics (Oxford, England)2015
Taxator-tk: precise taxonomic assignment of metagenomes by fast approximation of evolutionary neighborhoods.
Article in Bioinformatics (Oxford, England), 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 78 papers.
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Who cites it
78 citing papers in PubMed, 157 citations in OpenAlex.
- A bacterial pangenome association study identifies a role for polyamine metabolism and alkaline tolerance in middle ear infections.PLoS pathogens · 2026Article
- Metagenomic sequencing and binning reveal carbon cycling microorganisms and gene functions in park environments.BMC microbiology · 2026Article
- Upregulated jasmonate signaling shifts Arabidopsis microbiota interactions and stress adaptations through a positive feedback loop.The ISME journal · 2026Article
- The engineering of TBBPA-degrading synthetic microbiomes with integrated strategies.NPJ biofilms and microbiomes · 2025Article
- Metagenomic analysis to identify unique microbes in the rhizosphere of basmati rice (Oryza sativa L.) accessions.Scientific reports · 2025Article
- Yanomami skin microbiome complexity challenges prevailing concepts of healthy skin.Nature communications · 2025Article
- Metronidazole response profiles of Gardnerella species are congruent with phylogenetic and comparative genomic analyses.Genome medicine · 2025Article
- A review of neural networks for metagenomic binning.Briefings in bioinformatics · 2025Review
- Eradication of Helicobacter pylori reshapes gut microbiota and facilitates the evolution of antimicrobial resistance through gene transfer and genomic mutations in the gut.BMC microbiology · 2025Article
- Riverine antibiotic resistome along an anthropogenic gradient.Frontiers in microbiology · 2025Article
- The hidden nitrogen nexus: stochastic assembly and linear gene synergies drive urban park microbial networks.Frontiers in microbiology · 2025Article
- Spatial analysis of murine microbiota and bile acid metabolism during amoxicillin treatment.Cell reports · 2024Article
- Genomic and induction evidence for bacteriophage contributions to sargassum-bacteria symbioses.Microbiome · 2024Article
- Rich microbial and depolymerising diversity in Antarctic krill gut.Microbiology spectrum · 2024Article
- Article
- Viral Communities Contribute More to the Lysis of Antibiotic-Resistant Bacteria than the Transduction of Antibiotic Resistance Genes in Anaerobic Digestion Revealed by Metagenomics.Environmental science & technology · 2024Article
- Fecal microbial gene transfer contributes to the high-grain diet-induced augmentation of aminoglycoside resistance in dairy cattle.mSystems · 2024Article
- Nitrate-dependent antimony oxidase in an uncultured Symbiobacteriaceae member.The ISME journal · 2024Article
- Gut microbiota enhance energy accumulation of black-necked crane to cope with impending migration.Applied microbiology and biotechnology · 2023Article
- Potential of Microbial Communities to Perform Dehalogenation Processes in Natural and Anthropogenically Modified Environments-A Metagenomic Study.Microorganisms · 2023Article
18 more citing papers are in PubMed but not listed here.
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
motivationMetagenomics characterizes microbial communities by random shotgun sequencing of DNA isolated directly from an environment of interest. An essential step in computational metagenome analysis is taxonomic sequence assignment, which allows identifying the sequenced community members and reconstructing taxonomic bins with sequence data for the individual taxa. For the massive datasets generated by next-generation sequencing technologies, this cannot be performed with de-novo phylogenetic inference methods. We describe an algorithm and the accompanying software, taxator-tk, which performs taxonomic sequence assignment by fast approximate determination of evolutionary neighbors from sequence similarities.
resultsTaxator-tk was precise in its taxonomic assignment across all ranks and taxa for a range of evolutionary distances and for short as well as for long sequences. In addition to the taxonomic binning of metagenomes, it is well suited for profiling microbial communities from metagenome samples because it identifies bacterial, archaeal and eukaryotic community members without being affected by varying primer binding strengths, as in marker gene amplification, or copy number variations of marker genes across different taxa. Taxator-tk has an efficient, parallelized implementation that allows the assignment of 6 Gb of sequence data per day on a standard multiprocessor system with 10 CPU cores and microbial RefSeq as the genomic reference data.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.