Strain identifier

BacDive ID: 2872

Type strain: Yes

Species: Proteiniclasticum ruminis

Strain Designation: D3RC-2

Strain history: X. Dong D3RC-2.

NCBI tax ID(s): 1410668 (strain), 398199 (species)

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General

@ref: 17757

BacDive-ID: 2872

DSM-Number: 24773

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-negative, rod-shaped

description: Proteiniclasticum ruminis D3RC-2 is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from Yak rumen.

NCBI tax id

NCBI tax idMatching level
398199species
1410668strain

strain history

@refhistory
17757<- JCM <- X. Dong; D3RC-2
67770X. Dong D3RC-2.

doi: 10.13145/bacdive2872.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Clostridia
  • order: Eubacteriales
  • family: Clostridiaceae
  • genus: Proteiniclasticum
  • species: Proteiniclasticum ruminis
  • full scientific name: Proteiniclasticum ruminis Zhang et al. 2010

@ref: 17757

domain: Bacteria

phylum: Firmicutes

class: Clostridia

order: Clostridiales

family: Clostridiaceae

genus: Proteiniclasticum

species: Proteiniclasticum ruminis

full scientific name: Proteiniclasticum ruminis Zhang et al. 2010

strain designation: D3RC-2

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
29371negative0.6-2 µm0.5-0.8 µmrod-shapedno
69480positive99.726

pigmentation

  • @ref: 29371
  • production: no

Culture and growth conditions

culture medium

  • @ref: 17757
  • name: WILKINS-CHALGREN ANAEROBE BROTH (DSMZ Medium 339)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/339
  • composition: Name: WILKINS-CHALGREN ANAEROBE BROTH (DSMZ Medium 339) Composition: dehydrated Wilkins-Chalgren medium 33.0 g/l L-Cysteine HCl 0.3 g/l Sodium resazurin 0.0005 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
17757positivegrowth37mesophilic
29371positivegrowth24-46
29371positiveoptimum38-39mesophilic
67770positivegrowth37mesophilic

culture pH

@refabilitytypepHPH range
29371positivegrowth5.6-8.7alkaliphile
29371positiveoptimum7-7.3

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
17757anaerobe
29371anaerobe
69480anaerobe98.287

spore formation

@refspore formationconfidence
29371no
69480no98.817

observation

  • @ref: 29371
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2937127570histidine+carbon source
2937125017leucine+carbon source
2937128044phenylalanine+carbon source
2937117822serine+carbon source
2937126986threonine+carbon source
293714853esculin+hydrolysis
6838016199urea-hydrolysis
6838029016arginine-hydrolysis
6838016024D-mannose-fermentation
6838016634raffinose-fermentation
6838029985L-glutamate-degradation
6838017632nitrate-reduction
6838027897tryptophan-energy source

metabolite production

  • @ref: 68380
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 68380
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
68380serine arylamidase-
68380glutamyl-glutamate arylamidase-
68380histidine arylamidase-
68380glycin arylamidase-
68380alanine arylamidase-3.4.11.2
68380tyrosine arylamidase-
68380pyrrolidonyl arylamidase-3.4.19.3
68380leucine arylamidase-3.4.11.1
68380phenylalanine arylamidase-
68380leucyl glycin arylamidase-3.4.11.1
68380proline-arylamidase-3.4.11.5
68380L-arginine arylamidase-
68380alkaline phosphatase-3.1.3.1
68380tryptophan deaminase-4.1.99.1
68380alpha-fucosidase-3.2.1.51
68380glutamate decarboxylase-4.1.1.15
68380N-acetyl-beta-glucosaminidase-3.2.1.52
68380beta-glucuronidase-3.2.1.31
68380alpha-arabinosidase-3.2.1.55
68380beta-glucosidase-3.2.1.21
68380alpha-glucosidase+3.2.1.20
68380beta-Galactosidase 6-phosphate-
68380beta-galactosidase-3.2.1.23
68380alpha-galactosidase+3.2.1.22
68380arginine dihydrolase-3.5.3.6
68380urease-3.5.1.5

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
17757--+--+-----------------------

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
17757Yak rumenChinaCHNAsia
67770Yak rumen

isolation source categories

Cat1Cat2Cat3
#Host#Mammals#Bovinae (Cow, Cattle)
#Host Body-Site#Organ#Rumen

taxonmaps

  • @ref: 69479
  • File name: preview.99_693.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_34;96_428;97_487;98_558;99_693&stattab=map
  • Last taxonomy: Proteiniclasticum ruminis subclade
  • 16S sequence: DQ852338
  • Sequence Identity:
  • Total samples: 2227
  • soil counts: 211
  • aquatic counts: 1488
  • animal counts: 424
  • plant counts: 104

Safety information

risk assessment

  • @ref: 17757
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 17757
  • description: Clostridium sp. D3RC-2 16S ribosomal RNA gene, partial sequence
  • accession: DQ852338
  • length: 1516
  • database: ena
  • NCBI tax ID: 1410668

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Proteiniclasticum ruminis DSM 247731410668.3wgspatric1410668
66792Proteiniclasticum ruminis strain CGMCC 1.5058398199.5wgspatric398199
66792Proteiniclasticum ruminis DSM 247732561511080draftimg1410668
66792Proteiniclasticum ruminis CGMCC 1.50582675903137draftimg398199
67770Proteiniclasticum ruminis CGMCC 1.5058GCA_900099635scaffoldncbi398199
67770Proteiniclasticum ruminis DSM 24773GCA_000701905scaffoldncbi1410668

GC content

@refGC-contentmethod
1775741.0high performance liquid chromatography (HPLC)
2937141
6777041high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno74no
motileyes65.014yes
gram-positiveyes52.909yes
anaerobicyes98.149yes
halophileno59.757no
spore-formingno64.912yes
glucose-utilyes91.52no
thermophileno84.828yes
aerobicno96.789yes
flagellatedno64.487no
glucose-fermentyes69.217no

External links

@ref: 17757

culture collection no.: DSM 24773, CGMCC 1.5058, JCM 14817, KCTC 15188

straininfo link

  • @ref: 72396
  • straininfo: 407543

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19915115Proteiniclasticum ruminis gen. nov., sp. nov., a strictly anaerobic proteolytic bacterium isolated from yak rumen.Zhang K, Song L, Dong XInt J Syst Evol Microbiol10.1099/ijs.0.011759-02009Animals, Bacteria, Anaerobic/*classification/genetics/*isolation & purification/metabolism, Cattle/*microbiology, Cellulose/metabolism, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Rumen/*microbiology, Sodium Chloride/*metabolismMetabolism
Phylogeny24048874Youngiibacter fragilis gen. nov., sp. nov., isolated from natural gas production-water and reclassification of Acetivibrio multivorans as Youngiibacter multivorans comb. nov.Lawson PA, Wawrik B, Allen TD, Johnson CN, Marks CR, Tanner RS, Harriman BH, Strapoc D, Callaghan AVInt J Syst Evol Microbiol10.1099/ijs.0.053728-02013Alaska, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Gram-Negative Anaerobic Straight, Curved, and Helical Rods/*classification/genetics/isolation & purification, Molecular Sequence Data, Natural Gas/*microbiology, Nucleic Acid Hybridization, Peptidoglycan/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Water/*analysis, Water MicrobiologyGenetics
Phylogeny34401954Proteiniclasticum sediminis sp. nov., an obligate anaerobic bacterium isolated from anaerobic sludge.Liu J, Bao Y, Zhang X, Zhang K, Chen S, Wu H, He JAntonie Van Leeuwenhoek10.1007/s10482-021-01620-92021Anaerobiosis, Bacterial Typing Techniques, Base Composition, Clostridiaceae, DNA, Bacterial/genetics, *Fatty Acids, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *SewageTranscriptome
Phylogeny35394905Proteiniclasticum aestuarii sp. nov., isolated from tidal flat sediment, and emended descriptions of the genus Proteiniclasticum and Proteiniclasticum ruminis.Namirimu T, Yang JA, Yang SH, Yu J, Kim YJ, Kwon KKInt J Syst Evol Microbiol10.1099/ijsem.0.0052752022Bacteria, Anaerobic/genetics, Bacterial Typing Techniques, Base Composition, Clostridiaceae, DNA, Bacterial/genetics, *Fatty Acids/chemistry, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, *Seawater/microbiology, Sequence Analysis, DNATranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
17757Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 24773)https://www.dsmz.de/collection/catalogue/details/culture/DSM-24773
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
29371Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2578028776041
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 updates33211880Nucleic Acids Res. 49: D498-D508 2020
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68380Automatically annotated from API rID32A
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)
72396Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID407543.1StrainInfo: A central database for resolving microbial strain identifiers