Evidence map›Paper›PMID 25780503›Full record

ArticleStandards in genomic sciences2014

Complete genome sequence of Planctomyces brasiliensis type strain (DSM 5305(T)), phylogenomic analysis and reclassification of Planctomycetes including the descriptions of Gimesia gen. nov., Planctopirus gen. nov. and Rubinisphaera gen. nov. and emended descriptions of the order Planctomycetales and the family Planctomycetaceae.

Carmen Scheuner, Brian J Tindall, Megan Lu, Matt Nolan, Alla Lapidus, Jan-Fang Cheng, Lynne Goodwin, Sam Pitluck, Marcel Huntemann, Konstantinos Liolios and 20 more

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Standards in genomic sciences, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers, 1 of them a synthesis that pooled it.

0numbers the graph read from it
0cells of the map it votes in
25citing papers in PubMed, 1 pooled it
4.8field-weighted citation impact, top 4% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

25 citing papers in PubMed, 1 synthesis or guideline pooled it, 56 citations in OpenAlex.

  1. Pooled it
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  12. International journal of systematic and evolutionary microbiology · 2020
    Article
  13. Article
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  15. Article
  16. Tuwongella immobilis gen. nov., sp. nov., a novel non-motile bacterium within the phylum Planctomycetes.International journal of systematic and evolutionary microbiology · 2017
    Article
  17. Draft genome sequences ofStandards in genomic sciences · 2017
    Article
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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

30 authors at 8 institutions in 5 countries.

Carmen ScheunerDSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany.
Brian J TindallDSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany.
Megan LuDOE Joint Genome Institute, Walnut Creek, California, USA ; Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA.
Matt NolanDOE Joint Genome Institute, Walnut Creek, California, USA.
Alla LapidusDOE Joint Genome Institute, Walnut Creek, California, USA.
Jan-Fang ChengDOE Joint Genome Institute, Walnut Creek, California, USA.
Lynne GoodwinDOE Joint Genome Institute, Walnut Creek, California, USA ; Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA.
Sam PitluckDOE Joint Genome Institute, Walnut Creek, California, USA.
Marcel HuntemannDOE Joint Genome Institute, Walnut Creek, California, USA.
Konstantinos LioliosDOE Joint Genome Institute, Walnut Creek, California, USA.
Ioanna PaganiDOE Joint Genome Institute, Walnut Creek, California, USA.
Konstantinos MavromatisDOE Joint Genome Institute, Walnut Creek, California, USA.
Natalia IvanovaDOE Joint Genome Institute, Walnut Creek, California, USA.
Amrita PatiDOE Joint Genome Institute, Walnut Creek, California, USA.
Amy ChenBiological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA.
Krishna PalaniappanBiological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA.
Cynthia D JeffriesDOE Joint Genome Institute, Walnut Creek, California, USA ; Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA.
Loren HauserDOE Joint Genome Institute, Walnut Creek, California, USA ; Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA.
Miriam LandDOE Joint Genome Institute, Walnut Creek, California, USA ; Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA.
Romano MwirichiaJomo Kenyatta University of Agriculture and Technology, Juja, Kenya.
Manfred RohdeHZI - Helmholtz Centre for Infection Research, Braunschweig, Germany.
Birte AbtDSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany.
John C DetterDOE Joint Genome Institute, Walnut Creek, California, USA ; Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA.
Tanja WoykeDOE Joint Genome Institute, Walnut Creek, California, USA.
Jonathan A EisenDOE Joint Genome Institute, Walnut Creek, California, USA ; University of California Davis Genome Center, Davis, California, USA.
Victor MarkowitzBiological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA.
Philip HugenholtzDOE Joint Genome Institute, Walnut Creek, California, USA ; Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia.
Markus GökerDSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany.
Nikos C KyrpidesDOE Joint Genome Institute, Walnut Creek, California, USA ; Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia.
Hans-Peter KlenkDSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany.
Joint Genome Institute · USLeibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures · DELawrence Berkeley National Laboratory · USLos Alamos National Laboratory · USOak Ridge National Laboratory · USHelmholtz Centre for Infection Research · DEJomo Kenyatta University of Agriculture and Technology · KEKing Abdulaziz University · SA

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Planctomyces brasiliensis Schlesner 1990 belongs to the order Planctomycetales, which differs from other bacterial taxa by several distinctive features such as internal cell compartmentalization, multiplication by forming buds directly from the spherical, ovoid or pear-shaped mother cell and a cell wall consisting of a proteinaceous layer rather than a peptidoglycan layer. The first strains of P. brasiliensis, including the type strain IFAM 1448(T), were isolated from a water sample of Lagoa Vermelha, a salt pit near Rio de Janeiro, Brasil. This is the second completed genome sequence of a type strain of the genus Planctomyces to be published and the sixth type strain genome sequence from the family Planctomycetaceae. The 6,006,602 bp long genome with its 4,811 protein-coding and 54 RNA genes is a part of the G enomic E ncyclopedia of Bacteria and Archaea project. Phylogenomic analyses indicate that the classification within the Planctomycetaceae is partially in conflict with its evolutionary history, as the positioning of Schlesneria renders the genus Planctomyces paraphyletic. A re-analysis of published fatty-acid measurements also does not support the current arrangement of the two genera. A quantitative comparison of phylogenetic and phenotypic aspects indicates that the three Planctomyces species with type strains available in public culture collections should be placed in separate genera. Thus the genera Gimesia, Planctopirus and Rubinisphaera are proposed to accommodate P. maris, P. limnophilus and P. brasiliensis, respectively. Pronounced differences between the reported G + C content of Gemmata obscuriglobus, Singulisphaera acidiphila and Zavarzinella formosa and G + C content calculated from their genome sequences call for emendation of their species descriptions. In addition to other features, the range of G + C values reported for the genera within the Planctomycetaceae indicates that the descriptions of the family and the order should be emended.

Indexed as

GEBAGram-negativeHalotolerantNon-peptidoglycan bacteriaPlanctomycetalesPlanctomycetesStalked bacteriaTaxonomic descriptions

Identifiers

PMID25780503
PMCPMC4334474
OpenAlexW2111570072

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.