Strain identifier

BacDive ID: 14087

Type strain: Yes

Species: Solirubrobacter pauli

Strain Designation: B33D1

Strain history: CIP <- 2003, R. Upchurch, Georgia Univ., Athens, USA: strain B33D1

NCBI tax ID(s): 166793 (species)

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General

@ref: 5617

BacDive-ID: 14087

DSM-Number: 14954

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

description: Solirubrobacter pauli B33D1 is a spore-forming, mesophilic, Gram-positive bacterium that was isolated from burrow of the epigeic earthworm Lumbricus rubellus in an agricultural soil.

NCBI tax id

  • NCBI tax id: 166793
  • Matching level: species

strain history

@refhistory
5617<- W. B. Whitman, Univ. of Georgia, Athens, USA; B33D1 <- M. A. Furlong, Dept. Natural Sci., Clayton College and State Univ., USA
332002003, R. Upchurch, Georgia Univ., Athens, USA: strain B33D1
67770KCTC 9974 <-- W. B. Whitman B33D1.
121638CIP <- 2003, R. Upchurch, Georgia Univ., Athens, USA: strain B33D1

doi: 10.13145/bacdive14087.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Thermoleophilia
  • order: Solirubrobacterales
  • family: Solirubrobacteraceae
  • genus: Solirubrobacter
  • species: Solirubrobacter pauli
  • full scientific name: Solirubrobacter pauli Singleton et al. 2003

@ref: 5617

domain: Bacteria

phylum: Actinobacteria

class: Thermoleophilia

order: Solirubrobacterales

family: Solirubrobacteraceae

genus: Solirubrobacter

species: Solirubrobacter pauli

full scientific name: Solirubrobacter pauli Singleton et al. 2003

strain designation: B33D1

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480positive99.691
121638positiverod-shapedyes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5617NUTRIENT AGAR (DSMZ Medium 1)yeshttps://mediadive.dsmz.de/medium/1Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
33200MEDIUM 328- for nutrient agaryesDistilled water make up to (1000.000 ml);Agar (15.000 g);Peptone (5.000g);Beef extract (3.000 g)
121638CIP Medium 328yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=328

culture temp

@refgrowthtypetemperaturerange
5617positivegrowth28mesophilic
33200positivegrowth22psychrophilic
67770positivegrowth28mesophilic
121638positivegrowth15-37
121638nogrowth10psychrophilic
121638nogrowth41thermophilic
121638nogrowth45thermophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481yes90
69480no99.469

halophily

@refsaltgrowthtested relationconcentration
121638NaClpositivegrowth0 %
121638NaClnogrowth2 %
121638NaClnogrowth4 %
121638NaClnogrowth6 %
121638NaClnogrowth8 %
121638NaClnogrowth10 %

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-fucose-builds acid from28847
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
68371cellobiose-builds acid from17057
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
68371L-sorbose-builds acid from17266
68371D-mannose-builds acid from16024
68371D-fructose-builds acid from15824
68371D-glucose-builds acid from17634
68371D-galactose-builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose-builds acid from65327
68371D-ribose-builds acid from16988
68371L-arabinose-builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754
121638citrate-carbon source16947
121638esculin+hydrolysis4853
121638hippurate-hydrolysis606565
121638nitrate-reduction17632
121638nitrite-reduction16301
121638nitrate-respiration17632

antibiotic resistance

  • @ref: 121638
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

  • @ref: 121638
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12163815688acetoin-
12163817234glucose-

enzymes

@refvalueactivityec
121638oxidase-
121638beta-galactosidase+3.2.1.23
121638alcohol dehydrogenase-1.1.1.1
121638gelatinase-
121638amylase+
121638DNase-
121638caseinase+3.4.21.50
121638catalase+1.11.1.6
121638tween esterase-
121638gamma-glutamyltransferase-2.3.2.2
121638lecithinase-
121638lipase-
121638lysine decarboxylase-4.1.1.18
121638ornithine decarboxylase-4.1.1.17
121638phenylalanine ammonia-lyase-4.3.1.24
121638protease-
121638tryptophan deaminase-
121638urease-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
121638-+++-++---++-+-++---

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
121638------------------------+------------------------

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinentisolation date
5617burrow of the epigeic earthworm Lumbricus rubellus in an agricultural soilLumbricus rubellusGeorgia, AthensUSAUSANorth America
67770Burrow of the epigeic earthworm Lumbricus rubellus in agricultural soilLumbricus rubellusAthens, GAUSAUSANorth America
121638Environment, Burrow of Lumbricus rubellus in agricultural soilAthens, GeorgiaUnited States of AmericaUSANorth America1996

isolation source categories

Cat1Cat2Cat3
#Engineered#Agriculture
#Environmental#Terrestrial#Soil
#Host#Invertebrates (Other)#Annelida

taxonmaps

  • @ref: 69479
  • File name: preview.99_28756.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_373;96_1692;97_2026;98_20298;99_28756&stattab=map
  • Last taxonomy: Solirubrobacter pauli subclade
  • 16S sequence: AY039806
  • Sequence Identity:
  • Total samples: 817
  • soil counts: 566
  • aquatic counts: 22
  • animal counts: 52
  • plant counts: 177

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
56171Risk group (German classification)
1216381Risk group (French classification)

Sequence information

16S sequences

  • @ref: 5617
  • description: Earthworm burrow bacterium B33D1 16S ribosomal RNA gene, partial sequence
  • accession: AY039806
  • length: 1366
  • database: ena
  • NCBI tax ID: 166793

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Solirubrobacter pauli strain DSM 14954166793.3wgspatric166793
66792Solirubrobacter pauli DSM 149542737471645draftimg166793
67770Solirubrobacter pauli DSM 14954GCA_003633755scaffoldncbi166793

GC content

  • @ref: 67770
  • GC-content: 71.6-72
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes90no
motileyes70.887no
gram-positiveyes83.404no
anaerobicno97.941no
aerobicyes86.488no
halophileno94.815no
spore-formingno82.562no
thermophileno98.101yes
glucose-utilyes86.95no
flagellatedno88.122no
glucose-fermentno86.471no

External links

@ref: 5617

culture collection no.: DSM 14954, ATCC BAA 492, JCM 13025, CIP 108104, KCTC 9974

straininfo link

  • @ref: 83255
  • straininfo: 100956

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny12710617Solirubrobacter pauli gen. nov., sp. nov., a mesophilic bacterium within the Rubrobacteridae related to common soil clones.Singleton DR, Furlong MA, Peacock AD, White DC, Coleman DC, Whitman WBInt J Syst Evol Microbiol10.1099/ijs.0.02438-02003Actinobacteria/*classification/genetics/isolation & purification/physiology, Microscopy, Phase-Contrast, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, TemperatureGenetics
Phylogeny17625174Solirubrobacter soli sp. nov., isolated from soil of a ginseng field.Kim MK, Na JR, Lee TH, Im WT, Soung NK, Yang DCInt J Syst Evol Microbiol10.1099/ijs.0.64715-02007Actinobacteria/chemistry/*classification/*isolation & purification/physiology, Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Genes, rRNA, Korea, Locomotion, Molecular Sequence Data, Panax, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, *Soil Microbiology, Spores, Bacterial, Vitamin K 2/analysisGenetics
Phylogeny21148679Solirubrobacter ginsenosidimutans sp. nov., isolated from soil of a ginseng field.An DS, Wang L, Kim MS, Bae HM, Lee ST, Im WTInt J Syst Evol Microbiol10.1099/ijs.0.028431-02010Actinobacteria/*classification/genetics/*isolation & purification/metabolism, Base Composition, China, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/metabolism, Ginsenosides/metabolism, Molecular Sequence Data, Panax/*microbiology, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil MicrobiologyMetabolism
Phylogeny24254741Solirubrobacter phytolaccae sp. nov., an endophytic bacterium isolated from roots of Phytolacca acinosa Roxb.Wei L, Ouyang S, Wang Y, Shen X, Zhang LInt J Syst Evol Microbiol10.1099/ijs.0.057554-02013Actinobacteria/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, Phytolacca/*microbiology, Plant Roots/microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryGenetics
Phylogeny24846053Solirubrobacter taibaiensis sp. nov., isolated from a stem of Phytolacca acinosa Roxb.Zhang L, Zhu L, Si M, Li C, Zhao L, Wei Y, Shen XAntonie Van Leeuwenhoek10.1007/s10482-014-0194-42014Actinobacteria/*classification/genetics/*isolation & purification/physiology, Aerobiosis, Bacterial Typing Techniques, Base Composition, China, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Hydrogen-Ion Concentration, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Phytolacca/*microbiology, Plant Stems/microbiology, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride/metabolism, TemperatureGenetics

Reference

@idauthorscataloguedoi/urltitle
5617Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 14954)https://www.dsmz.de/collection/catalogue/details/culture/DSM-14954
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
33200Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5690
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
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
83255Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID100956.1StrainInfo: A central database for resolving microbial strain identifiers
121638Curators of the CIPCollection of Institut Pasteur (CIP 108104)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108104