Strain identifier

BacDive ID: 1777

Type strain: Yes

Species: Afipia clevelandensis

Strain Designation: Cleveland clinic foundation strain, 411m, B91-007353, F6703, G1849

Strain history: CIP <- 1992, ATCC <- D.J. Brenner, CDC: strain B91-007353 <- G.S. Hall: strain G1849, F6703

NCBI tax ID(s): 883079 (strain), 1034 (species)

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General

@ref: 3117

BacDive-ID: 1777

DSM-Number: 7315

keywords: genome sequence, 16S sequence, Bacteria, Gram-negative

description: Afipia clevelandensis Cleveland clinic foundation strain is a Gram-negative bacterium that was isolated from human tibia, biopsy.

NCBI tax id

NCBI tax idMatching level
883079strain
1034species

strain history

@refhistory
3117<- ATCC <- D.J. Brenner; B91-007353 <- G.S. Hall
118308CIP <- 1992, ATCC <- D.J. Brenner, CDC: strain B91-007353 <- G.S. Hall: strain G1849, F6703

doi: 10.13145/bacdive1777.20240916.9.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Hyphomicrobiales
  • family: Nitrobacteraceae
  • genus: Afipia
  • species: Afipia clevelandensis
  • full scientific name: Afipia clevelandensis Brenner et al. 1992

@ref: 3117

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Nitrobacteraceae

genus: Afipia

species: Afipia clevelandensis

full scientific name: Afipia clevelandensis Brenner et al. 1992

strain designation: Cleveland clinic foundation strain, 411m, B91-007353, F6703, G1849

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
118308negativerod-shapedyes
69480negative98.813

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
3117BCYE-AGAR (DSMZ Medium 585)yeshttps://mediadive.dsmz.de/medium/585Name: BCYE AGAR (DSMZ Medium 585) Composition: OXOID Legionella CYE-Agar base
40686MEDIUM 23 - for Afipia and LegionellayesDistilled water make up to (1000.000 ml);Legionella agar (37.000 g);Legionella - enrichment mixture (10.000 ml)
118308CIP Medium 23yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=23

culture temp

@refgrowthtypetemperature
3117positivegrowth28
40686positivegrowth30
50091positivegrowth37
118308positivegrowth30
118308nogrowth10
118308nogrowth15
118308nogrowth41

Physiology and metabolism

spore formation

  • @ref: 69481
  • spore formation: no
  • confidence: 100

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
11830817632nitrate-reduction
11830816301nitrite-reduction
11830815792malonate-assimilation
11830817234glucose-degradation
11830817632nitrate-respiration

enzymes

@refvalueactivityec
118308oxidase+
118308alcohol dehydrogenase-1.1.1.1
118308catalase-1.11.1.6
118308lysine decarboxylase-4.1.1.18
118308ornithine decarboxylase-4.1.1.17
118308urease+3.5.1.5

fatty acid profile

  • @reffatty acidpercentageECL
    50091C16:05.516
    50091C17:00.717
    50091C18:012.218
    5009111 methyl 18:1 ω7c13.318.081
    50091C16:1 ω7c9.215.819
    50091C17:0 CYCLO23.116.888
    50091C18:1 ω7c /12t/9t26.617.824
    50091C19:0 CYCLO ω8c8.618.9
    50091C20:1 ω7c0.919.833
  • type of FA analysis: whole cell analysis
  • method/protocol: CCUG
  • @reffatty acidpercentageECL
    50091C14:00.714
    50091C16:07.116
    50091C18:012.418
    5009111 methyl 18:1 ω7c6.818.081
    50091C16:1 ω7c19.515.819
    50091C17:0 CYCLO16.316.888
    50091C18:1 ω7c /12t/9t28.517.824
    50091C18:2 ω6,9c/C18:0 ANTE3.517.724
    50091C19:0 CYCLO ω8c2.618.9
    50091C20:1 ω7c1.419.833
    50091Unidentified0.313.742
    50091Unidentified0.418.441
    50091Unidentified0.619.785
  • type of FA analysis: whole cell analysis
  • method/protocol: CCUG

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling date
3117human tibia, biopsyOhioUSAUSANorth America
50091Tibial biopsy,male,age 69yr,diedOhioUSAUSANorth America1988
118308Human, Tibial biopsy

isolation source categories

Cat1Cat2Cat3
#Infection#Patient#Biopsy
#Host#Human
#Host Body-Site#Limb#Leg

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
31172Risk group (German classification)
1183081Risk group (French classification)

Sequence information

16S sequences

  • @ref: 20218
  • description: Afipia clevelandensis strain B-91-007353 16S ribosomal RNA gene, partial sequence
  • accession: M69186
  • length: 1425
  • database: nuccore
  • NCBI tax ID: 883079

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Afipia clevelandensis ATCC 49720GCA_000336555scaffoldncbi883079
66792Afipia clevelandensis ATCC 49720883079.3wgspatric883079
66792Afipia clevelandensis ATCC 497202537561906draftimg883079

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69481spore-formingspore-formingAbility to form endo- or exosporesno100no
69480gram-positivegram-positivePositive reaction to Gram-stainingno98.813no
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no93.76no
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes85.933no
69480spore-formingspore-formingAbility to form endo- or exosporesno84.983no
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno98.999yes
69480flagellatedmotile2+Ability to perform flagellated movementyes75.511no

External links

@ref: 3117

culture collection no.: CCUG 30457, DSM 7315, ATCC 49720, CIP 103516

straininfo link

  • @ref: 71424
  • straininfo: 12657

literature

  • topic: Phylogeny
  • Pubmed-ID: 13130002
  • title: Bosea minatitlanensis sp. nov., a strictly aerobic bacterium isolated from an anaerobic digester.
  • authors: Ouattara AS, Assih EA, Thierry S, Cayol JL, Labat M, Monroy O, Macarie H
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.02540-0
  • year: 2003
  • mesh: Aerobiosis, Bradyrhizobiaceae/classification/genetics/*isolation & purification/metabolism, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/analysis, Genes, Bacterial, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sewage/microbiology, Species Specificity
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
3117Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 7315)https://www.dsmz.de/collection/catalogue/details/culture/DSM-7315
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
40686Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/15322
50091Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 30457)https://www.ccug.se/strain?id=30457
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)
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
71424Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID12657.1StrainInfo: A central database for resolving microbial strain identifiers
118308Curators of the CIPCollection of Institut Pasteur (CIP 103516)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103516