Name: Afipia massiliensis 34633
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 1781

Type strain:

Species: Afipia massiliensis

Strain Designation: 34633

Culture col. no.: DSM 17498, CCUG 45153, CIP 107022

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

NCBI tax ID(s): 211460 (species)

SI-ID 100487

CCUG 45153, CIP 107022, DSM 17498

Special Collections

Section

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

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

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Pseudomonadota*
	Class	*Alphaproteobacteria*
	Order	*Hyphomicrobiales*
	Family	*Nitrobacteraceae*
	Genus	*Afipia*
	Species	**Afipia massiliensis**
	Full Scientific Name (LPSN)	Afipia massiliensis La Scola et al. 2002

Information on morphological and physiological properties Morphology

[Ref.: #23321]	Gram stain	negative
[Ref.: #120848]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %98.014

[Ref.: #23321]	Cell shape	rod-shaped
[Ref.: #120848]	Cell shape	rod-shaped

[Ref.: #23321]	Motility	yes
[Ref.: #120848]	Motility	yes

[Ref.: #23321]	Flagellum arrangement	monotrichous, polar

[Ref.: #23321]	Type of hemolysis	gamma
[Ref.: #23321]	Colony color	grey-white, opaque
[Ref.: #23321]	Cultivation medium used	BCYE agar

[Ref.: #56671]	Incubation period	2 days

Information on culture and growth conditions Culture and growth conditions

[Ref.: #7025]

Culture medium

BCYE-AGAR (DSMZ Medium 585)

[Ref.: #7025]

Culture medium growth

[Ref.: #7025]

Culture medium link

Medium recipe at MediaDive

[Ref.: #7025]

Culture medium composition

expand / minimize

[Ref.: #23321]

Culture medium

BCYE agar

[Ref.: #23321]

Culture medium growth

[Ref.: #34061]

Culture medium

MEDIUM 23 - for Afipia and Legionella

[Ref.: #34061]

Culture medium growth

[Ref.: #34061]

Culture medium composition

expand / minimize

[Ref.: #120848]

Culture medium

CIP Medium 23

[Ref.: #120848]

Culture medium growth

[Ref.: #120848]

Culture medium link

Medium recipe provided by DSMZ

	Kind of temperature		Temperature
[Ref.: #7025]		growth	28 °C
[Ref.: #23321]	no	growth	35 °C
[Ref.: #23321]	no	growth	37 °C
[Ref.: #23321]		growth	25-30 °C
[Ref.: #23321]	no	growth	42 °C
[Ref.: #34061]		growth	25 °C
[Ref.: #56671]		growth	30 °C
[Ref.: #120848]		growth	22-30 °C
[Ref.: #120848]	no	growth	15 °C
[Ref.: #120848]	no	growth	37 °C
[Ref.: #120848]	no	growth	41 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #56671]	Oxygen tolerance	aerobe
[Ref.: #120848]	Oxygen tolerance	facultative anaerobe

[Ref.: #69481]

Ability of spore formation

no Confidence in %100

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #23321]		NaCl	no	growth	6	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #23321]	adipate ChEBI	+	assimilation
[Ref.: #23321]	arabinose ChEBI	-	assimilation
[Ref.: #23321]	citrate ChEBI	-	assimilation
[Ref.: #23321]	esculin ChEBI	-	hydrolysis
[Ref.: #23321]	fructose ChEBI	-	builds acid from
[Ref.: #23321]	fructose ChEBI	-	fermentation
[Ref.: #23321]	fructose ChEBI	-	oxidation
[Ref.: #23321]	gelatin ChEBI	-	hydrolysis
[Ref.: #23321]	gluconate ChEBI	-	assimilation
[Ref.: #23321]	glucose ChEBI	-	builds acid from
[Ref.: #23321]	glucose ChEBI	-	fermentation
[Ref.: #23321]	glucose ChEBI	-	oxidation
[Ref.: #120848]	hippurate ChEBI	+	hydrolysis
[Ref.: #23321]	malate ChEBI	-	assimilation
[Ref.: #23321]	maltose ChEBI	-	builds acid from
[Ref.: #23321]	maltose ChEBI	-	fermentation
[Ref.: #23321]	maltose ChEBI	-	oxidation
[Ref.: #23321]	mannitol ChEBI	-	builds acid from
[Ref.: #23321]	mannitol ChEBI	-	fermentation
[Ref.: #23321]	mannitol ChEBI	-	oxidation
[Ref.: #23321]	mannose ChEBI	-	builds acid from
[Ref.: #23321]	mannose ChEBI	-	fermentation
[Ref.: #23321]	mannose ChEBI	-	oxidation
[Ref.: #23321]	N-acetylglucosamine ChEBI	-	assimilation
[Ref.: #23321]	nitrate ChEBI	+	reduction
[Ref.: #120848]	nitrate ChEBI	+	reduction
[Ref.: #120848]	nitrite ChEBI	-	reduction
[Ref.: #23321]	phenylacetate ChEBI	-	assimilation
[Ref.: #23321]	sucrose ChEBI	-	builds acid from
[Ref.: #23321]	sucrose ChEBI	-	fermentation
[Ref.: #23321]	sucrose ChEBI	-	oxidation
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Antibiotic sensitivity	Concentration
[Ref.: #23321]	amikacin ChEBI	yes	2	µg/mL (MIC)
[Ref.: #23321]	amoxicillin ChEBI	yes	32	µg/mL (MIC)
[Ref.: #23321]	cefalotin ChEBI	yes	2	µg/mL (MIC)
[Ref.: #23321]	cefepime ChEBI	yes	4	µg/mL (MIC)
[Ref.: #23321]	cefoxitin ChEBI	yes	32	µg/mL (MIC)
[Ref.: #23321]	ceftazidime ChEBI	yes	32	µg/mL (MIC)
[Ref.: #23321]	ceftriaxone ChEBI	yes	1	µg/mL (MIC)
[Ref.: #23321]	ciprofloxacin ChEBI	yes	2	µg/mL (MIC)
[Ref.: #23321]	co-trimoxazole ChEBI	yes	16	µg/mL (MIC)
[Ref.: #23321]	doxycycline ChEBI	yes	16	µg/mL (MIC)
[Ref.: #23321]	erythromycin ChEBI	yes	16	µg/mL (MIC)
[Ref.: #23321]	gentamicin ChEBI	yes	2	µg/mL (MIC)
[Ref.: #23321]	imipenem ChEBI	yes	0.5	µg/mL (MIC)
[Ref.: #23321]	netilmycin ChEBI	yes	32	µg/mL (MIC)
[Ref.: #23321]	penicillin ChEBI	yes	16	µg/mL (MIC)
[Ref.: #23321]	piperacillin ChEBI	yes	128	µg/mL (MIC)
[Ref.: #23321]	rifampicin ChEBI	yes	1	µg/mL (MIC)
[Ref.: #23321]	ticarcillin ChEBI	yes	128	µg/mL (MIC)
[Ref.: #23321]	tobramycin ChEBI	yes	2	µg/mL (MIC)
[Ref.: #23321]	vancomycin ChEBI	yes	256	µg/mL (MIC)
	Only first 10 entries are displayed. Click here to see all.

	Antibiotica	Group ID of combined antibiotics	Metabolite	Antibiotic sensitivity	Concentration
[Ref.: #23321]		12	amoxicillin ChEBI	yes	32	µg/mL (MIC)
[Ref.: #23321]		12	clavulanic acid ChEBI	yes	32	µg/mL (MIC)

	Metabolite production	Metabolite	Production
[Ref.: #23321]		hydrogen sulfide ChEBI	no
[Ref.: #120848]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #120848]	alcohol dehydrogenase	-	1.1.1.1
[Ref.: #68382]	alkaline phosphatase	+	3.1.3.1	* from API zym
[Ref.: #68382]	alpha-chymotrypsin	-	3.4.21.1	* from API zym
[Ref.: #68382]	alpha-fucosidase	-	3.2.1.51	* from API zym
[Ref.: #68382]	alpha-galactosidase	-	3.2.1.22	* from API zym
[Ref.: #68382]	alpha-glucosidase	-	3.2.1.20	* from API zym
[Ref.: #68382]	alpha-mannosidase	-	3.2.1.24	* from API zym
[Ref.: #23321]	arginine dihydrolase	-	3.5.3.6
[Ref.: #23321]	beta-galactosidase	-	3.2.1.23
[Ref.: #68382]	beta-galactosidase	-	3.2.1.23	* from API zym
[Ref.: #68382]	beta-glucosidase	-	3.2.1.21	* from API zym
[Ref.: #68382]	beta-glucuronidase	-	3.2.1.31	* from API zym
[Ref.: #23321]	catalase	+/-	1.11.1.6
[Ref.: #120848]	catalase	+	1.11.1.6
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #23321]	cytochrome oxidase	+	1.9.3.1
[Ref.: #68382]	esterase (C 4)	+		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	+		* from API zym
[Ref.: #120848]	gamma-glutamyltransferase	+	2.3.2.2
[Ref.: #120848]	gelatinase	-
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #120848]	lysine decarboxylase	-	4.1.1.18
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #120848]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #120848]	oxidase	+
[Ref.: #68382]	trypsin	+	3.4.21.4	* from API zym
[Ref.: #23321]	urease	+	3.5.1.5
[Ref.: #120848]	urease	+	3.5.1.5
[Ref.: #68382]	valine arylamidase	-		* from API zym
	Only first 10 entries are displayed. Click here to see all.

API® zym:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Control	2-naphthyl phosphateAlkaline phosphatase	2-naphthyl butyrateEsterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	2-naphthyl myristateLipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	N-benzoyl-DL-arginine-2-naphthylamideTrypsin	N-glutaryl-phenylalanine-2-naphthylamidealpha- Chymotrypsin	2-naphthyl phosphateAcid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	6-Br-2-naphthyl-alphaD-galactpyranosidealpha- Galactosidase	2-naphthyl-betaD-galactpyranosidebeta- Galactosidase	Naphthol-AS-BI-betaD-glucuronidebeta- Glucuronidase	2-naphthyl-alphaD-glucopyranosidealpha- Glucosidase	6-Br-2-naphthyl-betaD-glucopyranosidebeta- Glucosidase	1-naphthyl-N-acetyl-betaD-glucosaminideN-acetyl-beta- glucosaminidase	6-Br-2-naphthyl-alphaD-mannopyranosidealpha- Mannosidase	2-naphthyl-alphaL-fucopyranosidealpha- Fucosidase
[Ref.: #120848]	10005	-	+	+	+	-	+	-	-	+	-	+	+	-	-	-	-	-	-	-	-

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #7025]	Sample type/isolated from	water supply of hospital
[Ref.: #7025]	Geographic location (country and/or sea, region)	Marseille
[Ref.: #7025]	Country	France
[Ref.: #7025]	Country ISO 3 Code	FRA
[Ref.: #7025]	Continent	Europe

[Ref.: #23321]	Sample type/isolated from	water supply of the La Timone Hospital Centre

[Ref.: #56671]	Sample type/isolated from	Water supply
[Ref.: #56671]	Geographic location (country and/or sea, region)	Marseille,La Timone
[Ref.: #56671]	Country	France
[Ref.: #56671]	Country ISO 3 Code	FRA
[Ref.: #56671]	Continent	Europe

[Ref.: #120848]	Sample type/isolated from	Environment, Drinking water
[Ref.: #120848]	Geographic location (country and/or sea, region)	Marseille
[Ref.: #120848]	Country	France
[Ref.: #120848]	Country ISO 3 Code	FRA
[Ref.: #120848]	Continent	Europe
[Ref.: #120848]	Isolation date	1998
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	-
#Infection	#Medical environment	#Clinic

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AY568510 (>99% sequence identity) for Afipia from Microbeatlas

Aquatic Samples	84
Soil Samples	379
Animal Samples	54
Plant Samples	263
Total Samples	780

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #7025]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #120848]	Biosafety level	1	Risk group (French classification)

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #7025]	Uncultured Afipia sp. clone NW-12 16S ribosomal RNA gene, partial sequence	AY568510	1487	GenBank ENA	218203 tax ID
[Ref.: #23321]	Afipia massiliensis 16S ribosomal RNA gene, partial sequence	AY029562	1375	GenBank ENA	1211024 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Afipia massiliensis DSM 17498	GCA_014203115	contig	GenBank ENA	211460 tax ID	*
[Ref.: #66792]	Afipia massiliensis strain DSM 17498	211460.6	wgs	PATRIC	211460 tax ID	*
[Ref.: #66792]	Afipia massiliensis DSM 17498	2861716478	draft	JGI IMG/M	211460 tax ID	*

[Ref.: #7025]	GC-content	60.2 mol%
[Ref.: #23321]	GC-content	60.2 mol%	high performance liquid chromatography (HPLC)

Data predicted using genome information as a basis Genome-based predictions

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Afipia massiliensis strain DSM 17498 PATRIC: 211460.5
[Ref.: #69481]	spore-forming	spore-formingⓘ	no	100	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Afipia massiliensis strain DSM 17498 PATRIC: 211460.6
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	98.014	no
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	91.836	yes
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	86.876	no
[Ref.: #69480]	aerobic	aerobicⓘ	yes	83.632	no
[Ref.: #69480]	thermophilic	thermophileⓘ	no	97.324	no
[Ref.: #69480]	flagellated	motile2+ⓘ	yes	77.185	yes

Availability in culture collections External links

[Ref.: #7025]

Culture collection no.

DSM 17498, CCUG 45153, CIP 107022

[Ref.: #71428]

SI-ID 100487

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Description 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 D	Int J Syst Evol Microbiol	10.1099/00207713-52-5-1773	2002	*

References

#7025

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 17498

#20215

Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.: List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. IJSEM ( DOI 10.1099/ijsem.0.004332 )

#23321

Bernard La Scola, Marie-Noelle Mallet, Patrick A D Grimont, Didier Raoult: Description of Afipia birgiae sp. nov. and Afipia massiliensis sp. nov. and recognition of Afipia felis genospecies A.. IJSEM 52: 1773 - 1782 2002 ( DOI 10.1099/00207713-52-5-1773 , PubMed 12361286 )

#34061 ; Curators of the CIP;
#56671 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 45153

#66792

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#68382

Automatically annotated from API zym .

#69479

João 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.: MicrobeAtlas 1.0 beta .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#71428

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID100487.1 )

#120848 Collection of Institut Pasteur ; Curators of the CIP; CIP 107022
* These data were automatically processed and therefore are not curated

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Afipia massiliensis strain DSM 17498

Afipia massiliensis strain DSM 17498

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