Name: Comamonas badia No.12
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 2931

Type strain:

Species: Comamonas badia

Strain Designation: No.12

Culture col. no.: DSM 17552, IAM 14839, KCTC 12244, CCUG 51443, JCM 21345, CIP 108817

Strain history: CIP <- 2005, IAM <- Y. Tago

NCBI tax ID(s): 1121348 (strain), 265291 (species)

SI-ID 131035

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

Section

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

motile
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	*Betaproteobacteria*
	Order	*Burkholderiales*
	Family	*Comamonadaceae*
	Genus	*Comamonas*
	Species	**Comamonas badia**
	Full Scientific Name (LPSN)	Comamonas badia Tago and Yokota 2005

Information on morphological and physiological properties Morphology

[Ref.: #116700]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %100

[Ref.: #116700]	Cell shape	rod-shaped

[Ref.: #116700]	Motility	yes
[Ref.: #69480]	Motility	yes Confidence in %95.07

[Ref.: #116700]	Pigment production	no
[Ref.: #116700]	Pigment name	Pyocyanin

Information on culture and growth conditions Culture and growth conditions

[Ref.: #6968]

Culture medium

TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)

[Ref.: #6968]

Culture medium growth

[Ref.: #6968]

Culture medium link

Medium recipe at MediaDive

[Ref.: #6968]

Culture medium composition

expand / minimize

[Ref.: #6968]

Culture medium

LB (Luria-Bertani) MEDIUM (DSMZ Medium 381)

[Ref.: #6968]

Culture medium growth

[Ref.: #6968]

Culture medium link

Medium recipe at MediaDive

[Ref.: #6968]

Culture medium composition

expand / minimize

[Ref.: #38320]

Culture medium

MEDIUM 29- Brain heart agar

[Ref.: #38320]

Culture medium growth

[Ref.: #38320]

Culture medium composition

expand / minimize

[Ref.: #116700]

Culture medium

CIP Medium 368

[Ref.: #116700]

Culture medium growth

[Ref.: #116700]

Culture medium link

Medium recipe provided by DSMZ

[Ref.: #116700]

Culture medium

CIP Medium 29

[Ref.: #116700]

Culture medium growth

[Ref.: #116700]

Culture medium link

Medium recipe provided by DSMZ

	Kind of temperature		Temperature
[Ref.: #6968]		growth	28 °C
[Ref.: #38320]		growth	30 °C
[Ref.: #59190]		growth	30 °C
[Ref.: #67770]		growth	27 °C
[Ref.: #116700]		growth	25-30 °C
[Ref.: #116700]	no	growth	5 °C
[Ref.: #116700]	no	growth	10 °C
[Ref.: #116700]	no	growth	37 °C
[Ref.: #116700]	no	growth	41 °C

[Ref.: #6968]	Temperature range	mesophilic
[Ref.: #38320]	Temperature range	mesophilic
[Ref.: #59190]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic
[Ref.: #116700]	Temperature range	mesophilic
[Ref.: #116700]	Temperature range	psychrophilic
[Ref.: #116700]	Temperature range	mesophilic
[Ref.: #116700]	Temperature range	thermophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #59190]	Oxygen tolerance	aerobe
[Ref.: #116700]	Oxygen tolerance	obligate aerobe

[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.993

	Salt	Tested relation		Salt conc.
[Ref.: #116700]	NaCl		growth	0-2	%
[Ref.: #116700]	NaCl	no	growth	4	%
[Ref.: #116700]	NaCl	no	growth	6	%
[Ref.: #116700]	NaCl	no	growth	8	%
[Ref.: #116700]	NaCl	no	growth	10	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68369]	adipate ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	arginine ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #116700]	citrate ChEBI	-	carbon source
[Ref.: #68369]	D-glucose ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	D-glucose ChEBI	-	fermentation	* from API 20NE
[Ref.: #68369]	D-mannitol ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	D-mannose ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	decanoate ChEBI	-	assimilation	* from API 20NE
[Ref.: #116700]	esculin ChEBI	-	hydrolysis
[Ref.: #68369]	esculin ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #68369]	gelatin ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #68369]	gluconate ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	L-arabinose ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	malate ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	maltose ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	N-acetylglucosamine ChEBI	-	assimilation	* from API 20NE
[Ref.: #116700]	nitrate ChEBI	-	reduction
[Ref.: #116700]	nitrate ChEBI	-	respiration
[Ref.: #68369]	nitrate ChEBI	-	reduction	* from API 20NE
[Ref.: #116700]	nitrite ChEBI	-	reduction
[Ref.: #68369]	tryptophan ChEBI	-	energy source	* from API 20NE
[Ref.: #68369]	urea ChEBI	-	hydrolysis	* from API 20NE
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #116700]		indole ChEBI	no
[Ref.: #68369]		indole ChEBI	no	* from API 20NE

	Physiological tests	Metabolite	Indole test
[Ref.: #68369]		indole ChEBI	-	* from API 20NE

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	-	3.1.3.2	* from API zym
[Ref.: #116700]	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.: #116700]	amylase	-
[Ref.: #68369]	arginine dihydrolase	-	3.5.3.6	* from API 20NE
[Ref.: #116700]	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, API 20NE
[Ref.: #68382]	beta-glucuronidase	-	3.2.1.31	* from API zym
[Ref.: #116700]	caseinase	-	3.4.21.50
[Ref.: #116700]	catalase	+	1.11.1.6
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #68369]	cytochrome oxidase	+	1.9.3.1	* from API 20NE
[Ref.: #116700]	DNase	-
[Ref.: #68382]	esterase (C 4)	+		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	+		* from API zym
[Ref.: #116700]	gelatinase	-
[Ref.: #68369]	gelatinase	-		* from API 20NE
[Ref.: #116700]	lecithinase	-
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #116700]	lipase	-
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #116700]	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.: #116700]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #116700]	oxidase	+
[Ref.: #116700]	protease	+
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #116700]	tryptophan deaminase	-
[Ref.: #116700]	tween esterase	+
[Ref.: #116700]	urease	-	3.5.1.5
[Ref.: #68369]	urease	-	3.5.1.5	* from API 20NE
[Ref.: #68382]	valine arylamidase	-		* from API zym
	Only first 10 entries are displayed. Click here to see all.

API® 20NE:

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

	API ID	Reduction of nitratesNO3	Indole productionTRP	Fermentation of D-glucoseGLU_ Ferm	Arginine dihydrolaseADH (Arg)	Urease/urea hydrolysisURE	Esculin hydrolysis/beta-GlucosidaseESC	Gelatinase/gelatin hydrolysisGEL	beta-GalactosidasePNPG	Assimilation of D-glucoseGLU_ Assim	Assimilation of L-arabinoseARA	Assimilation of D-mannoseMNE	Assimilation of D-mannitolMAN	Assimilation of N-acetyl-glucosamineNAG	Assimilation of maltoseMAL	Assimilation of gluconateGNT	Assimilation of capric acidCAP	Assimilation adipic acidADI	Assimilation of malic acidMLT	Assimilation of citric acidCIT	Assimilation of phenyl-acetic acidPAC	Cytochrome oxidaseOX
[Ref.: #6968]	23232	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	+

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.: #116700]	11481	-	-	+	+	-	+	-	-	-	-	-	+	-	-	-	-	-	-	-	-

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

[Ref.: #6968]	Sample type/isolated from	activated sludge
[Ref.: #6968]	Geographic location (country and/or sea, region)	Kawasaki, Kanagawa Pre.
[Ref.: #6968]	Country	Japan
[Ref.: #6968]	Country ISO 3 Code	JPN
[Ref.: #6968]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Activated sludge
[Ref.: #67770]	Geographic location (country and/or sea, region)	Noborito, Kawasaki, Kanagawa Pref.
[Ref.: #67770]	Country	Japan
[Ref.: #67770]	Country ISO 3 Code	JPN
[Ref.: #67770]	Continent	Asia

[Ref.: #116700]	Sample type/isolated from	Environment, Activated sludge
[Ref.: #116700]	Geographic location (country and/or sea, region)	Kawasaki, Kanagawa
[Ref.: #116700]	Country	Japan
[Ref.: #116700]	Country ISO 3 Code	JPN
[Ref.: #116700]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Engineered

#Waste

#Activated sludge

What are isolation sources categories?

[Ref.: #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

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

[Ref.: #6968]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #116700]	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.: #6968]	Comamonas badia gene for 16S rRNA, partial sequence	AB164432	1496	ENA	265291 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Comamonas badia DSM 17552 DSM 17552	GCA_000484635	contig	GenBank	1121348 tax ID
[Ref.: #66792]	Comamonas badia DSM 17552	1121348.4	wgs	PATRIC	1121348 tax ID	*
[Ref.: #66792]	Comamonas badia DSM 17552	2528768012	draft	JGI IMG/M	1121348 tax ID	*

[Ref.: #67770]

GC-content

66.3 mol%

high performance liquid chromatography (HPLC)

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: Comamonas badia DSM 17552 PATRIC: 1121348.4
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Comamonas badia DSM 17552 PATRIC: 1121348.4
[Ref.: #69480]	motile	yes	89.431	no
[Ref.: #69480]	flagellated	yes	56.394	no
[Ref.: #69480]	gram-positive	no	98.438	no
[Ref.: #69480]	anaerobic	no	98.613	yes
[Ref.: #69480]	aerobic	yes	90.391	yes
[Ref.: #69480]	halophile	no	89.695	no
[Ref.: #69480]	spore-forming	no	93.857	no
[Ref.: #69480]	thermophile	no	91.627	yes
[Ref.: #69480]	glucose-util	no	89.272	no
[Ref.: #69480]	glucose-ferment	no	91.293	no

Availability in culture collections External links

[Ref.: #6968]

Culture collection no.

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

[Ref.: #72454]

SI-ID 131035

Literature:

Topic	Title	Authors	Journal	DOI	Year
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

#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) .

#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 .

#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 )

#72454

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-ID131035.1 )

#116700 Collection of Institut Pasteur ; Curators of the CIP; CIP 108817
* These data were automatically processed and therefore are not curated

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Comamonas badia DSM 17552

Comamonas badia DSM 17552

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