Strain identifier

BacDive ID: 134936

Type strain: Yes

Species: Zoogloea ramigera

Strain history: CIP <- 2001, NCIMB <- ATCC <- N.C. Dondero

NCBI tax ID(s): 350 (species)

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General

@ref: 33613

BacDive-ID: 134936

keywords: genome sequence, Bacteria, aerobe, mesophilic, motile

description: Zoogloea ramigera CIP 107119 is an aerobe, mesophilic, motile bacterium of the family Zoogloeaceae.

NCBI tax id

  • NCBI tax id: 350
  • Matching level: species

strain history

  • @ref: 33613
  • history: CIP <- 2001, NCIMB <- ATCC <- N.C. Dondero

doi: 10.13145/bacdive134936.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Rhodocyclales
  • family: Zoogloeaceae
  • genus: Zoogloea
  • species: Zoogloea ramigera
  • full scientific name: Zoogloea ramigera Itzigsohn 1868 (Approved Lists 1980)

@ref: 33613

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Rhodocyclales

family: Zoogloeaceae

genus: Zoogloea

species: Zoogloea ramigera

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes99.107
6948099.998negative
33613yesnegativerod-shaped

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
33613MEDIUM 394 - for Zoogloea ramigerayesDistilled water make up to (1000.000 ml);Agar (15.000 g);Yeast extract (2.500 g);Peptone (2.500 g)
33613CIP Medium 6yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=6

culture temp

@refgrowthtypetemperaturerange
33613positivegrowth25mesophilic
52774positivegrowth30mesophilic
33613positivegrowth25-37mesophilic
33613nogrowth5psychrophilic
33613nogrowth10psychrophilic
33613nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 52774
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.989

halophily

@refsaltgrowthtested relationconcentration
33613NaClpositivegrowth0 %
33613NaClnogrowth2 %
33613NaClnogrowth4 %
33613NaClnogrowth6 %
33613NaClnogrowth8 %
33613NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3361316947citrate-carbon source
336134853esculin-hydrolysis
3361317632nitrate-reduction
3361316301nitrite-reduction
3361317632nitrate+respiration

antibiotic resistance

  • @ref: 33613
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

  • @ref: 33613
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
33613oxidase+
33613beta-galactosidase-3.2.1.23
33613alcohol dehydrogenase-1.1.1.1
33613gelatinase-
33613amylase-
33613DNase-
33613caseinase-3.4.21.50
33613catalase-1.11.1.6
33613tween esterase-
33613lecithinase-
33613lipase-
33613lysine decarboxylase-4.1.1.18
33613ornithine decarboxylase-4.1.1.17
33613urease+3.5.1.5
68382alkaline phosphatase-3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)-
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase-3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase-3.2.1.20
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
33613--+--+-----+--------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
33613++--+--+-++++------------------+----------------------------+--------------+------------------+----

Isolation, sampling and environmental information

isolation

@refcountryorigin.countrycontinentsample typegeographic location
33613USAUSANorth America
52774USAUSANorth AmericaTrickling filter sampleNew Jersey,Freehold
33613United States of AmericaUSANorth AmericaBranched Zoogloea from trickling filter sample

isolation source categories

  • Cat1: #Engineered
  • Cat2: #Waste
  • Cat3: #Water treatment plant

Safety information

risk assessment

  • @ref: 33613
  • biosafety level: 1
  • biosafety level comment: Risk group (French classification)

Sequence information

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Zoogloea ramigera ATCC 19544GCA_008125065scaffoldncbi350
66792Zoogloea ramigera strain ATCC 19544350.4wgspatric350
66792Zoogloea ramigera ATCC 195442596583626draftimg350

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes89.206no
flagellatedyes79.295no
gram-positiveno98.678no
anaerobicno98.709no
aerobicyes89.689no
halophileno93.324no
spore-formingno93.693no
thermophileno99.552yes
glucose-utilyes92.244no
glucose-fermentno90.589no

External links

@ref: 33613

culture collection no.: CIP 107119, NCIMB 10706, ATCC 19544, IAM 12136, CCUG 35504

straininfo link

  • @ref: 92370
  • straininfo: 6464

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny7574608The abundance of Zoogloea ramigera in sewage treatment plants.Rossello-Mora RA, Wagner M, Amann R, Schleifer KHAppl Environ Microbiol10.1128/aem.61.2.702-707.19951995Base Sequence, DNA, Bacterial/genetics, In Situ Hybridization, Molecular Probe Techniques/statistics & numerical data, Molecular Sequence Data, Oligonucleotide Probes/genetics, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sensitivity and Specificity, *Sewage, Zoogloea/classification/genetics/*isolation & purificationGenetics
Phylogeny8240962Molecular systematics of the genus Zoogloea and emendation of the genus.Shin YK, Hiraishi A, Sugiyama JInt J Syst Bacteriol10.1099/00207713-43-4-8261993Base Composition, Base Sequence, DNA, Ribosomal/*genetics, Genome, Bacterial, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/*genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Zoogloea/*classification/*geneticsGenetics
Enzymology11791830Immunological methods for the study of Zoogloea strains in natural environments.Lu F, Lukasik J, Farrah SRWater Res10.1016/s0043-1354(01)00141-52001Biofilms, DNA, Bacterial/analysis, Environmental Monitoring/methods, Immunoassay, Population Dynamics, Reverse Transcriptase Polymerase Chain Reaction, Waste Disposal, Fluid, *Water Purification, Zoogloea/genetics/*immunology
Phylogeny25342113Zoogloea oleivorans sp. nov., a floc-forming, petroleum hydrocarbon-degrading bacterium isolated from biofilm.Farkas M, Tancsics A, Kriszt B, Benedek T, Toth EM, Keki Z, Veres PG, Szoboszlay SInt J Syst Evol Microbiol10.1099/ijs.0.068486-02014Bacterial Typing Techniques, Base Composition, Biodegradation, Environmental, *Biofilms, DNA, Bacterial/genetics, Fatty Acids/chemistry, Hungary, Hydrocarbons/metabolism, Molecular Sequence Data, Nucleic Acid Hybridization, Petroleum/*microbiology, Phosphatidylethanolamines/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Ubiquinone/chemistry, Zoogloea/*classification/genetics/isolation & purificationGenetics
Phylogeny32841112Zoogloea dura sp. nov., a N2-fixing bacterium isolated from forest soil and emendation of the genus Zoogloea and the species Zoogloea oryzae and Zoogloea ramigera.Dahal RH, Chaudhary DK, Kim DU, Kim JInt J Syst Evol Microbiol10.1099/ijsem.0.0044162020Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Forests, Nitrogen Fixation, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/chemistry, Zoogloea/*classification/isolation & purificationTranscriptome

Reference

@idauthorstitledoi/urlcataloguejournalpubmed
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
33613Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107119Collection of Institut Pasteur (CIP 107119)
52774Curators of the CCUGhttps://www.ccug.se/strain?id=35504Culture Collection University of Gothenburg (CCUG) (CCUG 35504)
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar SchomburgBRENDA, the ELIXIR core data resource in 2021: new developments and updates10.1093/nar/gkaa1025Nucleic Acids Res. 49: D498-D508 202033211880
68382Automatically annotated from API zym
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
92370Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID6464.1