Comprehensive ecosystem-specific 16S rRNA gene databases with automated taxonomy assignment (AutoTax) provide species-level resolution in microbial ecology

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Resumé

High-throughput 16S rRNA gene amplicon sequencing is an indispensable 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 lack of a systematic and comprehensive taxonomic classification for most environmental bacteria. Here we combine high-quality and high-throughput full-length 16S rRNA gene sequencing with a novel sequence identity-based approach for automated taxonomy assignment (AutoTax) to create robust, near-complete 16S rRNA gene databases for complex environmental ecosystems. To demonstrate the benefit of the approach, we created an ecosystem-specific database for wastewater treatment systems and anaerobic digesters. The novel approach allows consistent species-level classification of 16S rRNA amplicons sequence variants and the design of highly specific oligonucleotide probes for fluorescence in situ hybridization, which can reveal in situ properties of microbes at unprecedented taxonomic resolution.
OriginalsprogEngelsk
TidsskriftbioRxiv
DOI
StatusUdgivet - 2019

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Ecology
rRNA Genes
Ecosystem
Databases
Oligonucleotide Probes
Waste Water
Fluorescence In Situ Hybridization
Bacteria

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title = "Comprehensive ecosystem-specific 16S rRNA gene databases with automated taxonomy assignment (AutoTax) provide species-level resolution in microbial ecology",
abstract = "High-throughput 16S rRNA gene amplicon sequencing is an indispensable 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 lack of a systematic and comprehensive taxonomic classification for most environmental bacteria. Here we combine high-quality and high-throughput full-length 16S rRNA gene sequencing with a novel sequence identity-based approach for automated taxonomy assignment (AutoTax) to create robust, near-complete 16S rRNA gene databases for complex environmental ecosystems. To demonstrate the benefit of the approach, we created an ecosystem-specific database for wastewater treatment systems and anaerobic digesters. The novel approach allows consistent species-level classification of 16S rRNA amplicons sequence variants and the design of highly specific oligonucleotide probes for fluorescence in situ hybridization, which can reveal in situ properties of microbes at unprecedented taxonomic resolution.",
author = "Dueholm, {Morten Simonsen} and Andersen, {Kasper Skytte} and Francesca Petriglieri and McIlroy, {Simon Jon} and Nierychlo, {Marta Anna} and Petersen, {Jette Fischer} and Kristensen, {Jannie Munk} and Erika Yashiro and Karst, {S{\o}ren Michael} and Mads Albertsen and Nielsen, {Per Halkj{\ae}r}",
year = "2019",
doi = "10.1101/672873",
language = "English",
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TY - JOUR

T1 - Comprehensive ecosystem-specific 16S rRNA gene databases with automated taxonomy assignment (AutoTax) provide species-level resolution in microbial ecology

AU - Dueholm, Morten Simonsen

AU - Andersen, Kasper Skytte

AU - Petriglieri, Francesca

AU - McIlroy, Simon Jon

AU - Nierychlo, Marta Anna

AU - Petersen, Jette Fischer

AU - Kristensen, Jannie Munk

AU - Yashiro, Erika

AU - Karst, Søren Michael

AU - Albertsen, Mads

AU - Nielsen, Per Halkjær

PY - 2019

Y1 - 2019

N2 - High-throughput 16S rRNA gene amplicon sequencing is an indispensable 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 lack of a systematic and comprehensive taxonomic classification for most environmental bacteria. Here we combine high-quality and high-throughput full-length 16S rRNA gene sequencing with a novel sequence identity-based approach for automated taxonomy assignment (AutoTax) to create robust, near-complete 16S rRNA gene databases for complex environmental ecosystems. To demonstrate the benefit of the approach, we created an ecosystem-specific database for wastewater treatment systems and anaerobic digesters. The novel approach allows consistent species-level classification of 16S rRNA amplicons sequence variants and the design of highly specific oligonucleotide probes for fluorescence in situ hybridization, which can reveal in situ properties of microbes at unprecedented taxonomic resolution.

AB - High-throughput 16S rRNA gene amplicon sequencing is an indispensable 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 lack of a systematic and comprehensive taxonomic classification for most environmental bacteria. Here we combine high-quality and high-throughput full-length 16S rRNA gene sequencing with a novel sequence identity-based approach for automated taxonomy assignment (AutoTax) to create robust, near-complete 16S rRNA gene databases for complex environmental ecosystems. To demonstrate the benefit of the approach, we created an ecosystem-specific database for wastewater treatment systems and anaerobic digesters. The novel approach allows consistent species-level classification of 16S rRNA amplicons sequence variants and the design of highly specific oligonucleotide probes for fluorescence in situ hybridization, which can reveal in situ properties of microbes at unprecedented taxonomic resolution.

U2 - 10.1101/672873

DO - 10.1101/672873

M3 - Journal article

JO - bioRxiv

JF - bioRxiv

ER -