Strain identifier

BacDive ID: 3921

Type strain: Yes

Species: Demetria terragena

Strain Designation: 2002-46

Strain history: CIP <- 1998, I. Groth, Hans Knöll Inst., Jena, Germany: strain HKI 0089

NCBI tax ID(s): 1121385 (strain), 63959 (species)

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General

@ref: 4285

BacDive-ID: 3921

DSM-Number: 11295

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

description: Demetria terragena 2002-46 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from compost soil.

NCBI tax id

NCBI tax idMatching level
1121385strain
63959species

strain history

@refhistory
4285<- I. Groth, 2002-46 (= HKI 0089)
67770CIP 105501 <-- I. Groth HKI 0089 (=strain 2002-46).
123466CIP <- 1998, I. Groth, Hans Knöll Inst., Jena, Germany: strain HKI 0089

doi: 10.13145/bacdive3921.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Dermacoccaceae
  • genus: Demetria
  • species: Demetria terragena
  • full scientific name: Demetria terragena Groth et al. 1997

@ref: 4285

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Dermacoccaceae

genus: Demetria

species: Demetria terragena

full scientific name: Demetria terragena Groth et al. 1997 emend. Nouioui et al. 2018

strain designation: 2002-46

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480positive100
123466positiverod-shapedno

colony morphology

@refcolony colorincubation periodmedium used
18435Light ivory (1015)10-14 daysISP 2
18435Light ivory (1015)10-14 daysISP 3
18435Light ivory (1015)10-14 daysISP 4
18435Light ivory (1015)10-14 daysISP 5
18435Light ivory (1015)10-14 daysISP 6
18435Light ivory (1015)10-14 daysISP 7
123466

multicellular morphology

@refforms multicellular complexmedium name
18435noISP 2
18435noISP 3
18435noISP 4
18435noISP 5
18435noISP 6
18435noISP 7

multimedia

@refmultimedia contentcaptionintellectual property rights
66793EM_DSM_11295_1.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_11295_2.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_11295_3.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_11295_4.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_11295_5.jpgelectron microscopic image© HZI/Manfred Rohde

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
4285RICH 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
18435ISP 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
18435ISP 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:
18435ISP 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
18435ISP 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
18435ISP 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
18435ISP 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
35827MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
123466CIP Medium 234yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=234
123466CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3
123466CIP Medium 167yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=167

culture temp

@refgrowthtypetemperaturerange
4285positivegrowth28mesophilic
35827positivegrowth30mesophilic
54686positivegrowth30mesophilic
67770positivegrowth28mesophilic
123466positivegrowth25-30mesophilic
123466nogrowth10psychrophilic
123466nogrowth41thermophilic
123466nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
54686aerobe
123466obligate aerobe

spore formation

@refspore formationconfidence
69481no91
69480no99.997

compound production

@refcompound
20216Prolylglycin
20216Prolylvalin

halophily

@refsaltgrowthtested relationconcentration
18435NaClpositivemaximum5 %
123466NaClpositivegrowth2 %
123466NaClnogrowth0 %
123466NaClnogrowth4 %
123466NaClnogrowth6 %
123466NaClnogrowth8 %
123466NaClnogrowth10 %

murein

  • @ref: 4285
  • murein short key: A11.36
  • type: A4alpha L-Lys-L-Ser-D-Asp

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1843562968cellulose+
1843516634raffinose-
1843526546rhamnose+
1843528757fructose+
1843529864mannitol+
1843517268myo-inositol+
1843518222xylose-
1843517992sucrose+
1843522599arabinose-
1843517234glucose+
683685291gelatin+hydrolysis
6836827897tryptophan-energy source
6836816199urea-hydrolysis
6836816947citrate-assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine-hydrolysis
12346616947citrate-carbon source
1234664853esculin-hydrolysis
123466606565hippurate+hydrolysis
12346617632nitrate-reduction
12346616301nitrite-reduction
6837917632nitrate-reduction
683794853esculin-hydrolysis
6837916199urea-hydrolysis
683795291gelatin+hydrolysis
6837917634D-glucose-fermentation
6837916988D-ribose-fermentation
6837965327D-xylose-fermentation
6837916899D-mannitol-fermentation
6837917306maltose-fermentation
6837917716lactose-fermentation
6837917992sucrose-fermentation
6837928087glycogen-fermentation

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinyes
6836835581indoleno
6836816136hydrogen sulfideno
12346635581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole testmethylred-test
6836815688acetoin+
6836835581indole-
12346615688acetoin-
12346617234glucose-

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
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
68382acid phosphatase+3.1.3.2
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)+
68382esterase lipase (C 8)+
68382alkaline phosphatase+3.1.3.1
68379gelatinase+
68379urease-3.5.1.5
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
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
123466oxidase-
123466alcohol dehydrogenase-1.1.1.1
123466gelatinase+/-
123466amylase-
123466DNase-
123466caseinase+3.4.21.50
123466catalase+1.11.1.6
123466tween esterase+
123466gamma-glutamyltransferase+2.3.2.2
123466lecithinase-
123466lipase-
123466lysine decarboxylase-4.1.1.18
123466ornithine decarboxylase-4.1.1.17
123466phenylalanine ammonia-lyase-4.3.1.24
123466tryptophan deaminase-
123466urease-3.5.1.5

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
18435-+++--+---+--------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
18435+-++++++++----+--+-
123466+++++----++---+-----

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
18435---------++

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
123466+++++-+++++++-++-++++++-+++-+++++++++---+------+++++-++-+-+++---+--------+-+--+++-+---+-+++++++----

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
4285compost soilJenaGermanyDEUEurope
54686Compost soilGermanyDEUEurope
67770Compost soilnear JenaGermanyDEUEurope
123466Environment, Compost soilJenaGermanyDEUEurope1992

isolation source categories

Cat1Cat2Cat3
#Engineered#Biodegradation#Composting
#Environmental#Terrestrial#Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_1475.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_844;97_986;98_1164;99_1475&stattab=map
  • Last taxonomy: Demetria terragena subclade
  • 16S sequence: Y14152
  • Sequence Identity:
  • Total samples: 624
  • soil counts: 161
  • aquatic counts: 170
  • animal counts: 259
  • plant counts: 34

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
184351German classification
42851Risk group (German classification)
1234661Risk group (French classification)

Sequence information

16S sequences

  • @ref: 4285
  • description: Demetria terragena 16S rRNA gene, partial
  • accession: Y14152
  • length: 1457
  • database: ena
  • NCBI tax ID: 63959

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Demetria terragena DSM 112951121385.3wgspatric1121385
66792Demetria terragena DSM 112952521172561draftimg1121385
67770Demetria terragena DSM 11295GCA_000376825contigncbi1121385

GC content

@refGC-contentmethod
428566high performance liquid chromatography (HPLC)
6777064.7genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno91no
motileno92.089no
flagellatedno97.348no
gram-positiveyes93.707no
anaerobicno98.948no
aerobicyes93.558no
halophileno82.539no
spore-formingno90.64no
glucose-utilyes89.763no
thermophileno98.059yes
glucose-fermentno90.18yes

External links

@ref: 4285

culture collection no.: CCUG 39179, CCM 4700, CIP 105501, JCM 11480, DSM 11295, IFO 16164, NBRC 16164, HKI 0089, NCIMB 13517

straininfo link

  • @ref: 73430
  • straininfo: 49068

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny9336919Demetria terragena gen. nov., sp. nov., a new genus of actinomycetes isolated from compost soil.Groth I, Schumann P, Rainey FA, Martin K, Schuetze B, Augsten KInt J Syst Bacteriol10.1099/00207713-47-4-11291997Actinomycetaceae/chemistry/*classification/genetics/metabolism/ultrastructure, Base Composition, Cell Wall/chemistry, DNA, Bacterial/analysis, Fatty Acids/analysis, Microscopy, Electron, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/analysis, Terminology as TopicGenetics
Phylogeny21075908Calidifontibacter indicus gen. nov., sp. nov., a member of the family Dermacoccaceae isolated from a hot spring, and emended description of the family Dermacoccaceae.Ruckmani A, Kaur I, Schumann P, Klenk HP, Mayilraj SInt J Syst Evol Microbiol10.1099/ijs.0.025593-02010Actinomycetales/*classification/genetics/*isolation & purification/physiology, Amino Acids/analysis, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Hot Springs/*microbiology, India, Molecular Sequence Data, Phospholipids/analysis, Phylogeny, Pigments, Biological/metabolism, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analysisGenetics
Phylogeny28920829Allobranchiibius huperziae gen. nov., sp. nov., a member of Dermacoccaceae isolated from the root of a medicinal plant Huperzia serrata (Thunb.).Ai MJ, Sun Y, Sun HM, Liu HY, Yu LY, Zhang YQInt J Syst Evol Microbiol10.1099/ijsem.0.0022842017Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Glycolipids/chemistry, Huperzia/*microbiology, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, Plant Roots/*microbiology, Plants, Medicinal/microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNATranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
4285Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 11295)https://www.dsmz.de/collection/catalogue/details/culture/DSM-11295
18435Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM11295.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
20216Curators of the HKIhttp://www.leibniz-hki.de/de/Collection Description Leibniz-Institut für Naturstoff-Forschung und Infektionsbiologie e. V. Hans-Knöll-Institut (HKI)
35827Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/17527
54686Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 39179)https://www.ccug.se/strain?id=39179
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
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68368Automatically annotated from API 20E
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)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
73430Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID49068.1StrainInfo: A central database for resolving microbial strain identifiers
123466Curators of the CIPCollection of Institut Pasteur (CIP 105501)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105501