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Complete genome sequence of DSM 30083T, the type strain (U5/41T) of Escherichia coli, and a proposal for delineating subspecies in microbial taxonomy

Overview of attention for article published in Standards in Genomic Sciences, December 2014
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About this Attention Score

  • Above-average Attention Score compared to outputs of the same age (59th percentile)

Mentioned by

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5 Wikipedia pages

Citations

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301 Dimensions

Readers on

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235 Mendeley
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Title
Complete genome sequence of DSM 30083T, the type strain (U5/41T) of Escherichia coli, and a proposal for delineating subspecies in microbial taxonomy
Published in
Standards in Genomic Sciences, December 2014
DOI 10.1186/1944-3277-9-2
Pubmed ID
Authors

Jan P Meier-Kolthoff, Richard L Hahnke, Jörn Petersen, Carmen Scheuner, Victoria Michael, Anne Fiebig, Christine Rohde, Manfred Rohde, Berthold Fartmann, Lynne A Goodwin, Olga Chertkov, TBK Reddy, Amrita Pati, Natalia N Ivanova, Victor Markowitz, Nikos C Kyrpides, Tanja Woyke, Markus Göker, Hans-Peter Klenk

Abstract

Although Escherichia coli is the most widely studied bacterial model organism and often considered to be the model bacterium per se, its type strain was until now forgotten from microbial genomics. As a part of the G enomic E ncyclopedia of B acteria and A rchaea project, we here describe the features of E. coli DSM 30083(T) together with its genome sequence and annotation as well as novel aspects of its phenotype. The 5,038,133 bp containing genome sequence includes 4,762 protein-coding genes and 175 RNA genes as well as a single plasmid. Affiliation of a set of 250 genome-sequenced E. coli strains, Shigella and outgroup strains to the type strain of E. coli was investigated using digital DNA:DNA-hybridization (dDDH) similarities and differences in genomic G+C content. As in the majority of previous studies, results show Shigella spp. embedded within E. coli and in most cases forming a single subgroup of it. Phylogenomic trees also recover the proposed E. coli phylotypes as monophyla with minor exceptions and place DSM 30083(T) in phylotype B2 with E. coli S88 as its closest neighbor. The widely used lab strain K-12 is not only genomically but also physiologically strongly different from the type strain. The phylotypes do not express a uniform level of character divergence as measured using dDDH, however, thus an alternative arrangement is proposed and discussed in the context of bacterial subspecies. Analyses of the genome sequences of a large number of E. coli strains and of strains from > 100 other bacterial genera indicate a value of 79-80% dDDH as the most promising threshold for delineating subspecies, which in turn suggests the presence of five subspecies within E. coli.

Mendeley readers

The data shown below were compiled from readership statistics for 235 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Germany 2 <1%
United Kingdom 1 <1%
New Zealand 1 <1%
Mexico 1 <1%
Belgium 1 <1%
Denmark 1 <1%
United States 1 <1%
Unknown 227 97%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 45 19%
Researcher 42 18%
Student > Bachelor 37 16%
Student > Master 32 14%
Student > Doctoral Student 15 6%
Other 29 12%
Unknown 35 15%
Readers by discipline Count As %
Agricultural and Biological Sciences 77 33%
Biochemistry, Genetics and Molecular Biology 57 24%
Immunology and Microbiology 16 7%
Medicine and Dentistry 11 5%
Engineering 6 3%
Other 22 9%
Unknown 46 20%

Attention Score in Context

This research output has an Altmetric Attention Score of 3. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 02 February 2021.
All research outputs
#6,542,523
of 20,194,585 outputs
Outputs from Standards in Genomic Sciences
#132
of 548 outputs
Outputs of similar age
#83,310
of 248,055 outputs
Outputs of similar age from Standards in Genomic Sciences
#1
of 1 outputs
Altmetric has tracked 20,194,585 research outputs across all sources so far. This one is in the 45th percentile – i.e., 45% of other outputs scored the same or lower than it.
So far Altmetric has tracked 548 research outputs from this source. They receive a mean Attention Score of 2.6. This one has gotten more attention than average, scoring higher than 57% of its peers.
Older research outputs will score higher simply because they've had more time to accumulate mentions. To account for age we can compare this Altmetric Attention Score to the 248,055 tracked outputs that were published within six weeks on either side of this one in any source. This one has gotten more attention than average, scoring higher than 59% of its contemporaries.
We're also able to compare this research output to 1 others from the same source and published within six weeks on either side of this one. This one has scored higher than all of them