Strain identifier

BacDive ID: 1678

Type strain: Yes

Species: Beutenbergia cavernae

Strain Designation: 2163-026

Strain history: CIP <- 1999, I. Groth, Hans Knöll Inst., Jena, Germany: strain HKI 0122

NCBI tax ID(s): 471853 (strain), 84757 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 4698

BacDive-ID: 1678

DSM-Number: 12333

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic

description: Beutenbergia cavernae 2163-026 is an aerobe, mesophilic bacterium that was isolated from cave, soil between rocks.

NCBI tax id

NCBI tax idMatching level
471853strain
84757species

strain history

@refhistory
4698<- I. Groth <- Ch. Weigel; 2163-026 (= HKI 0122)
67770CIP 106362 <-- I. Groth HKI 0122 (=strain 2163-026).
117221CIP <- 1999, I. Groth, Hans Knöll Inst., Jena, Germany: strain HKI 0122

doi: 10.13145/bacdive1678.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Beutenbergiaceae
  • genus: Beutenbergia
  • species: Beutenbergia cavernae
  • full scientific name: Beutenbergia cavernae Groth et al. 1999

@ref: 4698

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Beutenbergiaceae

genus: Beutenbergia

species: Beutenbergia cavernae

full scientific name: Beutenbergia cavernae Groth et al. 1999 emend. Nouioui et al. 2018

strain designation: 2163-026

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no91.8
69480100positive
117221nopositiverod-shaped

colony morphology

@refcolony colorincubation periodmedium used
19736Zinc yellow (1018)10-14 days5006
1973610-14 daysISP 2
1973610-14 daysISP 3
1973610-14 daysISP 4
117221

multicellular morphology

@refforms multicellular complexmedium name
19736no5006
19736noISP 2
19736noISP 3
19736noISP 4

multimedia

  • @ref: 66793
  • multimedia content: EM_DSM_12333_1.jpg
  • caption: electron microscopic image
  • intellectual property rights: © HZI/Manfred Rohde

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
4698RICH 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
197365006yesMedium: 5006 Name: Composition (g/l) Sucrose 3,0 Dextrin 15,0 Meat extract 1,0 Yeast extract 2,0 Tryptone soy broth (Oxoid) 5,0 NaCl 0,5 K2HPO4 0,5 MgSO4 x 7 H2O 0,5 FeSO4 x 7 H2O 0,01 Agar 20,0 Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7,3 Usage: Maintenance Organisms: All Actinomycetes
19736ISP 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
19736ISP 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:
19736ISP 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
32959MEDIUM 29- Brain heart agaryesDistilled water make up to (1000.000 ml);Brain heart infusion agar (52.000 g)
117221CIP Medium 29yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=29

culture temp

@refgrowthtypetemperaturerange
19736positiveoptimum28mesophilic
4698positivegrowth28mesophilic
32959positivegrowth30mesophilic
55688positivegrowth30mesophilic
67770positivegrowth28mesophilic
117221positivegrowth15-37
117221nogrowth10psychrophilic
117221nogrowth41thermophilic
117221nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
55688aerobe
117221obligate aerobe

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 99.882

halophily

@refsaltgrowthtested relationconcentration
19736NaClpositivemaximum5 %
117221NaClpositivegrowth2-4 %
117221NaClnogrowth6 %
117221NaClnogrowth8 %
117221NaClnogrowth10 %

murein

  • @ref: 4698
  • murein short key: A11.54
  • type: A4alpha L-Lys-L-Glu

observation

  • @ref: 67770
  • observation: quinones: MK-8(H4), MK-8(2)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1973662968cellulose+
1973616634raffinose+
1973626546rhamnose+
1973628757fructose+
1973629864mannitol+
1973617268myo-inositol+
1973618222xylose+
1973617992sucrose+
1973622599arabinose+
1973617234glucose+
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate-builds acid from
6837118403L-arabitol+builds acid from
6837118333D-arabitol+builds acid from
6837118287L-fucose+builds acid from
6837128847D-fucose+builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose+builds acid from
6837132528turanose+builds acid from
6837128066gentiobiose+builds acid from
6837117151xylitol+builds acid from
6837128087glycogen-builds acid from
6837128017starch-builds acid from
6837116634raffinose+builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837127082trehalose+builds acid from
6837117992sucrose+builds acid from
6837128053melibiose+builds acid from
6837117716lactose+builds acid from
6837117306maltose+builds acid from
6837117057cellobiose+builds acid from
6837117814salicin+builds acid from
683714853esculin+builds acid from
6837118305arbutin-builds acid from
6837127613amygdalin-builds acid from
6837159640N-acetylglucosamine-builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837143943methyl alpha-D-mannoside+builds acid from
6837117924D-sorbitol-builds acid from
6837116899D-mannitol-builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose+builds acid from
6837117266L-sorbose-builds acid from
6837116024D-mannose+builds acid from
6837115824D-fructose+builds acid from
6837117634D-glucose+builds acid from
6837112936D-galactose+builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol+builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose+builds acid from
6837116988D-ribose+builds acid from
6837130849L-arabinose+builds acid from
6837117108D-arabinose+builds acid from
6837117113erythritol-builds acid from
6837117754glycerol+builds acid from
683685291gelatin-hydrolysis
6836827897tryptophan-energy source
6836816199urea+hydrolysis
6836816947citrate-assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine-hydrolysis
11722116947citrate-carbon source
1172214853esculin+hydrolysis
117221606565hippurate-hydrolysis
11722117632nitrate+reduction
11722116301nitrite-reduction
6837917632nitrate-reduction
6837916199urea+hydrolysis
683795291gelatin-hydrolysis
6837917634D-glucose-fermentation
6837916988D-ribose-fermentation
6837965327D-xylose-fermentation
6837916899D-mannitol-fermentation
6837917306maltose+fermentation
6837917716lactose-fermentation
6837917992sucrose+fermentation
6837928087glycogen-fermentation

antibiotic resistance

  • @ref: 117221
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinyes
6836835581indoleno
6836816136hydrogen sulfideno
11722135581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole testmethylred-test
6836815688acetoin+
6836835581indole-
11722115688acetoin-
11722117234glucose-

enzymes

@refvalueactivityec
68382alpha-mannosidase+3.2.1.24
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382beta-glucosidase-3.2.1.21
68382alpha-glucosidase+3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase+3.2.1.23
68382alpha-galactosidase+3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
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)-
68382alkaline phosphatase+3.1.3.1
68379gelatinase-
68379urease+3.5.1.5
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
68368gelatinase-
68368tryptophan deaminase-4.1.99.1
68368urease+3.5.1.5
68368ornithine decarboxylase-4.1.1.17
68368lysine decarboxylase-4.1.1.18
68368arginine dihydrolase-3.5.3.6
68368beta-galactosidase-3.2.1.23
117221oxidase-
117221beta-galactosidase-3.2.1.23
117221alcohol dehydrogenase-1.1.1.1
117221gelatinase+/-
117221amylase-
117221DNase-
117221caseinase+3.4.21.50
117221catalase+1.11.1.6
117221tween esterase-
117221gamma-glutamyltransferase-2.3.2.2
117221lecithinase-
117221lipase-
117221lysine decarboxylase-4.1.1.18
117221ornithine decarboxylase-4.1.1.17
117221phenylalanine ammonia-lyase-4.3.1.24
117221protease-
117221tryptophan deaminase-
117221urease-3.5.1.5

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
19736---+-++-+/-+-----+-+-

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
19736+---+----++++-+-++-
117221+++-+----++++-+-+++-

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
19736------+--+-

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
117221+-++++-+-++++-+----+----++++++++--+--++++-++++---

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
4698cave, soil between rocksChina, Guilin, "cave of the reed flutes"ChinaCHNAsia
55688Cave,soil between rocksChinaCHNAsia
67770Soil between rocks, Reed Flute Cavenear Guilin GuangxiChinaCHNAsia
117221Environment, Soil, cellarGuilinChinaCHNAsia1997

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_2096.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_1152;97_1352;98_1639;99_2096&stattab=map
  • Last taxonomy: Beutenbergia cavernae subclade
  • 16S sequence: Y18378
  • Sequence Identity:
  • Total samples: 866
  • soil counts: 443
  • aquatic counts: 228
  • animal counts: 157
  • plant counts: 38

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
46981Risk group (German classification)
197361Risk group (German classification)
1172211Risk group (French classification)

Sequence information

16S sequences

  • @ref: 4698
  • description: Beutenbergia cavernosa 16S rRNA gene
  • accession: Y18378
  • length: 1485
  • database: ena
  • NCBI tax ID: 471853

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Beutenbergia cavernae DSM 12333GCA_000023105completencbi471853
66792Beutenbergia cavernae DSM 12333471853.5completepatric471853
66792Beutenbergia cavernae HKI 0122, DSM 12333643692008completeimg471853

GC content

@refGC-contentmethod
469871.4high performance liquid chromatography (HPLC)
6777071high performance liquid chromatography (HPLC)
6777073.12genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno76no
motileno90.99no
flagellatedno98.579no
gram-positiveyes90.8no
anaerobicno99.063yes
aerobicyes92.109yes
halophileno92.533no
spore-formingno90.084no
thermophileno98.029no
glucose-utilyes87.239no
glucose-fermentno86.913yes

External links

@ref: 4698

culture collection no.: DSM 12333, ATCC BAA 8, IFO 16432, NBRC 16432, CCUG 43141, HKI 0122, JCM 11478, CIP 106362, NCIMB 13614

straininfo link

  • @ref: 71325
  • straininfo: 44250

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny10555355Beutenbergia cavernae gen. nov., sp. nov., an L-lysine-containing actinomycete isolated from a cave.Groth I, Schumann P, Schuetze B, Augsten K, Kramer I, Stackebrandt EInt J Syst Bacteriol10.1099/00207713-49-4-17331999Actinomycetales/*chemistry/*classification/isolation & purification/physiology, Bacterial Typing Techniques, Cell Wall/chemistry, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Ecosystem, Lipids/analysis, Lysine/*analysis, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil MicrobiologyGenetics
Genetics21304633Complete genome sequence of Beutenbergia cavernae type strain (HKI 0122).Land M, Pukall R, Abt B, Goker M, Rohde M, Glavina Del Rio T, Tice H, Copeland A, Cheng JF, Lucas S, Chen F, Nolan M, Bruce D, Goodwin L, Pitluck S, Ivanova N, Mavromatis K, Ovchinnikova G, Pati A, Chen A, Palaniappan K, Hauser L, Chang YJ, Jefferies CC, Saunders E, Brettin T, Detter JC, Han C, Chain P, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Lapidus AStand Genomic Sci10.4056/sigs.11622009

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
4698Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 12333)https://www.dsmz.de/collection/catalogue/details/culture/DSM-12333
19736Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM12333.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
32959Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/18484
55688Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 43141)https://www.ccug.se/strain?id=43141
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)
66793Mukherjee et al.10.1038/nbt.3886GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life 35: 676-683 201728604660
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/
68368Automatically annotated from API 20E
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)
71325Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID44250.1StrainInfo: A central database for resolving microbial strain identifiers
117221Curators of the CIPCollection of Institut Pasteur (CIP 106362)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106362