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Strain identifier

BacDive ID: 11739

Type strain: Yes

Species: Rodentibacter pneumotropicus

Strain Designation: P 421

Strain history: CCUG 12398 <-- W. Frederiksen P421.

NCBI tax ID(s): 1122936 (strain), 758 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 15688

BacDive-ID: 11739

DSM-Number: 21403

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

description: Rodentibacter pneumotropicus P 421 is a mesophilic, Gram-negative bacterium that was isolated from mouse lung.

NCBI tax id

NCBI tax idMatching level
1122936strain
758species

strain history

doi: 10.13145/bacdive11739.20221219.7.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Pasteurellales
  • family: Pasteurellaceae
  • genus: Rodentibacter
  • species: Rodentibacter pneumotropicus
  • full scientific name: Rodentibacter pneumotropicus (Jawetz 1950) Adhikary et al. 2017
  • synonyms

    • @ref: 20215
    • synonym: Pasteurella pneumotropica

@ref: 15688

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Pasteurellales

family: Pasteurellaceae

genus: Rodentibacter

species: Rodentibacter pneumotropicus

full scientific name: Rodentibacter pneumotropicus (Jawetz 1950) Adhikary et al. 2017

strain designation: P 421

type strain: yes

Morphology

cell morphology

@refgram stainmotilityconfidence
43243negativeno
69480negative99.49

colony morphology

@reftype of hemolysisincubation periodcolony sizecolony shapemedium used
15688gamma1-2 days
43243gamma1 day1-2 mmcircularBovine blood agar

pigmentation

  • @ref: 43243
  • production: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
15688BHI MEDIUM (DSMZ Medium 215)yeshttps://mediadive.dsmz.de/medium/215Name: BHI MEDIUM (DSMZ Medium 215) Composition: Brain heart infusion 37.0 g/l Distilled water
15688COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)yeshttps://mediadive.dsmz.de/medium/693Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base
37613MEDIUM 118 - for Pasteurella, Actinobacillus and Psychrobacter frigidicolayesDistilled water make up to (1000.000 ml);Yeast extract (1.000 g);Tryptocasein soy agar (40.000 g)
43243MacConkey agarno
43243Bovine blood agaryes

culture temp

@refgrowthtypetemperaturerange
15688positivegrowth37mesophilic
37613positivegrowth37mesophilic
67770positivegrowth30mesophilic

Physiology and metabolism

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 99.475

halophily

  • @ref: 69480
  • halophily level: non-halophilic
  • confidence: 95.925

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4324317234glucose+fermentation
4324317632nitrate+reduction
4324316947citrate-carbon source
4324317234glucose-fermentation
4324316537galactarate+builds acid from
4324315792malonate+builds base from
4324315226tetrathionate-reduction
4324353424tween 20-hydrolysis
4324348095(-)-D-fructose+builds acid from
4324312936D-galactose+builds acid from
4324317306maltose+builds acid from
4324317634(+)-D-glucose+builds acid from
4324348095(-)-D-fructose-builds gas from
4324312936D-galactose-builds gas from
4324317306maltose-builds gas from
4324317634(+)-D-glucose-builds gas from
4324317113erythritol-builds acid from
4324315963ribitol-builds acid from
4324317151xylitol-builds acid from
4324318333(+)-D-arabitol-builds acid from
4324365328(-)-L-xylose-builds acid from
4324316813galactitol-builds acid from
4324317924(-)-D-sorbitol-builds acid from
4324328847(+)-D-fucose-builds acid from
4324362345L-rhamnose-builds acid from
4324317266(-)-L-sorbose-builds acid from
4324317057cellobiose-builds acid from
432436731melezitose-builds acid from
43243(+)-D-glycogen-builds acid from
4324315443inulin-builds acid from
432434853esculin-builds acid from
4324327613amygdalin-builds acid from
4324318305arbutin-builds acid from
4324328066gentiobiose-builds acid from
4324317814salicin-builds acid from
4324332528turanose-builds acid from
4324353426tween 80-hydrolysis
4324317108D-arabinose-builds acid from
4324330849L-arabinose-builds acid from
4324316988(-)-D-ribose+builds acid from
4324365327D-xylose+builds acid from
4324317268myo-inositol+/-builds acid from
4324316899D-mannitol-builds acid from
4324318287L-fucose+builds acid from
4324316024D-mannose+builds acid from
4324317716lactose-builds acid from
4324317992sucrose+builds acid from
4324327082trehalose+builds acid from
4324323652dextrin+builds acid from
4324317634(-)-D-glucose+builds acid from
6837717306maltose+builds acid from
6837715824D-fructose+builds acid from
6837717634D-glucose+builds acid from
6836830849L-arabinose-fermentation
6836827613amygdalin-fermentation
6836828053melibiose-fermentation
6836817992sucrose-fermentation
6836862345L-rhamnose-fermentation
6836830911sorbitol-fermentation
6836817268myo-inositol-fermentation
6836816899D-mannitol-fermentation
6836817634D-glucose-fermentation
683685291gelatin-hydrolysis
6836827897tryptophan-energy source
6836816199urea+hydrolysis
6836816947citrate-assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine-hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
432438337porphyrinyes
4324315688acetoinno
6836815688acetoinno
6836835581indoleno
6836816136hydrogen sulfideno

metabolite tests

@refChebi-IDmetabolitemethylred-testvoges-proskauer-testindole test
4324317234glucose-
4324315688acetoin-
6836815688acetoin-
6836835581indole-

enzymes

@refvalueactivityec
15688catalase+1.11.1.6
15688cytochrome-c oxidase+1.9.3.1
43243catalase+1.11.1.6
43243cytochrome oxidase+1.9.3.1
43243urease+3.5.1.5
43243alkaline phosphatase+3.1.3.1
43243arginine dihydrolase-3.5.3.6
43243phenylalanine deaminase-4.3.1.5
43243gelatinase-
43243beta-glucosidase-3.2.1.21
43243alpha-fucosidase-3.2.1.51
43243beta-xylosidase-
43243alpha-mannosidase-3.2.1.24
43243lysine decarboxylase-4.1.1.18
43243ornithine decarboxylase+4.1.1.17
43243beta-galactosidase+3.2.1.23
43243alpha-glucosidase+3.2.1.20
43243alpha-galactosidase+/-3.2.1.22
43243alanine aminopeptidase+
43243beta-glucuronidase-3.2.1.31
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase-3.2.1.21
68382alpha-glucosidase-3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase-
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase-
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)-
68382esterase (C 4)-
68382alkaline phosphatase+3.1.3.1
68377gamma-glutamyltransferase+2.3.2.2
68377alkaline phosphatase+3.1.3.1
68368cytochrome oxidase+1.9.3.1
68368gelatinase-
68368tryptophan deaminase-4.1.99.1
68368urease+3.5.1.5
68368ornithine decarboxylase-4.1.1.17
68368lysine decarboxylase-4.1.1.18
68368arginine dihydrolase-3.5.3.6
68368beta-galactosidase-3.2.1.23

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
45690-+---+----+---------

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARAOX
45690------+-------------+

API NH

@refPENGLUFRUMALSACODCURELIPPALbeta GALProAGGTIND
15688++++-+-++-++-
15688++++-+/--++-++-
15688-++++-+-++-++
15688-++++-+/--++-++

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentsampling dategeographic location
15688mouse lungUSAUSANorth America
43243mouse samples
45690Mouse lungUSAUSANorth America1950San Francisco
67770Mouse lungUSAUSANorth AmericaSan Francisco

isolation source categories

Cat1Cat2Cat3
#Host#Mammals#Muridae (Mouse/Rat)
#Host Body-Site#Oral cavity and airways#Lung

taxonmaps

  • @ref: 69479
  • File name: preview.99_941.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_18;96_552;97_638;98_737;99_941&stattab=map
  • Last taxonomy: Rodentibacter pneumotropicus subclade
  • 16S sequence: M75083
  • Sequence Identity:
  • Total samples: 1467
  • soil counts: 5
  • aquatic counts: 12
  • animal counts: 1440
  • plant counts: 10

Safety information

risk assessment

  • @ref: 15688
  • biosafety level: 2
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Pasteurella pneumotropica partial 16S rRNA gene, strain P421AJ438681429ena758
20218Pasteurella pneumotropica 16S ribosomal RNA gene, partial sequenceAY634677483ena758
20218Pasteurella pneumotropica strain NCTC 8141 16S ribosomal RNA gene, partial sequenceM750831471ena758
15688Rodentibacter pneumotropicus strain NCTC 8141 16S ribosomal RNA gene, partial sequenceAY3629241356ena758

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pasteurella pneumotropica DSM 214031122936.3wgspatric1122936
66792Pasteurella pneumotropica strain ATCC 35149758.7wgspatric758
66792Rodentibacter pneumotropicus ATCC 351492585428040draftimg758
66792Rodentibacter pneumotropicus DSM 214032515154191draftimg1122936
67770Rodentibacter pneumotropicus DSM 21403 DSM 21403GCA_000379905scaffoldncbi1122936
67770Rodentibacter pneumotropicus ATCC 35149GCA_000730685contigncbi758
66792Clostridioides difficile -GCA_900002555scaffoldpatric1496
66792Streptococcus pneumoniae 2842STDY5881865GCA_900024295scaffoldpatric1313

GC content

@refGC-contentmethod
4324340
1568840sequence analysis

External links

@ref: 15688

culture collection no.: DSM 21403, ATCC 35149, CCUG 12398, CIP 66.16, JCM 14074, LMG 4224, NCTC 8141, MCCM 00234, BCRC 11902

straininfo link

@refpassport
20218http://www.straininfo.net/strains/52970
20218http://www.straininfo.net/strains/52972
20218http://www.straininfo.net/strains/234448
20218http://www.straininfo.net/strains/699452
20218http://www.straininfo.net/strains/52969
20218http://www.straininfo.net/strains/52976

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Enzymology15897620Identification procedure for Pasteurella pneumotropica in microbiologic monitoring of laboratory animals.Hayashimoto N, Aiba T, Itoh K, Kato M, Kawamoto E, Kiyokawa S, Morichika Y, Muraguchi T, Narita T, Okajima Y, Takakura A, Itoh TExp Anim10.1538/expanim.54.1232005Animals, Animals, Laboratory/*microbiology, Bacteriological Techniques, Cricetinae, Guinea Pigs, Japan, Mice, Pasteurella pneumotropica/genetics/*isolation & purification, Polymerase Chain Reaction, Rabbits, RatsPhylogeny
Phylogeny16187154Genetic diversity on 16S rDNA sequence and phylogenic tree analysis in Pasteurella pneumotropica strains isolated from laboratory animals.Hayashimoto N, Takakura A, Itoh TCurr Microbiol10.1007/s00284-005-4541-62005Animals, Animals, Laboratory/*microbiology, Cricetinae, DNA, Bacterial/analysis, DNA, Ribosomal/*analysis, *Genetic Variation, Guinea Pigs, Mice, Molecular Sequence Data, Pasteurella/*classification/genetics/isolation & purification, Phylogeny, RNA, Ribosomal, 16S/*analysis/genetics, Rabbits, Rats, Sequence AnalysisGenetics
Phylogeny17430628Ultrastructural characteristics of the external surfaces of Pasteurella pneumotropica from mice and Pasteurella multocida from rabbits.Kawamoto E, Okiyama E, Sasaki H, Sawada T, Mikazuki K, Ueshiba HLab Anim10.1258/0023677077803780872007Animals, Cell Membrane/ultrastructure, Mice/*microbiology, Pasteurella multocida/isolation & purification/*ultrastructure, Pasteurella pneumotropica/isolation & purification/*ultrastructure, Rabbits/*microbiology, Species SpecificityEnzymology
18256519Experimental infection studies of Pasteurella pneumotropica and V-factor dependent Pasteurellaceae for F344-rnu rats.Hayashimoto N, Yasuda M, Ueno M, Goto K, Takakura AExp Anim10.1538/expanim.57.572008Animals, Female, Immunologic Deficiency Syndromes/veterinary, Pasteurella pneumotropica/*pathogenicity, Pasteurellaceae/*pathogenicity, Pasteurellaceae Infections/microbiology/*veterinary, Rats, *Rats, Inbred F344, Rats, Mutant Strains, *Rodent Diseases/microbiology
Metabolism19363112Identification and characterization of hemolysin-like proteins similar to RTX toxin in Pasteurella pneumotropica.Sasaki H, Kawamoto E, Tanaka Y, Sawada T, Kunita S, Yagami KJ Bacteriol10.1128/JB.01527-082009Amino Acid Sequence, Animals, Bacterial Proteins/genetics/metabolism/*pharmacology, Blotting, Southern, Erythrocytes/drug effects, Escherichia coli/genetics/metabolism, Hemoglobins/analysis, Hemolysin Proteins/genetics/metabolism/*pharmacology, Hemolysis/drug effects, Mice, Molecular Sequence Data, Operon/genetics, Pasteurella pneumotropica/genetics/*metabolism, Polymerase Chain Reaction, Rats, Recombinant Proteins/genetics/metabolism/pharmacology, Sequence Analysis, DNA, SheepPathogenicity
Enzymology21410992Molecular and virulence characteristics of an outer membrane-associated RTX exoprotein in Pasteurella pneumotropica.Sasaki H, Ishikawa H, Sato T, Sekiguchi S, Amao H, Kawamoto E, Matsumoto T, Shirama KBMC Microbiol10.1186/1471-2180-11-552011Animals, Bacterial Outer Membrane Proteins/genetics/isolation & purification/metabolism/toxicity, Bacterial Toxins/*genetics/isolation & purification/metabolism/*toxicity, Cell Line, DNA, Bacterial/chemistry/genetics, Erythrocytes/drug effects, Hemagglutination, Macrophages/drug effects, Mice, Molecular Sequence Data, Pasteurella pneumotropica/*genetics/metabolism/*pathogenicity, Protein Transport, Recombinant Proteins/genetics/isolation & purification/toxicity, Sequence Alignment, Sequence Analysis, DNA, Sheep, VirulencePhylogeny
Pathogenicity22041283Pathogenicity of Pasteurella pneumotropica in immunodeficient NOD/ShiJic-scid/Jcl and immunocompetent Crlj:CD1 (ICR) mice.Kawamoto E, Sasaki H, Okiyama E, Kanai T, Ueshiba H, Ohnishi N, Sawada T, Hayashimoto N, Takakura A, Itoh TExp Anim10.1538/expanim.60.4632011Animals, Disease Models, Animal, Host-Pathogen Interactions, *Immunocompetence, *Immunocompromised Host, Mice, Mice, Inbred ICR/*immunology/*microbiology, Mice, Inbred NOD/*immunology/*microbiology, Mice, SCID/*immunology/*microbiology, Pasteurella Infections/*immunology/*microbiology/pathology/physiopathology, Pasteurella pneumotropica/isolation & purification/*pathogenicity, Respiratory System/microbiology/pathology, VirulenceEnzymology
Genetics25103762Draft Genome Sequence of the Rodent Opportunistic Pathogen Pasteurella pneumotropica ATCC 35149T.Sasaki H, Ishikawa H, Asano R, Ueshiba H, Matsumoto T, Boot R, Kawamoto EGenome Announc10.1128/genomeA.00771-142014
Phylogeny27402782Identification of a virulence determinant that is conserved in the Jawetz and Heyl biotypes of [Pasteurella] pneumotropica.Sasaki H, Ishikawa H, Terayama H, Asano R, Kawamoto E, Ishibashi H, Boot RPathog Dis10.1093/femspd/ftw0662016Genes, Bacterial, Pasteurella Infections/*microbiology, Pasteurella pneumotropica/classification/*pathogenicity/*physiology, Virulence/genetics, *Virulence Factors/genetics
Phylogeny28629498Rodentibacter gen. nov. including Rodentibacter pneumotropicus comb. nov., Rodentibacter heylii sp. nov., Rodentibacter myodis sp. nov., Rodentibacter ratti sp. nov., Rodentibacter heidelbergensis sp. nov., Rodentibacter trehalosifermentans sp. nov., Rodentibacter rarus sp. nov., Rodentibacter mrazii and two genomospecies.Adhikary S, Nicklas W, Bisgaard M, Boot R, Kuhnert P, Waberschek T, Aalbaek B, Korczak B, Christensen HInt J Syst Evol Microbiol10.1099/ijsem.0.0018662017Animals, Bacterial Typing Techniques, DNA, Bacterial/genetics, Genes, Bacterial, Nucleic Acid Hybridization, Pasteurellaceae/*classification/genetics/isolation & purification, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rodentia/*microbiology, Sequence Analysis, DNATranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
15688Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21403)https://www.dsmz.de/collection/catalogue/details/culture/DSM-21403
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
37613Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/10238
43243Sadhana Adhikary, Werner Nicklas, Magne Bisgaard, Ron Boot, Peter Kuhnert, Torsten Waberschek, Bent Aalbaek, Bozena Korczak and Henrik Christensen10.1099/ijsem.0.001866Rodentibacter gen. nov. including Rodentibacter pneumotropicus comb. nov., Rodentibacter heylii sp. nov., Rodentibacter myodis sp. nov., Rodentibacter ratti sp. nov., Rodentibacter heidelbergensis sp. nov., Rodentibacter trehalosifermentans sp. nov., Rodentibacter rarus sp. nov., Rodentibacter mrazii and two genomospeciesIJSEM 67: 1793-1806 201728629498
45690Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 12398)https://www.ccug.se/strain?id=12398
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/
68368Automatically annotated from API 20E
68377Automatically annotated from API NH
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)