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The SILVA ribosomal RNA gene database project: improved data processing and web-based tools
TLDR
The extensively curated SILVA taxonomy and the new non-redundant SILVA datasets provide an ideal reference for high-throughput classification of data from next-generation sequencing approaches. Expand
SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB
TLDR
SILVA (from Latin silva, forest), was implemented to provide a central comprehensive web resource for up to date, quality controlled databases of aligned rRNA sequences from the Bacteria, Archaea and Eukarya domains. Expand
SINA: Accurate high-throughput multiple sequence alignment of ribosomal RNA genes
TLDR
The SILVA Incremental Aligner (SINA) used to align the rRNA gene databases provided by the SILVA ribosomal RNA project was evaluated and was able to achieve higher accuracy than PyNAST and mothur in all performed benchmarks. Expand
Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies
TLDR
The results of this study may be used as a guideline for selecting primer pairs with the best overall coverage and phylum spectrum for specific applications, therefore reducing the bias in PCR-based microbial diversity studies. Expand
Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences
TLDR
This article proposes rational taxonomic boundaries for high taxa of bacteria and archaea on the basis of 16S rRNA gene sequence identities and suggests a rationale for the circumscription of uncultured taxa that is compatible with the taxonomy of cultured bacteria and Archaea. Expand
The All-Species Living Tree project: a 16S rRNA-based phylogenetic tree of all sequenced type strains.
TLDR
The signing authors together with the journal Systematic and Applied Microbiology (SAM) have started an ambitious project to reconstruct a single 16S rRNA tree harboring all sequenced type strains of the hitherto classified species of Archaea and Bacteria. Expand
Substrate-Controlled Succession of Marine Bacterioplankton Populations Induced by a Phytoplankton Bloom
TLDR
The bacterioplankton response to a diatom bloom in the North Sea is investigated and a dynamic succession of populations at genus-level resolution is observed, revealing how planktonic species, despite their seemingly homogeneous habitat, can evade extinction by direct competition. Expand
Bacterioplankton Compositions of Lakes and Oceans: a First Comparison Based on Fluorescence In Situ Hybridization
TLDR
FISH with rRNA-targeted oligonucleotide probes was used to investigate the phylogenetic composition of bacterioplankton communities in several freshwater and marine samples, finding that Beta subclass proteobacteria constituted a dominant fraction in freshwater systems and members of the Cytophaga-Flavobacterium cluster were the most abundant group detected in the marine systems. Expand
Comparative 16S rRNA Analysis of Lake Bacterioplankton Reveals Globally Distributed Phylogenetic Clusters Including an Abundant Group of Actinobacteria
TLDR
A combination of phylogenetic analysis and FISH was used to reveal 16 globally distributed sequence clusters and to confirm the broad distribution, abundance, and high biomass of members of the class Actinobacteria in freshwater ecosystems. Expand
The SILVA and “All-species Living Tree Project (LTP)” taxonomic frameworks
TLDR
The improvements the SILVA taxonomy has undergone in the last 3 years are described, focusing on the curation process, the various resources used for curation and the comparison of the SILva taxonomy with Greengenes and RDP-II taxonomies. Expand
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