Strain identifier

BacDive ID: 2234

Type strain: Yes

Species: Cardiobacterium valvarum

Strain history: CIP <- 2004, CCUG <- 2003, X. Han, M.D. Anderson Cancer Center, Houston, Texas, USA: strain MDA 3079

NCBI tax ID(s): 194702 (species)

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General

@ref: 6817

BacDive-ID: 2234

DSM-Number: 17211

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

description: Cardiobacterium valvarum DSM 17211 is a microaerophile, mesophilic, Gram-negative bacterium that was isolated from Human blood, patient with vegetation on aortic valve.

NCBI tax id

  • NCBI tax id: 194702
  • Matching level: species

strain history

@refhistory
6817<- CCUG; CCUG 48245 <- X. Y. Han, Univ. Texas; MDA 3079
123791CIP <- 2004, CCUG <- 2003, X. Han, M.D. Anderson Cancer Center, Houston, Texas, USA: strain MDA 3079

doi: 10.13145/bacdive2234.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Cardiobacteriales
  • family: Cardiobacteriaceae
  • genus: Cardiobacterium
  • species: Cardiobacterium valvarum
  • full scientific name: Cardiobacterium valvarum Han et al. 2004

@ref: 6817

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Cardiobacteriales

family: Cardiobacteriaceae

genus: Cardiobacterium

species: Cardiobacterium valvarum

full scientific name: Cardiobacterium valvarum Han et al. 2004 emend. Han and Falsen 2005

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480negative99.998
123791negativerod-shapedno

colony morphology

@refincubation periodhemolysis ability
580502-3 days
1237911

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6817COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium693.pdf
6817FASTIDIOUS ANAEROBE AGAR (DSMZ Medium 1203)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium1203.pdf
40022MEDIUM 6 - Columbia agar with 10 % horse bloodyesDistilled water make up to (1000.000 ml);Columbia agar (39.000 g);Horseblood (100.000 ml)
123791CIP Medium 6yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=6

culture temp

@refgrowthtypetemperaturerange
6817positivegrowth37mesophilic
40022positivegrowth37mesophilic
58050positivegrowth37mesophilic
123791positivegrowth25-37mesophilic
123791nogrowth10psychrophilic
123791nogrowth41thermophilic
123791nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
6817microaerophile
58050microaerophile

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 99.995

halophily

  • @ref: 123791
  • salt: NaCl
  • growth: no
  • tested relation: growth
  • concentration: 6.5 %

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 2-ketogluconate-builds acid from
68371gluconate-builds acid from24265
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose-builds acid from18287
68371D-fucose-builds acid from28847
68371D-lyxose-builds acid from62318
68371turanose-builds acid from32528
68371gentiobiose-builds acid from28066
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
68371cellobiose-builds acid from17057
68371salicin-builds acid from17814
68371esculin-builds acid from4853
68371arbutin-builds acid from18305
68371amygdalin-builds acid from27613
68371N-acetylglucosamine-builds acid from59640
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
68371D-galactose-builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose-builds acid from65327
68371L-arabinose-builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754
123791esculin-hydrolysis4853
123791hippurate+hydrolysis606565
123791nitrate-reduction17632
123791nitrite+reduction16301
68373urea-hydrolysis16199
68373nitrate-reduction17632
68373hippurate-hydrolysis606565
68373D-glucose-assimilation17634
68373acetate-assimilation30089
68373propionate-assimilation17272
68373malate-assimilation25115
68373citrate-assimilation16947
68377D-glucose+builds acid from17634
68377D-fructose+builds acid from15824
68377maltose+builds acid from17306
68377ornithine-degradation18257

antibiotic resistance

@refChEBImetaboliteis antibioticis sensitivesensitivity conc.
6837348923erythromycinyesyes14 µg
68373474053cefazolinyesyes224 µg
68373100147nalidixic acidyesyes84 µg

metabolite production

  • @ref: 68373
  • Chebi-ID: 16136
  • metabolite: hydrogen sulfide
  • production: no

enzymes

@refvalueactivityec
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
68377beta-galactosidase-3.2.1.23
68377ornithine decarboxylase-4.1.1.17
68373catalase-1.11.1.6
68373alkaline phosphatase+3.1.3.1
68373L-aspartate arylamidase+3.4.11.21
68373L-arginine arylamidase+
68373pyrrolidonyl arylamidase+3.4.19.3
68373gamma-glutamyltransferase-2.3.2.2
68373esterase+
68373urease-3.5.1.5
123791oxidase+
123791beta-galactosidase-3.2.1.23
123791alcohol dehydrogenase-1.1.1.1
123791catalase-1.11.1.6
123791gamma-glutamyltransferase-2.3.2.2
123791lysine decarboxylase-4.1.1.18
123791ornithine decarboxylase-4.1.1.17

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
123791-+++-+--+-++---+----

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
123791----+/------+/-+/-+/-----+/-+/---------+/---+/-+/----+/------+/-------+/-

API CAM

@refURENITESTHIPGGTTTCPYRAArgAAspAPALH2SGLUSUTNALCFZACEPROPMLTCITEROCAT
6817--+---++++--+--------
6817--+--+++++-----------

API NH

@refPENGLUFRUMALSACODCURELIPPALbeta GALProAGGTIND
6817-++++---+-+++
6817++++--+/-+---+-
6817-++++--+/-+---+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitudesampling dateisolation date
6817Human blood, patient with vegetation on aortic valveHoustonUSAUSANorth America29.7499-95.3584
58050Human blood,endocarditis,ruptures cerebr. aneurysmTexas,HoustonUSAUSANorth America2001-11-15
123791Human, BloodHouston, TexasUnited States of AmericaUSANorth America2001

isolation source categories

Cat1Cat2Cat3
#Infection#Patient
#Host#Human
#Host Body-Site#Organ#Heart
#Host Body Product#Fluids#Blood

taxonmaps

  • @ref: 69479
  • File name: preview.99_14343.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_183;96_7393;97_8871;98_10875;99_14343&stattab=map
  • Last taxonomy: Cardiobacterium
  • 16S sequence: AF506987
  • Sequence Identity:
  • Total samples: 28557
  • soil counts: 418
  • aquatic counts: 546
  • animal counts: 27464
  • plant counts: 129

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
68172Risk group (German classification)
1237912Risk group (French classification)

Sequence information

16S sequences

  • @ref: 6817
  • description: Cardiobacterium valvarum 16S ribosomal RNA gene, partial sequence
  • accession: AF506987
  • length: 1493
  • database: ena
  • NCBI tax ID: 194702

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Cardiobacterium valvarum NCTC13294GCA_900460955contigncbi194702
66792Cardiobacterium valvarum strain NCTC13294194702.3wgspatric194702
66792Cardiobacterium valvarum NCTC 132942808606637draftimg194702

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno86no
motileno85.44no
gram-positiveno98.221no
anaerobicno94.967no
aerobicno95.845yes
halophileno56.429no
spore-formingno97.985no
glucose-utilyes62.251yes
flagellatedno95.53no
thermophileno98.835yes
glucose-fermentno56.174no

External links

@ref: 6817

culture collection no.: DSM 17211, ATCC BAA 694, CCUG 48245, CIP 108480, MDA 3079, NCTC 13294

straininfo link

  • @ref: 71796
  • straininfo: 134280

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
6817Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17211)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17211
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
40022Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6223
58050Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 48245)https://www.ccug.se/strain?id=48245
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 updatesNucleic Acids Res. 49: D498-D508 202033211880
68371Automatically annotated from API 50CH acid
68373Automatically annotated from API CAM
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)
71796Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID134280.1StrainInfo: A central database for resolving microbial strain identifiers
123791Curators of the CIPCollection of Institut Pasteur (CIP 108480)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108480