Strain identifier

BacDive ID: 1781

Type strain: Yes

Species: Afipia massiliensis

Strain Designation: 34633

Strain history: CIP <- 2001, B. La Scola, Timone Hosp., Marseille, France: strain 34633

NCBI tax ID(s): 211460 (species)

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General

@ref: 7025

BacDive-ID: 1781

DSM-Number: 17498

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

description: Afipia massiliensis 34633 is an aerobe, Gram-negative, motile bacterium that was isolated from water supply of hospital.

NCBI tax id

  • NCBI tax id: 211460
  • Matching level: species

strain history

@refhistory
7025<- B. La Scola; 34633
340612001, B. La Scola, Fac. Medicine, Marseille, France: strain 34633
120848CIP <- 2001, B. La Scola, Timone Hosp., Marseille, France: strain 34633

doi: 10.13145/bacdive1781.20240916.9.1

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

@ref: 7025

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Nitrobacteraceae

genus: Afipia

species: Afipia massiliensis

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

strain designation: 34633

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityflagellum arrangementconfidence
23321negativerod-shapedyesmonotrichous, polar
120848negativerod-shapedyes
69480negative98.014

colony morphology

@reftype of hemolysiscolony colormedium usedincubation period
23321gammagrey-white, opaqueBCYE agar
566712 days

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7025BCYE-AGAR (DSMZ Medium 585)yeshttps://mediadive.dsmz.de/medium/585Name: BCYE AGAR (DSMZ Medium 585) Composition: OXOID Legionella CYE-Agar base
23321BCYE agaryes
34061MEDIUM 23 - for Afipia and LegionellayesDistilled water make up to (1000.000 ml);Legionella agar (37.000 g);Legionella - enrichment mixture (10.000 ml)
120848CIP Medium 23yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=23

culture temp

@refgrowthtypetemperature
7025positivegrowth28
23321nogrowth35
23321nogrowth37
23321positivegrowth25-30
23321nogrowth42
34061positivegrowth25
56671positivegrowth30
120848positivegrowth22-30
120848nogrowth15
120848nogrowth37
120848nogrowth41

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
56671aerobe
120848facultative anaerobe

spore formation

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

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
120848606565hippurate+hydrolysis
12084817632nitrate+reduction
12084816301nitrite-reduction

antibiotic resistance

@refChEBImetaboliteis antibioticis sensitivesensitivity conc.group ID
23321471744imipenemyesyes0.5 µg/mL (MIC)
2332129007ceftriaxoneyesyes1 µg/mL (MIC)
2332128077rifampicinyesyes1 µg/mL (MIC)
233218232piperacillinyesyes128 µg/mL (MIC)
233219587ticarcillinyesyes128 µg/mL (MIC)
233213770co-trimoxazoleyesyes16 µg/mL (MIC)
2332150845doxycyclineyesyes16 µg/mL (MIC)
2332148923erythromycinyesyes16 µg/mL (MIC)
2332117334penicillinyesyes16 µg/mL (MIC)
233212637amikacinyesyes2 µg/mL (MIC)
23321124991cefalotinyesyes2 µg/mL (MIC)
23321100241ciprofloxacinyesyes2 µg/mL (MIC)
2332117833gentamicinyesyes2 µg/mL (MIC)
2332128864tobramycinyesyes2 µg/mL (MIC)
2332128001vancomycinyesyes256 µg/mL (MIC)
233212676amoxicillinyesyes32 µg/mL (MIC)
233212676amoxicillinyesyes32 µg/mL (MIC)12
23321209807cefoxitinyesyes32 µg/mL (MIC)
233213508ceftazidimeyesyes32 µg/mL (MIC)
233217528netilmycinyesyes32 µg/mL (MIC)
23321478164cefepimeyesyes4 µg/mL (MIC)
2332148947clavulanic acidyesyes32 µg/mL (MIC)12

metabolite production

@refChebi-IDmetaboliteproduction
2332116136hydrogen sulfideno
12084835581indoleno

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
120848oxidase+
120848alcohol dehydrogenase-1.1.1.1
120848gelatinase-
120848catalase+1.11.1.6
120848gamma-glutamyltransferase+2.3.2.2
120848lysine decarboxylase-4.1.1.18
120848ornithine decarboxylase-4.1.1.17
120848urease+3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
120848-+++-+--+-++--------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
7025water supply of hospitalMarseilleFranceFRAEurope
23321water supply of the La Timone Hospital Centre
56671Water supplyMarseille,La TimoneFranceFRAEurope
120848Environment, Drinking waterMarseilleFranceFRAEurope1998

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_7957.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_86;96_297;97_1907;98_2342;99_7957&stattab=map
  • Last taxonomy: Afipia
  • 16S sequence: AY568510
  • Sequence Identity:
  • Total samples: 780
  • soil counts: 379
  • aquatic counts: 84
  • animal counts: 54
  • plant counts: 263

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
70251Risk group (German classification)
1208481Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
23321Afipia massiliensis 16S ribosomal RNA gene, partial sequenceAY0295621375nuccore1211024
7025Uncultured Afipia sp. clone NW-12 16S ribosomal RNA gene, partial sequenceAY5685101487nuccore218203

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Afipia massiliensis DSM 17498GCA_014203115contigncbi211460
66792Afipia massiliensis strain DSM 17498211460.6wgspatric211460
66792Afipia massiliensis DSM 174982861716478draftimg211460

GC content

@refGC-contentmethod
702560.2
2332160.2high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69481spore-formingspore-formingAbility to form endo- or exosporesno100no
69480gram-positivegram-positivePositive reaction to Gram-stainingno98.014no
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no91.836yes
69480spore-formingspore-formingAbility to form endo- or exosporesno86.876no
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes83.632no
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno97.324no
69480flagellatedmotile2+Ability to perform flagellated movementyes77.185yes

External links

@ref: 7025

culture collection no.: DSM 17498, CCUG 45153, CIP 107022

straininfo link

  • @ref: 71428
  • straininfo: 100487

literature

  • topic: Phylogeny
  • Pubmed-ID: 12361286
  • title: Description of Afipia birgiae sp. nov. and Afipia massiliensis sp. nov. and recognition of Afipia felis genospecies A.
  • authors: La Scola B, Mallet MN, Grimont PAD, Raoult D
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/00207713-52-5-1773
  • year: 2002
  • mesh: Afipia/*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 Supply
  • topic2: Pathogenicity

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
7025Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17498)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17498
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
34061Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/19217
56671Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 45153)https://www.ccug.se/strain?id=45153
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)
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
71428Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID100487.1StrainInfo: A central database for resolving microbial strain identifiers
120848Curators of the CIPCollection of Institut Pasteur (CIP 107022)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107022