Strain identifier

BacDive ID: 2978

Type strain: Yes

Species: Malikia granosa

Strain Designation: P1

Strain history: CIP <- 2003, DSMZ <- M. Wagner: strain P1

NCBI tax ID(s): 263067 (species)

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General

@ref: 5912

BacDive-ID: 2978

DSM-Number: 15619

keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, mesophilic, motile

description: Malikia granosa P1 is an obligate aerobe, mesophilic, motile bacterium that was isolated from activated sludge.

NCBI tax id

  • NCBI tax id: 263067
  • Matching level: species

strain history

@refhistory
5912<- S. Spring; P1 <- M. Wagner
67770DSM 15619 <-- S. Spring P1.
119727CIP <- 2003, DSMZ <- M. Wagner: strain P1

doi: 10.13145/bacdive2978.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Burkholderiales
  • family: Comamonadaceae
  • genus: Malikia
  • species: Malikia granosa
  • full scientific name: Malikia granosa Spring et al. 2005

@ref: 5912

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Comamonadaceae

genus: Malikia

species: Malikia granosa

full scientific name: Malikia granosa Spring et al. 2005

strain designation: P1

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes92.819
69480100negative
119727yesnegativerod-shaped

pigmentation

  • @ref: 119727
  • production: no
  • name: Pyocyanin

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5912R2A MEDIUM (DSMZ Medium 830)yeshttps://mediadive.dsmz.de/medium/830Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
5912NUTRIENT 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
33210MEDIUM 566- Reasoner's 2A agar for Flavobacterium micromatiyesDistilled water make up to (1000.000 ml);R2A agar (18.200 g)
119727CIP Medium 566yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=566

culture temp

@refgrowthtypetemperaturerange
5912positivegrowth28mesophilic
33210positivegrowth30mesophilic
67770positivegrowth35mesophilic
119727positivegrowth10-41
119727nogrowth5psychrophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 119727
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.997

halophily

@refsaltgrowthtested relationconcentration
119727NaClpositivegrowth0 %
119727NaClnogrowth2 %
119727NaClnogrowth4 %
119727NaClnogrowth6 %
119727NaClnogrowth8 %
119727NaClnogrowth10 %

observation

  • @ref: 67770
  • observation: quinones: Q-8

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
11972716947citrate-carbon source
1197274853esculin-hydrolysis
11972717632nitrate+reduction
11972716301nitrite-reduction
11972717632nitrate-respiration

antibiotic resistance

  • @ref: 119727
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

  • @ref: 119727
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
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
119727oxidase+
119727beta-galactosidase-3.2.1.23
119727alcohol dehydrogenase-1.1.1.1
119727gelatinase-
119727amylase-
119727DNase+
119727caseinase-3.4.21.50
119727catalase+1.11.1.6
119727tween esterase-
119727lecithinase-
119727lipase-
119727lysine decarboxylase-4.1.1.18
119727ornithine decarboxylase-4.1.1.17
119727protease-
119727tryptophan deaminase-
119727urease-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
119727-+++-+----++---+----

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
5912activated sludgeMunich, Kläranlage GroßlappenGermanyDEUEurope
67770Activated sludge in a wastewater treatment plantMunichGermanyDEUEurope
119727Environment, Activated sludgeMünchenGermanyDEUEurope1994

isolation source categories

  • Cat1: #Engineered
  • Cat2: #Waste
  • Cat3: #Activated sludge

taxonmaps

  • @ref: 69479
  • File name: preview.99_42391.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_1;96_872;97_3698;98_30803;99_42391&stattab=map
  • Last taxonomy: Malikia granosa
  • 16S sequence: AJ627188
  • Sequence Identity:
  • Total samples: 312
  • soil counts: 13
  • aquatic counts: 269
  • animal counts: 15
  • plant counts: 15

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
59121Risk group (German classification)
1197271Risk group (French classification)

Sequence information

16S sequences

  • @ref: 20218
  • description: Malikia granosa 16S rRNA gene, type strain P1
  • accession: AJ627188
  • length: 1525
  • database: ena
  • NCBI tax ID: 263067

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Malikia granosa strain P1263067.3wgspatric263067
66792Malikia granosa P12887120766draftimg263067
67770Malikia granosa P1GCA_002980595contigncbi263067

GC content

@refGC-contentmethod
591267
6777067high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes88.881no
gram-positiveno98.702no
anaerobicno95.391no
aerobicyes88.381no
halophileno93.19no
spore-formingno94.7no
glucose-utilno50no
flagellatedyes63.109no
thermophileno94.236yes
glucose-fermentno87.451no

External links

@ref: 5912

culture collection no.: DSM 15619, CIP 108194, JCM 12706, CCUG 64012

straininfo link

  • @ref: 72500
  • straininfo: 138011

literature

  • topic: Phylogeny
  • Pubmed-ID: 15774634
  • title: Malikia granosa gen. nov., sp. nov., a novel polyhydroxyalkanoate- and polyphosphate-accumulating bacterium isolated from activated sludge, and reclassification of Pseudomonas spinosa as Malikia spinosa comb. nov.
  • authors: Spring S, Wagner M, Schumann P, Kampfer P
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.63356-0
  • year: 2005
  • mesh: Comamonadaceae/*classification/genetics/isolation & purification, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, Polyesters/*metabolism, Polyphosphates/*metabolism, Pseudomonas/*classification/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sewage/*microbiology
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
5912Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15619)https://www.dsmz.de/collection/catalogue/details/culture/DSM-15619
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
33210Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5789
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/
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
72500Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID138011.1StrainInfo: A central database for resolving microbial strain identifiers
119727Curators of the CIPCollection of Institut Pasteur (CIP 108194)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108194