Strain identifier

BacDive ID: 2133

Type strain: Yes

Species: Campylobacter gracilis

Strain history: ATCC 33236 <-- A. C. R. Tanner FDC 1084.

NCBI tax ID(s): 824 (species)

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General

@ref: 8151

BacDive-ID: 2133

DSM-Number: 19528

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

description: Campylobacter gracilis DSM 19528 is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from human gingival sulcus.

NCBI tax id

  • NCBI tax id: 824
  • Matching level: species

strain history

@refhistory
8151<- JCM; JCM 8538 <- ATCC; ATCC 33236 <- A. C. R. Tanner; FDC 1084 (Bacteroides gracilis)
67770ATCC 33236 <-- A. C. R. Tanner FDC 1084.

doi: 10.13145/bacdive2133.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Epsilonproteobacteria
  • order: Campylobacterales
  • family: Campylobacteraceae
  • genus: Campylobacter
  • species: Campylobacter gracilis
  • full scientific name: Campylobacter gracilis (Tanner et al. 1981) Vandamme et al. 1995
  • synonyms

    • @ref: 20215
    • synonym: Bacteroides gracilis

@ref: 8151

domain: Bacteria

phylum: Proteobacteria

class: Epsilonproteobacteria

order: Campylobacterales

family: Campylobacteraceae

genus: Campylobacter

species: Campylobacter gracilis

full scientific name: Campylobacter gracilis (Tanner et al. 1981) Vandamme et al. 1995

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • gram stain: negative
  • confidence: 99.992

colony morphology

  • @ref: 8151
  • incubation period: 3-7 days

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8151COLUMBIA 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
8151CHOPPED MEAT MEDIUM (DSMZ Medium 78)yeshttps://mediadive.dsmz.de/medium/78Name: CHOPPED MEAT MEDIUM (DSMZ Medium 78) Composition: Ground beef 500.0 g/l Casitone 30.0 g/l Agar 15.0 g/l Ethanol 9.5 g/l (optional) K2HPO4 5.0 g/l Yeast extract 5.0 g/l L-Cysteine HCl 0.5 g/l Haemin 0.005 g/l (optional) Resazurin 0.001 g/l Vitamin K3 0.0005 g/l (optional) Vitamin K1 (optional) NaOH (optional) Distilled water
8151BTU MEDIUM (DSMZ Medium 413)yeshttps://mediadive.dsmz.de/medium/413Name: BTU MEDIUM (DSMZ Medium 413) Composition: Ground beef 500.0 g/l Casitone 30.0 g/l Agar 15.0 g/l K2HPO4 5.0 g/l Yeast extract 5.0 g/l Na-formiate 1.8 g/l Na-fumarate 1.8 g/l L-Cysteine HCl 0.5 g/l Ethanol 0.19 g/l Vitamin K3 0.05 g/l Hemin 0.005 g/l Resazurin 0.001 g/l Vitamin K1 NaOH Distilled water

culture temp

@refgrowthtypetemperaturerange
8151positivegrowth37mesophilic
48907positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
8151anaerobe
48907anaerobe

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 99.999

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6837316199urea-hydrolysis
68373606565hippurate-hydrolysis
6837317634D-glucose-assimilation
6837330031succinate-assimilation
6837330089acetate-assimilation
6837317272propionate-assimilation
6837316947citrate-assimilation

antibiotic resistance

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

enzymes

@refvalueactivityec
68373catalase+1.11.1.6
68373alkaline phosphatase-3.1.3.1
68373L-aspartate arylamidase+3.4.11.21
68373pyrrolidonyl arylamidase-3.4.19.3
68373gamma-glutamyltransferase-2.3.2.2
68373urease-3.5.1.5

fatty acid profile

  • @reffatty acidpercentageECL
    48907C10:00.410
    48907C12:012.712
    48907C13:00.213
    48907C14:015.214
    48907C16:011.116
    48907C18:00.318
    48907C13:0 3OH/C15:1 i I/H114.469
    48907C13:0 ISO 2OH0.613.814
    48907C13:1 at 12-130.212.931
    48907C14:0 3OH/C16:1 ISO I4.615.485
    48907C16:0 3OH2.517.52
    48907C16:0 aldehyde414.949
    48907C16:1 ω7c5.215.819
    48907C17:1 ISO I/C16:0 DMA19.916.481
    48907C18:1 ω7c /12t/9t12.917.824
    48907C18:1 ω7c DMA5.318.282
    48907C18:2 ω6,9c/C18:0 ANTE0.417.724
    48907C19:1 ISO I0.518.473
    48907Unidentified0.212.471
    48907Unidentified0.413.933
    48907Unidentified0.114.779
    48907Unidentified0.214.889
    48907Unidentified0.916.286
    48907Unidentified1.516.804
  • type of FA analysis: whole cell analysis
  • method/protocol: CCUG
  • @reffatty acidpercentageECL
    48907C12:013.712
    48907C14:016.614
    48907C16:012.616
    48907C14:0 3OH/C16:1 ISO I4.815.485
    48907C16:0 aldehyde4.514.949
    48907C16:1 ω7c4.915.819
    48907C17:1 ISO I/C16:0 DMA22.616.481
    48907C18:1 ω7c /12t/9t14.517.824
    48907C18:1 ω7c DMA5.818.282
  • type of FA analysis: whole cell analysis
  • method/protocol: CCUG

API CAM

@refURENITESTHIPGGTTTCPYRAArgAAspAPALH2SGLUSUTNALCFZACEPROPMLTCITEROCAT
8151--+-----+-+------+/---+
8151-+---+--+-+---------+
8151-------+/-+-----------

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentsampling date
8151human gingival sulcusUSAUSANorth America
48907Human gingival sulcusUSAUSANorth America1977
67770Human gingival sulcus

isolation source categories

Cat1Cat2Cat3
#Host#Human
#Host Body-Site#Oral cavity and airways#Gingiva
#Infection#Patient
#Host Body-Site#Other#Wound

taxonmaps

  • @ref: 69479
  • File name: preview.99_1796.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15775;96_1019;97_1189;98_1420;99_1796&stattab=map
  • Last taxonomy: Campylobacter gracilis subclade
  • 16S sequence: JX912515
  • Sequence Identity:
  • Total samples: 49179
  • soil counts: 708
  • aquatic counts: 933
  • animal counts: 47229
  • plant counts: 309

Safety information

risk assessment

  • @ref: 8151
  • biosafety level: 2
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Campylobacter gracilis strain ATCC 33236 16S ribosomal RNA (rrs) gene, partial sequenceDQ1741681341ena824
20218Bacteroides gracilis, complete 16S ribosomal RNAL043201450ena824
8151Campylobacter gracilis strain ATCC 33236 16S ribosomal RNA gene, partial sequenceJX9125151435ena824
67770Campylobacter gracilis gene for 16S ribosomal RNA, partial sequence, strain: JCM 8538AB9718151474ena824

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Campylobacter gracilis ATCC 33236GCA_001190745completencbi824
66792Campylobacter gracilis RM3268553220.3wgspatric553220
66792Campylobacter gracilis strain ATCC 33236824.5completepatric824
66792Campylobacter gracilis strain NCTC12738824.36wgspatric824
66792Campylobacter gracilis ATCC 332362645727670completeimg824
66792Campylobacter gracilis NCTC 127382808606742draftimg824
66792Campylobacter gracilis ATCC 33236645951857draftimg553220
67770Campylobacter gracilis NCTC12738GCA_900446335contigncbi824
66792Campylobacter gracilis strain FDAARGOS_1548824.194completepatric824
66792Campylobacter gracilis strain FDAARGOS_1548824.193completepatric824

GC content

@refGC-content
815144
6777045

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno82no
motileno87.435no
flagellatedno90.841no
gram-positiveno97.68no
anaerobicyes84.216no
aerobicno97.929yes
halophileno80.713no
spore-formingno97.218no
thermophileno95.106yes
glucose-utilno89.211yes
glucose-fermentno84.425no

External links

@ref: 8151

culture collection no.: DSM 19528, ATCC 33236, JCM 8538, CCUG 27720, NCTC 12738, FDC 1084, KCTC 15224

straininfo link

  • @ref: 71761
  • straininfo: 45949

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny6490858Comparison of strains of gram-negative, anaerobic, agar-corroding rods isolated from soft tissue infections in cats and dogs with type strains of Bacteroides gracilis, Wolinella recta, Wolinella succinogenes, and Campylobacter concisus.Love DN, Jones RF, Bailey M, Calverley AJ Clin Microbiol10.1128/jcm.20.4.747-750.19841984Agar, Animals, Bacteria/classification/*isolation & purification, Bacterial Infections/microbiology/*veterinary, Bacteroides/*isolation & purification, Campylobacter/*isolation & purification, Cat Diseases/*microbiology, Cats, Dog Diseases/*microbiology, DogsEnzymology
Genetics26383656Complete Genome Sequence of Campylobacter gracilis ATCC 33236T.Miller WG, Yee EGenome Announc10.1128/genomeA.01087-152015

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
8151Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19528)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19528
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
48907Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 27720)https://www.ccug.se/strain?id=27720
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/
68373Automatically annotated from API CAM
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)
71761Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID45949.1StrainInfo: A central database for resolving microbial strain identifiers