Strain identifier

BacDive ID: 2973

Type strain: Yes

Species: Hylemonella gracilis

Strain Designation: D4

Strain history: CIP <- 2002, NBRC <- ATCC <- E. Canale-Parola: strain D4

NCBI tax ID(s): 887062 (strain), 80880 (species)

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General

@ref: 3494

BacDive-ID: 2973

DSM-Number: 9158

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

description: Hylemonella gracilis D4 is a mesophilic, Gram-negative, motile bacterium that was isolated from pondwater.

NCBI tax id

NCBI tax idMatching level
80880species
887062strain

strain history

@refhistory
3494<- ATCC <- E. Canale-Parola, D4
119719CIP <- 2002, NBRC <- ATCC <- E. Canale-Parola: strain D4

doi: 10.13145/bacdive2973.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Burkholderiales
  • family: Comamonadaceae
  • genus: Hylemonella
  • species: Hylemonella gracilis
  • full scientific name: Hylemonella gracilis (Canale-Parola et al. 1966) Spring et al. 2004

  • synonyms

    @refsynonym
    20215Aquaspirillum gracile
    20215Spirillum gracile

@ref: 3494

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Comamonadaceae

genus: Hylemonella

species: Hylemonella gracilis

full scientific name: Hylemonella gracilis (Canale-Parola et al. 1966) Spring et al. 2004

strain designation: D4

type strain: yes

Morphology

cell morphology

  • @ref: 119719
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
3494SPIRILLUM GRACILE MEDIUM (DSMZ Medium 654)yeshttps://mediadive.dsmz.de/medium/654Name: SPIRILLUM GRACILE MEDIUM (DSMZ Medium 654) Composition: Agar 15.0 g/l Peptone 5.0 g/l Yeast extract 0.5 g/l K2HPO4 0.1 g/l Tween 80 0.02 g/l Tap water
36635MEDIUM 14 - Williams and Rittenberg medium for Aquaspirillum genusyesDistilled water make up to (1000.000 ml);Agar (13.000 g);Yeast extract (3.000 g);Peptone (5.000 g);Beef extract (3.000 g)
119719CIP Medium 14yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=14

culture temp

@refgrowthtypetemperaturerange
3494positivegrowth30mesophilic
36635positivegrowth30mesophilic
119719positivegrowth22-37
119719nogrowth5psychrophilic
119719nogrowth15psychrophilic
119719nogrowth41thermophilic

Physiology and metabolism

halophily

@refsaltgrowthtested relationconcentration
119719NaClpositivegrowth0 %
119719NaClnogrowth2 %
119719NaClnogrowth4 %
119719NaClnogrowth6 %
119719NaClnogrowth8 %
119719NaClnogrowth10 %

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
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
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
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754
119719citrate-carbon source16947
119719esculin-hydrolysis4853
119719glucose-fermentation17234
119719lactose-fermentation17716
119719nitrate-reduction17632
119719nitrite-reduction16301
119719sodium thiosulfate-builds gas from132112

antibiotic resistance

  • @ref: 119719
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

  • @ref: 119719
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11971915688acetoin-
11971917234glucose-

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
119719oxidase+
119719beta-galactosidase+3.2.1.23
119719alcohol dehydrogenase-1.1.1.1
119719gelatinase-
119719catalase+1.11.1.6
119719gamma-glutamyltransferase-2.3.2.2
119719lysine decarboxylase-4.1.1.18
119719ornithine decarboxylase-4.1.1.17
119719phenylalanine ammonia-lyase-4.3.1.24
119719tryptophan deaminase-
119719urease-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
119719-+++-+----++--------

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
119719---+/------+/-------------------+-------------------+/-

Isolation, sampling and environmental information

isolation

@refsample type
3494pondwater
60833Pondwater
119719Environment, Pondwater

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Aquatic
  • Cat3: #Pond (small)

taxonmaps

  • @ref: 69479
  • File name: preview.99_3015.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_1;96_1585;97_1891;98_2321;99_3015&stattab=map
  • Last taxonomy: Hylemonella gracilis subclade
  • 16S sequence: AF078753
  • Sequence Identity:
  • Total samples: 7561
  • soil counts: 1556
  • aquatic counts: 4404
  • animal counts: 993
  • plant counts: 608

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
34941Risk group (German classification)
1197191Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Aquaspirillum gracile 16S ribosomal RNA gene, partial sequenceAF0787531487ena887062
20218Hylemonella gracilis gene for 16S rRNA, partial sequence, strain: NBRC 14920AB6807061449ena80880

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Hylemonella gracilis ATCC 19624GCA_000211835contigncbi887062
66792Hylemonella gracilis ATCC 19624887062.3wgspatric887062
66792Hylemonella gracilis Canale-Parola D4, ATCC 19624651324043draftimg887062

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes89.487no
flagellatedyes77.912no
gram-positiveno98.729no
anaerobicno98.534no
halophileno93.962no
spore-formingno96.617no
thermophileno95.237no
glucose-utilyes57.815no
aerobicyes94.123no
glucose-fermentno88.428no

External links

@ref: 3494

culture collection no.: DSM 9158, ATCC 19624, CCUG 56031, LMG 8201, NBRC 14920, IFO 14920, CIP 107756

straininfo link

  • @ref: 72495
  • straininfo: 92577

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Metabolism4369249Sugar catabolism in Aquaspirillum gracile.Laughon BE, Krieg NRJ Bacteriol10.1128/jb.119.3.691-697.19741974Alcohol Oxidoreductases/metabolism, Aldehyde-Lyases/metabolism, Arabinose/metabolism, Carbohydrate Epimerases/metabolism, *Carbohydrate Metabolism, Cell-Free System, Chromatography, Gas, Chromatography, Paper, Fresh Water, Galactose/metabolism, Gluconates/biosynthesis/metabolism, Glucose/metabolism, Hydro-Lyases/metabolism, Phosphotransferases/metabolism, Spirillum/enzymology/*metabolism, Stereoisomerism, Sugar Acids/biosynthesis, *Water MicrobiologyEnzymology
Phylogeny14742465Ottowia thiooxydans gen. nov., sp. nov., a novel facultatively anaerobic, N2O-producing bacterium isolated from activated sludge, and transfer of Aquaspirillum gracile to Hylemonella gracilis gen. nov., comb. nov.Spring S, Jackel U, Wagner M, Kampfer PInt J Syst Evol Microbiol10.1099/ijs.0.02727-02004Betaproteobacteria/*classification/genetics/growth & development, Burkholderiaceae/*classification/genetics/growth & development/isolation & purification, Cell Division/drug effects, DNA, Ribosomal/genetics, Molecular Sequence Data, Nitrogen Oxides/*metabolism, Phylogeny, RNA, Ribosomal, 16S/genetics, Sewage/*microbiology, Thiosulfates/pharmacologyGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
3494Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 9158)https://www.dsmz.de/collection/catalogue/details/culture/DSM-9158
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
36635Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5226
60833Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 56031)https://www.ccug.se/strain?id=56031
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
68371Automatically annotated from API 50CH acid
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
72495Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID92577.1StrainInfo: A central database for resolving microbial strain identifiers
119719Curators of the CIPCollection of Institut Pasteur (CIP 107756)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107756