Strain identifier

BacDive ID: 1780

Type strain: Yes

Species: Afipia broomeae

Strain Designation: B91-007286

Strain history: CIP <- 1992, ATCC <- D.J. Brenner, CDC: strain B91-007286 <- Nat. Hlth. Inst., New Zealand: strain F186, GO 382

NCBI tax ID(s): 883078 (strain), 56946 (species)

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General

@ref: 3002

BacDive-ID: 1780

DSM-Number: 7327

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

description: Afipia broomeae B91-007286 is an obligate aerobe, Gram-negative bacterium that was isolated from sputum.

NCBI tax id

NCBI tax idMatching level
56946species
883078strain

strain history

@refhistory
3002<- ATCC <- D.J. Brenner; B91-007286 <- Natl. Health Inst. Wellington
117059CIP <- 1992, ATCC <- D.J. Brenner, CDC: strain B91-007286 <- Nat. Hlth. Inst., New Zealand: strain F186, GO 382

doi: 10.13145/bacdive1780.20240916.9.1

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 broomeae
  • full scientific name: Afipia broomeae Brenner et al. 1992

@ref: 3002

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Nitrobacteraceae

genus: Afipia

species: Afipia broomeae

full scientific name: Afipia broomeae Brenner et al. 1992

strain designation: B91-007286

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
117059negativerod-shapedyes
69480negative98.514

colony morphology

  • @ref: 3002
  • incubation period: 2-3 days

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
3002BCYE-AGAR (DSMZ Medium 585)yeshttps://mediadive.dsmz.de/medium/585Name: BCYE AGAR (DSMZ Medium 585) Composition: OXOID Legionella CYE-Agar base
40642MEDIUM 23 - for Afipia and LegionellayesDistilled water make up to (1000.000 ml);Legionella agar (37.000 g);Legionella - enrichment mixture (10.000 ml)
117059CIP Medium 23yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=23

culture temp

@refgrowthtypetemperature
3002positivegrowth28
40642positivegrowth30
50092positivegrowth37
117059positivegrowth15-37
117059nogrowth41

Physiology and metabolism

oxygen tolerance

  • @ref: 117059
  • oxygen tolerance: obligate aerobe

spore formation

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

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
117059hippurate+hydrolysis606565
117059nitrate-reduction17632
117059nitrite-reduction16301
117059malonate-assimilation15792
117059glucose-degradation17234

metabolite production

  • @ref: 117059
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
3002catalase+1.11.1.6
3002cytochrome-c oxidase+1.9.3.1
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
117059oxidase+
117059alcohol dehydrogenase-1.1.1.1
117059gelatinase-
117059gamma-glutamyltransferase-2.3.2.2
117059lysine decarboxylase-4.1.1.18
117059ornithine decarboxylase-4.1.1.17
117059tryptophan deaminase-
117059urease+3.5.1.5

fatty acid profile

  • fatty acids

    @reffatty acidpercentageECL
    50092C15:00.515
    50092C16:05.216
    50092C17:03.517
    50092C18:015.718
    50092C19:0119
    50092C20:00.420
    5009211 methyl 18:1 ω7c12.818.081
    50092C16:1 ω7c4.815.819
    50092C17:0 ANTEISO DMA1.717.195
    50092C17:0 CYCLO19.916.888
    50092C17:1 ω9c0.616.773
    50092C18:1 ω6c1.717.858
    50092C18:1 ω7c /12t/9t12.917.824
    50092C19:0 CYCLO ω8c15.418.9
    50092Unidentified0.518.131
    50092Unidentified0.718.309
    50092Unidentified0.918.783
    50092Unidentified0.919.818
    50092Unidentified0.619.874
  • type of FA analysis: whole cell analysis
  • method/protocol: CCUG

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
117059--++-+--+--+--------

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
117059-------------------------------------------------

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentsampling date
3002sputumNew ZealandNZLAustralia and Oceania
50092Human sputumNew ZealandNZLAustralia and Oceania1981
117059Human, Sputum

isolation source categories

  • Cat1: #Host Body Product
  • Cat2: #Fluids
  • Cat3: #Sputum

taxonmaps

  • @ref: 69479
  • File name: preview.99_3048.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_86;96_297;97_1907;98_2342;99_3048&stattab=map
  • Last taxonomy: Bradyrhizobiaceae
  • 16S sequence: U87759
  • Sequence Identity:
  • Total samples: 4226
  • soil counts: 1896
  • aquatic counts: 1311
  • animal counts: 501
  • plant counts: 518

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
30022Risk group (German classification)
1170591Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Afipia broomeae strain F186 16S ribosomal RNA gene, partial sequenceU877591401nuccore883078
124043Afipia broomeae partial 16S rRNA gene, isolate strain #15 (MBG-DUTH)/DSM 7327 (ELTE)OU548669801nuccore56946

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Afipia broomeae ATCC 49717GCA_000314675scaffoldncbi883078
66792Afipia broomeae ATCC 49717883078.3wgspatric883078
66792Afipia broomeae ATCC 497172537561905draftimg883078

GC content

  • @ref: 3002
  • GC-content: 61.5

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69481spore-formingspore-formingAbility to form endo- or exosporesno100no
69480gram-positivegram-positivePositive reaction to Gram-stainingno98.514no
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no94.728no
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes89.409yes
69480spore-formingspore-formingAbility to form endo- or exosporesno89.435no
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno97.444yes
69480flagellatedmotile2+Ability to perform flagellated movementyes69.015no

External links

@ref: 3002

culture collection no.: DSM 7327, ATCC 49717, CCUG 30458, CIP 103517

straininfo link

  • @ref: 71427
  • straininfo: 12659

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
3002Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 7327)https://www.dsmz.de/collection/catalogue/details/culture/DSM-7327
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
40642Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/15324
50092Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 30458)https://www.ccug.se/strain?id=30458
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
71427Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID12659.1StrainInfo: A central database for resolving microbial strain identifiers
117059Curators of the CIPCollection of Institut Pasteur (CIP 103517)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103517
124043Dr. Isabel Schober, Dr. Julia KoblitzData extracted from sequence databases, automatically matched based on designation and taxonomy