Evidence map›Paper›PMID 25197484›Full record

ArticleStandards in genomic sciences2014

Genome sequence of the mud-dwelling archaeon Methanoplanus limicola type strain (DSM 2279(T)), reclassification of Methanoplanus petrolearius as Methanolacinia petrolearia and emended descriptions of the genera Methanoplanus and Methanolacinia.

Markus Göker, Megan Lu, Anne Fiebig, Matt Nolan, Alla Lapidus, Hope Tice, Tijana Glavina Del Rio, Jan-Fang Cheng, Cliff Han, Roxanne Tapia and 24 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 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing papers in PubMed
1.1field-weighted citation impact, top 23% 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

2 citing papers in PubMed, 18 citations in OpenAlex.

  1. Article
  2. Article
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

34 authors at 10 institutions in 6 countries.

Markus GökerLeibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.
Megan LuDOE Joint Genome Institute, Walnut Creek, California, USA ; Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA.
Anne FiebigLeibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.
Matt NolanDOE Joint Genome Institute, Walnut Creek, California, USA.
Alla LapidusT. Dobzhansky Center for Genome Bionformatics, St. Petersburg State University, St. Petersburg, Russia ; Algorithmic Biology Lab, St. Petersburg Academic University, St. Petersburg, Russia.
Hope TiceDOE Joint Genome Institute, Walnut Creek, California, USA.
Tijana Glavina Del RioDOE Joint Genome Institute, Walnut Creek, California, USA.
Jan-Fang ChengDOE Joint Genome Institute, Walnut Creek, California, USA.
Cliff HanDOE Joint Genome Institute, Walnut Creek, California, USA ; Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA.
Roxanne TapiaDOE Joint Genome Institute, Walnut Creek, California, USA ; Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA.
Lynne A 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.
Konstantinos LioliosDOE Joint Genome Institute, Walnut Creek, California, USA.
Konstantinos MavromatisDOE Joint Genome Institute, Walnut Creek, California, USA.
Ioanna PaganiDOE Joint Genome Institute, Walnut Creek, California, USA.
Natalia IvanovaDOE Joint Genome Institute, Walnut Creek, California, USA.
Natalia MikhailovaDOE 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.
Miriam LandDOE Joint Genome Institute, Walnut Creek, California, USA ; Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA.
Shanmugam MayilrajMTCC - Microbial Type Culture Collection & Gene Bank, CSIR-Institute of Microbial Technology, Chandigarh, India.
Manfred RohdeHZI - Helmholtz Centre for Infection Research, Braunschweig, Germany.
John C DetterDOE Joint Genome Institute, Walnut Creek, California, USA ; Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA.
Boyke BunkLeibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.
Stefan SpringLeibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.
Reinhard WirthUniversity of Regensburg, Microbiology - Archaeenzentrum, Regensburg, Germany.
Tanja WoykeDOE Joint Genome Institute, Walnut Creek, California, USA.
James BristowDOE 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.
Nikos C KyrpidesDOE Joint Genome Institute, Walnut Creek, California, USA ; Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia.
Hans-Peter KlenkLeibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.
Joint Genome Institute · USLeibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures · DELawrence Berkeley National Laboratory · USHelmholtz Centre for Infection Research · DEInstitute of Microbial Technology · INKing Abdulaziz University · SALos Alamos National Laboratory · USSaint Petersburg Academic University · RUUniversity of Queensland · AUUniversity of Regensburg · DE

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Methanoplanus limicola Wildgruber et al. 1984 is a mesophilic methanogen that was isolated from a swamp composed of drilling waste near Naples, Italy, shortly after the Archaea were recognized as a separate domain of life. Methanoplanus is the type genus in the family Methanoplanaceae, a taxon that felt into disuse since modern 16S rRNA gene sequences-based taxonomy was established. Methanoplanus is now placed within the Methanomicrobiaceae, a family that is so far poorly characterized at the genome level. The only other type strain of the genus with a sequenced genome, Methanoplanus petrolearius SEBR 4847(T), turned out to be misclassified and required reclassification to Methanolacinia. Both, Methanoplanus and Methanolacinia, needed taxonomic emendations due to a significant deviation of the G+C content of their genomes from previously published (pre-genome-sequence era) values. Until now genome sequences were published for only four of the 33 species with validly published names in the Methanomicrobiaceae. Here we describe the features of M. limicola, together with the improved-high-quality draft genome sequence and annotation of the type strain, M3(T). The 3,200,946 bp long chromosome (permanent draft sequence) with its 3,064 protein-coding and 65 RNA genes is a part of the G enomic E ncyclopedia of B acteria and Archaea project.

Indexed as

anaerobicGEBAimproved-high-quality draftmesophilicmethanogenMethanomicrobiaceaemotileswamp

Identifiers

PMID25197484
PMCPMC4149034
OpenAlexW2042255328

What OpenQuestion holds

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Registered trials

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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.