Strain identifier
BacDive ID: 11952
Type strain:
Species: Kurthia sibirica
Strain Designation: 13-2
Strain history: CIP <- 1990, CCM <- V.L. Belikova: strain 13-2
NCBI tax ID(s): 202750 (species)
General
@ref: 1750
BacDive-ID: 11952
DSM-Number: 4747
keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, mesophilic, Gram-positive
description: Kurthia sibirica 13-2 is an obligate aerobe, mesophilic, Gram-positive bacterium that was isolated from large intestine of Magadan mammoth found in permafrost.
NCBI tax id
- NCBI tax id: 202750
- Matching level: species
strain history
@ref | history |
---|---|
1750 | <- CCM <- V.L. Belikova, 13-2 |
67770 | CCM 3477 <-- V. L. Belikova 13-22. |
122597 | CIP <- 1990, CCM <- V.L. Belikova: strain 13-2 |
doi: 10.13145/bacdive11952.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacillota
- domain: Bacteria
- phylum: Bacillota
- class: Bacilli
- order: Caryophanales
- family: Caryophanaceae
- genus: Kurthia
- species: Kurthia sibirica
- full scientific name: Kurthia sibirica Belikova et al. 1988
@ref: 1750
domain: Bacteria
phylum: Firmicutes
class: Bacilli
order: Bacillales
family: Caryophanaceae
genus: Kurthia
species: Kurthia sibirica
full scientific name: Kurthia sibirica Belikova et al. 1988
strain designation: 13-2
type strain: yes
Morphology
cell morphology
@ref | gram stain | confidence | cell shape | motility |
---|---|---|---|---|
69480 | positive | 100 | ||
122597 | positive | rod-shaped | yes |
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
1750 | TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) | yes | https://mediadive.dsmz.de/medium/92 | Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water |
35535 | MEDIUM 3 - Columbia agar | yes | Columbia agar (39.000 g);distilled water (1000.000 ml) | |
122597 | CIP Medium 3 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
1750 | positive | growth | 25 | mesophilic |
35535 | positive | growth | 30 | mesophilic |
67770 | positive | growth | 17 | psychrophilic |
122597 | positive | growth | 10-25 | psychrophilic |
122597 | no | growth | 37 | mesophilic |
122597 | no | growth | 41 | thermophilic |
122597 | no | growth | 45 | thermophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 122597
- oxygen tolerance: obligate aerobe
spore formation
- @ref: 69480
- spore formation: no
- confidence: 92.767
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
122597 | NaCl | positive | growth | 0-4 % |
122597 | NaCl | no | growth | 6 % |
122597 | NaCl | no | growth | 8 % |
122597 | NaCl | no | growth | 10 % |
murein
- @ref: 1750
- murein short key: A11.31
- type: A4alpha L-Lys-D-Asp
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 | L-fucose | - | builds acid from | 18287 |
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 | esculin | - | builds acid from | 4853 |
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 | D-mannitol | - | builds acid from | 16899 |
68371 | myo-inositol | - | builds acid from | 17268 |
68371 | galactitol | - | builds acid from | 16813 |
68371 | L-rhamnose | - | builds acid from | 62345 |
68371 | L-sorbose | - | builds acid from | 17266 |
68371 | D-mannose | - | builds acid from | 16024 |
68371 | D-fructose | - | builds acid from | 15824 |
68371 | D-glucose | - | builds acid from | 17634 |
68371 | D-galactose | - | builds acid from | 12936 |
68371 | methyl beta-D-xylopyranoside | - | builds acid from | 74863 |
68371 | ribitol | - | builds acid from | 15963 |
68371 | L-xylose | - | builds acid from | 65328 |
68371 | D-xylose | - | builds acid from | 65327 |
68371 | D-ribose | - | builds acid from | 16988 |
68371 | L-arabinose | - | builds acid from | 30849 |
68371 | D-arabinose | - | builds acid from | 17108 |
68371 | erythritol | - | builds acid from | 17113 |
68371 | glycerol | - | builds acid from | 17754 |
122597 | esculin | - | hydrolysis | 4853 |
122597 | nitrate | - | reduction | 17632 |
122597 | nitrite | - | reduction | 16301 |
122597 | glucose | - | degradation | 17234 |
metabolite production
- @ref: 122597
- Chebi-ID: 35581
- metabolite: indole
- production: no
enzymes
@ref | value | activity | ec |
---|---|---|---|
122597 | oxidase | - | |
122597 | beta-galactosidase | - | 3.2.1.23 |
122597 | alcohol dehydrogenase | - | 1.1.1.1 |
122597 | gelatinase | - | |
122597 | amylase | - | |
122597 | DNase | - | |
122597 | caseinase | - | 3.4.21.50 |
122597 | catalase | + | 1.11.1.6 |
122597 | tween esterase | - | |
122597 | lecithinase | - | |
122597 | lysine decarboxylase | - | 4.1.1.18 |
122597 | ornithine decarboxylase | - | 4.1.1.17 |
122597 | 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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
122597 | - | - | + | + | - | - | - | - | - | - | + | + | - | - | - | - | - | - | - | - |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
122597 | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
1750 | large intestine of Magadan (Susuman) mammoth found in permafrost | Sibiria | Russia | RUS | Asia |
122597 | Animal, Mammoth found in permafrost, large intestine | Siberia | Russian Federation | RUS | Europe |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Environmental | #Terrestrial | #Permafrost |
#Host | #Mammals | |
#Host Body-Site | #Gastrointestinal tract | #Large intestine |
taxonmaps
- @ref: 69479
- File name: preview.99_34149.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_3;96_393;97_20198;98_25244;99_34149&stattab=map
- Last taxonomy: Kurthia sibirica subclade
- 16S sequence: JN600481
- Sequence Identity:
- Total samples: 179
- soil counts: 7
- aquatic counts: 16
- animal counts: 150
- plant counts: 6
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
1750 | 1 | Risk group (German classification) |
122597 | 1 | Risk group (French classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Kurthia sibirica 16S rRNA gene, type strain DSM 4747T | AJ605774 | 1536 | ena | 202750 |
20218 | Kurthia sibirica DSM:4747 16S ribosomal RNA gene, partial sequence | JN600481 | 1474 | ena | 202750 |
20218 | Kurthia sibirica gene for 16S rRNA, partial sequence | AB271741 | 1477 | ena | 202750 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Kurthia sibirica NBRC 101530 | GCA_007989725 | contig | ncbi | 202750 |
66792 | Kurthia sibirica strain ATCC 49154 | 202750.4 | wgs | patric | 202750 |
66792 | Kurthia sibirica strain NBRC 101530 | 202750.5 | wgs | patric | 202750 |
66792 | Kurthia sibirica ATCC 49154 | 2891118952 | draft | img | 202750 |
67770 | Kurthia sibirica ATCC 49154 | GCA_003143975 | contig | ncbi | 202750 |
GC content
- @ref: 1750
- GC-content: 36.9
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | yes | 69 | no |
motile | yes | 85.556 | no |
gram-positive | yes | 91.91 | no |
anaerobic | no | 98.95 | no |
aerobic | yes | 93.126 | no |
halophile | no | 75.362 | no |
spore-forming | yes | 88.896 | no |
glucose-util | yes | 82.711 | no |
flagellated | yes | 75.695 | no |
thermophile | no | 93.173 | yes |
glucose-ferment | no | 84.831 | no |
External links
@ref: 1750
culture collection no.: DSM 4747, ATCC 49154, CCM 3477, VKM V-1549, JCM 8563, BCRC 17017, CIP 103418, LMG 17317, NBRC 101530, NCIMB 13254, NRRL B-41083, VKM B-1549
straininfo link
- @ref: 81165
- straininfo: 9243
literature
topic | Pubmed-ID | title | authors | journal | year | mesh | topic2 | DOI |
---|---|---|---|---|---|---|---|---|
Phylogeny | 3102908 | [New species of bacteria in the genus Kurthia--Kurthia sibirica sp. nov]. | Belikova VA, Cherevach NV, Kalakutskii LV | Mikrobiologiia | 1986 | Actinomycetales/*classification/isolation & purification/physiology, Animals, Elephants, Fossils, Phenotype, Siberia | Phenotype | |
Phylogeny | 24108326 | Kurthia huakuii sp. nov., isolated from biogas slurry, and emended description of the genus Kurthia. | Ruan Z, Wang Y, Song J, Jiang S, Wang H, Li Y, Zhao B, Jiang R, Zhao B | Int J Syst Evol Microbiol | 2013 | Bacterial Typing Techniques, Base Composition, Biofuels/*microbiology, Bioreactors/microbiology, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Glycolipids/chemistry, Molecular Sequence Data, *Phylogeny, Planococcaceae/*classification/genetics/isolation & purification, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry | Genetics | 10.1099/ijs.0.056044-0 |
Phylogeny | 29299848 | Kurthia ruminicola sp. nov., isolated from the rumen contents of a Holstein cow. | Kim MK, Kim ET, Kim SB, Jeong HY, Park BY, Srinivasan S | J Microbiol | 2018 | Animals, Bacterial Typing Techniques, Base Composition, Cattle/*microbiology, DNA, Bacterial/genetics, Fatty Acids/chemistry/metabolism, Phospholipids/metabolism, Phylogeny, Planococcaceae/classification/genetics/*isolation & purification/metabolism, RNA, Ribosomal, 16S/genetics, Rumen/*microbiology | Metabolism | 10.1007/s12275-018-7285-2 |
Genetics | 30533891 | Draft Genome Sequence of the Psychrotolerant Bacterium Kurthia sibirica ATCC 49154(T). | Goen AE, Silverwood T, Underriner A, Trachtenberg AM, Kelley C, MacLea KS | Microbiol Resour Announc | 2018 | 10.1128/MRA.00841-18 |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
1750 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 4747) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-4747 | |||
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 | |
35535 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/15214 | ||||
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 | |
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) | |||
81165 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID9243.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
122597 | Curators of the CIP | Collection of Institut Pasteur (CIP 103418) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103418 |