Strain identifier

BacDive ID: 3198

Type strain: Yes

Species: Corynebacterium appendicis

Strain history: CIP <- 2002, DSMZ <- A.F. Yassin, Bonn Univ., Bonn, Germany: strain IMMIB R-3491

NCBI tax ID(s): 1161099 (strain), 163202 (species)

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General

@ref: 11737

BacDive-ID: 3198

DSM-Number: 44531

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

description: Corynebacterium appendicis DSM 44531 is a microaerophile, mesophilic, Gram-positive human pathogen that was isolated from abdominal swab of a patient with appendicitis.

NCBI tax id

NCBI tax idMatching level
163202species
1161099strain

strain history

@refhistory
11737<- A. F. Yassin, Univ. Bonn; IMMIB R-3491
67770DSM 44531 <-- A. F. Yassin IMMIB R-3491.
116424CIP <- 2002, DSMZ <- A.F. Yassin, Bonn Univ., Bonn, Germany: strain IMMIB R-3491

doi: 10.13145/bacdive3198.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Mycobacteriales
  • family: Corynebacteriaceae
  • genus: Corynebacterium
  • species: Corynebacterium appendicis
  • full scientific name: Corynebacterium appendicis Yassin et al. 2002

@ref: 11737

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Corynebacteriaceae

genus: Corynebacterium

species: Corynebacterium appendicis

full scientific name: Corynebacterium appendicis Yassin et al. 2002 emend. Nouioui et al. 2018

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotility
23187positivepleomorphic-shapedno
116424positiverod-shapedno

colony morphology

@refcolony colorincubation periodmedium usedtype of hemolysiscolony size
20069Beige (1001)10-14 daysISP 2
20069Beige (1001)10-14 daysISP 3
20069Beige (1001)10-14 daysISP 4
20069Beige (1001)10-14 daysISP 5
20069Beige (1001)10-14 daysISP 6
20069Beige (1001)10-14 daysISP 7
23187greyish2 daysColumbia blood agar supplemented with 5% sheep bloodgamma<0.5 mm
116424

multicellular morphology

@refforms multicellular complexmedium name
20069noISP 2
20069noISP 3
20069noISP 4
20069noISP 5
20069noISP 6
20069noISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11737TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://mediadive.dsmz.de/medium/535Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
11737COLUMBIA 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
20069ISP 2yesName: ISP 2 / Yeast Malt Agar (5265); 5265 Composition Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l Agar 15.0 g/l Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.0 Usage: Maintenance and Taxonomy Organisms: All Actinomycetes
20069ISP 3yesName: ISP 3; 5315 Composition Dog oat flakes 20.0 g/l Trace element solution (5314) 2.5 ml/l Agar 18.0 g/l Preparation: Oat flakes are cooked for 20 minutes, trace element solution and agar are added (in the case of non rolled oat flakes the suspension has to bee filtrated). Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.8 Usage: Maintenance and taxonomy (e.g. SEM As liquid medium for metabolite production) Organisms: All Actinomycetes Trace element solution 5314 Name: Trace element solution 5314; 5314 Composition CaCl2 x H2O 3.0 g/l Fe-III-citrate 1.0 g/l MnSO4 0.2 g/l ZnCl2 0.1 g/l CuSO4 x 5 H2O 0.025 g/l Sodium tetra borate 0.2 g/l CoCl2 x 6 H2O 0.004 g/l Sodium molybdate 0.01 g/l Preparation: Use double destillated water. Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Trace element solution for different media Organisms:
20069ISP 4yesName: ISP 4; DSM 547 Solution I: Difco soluble starch, 10.0 g. Make a paste of the starch with a small amount of cold distilled water and bring to a volume of 500 ml. Solution II: CaCO3 2.0 g K2HPO4 (anhydrous) 1.0 g MgSO4 x 7 H2O 1.0 g NaCl 1.0 g (NH4)2SO4 2.0 g Distilled water 500.0 ml Trace salt solution (see below) 1.0 ml The pH should be between 7.0 and 7.4. Do not adjust if it is within this range. Mix solutions I and II together. Add 20.0 g agar. Liquify agar by steaming at 100°C for 10 to 20 min. Trace element solution: FeSO4 x 7 H2O 0.1 g MnCl2 x 4 H2O 0.1 g ZnSO4 x 7 H2O 0.1 g Distilled water 100.0 ml
20069ISP 5yesName: ISP 5 (5323) Composition L-Asparagine 1.0 g/l Glycerol 10.0 g/l K2HPO4 1.0 g/l Salt solution (see preparation) 1.0 ml/l Agar 20.0 g/l Preparation: Salt solution 1.0 g FeSO4 x 7 H2O 1.0 g MnCl2 x 4 H2O 1.0 g ZNSO4 x 7 H2O in 100 ml water Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.2 Usage: Maintenance and taxonomy Organisms: All Actinomycetes
20069ISP 6yesName: ISP 6 (5318) Composition Peptone 15.0 g/l Proteose peptose 5.0 g/l Ferric ammonium citrate 0.5 g/l Sodium glycerophosphate 1.0 g/l Sodium thiosulfate 0.08 g/l Yeast extract 1.0 g/l Agar 15.0 g/l Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigments Organisms: All Actinomycetes
20069ISP 7yesName: ISP 7 (5322) Composition Glycerol 15.0 g/l L-Tyrosine 0.5 g/l L-Asparagine 1.0 g/l K2HPO4 0.5 g/l NaCl 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Trace element solution 5343 1.0 ml/l Agar 20.0 Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.3 Usage: Production of melanoid pigments Organisms: All Actinomycetes
23187Columbia blood agar supplemented with 5% sheep bloodyes
40563MEDIUM 45 - for Columbia agar with sheep bloodyesDistilled water make up to (1000.000 ml);Columbia agar (39.000 g);Sheepblood (100.000 ml)
116424CIP Medium 45yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=45

culture temp

@refgrowthtypetemperaturerange
20069positiveoptimum37mesophilic
11737positivegrowth37mesophilic
40563positivegrowth37mesophilic
58075positivegrowth37mesophilic
67770positivegrowth37mesophilic
116424positivegrowth25-45
116424nogrowth10psychrophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
11737microaerophile
23187facultative anaerobe
58075microaerophile

spore formation

  • @ref: 23187
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
116424NaClpositivegrowth0 %
116424NaClnogrowth2 %
116424NaClnogrowth4 %
116424NaClnogrowth6 %
116424NaClnogrowth8 %
116424NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2006917234glucose+
2006922599arabinose-
2006917992sucrose-
2006918222xylose-
2006917268myo-inositol+
2006929864mannitol+
2006928757fructose-
2006926546rhamnose-
2006916634raffinose-
2006962968cellulose+
2318722599arabinose-builds acid from
2318722605arabinitol-builds acid from
2318717057cellobiose-builds acid from
2318728087glycogen-builds acid from
2318715443inulin-builds acid from
2318717716lactose-builds acid from
2318729864mannitol-builds acid from
231876731melezitose-builds acid from
2318728053melibiose-builds acid from
2318727941pullulan-builds acid from
2318716634raffinose-builds acid from
2318726546rhamnose-builds acid from
2318733942ribose-builds acid from
2318717814salicin-builds acid from
2318730911sorbitol-builds acid from
2318717992sucrose-builds acid from
2318733954tagatose-builds acid from
2318727082trehalose-builds acid from
2318718222xylose-builds acid from
2318727897tryptophan-energy source
231874853esculin-hydrolysis
231875291gelatin-hydrolysis
23187606565hippurate-hydrolysis
2318728017starch-hydrolysis
2318717234glucose+builds acid from
2318717306maltose+builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837118287L-fucose-builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose-builds acid from
6837132528turanose-builds acid from
6837128066gentiobiose-builds acid from
6837117151xylitol-builds acid from
6837128087glycogen-builds acid from
6837128017starch-builds acid from
6837116634raffinose-builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837127082trehalose-builds acid from
6837117992sucrose-builds acid from
6837128053melibiose-builds acid from
6837117716lactose-builds acid from
6837117306maltose-builds acid from
6837117057cellobiose-builds acid from
6837117814salicin-builds acid from
683714853esculin-builds acid from
6837118305arbutin-builds acid from
6837127613amygdalin-builds acid from
6837159640N-acetylglucosamine-builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-builds acid from
6837116899D-mannitol-builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose-builds acid from
6837117266L-sorbose-builds acid from
6837116024D-mannose-builds acid from
6837115824D-fructose-builds acid from
6837117634D-glucose-builds acid from
6837112936D-galactose-builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose-builds acid from
6837116988D-ribose-builds acid from
6837130849L-arabinose-builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol-builds acid from
6836925115malate-assimilation
6836917128adipate-assimilation
6836927689decanoate-assimilation
6836924265gluconate-assimilation
6836917306maltose-assimilation
6836959640N-acetylglucosamine-assimilation
6836916899D-mannitol-assimilation
6836916024D-mannose-assimilation
6836930849L-arabinose-assimilation
6836917634D-glucose-assimilation
6836916199urea+hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate+reduction
11642416947citrate-carbon source
1164244853esculin-hydrolysis
116424606565hippurate-hydrolysis
11642417632nitrate-reduction
11642416301nitrite-reduction
11642445285pyrazinamide+hydrolysis
11642417632nitrate-respiration
6837917632nitrate-reduction
683794853esculin-hydrolysis
6837916199urea+hydrolysis
683795291gelatin-hydrolysis
6837917634D-glucose-fermentation
6837916988D-ribose-fermentation
6837965327D-xylose-fermentation
6837916899D-mannitol-fermentation
6837917306maltose-fermentation
6837917716lactose-fermentation
6837917992sucrose-fermentation
6837928087glycogen-fermentation

antibiotic resistance

  • @ref: 116424
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

@refChebi-IDmetaboliteproduction
2318735581indoleno
6836935581indoleno
11642435581indoleno

metabolite tests

@refChebi-IDmetaboliteindole testvoges-proskauer-testmethylred-test
2318735581indole-
6836935581indole-
11642415688acetoin-
11642417234glucose-

enzymes

@refvalueactivityec
23187acid phosphatase-3.1.3.2
23187alkaline phosphatase+3.1.3.1
23187alpha-fucosidase-3.2.1.51
23187alpha-galactosidase-3.2.1.22
23187alpha-glucosidase-3.2.1.20
23187alpha-mannosidase-3.2.1.24
23187arginine dihydrolase-3.5.3.6
23187beta-galactosidase-3.2.1.23
23187beta-glucosidase-3.2.1.21
23187beta-glucuronidase-3.2.1.31
23187catalase+1.11.1.6
23187chymotrypsin-3.4.4.5
23187cystine arylamidase-3.4.11.3
23187esterase (C 4)-
23187esterase lipase (C 8)-
23187glycyl tryptophan arylamidase-
23187leucine arylamidase-3.4.11.1
23187lipase (C 14)-
23187N-acetyl-beta-glucosaminidase-3.2.1.52
23187naphthol-AS-BI-phosphohydrolase-
23187nitrate reductase-1.7.99.4
23187pyrazinamidase+3.5.1.B15
23187pyroglutamic acid arylamidase-
23187pyrrolidonyl arylamidase-3.4.19.3
23187trypsin-3.4.21.4
23187tryptophan deaminase-4.1.99.1
23187urease+3.5.1.5
23187valine arylamidase-
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
68382acid phosphatase-3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382valine arylamidase-
68382lipase (C 14)-
68379gelatinase-
68379urease+3.5.1.5
68379beta-glucosidase-3.2.1.21
68379N-acetyl-beta-glucosaminidase-3.2.1.52
68379alpha-glucosidase-3.2.1.20
68379beta-galactosidase-3.2.1.23
68379beta-glucuronidase-3.2.1.31
68379alkaline phosphatase-3.1.3.1
68379pyrrolidonyl arylamidase-3.4.19.3
68379pyrazinamidase-3.5.1.B15
68369urease+3.5.1.5
68369arginine dihydrolase-3.5.3.6
116424oxidase-
116424beta-galactosidase-3.2.1.23
116424alcohol dehydrogenase-1.1.1.1
116424gelatinase-
116424amylase-
116424DNase-
116424caseinase-3.4.21.50
116424catalase+1.11.1.6
116424tween esterase-
116424gamma-glutamyltransferase+2.3.2.2
116424lecithinase-
116424lipase-
116424lysine decarboxylase-4.1.1.18
116424ornithine decarboxylase-4.1.1.17
116424phenylalanine ammonia-lyase-4.3.1.24
116424tryptophan deaminase-
116424urease+3.5.1.5

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
20069---------+---------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
20069-++-+-++-----------
11737+/--------------------
116424-++-+-----+---------

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPAC
11737+---++/-+/------------+/--

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
116424------------------------------------------------+/-

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
116424---------------------------------------------------------------------------------------------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
11737abdominal swab of a patient with appendicitisHamburgGermanyDEUEurope
23187abdominal swab of a patient with appendicitis accompanied with abscess formation
58075Human abdominal swab,appendicitis and abscessGermanyDEUEurope
67770Abdominal swab of a patient with appendicitis with abscess formation
116424Abdominal swab of a patient with appendicitisHamburgGermanyDEUEurope2001

isolation source categories

Cat1Cat2Cat3
#Infection#Patient#Swab
#Host Body-Site#Gastrointestinal tract#Large intestine
#Host Body-Site#Other#Abdomen
#Host Body-Site#Other#Abscess

taxonmaps

  • @ref: 69479
  • File name: preview.99_5117.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_386;97_489;98_560;99_5117&stattab=map
  • Last taxonomy: Corynebacterium appendicis
  • 16S sequence: AJ314919
  • Sequence Identity:
  • Total samples: 6944
  • soil counts: 60
  • aquatic counts: 234
  • animal counts: 6631
  • plant counts: 19

Safety information

risk assessment

@refpathogenicity humanbiosafety levelbiosafety level comment
11737yes, in single cases1Risk group (German classification)
200692German classification
1164242Risk group (French classification)

Sequence information

16S sequences

  • @ref: 11737
  • description: Corynebacterium appendicis partial 16S rRNA gene, strain DSM 44531T
  • accession: AJ314919
  • length: 1470
  • database: ena
  • NCBI tax ID: 1161099

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Corynebacterium appendicis CIP 107643 strain DSM 445311161099.3wgspatric1161099
66792Corynebacterium appendicis DSM 445312681813517draftimg1161099
66792Corynebacterium appendicis CIP 1076432512047050draftimg1161099
67770Corynebacterium appendicis CIP 107643 DSM 44531GCA_900156665contigncbi1161099

GC content

@refGC-contentmethod
1173765.8
6777065.7-65.9high performance liquid chromatography (HPLC)
6777064.3genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno93.702no
gram-positiveyes94.499yes
anaerobicno99.195no
aerobicno73.114yes
halophileyes83.921no
spore-formingno92.447yes
flagellatedno96.535yes
thermophileno95.893yes
glucose-utilyes83.612no
glucose-fermentno75.83no

External links

@ref: 11737

culture collection no.: DSM 44531, JCM 11765, NRRL B-24151, CCUG 48298, IMMIB R-3491, CIP 107643

straininfo link

  • @ref: 72714
  • straininfo: 87993

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny12148623Corynebacterium appendicis sp. nov.Yassin AF, Steiner U, Ludwig WInt J Syst Evol Microbiol10.1099/00207713-52-4-11652002Appendicitis/*microbiology, Bacterial Typing Techniques, Corynebacterium/chemistry/*classification/genetics/metabolism, Corynebacterium Infections/microbiology, DNA, Ribosomal/analysis, Genes, rRNA, Humans, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAPathogenicity
Phylogeny29148360Corynebacterium godavarianum sp. nov., isolated from the Godavari river, India.Jani K, Khare K, Senik S, Karodi P, Vemuluri VR, Bandal J, Shouche Y, Rale V, Sharma AInt J Syst Evol Microbiol10.1099/ijsem.0.0024912017Bacterial Typing Techniques, Base Composition, Corynebacterium/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Humans, India, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Religion, Rivers/*microbiology, Sequence Analysis, DNA, *Water MicrobiologyPathogenicity

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
11737Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44531)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44531
20069Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44531.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
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
23187A F Yassin, U Steiner, W Ludwig10.1099/00207713-52-4-1165Corynebacterium appendicis sp. nov.IJSEM 52: 1165-1169 200212148623
40563Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5101
58075Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 48298)https://www.ccug.se/strain?id=48298
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/
68369Automatically annotated from API 20NE
68371Automatically annotated from API 50CH acid
68379Automatically annotated from API Coryne
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
72714Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID87993.1StrainInfo: A central database for resolving microbial strain identifiers
116424Curators of the CIPCollection of Institut Pasteur (CIP 107643)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107643