Evidence map›Paper›PMID 24416233›Full record

ArticlePloS one2014

Comparative genomics of cultured and uncultured strains suggests genes essential for free-living growth of Liberibacter.

Jennie R Fagen, Michael T Leonard, Connor M McCullough, Janaka N Edirisinghe, Christopher S Henry, Michael J Davis, Eric W Triplett

Abstract readComparative Study
In one paragraph

Article in PloS one, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers, 1 of them a synthesis that pooled it.

0numbers the graph read from it
0cells of the map it votes in
41citing papers in PubMed, 1 pooled it
–field-weighted citation impact
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

41 citing papers in PubMed, 1 synthesis or guideline pooled it.

  1. Pooled it
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  8. MAGs-centric crack: how long will, spore-positiveFrontiers in microbiology · 2024
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  9. The Microbial Connection to Sustainable Agriculture.Plants (Basel, Switzerland) · 2023
    Review
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  12. Interactions ofInternational journal of molecular sciences · 2022
    Review
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  15. An Overview of the Mechanisms Against "Frontiers in microbiology · 2022
    Review
  16. Article
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  18. 'Frontiers in microbiology · 2021
    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

7 authors.

Jennie R FagenMicrobiology and Cell Science Department, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, Florida, United States of America.
Michael T LeonardMicrobiology and Cell Science Department, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, Florida, United States of America.
Connor M McCulloughMicrobiology and Cell Science Department, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, Florida, United States of America.
Janaka N EdirisingheMathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, United States of America.
Christopher S HenryMathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, United States of America.
Michael J DavisPlant Pathology Department, Citrus Research and Development Center, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, Florida, United States of America.
Eric W TriplettMicrobiology and Cell Science Department, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, Florida, United States of America.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

The full genomes of two uncultured plant pathogenic Liberibacter, Ca. Liberibacter asiaticus and Ca. Liberibacter solanacearum, are publicly available. Recently, the larger genome of a closely related cultured strain, Liberibacter crescens BT-1, was described. To gain insights into our current inability to culture most Liberibacter, a comparative genomics analysis was done based on the RAST, KEGG, and manual annotations of these three organisms. In addition, pathogenicity genes were examined in all three bacteria. Key deficiencies were identified in Ca. L. asiaticus and Ca. L. solanacearum that might suggest why these organisms have not yet been cultured. Over 100 genes involved in amino acid and vitamin synthesis were annotated exclusively in L. crescens BT-1. However, none of these deficiencies are limiting in the rich media used to date. Other genes exclusive to L. crescens BT-1 include those involved in cell division, the stringent response regulatory pathway, and multiple two component regulatory systems. These results indicate that L. crescens is capable of growth under a much wider range of conditions than the uncultured Liberibacter strains. No outstanding differences were noted in pathogenicity-associated systems, suggesting that L. crescens BT-1 may be a plant pathogen on an as yet unidentified host.

Indexed as

GenomicsCarbonCell MembraneCulture TechniquesElectron TransportGenes, BacterialGenes, EssentialHomeostasisRhizobiaceaeSpecies SpecificityCarbon

Identifiers

PMID24416233
PMCPMC3885570

What OpenQuestion holds

Textmetadata
LicenceCC0
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.