Strain identifier

BacDive ID: 132605

Type strain: Yes

Species: Cutibacterium namnetense

Strain history: <- S. Corvec, Nantes Univ. Hospital, Bacteriology Unit, France <- P. Bremer

NCBI tax ID(s): 1574624 (species)

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General

@ref: 24394

BacDive-ID: 132605

DSM-Number: 29427

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-positive, pleomorphic-shaped, colony-forming, human pathogen

description: Cutibacterium namnetense DSM 29427 is an anaerobe, mesophilic, Gram-positive human pathogen that forms circular colonies and was isolated from surgical samples of human bone infection.

NCBI tax id

  • NCBI tax id: 1574624
  • Matching level: species

strain history

  • @ref: 24394
  • history: <- S. Corvec, Nantes Univ. Hospital, Bacteriology Unit, France <- P. Bremer

doi: 10.13145/bacdive132605.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Propionibacteriales
  • family: Propionibacteriaceae
  • genus: Cutibacterium
  • species: Cutibacterium namnetense
  • full scientific name: Cutibacterium namnetense (Aubin et al. 2016) Nouioui et al. 2018

  • synonyms

    • @ref: 20215
    • synonym: Propionibacterium namnetense

@ref: 24394

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Propionibacteriaceae

genus: Cutibacterium

species: Cutibacterium namnetense

full scientific name: Cutibacterium namnetense (Aubin et al. 2016) Nouioui et al. 2018

type strain: yes

Morphology

cell morphology

  • @ref: 43105
  • gram stain: positive
  • cell length: 1.5-7 µm
  • cell width: 0.7-0.8 µm
  • cell shape: pleomorphic-shaped
  • motility: no

colony morphology

@refcolony sizecolony colorcolony shapeincubation periodmedium used
431052 mmpale cream to orange-salmoncircular6 daysSchaedler blood agar
633262 days

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
43105Schaedler blood agaryes
24394PYG MEDIUM (MODIFIED) (DSMZ Medium 104)yeshttps://mediadive.dsmz.de/medium/104Name: PYG MEDIUM (modified) (DSMZ Medium 104) Composition: Yeast extract 10.0 g/l Peptone 5.0 g/l Trypticase peptone 5.0 g/l Beef extract 5.0 g/l Glucose 5.0 g/l L-Cysteine HCl x H2O 0.5 g/l NaHCO3 0.4 g/l NaCl 0.08 g/l K2HPO4 0.04 g/l KH2PO4 0.04 g/l MgSO4 x 7 H2O 0.02 g/l CaCl2 x 2 H2O 0.01 g/l Hemin 0.005 g/l Ethanol 0.0038 g/l Resazurin 0.001 g/l Tween 80 Vitamin K1 NaOH Distilled water

culture temp

@refgrowthtypetemperaturerange
43105positiveoptimum35mesophilic
43105positivegrowth20-42
63326positivegrowth37mesophilic
24394positivegrowth37mesophilic

culture pH

  • @ref: 43105
  • ability: positive
  • type: growth
  • pH: 4.0-10.0
  • PH range: alkaliphile

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
43105anaerobe
43105aerotolerant
63326anaerobe

spore formation

  • @ref: 43105
  • spore formation: no

halophily

  • @ref: 43105
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 4 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4310517632nitrate+reduction
4310517634D-glucose+assimilation
4310516988D-ribose+assimilation
431055291gelatin+hydrolysis
4310517716lactose-assimilation
4310517306maltose-assimilation
4310516899D-mannitol-assimilation
4310517992sucrose-assimilation
431054853esculin-hydrolysis
43105506227N-acetylglucosamine+respiration
4310563154N-acetyl-beta-D-mannosamine+respiration
4310517057cellobiose+respiration
4310523652dextrin+respiration
4310517113erythritol+respiration
4310515824D-fructose+respiration
4310512936D-galactose+respiration
4310515903beta-d-glucose+respiration
4310514314D-glucose 6-phosphate+respiration
4310517754glycerol+respiration
4310561993maltotriose+respiration
4310516024D-mannose+respiration
43105320055methyl beta-D-glucopyranoside+respiration
4310517540methyl beta-D-galactoside+respiration
4310518394palatinose+respiration
4310517924D-sorbitol+respiration
4310517992sucrose+respiration
4310527082trehalose+respiration
4310532528turanose+respiration
43105167632-oxobutanoate+respiration
4310524996lactate+respiration
4310516651(S)-lactate+respiration
4310515361pyruvate+respiration
4310551850methyl pyruvate+respiration
43105143136succinamate+respiration
4310530031succinate+respiration
4310575146monomethyl succinate+respiration
4310521217L-alaninamide+respiration
43105172562-deoxyadenosine+respiration
4310517748thymidine+respiration
4310516704uridine+respiration
6838016199urea+hydrolysis
6838029016arginine-hydrolysis
6838016024D-mannose-fermentation
6838016634raffinose-fermentation
6838029985L-glutamate-degradation
6838017632nitrate+reduction
6838027897tryptophan+energy source

metabolite production

@refChebi-IDmetaboliteproduction
4310535581indoleyes
6838035581indoleyes

metabolite tests

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

enzymes

@refvalueactivityec
43105N-acetyl-beta-glucosaminidase+3.2.1.52
43105alpha-glucosidase+3.2.1.20
43105beta-galactosidase+3.2.1.23
43105alanine arylamidase+3.4.11.2
43105glycin arylamidase+
43105serine arylamidase+
43105alkaline phosphatase-3.1.3.1
43105alpha-arabinosidase-3.2.1.55
43105arginine arylamidase-
43105arginine dihydrolase-3.5.3.6
43105beta-glucuronidase-3.2.1.31
431056-phospho-beta-galactosidase-3.2.1.85
43105glutamate decarboxylase-4.1.1.15
43105alpha-fucosidase-3.2.1.51
43105histidine arylamidase-
43105leucine arylamidase-3.4.11.1
43105phenylalanine arylamidase-
43105proline-arylamidase-3.4.11.5
43105pyroglutamic acid arylamidase-
43105tyrosine arylamidase-
43105urease-3.5.1.5
43105catalase+1.11.1.6
43105alpha-galactosidase+/-3.2.1.22
43105pyrazinamidase+3.5.1.B15
43105pyrrolidonyl arylamidase-3.4.19.3
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
68380beta-Galactosidase 6-phosphate-
68380alpha-galactosidase-3.2.1.22
68380arginine dihydrolase-3.5.3.6
68380urease+3.5.1.5

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    43105C15:0 iso57.6
    43105C15:0 anteiso12
    43105C17:0 iso14.7
  • type of FA analysis: whole cell analysis
  • incubation medium: brain heart infusion agar (Difco)
  • agar/liquid: agar
  • incubation temperature: 37
  • incubation time: 2
  • system: MIS MIDI
  • instrument: Hewlett Packard HP 5890
  • cutoff value:

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
24394+--+/--+/---------++--+-----++--+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling date
24394surgical samples of human bone infectionNantesFranceFRAEurope
43105clinical bone samples recovered from a 21-year-old male patient during the surgical treatment of a tibia external fixator infectionNantesFranceFRAEurope
63326Human bone infection,tissue sampleNantesFranceFRAEurope2013-07-25

isolation source categories

Cat1Cat2Cat3
#Infection#Disease
#Host#Human
#Host Body-Site#Other#Bone

taxonmaps

  • @ref: 69479
  • File name: preview.99_5860.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15360;96_410;97_465;98_535;99_5860&stattab=map
  • Last taxonomy: Cutibacterium namnetense
  • 16S sequence: KM507346
  • Sequence Identity:
  • Total samples: 9006
  • soil counts: 79
  • aquatic counts: 295
  • animal counts: 8581
  • plant counts: 51

Safety information

risk assessment

  • @ref: 24394
  • pathogenicity human: yes, in single cases
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 24394
  • description: [Propionibacterium] namnetense strain NTS 31307302 16S ribosomal RNA gene, partial sequence
  • accession: KM507346
  • length: 1424
  • database: ena
  • NCBI tax ID: 1574624

Genome sequences

  • @ref: 66792
  • description: Propionibacterium namnetense strain NTS 31307302
  • accession: 1574624.3
  • assembly level: wgs
  • database: patric
  • NCBI tax ID: 1574624

GC content

@refGC-contentmethod
4310559.7
2439459.7high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno95.226no
gram-positiveyes92.277yes
anaerobicyes61.651no
aerobicno86.411yes
halophileno81.721no
spore-formingno90.005yes
glucose-utilyes91.301yes
flagellatedno98.495yes
thermophileno79.246yes
glucose-fermentyes77.448no

External links

@ref: 24394

culture collection no.: DSM 29427, CCUG 66358, NTS 31307302

straininfo link

  • @ref: 90920
  • straininfo: 401705

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny27259292Propionibacterium namnetense sp. nov., isolated from a human bone infection.Aubin GG, Bemer P, Kambarev S, Patel NB, Lemenand O, Caillon J, Lawson PA, Corvec SInt J Syst Evol Microbiol10.1099/ijsem.0.0012042016Bacterial Typing Techniques, Base Composition, Bone Diseases, Infectious/*microbiology, DNA, Bacterial/genetics, Fatty Acids/chemistry, France, Humans, Male, Nucleic Acid Hybridization, *Phylogeny, Propionibacterium/*classification/genetics/isolation & purification, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Young AdultPathogenicity
Genetics27516511Draft Genome Sequence of Highly Rifampin-Resistant Propionibacterium namnetense NTS 31307302T Isolated from a Patient with a Bone Infection.Aubin GG, Kambarev S, Bemer P, Lawson PA, Corvec SGenome Announc10.1128/genomeA.00819-162016Phylogeny

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
24394Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-29427Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 29427)
43105Guillaume Ghislain Aubin, Pascale Bemer, Stanimir Kambarev, Nisha B. Patel, Olivier Lemenand, Jocelyne Caillon, Paul A. Lawson, Stephane CorvecPropionibacterium namnetense sp. nov., isolated from a human bone infection10.1099/ijsem.0.001204IJSEM 66: 3393-3399 201627259292
63326Curators of the CCUGhttps://www.ccug.se/strain?id=66358Culture Collection University of Gothenburg (CCUG) (CCUG 66358)
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
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
90920Reimer, 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-ID401705.1