Name: Afipia birgiae 34632
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 1782

Type strain:

Species: Afipia birgiae

Strain Designation: 34632

Culture col. no.: DSM 17499, CCUG 43108, CIP 106344

Strain history: CIP <- 1999, B. La Scola, NRC, Timone Hosp., Marseille, France: strain 34632

NCBI tax ID(s): 151414 (species)

SI-ID 100486

CCUG 43108, CIP 106344, DSM 17499

Special Collections

Section

Afipia birgiae 34632 is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from water supply of hospital.

Gram-negative
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 birgiae**
	Full Scientific Name (LPSN)	Afipia birgiae La Scola et al. 2002

Information on morphological and physiological properties Morphology

[Ref.: #23321]	Gram stain	negative
[Ref.: #116820]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %97.813

[Ref.: #23321]	Cell shape	rod-shaped
[Ref.: #116820]	Cell shape	rod-shaped

[Ref.: #23321]	Motility	no
[Ref.: #116820]	Motility	no

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

Information on culture and growth conditions Culture and growth conditions

[Ref.: #7026]

Culture medium

BCYE-AGAR (DSMZ Medium 585)

[Ref.: #7026]

Culture medium growth

[Ref.: #7026]

Culture medium link

Medium recipe at MediaDive

[Ref.: #7026]

Culture medium composition

expand / minimize

[Ref.: #38619]

Culture medium

MEDIUM 23 - for Afipia and Legionella

[Ref.: #38619]

Culture medium growth

[Ref.: #38619]

Culture medium composition

expand / minimize

[Ref.: #116820]

Culture medium

CIP Medium 23

[Ref.: #116820]

Culture medium growth

[Ref.: #116820]

Culture medium link

Medium recipe provided by DSMZ

	Kind of temperature		Temperature
[Ref.: #7026]		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.: #38619]		growth	25 °C
[Ref.: #55666]		growth	30 °C
[Ref.: #116820]		growth	15-30 °C
[Ref.: #116820]	no	growth	37 °C
[Ref.: #116820]	no	growth	41 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #55666]	Oxygen tolerance	aerobe
[Ref.: #116820]	Oxygen tolerance	facultative anaerobe

	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.: #116820]	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.: #116820]	nitrate ChEBI	+	reduction
[Ref.: #116820]	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	64	µg/mL (MIC)
[Ref.: #23321]	cefalotin ChEBI	yes	4	µg/mL (MIC)
[Ref.: #23321]	cefepime ChEBI	yes	8	µg/mL (MIC)
[Ref.: #23321]	cefoxitin ChEBI	yes	0.5	µg/mL (MIC)
[Ref.: #23321]	ceftazidime ChEBI	yes	4	µg/mL (MIC)
[Ref.: #23321]	ceftriaxone ChEBI	yes	0.25	µg/mL (MIC)
[Ref.: #23321]	ciprofloxacin ChEBI	yes	2	µg/mL (MIC)
[Ref.: #23321]	co-trimoxazole ChEBI	yes	256	µg/mL (MIC)
[Ref.: #23321]	doxycycline ChEBI	yes	4	µg/mL (MIC)
[Ref.: #23321]	erythromycin ChEBI	yes	64	µg/mL (MIC)
[Ref.: #23321]	gentamicin ChEBI	yes	0.25	µg/mL (MIC)
[Ref.: #23321]	imipenem ChEBI	yes	0.5	µg/mL (MIC)
[Ref.: #23321]	netilmycin ChEBI	yes	0.25	µg/mL (MIC)
[Ref.: #23321]	penicillin ChEBI	yes	256	µg/mL (MIC)
[Ref.: #23321]	piperacillin ChEBI	yes	256	µg/mL (MIC)
[Ref.: #23321]	rifampicin ChEBI	yes	1	µg/mL (MIC)
[Ref.: #23321]	ticarcillin ChEBI	yes	256	µg/mL (MIC)
[Ref.: #23321]	tobramycin ChEBI	yes	0.25	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]		13	amoxicillin ChEBI	yes	0.5	µg/mL (MIC)
[Ref.: #23321]		13	clavulanic acid ChEBI	yes	0.5	µg/mL (MIC)

	Metabolite production	Metabolite	Production
[Ref.: #23321]		hydrogen sulfide ChEBI	no
[Ref.: #116820]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #116820]	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.: #116820]	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.: #116820]	gamma-glutamyltransferase	-	2.3.2.2
[Ref.: #68382]	leucine arylamidase	-	3.4.11.1	* from API zym
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #116820]	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.: #116820]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #116820]	oxidase	+
[Ref.: #68382]	trypsin	+	3.4.21.4	* from API zym
[Ref.: #116820]	tween esterase	-
[Ref.: #23321]	urease	+	3.5.1.5
[Ref.: #116820]	urease	+	3.5.1.5
[Ref.: #68382]	valine arylamidase	-		* from API zym
	Only first 10 entries are displayed. Click here to see all.

Fatty acid profile

Metadata FA analysis

Reference

[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:

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.: #116820]	9420	-	-	+	+	-	-	-	-	+	-	+	+	-	-	-	-	-	-	-	-

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

[Ref.: #7026]	Sample type/isolated from	water supply of hospital
[Ref.: #7026]	Geographic location (country and/or sea, region)	Marseille
[Ref.: #7026]	Country	France
[Ref.: #7026]	Country ISO 3 Code	FRA
[Ref.: #7026]	Continent	Europe

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

[Ref.: #55666]	Sample type/isolated from	Water supply of La Timone Hospital Centre
[Ref.: #55666]	Geographic location (country and/or sea, region)	Marseille
[Ref.: #55666]	Country	France
[Ref.: #55666]	Country ISO 3 Code	FRA
[Ref.: #55666]	Continent	Europe

[Ref.: #116820]	Sample type/isolated from	Environment, Water tank
[Ref.: #116820]	Geographic location (country and/or sea, region)	Marseille
[Ref.: #116820]	Country	France
[Ref.: #116820]	Country ISO 3 Code	FRA
[Ref.: #116820]	Continent	Europe
[Ref.: #116820]	Isolation date	1999
* 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 AF288304 (>99% sequence identity) for Bradyrhizobiaceae from Microbeatlas

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

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

[Ref.: #7026]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #116820]	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.: #7026]	Alpha proteobacterium 34632 16S ribosomal RNA gene, partial sequence	AF288304	1426	GenBank ENA	1197906 tax ID
[Ref.: #124043]	Afipia birgiae partial 16S rRNA gene, isolate strain #14 (MBG-DUTH)/DSM 17499 (ELTE)	OU548668	821	GenBank ENA	151414 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Afipia birgiae 34632	GCA_000308295	contig	GenBank ENA	1197906 tax ID	*
[Ref.: #66792]	Afipia birgiae 34632	1197906.5	wgs	PATRIC	1197906 tax ID	*
[Ref.: #66792]	Afipia birgiae 34632	2551306146	draft	JGI IMG/M	1197906 tax ID	*

[Ref.: #7026]	GC-content	59.3 mol%
[Ref.: #23321]	GC-content	59.3 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 Diaspora project based on: Afipia birgiae 34632 34632 NCBI: GCA_000308295.2
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	97.813	yes
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	93.891	no
[Ref.: #69480]	aerobic	aerobicⓘ	yes	86.369	no
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	82.618	no
[Ref.: #69480]	thermophilic	thermophileⓘ	no	97.825	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	yes	78.265	no

Availability in culture collections External links

[Ref.: #7026]

Culture collection no.

DSM 17499, CCUG 43108, CIP 106344

[Ref.: #71429]

SI-ID 100486

Literature:

Topic	Title	Authors	Journal	DOI	Year
Genetics	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	*
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

#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 .

#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) .

#71429

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-ID100486.1 )

#116820 Collection of Institut Pasteur ; Curators of the CIP; CIP 106344

#124043

Dr. Isabel Schober, Dr. Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .

* These data were automatically processed and therefore are not curated

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Afipia birgiae 34632 34632

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