Afipia massiliensis (DSM 17498, CCUG 45153, CIP 107022)

Name: Afipia massiliensis (DSM 17498, CCUG 45153, CIP 107022)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 1781

Type strain

Strain Designation 34633

Culture col. no. DSM 17498 CCUG 45153 CIP 107022 34633

NCBI tax ID(s) 211460

Special Collections DSMZ CCUG CIP Literature strains

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

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

Name and taxonomic classification

SI-ID 100487

CCUG 45153,CIP 107022,DSM 17498

@ref 20215

Last LPSN update 2025-12-16 09:47:11

Domain Pseudomonadati

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Hyphomicrobiales

Family Nitrobacteraceae

Genus Afipia

Species Afipia massiliensis

Full scientific name Afipia massiliensis La Scola et al. 2002

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Flagellum arrangement	Confidence
23321	negative	rod-shaped	monotrichous, polar
120848	negative	rod-shaped
125438	negative			98.014
125439	negative			99.8

Colony morphology

@ref	Type of hemolysis	Colony color	Medium used	Incubation period
23321	gamma	grey-white, opaque	BCYE agar
56671				2 days

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
7025	BCYE-AGAR (DSMZ Medium 585)	Medium recipe at MediaDive	Name: BCYE AGAR (DSMZ Medium 585) Composition: OXOID Legionella CYE-Agar base
23321	BCYE agar
34061	MEDIUM 23 - for Afipia and Legionella		Distilled water make up to (1000.000 ml);Legionella agar (37.000 g);Legionella - enrichment mixture (10.000 ml)
120848	CIP Medium 23	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
7025	positive	growth	28	mesophilic
23321	negative	growth	35
23321	negative	growth	37
23321	positive	growth	25-30	mesophilic
23321	negative	growth	42
34061	positive	growth	25	mesophilic
56671	positive	growth	30	mesophilic
120848	positive	growth	22-30
120848	negative	growth	15
120848	negative	growth	37
120848	negative	growth	41

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
56671	aerobe
120848	facultative anaerobe
125439	obligate aerobe	97.6

Spore formation

@ref	Spore formation	Confidence
125439		98.9

Halophily

@ref	Salt	Growth	Tested relation	Concentration
23321	NaCl		growth	6 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
23321	17128 ChEBI	adipate	+	assimilation
23321	22599 ChEBI	arabinose	-	assimilation
23321	16947 ChEBI	citrate	-	assimilation
23321	4853 ChEBI	esculin	-	hydrolysis
23321	28757 ChEBI	fructose	-	builds acid from
23321	28757 ChEBI	fructose	-	fermentation
23321	28757 ChEBI	fructose	-	oxidation
23321	5291 ChEBI	gelatin	-	hydrolysis
23321	24265 ChEBI	gluconate	-	assimilation
23321	17234 ChEBI	glucose	-	builds acid from
23321	17234 ChEBI	glucose	-	fermentation
23321	17234 ChEBI	glucose	-	oxidation
120848	606565 ChEBI	hippurate	+	hydrolysis
23321	25115 ChEBI	malate	-	assimilation
23321	17306 ChEBI	maltose	-	builds acid from
23321	17306 ChEBI	maltose	-	fermentation
23321	17306 ChEBI	maltose	-	oxidation
23321	29864 ChEBI	mannitol	-	builds acid from
23321	29864 ChEBI	mannitol	-	fermentation
23321	29864 ChEBI	mannitol	-	oxidation
23321	37684 ChEBI	mannose	-	builds acid from
23321	37684 ChEBI	mannose	-	fermentation
23321	37684 ChEBI	mannose	-	oxidation
23321	506227 ChEBI	N-acetylglucosamine	-	assimilation
23321	17632 ChEBI	nitrate	+	reduction
120848	17632 ChEBI	nitrate	+	reduction
120848	16301 ChEBI	nitrite	-	reduction
23321	18401 ChEBI	phenylacetate	-	assimilation
23321	17992 ChEBI	sucrose	-	builds acid from
23321	17992 ChEBI	sucrose	-	fermentation
23321	17992 ChEBI	sucrose	-	oxidation

Antibiotic resistance

@ref	ChEBI	Group ID	Metabolite	Sensitivity conc.
23321	2637		amikacin	2 µg/mL (MIC)
23321	2676		amoxicillin	32 µg/mL (MIC)
23321	2676	12	amoxicillin	32 µg/mL (MIC)
23321	124991		cefalotin	2 µg/mL (MIC)
23321	478164		cefepime	4 µg/mL (MIC)
23321	209807		cefoxitin	32 µg/mL (MIC)
23321	3508		ceftazidime	32 µg/mL (MIC)
23321	29007		ceftriaxone	1 µg/mL (MIC)
23321	100241		ciprofloxacin	2 µg/mL (MIC)
23321	48947	12	clavulanic acid	32 µg/mL (MIC)
23321	3770		co-trimoxazole	16 µg/mL (MIC)
23321	50845		doxycycline	16 µg/mL (MIC)
23321	48923		erythromycin	16 µg/mL (MIC)
23321	17833		gentamicin	2 µg/mL (MIC)
23321	471744		imipenem	0.5 µg/mL (MIC)
23321	7528		netilmycin	32 µg/mL (MIC)
23321	17334		penicillin	16 µg/mL (MIC)
23321	8232		piperacillin	128 µg/mL (MIC)
23321	28077		rifampicin	1 µg/mL (MIC)
23321	9587		ticarcillin	128 µg/mL (MIC)
23321	28864		tobramycin	2 µg/mL (MIC)
23321	28001		vancomycin	256 µg/mL (MIC)

Metabolite production

@ref	Chebi-ID	Metabolite	Production
23321	16136 ChEBI	hydrogen sulfide
120848	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
120848	alcohol dehydrogenase	-	1.1.1.1
68382	alkaline phosphatase	+	3.1.3.1	from API zym
68382	alpha-chymotrypsin	-	3.4.21.1	from API zym
68382	alpha-fucosidase	-	3.2.1.51	from API zym
68382	alpha-galactosidase	-	3.2.1.22	from API zym
68382	alpha-glucosidase	-	3.2.1.20	from API zym
68382	alpha-mannosidase	-	3.2.1.24	from API zym
23321	arginine dihydrolase	-	3.5.3.6
23321	beta-galactosidase	-	3.2.1.23
68382	beta-galactosidase	-	3.2.1.23	from API zym
68382	beta-glucosidase	-	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
23321	catalase	+/-	1.11.1.6
120848	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
23321	cytochrome oxidase	+	1.9.3.1
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
120848	gamma-glutamyltransferase	+	2.3.2.2
120848	gelatinase	-
68382	leucine arylamidase	+	3.4.11.1	from API zym
68382	lipase (C 14)	-		from API zym
120848	lysine decarboxylase	-	4.1.1.18
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
120848	ornithine decarboxylase	-	4.1.1.17
120848	oxidase	+
68382	trypsin	+	3.4.21.4	from API zym
23321	urease	+	3.5.1.5
120848	urease	+	3.5.1.5
68382	valine arylamidase	-		from API zym

API zym

@ref	Control	Alkaline phosphatase	Esterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	Lipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	Trypsin	alpha- Chymotrypsin	Acid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	alpha- Galactosidase	beta- Galactosidase	beta- Glucuronidase	alpha- Glucosidase	beta- Glucosidase	N-acetyl-beta- glucosaminidase	alpha- Mannosidase	alpha- Fucosidase
120848	-	+	+	+	-	+	-	-	+	-	+	+	-	-	-	-	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	-
#Infection	#Medical environment	#Clinic

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Isolation date
7025	water supply of hospital	Marseille	France	FRA	Europe
23321	water supply of the La Timone Hospital Centre
56671	Water supply	Marseille,La Timone	France	FRA	Europe
120848	Environment, Drinking water	Marseille	France	FRA	Europe	1998

Taxonmaps

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

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
7025	1	Risk group (German classification) According to TRBA 466
120848	1	Risk group (French classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM1420311v1 assembly for Afipia massiliensis DSM 17498	contig	GCA_014203115	211460.6	2861716478	211460	55.29

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
23321	Afipia massiliensis 16S ribosomal RNA gene, partial sequence	AY029562	1375		1211024
7025	Uncultured Afipia sp. clone NW-12 16S ribosomal RNA gene, partial sequence	AY568510	1487		218203

GC content

@ref	GC-content (mol%)	Method
7025	60.2
23321	60.2	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Afipia massiliensis DSM 17498
NCBI: GCA_014203115

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	98.90	no
125439	motility	BacteriaNetⓘ	yes	78.50	no
125439	gram_stain	BacteriaNetⓘ	negative	99.80	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	97.60	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Afipia massiliensis strain DSM 17498
PATRIC: 211460.6

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.01	no
125438	anaerobic	anaerobicⓘ	no	91.84	yes
125438	spore-forming	spore-formingⓘ	no	86.88	no
125438	aerobic	aerobicⓘ	yes	83.63	no
125438	thermophilic	thermophileⓘ	no	97.32	no
125438	flagellated	motile2+ⓘ	yes	77.19	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Usefulness of rpoB gene sequencing for identification of Afipia and Bosea species, including a strategy for choosing discriminative partial sequences.	Khamis A, Colson P, Raoult D, Scola BL.	Appl Environ Microbiol	10.1128/aem.69.11.6740-6749.2003	2003
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 .
#120848	Collection of Institut Pasteur ; Curators of the CIP; CIP 107022
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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Afipia massiliensis (DSM 17498, CCUG 45153, CIP 107022)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Metabolite utilization

Antibiotic resistance

Metabolite production

Enzymes

API zym

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_014203115

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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