Herbaspirillum chlorophenolicum (DSM 17796, IAM 15024, JCM 21487)

Name: Herbaspirillum chlorophenolicum (DSM 17796, IAM 15024, JCM 21487)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 11366

Type strain

Strain Designation CPW301

Culture col. no. DSM 17796 IAM 15024 JCM 21487 KCTC 12096 NBRC 102525 4 more

NCBI tax ID(s) 1349766 211589

Special Collections DSMZ CCUG JCM KCTC CIP Literature strains UCCCB

History <- S.-T. Lee, KAIST; CPW301 <- H.-S. Bae, Dept. of Biol. Sci., LSU, LA, USA IAM 15024 <-- W.-T. Im CPW301. <- ST Lee, KAIST Lee S.-T., Korea Advanced Institute of Science and Technology; CPW301 < Bae H.-S., Deptartment of Biological Sciences., LSU, LA, USA CIP <- 2004, KCTC <- S.T. Lee, KAIST, Korea: strain CPW301

Links

Herbaspirillum chlorophenolicum CPW301 is an aerobe, Gram-negative, motile bacterium that was isolated from soil sediment collected at a stream near an industrial region.

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

Name and taxonomic classification

SI-ID 107096

KCTC 12096,IAM 15024,LMG 22686,CIP 108432,CCUG 52898,JCM 21487,DSM 17796,NBRC 102525

@ref 20215

Last LPSN update 2026-02-09 11:20:32

Domain Bacteria

Phylum Pseudomonadota

Class Betaproteobacteria

Order Burkholderiales

Family Oxalobacteraceae

Genus Herbaspirillum

Species Herbaspirillum chlorophenolicum

Full scientific name Herbaspirillum chlorophenolicum Im et al. 2004

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
30000	negative	2.3 µm	0.7 µm	rod-shaped
67771	negative
118240	negative			rod-shaped
125438	negative				97.994
125439	negative				99.7

Pigmentation

@ref	Production	Name
118240		Pyocyanin

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
7191	NUTRIENT AGAR (DSMZ Medium 1)	Medium recipe at MediaDive	Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
33241	MEDIUM 328- for nutrient agar		Distilled water make up to (1000.000 ml);Agar (15.000 g);Peptone (5.000g);Beef extract (3.000 g)
118240	CIP Medium 328	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
7191	positive	growth	28
30000	positive	optimum	30
33241	positive	growth	30
59716	positive	growth	30
67770	positive	growth	30
67771	positive	growth	30
67772	positive	optimum	28
118240	positive	growth	5-30
118240	negative	growth	37
118240	negative	growth	41

Culture pH

@ref	Ability	Type	PH
67772	positive	maximum	8.0
67772	positive	minimum	6.0
30000	positive	optimum	6.5
30000	positive	growth	06-08

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
30000	aerobe
59716	aerobe
67771	aerobe
118240	obligate aerobe

Spore formation

@ref	Spore formation	Confidence
125439		99.5

Halophily

@ref	Salt	Growth	Tested relation	Concentration
118240	NaCl	positive	growth	0-4 %
118240	NaCl		growth	6 %
118240	NaCl		growth	8 %
118240	NaCl		growth	10 %

Observation

@ref	Observation
67770	quinones: Q-8
67771	quinones: Q-8

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68369	17128 ChEBI	adipate	-	assimilation	from API 20NE
68371	27613 ChEBI	amygdalin	-	builds acid from	from API 50CH acid
68371	18305 ChEBI	arbutin	-	builds acid from	from API 50CH acid
68369	29016 ChEBI	arginine	-	hydrolysis	from API 20NE
68371	17057 ChEBI	cellobiose	-	builds acid from	from API 50CH acid
118240	16947 ChEBI	citrate	+	carbon source
68371	17108 ChEBI	D-arabinose	-	builds acid from	from API 50CH acid
68371	18333 ChEBI	D-arabitol	-	builds acid from	from API 50CH acid
68371	15824 ChEBI	D-fructose	-	builds acid from	from API 50CH acid
68371	28847 ChEBI	D-fucose	-	builds acid from	from API 50CH acid
68371	12936 ChEBI	D-galactose	-	builds acid from	from API 50CH acid
68371	17634 ChEBI	D-glucose	-	builds acid from	from API 50CH acid
68369	17634 ChEBI	D-glucose	+	assimilation	from API 20NE
68369	17634 ChEBI	D-glucose	-	fermentation	from API 20NE
68371	62318 ChEBI	D-lyxose	-	builds acid from	from API 50CH acid
68371	16899 ChEBI	D-mannitol	-	builds acid from	from API 50CH acid
68369	16899 ChEBI	D-mannitol	+	assimilation	from API 20NE
68371	16024 ChEBI	D-mannose	-	builds acid from	from API 50CH acid
68369	16024 ChEBI	D-mannose	-	assimilation	from API 20NE
68371	16988 ChEBI	D-ribose	-	builds acid from	from API 50CH acid
68371	17924 ChEBI	D-sorbitol	-	builds acid from	from API 50CH acid
68371	16443 ChEBI	D-tagatose	-	builds acid from	from API 50CH acid
68371	65327 ChEBI	D-xylose	-	builds acid from	from API 50CH acid
68369	27689 ChEBI	decanoate	+	assimilation	from API 20NE
68371	17113 ChEBI	erythritol	-	builds acid from	from API 50CH acid
118240	4853 ChEBI	esculin	-	hydrolysis
68371	4853 ChEBI	esculin	-	builds acid from	from API 50CH acid
68369	4853 ChEBI	esculin	-	hydrolysis	from API 20NE
68371	16813 ChEBI	galactitol	-	builds acid from	from API 50CH acid
68369	5291 ChEBI	gelatin	-	hydrolysis	from API 20NE
68371	28066 ChEBI	gentiobiose	-	builds acid from	from API 50CH acid
68371	24265 ChEBI	gluconate	-	builds acid from	from API 50CH acid
68369	24265 ChEBI	gluconate	+	assimilation	from API 20NE
68371	17754 ChEBI	glycerol	-	builds acid from	from API 50CH acid
68371	28087 ChEBI	glycogen	-	builds acid from	from API 50CH acid
68371	15443 ChEBI	inulin	-	builds acid from	from API 50CH acid
68371	30849 ChEBI	L-arabinose	-	builds acid from	from API 50CH acid
68369	30849 ChEBI	L-arabinose	+	assimilation	from API 20NE
68371	18403 ChEBI	L-arabitol	-	builds acid from	from API 50CH acid
68371	18287 ChEBI	L-fucose	-	builds acid from	from API 50CH acid
68371	62345 ChEBI	L-rhamnose	-	builds acid from	from API 50CH acid
68371	17266 ChEBI	L-sorbose	-	builds acid from	from API 50CH acid
68371	65328 ChEBI	L-xylose	-	builds acid from	from API 50CH acid
68371	17716 ChEBI	lactose	-	builds acid from	from API 50CH acid
68369	25115 ChEBI	malate	+	assimilation	from API 20NE
68371	17306 ChEBI	maltose	-	builds acid from	from API 50CH acid
68369	17306 ChEBI	maltose	-	assimilation	from API 20NE
68371	6731 ChEBI	melezitose	-	builds acid from	from API 50CH acid
68371	28053 ChEBI	melibiose	-	builds acid from	from API 50CH acid
68371	320061 ChEBI	methyl alpha-D-glucopyranoside	-	builds acid from	from API 50CH acid
68371	43943 ChEBI	methyl alpha-D-mannoside	-	builds acid from	from API 50CH acid
68371	74863 ChEBI	methyl beta-D-xylopyranoside	-	builds acid from	from API 50CH acid
68371	17268 ChEBI	myo-inositol	-	builds acid from	from API 50CH acid
30000	506227 ChEBI	N-acetylglucosamine	+	carbon source
68371	59640 ChEBI	N-acetylglucosamine	-	builds acid from	from API 50CH acid
68369	59640 ChEBI	N-acetylglucosamine	+	assimilation	from API 20NE
118240	17632 ChEBI	nitrate	-	reduction
118240	17632 ChEBI	nitrate	-	respiration
68369	17632 ChEBI	nitrate	-	reduction	from API 20NE
118240	16301 ChEBI	nitrite	-	reduction
68371		Potassium 2-ketogluconate	-	builds acid from	from API 50CH acid
68371		Potassium 5-ketogluconate	-	builds acid from	from API 50CH acid
68371	16634 ChEBI	raffinose	-	builds acid from	from API 50CH acid
68371	15963 ChEBI	ribitol	-	builds acid from	from API 50CH acid
68371	17814 ChEBI	salicin	-	builds acid from	from API 50CH acid
68371	28017 ChEBI	starch	-	builds acid from	from API 50CH acid
68371	17992 ChEBI	sucrose	-	builds acid from	from API 50CH acid
68371	27082 ChEBI	trehalose	-	builds acid from	from API 50CH acid
68369	27897 ChEBI	tryptophan	-	energy source	from API 20NE
68371	32528 ChEBI	turanose	-	builds acid from	from API 50CH acid
30000	16199 ChEBI	urea	+	carbon source
68369	16199 ChEBI	urea	-	hydrolysis	from API 20NE
68371	17151 ChEBI	xylitol	-	builds acid from	from API 50CH acid

Antibiotic resistance

@ref	Metabolite	Is sensitive	Is resistant
118240	0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)

Metabolite production

@ref	Chebi-ID	Metabolite	Production
118240	35581 ChEBI	indole
68369	35581 ChEBI	indole		from API 20NE

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
118240	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
118240	amylase	-
68369	arginine dihydrolase	-	3.5.3.6	from API 20NE
68382	beta-galactosidase	-	3.2.1.23	from API zym
118240	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
118240	caseinase	-	3.4.21.50
30000	catalase	+	1.11.1.6
118240	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
30000	cytochrome oxidase	+	1.9.3.1
68369	cytochrome oxidase	+	1.9.3.1	from API 20NE
118240	DNase	-
68382	esterase (C 4)	+		from API zym
118240	gelatinase	-
68369	gelatinase	-		from API 20NE
118240	lecithinase	-
68382	leucine arylamidase	+	3.4.11.1	from API zym
118240	lipase	-
68382	lipase (C 14)	-		from API zym
118240	lysine decarboxylase	-	4.1.1.18
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
118240	ornithine decarboxylase	-	4.1.1.17
118240	oxidase	-
118240	protease	-
68382	trypsin	-	3.4.21.4	from API zym
118240	tryptophan deaminase	-
118240	tween esterase	+
30000	urease	+	3.5.1.5
118240	urease	-	3.5.1.5
68369	urease	-	3.5.1.5	from API 20NE

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
59716	-	+	+	-	-	+	-	-	-	-	+	-	-	-	-	-	-	-	-	-
118240	-	+	+	+	-	+	+	-	-	-	+	+	-	-	-	-	-	-	-	-

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
59716	-	-	-	-	-	-	-	-	+	+	-	+	+	-	+	+	-	+	+	+	+

API 50CHac

@ref	ControlQ	GLY	ERY	DARA	LARA	RIB	DXYL	LXYL	ADO	MDX	GAL	GLU	FRU	MNE	SBE	RHA	DUL	INO	MAN	SOR	MDM	MDG	NAG	AMY	ARB	ESC	SAL	CEL	MAL	LAC	MEL	SAC	TRE	INU	MLZ	RAF	AMD	GLYG	XLT	GEN	TUR	LYX	TAG	DFUC	LFUC	DARL	LARL	GNT	2KG	5KG
118240	not determinedn.d.	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Industrial	-
#Environmental	#Aquatic	-
#Environmental	#Terrestrial	#Sediment
#Environmental	#Terrestrial	#Soil

Isolation

@ref	Sample type	Sampling date	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude
7191	soil sediment collected at a stream near an industrial region		Cheongju	Republic of Korea	KOR	Asia
59716	Soil sediment		industrial region of Cheongju	Republic of Korea	KOR	Asia
67770	Industrial stream near Chungju industry complex			Republic of Korea	KOR	Asia
67771	From soil			Republic of Korea	KOR	Asia
67772	Soil sediment collected from a stream near an industrial region	1997	North Chungcheong Province, Cheongju	Republic of Korea	KOR	Asia	36.6333	127.483 36.6333/127.483
118240	Environment, Soil		Cheongju, Chungbuk	Republic of Korea	KOR	Asia

Taxonmaps

69479

Global distribution of 16S sequence AB681859 (>99% sequence identity) for Herbaspirillum from Microbeatlas

Aquatic Samples	163
Soil Samples	183
Animal Samples	75
Plant Samples	429
Total Samples	850

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
7191	1	Risk group (German classification) According to TRBA 466
67772	1
118240	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	ASM157116v1 assembly for Herbaspirillum chlorophenolicum NBRC 102525	contig	GCA_001571165	1349766.3	2731957620	1349766	53.57
67770	ASM118995v1 assembly for Herbaspirillum chlorophenolicum CPW301	contig	GCA_001189955		2645727693	211589	33.9

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20218	Herbaspirillum chlorophenolicum gene for 16S rRNA, partial sequence, strain: NBRC 102525	AB681859	1458		211589
7191	Herbaspirillum chlorophenolicum gene for 16S rRNA, partial sequence	AB094401	1474		211589

GC content

@ref	GC-content (mol%)	Method
7191	61.3	high performance liquid chromatography (HPLC)
30000	61.3
67771	60.0

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Herbaspirillum chlorophenolicum NBRC 102525
NCBI: GCA_001571165

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	99.50	no
125439	motility	BacteriaNetⓘ	yes	88.20	no
125439	gram_stain	BacteriaNetⓘ	negative	99.70	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	88.30	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Herbaspirillum chlorophenolicum NBRC 102525
PATRIC: 1349766.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	97.99	yes
125438	anaerobic	anaerobicⓘ	no	98.67	yes
125438	spore-forming	spore-formingⓘ	no	89.38	no
125438	aerobic	aerobicⓘ	yes	86.68	yes
125438	thermophilic	thermophileⓘ	no	97.56	yes
125438	flagellated	motile2+ⓘ	yes	76.20	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Development of innovative pediocin PA-1 by DNA shuffling among class IIa bacteriocins.	Tominaga T, Hatakeyama Y.	Appl Environ Microbiol	10.1128/aem.00558-07	2007
Phylogeny	Herbaspirillum piri sp. nov., isolated from bark of a pear tree.	Xu G, Chang J, Xue H, Guo M, Piao CG, Li Y	Int J Syst Evol Microbiol	10.1099/ijsem.0.003050	2018
Phylogeny	Herbaspirillum robiniae sp. nov., isolated from root nodules of Robinia pseudoacacia in a lead-zinc mine.	Fan MC, Guo YQ, Zhang LP, Zhu YM, Chen WM, Lin YB, Wei GH	Int J Syst Evol Microbiol	10.1099/ijsem.0.002666	2018
Phylogeny	Herbaspirillum chlorophenolicum sp. nov., a 4-chlorophenol-degrading bacterium.	Im WT, Bae HS, Yokota A, Lee ST	Int J Syst Evol Microbiol	10.1099/ijs.0.02812-0	2004

References

#7191	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 17796
#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 )
#26365	IJSEM 851 2004 ( DOI 10.1099/ijs.0.02812-0 , PubMed 15143035 )
#30000	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 #26365
#33241	; Curators of the CIP;
#59716	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 52898
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#67771	Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;
#67772	The University of Coimbra Bacteria Culture Collection (UCCCB) ; Curators of the UCCCB;
#68369	Automatically annotated from API 20NE .
#68371	Automatically annotated from API 50CH acid .
#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 .
#118240	Collection of Institut Pasteur ; Curators of the CIP; CIP 108432
#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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Herbaspirillum chlorophenolicum (DSM 17796, IAM 15024, JCM 21487)

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

Metabolite tests

Enzymes

API zym

API 20NE

API 50CHac

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_001571165

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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