Strain identifier

BacDive ID: 5504

Type strain: Yes

Species: Cloacibacterium normanense

Strain history: CIP <- 2005, CCUG <- P.A. Lawson, UK <- Tanner, USA: strain NRS1

NCBI tax ID(s): 237258 (species)

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General

@ref: 6138

BacDive-ID: 5504

DSM-Number: 15886

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

description: Cloacibacterium normanense DSM 15886 is a facultative anaerobe, mesophilic, Gram-negative bacterium that was isolated from untreated municipal wastewater.

NCBI tax id

  • NCBI tax id: 237258
  • Matching level: species

strain history

@refhistory
6138<- R. S. Tanner; NRS1 <- T. D. Allen
121351CIP <- 2005, CCUG <- P.A. Lawson, UK <- Tanner, USA: strain NRS1

doi: 10.13145/bacdive5504.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Flavobacteriia
  • order: Flavobacteriales
  • family: Weeksellaceae
  • genus: Cloacibacterium
  • species: Cloacibacterium normanense
  • full scientific name: Cloacibacterium normanense Allen et al. 2006

@ref: 6138

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Weeksellaceae

genus: Cloacibacterium

species: Cloacibacterium normanense

full scientific name: Cloacibacterium normanense Allen et al. 2006

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell shapemotility
31763negative05-27 µmrod-shapedno
121351negativerod-shapedno

colony morphology

  • @ref: 121351

pigmentation

  • @ref: 31763
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6138NUTRIENT AGAR (DSMZ Medium 1)yeshttps://mediadive.dsmz.de/medium/1Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
40491MEDIUM 6 - Columbia agar with 10 % horse bloodyesDistilled water make up to (1000.000 ml);Columbia agar (39.000 g);Horseblood (100.000 ml)
121351CIP Medium 6yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=6

culture temp

@refgrowthtypetemperaturerange
6138positivegrowth30-37mesophilic
31763positivegrowth18-36
31763positiveoptimum30mesophilic
40491positivegrowth37mesophilic
57139positivegrowth37mesophilic
121351positivegrowth25-37mesophilic
121351nogrowth41thermophilic

culture pH

@refabilitytypepH
31763positivegrowth06-08
31763positiveoptimum07-08

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31763facultative anaerobe
57139aerobe
57139microaerophile
121351facultative anaerobe

spore formation

  • @ref: 31763
  • spore formation: no

observation

  • @ref: 31763
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3176340585alpha-cyclodextrin+carbon source
3176337684mannose+carbon source
317634853esculin+hydrolysis
12135115824D-fructose-degradation
12135117634D-glucose+degradation
12135116024D-mannose+degradation
12135117716lactose-degradation
12135117306maltose+degradation
12135117992sucrose-degradation
121351606565hippurate+hydrolysis
12135117632nitrate-builds gas from
12135117632nitrate-reduction
12135116301nitrite-builds gas from
12135116301nitrite-reduction
12135117632nitrate+respiration

metabolite production

@refChebi-IDmetaboliteproduction
3176335581indoleyes
12135135581indoleno

metabolite tests

  • @ref: 31763
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: +

enzymes

@refvalueactivityec
31763catalase+1.11.1.6
31763cytochrome oxidase+1.9.3.1
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
121351oxidase-
121351beta-galactosidase+3.2.1.23
121351alcohol dehydrogenase-1.1.1.1
121351gelatinase-
121351amylase+
121351DNase+
121351caseinase-3.4.21.50
121351catalase+1.11.1.6
121351tween esterase-
121351gamma-glutamyltransferase+2.3.2.2
121351lecithinase-
121351lipase-
121351lysine decarboxylase-4.1.1.18
121351ornithine decarboxylase-4.1.1.17
121351urease-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
121351-+++-++---++---+----

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
6138untreated municipal wastewaterOklahoma, NormanUSAUSANorth America
57139Untreated wastewater,water treatment plantOK,NormanUSAUSANorth America
121351Environment, Wastewater, untreated, treatment plantUnited States of AmericaUSANorth America

isolation source categories

  • Cat1: #Engineered
  • Cat2: #Waste
  • Cat3: #Wastewater

taxonmaps

  • @ref: 69479
  • File name: preview.99_462.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_76;96_305;97_339;98_382;99_462&stattab=map
  • Last taxonomy: Cloacibacterium normanense
  • 16S sequence: AJ575430
  • Sequence Identity:
  • Total samples: 10943
  • soil counts: 350
  • aquatic counts: 4936
  • animal counts: 5409
  • plant counts: 248

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
61381Risk group (German classification)
1213511Risk group (French classification)

Sequence information

16S sequences

  • @ref: 6138
  • description: Cloacibacterium normanense partial 16S rRNA gene, type strain CCUG 46293
  • accession: AJ575430
  • length: 1475
  • database: ena
  • NCBI tax ID: 237258

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Cloacibacterium normanense DSM 15886GCA_900104195scaffoldncbi237258
66792Cloacibacterium normanense strain DSM 15886237258.25wgspatric237258
66792Cloacibacterium normanense DSM 158862634166320draftimg237258

GC content

  • @ref: 6138
  • GC-content: 31

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno92.281yes
flagellatedno96.929no
gram-positiveno98.451no
anaerobicno96.433no
aerobicyes72.229no
halophileno94.204no
spore-formingno96.407yes
glucose-fermentno90.703no
thermophileno99.117yes
glucose-utilyes85.556no

External links

@ref: 6138

culture collection no.: DSM 15886, ATCC BAA 825, CCUG 46293, CIP 108613, NRS 1

straininfo link

  • @ref: 74989
  • straininfo: 289357

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16738108Cloacibacterium normanense gen. nov., sp. nov., a novel bacterium in the family Flavobacteriaceae isolated from municipal wastewater.Allen TD, Lawson PA, Collins MD, Falsen E, Tanner RSInt J Syst Evol Microbiol10.1099/ijs.0.64218-02006Base Composition, DNA, Bacterial/chemistry, Flavobacteriaceae/*classification/genetics/isolation & purification, Molecular Sequence Data, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sweden, *Waste Disposal, Fluid, Water MicrobiologyGenetics
Phylogeny19819999Cloacibacterium rupense sp. nov., isolated from freshwater lake sediment.Cao SJ, Deng CP, Li BZ, Dong XQ, Yuan HLInt J Syst Evol Microbiol10.1099/ijs.0.017681-02009DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/metabolism, Flavobacteriaceae/*classification/genetics/*isolation & purification/metabolism, Fresh Water/*microbiology, Geologic Sediments/*microbiology, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/geneticsMetabolism
Phylogeny28150572Cloacibacterium caeni sp. nov., isolated from activated sludge.Chun BH, Lee Y, Jin HM, Jeon COInt J Syst Evol Microbiol10.1099/ijsem.0.0018412017Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flavobacteriaceae/*classification/genetics/isolation & purification, Nucleic Acid Hybridization, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Sewage/*microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
6138Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15886)https://www.dsmz.de/collection/catalogue/details/culture/DSM-15886
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
31763Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2803628776041
40491Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6261
57139Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 46293)https://www.ccug.se/strain?id=46293
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 updates33211880Nucleic Acids Res. 49: D498-D508 2020
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
74989Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID289357.1StrainInfo: A central database for resolving microbial strain identifiers
121351Curators of the CIPCollection of Institut Pasteur (CIP 108613)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108613