Afipia clevelandensis (CCUG 30457, DSM 7315, ATCC 49720)

Name: Afipia clevelandensis (CCUG 30457, DSM 7315, ATCC 49720)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 1777

Type strain

Strain Designation Cleveland clinic foundation strain, 411m, B91-007353, F6703, G1849

Culture col. no. CCUG 30457 DSM 7315 ATCC 49720 Cleveland clinic foundation strain 411m 4 more

NCBI tax ID(s) 883079 1034

Special Collections DSMZ CCUG CIP

Links

Afipia clevelandensis Cleveland clinic foundation strain is a mesophilic, Gram-negative, motile prokaryote that was isolated from human tibia, biopsy.

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

Name and taxonomic classification

SI-ID 12657

LMG 18883,ATCC 49720,CIP 103516,DSM 7315,NCTC 12721,CCUG 30457

@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 clevelandensis

Full scientific name Afipia clevelandensis Brenner et al. 1992

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
118308	negative	rod-shaped
125438	negative		98.813
125439	negative		99.9

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
3117	BCYE-AGAR (DSMZ Medium 585)	Medium recipe at MediaDive	Name: BCYE AGAR (DSMZ Medium 585) Composition: OXOID Legionella CYE-Agar base
40686	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)
118308	CIP Medium 23	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
3117	positive	growth	28	mesophilic
40686	positive	growth	30	mesophilic
50091	positive	growth	37	mesophilic
118308	positive	growth	30	mesophilic
118308	negative	growth	10
118308	negative	growth	15
118308	negative	growth	41

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	95.9

Spore formation

@ref	Spore formation	Confidence
125439		99.2

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
118308	17234 ChEBI	glucose	-	degradation
118308	15792 ChEBI	malonate	-	assimilation
118308	17632 ChEBI	nitrate	-	reduction
118308	17632 ChEBI	nitrate	-	respiration
118308	16301 ChEBI	nitrite	-	reduction

Enzymes

@ref	Value	Activity	Ec
118308	alcohol dehydrogenase	-	1.1.1.1
118308	catalase	-	1.11.1.6
118308	lysine decarboxylase	-	4.1.1.18
118308	ornithine decarboxylase	-	4.1.1.17
118308	oxidase	+
118308	urease	+	3.5.1.5

Fatty acid profile

Metadata FA analysis

@ref

50091

Fatty acid	Percentage	ECL
C18:1 ω7c /12t/9t	26.6	17.824
C17:0 CYCLO	23.1	16.888
11 methyl 18:1 ω7c	13.3	18.081
C18:0	12.2	18
C16:1 ω7c	9.2	15.819
C19:0 CYCLO ω8c	8.6	18.9
C16:0	5.5	16
C20:1 ω7c	0.9	19.833
C17:0	0.7	17

Metadata FA analysis

@ref

50091

Fatty acid	Percentage	ECL
C18:1 ω7c /12t/9t	28.5	17.824
C16:1 ω7c	19.5	15.819
C17:0 CYCLO	16.3	16.888
C18:0	12.4	18
C16:0	7.1	16
11 methyl 18:1 ω7c	6.8	18.081
C18:2 ω6,9c/C18:0 ANTE	3.5	17.724
C19:0 CYCLO ω8c	2.6	18.9
C20:1 ω7c	1.4	19.833
C14:0	0.7	14
Unidentified	0.6	19.785
Unidentified	0.4	18.441
Unidentified	0.3	13.742

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Infection	#Patient	#Biopsy
#Host	#Human	-
#Host Body-Site	#Limb	#Leg

Isolation

@ref	Sample type	Sampling date	Geographic location	Country	Country ISO 3 Code	Continent
3117	human tibia, biopsy		Ohio	USA	USA	North America
50091	Tibial biopsy,male,age 69yr,died	1988	Ohio	USA	USA	North America
118308	Human, Tibial biopsy

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
3117	2	Risk group (German classification) According to TRBA 466
118308	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	Afip_clev_ATCC49720_G12581_V1 assembly for Afipia clevelandensis ATCC 49720	scaffold	GCA_000336555	883079.3	2537561906	883079	59.09

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20218	Afipia clevelandensis strain B-91-007353 16S ribosomal RNA gene, partial sequence	M69186	1425		883079

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Afipia clevelandensis ATCC 49720
NCBI: GCA_000336555

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	99.20	no
125439	motility	BacteriaNetⓘ	yes	77.40	no
125439	gram_stain	BacteriaNetⓘ	negative	99.90	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	95.90	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Afipia clevelandensis ATCC 49720 ATCC 49720
NCBI: GCA_000336555.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.81	no
125438	anaerobic	anaerobicⓘ	no	93.76	no
125438	aerobic	aerobicⓘ	yes	85.93	no
125438	spore-forming	spore-formingⓘ	no	84.98	no
125438	thermophilic	thermophileⓘ	no	99.00	yes
125438	flagellated	motile2+ⓘ	yes	75.51	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Reclassification of Pseudomonas boreopolis Gray and Thornton 1928 (Approved Lists 1980) as Xanthomonas boreopolis comb. nov. and Pseudomonas carboxydohydrogena (ex Sanjieva and Zavarzin 1971) Meyer et al. 1980 as Afipia carboxydohydrogena comb. nov. based on comparative genomic analysis.	Fatahi-Bafghi M.	Int J Syst Evol Microbiol	10.1099/ijsem.0.006865	2025
Genetics	Genome sequencing and annotation of Afipia septicemium strain OHSU_II.	Yang P, Hung GC, Lei H, Li T, Li B, Tsai S, Lo SC.	Genom Data	10.1016/j.gdata.2014.06.001	2014
	Identification of Bradyrhizobium elkanii Genes Involved in Incompatibility with Vigna radiata.	Nguyen HP, Miwa H, Kaneko T, Sato S, Okazaki S.	Genes (Basel)	10.3390/genes8120374	2017
	Isoprenoid quinones of "Afipia" spp.	Moss CW, Daneshvar MI, Hollis DG, Birkness KA.	J Clin Microbiol	10.1128/jcm.29.12.2904-2905.1991	1991
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
Enzymology	Detection of Ehrlichia chaffeensis in human tissue by using a species-specific monoclonal antibody.	Yu X, Brouqui P, Dumler JS, Raoult D.	J Clin Microbiol	10.1128/jcm.31.12.3284-3288.1993	1993
Phylogeny	Proposal of Afipia gen. nov., with Afipia felis sp. nov. (formerly the cat scratch disease bacillus), Afipia clevelandensis sp. nov. (formerly the Cleveland Clinic Foundation strain), Afipia broomeae sp. nov., and three unnamed genospecies.	Brenner DJ, Hollis DG, Moss CW, English CK, Hall GS, Vincent J, Radosevic J, Birkness KA, Bibb WF, Quinn FD.	J Clin Microbiol	10.1128/jcm.29.11.2450-2460.1991	1991
Phylogeny	Bosea minatitlanensis sp. nov., a strictly aerobic bacterium isolated from an anaerobic digester.	Ouattara AS, Assih EA, Thierry S, Cayol JL, Labat M, Monroy O, Macarie H	Int J Syst Evol Microbiol	10.1099/ijs.0.02540-0	2003

References

#3117	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 7315
#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 )
#20218	Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )
#40686	; Curators of the CIP;
#50091	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 30457
#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) .
#118308	Collection of Institut Pasteur ; Curators of the CIP; CIP 103516
#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 )

Rate our new design

Content

About us

Afipia clevelandensis (CCUG 30457, DSM 7315, ATCC 49720)

Name and taxonomic classification