Comamonas badia (DSM 17552, IAM 14839, KCTC 12244)

Name: Comamonas badia (DSM 17552, IAM 14839, KCTC 12244)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 2931

Type strain

Strain Designation No.12

Culture col. no. DSM 17552 IAM 14839 KCTC 12244 CCUG 51443 No.12 2 more

NCBI tax ID(s) 1121348 265291

Special Collections DSMZ CCUG JCM KCTC CIP

History DSMZ <- A. Yokota <- Y. Tago; No.12 JCM <-- IAM 14839 <-- Y. Tago and A. Yokota. CIP <- 2005, IAM <- Y. Tago

Links

Comamonas badia No.12 is an aerobe, Gram-negative, motile bacterium that was isolated from activated sludge.

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

Name and taxonomic classification

SI-ID 131035

IAM 14839,KCTC 12244,DSM 17552,CCUG 51443,JCM 21345,CIP 108817

@ref 20215

Last LPSN update 2026-05-29 08:25:35

Domain Bacteria

Phylum Pseudomonadota

Class Betaproteobacteria

Order Burkholderiales

Family Comamonadaceae

Genus Comamonas

Species Comamonas badia

Full scientific name Comamonas badia Tago and Yokota 2005

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
116700	negative	rod-shaped
125439	negative		98.017
125438	negative		95.364

Pigmentation

@ref	Production	Name
116700		Pyocyanin

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
6968	TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)	Medium recipe at MediaDive	Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
6968	LB (Luria-Bertani) MEDIUM (DSMZ Medium 381)	Medium recipe at MediaDive	Name: LB (Luria-Bertani) MEDIUM (DSMZ Medium 381) Composition: Agar 20.0 g/l NaCl 10.0 g/l Tryptone 10.0 g/l Yeast extract 5.0 g/l Distilled water
38320	MEDIUM 29- Brain heart agar		Distilled water make up to (1000.000 ml);Brain heart infusion agar (52.000 g)
116700	CIP Medium 368	Medium recipe at CIP
116700	CIP Medium 29	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
6968	positive	growth	28
38320	positive	growth	30
59190	positive	growth	30
67770	positive	growth	27
116700	positive	growth	25-30
116700	negative	growth	5
116700	negative	growth	10
116700	negative	growth	37
116700	negative	growth	41

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
59190	aerobe
116700	obligate aerobe
125439	obligate aerobe	98.797

Spore formation

@ref	Spore formation	Confidence
125439		99.64
125438		92.299

Halophily

@ref	Salt	Growth	Tested relation	Concentration
116700	NaCl	positive	growth	0-2 %
116700	NaCl		growth	4 %
116700	NaCl		growth	6 %
116700	NaCl		growth	8 %
116700	NaCl		growth	10 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68369	17128 ChEBI	adipate	-	assimilation	from API 20NE
68369	29016 ChEBI	arginine	-	hydrolysis	from API 20NE
116700	16947 ChEBI	citrate	-	carbon source
68369	17634 ChEBI	D-glucose	-	assimilation	from API 20NE
68369	17634 ChEBI	D-glucose	-	fermentation	from API 20NE
68369	16899 ChEBI	D-mannitol	-	assimilation	from API 20NE
68369	16024 ChEBI	D-mannose	-	assimilation	from API 20NE
68369	27689 ChEBI	decanoate	-	assimilation	from API 20NE
116700	4853 ChEBI	esculin	-	hydrolysis
68369	4853 ChEBI	esculin	-	hydrolysis	from API 20NE
68369	5291 ChEBI	gelatin	-	hydrolysis	from API 20NE
68369	24265 ChEBI	gluconate	-	assimilation	from API 20NE
68369	30849 ChEBI	L-arabinose	-	assimilation	from API 20NE
68369	25115 ChEBI	malate	-	assimilation	from API 20NE
68369	17306 ChEBI	maltose	-	assimilation	from API 20NE
68369	59640 ChEBI	N-acetylglucosamine	-	assimilation	from API 20NE
116700	17632 ChEBI	nitrate	-	reduction
116700	17632 ChEBI	nitrate	-	respiration
68369	17632 ChEBI	nitrate	-	reduction	from API 20NE
116700	16301 ChEBI	nitrite	-	reduction
68369	27897 ChEBI	tryptophan	-	energy source	from API 20NE
68369	16199 ChEBI	urea	-	hydrolysis	from API 20NE

Metabolite production

@ref	Chebi-ID	Metabolite	Production
68369	35581 ChEBI	indole		from API 20NE
116700	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test
68369	35581 ChEBI	indole	-	from API 20NE

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	-	3.1.3.2	from API zym
116700	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
116700	amylase	-
68369	arginine dihydrolase	-	3.5.3.6	from API 20NE
68382	beta-galactosidase	-	3.2.1.23	from API zym
116700	beta-galactosidase	-	3.2.1.23
68382	beta-glucosidase	-	3.2.1.21	from API zym
68369	beta-glucosidase	-	3.2.1.21	from API 20NE
68382	beta-glucuronidase	-	3.2.1.31	from API zym
116700	caseinase	-	3.4.21.50
116700	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
68369	cytochrome oxidase	+	1.9.3.1	from API 20NE
116700	DNase	-
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
116700	gelatinase	-
68369	gelatinase	-		from API 20NE
116700	lecithinase	-
68382	leucine arylamidase	+	3.4.11.1	from API zym
116700	lipase	-
68382	lipase (C 14)	-		from API zym
116700	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
116700	ornithine decarboxylase	-	4.1.1.17
116700	oxidase	+
116700	protease	+
68382	trypsin	-	3.4.21.4	from API zym
116700	tryptophan deaminase	-
116700	tween esterase	+
116700	urease	-	3.5.1.5
68369	urease	-	3.5.1.5	from API 20NE
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
116700	-	-	+	+	-	+	-	-	-	-	-	+	-	-	-	-	-	-	-	-

API 20NE

@ref	Reduction of nitratesNO3	TRP	GLU_ Ferm	ADH (Arg)	URE	ESC	GEL	PNPG	GLU_ Assim	ARA	MNE	MAN	NAG	MAL	GNT	CAP	ADI	MLT	CIT	PAC	OX
6968	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	+

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Waste	#Activated sludge

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
6968	activated sludge	Kawasaki, Kanagawa Pre.	Japan	JPN	Asia
67770	Activated sludge	Noborito, Kawasaki, Kanagawa Pref.	Japan	JPN	Asia
116700	Environment, Activated sludge	Kawasaki, Kanagawa	Japan	JPN	Asia

Taxonmaps

69479

Global distribution of 16S sequence AB164432 (>99% sequence identity) for Comamonas badia subclade from Microbeatlas

Aquatic Samples	2420
Soil Samples	996
Animal Samples	200
Plant Samples	158
Total Samples	3774

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
6968	1	Risk group (German classification) According to TRBA 466
116700	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
67770	ASM48463v1 assembly for Comamonas badia DSM 17552	contig	GCA_000484635	1121348.4	2528768012	1121348	74.23

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
6968	Comamonas badia gene for 16S rRNA, partial sequence	AB164432	1496		265291

GC content

@ref	GC-content (mol%)	Method
67770	66.3	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM48463v1 assembly for Comamonas badia DSM 17552
BV-BRC: 1121348.4

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	98.80	no
125439	gram_stain	BacteriaNetⓘ	negative	98.02	no
125439	motility	BacteriaNetⓘ	yes	81.35	no
125439	spore_formation	BacteriaNetⓘ	no	99.64	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Comamonas badia DSM 17552
PATRIC: 1121348.4

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	95.36	no
125438	anaerobic	anaerobicⓘ	no	95.89	yes
125438	spore-forming	spore-formingⓘ	no	92.30	no
125438	aerobic	aerobicⓘ	yes	83.78	yes
125438	thermophilic	thermophileⓘ	no	96.22	yes
125438	flagellated	motile2+ⓘ	yes	82.72	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Nanopore Long-Read Guided Complete Genome Assembly of Hydrogenophaga intermedia, and Genomic Insights into 4-Aminobenzenesulfonate, p-Aminobenzoic Acid and Hydrogen Metabolism in the Genus Hydrogenophaga.	Gan HM, Lee YP, Austin CM.	Front Microbiol	10.3389/fmicb.2017.01880	2017
	The Emergence of the Genus Comamonas as Important Opportunistic Pathogens.	Ryan MP, Sevjahova L, Gorman R, White S.	Pathogens	10.3390/pathogens11091032	2022
Metabolism	Metagenomic Analyses of the Autotrophic Fe(II)-Oxidizing, Nitrate-Reducing Enrichment Culture KS.	He S, Tominski C, Kappler A, Behrens S, Roden EE.	Appl Environ Microbiol	10.1128/aem.03493-15	2016
Genetics	Dakarella massiliensis gen. nov., sp. nov., strain ND3^T: a new bacterial genus isolated from the female genital tract.	Dione N, Rathored J, Tomei E, Lagier JC, Khelaifia S, Robert C, Bretelle F, Raoult D, Fournier PE, Fenollar F.	New Microbes New Infect	10.1016/j.nmni.2017.05.003	2017
Phylogeny	Comamonas flocculans sp. nov., a Floc-Forming Bacterium Isolated from Livestock Wastewater.	Kim DH, Han KI, Kwon HJ, Kim MG, Kim YG, Choi DH, Lee KC, Suh MK, Kim HS, Lee JS, Kim JG	Curr Microbiol	10.1007/s00284-020-01940-5	2020
Phylogeny	Comamonas badia sp. nov., a floc-forming bacterium isolated from activated sludge.	Tago Y, Yokota A	J Gen Appl Microbiol	10.2323/jgam.50.243	2004

References

#6968	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 17552
#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 )
#38320	; Curators of the CIP;
#59190	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 51443
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#68369	Automatically annotated from API 20NE .
#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 .
#116700	Collection of Institut Pasteur ; Curators of the CIP; CIP 108817
#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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Comamonas badia (DSM 17552, IAM 14839, KCTC 12244)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API zym

API 20NE

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000484635

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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