Strain identifier
BacDive ID: 7488
Type strain:
Species: Salinibacterium amurskyense
Strain history: CIP <- 2004, KCTC <- KMM
NCBI tax ID(s): 205941 (species)
General
@ref: 6429
BacDive-ID: 7488
DSM-Number: 16400
keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, mesophilic, Gram-positive
description: Salinibacterium amurskyense DSM 16400 is an obligate aerobe, mesophilic, Gram-positive bacterium that was isolated from seawater.
NCBI tax id
- NCBI tax id: 205941
- Matching level: species
strain history
@ref | history |
---|---|
6429 | <- S.-B. Kim <- KMM <- O. I. Nedashkovskaya |
67770 | KCTC 9931 <-- S. B. Kim <-- O. I. Nedashkovskaya KMM 3673. |
116347 | CIP <- 2004, KCTC <- KMM |
doi: 10.13145/bacdive7488.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/actinomycetota
- domain: Bacteria
- phylum: Actinomycetota
- class: Actinomycetes
- order: Micrococcales
- family: Microbacteriaceae
- genus: Salinibacterium
- species: Salinibacterium amurskyense
- full scientific name: Salinibacterium amurskyense Han et al. 2003
@ref: 6429
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Microbacteriaceae
genus: Salinibacterium
species: Salinibacterium amurskyense
full scientific name: Salinibacterium amurskyense Han et al. 2003
type strain: yes
Morphology
cell morphology
@ref | gram stain | confidence | cell shape | motility |
---|---|---|---|---|
69480 | positive | 100 | ||
116347 | positive | rod-shaped | no |
colony morphology
- @ref: 116347
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
6429 | BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) | yes | https://mediadive.dsmz.de/medium/514 | Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water |
33234 | Marine agar (MA) | yes | Distilled water make up to (1000.000 ml);Marine agar (55.100 g) | |
116347 | CIP Medium 13 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
6429 | positive | growth | 25-28 | mesophilic |
33234 | positive | growth | 30 | mesophilic |
67770 | positive | growth | 28 | mesophilic |
116347 | positive | growth | 10-30 | |
116347 | no | growth | 37 | mesophilic |
116347 | no | growth | 41 | thermophilic |
116347 | no | growth | 45 | thermophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 116347
- oxygen tolerance: obligate aerobe
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.998 |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
116347 | NaCl | positive | growth | 0-4 % |
116347 | NaCl | no | growth | 6 % |
116347 | NaCl | no | growth | 8 % |
116347 | NaCl | no | growth | 10 % |
observation
- @ref: 67770
- observation: quinones: MK-11
metabolite utilization
@ref | metabolite | utilization activity | kind of utilization tested | Chebi-ID |
---|---|---|---|---|
68371 | Potassium 5-ketogluconate | - | builds acid from | |
68371 | Potassium 2-ketogluconate | - | builds acid from | |
68371 | gluconate | - | builds acid from | 24265 |
68371 | L-arabitol | - | builds acid from | 18403 |
68371 | D-arabitol | - | builds acid from | 18333 |
68371 | D-fucose | - | builds acid from | 28847 |
68371 | D-tagatose | - | builds acid from | 16443 |
68371 | D-lyxose | - | builds acid from | 62318 |
68371 | turanose | - | builds acid from | 32528 |
68371 | gentiobiose | - | builds acid from | 28066 |
68371 | xylitol | - | builds acid from | 17151 |
68371 | glycogen | - | builds acid from | 28087 |
68371 | starch | - | builds acid from | 28017 |
68371 | raffinose | - | builds acid from | 16634 |
68371 | melezitose | - | builds acid from | 6731 |
68371 | inulin | - | builds acid from | 15443 |
68371 | trehalose | - | builds acid from | 27082 |
68371 | sucrose | - | builds acid from | 17992 |
68371 | melibiose | - | builds acid from | 28053 |
68371 | lactose | - | builds acid from | 17716 |
68371 | maltose | - | builds acid from | 17306 |
68371 | cellobiose | - | builds acid from | 17057 |
68371 | salicin | - | builds acid from | 17814 |
68371 | arbutin | - | builds acid from | 18305 |
68371 | amygdalin | - | builds acid from | 27613 |
68371 | N-acetylglucosamine | - | builds acid from | 59640 |
68371 | methyl alpha-D-glucopyranoside | - | builds acid from | 320061 |
68371 | methyl alpha-D-mannoside | - | builds acid from | 43943 |
68371 | D-sorbitol | - | builds acid from | 17924 |
68371 | myo-inositol | - | builds acid from | 17268 |
68371 | galactitol | - | builds acid from | 16813 |
68371 | L-sorbose | - | builds acid from | 17266 |
68371 | methyl beta-D-xylopyranoside | - | builds acid from | 74863 |
68371 | ribitol | - | builds acid from | 15963 |
68371 | L-xylose | - | builds acid from | 65328 |
68371 | L-arabinose | - | builds acid from | 30849 |
68371 | D-arabinose | - | builds acid from | 17108 |
68371 | erythritol | - | builds acid from | 17113 |
116347 | citrate | - | carbon source | 16947 |
116347 | esculin | - | hydrolysis | 4853 |
116347 | hippurate | - | hydrolysis | 606565 |
116347 | nitrate | - | reduction | 17632 |
116347 | nitrite | - | reduction | 16301 |
116347 | nitrate | - | respiration | 17632 |
metabolite production
- @ref: 116347
- Chebi-ID: 35581
- metabolite: indole
- production: no
metabolite tests
@ref | Chebi-ID | metabolite | voges-proskauer-test | methylred-test |
---|---|---|---|---|
116347 | 15688 | acetoin | - | |
116347 | 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 |
116347 | oxidase | - | |
116347 | beta-galactosidase | - | 3.2.1.23 |
116347 | alcohol dehydrogenase | - | 1.1.1.1 |
116347 | gelatinase | +/- | |
116347 | amylase | - | |
116347 | DNase | + | |
116347 | caseinase | - | 3.4.21.50 |
116347 | catalase | + | 1.11.1.6 |
116347 | tween esterase | - | |
116347 | gamma-glutamyltransferase | - | 2.3.2.2 |
116347 | lysine decarboxylase | - | 4.1.1.18 |
116347 | ornithine decarboxylase | - | 4.1.1.17 |
116347 | phenylalanine ammonia-lyase | - | 4.3.1.24 |
116347 | tryptophan deaminase | - | |
116347 | 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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
116347 | - | - | + | + | - | + | + | - | - | - | + | + | + | - | - | + | - | - | - | - |
API 50CHac
@ref | GLY | ERY | DARA | LARA | RIB | DXYL | LXYL | ADO | MDX | GAL | GLU | FRU | MNE | SBE | RHA | DUL | INO | MAN | SOR | MDM | MDG | NAG | AMY | ARB | ESC | SAL | CEL | MAL | LAC | MEL | SAC | TRE | INU | MLZ | RAF | AMD | GLYG | XLT | GEN | TUR | LYX | TAG | DFUC | LFUC | DARL | LARL | GNT | 2KG | 5KG |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
116347 | +/- | - | - | - | +/- | +/- | - | - | - | +/- | +/- | +/- | +/- | - | +/- | - | - | +/- | - | - | - | - | - | - | +/- | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | +/- | - | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
6429 | seawater | East Sea, Amursky Bay | Russia | RUS | Europe |
67770 | Seawater | Amursky Bay of the Gulf of Peter the Great | Russia | RUS | |
116347 | Environment, Sea water | Amursky bay | Sea of Japan |
isolation source categories
- Cat1: #Environmental
- Cat2: #Aquatic
- Cat3: #Marine
taxonmaps
- @ref: 69479
- File name: preview.99_5731.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_895;97_3383;98_4266;99_5731&stattab=map
- Last taxonomy: Salinibacterium amurskyense subclade
- 16S sequence: AF539697
- Sequence Identity:
- Total samples: 837
- soil counts: 348
- aquatic counts: 328
- animal counts: 65
- plant counts: 96
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
6429 | 1 | Risk group (German classification) |
116347 | 1 | Risk group (French classification) |
Sequence information
16S sequences
- @ref: 6429
- description: Marine bacterium KMM3673 16S ribosomal RNA gene, partial sequence
- accession: AF539697
- length: 1431
- database: ena
- NCBI tax ID: 205941
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Salinibacterium amurskyense KCTC 9931 | GCA_014652955 | contig | ncbi | 205941 |
66792 | Salinibacterium amurskyense strain DSM 16400 | 205941.3 | wgs | patric | 205941 |
66792 | Salinibacterium amurskyense strain JCM 12362 | 205941.4 | wgs | patric | 205941 |
66792 | Salinibacterium amurskyense strain KCTC 9931 | 205941.11 | wgs | patric | 205941 |
66792 | Salinibacterium amurskyense DSM 16400 | 2728369736 | draft | img | 205941 |
66792 | Salinibacterium amurskyense JCM 12362 | 2839424328 | draft | img | 205941 |
67770 | Salinibacterium amurskyense DSM 16400 | GCA_002797685 | contig | ncbi | 205941 |
67770 | Salinibacterium amurskyense JCM 12362 | GCA_003668745 | contig | ncbi | 205941 |
GC content
@ref | GC-content | method |
---|---|---|
6429 | 61 | |
67770 | 61 | thermal denaturation, midpoint method (Tm) |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | no | 90.889 | no |
gram-positive | yes | 92.564 | no |
anaerobic | no | 99.402 | no |
aerobic | yes | 94.545 | no |
halophile | no | 86.803 | no |
spore-forming | no | 94.751 | no |
glucose-util | yes | 84.63 | no |
flagellated | no | 97.601 | no |
thermophile | no | 99.496 | yes |
glucose-ferment | no | 87.237 | no |
External links
@ref: 6429
culture collection no.: DSM 16400, KCTC 9931, KMM 3673, JCM 12362, CIP 108377, IAM 15155, NBRC 100448
straininfo link
- @ref: 76934
- straininfo: 99608
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 14657146 | Salinibacterium amurskyense gen. nov., sp. nov., a novel genus of the family Microbacteriaceae from the marine environment. | Han SK, Nedashkovskaya OI, Mikhailov VV, Kim SB, Bae KS | Int J Syst Evol Microbiol | 10.1099/ijs.0.02627-0 | 2003 | Korea, Micrococcaceae/*classification/genetics/isolation & purification, Molecular Sequence Data, *Phylogeny, Seawater/microbiology, Species Specificity | Genetics |
Phylogeny | 19060050 | Salinibacterium xinjiangense sp. nov., a psychrophilic bacterium isolated from the China No. 1 glacier. | Zhang DC, Liu HC, Xin YH, Yu Y, Zhou PJ, Zhou YG | Int J Syst Evol Microbiol | 10.1099/ijs.0.65802-0 | 2008 | Actinomycetales/*classification/genetics/isolation & purification/*physiology, China, Ice Cover/*microbiology, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Species Specificity | Genetics |
Phylogeny | 22923118 | Homoserinimonas aerilata gen. nov., sp. nov., a novel member of the family Microbacteriaceae isolated from an air sample in Korea. | Kim SJ, Jang YH, Hamada M, Tamura T, Ahn JH, Weon HY, Suzuki K, Kwon SW | J Microbiol | 10.1007/s12275-012-2096-3 | 2012 | Actinomycetales/*classification/genetics/*isolation & purification/physiology, Aerobiosis, *Air Microbiology, Amino Acids/analysis, Base Composition, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Hydrogen-Ion Concentration, Locomotion, Molecular Sequence Data, Peptidoglycan/chemistry, Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Temperature, Vitamin K 2/analysis | Genetics |
Reference
@id | authors | catalogue | doi/url | title |
---|---|---|---|---|
6429 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16400) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-16400 | |
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 | |
33234 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/5992 | ||
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/ | ||
68371 | Automatically annotated from API 50CH acid | |||
68382 | Automatically annotated from API zym | |||
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 | |
76934 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID99608.1 | StrainInfo: A central database for resolving microbial strain identifiers | |
116347 | Curators of the CIP | Collection of Institut Pasteur (CIP 108377) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108377 |