Strain identifier

BacDive ID: 13652

Type strain: Yes

Species: Meinhardsimonia xiamenensis

Strain Designation: YBY-7

Strain history: <- X. Chen, Third Inst. Oceanography, State Oceanic Admin., China; YBY-7 <- D. Yin

NCBI tax ID(s): 990712 (species)

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General

@ref: 17674

BacDive-ID: 13652

DSM-Number: 24422

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

description: Meinhardsimonia xiamenensis YBY-7 is an aerobe, thermophilic, Gram-negative bacterium that was isolated from water from a terrestrial hot spring.

NCBI tax id

  • NCBI tax id: 990712
  • Matching level: species

strain history

  • @ref: 17674
  • history: <- X. Chen, Third Inst. Oceanography, State Oceanic Admin., China; YBY-7 <- D. Yin

doi: 10.13145/bacdive13652.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Rhodobacterales
  • family: Roseobacteraceae
  • genus: Meinhardsimonia
  • species: Meinhardsimonia xiamenensis
  • full scientific name: Meinhardsimonia xiamenensis (Yin et al. 2012) Hördt et al. 2020

  • synonyms

    • @ref: 20215
    • synonym: Albidovulum xiamenense

@ref: 17674

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Meinhardsimonia

species: Meinhardsimonia xiamenensis

full scientific name: Meinhardsimonia xiamenensis (Yin et al. 2012) Hördt et al. 2020

strain designation: YBY-7

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
30365negative4 µm0.5 µmrod-shapedyes
69480negative99.998

colony morphology

  • @ref: 17674
  • incubation period: 3-7 days

Culture and growth conditions

culture medium

  • @ref: 17674
  • name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/514
  • composition: Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
17674positivegrowth55thermophilic
30365positiveoptimum54thermophilic

culture pH

  • @ref: 30365
  • ability: positive
  • type: optimum
  • pH: 8

Physiology and metabolism

oxygen tolerance

  • @ref: 30365
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
30365no
69481no100
69480no99.995

halophily

@refsaltgrowthtested relationconcentration
30365NaClpositivegrowth0.25-5.5 %
30365NaClpositiveoptimum3 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3036530089acetate+carbon source
3036540585alpha-cyclodextrin+carbon source
3036518403L-arabitol+carbon source
3036517057cellobiose+carbon source
3036528757fructose+carbon source
3036517234glucose+carbon source
3036517754glycerol+carbon source
3036528087glycogen+carbon source
3036524996lactate+carbon source
3036517306maltose+carbon source
3036529864mannitol+carbon source
3036537684mannose+carbon source
3036517992sucrose+carbon source
3036517748thymidine+carbon source
3036527082trehalose+carbon source
3036553423tween 40+carbon source
3036553426tween 80+carbon source
3036517151xylitol+carbon source
303654853esculin+hydrolysis
3036517632nitrate+reduction

enzymes

@refvalueactivityec
30365acid phosphatase+3.1.3.2
30365alkaline phosphatase+3.1.3.1
30365alpha-galactosidase+3.2.1.22
30365catalase+1.11.1.6
30365cytochrome oxidase+1.9.3.1
30365urease+3.5.1.5

Isolation, sampling and environmental information

isolation

  • @ref: 17674
  • sample type: water from a terrestrial hot spring
  • geographic location: Fuijian Province, Xiamen city (24° 34' N 118° 04' E)
  • country: China
  • origin.country: CHN
  • continent: Asia
  • latitude: 24.5667
  • longitude: 118.067

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Thermal spring
#Environmental#Terrestrial
#Condition#Thermophilic (>45°C)

taxonmaps

  • @ref: 69479
  • File name: preview.99_92720.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_30434;97_48615;98_63811;99_92720&stattab=map
  • Last taxonomy: Albidovulum xiamenense subclade
  • 16S sequence: HQ709061
  • Sequence Identity:
  • Total samples: 121
  • soil counts: 23
  • aquatic counts: 60
  • animal counts: 38

Safety information

risk assessment

  • @ref: 17674
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 17674
  • description: Albidovulum xiamenense strain YBY-7 16S ribosomal RNA gene, partial sequence
  • accession: HQ709061
  • length: 1434
  • database: ena
  • NCBI tax ID: 990712

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Meinhardsimonia xiamenensis CGMCC 1.10789GCA_900102905scaffoldncbi990712
66792Meinhardsimonia xiamenensis DSM 24422GCA_003001835scaffoldncbi990712
66792Albidovulum xiamenense strain CGMCC 1.10789990712.3wgspatric990712
66792Albidovulum xiamenense strain DSM 24422990712.6wgspatric990712
66792Albidovulum xiamenense CGMCC 1.107892663762716draftimg990712
66792Albidovulum xiamenense DSM 244222593339294draftimg990712

GC content

@refGC-contentmethod
1767470.6high performance liquid chromatography (HPLC)
3036570.6

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno69.829no
flagellatedno87.634no
gram-positiveno98.564yes
anaerobicno97.398yes
aerobicyes83.654no
halophileyes70.705no
spore-formingno96.032no
glucose-fermentno91.499no
thermophileno57.852no
glucose-utilyes64.551no

External links

@ref: 17674

culture collection no.: DSM 24422, CGMCC 1.10789, LMG 26247, MCCC 1A06317

straininfo link

  • @ref: 82835
  • straininfo: 407901

literature

  • topic: Phylogeny
  • Pubmed-ID: 21890729
  • title: Albidovulum xiamenense sp. nov., a moderately thermophilic bacterium from a terrestrial hot spring.
  • authors: Yin D, Xiao J, Ao J, Ai C, Chen X
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.034454-0
  • year: 2011
  • mesh: Aerobiosis, Bacterial Typing Techniques, Base Composition, China, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Flagella/physiology, Hot Springs/*microbiology, Hydrogen-Ion Concentration, Locomotion, Microscopy, Electron, Transmission, Molecular Sequence Data, Phospholipids/analysis, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/*isolation & purification/physiology, Sequence Analysis, DNA, Sodium Chloride/metabolism, Temperature
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
17674Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 24422)https://www.dsmz.de/collection/catalogue/details/culture/DSM-24422
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
30365Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2670528776041
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updates33211880Nucleic Acids Res. 49: D498-D508 2020
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.https://microbeatlas.org/MicrobeAtlas 1.0 beta
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
82835Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID407901.1StrainInfo: A central database for resolving microbial strain identifiers