Strain identifier

BacDive ID: 11195

Type strain: Yes

Species: Nocardiopsis trehalosi

Strain history: CIP <- 2000, DSMZ <- VKM

NCBI tax ID(s): 1348638 (strain), 109329 (species)

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General

@ref: 11501

BacDive-ID: 11195

DSM-Number: 44380

keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, spore-forming, mesophilic, Gram-positive

description: Nocardiopsis trehalosi DSM 44380 is a facultative anaerobe, spore-forming, mesophilic bacterium that was isolated from soil.

NCBI tax id

NCBI tax idMatching level
1348638strain
109329species

strain history

@refhistory
11501<- L. Evtushenko, VKM
67770NRRL 12026 <-- Upjohn Co., USA.
123578CIP <- 2000, DSMZ <- VKM

doi: 10.13145/bacdive11195.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Streptosporangiales
  • family: Nocardiopsidaceae
  • genus: Nocardiopsis
  • species: Nocardiopsis trehalosi
  • full scientific name: Nocardiopsis trehalosi (ex Dolak et al. 1981) Evtushenko et al. 2000

@ref: 11501

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardiopsaceae

genus: Nocardiopsis

species: Nocardiopsis trehalosi

full scientific name: Nocardiopsis trehalosi (ex Dolak et al. 1981) Evtushenko et al. 2000 emend. Nouioui et al. 2018

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480positive100
123578positiverod-shapedno

colony morphology

@refcolony colorincubation periodmedium used
19656Beige10-14 daysISP 2
19656Beige10-14 daysISP 3
19656Beige10-14 daysISP 4
19656Beige10-14 daysISP 5
19656Beige10-14 daysISP 6
19656Beige10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
19656noISP 2
19656noISP 3
19656noISP 4
19656noISP 5
19656noISP 6
19656noISP 7

multimedia

  • @ref: 11501
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_44380.jpg
  • caption: Medium 65 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11501PEPTONE MEAT EXTRACT GLYCEROL AGAR (DSMZ Medium 250)yeshttps://mediadive.dsmz.de/medium/250Name: PEPTONE MEAT EXTRACT GLYCEROL AGAR (DSMZ Medium 250) Composition: Agar 20.0 g/l Proteose peptone no. 3 5.0 g/l Meat extract 3.0 g/l Glycerol Distilled water
11501GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)yeshttps://mediadive.dsmz.de/medium/65Name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) Composition: Agar 18.0 g/l Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l CaCO3 2.0 g/l Distilled water
19656ISP 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
19656ISP 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:
19656ISP 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
19656ISP 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
19656ISP 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
19656ISP 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
39517MEDIUM 57 - for Streptomyces, Nocardioides, Lentzea albidocapillata and Streptoverticillium reticulumyesDistilled water make up to (1000.000 ml);Agar (15.000 g);Glucose (4.000g);Yeast extract (4.000 g);Malt extract (10.000 g);Calcium carbonate (2.000 g)
11501BHI MEDIUM (DSMZ Medium 215)yeshttps://mediadive.dsmz.de/medium/215Name: BHI MEDIUM (DSMZ Medium 215) Composition: Brain heart infusion 37.0 g/l Distilled water
11501GPHF-MEDIUM (DSMZ Medium 553)yeshttps://mediadive.dsmz.de/medium/553Name: GPHF-MEDIUM (DSMZ Medium 553) Composition: Agar 20.0 g/l Glucose 10.0 g/l Beef extract 5.0 g/l Yeast extract 5.0 g/l Casein peptone 5.0 g/l CaCl2 x 2 H2O 0.74 g/l Distilled water
123578CIP Medium 57yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=57

culture temp

@refgrowthtypetemperaturerange
11501positivegrowth28mesophilic
39517positivegrowth30mesophilic
67770positivegrowth28mesophilic
123578positivegrowth25-41
123578nogrowth10psychrophilic
123578nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 123578
  • oxygen tolerance: facultative anaerobe

spore formation

@refspore formationconfidence
69481yes100
69480yes100

compound production

  • @ref: 11501
  • compound: 3 trehalosamine

halophily

@refsaltgrowthtested relationconcentration
123578NaClpositivegrowth0-4 %
123578NaClnogrowth6 %
123578NaClnogrowth8 %
123578NaClnogrowth10 %

observation

  • @ref: 67770
  • observation: quinones: MK-10(H4), MK-10(H6)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1965617234glucose+
1965622599arabinose+
1965617992sucrose+
1965618222xylose-
1965617268myo-inositol-
1965629864mannitol-
1965628757fructose-
1965626546rhamnose+
1965616634raffinose-
1965662968cellulose+
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
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
6837117754glycerol+builds acid from
683685291gelatin-hydrolysis
6836827897tryptophan-energy source
6836816199urea+hydrolysis
6836816947citrate+assimilation
6836818257ornithine+degradation
6836825094lysine+degradation
6836829016arginine+hydrolysis
12357816947citrate-carbon source
1235784853esculin+hydrolysis
123578606565hippurate-hydrolysis
12357817632nitrate+reduction
12357816301nitrite-reduction
12357817632nitrate+respiration

metabolite production

@refmetaboliteproductionChebi-ID
677703-trehalosamineyes
68368acetoinyes15688
68368indoleno35581
68368hydrogen sulfideno16136
123578indoleno35581

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole testmethylred-test
6836815688acetoin+
6836835581indole-
12357815688acetoin-
12357817234glucose-

enzymes

@refvalueactivityec
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
123578oxidase+
123578beta-galactosidase-3.2.1.23
123578alcohol dehydrogenase-1.1.1.1
123578gelatinase-
123578amylase+
123578DNase-
123578caseinase-3.4.21.50
123578catalase+1.11.1.6
123578tween esterase+
123578gamma-glutamyltransferase+2.3.2.2
123578lecithinase-
123578lipase-
123578lysine decarboxylase-4.1.1.18
123578ornithine decarboxylase-4.1.1.17
123578protease-
123578tryptophan deaminase-
123578urease+3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
68382cystine arylamidase+3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382naphthol-AS-BI-phosphohydrolase+
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase+3.2.1.20
68382beta-glucosidase+3.2.1.21
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382alpha-fucosidase-3.2.1.51

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
19656+-+-+++--+++--++++-
123578+++-+++---+---+++---

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
19656-++++-+--+-

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
123578++/---+--+-++++----+---+--+-++--++/-----+--+---------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
123578---------------+---++--+-------+-+-------------------------++---+----------+--+-------+-+-+--------

Isolation, sampling and environmental information

isolation

@refsample type
11501soil
123578Environment, Soil

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_6241.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_152;96_2971;97_3654;98_4622;99_6241&stattab=map
  • Last taxonomy: Nocardiopsis trehalosi subclade
  • 16S sequence: AF105972
  • Sequence Identity:
  • Total samples: 119
  • soil counts: 64
  • aquatic counts: 5
  • animal counts: 23
  • plant counts: 27

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
115011Risk group (German classification)
196561Risk group (German classification)
1235781Risk group (French classification)

Sequence information

16S sequences

  • @ref: 20218
  • description: Nocardiopsis trehalosi 16S ribosomal RNA gene, partial sequence
  • accession: AF105972
  • length: 1474
  • database: ena
  • NCBI tax ID: 109329

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Nocardiopsis trehalosi NBRC 142011348638.3wgspatric1348638
66792Nocardiopsis trehalosi NBRC 142012731957590draftimg1348638
67770Nocardiopsis trehalosi NBRC 14201GCA_001552555contigncbi1348638

GC content

  • @ref: 67770
  • GC-content: 75.2
  • method: genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileno93.339no
gram-positiveyes90.056no
anaerobicno99.203no
halophileno64.962no
spore-formingyes93.015no
thermophileno93.495no
glucose-utilyes88.248yes
aerobicyes95.055no
flagellatedno97.838no
glucose-fermentno92.244no

External links

@ref: 11501

culture collection no.: DSM 44380, CCRC 12529, CIP 106425, IFO 14201, JCM 3357, NBRC 14201, NRRL 12026, VKM Ac-942, BCRC 12529, CGMCC 4.1174, IFM 0242

straininfo link

  • @ref: 80444
  • straininfo: 50601

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny10826789Nocardiopsis tropica sp. nov., Nocardiopsis trehalosi sp. nov., nom. rev. and Nocardiopsis dassonvillei subsp. albirubida subsp. nov., comb. nov.Evtushenko LI, Taran VV, Akimov VN, Kroppenstedt RM, Tiedje JM, Stackebrandt EInt J Syst Evol Microbiol10.1099/00207713-50-1-732000Actinomycetales/chemistry/*classification/cytology/physiology, DNA, Bacterial/analysis/genetics, DNA, Ribosomal/analysis/genetics, Fatty Acids/analysis, Mathematics, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAGenetics
Phylogeny19406773Marinactinospora thermotolerans gen. nov., sp. nov., a marine actinomycete isolated from a sediment in the northern South China Sea.Tian XP, Tang SK, Dong JD, Zhang YQ, Xu LH, Zhang S, Li WJInt J Syst Evol Microbiol10.1099/ijs.0.005231-02009Actinomycetales/chemistry/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Geologic Sediments/*microbiology, Molecular Sequence Data, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Species Specificity, Vitamin K 2/analysisGenetics
Phylogeny25969384Nocardiopsis mangrovei sp. nov., isolated from mangrove sediment.Huang HQ, Xing SS, Yuan WD, Wang Y, Liu M, Sun QG, Lin XZ, Bao SXAntonie Van Leeuwenhoek10.1007/s10482-015-0447-x2015Actinobacteria/*classification/genetics/*isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, China, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Geologic Sediments/*microbiology, Hydrogen-Ion Concentration, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride/metabolism, TemperatureGenetics
Phylogeny27381319Nocardiopsissediminis sp. nov., isolated from mangrove sediment.Muangham S, Suksaard P, Mingma R, Matsumoto A, Takahashi Y, Duangmal KInt J Syst Evol Microbiol10.1099/ijsem.0.0012732016Actinomycetales/*classification/genetics/isolation & purification, Avicennia, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Thailand, Vitamin K 2/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
11501Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44380)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44380
19656Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44380.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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
39517Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/18554
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68368Automatically annotated from API 20E
68371Automatically annotated from API 50CH acid
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
80444Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID50601.1StrainInfo: A central database for resolving microbial strain identifiers
123578Curators of the CIPCollection of Institut Pasteur (CIP 106425)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106425