Strain identifier

BacDive ID: 1782

Type strain: Yes

Species: Afipia birgiae

Strain Designation: 34632

Strain history: CIP <- 1999, B. La Scola, NRC, Timone Hosp., Marseille, France: strain 34632

NCBI tax ID(s): 151414 (species)

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General

@ref: 7026

BacDive-ID: 1782

DSM-Number: 17499

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

description: Afipia birgiae 34632 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from water supply of hospital.

NCBI tax id

  • NCBI tax id: 151414
  • Matching level: species

strain history

@refhistory
7026<- B. La Scola
386191999, B. La Scola, NRC, Fac. Medicine, Marseille, France: strain 34632
116820CIP <- 1999, B. La Scola, NRC, Timone Hosp., Marseille, France: strain 34632

doi: 10.13145/bacdive1782.20230509.8.1

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 birgiae
  • full scientific name: Afipia birgiae La Scola et al. 2002

@ref: 7026

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Nitrobacteraceae

genus: Afipia

species: Afipia birgiae

full scientific name: Afipia birgiae La Scola et al. 2002

strain designation: 34632

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotility
23321negativerod-shapedno
116820negativerod-shapedno

colony morphology

  • @ref: 23321
  • type of hemolysis: gamma
  • colony color: grey-white, opaque
  • medium used: BCYE agar

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7026BCYE-AGAR (DSMZ Medium 585)yeshttps://mediadive.dsmz.de/medium/585Name: BCYE AGAR (DSMZ Medium 585) Composition: OXOID Legionella CYE-Agar base
38619MEDIUM 23 - for Afipia and LegionellayesDistilled water make up to (1000.000 ml);Legionella agar (37.000 g);Legionella - enrichment mixture (10.000 ml)
116820CIP Medium 23yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=23

culture temp

@refgrowthtypetemperaturerange
7026positivegrowth28mesophilic
23321nogrowth35mesophilic
23321nogrowth37mesophilic
23321positivegrowth25-30mesophilic
23321nogrowth42thermophilic
38619positivegrowth25mesophilic
55666positivegrowth30mesophilic
116820positivegrowth15-30
116820nogrowth37mesophilic
116820nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
55666aerobe
116820facultative anaerobe

halophily

  • @ref: 23321
  • salt: NaCl
  • growth: no
  • tested relation: growth
  • concentration: 6 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2332122599arabinose-assimilation
2332116947citrate-assimilation
2332124265gluconate-assimilation
2332125115malate-assimilation
23321506227N-acetylglucosamine-assimilation
2332118401phenylacetate-assimilation
2332128757fructose-builds acid from
2332117234glucose-builds acid from
2332117306maltose-builds acid from
2332129864mannitol-builds acid from
2332137684mannose-builds acid from
2332117992sucrose-builds acid from
2332128757fructose-fermentation
2332117234glucose-fermentation
2332117306maltose-fermentation
2332129864mannitol-fermentation
2332137684mannose-fermentation
2332117992sucrose-fermentation
233214853esculin-hydrolysis
233215291gelatin-hydrolysis
2332128757fructose-oxidation
2332117234glucose-oxidation
2332117306maltose-oxidation
2332129864mannitol-oxidation
2332137684mannose-oxidation
2332117992sucrose-oxidation
2332117128adipate+assimilation
2332117632nitrate+reduction
116820606565hippurate-hydrolysis
11682017632nitrate+reduction
11682016301nitrite-reduction

antibiotic resistance

@refChEBImetaboliteis antibioticis sensitivesensitivity conc.group ID
2332129007ceftriaxoneyesyes0.25 µg/mL (MIC)
2332117833gentamicinyesyes0.25 µg/mL (MIC)
233217528netilmycinyesyes0.25 µg/mL (MIC)
2332128864tobramycinyesyes0.25 µg/mL (MIC)
233212676amoxicillinyesyes0.5 µg/mL (MIC)13
23321209807cefoxitinyesyes0.5 µg/mL (MIC)
23321471744imipenemyesyes0.5 µg/mL (MIC)
2332128077rifampicinyesyes1 µg/mL (MIC)
233212637amikacinyesyes2 µg/mL (MIC)
23321100241ciprofloxacinyesyes2 µg/mL (MIC)
233213770co-trimoxazoleyesyes256 µg/mL (MIC)
2332117334penicillinyesyes256 µg/mL (MIC)
233218232piperacillinyesyes256 µg/mL (MIC)
233219587ticarcillinyesyes256 µg/mL (MIC)
2332128001vancomycinyesyes256 µg/mL (MIC)
233213508ceftazidimeyesyes4 µg/mL (MIC)
23321124991cefalotinyesyes4 µg/mL (MIC)
2332150845doxycyclineyesyes4 µg/mL (MIC)
233212676amoxicillinyesyes64 µg/mL (MIC)
2332148923erythromycinyesyes64 µg/mL (MIC)
23321478164cefepimeyesyes8 µg/mL (MIC)
2332148947clavulanic acidyesyes0.5 µg/mL (MIC)13

metabolite production

@refChebi-IDmetaboliteproduction
2332116136hydrogen sulfideno
11682035581indoleno

enzymes

@refvalueactivityec
23321arginine dihydrolase-3.5.3.6
23321beta-galactosidase-3.2.1.23
23321catalase+/-1.11.1.6
23321cytochrome oxidase+1.9.3.1
23321urease+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
116820oxidase+
116820alcohol dehydrogenase-1.1.1.1
116820catalase+1.11.1.6
116820tween esterase-
116820gamma-glutamyltransferase-2.3.2.2
116820lysine decarboxylase-4.1.1.18
116820ornithine decarboxylase-4.1.1.17
116820urease+3.5.1.5

fatty acid profile

  • fatty acids

    @reffatty acidpercentageECL
    55666C15:01.815
    55666C16:03.116
    55666C17:07.117
    55666C18:05.118
    5566611 methyl 18:1 ω7c7.818.081
    55666C16:1 ω7c15.315.819
    55666C17:0 CYCLO27.116.888
    55666C17:1 ω8c7.116.792
    55666C17:ISO 2OH3.717.875
    55666C18:1 ω7c /12t/9t16.217.824
    55666C19:0 CYCLO ω8c318.9
    55666unknown 18.7972.718.797
  • 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
116820--++----+-++--------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
7026water supply of hospitalMarseilleFranceFRAEurope
23321water supply of the La Timone Hospital Centre
55666Water supply of La Timone Hospital CentreMarseilleFranceFRAEurope
116820Environment, Water tankMarseilleFranceFRAEurope1999

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic
#Infection#Medical environment#Clinic

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: AF288304
  • 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
70261Risk group (German classification)
1168201Risk group (French classification)

Sequence information

16S sequences

  • @ref: 7026
  • description: Alpha proteobacterium 34632 16S ribosomal RNA gene, partial sequence
  • accession: AF288304
  • length: 1426
  • database: ena
  • NCBI tax ID: 1197906

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Afipia birgiae 34632GCA_000308295contigncbi1197906
66792Afipia birgiae 346321197906.5wgspatric1197906
66792Afipia birgiae 346322551306146draftimg1197906

GC content

@refGC-contentmethod
702659.3
2332159.3high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes76.046yes
flagellatedno54.004no
gram-positiveno98.47no
anaerobicno98.762yes
aerobicyes92.456yes
halophileno94.634no
spore-formingno95.326no
glucose-utilyes61.039no
thermophileno97.88no
glucose-fermentno92.979yes

External links

@ref: 7026

culture collection no.: DSM 17499, CCUG 43108, CIP 106344

straininfo link

  • @ref: 71429
  • straininfo: 100486

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny12361286Description of Afipia birgiae sp. nov. and Afipia massiliensis sp. nov. and recognition of Afipia felis genospecies A.La Scola B, Mallet MN, Grimont PAD, Raoult DInt J Syst Evol Microbiol10.1099/00207713-52-5-17732002Afipia/*classification/genetics/isolation & purification/pathogenicity, Base Composition, Cross Infection/microbiology, DNA, Bacterial/chemistry/genetics, Fatty Acids/analysis, Gram-Negative Bacterial Infections/microbiology, Humans, Phenotype, Phylogeny, Species Specificity, Water SupplyPathogenicity
Genetics23209256Genome sequence of Afipia birgiae, a rare bacterium associated with Amoebae.Pagnier I, Croce O, Robert C, Raoult D, La Scola BJ Bacteriol10.1128/JB.01918-122012Afipia/classification/*genetics/isolation & purification, Amoeba/*microbiology, Base Composition/genetics, DNA, Bacterial/genetics, *Genome, Bacterial, Molecular Sequence Data, RNA, Bacterial/genetics, Sequence Analysis, DNAPhylogeny

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
7026Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17499)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17499
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
23321Bernard La Scola, Marie-Noelle Mallet, Patrick A D Grimont, Didier Raoult10.1099/00207713-52-5-1773Description of Afipia birgiae sp. nov. and Afipia massiliensis sp. nov. and recognition of Afipia felis genospecies A.IJSEM 52: 1773-1782 200212361286
38619Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/18464
55666Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 43108)https://www.ccug.se/strain?id=43108
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)
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
71429Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID100486.1StrainInfo: A central database for resolving microbial strain identifiers
116820Curators of the CIPCollection of Institut Pasteur (CIP 106344)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106344