Strain identifier

BacDive ID: 235

Type strain: Yes

Species: Ignavigranum ruoffiae

Strain Designation: 1607-97

Strain history: CIP <- 1999, P. Campbell, CDC: strain 1607-97

NCBI tax ID(s): 89093 (species)

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General

@ref: 6061

BacDive-ID: 235

DSM-Number: 15695

keywords: genome sequence, 16S sequence, Bacteria, microaerophile, mesophilic, Gram-positive, coccus-shaped

description: Ignavigranum ruoffiae 1607-97 is a microaerophile, mesophilic, Gram-positive bacterium that was isolated from human wound.

NCBI tax id

  • NCBI tax id: 89093
  • Matching level: species

strain history

@refhistory
6061<- CCUG <- M. D. Collins <- R. R. Facklam, CDC
122315CIP <- 1999, P. Campbell, CDC: strain 1607-97

doi: 10.13145/bacdive235.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Lactobacillales
  • family: Aerococcaceae
  • genus: Ignavigranum
  • species: Ignavigranum ruoffiae
  • full scientific name: Ignavigranum ruoffiae Collins et al. 1999

@ref: 6061

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Lactobacillales

family: Aerococcaceae

genus: Ignavigranum

species: Ignavigranum ruoffiae

full scientific name: Ignavigranum ruoffiae Collins et al. 1999

strain designation: 1607-97

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
23253positivecoccus-shapedno
69480no96.706
69480positive100
122315positivecoccus-shapedno

colony morphology

  • @ref: 122315

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6061TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)yeshttps://mediadive.dsmz.de/medium/92Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water
6061COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)yeshttps://mediadive.dsmz.de/medium/693Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base
39388MEDIUM 6 - Columbia agar with 10 % horse bloodyesDistilled water make up to (1000.000 ml);Columbia agar (39.000 g);Horseblood (100.000 ml)
122315CIP Medium 6yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=6

culture temp

@refgrowthtypetemperaturerange
6061positivegrowth37mesophilic
23253positivegrowth45thermophilic
39388positivegrowth37mesophilic
53788positivegrowth37mesophilic
122315positivegrowth25-45
122315nogrowth10psychrophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
6061microaerophile
23253facultative anaerobe
53788microaerophile
122315facultative anaerobe

spore formation

@refspore formationconfidence
23253no
69481no100
69480no99.975

halophily

@refsaltgrowthtested relationconcentration
23253NaClpositivemaximum6.5 %
122315NaClpositivegrowth6.5 %

murein

  • @ref: 23253
  • type: A1alpha L-Lys-direct

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2325323456cyclodextrin-builds acid from
2325318333D-arabitol-builds acid from
2325316024D-mannose-builds acid from
2325316634raffinose-builds acid from
2325316988D-ribose-builds acid from
2325365327D-xylose-builds acid from
2325328087glycogen-builds acid from
2325330849L-arabinose-builds acid from
2325317716lactose-builds acid from
232536731melezitose-builds acid from
2325328053melibiose-builds acid from
2325327941pullulan-builds acid from
2325330911sorbitol-builds acid from
2325333954tagatose-builds acid from
2325327082trehalose-builds acid from
232534853esculin-hydrolysis
232535291gelatin-hydrolysis
23253606565hippurate-hydrolysis
2325328017starch-hydrolysis
2325317632nitrate-reduction
2325317234glucose+builds acid from
2325329864mannitol+/-builds acid from
2325317992sucrose+/-builds acid from
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837118287L-fucose-builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose-builds acid from
6837132528turanose-builds acid from
6837128066gentiobiose-builds acid from
6837117151xylitol-builds acid from
6837128087glycogen-builds acid from
6837128017starch-builds acid from
6837116634raffinose-builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837127082trehalose-builds acid from
6837128053melibiose-builds acid from
6837117716lactose-builds acid from
6837117306maltose+builds acid from
6837117057cellobiose+builds acid from
6837117814salicin+builds acid from
6837118305arbutin+builds acid from
6837127613amygdalin-builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose-builds acid from
6837117266L-sorbose-builds acid from
6837116024D-mannose+builds acid from
6837115824D-fructose+builds acid from
6837117634D-glucose+builds acid from
6837112936D-galactose-builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose-builds acid from
6837116988D-ribose+builds acid from
6837130849L-arabinose-builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol-builds acid from
1223154853esculin-hydrolysis
122315606565hippurate-hydrolysis
12231517632nitrate-reduction
12231516301nitrite-reduction

metabolite production

  • @ref: 23253
  • Chebi-ID: 15688
  • metabolite: acetoin
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-test
2325315688acetoin-
12231515688acetoin-

enzymes

@refvalueactivityec
23253alkaline phosphatase-3.1.3.1
23253alpha-fucosidase-3.2.1.51
23253alpha-galactosidase-3.2.1.22
23253arginine dihydrolase+3.5.3.6
23253beta-galactosidase-3.2.1.23
23253beta-glucuronidase-3.2.1.31
23253beta-mannosidase-3.2.1.25
23253catalase-1.11.1.6
23253chymotrypsin-3.4.4.5
23253cystine arylamidase-3.4.11.3
23253glycyl tryptophan arylamidase-
23253leucine arylamidase+3.4.11.1
23253lipase (C 14)-
23253pyrazinamidase-3.5.1.B15
23253pyroglutamic acid arylamidase+
23253tripeptide aminopeptidase-3.4.11.4
23253trypsin-3.4.21.4
23253urease+3.5.1.5
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
122315oxidase-
122315beta-galactosidase-3.2.1.23
122315alcohol dehydrogenase-1.1.1.1
122315catalase-1.11.1.6
122315gamma-glutamyltransferase-2.3.2.2
122315lysine decarboxylase-4.1.1.18
122315ornithine decarboxylase-4.1.1.17

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
122315-+++-+----++--------

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
122315----+-----+++----+/-+/---+/--++/-+++--+/----------------+/---

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentsampling dateisolation date
6061human woundUSAUSANorth America
53788Human woundUSAUSANorth America1995
122315Human, WoundUnited States of AmericaUSANorth America1996

isolation source categories

Cat1Cat2Cat3
#Host#Human
#Host Body-Site#Other#Wound

taxonmaps

  • @ref: 69479
  • File name: preview.99_82750.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_178;96_34635;97_43940;98_57459;99_82750&stattab=map
  • Last taxonomy: Ignavigranum ruoffiae subclade
  • 16S sequence: Y16426
  • Sequence Identity:
  • Total samples: 1262
  • soil counts: 123
  • aquatic counts: 64
  • animal counts: 1049
  • plant counts: 26

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
60612Risk group (German classification)
1223151Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Ignavigranum ruoffiae strain CCUG 37658 16S-23S ribosomal RNA intergenic spacer, complete sequenceJQ012778197ena89093
6061Ignavigranum ruoffiae 16S rRNA geneY164261417ena89093

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Ignavigranum ruoffiae DSM 15695GCA_900110675scaffoldncbi89093
66792Ignavigranum ruoffiae strain DSM 1569589093.3wgspatric89093
66792Ignavigranum ruoffiae DSM 156952634166308draftimg89093

GC content

@refGC-contentmethod
606140
2325340.00thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
glucose-fermentyes68.284no
motileno94.75no
flagellatedno97.773no
gram-positiveyes90.798no
anaerobicno87.901no
aerobicno91.718yes
halophileyes83.954no
spore-formingno93.555yes
thermophileno98.74no
glucose-utilyes84.737no

External links

@ref: 6061

culture collection no.: DSM 15695, ATCC 700630, CCUG 37658, CIP 105896

straininfo link

  • @ref: 69918
  • straininfo: 44048

literature

  • topic: Phylogeny
  • Pubmed-ID: 10028250
  • title: Ignavigranum ruoffiae sp. nov., isolated from human clinical specimens.
  • authors: Collins MD, Lawson PA, Monasterio R, Falsen E, Sjoden B, Facklam RR
  • journal: Int J Syst Bacteriol
  • DOI: 10.1099/00207713-49-1-97
  • year: 1999
  • mesh: Base Sequence, Gram-Positive Bacteria/*classification/isolation & purification, Humans, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/chemistry
  • topic2: Pathogenicity

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
6061Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15695)https://www.dsmz.de/collection/catalogue/details/culture/DSM-15695
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
23253Matthew D. Collins, Paul A. Lawson, Rafael Monasterio, Enevold Falsen, Berit Sjödén, Richard R. Facklam10.1099/00207713-49-1-97Ignavigranum ruoffiae sp. nov., isolated from human clinical specimensIJSEM 49: 97-101 199910028250
39388Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/17965
53788Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 37658)https://www.ccug.se/strain?id=37658
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
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
69918Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID44048.1StrainInfo: A central database for resolving microbial strain identifiers
122315Curators of the CIPCollection of Institut Pasteur (CIP 105896)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105896