Evidence map›Paper›PMID 27814683›Full record

ArticleBMC microbiology2016

Reclassification of the taxonomic status of SEMIA3007 isolated in Mexico B-11A Mex as Rhizobium leguminosarum bv. viceae by bioinformatic tools.

Luciano Takeshi Kishi, Camila Cesário Fernandes, Wellington Pine Omori, João Carlos Campanharo, Eliana Gertrudes de Macedo Lemos

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In one paragraph

Article in BMC microbiology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.

0numbers the graph read from it
0cells of the map it votes in
3citing papers in PubMed
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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

3 citing papers in PubMed.

  1. Pan-Resistome Insights into the Multidrug Resistance ofAntibiotics (Basel, Switzerland) · 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

5 authors.

Luciano Takeshi KishiDepartamento de Tecnologia, Laboratório de Bioquímica de Microrganismos e Planta - LBMP, UNESP - Universidade Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Via de Acesso Prof. Paulo Donato Castellane s/n, 14884-900, Jaboticabal, SP, Brazil.
Camila Cesário FernandesDepartamento de Tecnologia, Laboratório de Bioquímica de Microrganismos e Planta - LBMP, UNESP - Universidade Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Via de Acesso Prof. Paulo Donato Castellane s/n, 14884-900, Jaboticabal, SP, Brazil.
Wellington Pine OmoriDepartamento de Tecnologia, Laboratório de Bioquímica de Microrganismos e Planta - LBMP, UNESP - Universidade Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Via de Acesso Prof. Paulo Donato Castellane s/n, 14884-900, Jaboticabal, SP, Brazil.
João Carlos CampanharoDepartamento de Tecnologia, Laboratório de Bioquímica de Microrganismos e Planta - LBMP, UNESP - Universidade Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Via de Acesso Prof. Paulo Donato Castellane s/n, 14884-900, Jaboticabal, SP, Brazil.
Eliana Gertrudes de Macedo LemosDepartamento de Tecnologia, Laboratório de Bioquímica de Microrganismos e Planta - LBMP, UNESP - Universidade Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Via de Acesso Prof. Paulo Donato Castellane s/n, 14884-900, Jaboticabal, SP, Brazil. egerle@fcav.unesp.br.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

backgroundEvidence based on genomic sequences is extremely important to confirm the phylogenetic relationships within the Rhizobium group. SEMIA3007 was analyzed within the Mesorhizobium groups to define the underlying causes of taxonomic identification. We previously used biochemical tests and phenotypic taxonomic methods to identify bacteria, which can lead to erroneous classification. An improved understanding of bacterial strains such as the Mesorhizobium genus would increase our knowledge of classification and evolution of these species.

resultsIn this study, we sequenced the complete genome of SEMIA3007 and compared it with five other Mesorhizobium and two Rhizobium genomes. The genomes of isolated SEMIA3007 showed several orthologs with M. huakuii, M. erdmanii and M. loti. We identified SEMIA3007 as a Mesorhizobium by comparing the 16S rRNA gene and the complete genome.

conclusionOur ortholog, 16S rRNA gene and average nucleotide identity values (ANI) analysis all demonstrate SEMIA3007 is not Rhizobium leguminosarum bv. viceae. The results of the phylogenetic analysis clearly show SEMIA3007 is part of the Mesorhizobium group and suggest a reclassification is warranted.

Indexed as

Computational BiologyPhylogenyBase SequenceClassificationDNA, BacterialDNA, RibosomalGenome, BacterialMesorhizobiumMexicoMolecular Sequence AnnotationRhizobiumRhizobium leguminosarumRNA, Ribosomal, 16SSequence Analysis, DNADNA, BacterialDNA, RibosomalRNA, Ribosomal, 16SComparative analysisCore genomeGenome sequencingOrtholog genesPhylogenetic analysis

Identifiers

PMID27814683
PMCPMC5097390

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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.