Strain identifier
BacDive ID: 10459
Type strain:
Species: Formivibrio citricus
Strain Designation: CreCit1
Strain history: <- K. Tanaka, CreCit1
NCBI tax ID(s): 1121905 (strain), 83765 (species)
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 id | Matching level |
---|---|
1121905 | strain |
83765 | species |
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
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.999 |
Isolation, sampling and environmental information
isolation
- @ref: 2505
- sample type: anoxic fresh water mud
- country: Japan
- origin.country: JPN
- continent: Asia
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#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
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Formivibrio citricus DSM 6150 | GCA_900115065 | contig | ncbi | 83765 |
66792 | Formivibrio citricus strain DSM 6150 | 83765.3 | wgs | patric | 83765 |
66792 | Formivibrio citricus DSM 6150 | 2599185172 | draft | img | 83765 |
GC content
- @ref: 2505
- GC-content: 59.0
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | yes | 88.665 | no |
flagellated | yes | 70.528 | no |
gram-positive | no | 99.234 | no |
anaerobic | yes | 90.994 | yes |
halophile | no | 96.478 | no |
spore-forming | no | 93.898 | no |
thermophile | no | 95.89 | yes |
glucose-util | yes | 60.814 | no |
aerobic | no | 96.596 | yes |
glucose-ferment | no | 74.683 | no |
External links
@ref: 2505
culture collection no.: DSM 6150, ATCC 49791
straininfo link
- @ref: 79736
- straininfo: 42689
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 15280319 | Chitinibacter tainanensis gen. nov., sp. nov., a chitin-degrading aerobe from soil in Taiwan. | Chern LL, Stackebrandt E, Lee SF, Lee FL, Chen JK, Fu HM | Int J Syst Evol Microbiol | 10.1099/ijs.0.02834-0 | 2004 | Bacterial 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, Temperature | Enzymology |
Phylogeny | 16280491 | Silvimonas 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 ST | Int J Syst Evol Microbiol | 10.1099/ijs.0.63837-0 | 2005 | Bacteria, 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, DNA | Metabolism |
Phylogeny | 17329799 | Deefgea rivuli gen. nov., sp. nov., a member of the class Betaproteobacteria. | Stackebrandt E, Lang E, Cousin S, Pauker O, Brambilla E, Kroppenstedt R, Lunsdorf H | Int J Syst Evol Microbiol | 10.1099/ijs.0.64771-0 | 2007 | DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Genome, Bacterial, Germany, Molecular Sequence Data, Neisseriaceae/*classification/genetics/ultrastructure, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, *Water Microbiology | Genetics |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
2505 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 6150) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-6150 | |||
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
69479 | João 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 | |||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | |||
79736 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID42689.1 | StrainInfo: A central database for resolving microbial strain identifiers |