Strain identifier

BacDive ID: 10522

Type strain: Yes

Species: Microvirgula aerodenitrificans

Strain Designation: SGLY2

Strain history: CIP <- 2003, DSMZ <- LMG <- D. Patureau: strain SGLY2

NCBI tax ID(s): 1122240 (strain), 57480 (species)

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General

@ref: 5702

BacDive-ID: 10522

DSM-Number: 15089

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

description: Microvirgula aerodenitrificans SGLY2 is an aerobe, mesophilic, motile bacterium that was isolated from laboratory anoxic filter inoculated with activated sludge.

NCBI tax id

NCBI tax idMatching level
1122240strain
57480species

strain history

@refhistory
5702<- LMG <- D. Patureau; SGLY2
67770IAM 14991 <-- LMG 18919 <-- D. Patureau SGLY2.
116065CIP <- 2003, DSMZ <- LMG <- D. Patureau: strain SGLY2

doi: 10.13145/bacdive10522.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Neisseriales
  • family: Chromobacteriaceae
  • genus: Microvirgula
  • species: Microvirgula aerodenitrificans
  • full scientific name: Microvirgula aerodenitrificans Patureau et al. 1998

@ref: 5702

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Neisseriales

family: Chromobacteriaceae

genus: Microvirgula

species: Microvirgula aerodenitrificans

full scientific name: Microvirgula aerodenitrificans Patureau et al. 1998 emend. Cleenwerck et al. 2003

strain designation: SGLY2

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes92.815
69480100negative
116065yesnegativerod-shaped

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5702MICROVIRGULA MEDIUM (DSMZ Medium 957)yeshttps://mediadive.dsmz.de/medium/957Name: MICROVIRGULA MEDIUM (DSMZ Medium 957) Composition: Sodium succinate 1.5 g/l KNO3 1.5 g/l (NH4)2SO4 1.0 g/l KH2PO4 0.82 g/l K2HPO4 0.7 g/l MgSO4 x 7 H2O 0.5 g/l Yeast extract 0.25 g/l Distilled water
5702REACTIVATION WITH LIQUID MEDIUM 1 (DSMZ Medium 1a)yeshttps://mediadive.dsmz.de/medium/1aName: REACTIVATION WITH LIQUID MEDIUM 1 (DSMZ Medium 1a) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
42120MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
116065CIP Medium 328yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=328
116065CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
5702positivegrowth28mesophilic
42120positivegrowth30mesophilic
67770positivegrowth27mesophilic
116065positivegrowth15-37
116065nogrowth5psychrophilic
116065nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
5702aerobe
5702anaerobe
116065facultative anaerobe

spore formation

@refspore formationconfidence
69481no99
69480no99.999

halophily

@refsaltgrowthtested relationconcentration
116065NaClpositivegrowth0-4 %
116065NaClnogrowth6 %
116065NaClnogrowth8 %
116065NaClnogrowth10 %

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
68371gluconate-builds acid from24265
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose-builds acid from18287
68371D-fucose-builds acid from28847
68371D-tagatose-builds acid from16443
68371D-lyxose-builds acid from62318
68371turanose-builds acid from32528
68371gentiobiose-builds acid from28066
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose-builds acid from27082
68371sucrose-builds acid from17992
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
68371maltose-builds acid from17306
68371cellobiose-builds acid from17057
68371salicin-builds acid from17814
68371esculin-builds acid from4853
68371arbutin-builds acid from18305
68371amygdalin-builds acid from27613
68371N-acetylglucosamine-builds acid from59640
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371D-mannitol-builds acid from16899
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
68371D-mannose-builds acid from16024
68371D-fructose-builds acid from15824
68371D-glucose-builds acid from17634
68371D-galactose-builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose-builds acid from65327
68371D-ribose-builds acid from16988
68371L-arabinose-builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754
68368nitrate-reduction17632
68368D-glucose-fermentation17634
68368gelatin-hydrolysis5291
68368tryptophan-energy source27897
68368urea-hydrolysis16199
68368citrate-assimilation16947
68368ornithine-degradation18257
68368lysine-degradation25094
68368arginine-hydrolysis29016
116065D-arabinose-degradation17108
116065D-fructose-degradation15824
116065D-glucose-degradation17634
116065D-mannose-degradation16024
116065D-xylose-degradation65327
116065cellobiose-degradation17057
116065lactose-degradation17716
116065maltose-degradation17306
116065salicin-degradation17814
116065sucrose-degradation17992
116065citrate+carbon source16947
116065esculin-hydrolysis4853
116065glucose-fermentation17234
116065lactose-fermentation17716
116065nitrate-reduction17632
116065nitrite-reduction16301
116065sodium thiosulfate-builds gas from132112
116065nitrate+respiration17632
68376esculin-hydrolysis4853
68376D-arabitol-builds acid from18333
68376D-xylose-builds acid from65327
68376L-rhamnose-builds acid from62345
68376methyl alpha-D-glucopyranoside-builds acid from320061
68376D-ribose-builds acid from16988
68376glucose 1-phosphate-builds acid from29042
68376D-tagatose-builds acid from16443

antibiotic resistance

  • @ref: 116065
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

@refChebi-IDmetaboliteproduction
6836817997dinitrogenno
6836816301nitriteno
6836815688acetoinno
6836835581indoleno
6836816136hydrogen sulfideno
11606535581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole testmethylred-test
6836815688acetoin-
6836835581indole-
11606515688acetoin-
11606517234glucose-

enzymes

@refvalueactivityec
68376alpha-mannosidase-3.2.1.24
68376beta-glucosidase-3.2.1.21
68368gelatinase-
68368tryptophan deaminase-4.1.99.1
68368urease-3.5.1.5
68368ornithine decarboxylase-4.1.1.17
68368lysine decarboxylase-4.1.1.18
68368arginine dihydrolase-3.5.3.6
68368beta-galactosidase-3.2.1.23
116065oxidase+
116065beta-galactosidase-3.2.1.23
116065alcohol dehydrogenase+1.1.1.1
116065gelatinase-
116065amylase-
116065DNase-
116065caseinase-3.4.21.50
116065catalase+1.11.1.6
116065tween esterase-
116065gamma-glutamyltransferase+2.3.2.2
116065lecithinase-
116065lipase-
116065lysine decarboxylase-4.1.1.18
116065ornithine decarboxylase-4.1.1.17
116065phenylalanine ammonia-lyase-4.3.1.24
116065tryptophan deaminase-
116065urease-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
116065-+++-+----+---------

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUNO2N2
116065--------------

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
116065-------------------------------------------------

API LIST

@refDIMESCalpha MANDARLXYLRHAMDGRIBG1PTAG
116065----------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
116065------------------------------------------------+++--+--------+---------++-+++-+++-+----++++++-++-+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
5702laboratory anoxic filter inoculated with activated sludgeNarbonneFranceFRAEurope
67770Upflow anoxic filter previously inoculated with activated sludgeParisFranceFRAEurope
116065Environment, Laboratory anoxic filter inoculated with activated sludge

isolation source categories

Cat1Cat2Cat3
#Engineered#Laboratory
#Engineered#Waste#Activated sludge
#Condition#Anoxic (anaerobic)

taxonmaps

  • @ref: 69479
  • File name: preview.99_5074.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15355;96_2474;97_3019;98_3787;99_5074&stattab=map
  • Last taxonomy: Microvirgula
  • 16S sequence: U89333
  • Sequence Identity:
  • Total samples: 4775
  • soil counts: 416
  • aquatic counts: 2210
  • animal counts: 1828
  • plant counts: 321

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
57021Risk group (German classification)
1160651Risk group (French classification)

Sequence information

16S sequences

  • @ref: 5702
  • description: Microvirgula aerodenitrificans 16S ribosomal RNA gene, partial sequence
  • accession: U89333
  • length: 1501
  • database: ena
  • NCBI tax ID: 57480

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Microvirgula aerodenitrificans DSM 150891122240.3wgspatric1122240
66792Microvirgula aerodenitrificans DSM 150892556921007draftimg1122240
67770Microvirgula aerodenitrificans DSM 15089GCA_000620105scaffoldncbi1122240

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno99no
motileyes93.57no
flagellatedyes81.24no
gram-positiveno98.646no
anaerobicno95.606no
aerobicyes72.415no
halophileno91.544no
spore-formingno94.87no
thermophileno99.408yes
glucose-utilyes68.891no
glucose-fermentno85.127no

External links

@ref: 5702

culture collection no.: DSM 15089, CIP 108159, LMG 18919, JCM 21462, IAM 14991

straininfo link

  • @ref: 79798
  • straininfo: 12664

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny9734031Microvirgula aerodenitrificans gen. nov., sp. nov., a new gram-negative bacterium exhibiting co-respiration of oxygen and nitrogen oxides up to oxygen-saturated conditions.Patureau D, Godon JJ, Dabert P, Bouchez T, Bernet N, Delgenes JP, Moletta RInt J Syst Bacteriol10.1099/00207713-48-3-7751998Base Sequence, Gram-Negative Aerobic Rods and Cocci/*classification/metabolism, Molecular Sequence Data, Nitrogen Oxides/*metabolism, Oligonucleotide Probes, Oxygen/*metabolism, Phenotype, PhylogenyMetabolism
Genetics13130033Aquaspirillum dispar Hylemon et al. 1973 and Microvirgula aerodenitrificans Patureau et al. 1998 are subjective synonyms.Cleenwerck I, De Wachter M, Hoste B, Janssens D, Swings JInt J Syst Evol Microbiol10.1099/ijs.0.02675-02003DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/analysis, Molecular Sequence Data, Neisseriaceae/*classification/genetics/metabolism, Phenotype, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Terminology as TopicPhylogeny
Phylogeny27666417Microvirgula curvata sp. nov., isolated from hydrocarbon-contaminated soil, and emended description of the genus Microvirgula.Subhash Y, Park MJ, Lee SSInt J Syst Evol Microbiol10.1099/ijsem.0.0015122016Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, *Environmental Pollution, Fatty Acids/chemistry, Hydrocarbons/*analysis, Kuwait, Neisseriaceae/*classification/genetics/isolation & purification, Nucleic Acid Hybridization, Phosphatidylethanolamines/chemistry, Phosphatidylglycerols/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
5702Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15089)https://www.dsmz.de/collection/catalogue/details/culture/DSM-15089
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
42120Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5750
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 updatesNucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68368Automatically annotated from API 20E
68371Automatically annotated from API 50CH acid
68376Automatically annotated from API LIST
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
79798Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID12664.1StrainInfo: A central database for resolving microbial strain identifiers
116065Curators of the CIPCollection of Institut Pasteur (CIP 108159)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108159