Strain identifier

BacDive ID: 10459

Type strain: Yes

Species: Formivibrio citricus

Strain Designation: CreCit1

Strain history: <- K. Tanaka, CreCit1

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 2505

BacDive-ID: 10459

DSM-Number: 6150

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-negative

description: Formivibrio citricus CreCit1 is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from anoxic fresh water mud.

NCBI tax id

NCBI tax idMatching level
1121905strain
83765species

strain history

  • @ref: 2505
  • history: <- K. Tanaka, CreCit1

doi: 10.13145/bacdive10459.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Neisseriales
  • family: Chromobacteriaceae
  • genus: Formivibrio
  • species: Formivibrio citricus
  • full scientific name: Formivibrio citricus Tanaka et al. 1991

@ref: 2505

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Neisseriales

family: Chromobacteriaceae

genus: Formivibrio

species: Formivibrio citricus

full scientific name: Formivibrio citricus Tanaka et al. 1991

strain designation: CreCit1

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • gram stain: negative
  • confidence: 99.974

Culture and growth conditions

culture medium

  • @ref: 2505
  • name: FORMIVIBRIO MEDIUM (DSMZ Medium 505)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/505
  • composition: Name: FORMIVIBRIO MEDIUM (DSMZ Medium 505) Composition: Trisodium citrate x 2 H2O 2.99103 g/l Na2CO3 1.49551 g/l KH2PO4 1.39581 g/l NH4Cl 0.498505 g/l Na2S x 9 H2O 0.299103 g/l MgCl2 x 6 H2O 0.199402 g/l CaCl2 x 2 H2O 0.149552 g/l HCl 0.00249252 g/l FeCl2 x 4 H2O 0.00149551 g/l Sodium resazurin 0.000498505 g/l NaOH 0.000498504 g/l CoCl2 x 6 H2O 0.000189432 g/l Pyridoxine hydrochloride 9.97009e-05 g/l MnCl2 x 4 H2O 9.97009e-05 g/l ZnCl2 6.97906e-05 g/l Nicotinic acid 4.98504e-05 g/l Riboflavin 4.98504e-05 g/l p-Aminobenzoic acid 4.98504e-05 g/l Calcium D-(+)-pantothenate 4.98504e-05 g/l Thiamine HCl 4.98504e-05 g/l (DL)-alpha-Lipoic acid 4.98504e-05 g/l Na2MoO4 x 2 H2O 3.58923e-05 g/l NiCl2 x 6 H2O 2.39282e-05 g/l Biotin 1.99402e-05 g/l Folic acid 1.99402e-05 g/l H3BO3 5.98205e-06 g/l Na2WO4 x 2 H2O 3.98804e-06 g/l Na2SeO3 x 5 H2O 2.99103e-06 g/l CuCl2 x 2 H2O 1.99402e-06 g/l Vitamin B12 9.97009e-07 g/l Distilled water

culture temp

  • @ref: 2505
  • growth: positive
  • type: growth
  • temperature: 30
  • range: mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 2505
  • oxygen tolerance: anaerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.999

Isolation, sampling and environmental information

isolation

  • @ref: 2505
  • sample type: anoxic fresh water mud
  • country: Japan
  • origin.country: JPN
  • continent: Asia

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Freshwater
#Environmental#Terrestrial#Mud (Sludge)
#Condition#Anoxic (anaerobic)

taxonmaps

  • @ref: 69479
  • File name: preview.99_55710.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_168;96_24829;97_31086;98_39784;99_55710&stattab=map
  • Last taxonomy: Formivibrio citricus subclade
  • 16S sequence: Y17602
  • Sequence Identity:
  • Total samples: 5693
  • soil counts: 1024
  • aquatic counts: 4307
  • animal counts: 200
  • plant counts: 162

Safety information

risk assessment

  • @ref: 2505
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 2505
  • description: Formivibrio citricus 16S rRNA gene, partial
  • accession: Y17602
  • length: 1490
  • database: ena
  • NCBI tax ID: 83765

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Formivibrio citricus DSM 6150GCA_900115065contigncbi83765
66792Formivibrio citricus strain DSM 615083765.3wgspatric83765
66792Formivibrio citricus DSM 61502599185172draftimg83765

GC content

  • @ref: 2505
  • GC-content: 59.0

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes88.665no
flagellatedyes70.528no
gram-positiveno99.234no
anaerobicyes90.994yes
halophileno96.478no
spore-formingno93.898no
thermophileno95.89yes
glucose-utilyes60.814no
aerobicno96.596yes
glucose-fermentno74.683no

External links

@ref: 2505

culture collection no.: DSM 6150, ATCC 49791

straininfo link

  • @ref: 79736
  • straininfo: 42689

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15280319Chitinibacter tainanensis gen. nov., sp. nov., a chitin-degrading aerobe from soil in Taiwan.Chern LL, Stackebrandt E, Lee SF, Lee FL, Chen JK, Fu HMInt J Syst Evol Microbiol10.1099/ijs.0.02834-02004Bacterial Typing Techniques, Base Composition, Chitin/*metabolism, DNA, Bacterial/chemistry/isolation & purification, DNA, Ribosomal/chemistry, Fatty Acids/analysis, Flagella/ultrastructure, Genes, rRNA, Microscopy, Electron, Microscopy, Phase-Contrast, Molecular Sequence Data, Neisseriaceae/*classification/cytology/*isolation & purification/physiology, Phylogeny, Quinones/analysis, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, *Soil Microbiology, Taiwan, TemperatureEnzymology
Phylogeny16280491Silvimonas terrae gen. nov., sp. nov., a novel chitin-degrading facultative anaerobe belonging to the 'Betaproteobacteria'.Yang HC, Im WT, An DS, Park WS, Kim IS, Lee STInt J Syst Evol Microbiol10.1099/ijs.0.63837-02005Bacteria, Anaerobic, Base Composition, Biodegradation, Environmental, Chitin/*metabolism, DNA, Bacterial/analysis/chemistry/isolation & purification, DNA, Ribosomal/analysis/chemistry, Molecular Sequence Data, Neisseriaceae/classification/genetics/*metabolism/ultrastructure, Phylogeny, RNA, Ribosomal, 16S/analysis/genetics, Sequence Analysis, DNAMetabolism
Phylogeny17329799Deefgea rivuli gen. nov., sp. nov., a member of the class Betaproteobacteria.Stackebrandt E, Lang E, Cousin S, Pauker O, Brambilla E, Kroppenstedt R, Lunsdorf HInt J Syst Evol Microbiol10.1099/ijs.0.64771-02007DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Genome, Bacterial, Germany, Molecular Sequence Data, Neisseriaceae/*classification/genetics/ultrastructure, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, *Water MicrobiologyGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
2505Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 6150)https://www.dsmz.de/collection/catalogue/details/culture/DSM-6150
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
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 updatesNucleic Acids Res. 49: D498-D508 202033211880
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
79736Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID42689.1StrainInfo: A central database for resolving microbial strain identifiers