Strain identifier

BacDive ID: 132007

Type strain: Yes

Species: Thermobifida alba

Strain Designation: A-0077, 1900

Strain history: CIP <- 1998, JCM <- KCC: strain A-0077 <- K. Locci, IPV: strain 1900

NCBI tax ID(s): 53522 (species)

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: 11250

BacDive-ID: 132007

DSM-Number: 43795

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

description: Thermobifida alba A-0077 is an obligate aerobe, mesophilic, Gram-positive bacterium that was isolated from garden soil.

NCBI tax id

  • NCBI tax id: 53522
  • Matching level: species

strain history

@refhistory
11250<- NBRC; NBRC 16095 <- IFO; 16095 <- JCM; 3077 <- KACC; KCC A-0077 <- Inst. di Pathol. Veg., Italy; IPV 1900
67770KCC A-0077 <-- IPV 1900.
116180CIP <- 1998, JCM <- KCC: strain A-0077 <- K. Locci, IPV: strain 1900

doi: 10.13145/bacdive132007.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Streptosporangiales
  • family: Nocardiopsidaceae
  • genus: Thermobifida
  • species: Thermobifida alba
  • full scientific name: Thermobifida alba (Locci et al. 1967) Zhang et al. 1998
  • synonyms

    @refsynonym
    20215Actinobifida alba
    20215Thermomonospora mesouviformis
    20215Thermomonospora alba

@ref: 11250

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardiopsaceae

genus: Thermobifida

species: Thermobifida alba

full scientific name: Thermobifida alba (Locci et al. 1967) Zhang et al. 1998

strain designation: A-0077, 1900

type strain: yes

Morphology

cell morphology

  • @ref: 116180
  • gram stain: positive
  • cell shape: rod-shaped
  • motility: no

multimedia

  • @ref: 11250
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_43795.jpg
  • caption: Medium 65 37°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11250TRYPTICASE 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
39322MEDIUM 287 - for Thermobifida albayesDistilled water make up to (1000.000 ml);Iron (II) sulphate heptahydrate (0.500 g);Sodium nitrate (3.000 g);Magnesium sulphate heptahydrate (0.500 g);Agar (13.000 g);Yeast extract (2.000 g);Sucrose (30.000 g);Casamino acids (6.100 g);L-Tryptophan (0.020 g
11250GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium65.pdf
116180CIP Medium 287yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=287

culture temp

@refgrowthtypetemperaturerange
11250positivegrowth37mesophilic
39322positivegrowth37mesophilic
67770positivegrowth37mesophilic
116180positivegrowth22-41
116180nogrowth5psychrophilic
116180nogrowth15psychrophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 116180
  • oxygen tolerance: obligate aerobe

halophily

@refsaltgrowthtested relationconcentration
116180NaClpositivegrowth2 %
116180NaClnogrowth0 %
116180NaClnogrowth4 %
116180NaClnogrowth6 %
116180NaClnogrowth8 %
116180NaClnogrowth10 %

observation

  • @ref: 67770
  • observation: quinones: MK-10(H6), MK-10(H8), MK-10(H10), MK-11(H8)

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-tagatose-builds acid from16443
68371D-lyxose-builds acid from62318
68371turanose-builds acid from32528
68371gentiobiose-builds acid from28066
68371xylitol-builds acid from17151
68371glycogen+builds acid from28087
68371starch-builds acid from28017
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose-builds acid from27082
68371sucrose-builds acid from17992
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
68371maltose-builds acid from17306
68371salicin-builds acid from17814
68371esculin+builds acid from4853
68371arbutin-builds acid from18305
68371amygdalin-builds acid from27613
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
68371D-galactose-builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371L-arabinose-builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754
116180esculin+hydrolysis4853
116180nitrate-reduction17632
116180nitrite-reduction16301
116180glucose-degradation17234
116180nitrate-respiration17632

metabolite production

  • @ref: 116180
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11618015688acetoin-
11618017234glucose-

enzymes

@refvalueactivityec
116180oxidase-
116180alcohol dehydrogenase-1.1.1.1
116180gelatinase+
116180amylase+
116180DNase+
116180caseinase+3.4.21.50
116180catalase+1.11.1.6
116180tween esterase+
116180gamma-glutamyltransferase-2.3.2.2
116180lecithinase+
116180lipase+
116180lysine decarboxylase-4.1.1.18
116180ornithine decarboxylase-4.1.1.17
116180protease+
116180tryptophan deaminase-
116180urease-3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
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
68382acid phosphatase-3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase-3.2.1.22
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-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
116180-+++-+-----+--------

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
116180----+/-+/-----+/-+/-+/-+/-----------+-+/----------+-----+/------+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
11250garden soilMilanoItalyITAEurope
67770Garden soilMilanItalyITAEurope
116180Environment, Garden soil

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Soil
#Engineered#Agriculture#Garden

taxonmaps

  • @ref: 69479
  • File name: preview.99_80713.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_152;96_595;97_696;98_35937;99_80713&stattab=map
  • Last taxonomy: Thermobifida
  • 16S sequence: AF002260
  • Sequence Identity:
  • Total samples: 39
  • soil counts: 29
  • aquatic counts: 1
  • animal counts: 6
  • plant counts: 3

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
112501Risk group (German classification)
1161801Risk group (French classification)

Sequence information

16S sequences

  • @ref: 11250
  • description: Thermomonospora alba 16S ribosomal RNA gene, partial sequence
  • accession: AF002260
  • length: 1468
  • database: ena
  • NCBI tax ID: 53522

Genome sequences

  • @ref: 66792
  • description: Thermobifida alba DSM 43795
  • accession: GCA_023208015
  • assembly level: complete
  • database: ncbi
  • NCBI tax ID: 53522

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedno97.872no
gram-positiveyes90.08no
anaerobicno98.628no
aerobicyes83.886no
halophileno63.276no
spore-formingyes89.767no
motileno93.631no
glucose-fermentno92.675no
thermophileno92.52yes
glucose-utilyes84.326no

External links

@ref: 11250

culture collection no.: DSM 43795, CECT 3324, CIP 105591, CUB 1002, CUB 432, DSM 43310, IFM 1271, IFO (now NBRC) 15853, IFO (now NBRC) 16095, IMET 9528, IMSNU 22187, JCM 3077, KCC A-0077, KCTC 9618, NBRC 15853, NBRC 16095, NCIB 10169, IPV 1900, IFO 15853, IFO 16095, NCIMB 10169

straininfo link

  • @ref: 90393
  • straininfo: 50429

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny12148627Thermobifida cellulolytica sp. nov., a novel lignocellulose-decomposing actinomycete.Kukolya J, Nagy I, Laday M, Toth E, Oravecz O, Marialigeti K, Hornok LInt J Syst Evol Microbiol10.1099/00207713-52-4-11932002Actinomycetales/chemistry/*classification/genetics/physiology, Bacterial Typing Techniques, Base Composition, Cellulose/*metabolism, DNA, Ribosomal, Genes, rRNA, Lignin/*metabolism, Manure/microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, RNA, Ribosomal, 16S, *Refuse Disposal, Sequence Analysis, DNA, Spores, Bacterial/physiology/ultrastructureMetabolism
Metabolism32841608Biotransformation of cladribine by a nanostabilized extremophilic biocatalyst.Rivero CW, De Benedetti EC, Sambeth J, Trelles JAJ Biotechnol10.1016/j.jbiotec.2020.08.0122020Acrylic Resins, Antineoplastic Agents/therapeutic use, Biosynthetic Pathways, *Biotransformation, Cladribine/*metabolism/therapeutic use, Deoxyadenosines, Extremophiles/*physiology, Geobacillus, Leukemia, Hairy Cell/drug therapy, Nanocomposites, Temperature, Thermobifida/growth & development/metabolism

Reference

@idauthorscataloguedoi/urltitle
11250Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 43795)https://www.dsmz.de/collection/catalogue/details/culture/DSM-43795
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
39322Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/17627
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/
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
90393Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID50429.1StrainInfo: A central database for resolving microbial strain identifiers
116180Curators of the CIPCollection of Institut Pasteur (CIP 105591)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105591