Strain identifier

BacDive ID: 3851

Type strain: Yes

Species: Deinococcus proteolyticus

Strain Designation: MRP

Strain history: IAM 12141 <-- M. Kobatake strain MRP.

NCBI tax ID(s): 693977 (strain), 55148 (species)

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General

@ref: 8769

BacDive-ID: 3851

DSM-Number: 20540

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic

description: Deinococcus proteolyticus MRP is an aerobe, mesophilic bacterium that was isolated from faeces of Lama glama.

NCBI tax id

NCBI tax idMatching level
693977strain
55148species

strain history

@refhistory
8769<- CCM <- M. Kobatake, MRP
67770IAM 12141 <-- M. Kobatake strain MRP.

doi: 10.13145/bacdive3851.20250331.9.3

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/deinococcota
  • domain: Bacteria
  • phylum: Deinococcota
  • class: Deinococci
  • order: Deinococcales
  • family: Deinococcaceae
  • genus: Deinococcus
  • species: Deinococcus proteolyticus
  • full scientific name: Deinococcus proteolyticus (ex Kobatake et al. 1973) Brooks and Murray 1981

@ref: 8769

domain: Bacteria

phylum: Deinococcus-Thermus

class: Deinococci

order: Deinococcales

family: Deinococcaceae

genus: Deinococcus

species: Deinococcus proteolyticus

full scientific name: Deinococcus proteolyticus (ex Kobatake et al. 1973) Brooks and Murray 1981

strain designation: MRP

type strain: yes

Morphology

cell morphology

  • @ref: 125439
  • gram stain: negative
  • confidence: 98.1

multimedia

  • @ref: 66793
  • multimedia content: EM_DSM_20540_1.jpg
  • caption: electron microscopic image
  • intellectual property rights: © HZI/Manfred Rohde

Culture and growth conditions

culture medium

  • @ref: 8769
  • name: CORYNEBACTERIUM AGAR (DSMZ Medium 53)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/53
  • composition: Name: CORYNEBACTERIUM AGAR (DSMZ Medium 53) Composition: Agar 15.0 g/l Casein peptone 10.0 g/l NaCl 5.0 g/l Glucose 5.0 g/l Yeast extract 5.0 g/l Distilled water

culture temp

@refgrowthtypetemperature
8769positivegrowth30
58764positivegrowth30
67770positivegrowth30

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
58764aerobe
125439obligate aerobe98.1

spore formation

  • @ref: 125439
  • spore formation: no
  • confidence: 96.5

murein

  • @ref: 8769
  • murein short key: A21.01
  • type: A3ß L-Orn-Gly2-3

Isolation, sampling and environmental information

isolation

@refsample typehost species
8769faeces of Lama glamaLama glama
58764Lama glama feces

isolation source categories

Cat1Cat2Cat3
#Host#Mammals
#Host Body Product#Gastrointestinal tract#Feces (Stool)

taxonmaps

  • @ref: 69479
  • File name: preview.99_176994.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_181;96_599;97_701;98_817;99_176994&stattab=map
  • Last taxonomy: Deinococcus proteolyticus subclade
  • 16S sequence: Y11331
  • Sequence Identity:
  • Total samples: 48
  • soil counts: 2
  • aquatic counts: 1
  • animal counts: 44
  • plant counts: 1

Safety information

risk assessment

  • @ref: 8769
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 8769
  • description: D.proteolyticus 16S rRNA gene
  • accession: Y11331
  • length: 1466
  • database: nuccore
  • NCBI tax ID: 693977

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Deinococcus proteolyticus MRPGCA_000190555completencbi693977
66792Deinococcus proteolyticus MRP693977.14plasmidpatric693977
66792Deinococcus proteolyticus MRP693977.3completepatric693977
66792Deinococcus proteolyticus MRP693977.15plasmidpatric693977
66792Deinococcus proteolyticus MRP693977.17plasmidpatric693977
66792Deinococcus proteolyticus MRP693977.16plasmidpatric693977
66792Deinococcus proteolyticus MRP, DSM 20540649633035completeimg693977

GC content

@refGC-contentmethod
876965.0
6777065thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingno62.835no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no93.836yes
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes79.453no
125438spore-formingspore-formingAbility to form endo- or exosporesno75.25no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno85.791yes
125438motile2+flagellatedAbility to perform flagellated movementno74.361no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno96.5
125439BacteriaNetmotilityAbility to perform movementyes72.7
125439BacteriaNetgram_stainReaction to gram-stainingnegative98.1
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe98.1

External links

@ref: 8769

culture collection no.: DSM 20540, ATCC 35074, CCM 2703, CCUG 50161, IFO 15345, NCIMB 13154, UWO 1056, JCM 6276, BCRC 17377, HAMBI 2066, IAM 12141, NBRC 101906, NBRC 15345, VKM Ac-1939

straininfo link

  • @ref: 73361
  • straininfo: 105399

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19625434Deinococcus piscis sp. nov., a radiation-resistant bacterium isolated from a marine fish.Shashidhar R, Bandekar JRInt J Syst Evol Microbiol10.1099/ijs.0.003046-02009Animals, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Deinococcus/classification/genetics/*isolation & purification/*radiation effects, Fatty Acids/chemistry/metabolism, Molecular Sequence Data, Perciformes/*microbiology, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiologyGenetics
Metabolism29366718Production of aminoacyl prolines using the adenylation domain of nonribosomal peptide synthetase with class III polyphosphate kinase 2-mediated ATP regeneration.Suzuki S, Hara R, Kino KJ Biosci Bioeng10.1016/j.jbiosc.2017.12.0232018Adenosine Triphosphate/*metabolism, Amino Acids/*metabolism, *Aminoacylation, Catalytic Domain/genetics, Cloning, Molecular, Dipeptides/metabolism, Escherichia coli/metabolism, Peptide Synthases/*chemistry/genetics/*metabolism, Phosphotransferases (Phosphate Group Acceptor)/genetics/*metabolism, Proline/analogs & derivatives/*metabolism, Protein Domains/genetics, Protein Engineering, Recombinant Fusion Proteins/genetics/metabolismEnzymology

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
8769Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20540)https://www.dsmz.de/collection/catalogue/details/culture/DSM-20540
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
58764Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 50161)https://www.ccug.se/strain?id=50161
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)
66793Mukherjee et al.10.1038/nbt.3886GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life 35: 676-683 201728604660
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/
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
73361Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID105399.1StrainInfo: A central database for resolving microbial strain identifiers
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1