Strain identifier

BacDive ID: 140273

Type strain: Yes

Species: Treponema ruminis

Strain Designation: Ru1

Strain history: <- K. Newbrook, Univ. Liverpool, United Kingdom; Ru1 <- N.J. Evans {2009}

NCBI tax ID(s): 744515 (species)

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General

@ref: 42880

BacDive-ID: 140273

DSM-Number: 103462

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-negative, motile, helical-shaped, colony-forming

description: Treponema ruminis Ru1 is an anaerobe, mesophilic, Gram-negative bacterium that forms circular colonies and was isolated from rumen contents of a Holstein-Friesian bull from a dairy farm.

NCBI tax id

  • NCBI tax id: 744515
  • Matching level: species

strain history

  • @ref: 42880
  • history: <- K. Newbrook, Univ. Liverpool, United Kingdom; Ru1 <- N.J. Evans {2009}

doi: 10.13145/bacdive140273.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/spirochaetota
  • domain: Bacteria
  • phylum: Spirochaetota
  • class: Spirochaetia
  • order: Spirochaetales
  • family: Treponemataceae
  • genus: Treponema
  • species: Treponema ruminis
  • full scientific name: Treponema ruminis Newbrook et al. 2017

@ref: 42880

domain: Bacteria

phylum: Spirochaetes

class: Spirochaetia

order: Spirochaetales

family: Treponemataceae

genus: Treponema

species: Treponema ruminis

full scientific name: Treponema ruminis Newbrook et al. 2017

strain designation: Ru1

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityflagellum arrangementconfidence
43218negative5-9 µm0.4-0.5 µmhelical-shapedyesperitrichous
69480yes92.817
69480negative99.94

colony morphology

  • @ref: 43218
  • colony size: 0.2-0.5 mm
  • colony color: translucent
  • colony shape: circular
  • incubation period: 10 days
  • medium used: fastidious anaerobe agar

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
43218fastidious anaerobe agaryes
43218oral treponeme enrichment broth (Anaerobe Systems)yes
42880TREPONEMA RUMINIS MEDIUM (DSMZ Medium 212a)yeshttps://mediadive.dsmz.de/medium/212aName: TREPONEMA RUMINIS MEDIUM (DSMZ Medium 212a) Composition: Na2SO4 2.77778 g/l Trehalose 1.88492 g/l Maltose x H2O 1.78571 g/l Sucrose 1.68651 g/l Cellobiose 1.68651 g/l Na2CO3 1.4881 g/l Trypticase peptone 0.992061 g/l Ethanol 0.94246 g/l D-Glucose 0.793651 g/l D-Xylose 0.744048 g/l Na-pyruvate 0.496032 g/l KH2PO4 0.496031 g/l DL-Dithiothreitol 0.396825 g/l NaCl 0.396825 g/l NH4Cl 0.396825 g/l Starch 0.396825 g/l MgCl2 x 6 H2O 0.327381 g/l L-Cysteine HCl x H2O 0.297619 g/l CaCl2 x 2 H2O 0.0496031 g/l HCl 0.00248016 g/l FeCl2 x 4 H2O 0.0014881 g/l NaOH 0.000496032 g/l Sodium resazurin 0.000496031 g/l Pyridoxine hydrochloride 0.000297619 g/l Nicotinic acid 0.000198413 g/l Thiamine-HCl x 2 H2O 0.000198413 g/l CoCl2 x 6 H2O 0.000188492 g/l Vitamin B12 9.92064e-05 g/l Calcium pantothenate 9.92064e-05 g/l MnCl2 x 4 H2O 9.92064e-05 g/l p-Aminobenzoic acid 7.93651e-05 g/l ZnCl2 6.94444e-05 g/l Na2MoO4 x 2 H2O 3.57143e-05 g/l NiCl2 x 6 H2O 2.38095e-05 g/l D-(+)-biotin 1.98413e-05 g/l H3BO3 5.95238e-06 g/l Na2WO4 x 2 H2O 3.96825e-06 g/l Na2SeO3 x 5 H2O 2.97619e-06 g/l CuCl2 x 2 H2O 1.98413e-06 g/l iso-Valeric acid DL-2-Methylbutyric acid iso-Butyric acid n-Valeric acid Butyric acid Propionic acid Acetic acid Vitamin K1 Distilled water

culture temp

  • @ref: 42880
  • growth: positive
  • type: growth
  • temperature: 37
  • range: mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
43218anaerobe
69480anaerobe99.56

spore formation

@refspore formationconfidence
69481no100
69480no99.992

enzymes

@refvalueactivityec
43218esterase Lipase (C 8)+
43218leucine arylamidase+3.4.11.1
43218beta-galactosidase+3.2.1.23
43218beta-glucosidase+3.2.1.21
43218alkaline phosphatase-3.1.3.1
43218esterase (C 4)-
43218lipase (C 14)-
43218valine arylamidase-
43218cystine arylamidase-3.4.11.3
43218trypsin-3.4.21.4
43218chymotrypsin-3.4.4.5
43218acid phosphatase-3.1.3.2
43218naphthol-AS-BI-phosphohydrolase-
43218alpha-galactosidase-3.2.1.22
43218beta-glucuronidase-3.2.1.31
43218alpha-glucosidase-3.2.1.20
43218N-acetyl-beta-glucosaminidase-3.2.1.52
43218alpha-mannosidase-3.2.1.24
43218alpha-fucosidase-3.2.1.51

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentenrichment cultureenrichment culture composition
42880rumen contents of a Holstein-Friesian bull from a dairy farmCheshireUnited KingdomGBREurope
43218rumen contents of a Holstein-Friesian bull from a UK dairy farmoral treponeme enrichment broth (Anaerobe Systems)supplemented with 10 % (v/v) rabbit serum

isolation source categories

Cat1Cat2Cat3
#Engineered#Agriculture#Livestock (Husbandry)
#Host#Mammals#Bovinae (Cow, Cattle)
#Host Body-Site#Organ#Rumen

taxonmaps

  • @ref: 69479
  • File name: preview.99_72850.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_6418;96_31006;97_39221;98_51027;99_72850&stattab=map
  • Last taxonomy: Treponema ruminis subclade
  • 16S sequence: GU566698
  • Sequence Identity:
  • Total samples: 5978
  • soil counts: 259
  • aquatic counts: 12
  • animal counts: 5200
  • plant counts: 507

Safety information

risk assessment

  • @ref: 42880
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 42880
  • description: Treponema ruminis strain Ru1 16S ribosomal RNA gene, partial sequence
  • accession: GU566698
  • length: 1309
  • database: ena
  • NCBI tax ID: 744515

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Treponema ruminis RU1GCA_017161305completencbi744515
66792Treponema ruminis DSM 103462GCA_014201975scaffoldncbi744515
66792Treponema ruminis strain DSM 103462744515.3wgspatric744515
66792Treponema ruminis strain RU1744515.4completepatric744515
66792Treponema ruminis DSM 1034622861310463draftimg744515

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedno75.701no
gram-positiveno94.327no
anaerobicyes98.37yes
aerobicno97.102yes
halophileno87.947no
spore-formingno88.266no
thermophileno91.218no
glucose-utilyes72.538no
motileyes86.146yes
glucose-fermentyes58.611no

External links

@ref: 42880

culture collection no.: DSM 103462, NCTC 13847

straininfo link

  • @ref: 96579
  • straininfo: 408305

literature

  • topic: Phylogeny
  • Pubmed-ID: 28113049
  • title: Treponema ruminis sp. nov., a spirochaete isolated from the bovine rumen.
  • authors: Newbrook K, Staton GJ, Clegg SR, Birtles RJ, Carter SD, Evans NJ
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.001812
  • year: 2017
  • mesh: Animals, Bacterial Typing Techniques, Base Composition, Cattle/*microbiology, DNA, Bacterial/genetics, Male, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rumen/*microbiology, Sequence Analysis, DNA, Treponema/*classification/genetics/isolation & purification, United Kingdom
  • topic2: Transcriptome

Reference

@idauthorstitledoi/urlcataloguejournalpubmed
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
42880Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-103462Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 103462)
43218Kerry Newbrook, Gareth J. Staton, Simon R. Clegg, Richard J. Birtles, Stuart D. Carter, Nicholas J. EvansTreponema ruminis sp. nov., a spirochaete isolated from the bovine rumen10.1099/ijsem.0.001812IJSEM 67: 1349-1354 201728113049
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
96579Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID408305.1