Taxonomic parameters revisited : tarnished gold standards

By E. Stackebrandt. 2006

2,163 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/50b6c2ffe163a091511d9e857a1ce334184c7655

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Citations in the corpus

Microbial culturomics: paradigm shift in the human gut microbiome study. (2012, background): “7% was chosen to define a new bacterial species [11].”
Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. (2018, methodology): “In this two-step approach, the list of species that is required to compare to the strain in question using genome sequences is obtained using a 16S-based search [11]; only species showing 98.7% or higher 16S similarity are selected for calculating OGRIs [7, 13, 14].”
FunGene: the functional gene pipeline and repository (2013, background): “Using this 70% re-association species deﬁnition, Stackebrandt and Ebers found that strains of the same species almost always share more than 99% full-length 16S rRNA gene identity, while different species can share identical 16S gene sequences (Stackebrandt and Ebers, 2006).”
Comparative Analysis of Pyrosequencing and a Phylogenetic Microarray for Exploring Microbial Community Structures in the Human Distal Intestine (2009, unknown): “However, for species/strain-level resolution, either longer ribosomal sequences or additional experiments are required [52], unless there are distinct and identifiable differences between the variable regions of the particular organisms of interest.”
Ribosomal Database Project: data and tools for high throughput rRNA analysis (2013, background): “Because rRNA genes are too slowly evolving to reliably separate the validly named species (18), genus is the lowest rank presented in the RDP taxonomy.”
Uncultivated microbes in need of their own taxonomy (2017, background): “For the past decade, a cutoff value of about 98.6% (Stackebrandt and Ebers, 2006) using the almost full-length sequence to minimize the effect of sequencing errors (Yarza et al., 2014), has been accepted as the highest identity value that generally guarantees that two organisms belong to distinct…”
Minimum entropy decomposition: Unsupervised oligotyping for sensitive partitioning of high-throughput marker gene sequences (2014, background): “One solution is to increase the similarity threshold, as previously proposed (Stackebrandt and Ebers, 2006); however, this approach does not scale.”
Ongoing revolution in bacteriology: routine identification of bacteria by matrix-assisted laser desorption ionization time-of-flight mass spectrometry. (2009, background): “7% sequence similarity with the closest bacterial species sequence in GenBank [11]; it was correctly identified when its partial rpoB gene sequence yielded 97% sequence similarity with the closest bacterial species sequence in GenBank or a local database [10, 12].”
Diversity of endophytic actinomycetes in mandarin grown in northern Thailand, their phytohormone production potential and plant growth promoting activity (2013, background): “Stackebrandt and Ebers (2006) increased the recommended 16S rRNA gene sequence similarity from 97 to 98.7–99%, and approximately 20% of the 16S rRNA gene sequences in their study exhibited a similarity value > 99% with corresponding DDH values 70%.”
The All-Species Living Tree project: a 16S rRNA-based phylogenetic tree of all sequenced type strains. (2008, unknown): “7–99% [29].”
Exact sequence variants should replace operational taxonomic units in marker-gene data analysis (2017, background): “…often unacknowledged dual mandate is that OTUs struggle to serve both purposes well; the connection between OTUs and species is largely unfounded (Stackebrandt & Ebers, 2006), and the most common methods often output numbers of OTUs an order-of-magnitude higher than the number of strains present…”
EzTaxon: a web-based tool for the identification of prokaryotes based on 16S ribosomal RNA gene sequences. (2007, background): “More recently, Stackebrandt & Ebers (2006) proposed a more relaxed cut-off value of 98.7–99 %, after inspection of a large amount of recently published data.”