Strain identifier
BacDive ID: 5946
Type strain:
Species: Halorubrum distributum
Strain Designation: 4p
Strain history: CIP <- 2004, JCM <- 1998, VKM <- I. S. Zvyagintseva: strain 4p
NCBI tax ID(s): 267368 (species)
General
@ref: 17218
BacDive-ID: 5946
DSM-Number: 23453
keywords: genome sequence, 16S sequence, Archaea, mesophilic, Gram-negative, ovoid-shaped
description: Halorubrum distributum 4p is a mesophilic, Gram-negative, ovoid-shaped archaeon of the family Halorubraceae.
NCBI tax id
- NCBI tax id: 267368
- Matching level: species
strain history
@ref | history |
---|---|
67770 | VKM B-1739 <-- I. S. Zvyagintseva 4p. |
123471 | CIP <- 2004, JCM <- 1998, VKM <- I. S. Zvyagintseva: strain 4p |
doi: 10.13145/bacdive5946.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/archaea
- keyword: phylum/methanobacteriota
- domain: Archaea
- phylum: Methanobacteriota
- class: Halobacteria
- order: Haloferacales
- family: Halorubraceae
- genus: Halorubrum
- species: Halorubrum distributum
- full scientific name: Halorubrum distributum (Zvyagintseva and Tarasov 1989) Oren and Ventosa 1996
synonyms
@ref synonym 20215 Halobacterium distributus 20215 Halorubrum terrestre 20215 Halorubrum arcis 20215 Halorubrum litoreum 20215 Halorubrobacterium distributum 20215 Halobacterium distributum
@ref: 17218
domain: Archaea
phylum: Euryarchaeota
class: Halobacteria
order: Halobacteriales
family: Halorubraceae
genus: Halobacterium
species: Halobacterium distributum
full scientific name: Halorubrum distributum (Zvyagintseva and Tarasov 1989) Oren and Ventosa 1996
strain designation: 4p
type strain: no
Morphology
cell morphology
- @ref: 123471
- gram stain: negative
- cell shape: ovoid-shaped
- motility: no
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
17218 | HALOBACTERIA MEDIUM (DSMZ Medium 372) | yes | https://mediadive.dsmz.de/medium/372 | Name: HALOBACTERIA MEDIUM (DSMZ Medium 372) Composition: NaCl 200.0 g/l MgSO4 x 7 H2O 20.0 g/l Agar 20.0 g/l Yeast extract 5.0 g/l Casamino acids 5.0 g/l Na3-citrate 3.0 g/l KCl 2.0 g/l Na glutamate 1.0 g/l FeCl2 x 4 H2O 0.036 g/l MnCl2 x 4 H2O 0.00036 g/l Distilled water |
39994 | MEDIUM 223 - for Halorubrum saccharovorum and H. distributum | yes | Distilled water make up to (1000.000 ml);Sodium chloride (250.000 g);Potassium chloride (2.000 g);Iron (II) sulphate heptahydrate (0.050 g);Manganese II sulphate monohydrate (0.200 mg);Magnesium sulphate heptahydrate (20.000 g);Agar (20.000 g);Yeast extra | |
123471 | CIP Medium 223 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=223 | |
123471 | CIP Medium 330 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=330 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
17218 | positive | growth | 37 | mesophilic |
39994 | positive | growth | 37 | mesophilic |
67770 | positive | growth | 37 | mesophilic |
123471 | positive | growth | 25-45 | |
123471 | no | growth | 5 | psychrophilic |
123471 | no | growth | 15 | psychrophilic |
Physiology and metabolism
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
123471 | NaCl | no | growth | 0 % |
123471 | NaCl | no | growth | 2 % |
123471 | NaCl | no | growth | 4 % |
123471 | NaCl | no | growth | 6 % |
123471 | NaCl | no | growth | 8 % |
123471 | NaCl | no | growth | 10 % |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
123471 | 606565 | hippurate | + | hydrolysis |
123471 | 17632 | nitrate | - | reduction |
123471 | 16301 | nitrite | - | reduction |
metabolite production
- @ref: 123471
- Chebi-ID: 35581
- metabolite: indole
- production: no
metabolite tests
@ref | Chebi-ID | metabolite | voges-proskauer-test | methylred-test |
---|---|---|---|---|
123471 | 15688 | acetoin | - | |
123471 | 17234 | glucose | - |
enzymes
@ref | value | activity | ec |
---|---|---|---|
68382 | alpha-fucosidase | - | 3.2.1.51 |
68382 | alpha-mannosidase | - | 3.2.1.24 |
68382 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68382 | beta-glucosidase | - | 3.2.1.21 |
68382 | alpha-glucosidase | - | 3.2.1.20 |
68382 | beta-glucuronidase | - | 3.2.1.31 |
68382 | beta-galactosidase | - | 3.2.1.23 |
68382 | alpha-galactosidase | - | 3.2.1.22 |
68382 | naphthol-AS-BI-phosphohydrolase | + | |
68382 | acid phosphatase | - | 3.1.3.2 |
68382 | alpha-chymotrypsin | + | 3.4.21.1 |
68382 | trypsin | - | 3.4.21.4 |
68382 | cystine arylamidase | - | 3.4.11.3 |
68382 | valine arylamidase | - | |
68382 | leucine arylamidase | + | 3.4.11.1 |
68382 | lipase (C 14) | - | |
68382 | esterase lipase (C 8) | + | |
68382 | esterase (C 4) | + | |
68382 | alkaline phosphatase | + | 3.1.3.1 |
123471 | oxidase | + | |
123471 | beta-galactosidase | - | 3.2.1.23 |
123471 | alcohol dehydrogenase | - | 1.1.1.1 |
123471 | gelatinase | - | |
123471 | catalase | + | 1.11.1.6 |
123471 | gamma-glutamyltransferase | - | 2.3.2.2 |
123471 | lysine decarboxylase | - | 4.1.1.18 |
123471 | ornithine decarboxylase | - | 4.1.1.17 |
123471 | phenylalanine ammonia-lyase | - | 4.3.1.24 |
123471 | tryptophan deaminase | - | |
123471 | urease | - | 3.5.1.5 |
API zym
@ref | Control | Alkaline phosphatase | Esterase | Esterase Lipase | Lipase | Leucine arylamidase | Valine arylamidase | Cystine arylamidase | Trypsin | alpha- Chymotrypsin | Acid phosphatase | Naphthol-AS-BI-phosphohydrolase | alpha- Galactosidase | beta- Galactosidase | beta- Glucuronidase | alpha- Glucosidase | beta- Glucosidase | N-acetyl-beta- glucosaminidase | alpha- Mannosidase | alpha- Fucosidase |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
123471 | - | + | + | + | - | + | - | - | - | + | - | + | - | - | - | - | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | geographic location | country | origin.country | sample type | continent |
---|---|---|---|---|---|
39994 | Ashkhabad | USSR | TKM | ||
67770 | Ashgabat | Turkmenistan | TKM | Salt crust | Asia |
123471 | Ashkhabad | Turkmenistan | TKM | Salt crust | Asia |
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
17218 | 1 | Risk group (German classification) |
123471 | 1 | Risk group (French classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Halorubrum terrestre gene for 16S rRNA, complete sequence, strain: JCM 10247 | AB663422 | 1470 | ena | 267368 |
20218 | Halorubrum terrestre gene for 16S rRNA, partial sequence | AB090169 | 1467 | ena | 267368 |
67770 | Halobacterium distributum 16S ribosomal RNA (16S rRNA) | L26117 | 182 | ena | 29283 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Halorubrum terrestre JCM 10247 | 2554235509 | draft | img | 1227486 |
67770 | Halorubrum terrestre JCM 10247 | GCA_000337435 | contig | ncbi | 1227486 |
66792 | Halorubrum terrestre JCM 10247 | 1227486.3 | wgs | patric | 1227486 |
GC content
- @ref: 67770
- GC-content: 64.4
- method: thermal denaturation, midpoint method (Tm)
External links
@ref: 17218
culture collection no.: DSM 23453, JCM 10247, CGMCC 1.5397, CGMCC 1.8971, CIP 108318, VKM B-1739
straininfo link
- @ref: 75435
- straininfo: 389474
literature
topic | Pubmed-ID | title | authors | journal | year | mesh | topic2 | DOI |
---|---|---|---|---|---|---|---|---|
Phylogeny | 8992245 | [A new description of the type strain of Halobacterium distributum]. | Zviagintseva IS, Kudriashova EB, Bulygina ES | Mikrobiologiia | 1996 | Base Sequence, Halobacteriaceae/classification/genetics, Halobacterium/*classification/genetics, Molecular Sequence Data, RNA, Bacterial/*genetics, RNA, Ribosomal, 16S/*genetics, RNA, Ribosomal, 5S/*genetics, Sequence Homology, Nucleic Acid | Genetics | |
Phylogeny | 15023949 | Taxonomic study of Halorubrum distributum and proposal of Halorubrum terrestre sp. nov. | Ventosa A, Gutierrez MC, Kamekura M, Zvyagintseva IS, Oren A | Int J Syst Evol Microbiol | 2004 | Base Composition, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Halobacteriaceae/*classification/isolation & purification, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Soil Microbiology | Genetics | 10.1099/ijs.0.02621-0 |
Phylogeny | 31971502 | Genome-based analyses reveal a synonymy among Halorubrum distributum Zvyagintseva and Tarasov 1989; Oren and Ventosa 1996, Halorubrum terrestre Ventosa et al. 2004, Halorubrum arcis Xu et al. 2007 and Halorubrum litoreum Cui et al. 2007. Emended description of Halorubrum distributum Zvyagintseva and Tarasov 1989; Oren and Ventosa 1996. | Infante-Dominguez C, de la Haba RR, Corral P, Sanchez-Porro C, Arahal DR, Ventosa A | Int J Syst Evol Microbiol | 2020 | DNA, Archaeal/genetics, Genes, Archaeal, Halorubrum/*classification, Lipids/chemistry, Multilocus Sequence Typing, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA | Transcriptome | 10.1099/ijsem.0.003956 |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
17218 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23453) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-23453 | |||
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 | |
39994 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/5927 | ||||
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/ | ||||
68382 | Automatically annotated from API zym | |||||
75435 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID389474.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
123471 | Curators of the CIP | Collection of Institut Pasteur (CIP 108318) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108318 |