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Overview on our ARB/SILVA-related Projects

SSU Ref NR (non-redundant)

For users interested in representative (rRNA) sequence collections, the rapid growth of the datasets has led to immense hardware requirements paired with a significantly increased amount of time to analyse the data.

To compensate for this, the SILVA project now offers a non-redundant version of the SSU Ref dataset (SILVA SSU Ref NR). A 99% identity criterion was applied to sort out more than 50% of the sequences within the full SSU Ref.

Although significantly reduced in size, the SSU Ref NR is still a representative dataset offering a comprehensive high quality alignment and a fully classified tree reflecting the complete SILVA taxonomy, inlcuding sequences from all three domains of life. It represents the perfect starting point for your daily rRNA work based on ARB/SILVA - now again asking for just moderate hardware requirements.

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Eukaryotic Taxonomy Working Group (ETWG)

The Eukaryotic Taxonomy Working Group (ETWG) has been founded in October 2011 to create a unified taxonomy for Eukaryotes based on 18S/28S ribosomal RNA gene sequences. It is  now funded by the Gordon and Betty Moore Foundation as the UniEuk project.

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dsrAB@SILVA – high quality database of the functional marker genes encoding dissimilatory sulfite reductases


For users interested in dsrA/B-based amplicon surveys to study the microbial ecology of dsrAB-encoding sulfate/sulfite reducers or sulfur oxidizers, dsrAB@SILVA provides a curated dsrA and dsrB database accompanied by a GTDB-based taxonomy as based on 902 bacterial and 48 archaeal (metagenome-assambled) genomes. The database encompasses reductive bacterial-type dsrA/B, oxidative bacterial-type dsrA/B, and reductive archaeal-type dsrA/B.

Muhe Diao, Stefan Dyksma, Elif Koeksoy, David Kamanda Ngugi, Karthik Anantharaman, Alexander Loy, Michael Pester (2023) Global diversity and inferred ecophysiology of microorganisms with the potential for dissimilatory sulfate/sulfite reduction. Opens external link in new windowbioRxiv 2023.06.27.546762

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'The All-Species Living Tree' Project


The All-Species Living Tree is a regularly-updated 16S (SSU) rRNA-based phylogenetic tree harboring all sequenced type strains of the hitherto classified species of Archaea and Bacteria.

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Contextual Data (Metadata) for Environmental Sequences

Contextual data (metadata) is the set of data describing aspects like geographic location and habitat type from which a sequence was retrieved as well as the processing of the sample.

Following the Opens external link in new windowMIGS/MIMS and MIMARKS standards for environmental samples at least providing the GPS position (longitude, latitude), depth/altitude and time of sampling is highly recommended.

The SILVA team together with the Genomics Standards Consortium has started a project to facilitate and improve the integration of contextual data for environmental sequences with an emphasis on marker genes like ribosomal RNA sequence data.

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A Standard Operating Procedure for Phylogenetic Inference (SOPPI)

A Standard Operating Procedure offering a helping hand in working through the process of contextual data acquisition, alignment, phylogenetic tree reconstruction, presentation of trees and documentation.

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International Workshop on ribosomal RNA Technology, 2008

On April 7- 9, 2008 in Bremen, Germany, in five sessions, 26 leading international speakers and about 120 participants representing diverse disciplines discussed and summarized the current status of the rRNA-based technologies. 

Thirty years have passed since Carl Woese proposed three primary domains of life based on the phylogenetic analysis of the ribosomal RNA genes. It was now the time to strategize on the best ways of proceeding on both biological and technological fronts ...

Program, Speakers, Impressions, Reports, etc.