Afipia birgiae (DSM 17499, CCUG 43108, CIP 106344)

Name: Afipia birgiae (DSM 17499, CCUG 43108, CIP 106344)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 1782

Type strain

Strain Designation 34632

Culture col. no. DSM 17499 CCUG 43108 CIP 106344 34632

NCBI tax ID(s) 151414

Special Collections DSMZ CCUG CIP Literature strains

Links

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

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

Name and taxonomic classification

SI-ID 100486

CCUG 43108,CIP 106344,DSM 17499

@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 birgiae

Full scientific name Afipia birgiae La Scola et al. 2002

Morphology

Cell morphology

@ref	Gram stain	Cell shape
23321	negative	rod-shaped
116820	negative	rod-shaped
125438	negative
125439	negative

Colony morphology

@ref	Type of hemolysis	Colony color	Medium used
23321	gamma	grey-white, opaque	BCYE agar

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
7026	BCYE-AGAR (DSMZ Medium 585)	Medium recipe at MediaDive	Name: BCYE AGAR (DSMZ Medium 585) Composition: OXOID Legionella CYE-Agar base
38619	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)
116820	CIP Medium 23	Medium recipe at CIP
7026	NUTRIENT AGAR (DSMZ Medium 1)	Medium recipe at MediaDive	Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
7026	positive	growth	28	mesophilic
23321	negative	growth	35
23321	negative	growth	37
23321	positive	growth	25-30	mesophilic
23321	negative	growth	42
38619	positive	growth	25	mesophilic
55666	positive	growth	30	mesophilic
116820	positive	growth	15-30
116820	negative	growth	37
116820	negative	growth	41

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
55666	aerobe
116820	facultative anaerobe
125439	obligate aerobe

Spore formation

@ref	Spore formation	Confidence
125439		97.6

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
116820	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
116820	17632 ChEBI	nitrate	+	reduction
116820	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	Metabolite	Sensitivity conc.
23321	2637	amikacin	2 µg/mL (MIC)
23321	2676	amoxicillin	0.5 µg/mL (MIC)
23321	2676	amoxicillin	64 µg/mL (MIC)
23321	124991	cefalotin	4 µg/mL (MIC)
23321	478164	cefepime	8 µg/mL (MIC)
23321	209807	cefoxitin	0.5 µg/mL (MIC)
23321	3508	ceftazidime	4 µg/mL (MIC)
23321	29007	ceftriaxone	0.25 µg/mL (MIC)
23321	100241	ciprofloxacin	2 µg/mL (MIC)
23321	48947	clavulanic acid	0.5 µg/mL (MIC)
23321	3770	co-trimoxazole	256 µg/mL (MIC)
23321	50845	doxycycline	4 µg/mL (MIC)
23321	48923	erythromycin	64 µg/mL (MIC)
23321	17833	gentamicin	0.25 µg/mL (MIC)
23321	471744	imipenem	0.5 µg/mL (MIC)
23321	7528	netilmycin	0.25 µg/mL (MIC)
23321	17334	penicillin	256 µg/mL (MIC)
23321	8232	piperacillin	256 µg/mL (MIC)
23321	28077	rifampicin	1 µg/mL (MIC)
23321	9587	ticarcillin	256 µg/mL (MIC)
23321	28864	tobramycin	0.25 µg/mL (MIC)
23321	28001	vancomycin	256 µg/mL (MIC)

Metabolite production

@ref	Chebi-ID	Metabolite	Production
23321	16136 ChEBI	hydrogen sulfide
116820	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
116820	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
116820	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
116820	gamma-glutamyltransferase	-	2.3.2.2
68382	leucine arylamidase	-	3.4.11.1	from API zym
68382	lipase (C 14)	-		from API zym
116820	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
116820	ornithine decarboxylase	-	4.1.1.17
116820	oxidase	+
68382	trypsin	+	3.4.21.4	from API zym
116820	tween esterase	-
23321	urease	+	3.5.1.5
116820	urease	+	3.5.1.5
68382	valine arylamidase	-		from API zym

Fatty acid profile

Metadata FA analysis

@ref

55666

Fatty acid	Percentage	ECL
C17:0 CYCLO	27.1	16.888
C18:1 ω7c /12t/9t	16.2	17.824
C16:1 ω7c	15.3	15.819
11 methyl 18:1 ω7c	7.8	18.081
C17:0	7.1	17
C17:1 ω8c	7.1	16.792
C18:0	5.1	18
C17:ISO 2OH	3.7	17.875
C16:0	3.1	16
C19:0 CYCLO ω8c	3	18.9
unknown 18.797	2.7	18.797
C15:0	1.8	15

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
116820	-	-	+	+	-	-	-	-	+	-	+	+	-	-	-	-	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2
#Environmental	#Aquatic
#Infection	#Medical environment

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
7026	water supply of hospital	Marseille	France	FRA	Europe
23321	water supply of the La Timone Hospital Centre
55666	Water supply of La Timone Hospital Centre	Marseille	France	FRA	Europe
116820	Environment, Water tank	Marseille	France	FRA	Europe

Taxonmaps

69479

Global distribution of 16S sequence AF288304 (>99% sequence identity) for Bradyrhizobiaceae from Microbeatlas

Aquatic Samples	1311
Soil Samples	1896
Animal Samples	501
Plant Samples	518
Total Samples	4226

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
7026	1	Risk group (German classification) According to TRBA 466
116820	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	Ab_34632 assembly for Afipia birgiae 34632	scaffold	GCA_000308295	1197906.5	2551306146	1197906	48.49

Genome browser: GCA_000308295

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
7026	Alpha proteobacterium 34632 16S ribosomal RNA gene, partial sequence	AF288304	1426		1197906
124043	Afipia birgiae partial 16S rRNA gene, isolate strain #14 (MBG-DUTH)/DSM 17499 (ELTE)	OU548668	821		151414

GC content

@ref	GC-content (mol%)
7026	59.3
23321	59.3

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Afipia birgiae 34632
NCBI: GCA_000308295

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	97.60	no
125439	motility	BacteriaNetⓘ	yes	85.90	no
125439	gram_stain	BacteriaNetⓘ	negative	98.90	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	94.40	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Afipia birgiae 34632 34632
NCBI: GCA_000308295.2

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	97.81	yes
125438	anaerobic	anaerobicⓘ	no	93.89	no
125438	aerobic	aerobicⓘ	yes	86.37	no
125438	spore-forming	spore-formingⓘ	no	82.62	no
125438	thermophilic	thermophileⓘ	no	97.83	yes
125438	flagellated	motile2+ⓘ	yes	78.27	no

Literature

Title	Authors	Journal	DOI	Year
Comparative Investigation of 15 Xenobiotic-Metabolizing N-Acetyltransferase (NAT) Homologs from Bacteria.	Garefalaki V, Papavergi MG, Savvidou O, Papanikolaou G, Felfoldi T, Marialigeti K, Fakis G, Boukouvala S.	Appl Environ Microbiol	10.1128/aem.00819-21	2021
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
Genome sequence of Afipia birgiae, a rare bacterium associated with Amoebae.	Pagnier I, Croce O, Robert C, Raoult D, La Scola B	J Bacteriol	10.1128/JB.01918-12	2012
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

#7026	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 17499
#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 )
#38619	; Curators of the CIP;
#55666	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 43108
#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 .
#116820	Collection of Institut Pasteur ; Curators of the CIP; CIP 106344
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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 birgiae (DSM 17499, CCUG 43108, CIP 106344)

Name and taxonomic classification