Strain identifier
BacDive ID: 2424
Type strain: 
Species: Allochromatium vinosum
Strain Designation: D, Roelofsoen D
Strain history: <- C.B. van Niel <- P.A. Roelofsoen, D
NCBI tax ID(s): 572477 (strain), 1049 (species)
version 8.1 (current version)
General
@ref: 5
BacDive-ID: 2424
DSM-Number: 180
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic
description: Allochromatium vinosum D is an anaerobe, mesophilic bacterium that was isolated from ditch water.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 572477 | strain |
| 1049 | species |
strain history
- @ref: 5
- history: <- C.B. van Niel <- P.A. Roelofsoen, D
doi: 10.13145/bacdive2424.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Gammaproteobacteria
- order: Chromatiales
- family: Chromatiaceae
- genus: Allochromatium
- species: Allochromatium vinosum
- full scientific name: Allochromatium vinosum (Ehrenberg 1838) Imhoff et al. 1998
synonyms
@ref synonym 20215 Monas vinosa 20215 Chromatium vinosum
@ref: 5
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Chromatiales
family: Chromatiaceae
genus: Allochromatium
species: Allochromatium vinosum
full scientific name: Allochromatium vinosum (Ehrenberg 1838) Imhoff et al. 1998
strain designation: D, Roelofsoen D
type strain: yes
Culture and growth conditions
culture medium
- @ref: 5
- name: PFENNIG'S MEDIUM I (modified 1988, for purple sulfur bacteria) (DSMZ Medium 28)
- growth: yes
- link: https://mediadive.dsmz.de/medium/28
- composition: Name: PFENNIG'S MEDIUM I (DSMZ Medium 28) Composition: NaHCO3 1.5 g/l Na2S x 9 H2O 0.592592 g/l MgSO4 x 7 H2O 0.500001 g/l KCl 0.349999 g/l KH2PO4 0.349999 g/l Ammonium chloride 0.349999 g/l Pyruvic acid sodium salt 0.25 g/l Dextrose 0.25 g/l CaCl2 x 2 H2O 0.25 g/l Yeast extract 0.25 g/l Ammonium acetate 0.25 g/l Na2-EDTA 0.003 g/l Resazurin 0.00225 g/l FeSO4 x 7 H2O 0.0011 g/l Vitamin B12 0.001 g/l H3BO3 0.0003 g/l CoCl2 x 6 H2O 0.00019 g/l MnCl2 x 2 H2O 5e-05 g/l ZnCl2 4.2e-05 g/l NiCl2 x 6 H2O 2.4e-05 g/l Na2MoO4 x 2 H2O 1.8e-05 g/l CuCl2 x 2 H2O 2e-06 g/l Distilled water
culture temp
- @ref: 5
- growth: positive
- type: growth
- temperature: 25
- range: mesophilic
Physiology and metabolism
oxygen tolerance
- @ref: 5
- oxygen tolerance: anaerobe
Isolation, sampling and environmental information
isolation
- @ref: 5
- sample type: ditch water
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Freshwater |
| #Engineered | #Built environment |
taxonmaps
- @ref: 69479
- File name: preview.99_3612.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_169;96_1874;97_2251;98_2763;99_3612&stattab=map
- Last taxonomy: Allochromatium
- 16S sequence: FM178268
- Sequence Identity:
- Total samples: 671
- soil counts: 87
- aquatic counts: 525
- animal counts: 49
- plant counts: 10
Safety information
risk assessment
- @ref: 5
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 20218 | Allochromatium vinosum DSM 180 16S ribosomal RNA gene, partial sequence | FJ812038 | 1267 | ena | 572477 |
| 20218 | Allochromatium vinosum DSM 180 16S-23S ribosomal RNA intergenic spacer, partial sequence | FJ823965 | 420 | ena | 572477 |
| 20218 | Allochromatium vinosum partial 16S rRNA gene, type strain DSM 180T | FM178268 | 1462 | ena | 572477 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Allochromatium vinosum DSM 180 | GCA_000025485 | complete | ncbi | 572477 |
| 66792 | Allochromatium vinosum DSM 180 | 572477.4 | complete | patric | 572477 |
| 66792 | Allochromatium vinosum DSM 180 | 572477.21 | plasmid | patric | 572477 |
| 66792 | Allochromatium vinosum DSM 180 | 572477.22 | plasmid | patric | 572477 |
| 66792 | Allochromatium vinosum DSM 180 | 646564502 | complete | img | 572477 |
GC content
- @ref: 5
- GC-content: 64.3
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| motile | yes | 90.55 | no |
| flagellated | yes | 50.735 | no |
| gram-positive | no | 98.837 | no |
| anaerobic | yes | 97.152 | yes |
| aerobic | no | 95.396 | yes |
| halophile | no | 91.346 | no |
| spore-forming | no | 90.104 | no |
| thermophile | no | 93.572 | yes |
| glucose-util | yes | 69.414 | no |
| glucose-ferment | no | 81.238 | no |
External links
@ref: 5
culture collection no.: DSM 180, ATCC 17899
straininfo link
- @ref: 71974
- straininfo: 47074
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Enzymology | 7669805 | Electron paramagnetic resonance studies of ferric cytochrome c' from photosynthetic bacteria. | Fujii S, Yoshimura T, Kamada H, Yamaguchi K, Suzuki S, Shidara S, Takakuwa S | Biochim Biophys Acta | 10.1016/0167-4838(95)00092-9 | 1995 | Chromatium/*enzymology, Cytochrome-c Peroxidase/chemistry, Electron Spin Resonance Spectroscopy, Hydrogen-Ion Concentration, Peroxidases/*chemistry/isolation & purification, Rhodobacter capsulatus/*enzymology, Rhodopseudomonas/*enzymology, Rhodospirillum/*enzymology | Phylogeny |
| Metabolism | 8547347 | Spectroscopic characterization of nitrosylheme in nitric oxide complexes of ferric and ferrous cytochrome c' from photosynthetic bacteria. | Yoshimura T, Fujii S, Kamada H, Yamaguchi K, Suzuki S, Shidara S, Takakuwa S | Biochim Biophys Acta | 10.1016/0167-4838(95)00187-5 | 1996 | Cytochrome c Group/chemistry/*metabolism, Electron Spin Resonance Spectroscopy, Ferric Compounds/metabolism, Ferrous Compounds/metabolism, Heme/*analogs & derivatives/chemistry, Nitric Oxide/*metabolism, Photosynthesis, Rhodospirillales/*chemistry, Spectrophotometry | |
| Enzymology | 9004500 | Insertional gene inactivation in a phototrophic sulphur bacterium: APS-reductase-deficient mutants of Chromatium vinosum. | Dahl C | Microbiology (Reading) | 10.1099/13500872-142-12-3363 | 1996 | Chromatium/*enzymology/*genetics/growth & development, Cloning, Molecular, Conjugation, Genetic, DNA Primers, Escherichia coli, Genes, Bacterial, Genotype, *Mutagenesis, Insertional, Oxidoreductases/biosynthesis/*genetics/metabolism, *Oxidoreductases Acting on Sulfur Group Donors, Phenotype, Plasmids, Polymerase Chain Reaction, Recombinant Proteins/biosynthesis/metabolism, Recombination, Genetic, Restriction Mapping, Substrate Specificity, Sulfites/metabolism, Thiosulfates/metabolism | Metabolism |
| Enzymology | 9177478 | Cloning and sequencing of the gene encoding the high potential iron-sulfur protein (HiPIP) from the purple sulfur bacterium Chromatium vinosum. | Bruser T, Truper HG, Dahl C | Biochim Biophys Acta | 10.1016/s0167-4781(97)00033-x | 1997 | Amino Acid Sequence, Bacterial Proteins, Base Sequence, Chromatium/*genetics, Cloning, Molecular, DNA/*chemistry, *Genes, Bacterial, Iron-Sulfur Proteins/*genetics, Molecular Sequence Data, *Photosynthetic Reaction Center Complex Proteins, Protein Sorting Signals/genetics | Genetics |
| Metabolism | 15687204 | Novel genes of the dsr gene cluster and evidence for close interaction of Dsr proteins during sulfur oxidation in the phototrophic sulfur bacterium Allochromatium vinosum. | Dahl C, Engels S, Pott-Sperling AS, Schulte A, Sander J, Lubbe Y, Deuster O, Brune DC | J Bacteriol | 10.1128/JB.187.4.1392-1404.2005 | 2005 | Bacterial Proteins/genetics/isolation & purification/*metabolism, Blotting, Western, Chromatiaceae/*genetics/*metabolism, Cytochromes c/genetics/metabolism, DNA, Bacterial/chemistry, *Genes, Bacterial, Iron-Sulfur Proteins/genetics/metabolism, Membrane Proteins/genetics/metabolism, Molecular Sequence Data, Molecular Weight, Multigene Family, NADH, NADPH Oxidoreductases/genetics/metabolism, *Operon, Oxidation-Reduction, Oxidoreductases Acting on Sulfur Group Donors/isolation & purification, Protein Interaction Mapping, Protein Subunits/isolation & purification, Sequence Analysis, DNA, Sulfides/metabolism, Sulfur/*metabolism, Thiosulfates/metabolism, Transaminases/genetics/metabolism | Enzymology |
| Metabolism | 19557308 | Altered composition of Ralstonia eutropha poly(hydroxyalkanoate) through expression of PHA synthase from Allochromatium vinosum ATCC 35206. | Aneja KK, Ashby RD, Solaiman DK | Biotechnol Lett | 10.1007/s10529-009-0052-z | 2009 | Acyltransferases/genetics/*metabolism, Amino Acid Sequence, Chromatiaceae/*enzymology/genetics, Cloning, Molecular, Cupriavidus necator/*enzymology/genetics/*metabolism, DNA, Bacterial/chemistry/genetics, Gene Expression, Gene Order, Molecular Sequence Data, Polyhydroxyalkanoates/*chemistry/*metabolism, Recombinant Proteins/genetics/metabolism, Sequence Alignment, Sequence Analysis, DNA | Enzymology |
| Phylogeny | 21885227 | The genus Allochromatium (Chromatiales Chromatiaceae) revisited: a study on its intragenic structure based on multilocus sequence analysis (MLSA) and DNA-DNA hybridization (DDH). | Serrano W, Amann R, Rossello-Mora R, Herbert RA, Fischer U | Syst Appl Microbiol | 10.1016/j.syapm.2011.06.002 | 2011 | Bacterial Proteins/genetics, Bacterial Typing Techniques/*methods, Chromatiaceae/*classification/*genetics, DNA, Bacterial/analysis/genetics/isolation & purification, DNA, Ribosomal Spacer/genetics, Molecular Sequence Data, Multilocus Sequence Typing/*methods, Nucleic Acid Hybridization/*methods, Phylogeny, RNA, Ribosomal, 16S/genetics | Genetics |
| Genetics | 22675582 | Complete genome sequence of Allochromatium vinosum DSM 180(T). | Weissgerber T, Zigann R, Bruce D, Chang YJ, Detter JC, Han C, Hauser L, Jeffries CD, Land M, Munk AC, Tapia R, Dahl C | Stand Genomic Sci | 10.4056/sigs.2335270 | 2011 | ||
| Metabolism | 23873913 | Genome-wide transcriptional profiling of the purple sulfur bacterium Allochromatium vinosum DSM 180T during growth on different reduced sulfur compounds. | Weissgerber T, Dobler N, Polen T, Latus J, Stockdreher Y, Dahl C | J Bacteriol | 10.1128/JB.00154-13 | 2013 | Bacterial Proteins/genetics/*metabolism, Chromatiaceae/*genetics/*growth & development/metabolism, Culture Media/chemistry, *Gene Expression Profiling, *Gene Expression Regulation, Bacterial, Genes, Bacterial, *Genome, Bacterial, Hydrogensulfite Reductase/genetics/metabolism, Oligonucleotide Array Sequence Analysis, Oxidation-Reduction, Sulfides/metabolism, Sulfites/metabolism, Sulfur/metabolism, Sulfur Compounds/*metabolism, Thiosulfates/metabolism | Genetics |
| Phylogeny | 26025943 | Allochromatium humboldtianum sp. nov., isolated from soft coastal sediments. | Serrano W, Schrubbers J, Amann R, Fischer U | Int J Syst Evol Microbiol | 10.1099/ijs.0.000364 | 2015 | Bacterial Typing Techniques, Bacteriochlorophyll A/metabolism, Base Composition, Carotenoids/metabolism, Chromatiaceae/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Peru, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/microbiology, Sequence Analysis, DNA | Metabolism |
| Metabolism | 28042698 | Geochemically distinct carbon isotope distributions in Allochromatium vinosum DSM 180(T) grown photoautotrophically and photoheterotrophically. | Tang T, Mohr W, Sattin SR, Rogers DR, Girguis PR, Pearson A | Geobiology | 10.1111/gbi.12221 | 2017 | Acetates/metabolism, Amino Acids/analysis, Carbon Cycle, Carbon Dioxide/metabolism, Carbon Isotopes/*analysis, Chromatiaceae/*chemistry/*growth & development/metabolism, Fatty Acids/analysis, Phytol/analysis, Proteins/analysis, RNA, Bacterial/analysis | |
| Metabolism | 28853772 | Effect of Illumination Intensity and Inhibition of Carotenoid Biosynthesis on Assembly of Peripheral Light-Gathering Complexes in Purple Sulfur Bacteria C Allochromatium vinosum ATCC 17899. | Bol'shakov MA, Ashikhmin AA, Makhneva ZK, Moskalenko AA | Mikrobiologiia | 2016 | Bacterial Proteins/*biosynthesis/genetics, Carotenoids/*antagonists & inhibitors/biosynthesis, Chromatiaceae/drug effects/genetics/metabolism/*radiation effects, Culture Media/chemistry/pharmacology, Diphenylamine/pharmacology, Dose-Response Relationship, Radiation, Gene Expression, Ligases/genetics/metabolism, Light, Light-Harvesting Protein Complexes/*biosynthesis/genetics, Mixed Function Oxygenases/genetics/metabolism, Xanthophylls/antagonists & inhibitors/biosynthesis, zeta Carotene/antagonists & inhibitors/biosynthesis | Pathogenicity | |
| Metabolism | 30798412 | Structural study to analyze the DNA-binding properties of DsrC protein from the dsr operon of sulfur-oxidizing bacterium Allochromatium vinosum. | Ghosh S, Bagchi A | J Mol Model | 10.1007/s00894-019-3945-3 | 2019 | Amino Acid Motifs, Bacterial Proteins/*chemistry, Binding Sites, Chromatiaceae/*metabolism, DNA-Binding Proteins/*chemistry, Hydrogensulfite Reductase/*chemistry, Molecular Dynamics Simulation, Oxidation-Reduction, Promoter Regions, Genetic, Protein Domains, Sulfur/chemistry/metabolism | Enzymology |
| Metabolism | 32276557 | Protein dynamics and molecular motions study in relation to molecular interaction between proteins from sulfur oxidizing proteobacteria Allochromatium vinosum. | Ghosh S, Bagchi A | J Biomol Struct Dyn | 10.1080/07391102.2020.1754914 | 2020 | *Bacterial Proteins/genetics/metabolism, Chromatiaceae, Oxidation-Reduction, *Proteobacteria/metabolism, Sulfur | |
| Transcriptome | 34669148 | Complete genome of the thermophilic purple sulfur Bacterium Thermochromatium tepidum compared to Allochromatium vinosum and other Chromatiaceae. | Sattley WM, Swingley WD, Burchell BM, Dewey ED, Hayward MK, Renbarger TL, Shaffer KN, Stokes LM, Gurbani SA, Kujawa CM, Nuccio DA, Schladweiler J, Touchman JW, Wang-Otomo ZY, Blankenship RE, Madigan MT | Photosynth Res | 10.1007/s11120-021-00870-y | 2021 | *Chromatiaceae/genetics, Sequence Analysis, DNA, Sulfur |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 5 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 180) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-180 | |||
| 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 | |
| 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 | |||
| 71974 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID47074.1 | StrainInfo: A central database for resolving microbial strain identifiers |