Strain identifier
BacDive ID: 138190
Type strain:
Species: Halobacterium distributum
Strain history: CIP <- 1997, JCM <- VKM <- I.S. Zvyagintseva
NCBI tax ID(s): 1227468 (strain), 1227467 (strain), 29283 (species)
General
@ref: 39236
BacDive-ID: 138190
keywords: genome sequence, 16S sequence, Archaea, mesophilic, Gram-negative, rod-shaped
description: Halobacterium distributum CIP 105238 is a mesophilic, Gram-negative, rod-shaped archaeon of the family Halobacteriaceae.
NCBI tax id
NCBI tax id | Matching level |
---|---|
1227468 | strain |
29283 | species |
1227467 | strain |
strain history
@ref | history |
---|---|
67770 | VKM B-1733 <-- I. S. Zvyagintseva 1m. |
39236 | CIP <- 1997, JCM <- VKM <- I.S. Zvyagintseva |
doi: 10.13145/bacdive138190.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/archaea
- keyword: phylum/methanobacteriota
- domain: Archaea
- phylum: Methanobacteriota
- class: Halobacteria
- order: Halobacteriales
- family: Halobacteriaceae
- genus: Halobacterium
- species: Halobacterium distributum
- full scientific name: Halobacterium distributum corrig. Zvyagintseva and Tarasov 1989
synonyms
@ref synonym 20215 Halobacterium distributus 20215 Halorubrum terrestre 20215 Halorubrum arcis 20215 Halorubrum litoreum 20215 Halorubrobacterium distributum 20215 Halorubrum distributum
@ref: 39236
domain: Archaea
phylum: Euryarchaeota
class: Halobacteria
order: Halobacteriales
family: Halorubraceae
genus: Halorubrum
species: Halorubrum distributum
type strain: yes
Morphology
cell morphology
- @ref: 39236
- gram stain: negative
- cell shape: rod-shaped
- motility: no
Culture and growth conditions
culture medium
@ref | name | growth | composition | link |
---|---|---|---|---|
39236 | 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 | |
39236 | CIP Medium 223 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=223 | |
39236 | CIP Medium 232 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=232 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
39236 | positive | growth | 30 | mesophilic |
67770 | positive | growth | 37 | mesophilic |
39236 | positive | growth | 25-41 | |
39236 | no | growth | 5 | psychrophilic |
39236 | no | growth | 15 | psychrophilic |
39236 | no | growth | 45 | thermophilic |
Physiology and metabolism
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
39236 | 606565 | hippurate | + | hydrolysis |
39236 | 17632 | nitrate | - | reduction |
39236 | 16301 | nitrite | - | reduction |
antibiotic resistance
- @ref: 39236
- metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
- is antibiotic: yes
- is sensitive: yes
- is resistant: no
metabolite production
- @ref: 39236
- Chebi-ID: 35581
- metabolite: indole
- production: no
enzymes
@ref | value | activity | ec |
---|---|---|---|
39236 | oxidase | + | |
39236 | beta-galactosidase | + | 3.2.1.23 |
39236 | gelatinase | - | |
39236 | catalase | + | 1.11.1.6 |
39236 | gamma-glutamyltransferase | - | 2.3.2.2 |
39236 | phenylalanine ammonia-lyase | - | 4.3.1.24 |
39236 | tryptophan deaminase | - | |
39236 | urease | - | 3.5.1.5 |
68382 | alkaline phosphatase | + | 3.1.3.1 |
68382 | esterase (C 4) | + | |
68382 | esterase lipase (C 8) | + | |
68382 | lipase (C 14) | - | |
68382 | leucine arylamidase | + | 3.4.11.1 |
68382 | valine arylamidase | - | |
68382 | cystine arylamidase | + | 3.4.11.3 |
68382 | trypsin | - | 3.4.21.4 |
68382 | alpha-chymotrypsin | - | 3.4.21.1 |
68382 | acid phosphatase | - | 3.1.3.2 |
68382 | naphthol-AS-BI-phosphohydrolase | + | |
68382 | alpha-galactosidase | - | 3.2.1.22 |
68382 | beta-galactosidase | - | 3.2.1.23 |
68382 | beta-glucuronidase | - | 3.2.1.31 |
68382 | alpha-glucosidase | - | 3.2.1.20 |
68382 | beta-glucosidase | - | 3.2.1.21 |
68382 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68382 | alpha-mannosidase | - | 3.2.1.24 |
68382 | alpha-fucosidase | - | 3.2.1.51 |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
39236 | - | + | + | + | - | + | - | + | - | - | - | + | - | - | - | - | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | country | sample type | origin.country | continent |
---|---|---|---|---|
39236 | USSR | |||
67770 | Turkmenistan | Salt soil crust | TKM | Asia |
39236 | USSR | Environment, Salt soil crust in Turkmen |
Safety information
risk assessment
- @ref: 39236
- biosafety level: 1
- biosafety level comment: Risk group (French classification)
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
67770 | Halorubrum distributum 16S rRNA gene, complete sequence | D63572 | 1467 | ena | 29283 |
67770 | Halobacterium sp. (Halobacterium distributum) 16S ribosomal RNA sequence | L26170 | 181 | ena | 29283 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Halorubrum distributum JCM 10118 | GCA_000337335 | contig | ncbi | 1227468 |
67770 | Halorubrum distributum JCM 9100 | GCA_000337055 | contig | ncbi | 1227467 |
66792 | Halorubrum distributum JCM 9100 | 1227467.4 | wgs | patric | 1227467 |
66792 | Halorubrum distributum JCM 10118 | 1227468.4 | wgs | patric | 1227468 |
GC content
- @ref: 67770
- GC-content: 63.9
- method: thermal denaturation, midpoint method (Tm)
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
motile | no | 69.951 | no |
gram-positive | no | 97.61 | no |
anaerobic | no | 97.356 | no |
aerobic | yes | 86.837 | no |
halophile | yes | 89.384 | no |
spore-forming | no | 93.995 | no |
glucose-util | yes | 87.898 | no |
flagellated | no | 95.521 | no |
thermophile | no | 95.18 | yes |
glucose-ferment | no | 83.266 | no |
External links
@ref: 39236
culture collection no.: CIP 105238, ATCC 51197, JCM 9100, NCIMB 13203, VKM B-1733, CGMCC 1.3491, JCM 10118
straininfo link
@ref | straininfo |
---|---|
94970 | 46899 |
94971 | 312081 |
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 |
Reference
@id | authors | title | doi/url | catalogue | journal | pubmed |
---|---|---|---|---|---|---|
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | 10.1099/ijsem.0.004332 | |||
39236 | Curators of the CIP | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105238 | Collection of Institut Pasteur (CIP 105238) | |||
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |||
66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | 10.1093/nar/gkaa1025 | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
68382 | Automatically annotated from API zym | |||||
94970 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | StrainInfo: A central database for resolving microbial strain identifiers | 10.60712/SI-ID46899.1 | |||
94971 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | StrainInfo: A central database for resolving microbial strain identifiers | 10.60712/SI-ID312081.1 |