Strain identifier

BacDive ID: 6270

Type strain: Yes

Species: Knoellia subterranea

Strain Designation: 2163-021

Strain history: CIP <- 2000, I. Groth, Hans Knöll Institut, Jena, Germany: strain HKI 0120

NCBI tax ID(s): 1385521 (strain), 184882 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 4697

BacDive-ID: 6270

DSM-Number: 12332

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-positive

description: Knoellia subterranea 2163-021 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from cave, soil between rocks.

NCBI tax id

NCBI tax idMatching level
184882species
1385521strain

strain history

@refhistory
4697<- I. Groth; HKI 0120 <- Ch. Weigel; 2163-021
67770I. Groth HKI 0120 <-- Ch. Weigel 2163-021.
67771<- DSM <- I. Groth; HKI 0120 <- Ch. Weigel; 2163-021
123351CIP <- 2000, I. Groth, Hans Knöll Institut, Jena, Germany: strain HKI 0120

doi: 10.13145/bacdive6270.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Intrasporangiaceae
  • genus: Knoellia
  • species: Knoellia subterranea
  • full scientific name: Knoellia subterranea Groth et al. 2002

@ref: 4697

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Intrasporangiaceae

genus: Knoellia

species: Knoellia subterranea

full scientific name: Knoellia subterranea Groth et al. 2002

strain designation: 2163-021

type strain: yes

Morphology

cell morphology

@refgram stainmotilityconfidencecell shape
67771positive
69480no95.503
69480positive100
123351positivenorod-shaped

colony morphology

@refcolony colorincubation periodmedium used
18363Light ivory (1015)10-14 daysISP 2
18363Light ivory (1015)10-14 daysISP 3
18363Light ivory (1015)10-14 daysISP 4
18363Light ivory (1015)10-14 daysISP 5
18363Light ivory (1015)10-14 daysISP 6
18363Light ivory (1015)10-14 daysISP 7
580222 days
123351

multicellular morphology

@refforms multicellular complexmedium name
18363noISP 2
18363noISP 3
18363noISP 4
18363noISP 5
18363noISP 6
18363noISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
4697RICH MEDIUM (DSMZ Medium 736)yeshttps://mediadive.dsmz.de/medium/736Name: RICH MEDIUM (DSMZ Medium 736) Composition: Agar 20.0 g/l Bacto peptone 10.0 g/l Yeast extract 5.0 g/l Malt extract 5.0 g/l Casamino acids 5.0 g/l Glycerol 2.0 g/l Meat extract 2.0 g/l MgSO4 x 7 H2O 1.0 g/l Tween 80 0.05 g/l Distilled water
18363ISP 2yesName: ISP 2 / Yeast Malt Agar (5265); 5265 Composition Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l Agar 15.0 g/l Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.0 Usage: Maintenance and Taxonomy Organisms: All Actinomycetes
18363ISP 3yesName: ISP 3; 5315 Composition Dog oat flakes 20.0 g/l Trace element solution (5314) 2.5 ml/l Agar 18.0 g/l Preparation: Oat flakes are cooked for 20 minutes, trace element solution and agar are added (in the case of non rolled oat flakes the suspension has to bee filtrated). Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.8 Usage: Maintenance and taxonomy (e.g. SEM As liquid medium for metabolite production) Organisms: All Actinomycetes Trace element solution 5314 Name: Trace element solution 5314; 5314 Composition CaCl2 x H2O 3.0 g/l Fe-III-citrate 1.0 g/l MnSO4 0.2 g/l ZnCl2 0.1 g/l CuSO4 x 5 H2O 0.025 g/l Sodium tetra borate 0.2 g/l CoCl2 x 6 H2O 0.004 g/l Sodium molybdate 0.01 g/l Preparation: Use double destillated water. Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Trace element solution for different media Organisms:
18363ISP 4yesName: ISP 4; DSM 547 Solution I: Difco soluble starch, 10.0 g. Make a paste of the starch with a small amount of cold distilled water and bring to a volume of 500 ml. Solution II: CaCO3 2.0 g K2HPO4 (anhydrous) 1.0 g MgSO4 x 7 H2O 1.0 g NaCl 1.0 g (NH4)2SO4 2.0 g Distilled water 500.0 ml Trace salt solution (see below) 1.0 ml The pH should be between 7.0 and 7.4. Do not adjust if it is within this range. Mix solutions I and II together. Add 20.0 g agar. Liquify agar by steaming at 100°C for 10 to 20 min. Trace element solution: FeSO4 x 7 H2O 0.1 g MnCl2 x 4 H2O 0.1 g ZnSO4 x 7 H2O 0.1 g Distilled water 100.0 ml
18363ISP 5yesName: ISP 5 (5323) Composition L-Asparagine 1.0 g/l Glycerol 10.0 g/l K2HPO4 1.0 g/l Salt solution (see preparation) 1.0 ml/l Agar 20.0 g/l Preparation: Salt solution 1.0 g FeSO4 x 7 H2O 1.0 g MnCl2 x 4 H2O 1.0 g ZNSO4 x 7 H2O in 100 ml water Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.2 Usage: Maintenance and taxonomy Organisms: All Actinomycetes
18363ISP 6yesName: ISP 6 (5318) Composition Peptone 15.0 g/l Proteose peptose 5.0 g/l Ferric ammonium citrate 0.5 g/l Sodium glycerophosphate 1.0 g/l Sodium thiosulfate 0.08 g/l Yeast extract 1.0 g/l Agar 15.0 g/l Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigments Organisms: All Actinomycetes
18363ISP 7yesName: ISP 7 (5322) Composition Glycerol 15.0 g/l L-Tyrosine 0.5 g/l L-Asparagine 1.0 g/l K2HPO4 0.5 g/l NaCl 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Trace element solution 5343 1.0 ml/l Agar 20.0 Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.3 Usage: Production of melanoid pigments Organisms: All Actinomycetes
34059MEDIUM 29- Brain heart agaryesDistilled water make up to (1000.000 ml);Brain heart infusion agar (52.000 g)
123351CIP Medium 29yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=29

culture temp

@refgrowthtypetemperaturerange
18363positiveoptimum28mesophilic
4697positivegrowth28mesophilic
34059positivegrowth30mesophilic
58022positivegrowth30-37mesophilic
67770positivegrowth28mesophilic
67771positivegrowth28mesophilic
123351positivegrowth25-37mesophilic
123351nogrowth10psychrophilic
123351nogrowth41thermophilic
123351nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
58022aerobe
67771aerobe
123351obligate aerobe

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 99.982

halophily

@refsaltgrowthtested relationconcentration
123351NaClpositivegrowth2-4 %
123351NaClnogrowth0 %
123351NaClnogrowth8 %
123351NaClnogrowth10 %

murein

  • @ref: 4697
  • murein short key: A31
  • type: A1gamma m-Dpm-direct

observation

  • @ref: 67770
  • observation: quinones: MK-8(H4)

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
68371gluconate-builds acid from24265
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose-builds acid from18287
68371D-fucose-builds acid from28847
68371D-tagatose-builds acid from16443
68371xylitol-builds acid from17151
68371raffinose-builds acid from16634
68371inulin-builds acid from15443
68371melibiose-builds acid from28053
68371arbutin-builds acid from18305
68371N-acetylglucosamine-builds acid from59640
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371D-mannitol-builds acid from16899
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose-builds acid from65327
68371L-arabinose-builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754
123351citrate-carbon source16947
123351esculin+hydrolysis4853
123351hippurate-hydrolysis606565
123351nitrate+reduction17632
123351nitrite-reduction16301
123351nitrate-respiration17632
68379nitrate-reduction17632
68379esculin+hydrolysis4853
68379gelatin+hydrolysis5291
68379D-glucose-fermentation17634
68379D-ribose-fermentation16988
68379D-xylose-fermentation65327
68379D-mannitol-fermentation16899
68379maltose-fermentation17306
68379lactose-fermentation17716
68379sucrose+fermentation17992
68379glycogen-fermentation28087

metabolite production

  • @ref: 123351
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12335115688acetoin-
12335117234glucose-

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382beta-glucosidase+3.2.1.21
68382alpha-glucosidase+3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382alpha-galactosidase-3.2.1.22
68382alpha-chymotrypsin-3.4.21.1
68382trypsin+3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase+
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68379gelatinase+
68379beta-glucosidase+3.2.1.21
68379N-acetyl-beta-glucosaminidase+3.2.1.52
68379alpha-glucosidase+3.2.1.20
68379beta-galactosidase+3.2.1.23
68379beta-glucuronidase-3.2.1.31
68379alkaline phosphatase+3.1.3.1
68379pyrrolidonyl arylamidase-3.4.19.3
68379pyrazinamidase-3.5.1.B15
123351oxidase-
123351beta-galactosidase+3.2.1.23
123351alcohol dehydrogenase-1.1.1.1
123351gelatinase+
123351amylase+
123351DNase+
123351caseinase+3.4.21.50
123351catalase+1.11.1.6
123351tween esterase-
123351gamma-glutamyltransferase-2.3.2.2
123351lysine decarboxylase-4.1.1.18
123351ornithine decarboxylase-4.1.1.17
123351tryptophan deaminase-
123351urease-3.5.1.5

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
18363---+-+++++/-+------+-

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
18363+-+-++-+-+--+-++++-
123351-++-++-+--+---++----

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
123351----+/-----+/-+/-+/-+/----------+/--+/-+/-+/-+/-+/--+/-+/--+/--+/-+/--+/-+/-+/---------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling dateisolation date
4697cave, soil between rocksChina, guilin, "Cave of the reed flutes"ChinaCHNAsia
58022Cave,soil between rocksChinaCHNAsia1997
67771From cave, soil between rocksChinaCHNAsia
67770Soil, the Reed Flute Cave near GuilinGuangxiChinaCHNAsia
123351Environment, Cave, soil between rocksChinaCHNAsia1997

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Geologic
#Environmental#Terrestrial#Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_6222.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_1391;97_1657;98_2108;99_6222&stattab=map
  • Last taxonomy: Knoellia subterranea
  • 16S sequence: AJ294413
  • Sequence Identity:
  • Total samples: 416
  • soil counts: 24
  • aquatic counts: 15
  • animal counts: 372
  • plant counts: 5

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
183631
46971Risk group (German classification)
1233511Risk group (French classification)

Sequence information

16S sequences

  • @ref: 4697
  • description: Knoellia subterranea partial 16S rRNA gene, type strain HKI 0120
  • accession: AJ294413
  • length: 1479
  • database: ena
  • NCBI tax ID: 184882

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Knoellia subterranea KCTC 199371385521.3wgspatric1385521
66792Knoellia subterranea KCTC 199372634166482draftimg1385521
67770Knoellia subterranea KCTC 19937GCA_000768685contigncbi1385521

GC content

  • @ref: 4697
  • GC-content: 69
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes55no
motileno96.234no
gram-positiveyes92.381yes
anaerobicno97.68no
halophileno97.428no
spore-formingno89.454no
glucose-utilyes87.908no
thermophileno94.24yes
aerobicyes88.865no
flagellatedno98.208no
glucose-fermentno89.798no

External links

@ref: 4697

culture collection no.: CCUG 48178, HKI 0120, DSM 12332, CIP 106776, KCTC 19937, JCM 11537, IAM 15305, NBRC 100351

straininfo link

  • @ref: 75747
  • straininfo: 87906

literature

  • topic: Phylogeny
  • Pubmed-ID: 11837319
  • title: Knoellia sinensis gen. nov., sp. nov. and Knoellia subterranea sp. nov., two novel actinobacteria isolated from a cave.
  • authors: Groth I, Schumann P, Schutze B, Augsten K, Stackebrandt E
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/00207713-52-1-77
  • year: 2002
  • mesh: Actinobacteria/chemistry/*classification/genetics/physiology, DNA, Ribosomal/analysis, Diaminopimelic Acid/metabolism, Fatty Acids/analysis, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
4697Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 12332)https://www.dsmz.de/collection/catalogue/details/culture/DSM-12332
18363Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM12332.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
34059Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/18943
58022Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 48178)https://www.ccug.se/strain?id=48178
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
68371Automatically annotated from API 50CH acid
68379Automatically annotated from API Coryne
68382Automatically annotated from API zym
69479João 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
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
75747Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID87906.1StrainInfo: A central database for resolving microbial strain identifiers
123351Curators of the CIPCollection of Institut Pasteur (CIP 106776)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106776