Strain identifier

BacDive ID: 12585

Type strain: Yes

Species: Isoptericola hypogeus

Strain Designation: CD12E2-119

Strain history: CIP <- 2005, DSMZ <- I. Groth: strain HKI 0342 <- C. Weigel: strain CD12E2-119

NCBI tax ID(s): 300179 (species)

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General

@ref: 6633

BacDive-ID: 12585

DSM-Number: 16849

keywords: 16S sequence, Bacteria, microaerophile, mesophilic, Gram-positive, rod-shaped

description: Isoptericola hypogeus CD12E2-119 is a microaerophile, mesophilic, Gram-positive bacterium that was isolated from Tufa, catacomb Domitilla.

NCBI tax id

  • NCBI tax id: 300179
  • Matching level: species

strain history

@refhistory
6633<- I. Groth <- C. Weigel, CD12E2-119
67770NCIMB 14033 <-- I. Groth CD12-119 (=HKI 0342).
120035CIP <- 2005, DSMZ <- I. Groth: strain HKI 0342 <- C. Weigel: strain CD12E2-119

doi: 10.13145/bacdive12585.20250331.9.3

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Promicromonosporaceae
  • genus: Isoptericola
  • species: Isoptericola hypogeus
  • full scientific name: Isoptericola hypogeus Groth et al. 2005

@ref: 6633

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Promicromonosporaceae

genus: Isoptericola

species: Isoptericola hypogeus

full scientific name: Isoptericola hypogeus Groth et al. 2005

strain designation: CD12E2-119

type strain: yes

Morphology

cell morphology

@refgram staincell widthcell shapemotility
31470positive0.9 µmrod-shapedno
120035positiverod-shapedno

colony morphology

@refcolony colorincubation periodmedium used
18297Colorless10-14 daysISP 2
18297Light cadmium yellow10-14 daysISP 3
18297Light cadmium yellow10-14 daysISP 4
18297Light cadmium yellow10-14 daysISP 5
18297Sulfur yellow (1016)10-14 daysISP 6
18297Light cadmium yellow10-14 daysISP 7
120035

multicellular morphology

@refforms multicellular complexmedium name
18297noISP 2
18297noISP 3
18297noISP 4
18297noISP 5
18297noISP 6
18297noISP 7

pigmentation

  • @ref: 31470
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6633R2A MEDIUM (DSMZ Medium 830)yeshttps://mediadive.dsmz.de/medium/830Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
18297ISP 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
18297ISP 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:
18297ISP 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
18297ISP 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
18297ISP 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
18297ISP 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
37329MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
6633TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://mediadive.dsmz.de/medium/535Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
120035CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperature
6633positivegrowth28
18297positiveoptimum28
31470positivegrowth10-40
31470positiveoptimum28
37329positivegrowth30
67770positivegrowth28
120035positivegrowth10-37
120035nogrowth41
120035nogrowth45

culture pH

@refabilitytypepHPH range
31470positivegrowth06-09alkaliphile
31470positiveoptimum7.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31470microaerophile
120035obligate aerobe

halophily

@refsaltgrowthtested relationconcentration
31470NaClpositivegrowth<10 %
31470NaClpositiveoptimum5 %
120035NaClpositivegrowth0-10 %

murein

  • @ref: 6633
  • murein short key: A11.33
  • type: A4alpha L-Lys-D-Glu

observation

@refobservation
31470aggregates in clumps
67770quinones: MK-9(H2), MK-9, MK-9(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1829762968cellulose-
1829716634raffinose-
1829726546rhamnose+
1829728757fructose+
1829729864mannitol+
1829717268myo-inositol+
1829718222xylose-
1829717992sucrose+
1829722599arabinose-
1829717234glucose-
31470370543-hydroxybutyrate+carbon source
3147025115malate+carbon source
6837917992sucrose-fermentation
683795291gelatin+hydrolysis
683794853esculin+hydrolysis
12003516947citrate-carbon source
1200354853esculin+hydrolysis
120035606565hippurate+hydrolysis
12003517632nitrate+reduction
12003516301nitrite-reduction
12003517632nitrate-respiration
6837916199urea+hydrolysis

metabolite production

  • @ref: 120035
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12003515688acetoin-
12003517234glucose+

enzymes

@refvalueactivityec
68382alpha-mannosidase+3.2.1.24
68382beta-glucosidase+3.2.1.21
68382alpha-glucosidase+3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase+3.2.1.23
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase-3.1.3.2
68382trypsin-3.4.21.4
68382cystine arylamidase-3.4.11.3
68382leucine arylamidase+3.4.11.1
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase+3.1.3.1
120035oxidase-
120035beta-galactosidase+3.2.1.23
120035alcohol dehydrogenase-1.1.1.1
120035gelatinase+/-
120035amylase+
120035DNase-
120035caseinase+3.4.21.50
120035catalase+1.11.1.6
120035tween esterase-
120035gamma-glutamyltransferase+2.3.2.2
120035lecithinase-
120035lipase-
120035lysine decarboxylase-4.1.1.18
120035ornithine decarboxylase-4.1.1.17
120035phenylalanine ammonia-lyase-4.3.1.24
120035protease+
120035tryptophan deaminase-
120035urease-3.5.1.5
68379beta-glucosidase+3.2.1.21
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382lipase (C 14)-
68379gelatinase+
68379urease+3.5.1.5
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

API coryne

@refPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELSAC
18297--+-++/-+/-+++-

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
18297+++-++--+-+++-++++-
120035+++-+-----+-+-+++++-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
6633Tufa, catacomb DomitillaRomItalyITAEurope
67770Tufa from a burial chamber in the catacomb of DomitillaRomeItalyITAEurope
120035Tufa, Roman catacombDomitilla, RomeItalyITAEurope

isolation source categories

Cat1Cat2Cat3
#Engineered#Built environment
#Environmental#Terrestrial#Geologic

taxonmaps

  • @ref: 69479
  • File name: preview.99_3403.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_1778;97_2128;98_2608;99_3403&stattab=map
  • Last taxonomy: Isoptericola
  • 16S sequence: AJ854061
  • Sequence Identity:
  • Total samples: 1061
  • soil counts: 472
  • aquatic counts: 100
  • animal counts: 365
  • plant counts: 124

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
182971Risk group (German classification)
66331Risk group (German classification)
1200351Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
6633Isoptericola hypogeus 16S rRNA gene, type strain HKI 0342TAJ8540611426nuccore300179
124043Isoptericola hypogeus gene for 16S rRNA, partial sequence, strain: NBRC 104396.AB4892231476nuccore300179

GC content

@refGC-contentmethod
663373.8
6777073.8high performance liquid chromatography (HPLC)

External links

@ref: 6633

culture collection no.: DSM 16849, CIP 108902, HKI 0342, NBRC 104396, NCIMB 14033, JCM 15589, JCM 14325

straininfo link

  • @ref: 81799
  • straininfo: 237171

literature

  • topic: Phylogeny
  • Pubmed-ID: 16014507
  • title: Isoptericola hypogeus sp. nov., isolated from the Roman catacomb of Domitilla.
  • authors: Groth I, Schumann P, Schutze B, Gonzalez JM, Laiz L, Saiz-Jimenez C, Stackebrandt E
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.63632-0
  • year: 2005
  • mesh: Actinomycetales/*classification/genetics/*isolation & purification/physiology, Bacterial Typing Techniques, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genes, rRNA, Geologic Sediments/*microbiology, Italy, Molecular Sequence Data, *Mortuary Practice, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species Specificity
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
6633Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16849)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16849
18297Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM16849.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
31470Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2777028776041
37329Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6584
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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
81799Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID237171.1StrainInfo: A central database for resolving microbial strain identifiers
120035Curators of the CIPCollection of Institut Pasteur (CIP 108902)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108902
124043Isabel Schober, Julia KoblitzData extracted from sequence databases, automatically matched based on designation and taxonomy