Strain identifier
BacDive ID: 2963
Type strain: 
Species: Hydrogenophaga flava
Strain history: CIP <- 1989, DSM <- ATCC, Pseudomonas flava <- Lab. Microbiol. Delft, The Netherlands <- A. Manten
NCBI tax ID(s): 1349752 (strain), 65657 (species)
version 8.1 (current version)
General
@ref: 324
BacDive-ID: 2963
DSM-Number: 619
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, motile
description: Hydrogenophaga flava DSM 619 is a mesophilic, motile bacterium that was isolated from ditch mud.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 1349752 | strain |
| 65657 | species |
strain history
| @ref | history |
|---|---|
| 324 | <- ATCC <- Lab. Microbiol. Delft (Hydrogenomonas flava) |
| 67770 | IAM 14931 <-- DSM 619 <-- ATCC 33667 <-- LMD ("Hydrogenomonas flava") <-- A. Manten. |
| 119363 | CIP <- 1989, DSM <- ATCC, Pseudomonas flava <- Lab. Microbiol. Delft, The Netherlands <- A. Manten |
doi: 10.13145/bacdive2963.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Betaproteobacteria
- order: Burkholderiales
- family: Comamonadaceae
- genus: Hydrogenophaga
- species: Hydrogenophaga flava
- full scientific name: Hydrogenophaga flava (Niklewski 1910) Willems et al. 1989
synonyms
@ref synonym 20215 Pseudomonas flava 20215 Hydrogenomonas flava
@ref: 324
domain: Bacteria
phylum: Proteobacteria
class: Betaproteobacteria
order: Burkholderiales
family: Comamonadaceae
genus: Hydrogenophaga
species: Hydrogenophaga flava
full scientific name: Hydrogenophaga flava (Niklewski 1910) Willems et al. 1989
type strain: yes
Morphology
cell morphology
| @ref | motility | confidence | gram stain |
|---|---|---|---|
| 69480 | yes | 97.1 | |
| 69480 | 99.998 | negative |
Culture and growth conditions
culture medium
| @ref | name | growth | link | composition |
|---|---|---|---|---|
| 324 | MINERAL MEDIUM FOR CHEMOLITHOTROPHIC GROWTH (H-3) (DSMZ Medium 81) | yes | https://mediadive.dsmz.de/medium/81 | Name: MINERAL MEDIUM FOR CHEMOLITHOTROPHIC GROWTH (H-3) (DSMZ Medium 81) Composition: Agar 20.1005 g/l Na2HPO4 x 2 H2O 2.91457 g/l KH2PO4 2.31156 g/l NH4Cl 1.00503 g/l MgSO4 x 7 H2O 0.502512 g/l Ferric ammonium citrate 0.0502513 g/l CaCl2 x 2 H2O 0.0100503 g/l NaVO3 x H2O 0.00502512 g/l Calcium pantothenate 0.00251256 g/l Pyridoxine hydrochloride 0.00251256 g/l Nicotinic acid 0.00251256 g/l Thiamine-HCl x 2 H2O 0.00251256 g/l H3BO3 0.00150754 g/l CoCl2 x 6 H2O 0.00100503 g/l Riboflavin 0.000502513 g/l ZnSO4 x 7 H2O 0.000502513 g/l MnCl2 x 4 H2O 0.000150754 g/l Na2MoO4 x 2 H2O 0.000150754 g/l NiCl2 x 6 H2O 0.000100503 g/l CuCl2 x 2 H2O 5.02513e-05 g/l Vitamin B12 5.02513e-05 g/l Folic acid 1.00503e-05 g/l Biotin 5.02513e-06 g/l Distilled water |
| 324 | NUTRIENT AGAR (DSMZ Medium 1) | yes | https://mediadive.dsmz.de/medium/1 | Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water |
| 34235 | MEDIUM 18 - for Hydrogenophaga, Vogesella and Pseudomonas genera | yes | Distilled water make up to (1000.000 ml);Sodium chloride (3.000 g);Agar(12.000 g);Yeast extract (3.000 g);Peptone (0.600 g) | |
| 119363 | CIP Medium 18 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=18 |
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 324 | positive | growth | 30 | mesophilic |
| 34235 | positive | growth | 30 | mesophilic |
| 67770 | positive | growth | 30 | mesophilic |
Physiology and metabolism
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 100 |
| 69480 | no | 99.994 |
Isolation, sampling and environmental information
isolation
| @ref | sample type |
|---|---|
| 324 | ditch mud |
| 67770 | Ditch mud |
| 119363 | Environment, Ditch mud |
isolation source categories
- Cat1: #Environmental
- Cat2: #Terrestrial
- Cat3: #Mud (Sludge)
taxonmaps
- @ref: 69479
- File name: preview.99_1523.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_1;96_872;97_1019;98_1202;99_1523&stattab=map
- Last taxonomy: Hydrogenophaga
- 16S sequence: AF078771
- Sequence Identity:
- Total samples: 737
- soil counts: 9
- aquatic counts: 295
- animal counts: 23
- plant counts: 410
Safety information
risk assessment
| @ref | biosafety level | biosafety level comment |
|---|---|---|
| 324 | 1 | Risk group (German classification) |
| 119363 | 1 | Risk group (French classification) |
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 20218 | Hydrogenophaga flava gene for 16S rRNA, strain: DSM 619 | AB021420 | 1519 | ena | 65657 |
| 20218 | Hydrogenophaga flava 16S rRNA gene, strain DSM 619 | AJ420328 | 1494 | ena | 65657 |
| 20218 | Hydrogenophaga flava gene for 16S rRNA, partial sequence, strain: NBRC 102514 | AB681848 | 1454 | ena | 65657 |
| 324 | Hydrogenophaga flava 16S ribosomal RNA gene, partial sequence | AF078771 | 1513 | ena | 65657 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Hydrogenophaga flava NBRC 102514 | 1349752.3 | wgs | patric | 1349752 |
| 66792 | Hydrogenophaga flava NBRC 102514 | 2731957619 | draft | img | 1349752 |
| 67770 | Hydrogenophaga flava NBRC 102514 | GCA_001571145 | contig | ncbi | 1349752 |
GC content
- @ref: 324
- GC-content: 67.3
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| motile | yes | 90.112 | no |
| gram-positive | no | 99.176 | no |
| anaerobic | no | 97.343 | no |
| halophile | no | 96.503 | no |
| spore-forming | no | 95.15 | no |
| glucose-util | yes | 69.956 | no |
| aerobic | yes | 89.618 | no |
| flagellated | yes | 85.979 | no |
| thermophile | no | 97.844 | no |
| glucose-ferment | no | 89.565 | no |
External links
@ref: 324
culture collection no.: DSM 619, ATCC 33667, JCM 21413, BCRC 13889, CCM 4453, CCUG 1658, CCUG 22894, CECT 4106, CFBP 2438, CIP 103271, IAM 14931, KCTC 1648, LMG 2185, NBRC 102514
straininfo link
- @ref: 72485
- straininfo: 3010
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 21282897 | Hydrogenophaga temperata sp. nov., a betaproteobacterium isolated from compost in Korea. | Kim YJ, Kim MK, Weon HY, Kim HB, Yang DC | J Gen Appl Microbiol | 10.2323/jgam.56.419 | 2010 | *Bacterial Typing Techniques, Base Composition, Comamonadaceae/*classification/genetics/*isolation & purification/physiology, DNA, Bacterial/chemistry/genetics, Fatty Acids/analysis/chemistry, Genes, rRNA, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology | Genetics |
| Phylogeny | 26154498 | Hydrogenophaga luteola sp. nov. isolated from reed pond water. | Du J, Yang JE, Singh H, Akter S, Won K, Yin CS, Jin FX, Yi TH | Antonie Van Leeuwenhoek | 10.1007/s10482-015-0525-0 | 2015 | Aerobiosis, Bacterial Typing Techniques, Base Composition, China, Cluster Analysis, Comamonadaceae/*classification/genetics/*isolation & purification/physiology, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Locomotion, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, Ponds/*microbiology, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA | Genetics |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 324 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 619) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-619 | |||
| 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 | |||
| 20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | |
| 34235 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/15050 | ||||
| 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) | |||
| 67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
| 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 | |||
| 72485 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID3010.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
| 119363 | Curators of the CIP | Collection of Institut Pasteur (CIP 103271) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103271 |