Name: Aminobacter carboxidus DSM 17454
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 11862

Type strain:

Species: Aminobacter carboxidus

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

Strain history: CIP <- 2005, P. Kämpfer, Giessen Univ., Giessen, Germany <- I. Mc Donald, Waikato Univ., Hamilton, New-Zealand: strain CC495

NCBI tax ID(s): 305698 (species)

Other strains from Aminobacter carboxidus

A. carboxidus Z-1171, DSM 1086, ATCC 51424, CIP ... (type strain)

Section

Aminobacter carboxidus DSM 17454 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from soil of beech woodland.

Gram-negative
motile
rod-shaped
aerobe
mesophilic
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	*Phyllobacteriaceae*
	Genus	*Aminobacter*
	Species	**Aminobacter carboxidus**
	Full Scientific Name (LPSN)	Aminobacter carboxidus (Meyer et al. 1994 ex Nozhevnikova and Zavarzin 1974) Hördt et al. 2020

	Synonym	Aminobacter lissarensis
	Synonym	Carbophilus carboxidus

Information on morphological and physiological properties Morphology

[Ref.: #31512]	Gram stain	negative
[Ref.: #120627]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.972

[Ref.: #31512]	Cell length	1.4 µm

[Ref.: #31512]	Cell width	0.55 µm

[Ref.: #31512]	Cell shape	rod-shaped
[Ref.: #120627]	Cell shape	rod-shaped

[Ref.: #31512]	Motility	yes
[Ref.: #120627]	Motility	yes

[Ref.: #31512]	Pigment production	yes
[Ref.: #120627]	Pigment production	no
[Ref.: #120627]	Pigment name	Pyocyanin

Information on culture and growth conditions Culture and growth conditions

[Ref.: #6994]

Culture medium

R2A MEDIUM (DSMZ Medium 830)

[Ref.: #6994]

Culture medium growth

[Ref.: #6994]

Culture medium link

Medium recipe at MediaDive

[Ref.: #6994]

Culture medium composition

expand / minimize

[Ref.: #34007]

Culture medium

MEDIUM 72- for trypto casein soja agar

[Ref.: #34007]

Culture medium growth

[Ref.: #34007]

Culture medium composition

expand / minimize

[Ref.: #120627]

Culture medium

CIP Medium 72

[Ref.: #120627]

Culture medium growth

[Ref.: #120627]

Culture medium link

Medium recipe provided by DSMZ

[Ref.: #120627]

Culture medium

CIP Medium 566

[Ref.: #120627]

Culture medium growth

[Ref.: #120627]

Culture medium link

Medium recipe provided by DSMZ

	Kind of temperature		Temperature
[Ref.: #6994]		growth	28 °C
[Ref.: #31512]		growth	25 °C
[Ref.: #31512]		optimum	25 °C
[Ref.: #34007]		growth	25 °C
[Ref.: #58909]		growth	26-37 °C
[Ref.: #120627]	no	growth	37 °C
[Ref.: #120627]	no	growth	10 °C
[Ref.: #120627]	no	growth	5 °C
[Ref.: #120627]		growth	25-30 °C
[Ref.: #120627]	no	growth	41 °C

[Ref.: #6994]	Temperature range	mesophilic
[Ref.: #31512]	Temperature range	mesophilic
[Ref.: #34007]	Temperature range	mesophilic
[Ref.: #58909]	Temperature range	mesophilic
[Ref.: #120627]	Temperature range	mesophilic
[Ref.: #120627]	Temperature range	psychrophilic
[Ref.: #120627]	Temperature range	mesophilic
[Ref.: #120627]	Temperature range	thermophilic

	pH	Kind of pH		pH
[Ref.: #31512]			optimum	6.95
[Ref.: #31512]			growth	6.7-7.2

Information on physiology and metabolism Physiology and metabolism

[Ref.: #6994]	Oxygen tolerance	aerobe
[Ref.: #31512]	Oxygen tolerance	aerobe
[Ref.: #58909]	Oxygen tolerance	aerobe
[Ref.: #120627]	Oxygen tolerance	obligate aerobe

[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.982

	Salt	Tested relation		Salt conc.
[Ref.: #120627]	NaCl		growth	0-2	%
[Ref.: #120627]	NaCl	no	growth	4	%
[Ref.: #120627]	NaCl	no	growth	6	%
[Ref.: #120627]	NaCl	no	growth	8	%
[Ref.: #120627]	NaCl	no	growth	10	%

[Ref.: #31512]

Observation

aggregates in clumps

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #31512]	3-hydroxybutyrate ChEBI	+	carbon source
[Ref.: #31512]	acetate ChEBI	+	carbon source
[Ref.: #31512]	alanine ChEBI	+	carbon source
[Ref.: #31512]	arabinose ChEBI	+	carbon source
[Ref.: #31512]	aspartate ChEBI	+	carbon source
[Ref.: #31512]	cellobiose ChEBI	+	carbon source
[Ref.: #120627]	citrate ChEBI	-	carbon source
[Ref.: #31512]	D-tryptophan ChEBI	+	carbon source
[Ref.: #120627]	esculin ChEBI	-	hydrolysis
[Ref.: #31512]	fructose ChEBI	+	carbon source
[Ref.: #31512]	galactose ChEBI	+	carbon source
[Ref.: #31512]	glucose ChEBI	+	carbon source
[Ref.: #31512]	histidine ChEBI	+	carbon source
[Ref.: #31512]	lactate ChEBI	+	carbon source
[Ref.: #31512]	leucine ChEBI	+	carbon source
[Ref.: #31512]	maltose ChEBI	+	carbon source
[Ref.: #31512]	mannitol ChEBI	+	carbon source
[Ref.: #31512]	mannose ChEBI	+	carbon source
[Ref.: #31512]	N-acetylglucosamine ChEBI	+	carbon source
[Ref.: #120627]	nitrate ChEBI	+	reduction
[Ref.: #120627]	nitrate ChEBI	-	respiration
[Ref.: #120627]	nitrite ChEBI	+	reduction
[Ref.: #31512]	ornithine ChEBI	+	carbon source
[Ref.: #31512]	proline ChEBI	+	carbon source
[Ref.: #31512]	propionate ChEBI	+	carbon source
[Ref.: #31512]	pyruvate ChEBI	+	carbon source
[Ref.: #31512]	rhamnose ChEBI	+	carbon source
[Ref.: #31512]	ribose ChEBI	+	carbon source
[Ref.: #31512]	serine ChEBI	+	carbon source
[Ref.: #31512]	sorbitol ChEBI	+	carbon source
[Ref.: #31512]	sucrose ChEBI	+	carbon source
[Ref.: #31512]	trehalose ChEBI	+	carbon source
[Ref.: #31512]	xylose ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Antibiotica	Metabolite	Antibiotic sensitivity	Antibiotic resistance
[Ref.: #120627]		0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)	no	yes

	Metabolite production	Metabolite	Production
[Ref.: #120627]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #120627]	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.: #120627]	amylase	-
[Ref.: #120627]	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.: #120627]	caseinase	-	3.4.21.50
[Ref.: #120627]	catalase	+	1.11.1.6
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #120627]	DNase	-
[Ref.: #68382]	esterase (C 4)	+		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	-		* from API zym
[Ref.: #120627]	gelatinase	-
[Ref.: #120627]	lecithinase	-
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #120627]	lipase	-
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #120627]	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.: #120627]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #120627]	oxidase	+
[Ref.: #120627]	protease	-
[Ref.: #68382]	trypsin	+	3.4.21.4	* from API zym
[Ref.: #120627]	tryptophan deaminase	-
[Ref.: #120627]	tween esterase	-
[Ref.: #120627]	urease	+	3.5.1.5
[Ref.: #68382]	valine arylamidase	-		* from API zym
	Only first 10 entries are displayed. Click here to see all.

API® Biotype100:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	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
[Ref.: #120627]	2860	not determinedn.d.	+	+	+	+	+	-	-	+	-	-	+	-	-	+	+	+	+	-	+	+	-	+	-	+	+	-	+	-	-	-	-	+	+	+	-	+	+	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	+	-	-	+	-	-	+	-	+	-	-	-	-	-	-	+	-	+	-	+	-	-	-	-	-	-	-	+	-	-	+	-	+	+	+	+	-	+	+	-	-	+	-

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.: #120627]	11366	-	-	+	-	-	+	-	-	+	-	+	-	-	-	-	+	-	-	-	-

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

[Ref.: #6994]	Sample type/isolated from	soil of beech woodland
[Ref.: #6994]	Geographic location (country and/or sea, region)	County Down
[Ref.: #6994]	Continent	Europe

[Ref.: #58909]	Sample type/isolated from	Soil,unpolluted beech woodland soil
[Ref.: #58909]	Geographic location (country and/or sea, region)	Northern Ireland,County Down
[Ref.: #58909]	Country	United Kingdom
[Ref.: #58909]	Country ISO 3 Code	GBR
[Ref.: #58909]	Continent	Europe

[Ref.: #120627]	Sample type/isolated from	Environment, Soil, Beech woodland
[Ref.: #120627]	Geographic location (country and/or sea, region)	Lissara House, county Down
[Ref.: #120627]	Country	United Kingdom
[Ref.: #120627]	Country ISO 3 Code	GBR
[Ref.: #120627]	Continent	Europe
* marker position based on {}

Isolation sources categories

#Environmental	#Terrestrial	#Forest
#Environmental	#Terrestrial	#Soil

What are isolation sources categories?

[Ref.: #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

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

[Ref.: #6994]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #120627]	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.: #6994]	Aminobacter lissarensis strain CC495 16S ribosomal RNA gene, complete sequence	AF107722	1435	ENA	305698 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Aminobacter lissarensis DSM 17454	GCA_014207495	scaffold	GenBank	305698 tax ID	*
[Ref.: #66792]	Aminobacter lissarensis strain DSM 17454	305698.3	wgs	PATRIC	305698 tax ID	*
[Ref.: #66792]	Aminobacter lissarensis DSM 17454	2861412741	draft	JGI IMG/M	305698 tax ID	*

[Ref.: #31512]

GC-content

62.5 mol%

Data predicted using genome information as a basis Genome-based predictions

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Aminobacter lissarensis DSM 17454 NCBI: GCA_014207495.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Aminobacter lissarensis DSM 17454 NCBI: GCA_014207495.1
[Ref.: #69480]	flagellated	no	70.554	no
[Ref.: #69480]	gram-positive	no	97.676	yes
[Ref.: #69480]	anaerobic	no	98.917	no
[Ref.: #69480]	aerobic	yes	94.708	yes
[Ref.: #69480]	halophile	no	89.358	no
[Ref.: #69480]	spore-forming	no	94.666	no
[Ref.: #69480]	glucose-util	yes	93.72	yes
[Ref.: #69480]	thermophile	no	99.003	no
[Ref.: #69480]	motile	yes	89.953	yes
[Ref.: #69480]	glucose-ferment	no	89.97	no

Availability in culture collections External links

[Ref.: #6994]

Culture collection no.

DSM 17454, CCUG 50579, CIP 108661, NCIMB 13798, CC 495

Literature:

Topic	Title	Authors	Journal	DOI	Year
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	*
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	*
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	*

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 )

#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 (see below)

#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 .

#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) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#120627 Collection of Institut Pasteur ; Curators of the CIP; CIP 108661

#27808

IJSEM 1827 2005 ( DOI 10.1099/ijs.0.63716-0 , PubMed 16166673 )

* These data were automatically processed and therefore are not curated

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Aminobacter lissarensis DSM 17454

Aminobacter lissarensis DSM 17454

Change proposal

Change proposal