Strain identifier

BacDive ID: 133844

Type strain: Yes

Species: Endobacter medicaginis

Strain Designation: M1MS02, MIMS02

Strain history: CIP <- 2012, MH Ramirez-Bahena, IRNASA-CSIC, Salamanca, Spain: strain MIMS02

NCBI tax ID(s): 1181271 (species)

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General

@ref: 30659

BacDive-ID: 133844

keywords: genome sequence, 16S sequence, Bacteria, aerobe, Gram-negative, motile, rod-shaped

description: Endobacter medicaginis M1MS02 is an aerobe, Gram-negative, motile bacterium that was isolated from Plant, Root nodules of Medicago sativa.

NCBI tax id

  • NCBI tax id: 1181271
  • Matching level: species

strain history

  • @ref: 120868
  • history: CIP <- 2012, MH Ramirez-Bahena, IRNASA-CSIC, Salamanca, Spain: strain MIMS02

doi: 10.13145/bacdive133844.20240916.9.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Rhodospirillales
  • family: Acetobacteraceae
  • genus: Endobacter
  • species: Endobacter medicaginis
  • full scientific name: Endobacter medicaginis Ramírez-Bahena et al. 2013

@ref: 30659

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodospirillales

family: Acetobacteraceae

genus: Endobacter

species: Endobacter medicaginis

strain designation: M1MS02, MIMS02

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
30659negativerod-shapedyes
69480negative94.828
120868negativeovoid-shapedno

pigmentation

  • @ref: 30659
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
34724MEDIUM 600 - for Desovia neptuniaeyesDistilled water make up to (1000.000 ml);Magnesium sulphate heptahydrate (0.200 g);Agar (15.000 g);Yeast extract (3.000 g);Mannitol (10.000 g);Di Potassium monohydrogenophosphate (0.200 g)
120868CIP Medium 600yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=600

culture temp

@refgrowthtypetemperature
30659positivegrowth20-37
30659positiveoptimum28
34724positivegrowth30

culture pH

@refabilitytypepHPH range
30659positivegrowth3.5-7acidophile
30659positiveoptimum6

Physiology and metabolism

oxygen tolerance

  • @ref: 30659
  • oxygen tolerance: aerobe

spore formation

  • @ref: 30659
  • spore formation: no

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3065929987glutamate+carbon source
3065929864mannitol+carbon source
12086817632nitrate+reduction
12086816301nitrite-reduction

metabolite production

  • @ref: 120868
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
30659catalase+1.11.1.6
120868oxidase-
120868catalase+1.11.1.6
120868urease-3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
68382cystine arylamidase-3.4.11.3
68382trypsin+3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase-3.2.1.20
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
120868-+++-++-+-++--------

Isolation, sampling and environmental information

isolation

  • @ref: 120868
  • sample type: Plant, Root nodules of Medicago sativa
  • geographic location: Salamanca
  • country: Spain
  • origin.country: ESP
  • continent: Europe
  • isolation date: 2011

taxonmaps

  • @ref: 69479
  • File name: preview.99_153776.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_29;96_64;97_62978;98_101441;99_153776&stattab=map
  • Last taxonomy: Endobacter medicaginis subclade
  • 16S sequence: JQ436923
  • Sequence Identity:
  • Total samples: 2301
  • soil counts: 556
  • aquatic counts: 325
  • animal counts: 1194
  • plant counts: 226

Safety information

risk assessment

  • @ref: 120868
  • biosafety level: 1
  • biosafety level comment: Risk group (French classification)

Sequence information

16S sequences

  • @ref: 30659
  • description: Endobacter medicaginis strain M1MS02 16S ribosomal RNA gene, partial sequence
  • accession: JQ436923
  • length: 1492
  • database: nuccore
  • NCBI tax ID: 1181271

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Endobacter medicaginis CECT 8088GCA_014192375scaffoldncbi1181271
66792Endobacter medicaginis LMG 26838GCA_013376135contigncbi1181271
66792Endobacter medicaginis strain CECT 80881181271.5wgspatric1181271
66792Endobacter medicaginis strain LMG 268381181271.4wgspatric1181271
66792Endobacter medicaginis CECT 80882824439340draftimg1181271
66792Endobacter medicaginis M1MS02GCA_026341395contigncbi1181271

GC content

  • @ref: 30659
  • GC-content: 60.3

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69481spore-formingspore-formingAbility to form endo- or exosporesno68no
69480gram-positivegram-positivePositive reaction to Gram-stainingno94.828yes
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no90.021no
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes87.7yes
69480spore-formingspore-formingAbility to form endo- or exosporesno85.569yes
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno93.964yes
69480flagellatedmotile2+Ability to perform flagellated movementyes68.522no

External links

@ref: 30659

culture collection no.: LMG 26838, CECT 8088, CIP 110365

straininfo link

  • @ref: 91617
  • straininfo: 379236

literature

  • topic: Phylogeny
  • Pubmed-ID: 23002052
  • title: Endobacter medicaginis gen. nov., sp. nov., isolated from alfalfa nodules in an acidic soil.
  • authors: Ramirez-Bahena MH, Tejedor C, Martin I, Velazquez E, Peix A
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.041368-0
  • year: 2012
  • mesh: Acetobacteraceae/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, DNA, Ribosomal Spacer/genetics, Fatty Acids/analysis, Medicago sativa/*microbiology, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Root Nodules, Plant/*microbiology, Sequence Analysis, DNA, Spain, Ubiquinone/analysis
  • topic2: Genetics

Reference

@idauthorstitledoi/urlID_cross_referencepubmedcatalogue
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
30659Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172699028776041
34724Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/8216
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
68382Automatically annotated from API zym
69479João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
91617Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID379236.1
120868Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110365Collection of Institut Pasteur (CIP 110365)