Strain identifier

BacDive ID: 14036

Type strain: Yes

Species: Rubrobacter xylanophilus

Strain Designation: PRD-1

Strain history: CIP <- 1998, F. Nobre, Univ. Coimbra, Portugal: strain PRD-1

NCBI tax ID(s): 266117 (strain), 49319 (species)

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General

@ref: 3697

BacDive-ID: 14036

DSM-Number: 9941

keywords: genome sequence, 16S sequence, Bacteria, aerobe, thermophilic, Gram-positive, rod-shaped, colony-forming

description: Rubrobacter xylanophilus PRD-1 is an aerobe, thermophilic, Gram-positive bacterium that forms circular colonies and was isolated from thermally polluted industrial runoff.

NCBI tax id

NCBI tax idMatching level
49319species
266117strain

strain history

@refhistory
3697<- M.S. Da Costa, University of Coimbra
67770CIP 105412 <-- F. Nobre PRD-1.
123998CIP <- 1998, F. Nobre, Univ. Coimbra, Portugal: strain PRD-1

doi: 10.13145/bacdive14036.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Rubrobacteria
  • order: Rubrobacterales
  • family: Rubrobacteraceae
  • genus: Rubrobacter
  • species: Rubrobacter xylanophilus
  • full scientific name: Rubrobacter xylanophilus Carreto et al. 1996

@ref: 3697

domain: Bacteria

phylum: Actinobacteria

class: Rubrobacteria

order: Rubrobacterales

family: Rubrobacteraceae

genus: Rubrobacter

species: Rubrobacter xylanophilus

full scientific name: Rubrobacter xylanophilus Carreto et al. 1996 emend. Nouioui et al. 2018

strain designation: PRD-1

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
43368positive1-3 µm0.9-1 µmrod-shapedno
69480no95.405
69480positive99.999
123998positiverod-shapedno

colony morphology

  • @ref: 43368
  • colony size: 1.5-2 mm
  • colony color: light pink
  • colony shape: circular
  • medium used: Thermus medium

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
3697THERMUS 162 MEDIUM (DSMZ Medium 878)yeshttps://mediadive.dsmz.de/medium/878Name: THERMUS 162 MEDIUM (DSMZ Medium 878; with strain-specific modifications) Composition: Agar 28.0 g/l NaCl 10.0 g/l Na2HPO4 x 12 H2O 4.3 g/l Yeast extract 1.0 g/l Tryptone 1.0 g/l KH2PO4 0.544 g/l MgCl2 x 6 H2O 0.2 g/l Nitrilotriacetic acid 0.1 g/l CaSO4 x 2 H2O 0.04 g/l Fe(III) citrate 0.00122472 g/l MnSO4 x H2O 0.00114 g/l H3BO3 0.00025 g/l ZnSO4 x 7 H2O 0.00025 g/l CoCl2 x 6 H2O 2.25e-05 g/l CuSO4 x 5 H2O 1.25e-05 g/l Na2MoO4 x 2 H2O 1.25e-05 g/l H2SO4 Distilled water
38548MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
43368Thermus mediumyes
43368basal salts mediumyes
123998CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerangeconfidence
3697positivegrowth50thermophilic
38548positivegrowth60thermophilic
43368positivegrowth40-70thermophilic
43368positiveoptimum60thermophilic
67770positivegrowth60thermophilic
69480thermophilic95.319
123998positivegrowth45-55thermophilic
123998nogrowth10psychrophilic
123998nogrowth15psychrophilic
123998nogrowth25mesophilic
123998nogrowth30mesophilic
123998nogrowth37mesophilic

culture pH

@refabilitytypepHPH range
43368positivegrowth6-10alkaliphile
43368positivegrowth7.5-8

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
43368aerobe
123998obligate aerobe

spore formation

@refspore formationconfidence
43368no
69481yes100
69480no98.804

halophily

@refsaltgrowthtested relationconcentration
43368NaClpositivegrowth6 %
123998NaClpositivegrowth0-4 %
123998NaClnogrowth6 %
123998NaClnogrowth8 %
123998NaClnogrowth10 %

observation

  • @ref: 67770
  • observation: quinones: MK-8

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4336812936D-galactose+carbon source
43368911224-nitrophenyl alpha-D-glucopyranoside-degradation
43368902594-nitrophenyl beta-D-glucopyranoside-degradation
4336827856acetamide+carbon source
4336830089acetate+/-carbon source
4336815963ribitol-carbon source
4336818305arbutin+degradation
43368casein-degradation
4336862968cellulose-degradation
4336816947citrate-assimilation
4336817057cellobiose+growth
4336815824D-fructose+growth
4336817634D-glucose+growth
4336816899D-mannitol-carbon source
4336816024D-mannose+growth
4336828053melibiose+carbon source
4336816634raffinose+growth
4336817924D-sorbitol-assimilation
4336816551D-trehalose+growth
4336865327D-xylose+carbon source
4336816813galactitol+/-carbon source
433684767elastin-degradation
4336817113erythritol+growth
433684853esculin+degradation
433685054fibrin-degradation
433685291gelatin+degradation
4336817754glycerol-carbon source
43368606565hippurate+degradation
4336830849L-arabinose+growth
4336817196L-asparagine+growth
4336829985L-glutamate+growth
4336818050L-glutamine+/-carbon source
4336817203L-proline+growth
4336862345L-rhamnose+growth
4336817115L-serine-assimilation
4336817716lactose+growth
4336825115malate+growth
4336817268myo-inositol+carbon source
43368olive oil-degradation
4336885645p-nitrophenyl palmitate-degradation
4336815361pyruvate+growth
4336817814salicin+growth
4336828017starch-degradation
4336830031succinate+carbon source
4336817992sucrose+growth
4336853426tween 80-degradation
4336818186tyrosine-degradation
4336837166xylan+hydrolysis
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
6837116443D-tagatose-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
1239984853esculin+hydrolysis
123998606565hippurate+hydrolysis
12399817632nitrate+reduction
12399816301nitrite-reduction

metabolite production

  • @ref: 123998
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12399815688acetoin-
12399817234glucose-

enzymes

@refvalueactivityec
123998beta-galactosidase+3.2.1.23
123998alcohol dehydrogenase-1.1.1.1
123998amylase+
123998DNase-
123998caseinase-3.4.21.50
123998catalase+1.11.1.6
123998tween esterase-
123998gamma-glutamyltransferase-2.3.2.2
123998lecithinase-
123998lipase-
123998lysine decarboxylase-4.1.1.18
123998ornithine decarboxylase-4.1.1.17
123998phenylalanine ammonia-lyase-4.3.1.24
123998tryptophan deaminase-
123998urease-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
123998-+++-++---++-+-++---

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
123998--++++------------------+---------------+/--+/-------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
3697thermally polluted industrial runoffSalisburyUnited KingdomGBREurope
43368thermally polluted runoff (temperature 50°C) from a carpet factory in Wilton, Wiltshire near SalisburyWiltshireUnited KingdomGBREurope
67770Thermally polluted runoff (temperature, 50C)Wilton, WiltshireUnited KingdomGBREurope
123998Environment, Thermally polluted industrial runoff

isolation source categories

Cat1Cat2Cat3
#Engineered#Contamination
#Engineered#Waste#Industrial wastewater
#Condition#Thermophilic (>45°C)

taxonmaps

  • @ref: 69479
  • File name: preview.99_3517.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_408;96_1829;97_2197;98_2696;99_3517&stattab=map
  • Last taxonomy: Rubrobacter xylanophilus
  • 16S sequence: X87135
  • Sequence Identity:
  • Total samples: 2336
  • soil counts: 232
  • aquatic counts: 380
  • animal counts: 1583
  • plant counts: 141

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
36971Risk group (German classification)
1239981Risk group (French classification)

Sequence information

16S sequences

  • @ref: 3697
  • description: R.xylanophilus 16S rRNA gene
  • accession: X87135
  • length: 1509
  • database: ena
  • NCBI tax ID: 49319

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Rubrobacter xylanophilus DSM 9941GCA_000014185completencbi266117
66792Rubrobacter xylanophilus DSM 9941GCA_019448335chromosomencbi266117
66792Rubrobacter xylanophilus DSM 9941266117.34completepatric266117
66792Rubrobacter xylanophilus DSM 9941266117.10completepatric266117
66792Rubrobacter xylanophilus DSM 9941637000248completeimg266117

GC content

@refGC-contentmethod
4336867.6thermal denaturation, midpoint method (Tm)
6777070.5genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileno90.098no
flagellatedno98.856yes
gram-positiveyes84.303yes
anaerobicno86.072no
halophileyes57.312yes
spore-formingno91.083yes
glucose-utilyes88.855yes
aerobicyes86.312yes
thermophileyes98.982yes
glucose-fermentno88.287no

External links

@ref: 3697

culture collection no.: DSM 9941, IFO 16129, NBRC 16129, JCM 11954, CIP 105412, NBRC 100952

straininfo link

  • @ref: 83203
  • straininfo: 48721

literature

  • topic: Phylogeny
  • Pubmed-ID: 28290523
  • title: A phylogenetically distinctive and extremely heat stable light-driven proton pump from the eubacterium Rubrobacter xylanophilus DSM 9941(T).
  • authors: Kanehara K, Yoshizawa S, Tsukamoto T, Sudo Y
  • journal: Sci Rep
  • DOI: 10.1038/srep44427
  • year: 2017
  • mesh: Actinobacteria/chemistry/genetics, Hot Temperature, Hydrogen-Ion Concentration, Light, Light Signal Transduction, *Phylogeny, Proton Pumps/chemistry/*genetics, Rhodopsins, Microbial/*chemistry/genetics, Schiff Bases
  • topic2: Stress

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
3697Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 9941)https://www.dsmz.de/collection/catalogue/details/culture/DSM-9941
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
38548Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/17429
43368Laura Carreto, Edward Moore, M. Fernanda Nobre, Robin Wait, Paul W. Riley, Richard J, Sharp, Milton S. da Costa10.1099/00207713-46-2-460Rubrobacter xylanophilus sp. nov., a New Thermophilic Species Isolated from a Thermally Polluted EffluentIJSEM 1996: 460-465 46
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)
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/
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
83203Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID48721.1StrainInfo: A central database for resolving microbial strain identifiers
123998Curators of the CIPCollection of Institut Pasteur (CIP 105412)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105412