ArticlemBio2020
Generation of Comprehensive Ecosystem-Specific Reference Databases with Species-Level Resolution by High-Throughput Full-Length 16S rRNA Gene Sequencing and Automated Taxonomy Assignment (AutoTax).
Article in mBio, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 70 papers.
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Who cites it
70 citing papers in PubMed, 122 citations in OpenAlex.
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- CoSMIC: A hybrid approach for large-scale, high-resolution microbial profiling of novel niches.PloS one · 2026Article
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- Temperature-Driven Divergence in Microbial Consortia and Physicochemical Functionality: A Comparative Study of High- and Medium-TemperatureMicroorganisms · 2025Article
- MultiTax-human: an extensive and high-resolution human-related full-length 16S rRNA reference database and taxonomy.Microbiology spectrum · 2025Article
- Evaluating the efficiency of 16S-ITS-23S operon sequencing for species level resolution in microbial communities.Scientific reports · 2025Article
- Sewer microbiomes shape microbial community composition and dynamics of wastewater treatment plants.The ISME journal · 2025Article
- Novel insights into ORFV B2L DNA vaccine-mediated gut microbiota modulation and immune augmentation in rats.Frontiers in immunology · 2025Article
- Novel potential biomarkers for predicting childhood caries via metagenomic analysis.Frontiers in cellular and infection microbiology · 2025Article
- Bacterial community and filamentous population of industrial wastewater treatment plants in Belgium.Applied microbiology and biotechnology · 2024Article
- Evaluation of microbial diversity in the formation water of the producer and marginal wells in bokaro coal field.Scientific reports · 2024Article
- MIMt: a curated 16S rRNA reference database with less redundancy and higher accuracy at species-level identification.Environmental microbiome · 2024Article
- High accuracy meets high throughput for near full-length 16S ribosomal RNA amplicon sequencing on the Nanopore platform.PNAS nexus · 2024Article
- Polylactic acid micro/nanoplastic-induced hepatotoxicity: Investigating food and air sources via multi-omics.Environmental science and ecotechnology · 2024Article
10 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
8 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
High-throughput 16S rRNA gene amplicon sequencing is an essential method for studying the diversity and dynamics of microbial communities. However, this method is presently hampered by the lack of high-identity reference sequences for many environmental microbes in the public 16S rRNA gene reference databases and by the absence of a systematic and comprehensive taxonomy for the uncultured majority. Here, we demonstrate how high-throughput synthetic long-read sequencing can be applied to create ecosystem-specific full-length 16S rRNA gene amplicon sequence variant (FL-ASV) resolved reference databases that include high-identity references (>98.7% identity) for nearly all abundant bacteria (>0.01% relative abundance) using Danish wastewater treatment systems and anaerobic digesters as an example. In addition, we introduce a novel sequence identity-based approach for automated taxonomy assignment (AutoTax) that provides a complete seven-rank taxonomy for all reference sequences, using the SILVA taxonomy as a backbone, with stable placeholder names for unclassified taxa. The FL-ASVs are perfectly suited for the evaluation of taxonomic resolution and bias associated with primers commonly used for amplicon sequencing, allowing researchers to choose those that are ideal for their ecosystem. Reference databases processed with AutoTax greatly improves the classification of short-read 16S rRNA ASVs at the genus- and species-level, compared with the commonly used universal reference databases. Importantly, the placeholder names provide a way to explore the unclassified environmental taxa at different taxonomic ranks, which in combination with
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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.