Aminobacter carboxidus (DSM 17454, CCUG 50579, CIP 108661)

Name: Aminobacter carboxidus (DSM 17454, CCUG 50579, CIP 108661)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 11862

Type strain

Strain Designation CC 495

Culture col. no. DSM 17454 CCUG 50579 CIP 108661 NCIMB 13798 CC 495

NCBI tax ID(s) 376165

Special Collections DSMZ CCUG CIP Literature strains

History DSMZ <- P. Kämpfer <- I. R. McDonald; CC495 CIP <- 2005, P. Kämpfer, Giessen Univ., Giessen, Germany <- I. Mc Donald, Waikato Univ., Hamilton, New-Zealand: strain CC495

Links

Aminobacter carboxidus CC 495 is an aerobe, Gram-negative, motile bacterium that was isolated from soil of beech woodland.

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

Name and taxonomic classification

SI-ID 60980

NCIMB 13789,CCUG 50579,CIP 108661,DSM 17454

@ref 20215

Last LPSN update 2026-05-29 08:27:39

Domain Bacteria

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Hyphomicrobiales

Family Bartonellaceae

Genus Aminobacter

Species Aminobacter carboxidus

Full scientific name Aminobacter carboxidus (Meyer et al. 1994 ex Nozhevnikova and Zavarzin 1974) Hördt et al. 2020

Synonyms (2)

Aminobacter lissarensis
Carbophilus carboxidus

BacDive ID	Other strains from **Aminobacter carboxidus** (1)	Type strain
13540	A. carboxidus Z-1171, DSM 1086, ATCC 51424, CIP 105722 (type strain)

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
31512	negative	1.4 µm	0.55 µm	rod-shaped
120627	negative			rod-shaped
125439	negative				98.1
125438	negative				98.4

Pigmentation

@ref	Production	Name
31512
120627		Pyocyanin

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
6994	R2A MEDIUM (DSMZ Medium 830)	Medium recipe at MediaDive	Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
34007	MEDIUM 72- for trypto casein soja agar		Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
120627	CIP Medium 72	Medium recipe at CIP
120627	CIP Medium 566	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
6994	positive	growth	28
31512	positive	growth	25
31512	positive	optimum	25
34007	positive	growth	25
58909	positive	growth	26-37
120627	negative	growth	37
120627	negative	growth	10
120627	negative	growth	5
120627	positive	growth	25-30
120627	negative	growth	41

Culture pH

@ref	Ability	Type	PH
31512	positive	optimum	6.95
31512	positive	growth	6.7-7.2

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
6994	aerobe
31512	aerobe
58909	aerobe
120627	obligate aerobe
125439	obligate aerobe	99.389

Spore formation

@ref	Spore formation	Confidence
125439		99.577

Halophily

@ref	Salt	Growth	Tested relation	Concentration
120627	NaCl	positive	growth	0-2 %
120627	NaCl		growth	4 %
120627	NaCl		growth	6 %
120627	NaCl		growth	8 %
120627	NaCl		growth	10 %

Observation

31512

Observationaggregates in clumps

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
31512	37054 ChEBI	3-hydroxybutyrate	+	carbon source
31512	30089 ChEBI	acetate	+	carbon source
31512	16449 ChEBI	alanine	+	carbon source
31512	22599 ChEBI	arabinose	+	carbon source
31512	35391 ChEBI	aspartate	+	carbon source
31512	17057 ChEBI	cellobiose	+	carbon source
120627	16947 ChEBI	citrate	-	carbon source
31512	16296 ChEBI	D-tryptophan	+	carbon source
120627	4853 ChEBI	esculin	-	hydrolysis
31512	28757 ChEBI	fructose	+	carbon source
31512	28260 ChEBI	galactose	+	carbon source
31512	17234 ChEBI	glucose	+	carbon source
31512	27570 ChEBI	histidine	+	carbon source
31512	24996 ChEBI	lactate	+	carbon source
31512	25017 ChEBI	leucine	+	carbon source
31512	17306 ChEBI	maltose	+	carbon source
31512	29864 ChEBI	mannitol	+	carbon source
31512	37684 ChEBI	mannose	+	carbon source
31512	506227 ChEBI	N-acetylglucosamine	+	carbon source
120627	17632 ChEBI	nitrate	+	reduction
120627	17632 ChEBI	nitrate	-	respiration
120627	16301 ChEBI	nitrite	+	reduction
31512	18257 ChEBI	ornithine	+	carbon source
31512	26271 ChEBI	proline	+	carbon source
31512	17272 ChEBI	propionate	+	carbon source
31512	15361 ChEBI	pyruvate	+	carbon source
31512	26546 ChEBI	rhamnose	+	carbon source
31512	33942 ChEBI	ribose	+	carbon source
31512	17822 ChEBI	serine	+	carbon source
31512	30911 ChEBI	sorbitol	+	carbon source
31512	17992 ChEBI	sucrose	+	carbon source
31512	27082 ChEBI	trehalose	+	carbon source
31512	18222 ChEBI	xylose	+	carbon source

Antibiotic resistance

@ref	Metabolite	Is sensitive	Is resistant
120627	0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)

Metabolite production

@ref	Chebi-ID	Metabolite	Production
120627	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
120627	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
120627	amylase	-
68382	beta-galactosidase	-	3.2.1.23	from API zym
120627	beta-galactosidase	-	3.2.1.23
68382	beta-glucosidase	-	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
120627	caseinase	-	3.4.21.50
120627	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
120627	DNase	-
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	-		from API zym
120627	gelatinase	-
120627	lecithinase	-
68382	leucine arylamidase	+	3.4.11.1	from API zym
120627	lipase	-
68382	lipase (C 14)	-		from API zym
120627	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
120627	ornithine decarboxylase	-	4.1.1.17
120627	oxidase	+
120627	protease	-
68382	trypsin	+	3.4.21.4	from API zym
120627	tryptophan deaminase	-
120627	tween esterase	-
120627	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
120627	-	-	+	-	-	+	-	-	+	-	+	-	-	-	-	+	-	-	-	-

API biotype100

@ref	ControlQ	D-glucose as carbon sourceGLU	D-fructose as carbon sourceFRU	D-galactose as carbon sourceGAL	D-trehalose as carbon sourceTRE	D-mannose as carbon sourceMNE	L-sorbose as carbon sourceSBE	D-melibiose as carbon sourceMEL	sucrose as carbon sourceSAC	D-raffinose as carbon sourceRAF	maltotriose as carbon sourceMTE	maltose as carbon sourceMAL	lactose as carbon sourceLAC	lactulose as carbon sourceLTE	1-O-methyl-beta-galactopyranoside as carbon sourceMbGa	1-O-methyl-alpha-galactopyranoside as carbon sourceMaGa	D-cellobiose as carbon sourceCEL	gentiobiose as carbon sourceGEN	1-O-methyl-beta-D-glucopyranoside as carbon sourceMbGu	esculin as carbon sourceESC	D-ribose as carbon sourceRIB	L-arabinose as carbon sourceARA	D-xylose as carbon sourceXYL	palatinose as carbon sourcePLE	L-rhamnose as carbon sourceRHA	L-fucose as carbon sourceFUC	D-melezitose as carbon sourceMLZ	D-arabitol as carbon sourceDARL	L-arabitol as carbon sourceLARL	xylitol as carbon sourceXLT	dulcitol as carbon sourceDUL	D-tagatose as carbon sourceTAG	glycerol as carbon sourceGLY	myo-inositol as carbon sourceINO	D-mannitol as carbon sourceMAN	maltitol as carbon sourceMTL	D-turanose as carbon sourceTUR	D-sorbitol as carbon sourceSOR	adonitol as carbon sourceADO	hydroxyquinoline-beta-glucuronide as carbon sourceHBG	D-lyxose as carbon sourceLYX	i-erythritol as carbon sourceERY	1-O-methyl-alpha-D-glucoside as carbon sourceMDG	3-O-methyl-D-glucose as carbon source3MDG	D-saccharate as carbon sourceSAT	mucate as carbon sourceMUC	L-tartrate as carbon sourceLTAT	D-tartrate as carbon sourceDTAT	meso-tartrate as carbon sourceMTAT	D-malate as carbon sourceDMLT	L-malate as carbon sourceLMLT	cis-aconitate as carbon sourceCATE	trans-aconitate as carbon sourceTATE	tricarballylate as carbon sourceTTE	citrate as carbon sourceCIT	D-glucuronate as carbon sourceGRT	D-galacturonate as carbon sourceGAT	2-ketogluconate as carbon source2KG	5-ketogluconate as carbon source5KG	tryptophan as carbon sourceTRY	N-acetyl-D-glucosamine as carbon sourceNAG	D-gluconate as carbon sourceGNT	phenylacetate as carbon sourcePAC	protocatechuate as carbon sourcePAT	4-hydroxybenzoate as carbon sourcepOBE	quinate as carbon sourceQAT	gentisate as carbon sourceGTE	3-hydroxybenzoate as carbon sourcemOBE	benzoate as carbon sourceBAT	3-phenylpropionate as carbon sourcePPAT	m-coumarate as carbon sourceCMT	trigonelline as carbon sourceTGE	betaine as carbon sourceBET	putrescine as carbon sourcePCE	4-aminobutyrate as carbon sourceABT	histamine as carbon sourceHIN	DL-lactate as carbon sourceLAT	caprate as carbon sourceCAP	caprylate as carbon sourceCYT	L-histidine as carbon sourceHIS	succinate as carbon sourceSUC	fumarate as carbon sourceFUM	glutarate as carbon sourceGRE	DL-glycerate as carbon sourceGYT	5-aminovalerate as carbon sourceAVT	ethanolamine as carbon sourceETN	tryptamine as carbon sourceTTN	D-glucosamine as carbon sourceGLN	itaconate as carbon sourceITA	3-hydroxybutyrate as carbon source3OBU	L-aspartate as carbon sourceAPT	L-glutamate as carbon sourceGTT	L-proline as carbon sourcePRO	D-alanine as carbon sourceDALA	L-alanine as carbon sourceLALA	L-serine as carbon sourceSER	malonate as carbon sourceMNT	propionate as carbon sourcePROP	L-tyrosine as carbon sourceTYR	2-ketoglutarate as carbon source2KT
120627	not determinedn.d.	+	+	+	+	+	-	-	+	-	-	+	-	-	+	+	+	+	-	+	+	-	+	-	+	+	-	+	-	-	-	-	+	+	+	-	+	+	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	+	-	-	+	-	-	+	-	+	-	-	-	-	-	-	+	-	+	-	+	-	-	-	-	-	-	-	+	-	-	+	-	+	+	+	+	-	+	+	-	-	+	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Forest
#Environmental	#Terrestrial	#Soil

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
6994	soil of beech woodland	County Down			Europe
58909	Soil,unpolluted beech woodland soil	Northern Ireland,County Down	United Kingdom	GBR	Europe
120627	Environment, Soil, Beech woodland	Lissara House, county Down	United Kingdom	GBR	Europe

Taxonmaps

69479

Global distribution of 16S sequence AF107722 (>99% sequence identity) for Mesorhizobium from Microbeatlas

Aquatic Samples	308
Soil Samples	780
Animal Samples	145
Plant Samples	31
Total Samples	1264

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
6994	1	Risk group (German classification) According to TRBA 466
120627	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	ASM1420749v1 assembly for Aminobacter carboxidus DSM 17454	scaffold	GCA_014207495	305698.3	2861412741	305698	68.94

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
6994	Aminobacter lissarensis strain CC495 16S ribosomal RNA gene, complete sequence	AF107722	1435		305698

GC content

31512

GC-content (mol%)62.5

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM1420749v1 assembly for Aminobacter carboxidus DSM 17454
NCBI: GCA_014207495

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.39	no
125439	motility	BacteriaNetⓘ	yes	68.80	no
125439	gram_stain	BacteriaNetⓘ	negative	98.10	no
125439	spore_formation	BacteriaNetⓘ	no	99.58	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Aminobacter lissarensis DSM 17454
NCBI: GCA_014207495.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.40	no
125438	anaerobic	anaerobicⓘ	no	95.95	yes
125438	aerobic	aerobicⓘ	yes	84.10	no
125438	spore-forming	spore-formingⓘ	no	88.40	no
125438	thermophilic	thermophileⓘ	no	100.00	yes
125438	flagellated	motile2+ⓘ	yes	69.37	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Phylogenomic Reconstruction and Metabolic Potential of the Genus Aminobacter.	Artuso I, Turrini P, Pirolo M, Lugli GA, Ventura M, Visca P.	Microorganisms	10.3390/microorganisms9061332	2021
Phylogeny	Phylogenomic analysis and characterization of carbon monoxide utilization genes in the family Phyllobacteriaceae with reclassification of Aminobacter carboxidus (Meyer et al. 1993, Hordt et al. 2020) as Aminobacter lissarensis comb. nov. (McDonald et al. 2005).	Artuso I, Turrini P, Pirolo M, Lucidi M, Tescari M, Visaggio D, Mansi A, Lugli GA, Ventura M, Visca P	Syst Appl Microbiol	10.1016/j.syapm.2021.126199	2021
Metabolism	Analysis of genes involved in methyl halide degradation in Aminobacter lissarensis CC495.	Warner KL, Larkin MJ, Harper DB, Murrell JC, McDonald IR	FEMS Microbiol Lett	10.1016/j.femsle.2005.07.021	2005
Phylogeny	Aminobacter ciceronei sp. nov. and Aminobacter lissarensis sp. nov., isolated from various terrestrial environments.	McDonald IR, Kampfer P, Topp E, Warner KL, Cox MJ, Hancock TLC, Miller LG, Larkin MJ, Ducrocq V, Coulter C, Harper DB, Murrell JC, Oremland RS	Int J Syst Evol Microbiol	10.1099/ijs.0.63716-0	2005

References

#6994	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 17454
#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 )
#27808	IJSEM 1827 2005 ( DOI 10.1099/ijs.0.63716-0 , PubMed 16166673 )
#31512	Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #27808
#34007	; Curators of the CIP;
#58909	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 50579
#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 .
#120627	Collection of Institut Pasteur ; Curators of the CIP; CIP 108661
#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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Aminobacter carboxidus (DSM 17454, CCUG 50579, CIP 108661)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Antibiotic resistance

Metabolite production

Enzymes

API zym

API biotype100

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_014207495

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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