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, Gram-negative, rod-shaped

description: Afipia birgiae 34632 is an aerobe, Gram-negative, rod-shaped 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/bacdive1782.20240916.9.1

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 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 shapemotilityconfidence
23321negativerod-shapedno
116820negativerod-shapedno
69480negative97.813

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

@refgrowthtypetemperature
7026positivegrowth28
23321nogrowth35
23321nogrowth37
23321positivegrowth25-30
23321nogrowth42
38619positivegrowth25
55666positivegrowth30
116820positivegrowth15-30
116820nogrowth37
116820nogrowth41

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

@refdescriptionaccessionlengthdatabaseNCBI tax ID
7026Alpha proteobacterium 34632 16S ribosomal RNA gene, partial sequenceAF2883041426nuccore1197906
124043Afipia birgiae partial 16S rRNA gene, isolate strain #14 (MBG-DUTH)/DSM 17499 (ELTE)OU548668821nuccore151414

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

@reftraitmodeldescriptionpredictionconfidencetraining_data
69480gram-positivegram-positivePositive reaction to Gram-stainingno97.813yes
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no93.891no
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes86.369no
69480spore-formingspore-formingAbility to form endo- or exosporesno82.618no
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno97.825yes
69480flagellatedmotile2+Ability to perform flagellated movementyes78.265no

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
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)
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
124043Dr. Isabel Schober, Dr. Julia KoblitzData extracted from sequence databases, automatically matched based on designation and taxonomy