Strain identifier

BacDive ID: 385

Type strain: Yes

Species: Advenella incenata

Strain history: CIP <- 2005, CCUG <- 2001, PHLS, Göteborg, Sweden

NCBI tax ID(s): 267800 (species)

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General

@ref: 17385

BacDive-ID: 385

DSM-Number: 23814

keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, mesophilic, Gram-negative, rod-shaped

description: Advenella incenata DSM 23814 is an obligate aerobe, mesophilic, Gram-negative bacterium that was isolated from human sputum.

NCBI tax id

  • NCBI tax id: 267800
  • Matching level: species

strain history

@refhistory
17385<- CCUG <- PHLS, Göteborg, Sweden
120072CIP <- 2005, CCUG <- 2001, PHLS, Göteborg, Sweden

doi: 10.13145/bacdive385.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Burkholderiales
  • family: Alcaligenaceae
  • genus: Advenella
  • species: Advenella incenata
  • full scientific name: Advenella incenata Coenye et al. 2005

@ref: 17385

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Alcaligenaceae

genus: Advenella

species: Advenella incenata

full scientific name: Advenella incenata Coenye et al. 2005 emend. Gibello et al. 2009

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell shapeconfidencemotility
23283negative1-2 µmrod-shaped
69480negative99.992
120072negativerod-shapedno

colony morphology

@reftype of hemolysiscolony color
17385gamma
23283gammalight brown
120072

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
17385COLUMBIA 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
17385TRYPTICASE 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
40049MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
120072CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
17385positivegrowth37mesophilic
23283positivegrowth30-37mesophilic
40049positivegrowth30mesophilic
56700positivegrowth30-42
120072positivegrowth15-37
120072nogrowth5psychrophilic
120072nogrowth41thermophilic
120072nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 120072
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.995

halophily

@refsaltgrowthtested relationconcentration
23283NaClpositivegrowth0-3 %
120072NaClpositivegrowth0-6 %
120072NaClnogrowth8 %
120072NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2328327689decanoate-assimilation
2328316899D-mannitol-assimilation
2328316467L-arginine-assimilation
2328317306maltose-assimilation
2328337684mannose-assimilation
23283506227N-acetylglucosamine-assimilation
2328336405norleucine-assimilation
2328318401phenylacetate-assimilation
2328317992sucrose-assimilation
2328327082trehalose-assimilation
2328327856acetamide-growth
2328315963ribitol-growth
232833565cetrimide-growth
2328315824D-fructose-growth
2328317306maltose-growth
232834853esculin-hydrolysis
2328353426tween 80-hydrolysis
2328317632nitrate-reduction
2328316947citrate+assimilation
2328315589L-malate+assimilation
2328324996lactate+assimilation
6836925115malate+assimilation
6836917128adipate+assimilation
6836927689decanoate-assimilation
6836924265gluconate+assimilation
6836959640N-acetylglucosamine-assimilation
6836916899D-mannitol+assimilation
6836916024D-mannose-assimilation
6836930849L-arabinose+assimilation
6836917634D-glucose+assimilation
683695291gelatin-hydrolysis
683694853esculin-hydrolysis
6836916199urea+hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate-reduction
12007216947citrate+carbon source
1200724853esculin-hydrolysis
120072606565hippurate+hydrolysis
12007217632nitrate-builds gas from
12007217632nitrate-reduction
12007216301nitrite-builds gas from
12007216301nitrite-reduction
12007215792malonate+assimilation
12007217632nitrate-respiration

antibiotic resistance

  • @ref: 120072
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

@refChebi-IDmetaboliteproduction
2328335581indoleno
2328316136hydrogen sulfideno
6836935581indoleno
12007235581indoleno

metabolite tests

@refChebi-IDmetaboliteindole testvoges-proskauer-testmethylred-test
6836935581indole-
12007215688acetoin-
12007217234glucose-

enzymes

@refvalueactivityec
17385catalase+1.11.1.6
17385cytochrome-c oxidase+1.9.3.1
23283alkaline phosphatase+3.1.3.1
23283alpha-fucosidase-3.2.1.51
23283alpha-galactosidase-3.2.1.22
23283alpha-glucosidase-3.2.1.20
23283alpha-mannosidase-3.2.1.24
23283amylase-
23283arginine dihydrolase-3.5.3.6
23283beta-galactosidase-3.2.1.23
23283beta-glucosidase-3.2.1.21
23283beta-glucuronidase-3.2.1.31
23283catalase+1.11.1.6
23283chymotrypsin-3.4.4.5
23283cytochrome oxidase+1.9.3.1
23283DNase-
23283leucine arylamidase+3.4.11.1
23283lipase (C 14)-
23283lysine decarboxylase-4.1.1.18
23283N-acetyl-beta-glucosaminidase-3.2.1.52
23283ornithine decarboxylase-4.1.1.17
23283trypsin-3.4.21.4
23283valine 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
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
68369cytochrome oxidase+1.9.3.1
68369gelatinase-
68369beta-glucosidase-3.2.1.21
68369urease+3.5.1.5
68369arginine dihydrolase-3.5.3.6
120072oxidase+
120072beta-galactosidase+3.2.1.23
120072alcohol dehydrogenase-1.1.1.1
120072gelatinase-
120072amylase-
120072DNase-
120072caseinase-3.4.21.50
120072catalase+1.11.1.6
120072tween esterase-
120072gamma-glutamyltransferase+2.3.2.2
120072lecithinase-
120072lipase-
120072lysine decarboxylase-4.1.1.18
120072ornithine decarboxylase-4.1.1.17
120072phenylalanine ammonia-lyase-4.3.1.24
120072tryptophan deaminase-
120072urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
120072-+++-++---++--------

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
17385----+---++-+-+/-+-+++-+

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
120072+-+----------------+++-++------+------+---+-+-+++++++++++++-+-+-++++-----+-++-+++++----++++++++++++

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling dateisolation date
17385human sputumGöteborgSwedenSWEEurope
23283Human sputum, 69-year-old woman
56700Human sputum,69-yr-old womanGöteborgSwedenSWEEurope2001-04-01
120072Human, SputumGöteborgSwedenSWEEurope2001

isolation source categories

Cat1Cat2Cat3
#Host#Human#Female
#Host Body Product#Fluids#Sputum

taxonmaps

  • @ref: 69479
  • File name: preview.99_1770.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_7;96_1003;97_1169;98_1397;99_1770&stattab=map
  • Last taxonomy: Advenella
  • 16S sequence: AM944734
  • Sequence Identity:
  • Total samples: 2457
  • soil counts: 822
  • aquatic counts: 378
  • animal counts: 766
  • plant counts: 491

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
173852Risk group (German classification)
1200721Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
23283Advenella incenata strain LMG 22250 16S ribosomal RNA gene, partial sequenceAY569457734nuccore267800
17385Advenella incenata partial 16S rRNA gene, type strain CCUG 45225AM9447341341ena267800

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Advenella incenata DSM 23814GCA_004217095scaffoldncbi267800
66792Advenella incenata strain DSM 23814267800.3wgspatric267800
66792Advenella incenata DSM 238142802429727draftimg267800

GC content

  • @ref: 23283
  • GC-content: 54.2
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno77.391no
flagellatedno94.8no
gram-positiveno98.158no
anaerobicno99.353no
aerobicyes92.26no
halophileno80.18no
spore-formingno96.047no
glucose-utilyes58.076yes
thermophileno99.793yes
glucose-fermentno89.664yes

External links

@ref: 17385

culture collection no.: DSM 23814, CCUG 45225, LMG 22250, CIP 108657

straininfo link

  • @ref: 70065
  • straininfo: 110312

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15653883Advenella incenata gen. nov., sp. nov., a novel member of the Alcaligenaceae, isolated from various clinical samples.Coenye T, Vanlaere E, Samyn E, Falsen E, Larsson P, Vandamme PInt J Syst Evol Microbiol10.1099/ijs.0.63267-02005Adolescent, Adult, Alcaligenaceae/chemistry/*classification/genetics/isolation & purification, Animals, Bacterial Proteins/analysis, Cystic Fibrosis/*microbiology, DNA, Bacterial/analysis, Female, Gram-Negative Bacterial Infections/*microbiology/veterinary, Humans, Male, Middle Aged, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Random Amplified Polymorphic DNA Technique, Sequence Analysis, DNAPathogenicity
Phylogeny22307513Advenella faeciporci sp. nov., a nitrite-denitrifying bacterium isolated from nitrifying-denitrifying activated sludge collected from a laboratory-scale bioreactor treating piggery wastewater.Matsuoka M, Park S, An SY, Miyahara M, Kim SW, Kamino K, Fushinobu S, Yokota A, Wakagi T, Shoun HInt J Syst Evol Microbiol10.1099/ijs.0.037440-02012Alcaligenaceae/*classification/genetics/isolation & purification, Animals, Bacterial Typing Techniques, Base Composition, Bioreactors, DNA, Bacterial/genetics, Denitrification, Fatty Acids/analysis, Molecular Sequence Data, Nitrification, Nitrites, *Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sewage/*microbiology, Swine, Waste Water/*microbiologyGenetics
Phylogeny26620977Advenella alkanexedens sp. nov., an alkane-degrading bacterium isolated from biogas slurry samples.Wang H, Zhou S, Wang Y, Kong D, Guo X, Zhu J, Dong W, Ruan ZInt J Syst Evol Microbiol10.1099/ijsem.0.0008112015

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
17385Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23814)https://www.dsmz.de/collection/catalogue/details/culture/DSM-23814
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
23283Tom Coenye, Elke Vanlaere, Emly Samyn, Enevold Falsen, Peter Larsson, Peter Vandamme10.1099/ijs.0.63267-0Advenella incenata gen. nov., sp. nov., a novel member of the Alcaligenaceae, isolated from various clinical samplesIJSEM 55: 251-256 200515653883
40049Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6310
56700Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 45225)https://www.ccug.se/strain?id=45225
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)
68369Automatically annotated from API 20NE
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)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
70065Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID110312.1StrainInfo: A central database for resolving microbial strain identifiers
120072Curators of the CIPCollection of Institut Pasteur (CIP 108657)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108657