Name: Gordonia phthalatica QH-11
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 141149

Type strain:

Species: Gordonia phthalatica

Strain Designation: QH-11

Culture col. no.: CICC 24107, KCTC 39933, DSM 108671

Strain history: <- Decai Jin, Chinese Academy of Sciences

NCBI tax ID(s): 1136941 (species)

SI-ID 404484

DSM 108671

Section

Gordonia phthalatica QH-11 is an aerobe, Gram-positive, rod-shaped bacterium that forms irregular colonies and was isolated from activated sludge wastewater treatment plant.

colony-forming
Gram-positive
rod-shaped
aerobe
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	*Actinomycetota*
	Class	*Actinomycetes*
	Order	*Mycobacteriales*
	Family	*Gordoniaceae*
	Genus	*Gordonia*
	Species	**Gordonia phthalatica**
	Full Scientific Name (LPSN)	Gordonia phthalatica Jin et al. 2017

Information on morphological and physiological properties Morphology

[Ref.: #44070]	Gram stain	positive
[Ref.: #69480]	Gram stain	positive Confidence in %100

[Ref.: #44070]	Cell length	0.8-1.6 µm

[Ref.: #44070]	Cell width	0.3-0.5 µm

[Ref.: #44070]	Cell shape	rod-shaped

[Ref.: #44070]	Motility	no
[Ref.: #69480]	Motility	no Confidence in %97.474

[Ref.: #44070]	Colony color	creamy-white
[Ref.: #44070]	Colony shape	irregular
[Ref.: #44070]	Cultivation medium used	Nutrient agar

Information on culture and growth conditions Culture and growth conditions

[Ref.: #44070]

Culture medium

Nutrient agar (NA)

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Culture medium growth

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Culture medium

nurtient broth

[Ref.: #44070]

Culture medium growth

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Culture medium

NUTRIENT AGAR (DSMZ Medium 1)

[Ref.: #64975]

Culture medium growth

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Culture medium link

Medium recipe at MediaDive

[Ref.: #64975]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #44070]	growth	15-40 °C
[Ref.: #44070]	optimum	30 °C
[Ref.: #64975]	growth	30 °C
[Ref.: #67771]	growth	30 °C

[Ref.: #44070]	Temperature range	mesophilic
[Ref.: #64975]	Temperature range	mesophilic
[Ref.: #67771]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #44070]			optimum	7
[Ref.: #44070]			growth	5.0-10.0

Information on physiology and metabolism Physiology and metabolism

[Ref.: #44070]	Oxygen tolerance	aerobe
[Ref.: #67771]	Oxygen tolerance	aerobe

[Ref.: #44070]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %93
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.987

[Ref.: #44070]

Halophily / tolerance level

non-halophilic

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #44070]		NaCl		growth	0.8	%
[Ref.: #44070]		NaCl		optimum	0	%

[Ref.: #44070]

Observation

degradation of dibutyl phthalate

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #44070]	2-oxogluconate	-	fermentation
[Ref.: #44070]	5-dehydro-D-gluconate ChEBI	-	fermentation
[Ref.: #68369]	adipate ChEBI	+	assimilation	* from API 20NE
[Ref.: #44070]	amygdalin ChEBI	-	fermentation
[Ref.: #44070]	arbutin ChEBI	-	fermentation
[Ref.: #68369]	arginine ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #44070]	cellobiose ChEBI	-	fermentation
[Ref.: #44070]	D-arabinose ChEBI	-	fermentation
[Ref.: #44070]	D-arabitol ChEBI	-	fermentation
[Ref.: #44070]	D-fructose ChEBI	+	fermentation
[Ref.: #44070]	D-fucose ChEBI	-	fermentation
[Ref.: #44070]	D-galactose ChEBI	-	fermentation
[Ref.: #44070]	D-glucose ChEBI	+	fermentation
[Ref.: #68369]	D-glucose ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	D-glucose ChEBI	-	fermentation	* from API 20NE
[Ref.: #44070]	D-lyxose ChEBI	-	fermentation
[Ref.: #68369]	D-mannitol ChEBI	-	assimilation	* from API 20NE
[Ref.: #44070]	D-mannose ChEBI	-	fermentation
[Ref.: #68369]	D-mannose ChEBI	-	assimilation	* from API 20NE
[Ref.: #44070]	D-ribose ChEBI	-	fermentation
[Ref.: #44070]	D-tagatose ChEBI	-	fermentation
[Ref.: #44070]	D-xylose ChEBI	-	fermentation
[Ref.: #68369]	decanoate ChEBI	-	assimilation	* from API 20NE
[Ref.: #44070]	erythritol ChEBI	-	fermentation
[Ref.: #44070]	esculin ChEBI	+	fermentation
[Ref.: #68369]	esculin ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #44070]	galactitol ChEBI	-	fermentation
[Ref.: #44070]	gelatin ChEBI	-	hydrolysis
[Ref.: #68369]	gelatin ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #44070]	gentiobiose ChEBI	-	fermentation
[Ref.: #44070]	glycerol ChEBI	+	fermentation
[Ref.: #44070]	glycogen ChEBI	-	fermentation
[Ref.: #44070]	inulin ChEBI	-	fermentation
[Ref.: #44070]	L-arabinose ChEBI	-	fermentation
[Ref.: #68369]	L-arabinose ChEBI	-	assimilation	* from API 20NE
[Ref.: #44070]	L-arabitol ChEBI	-	fermentation
[Ref.: #44070]	L-fucose ChEBI	-	fermentation
[Ref.: #44070]	L-sorbose ChEBI	-	fermentation
[Ref.: #44070]	L-xylose ChEBI	-	fermentation
[Ref.: #44070]	lactose ChEBI	-	fermentation
[Ref.: #44070]	maltose ChEBI	-	fermentation
[Ref.: #68369]	maltose ChEBI	-	assimilation	* from API 20NE
[Ref.: #44070]	mannitol ChEBI	-	fermentation
[Ref.: #44070]	melezitose ChEBI	-	fermentation
[Ref.: #44070]	melibiose ChEBI	-	fermentation
[Ref.: #44070]	methyl alpha-D-glucopyranoside ChEBI	-	fermentation
[Ref.: #44070]	methyl alpha-D-mannoside ChEBI	-	fermentation
[Ref.: #44070]	methyl beta-D-xylopyranoside ChEBI	-	fermentation
[Ref.: #44070]	myo-inositol ChEBI	-	fermentation
[Ref.: #44070]	N-acetylglucosamine ChEBI	-	fermentation
[Ref.: #68369]	N-acetylglucosamine ChEBI	+	assimilation	* from API 20NE
[Ref.: #44070]	nitrate ChEBI	-	reduction
[Ref.: #68369]	nitrate ChEBI	-	reduction	* from API 20NE
[Ref.: #44070]	potassium gluconate ChEBI	-	fermentation
[Ref.: #44070]	raffinose ChEBI	-	fermentation
[Ref.: #44070]	rhamnose ChEBI	-	fermentation
[Ref.: #44070]	ribitol ChEBI	-	fermentation
[Ref.: #44070]	salicin ChEBI	-	fermentation
[Ref.: #44070]	sorbitol ChEBI	-	fermentation
[Ref.: #44070]	starch ChEBI	-	fermentation
[Ref.: #44070]	starch ChEBI	-	hydrolysis
[Ref.: #44070]	sucrose ChEBI	+	fermentation
[Ref.: #44070]	trehalose ChEBI	-	fermentation
[Ref.: #68369]	tryptophan ChEBI	-	energy source	* from API 20NE
[Ref.: #44070]	turanose ChEBI	-	fermentation
[Ref.: #68369]	urea ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #44070]	xylitol ChEBI	-	fermentation
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[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.: #44070]	acid phosphatase	+	3.1.3.2
[Ref.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #44070]	alkaline phosphatase	+	3.1.3.1
[Ref.: #68382]	alkaline phosphatase	-	3.1.3.1	* from API zym
[Ref.: #44070]	alpha-chymotrypsin	-	3.4.21.1
[Ref.: #68382]	alpha-chymotrypsin	-	3.4.21.1	* from API zym
[Ref.: #68382]	alpha-fucosidase	-	3.2.1.51	* from API zym
[Ref.: #44070]	alpha-galactosidase	-	3.2.1.22
[Ref.: #68382]	alpha-galactosidase	-	3.2.1.22	* from API zym
[Ref.: #44070]	alpha-glucosidase	+	3.2.1.20
[Ref.: #68382]	alpha-glucosidase	+	3.2.1.20	* from API zym
[Ref.: #44070]	alpha-mannosidase	-	3.2.1.24
[Ref.: #68382]	alpha-mannosidase	-	3.2.1.24	* from API zym
[Ref.: #68369]	arginine dihydrolase	-	3.5.3.6	* from API 20NE
[Ref.: #44070]	beta-D-fucosidase	-	3.2.1.38
[Ref.: #44070]	beta-galactosidase	-	3.2.1.23
[Ref.: #68382]	beta-galactosidase	-	3.2.1.23	* from API zym
[Ref.: #44070]	beta-glucosidase	+	3.2.1.21
[Ref.: #68369]	beta-glucosidase	-	3.2.1.21	* from API 20NE, API zym
[Ref.: #44070]	beta-glucuronidase	-	3.2.1.31
[Ref.: #68382]	beta-glucuronidase	-	3.2.1.31	* from API zym
[Ref.: #44070]	catalase	+	1.11.1.6
[Ref.: #44070]	cystine arylamidase	+	3.4.11.3
[Ref.: #44070]	cytochrome oxidase	-	1.9.3.1
[Ref.: #44070]	esterase (C 4)	+
[Ref.: #44070]	esterase Lipase (C 8)	+
[Ref.: #68369]	gelatinase	-		* from API 20NE
[Ref.: #44070]	leucine arylamidase	+	3.4.11.1
[Ref.: #44070]	lipase (C 14)	+
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #44070]	N-acetyl-beta-glucosaminidase	-	3.2.1.52
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API zym
[Ref.: #44070]	naphthol-AS-BI-phosphohydrolase	+
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #44070]	pyrazinamidase	-	3.5.1.B15
[Ref.: #44070]	pyrrolidonyl arylamidase	+	3.4.19.3
[Ref.: #44070]	trypsin	+	3.4.21.4
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #44070]	urease	-	3.5.1.5
[Ref.: #68369]	urease	-	3.5.1.5	* from API 20NE
[Ref.: #44070]	valine arylamidase	-
[Ref.: #68382]	valine arylamidase	-		* from API zym
	Only first 10 entries are displayed. Click here to see all.

Fatty acid profile

Metadata FA analysis

Reference

[Ref.: #44070]

Fatty acid	Percentage
C16:0	33.3
C17:1ω8c	23.4
C18:1ω9c	17.9
C16:1ω7c / C16:1ω6c	4.7
C17:0	4.5
C14:0	3.5
10-methyl C17:0	3.3
10-methyl C17:0	2.3
C15:1ω8c	1.1
C18:0	1

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.: #64975]	24793	-	-	-	-	-	-	-	-	+	-	-	-	+	-	+/-	-	+	+/-	+	+/-	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.: #64975]	14126	-	-	+/-	+/-	-	+/-	-	+/-	-	-	+	+	-	-	-	+	-	-	-	-

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

[Ref.: #44070]	Sample type/isolated from	activated sludge wastewater treatment plant
[Ref.: #44070]	Geographic location (country and/or sea, region)	Beijing
[Ref.: #44070]	Country	China
[Ref.: #44070]	Country ISO 3 Code	CHN
[Ref.: #44070]	Continent	Asia

[Ref.: #64975]	Sample type/isolated from	activated sludge of a municipal wastewater treatment plant
[Ref.: #64975]	Geographic location (country and/or sea, region)	Beijing
[Ref.: #64975]	Country	China
[Ref.: #64975]	Country ISO 3 Code	CHN
[Ref.: #64975]	Continent	Asia

[Ref.: #67771]	Sample type/isolated from	From activated sludge, wastewater treatment plant in Beijing
[Ref.: #67771]	Country	China
[Ref.: #67771]	Country ISO 3 Code	CHN
[Ref.: #67771]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Engineered	#Waste	#Activated sludge
#Engineered	#Waste	#Water treatment plant

What are isolation sources categories?

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

[Ref.: #64975]

Biosafety level

Risk group (German classification)
According to TRBA 466

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.: #64975]	Gordonia phthalatica strain QH-11, complete genome	CP011853	4428727	ENA	1136941 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Gordonia phthalatica QH-11	GCA_001305675	complete	GenBank	1136941 tax ID	*
[Ref.: #66792]	Gordonia phthalatica QH-11	2648501237	complete	JGI IMG/M	1136941 tax ID	*

[Ref.: #44070]

GC-content

68 mol%

genome sequence analysis

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: Gordonia phthalatica QH-11 NCBI: GCA_001305675.1
[Ref.: #69481]	spore-forming	no	93	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Gordonia phthalatica QH-11 NCBI: GCA_001305675.1
[Ref.: #69480]	motile	no	96.119	yes
[Ref.: #69480]	flagellated	no	98.754	no
[Ref.: #69480]	gram-positive	yes	91.351	no
[Ref.: #69480]	anaerobic	no	99.477	yes
[Ref.: #69480]	aerobic	yes	90.137	yes
[Ref.: #69480]	halophile	no	91.722	yes
[Ref.: #69480]	spore-forming	no	84.99	yes
[Ref.: #69480]	glucose-util	yes	89.771	no
[Ref.: #69480]	glucose-ferment	no	86.51	no
[Ref.: #69480]	thermophile	no	99.405	yes

Availability in culture collections External links

[Ref.: #64975]

Culture collection no.

CICC 24107, KCTC 39933, DSM 108671

[Ref.: #96869]

SI-ID 404484

Literature:

Topic	Title	Authors	Journal	DOI	Year
Metabolism	Bioremediation of dibutyl phthalate in a simulated agricultural ecosystem by Gordonia sp. strain QH-11 and the microbial ecological effects in soil.	Kong X, Jin D, Tai X, Yu H, Duan G, Yan X, Pan J, Song J, Deng Y	Sci Total Environ	10.1016/j.scitotenv.2019.02.385	2019	*
Phylogeny	Gordonia phthalatica sp. nov., a di-n-butyl phthalate-degrading bacterium isolated from activated sludge.	Jin D, Kong X, Jia M, Yu X, Wang X, Zhuang X, Deng Y, Bai Z	Int J Syst Evol Microbiol	10.1099/ijsem.0.002430	2017	*

References

#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 )

#44070

Decai Jin, Xiao Kong, Minghong Jia, Xiangyang Yu, Xinxin Wang, Xuliang Zhuang, Ye Deng and Zhihui Bai: Gordonia phthalatica sp. nov., a di-n-butyl phthalate-degrading bacterium isolated from activated sludge. IJSEM 67: 5128 - 5133 2017 ( DOI 10.1099/ijsem.0.002430 , PubMed 29068282 )

#64975

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 108671

#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) .

#67771 Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;

#68369

Automatically annotated from API 20NE .

#68382

Automatically annotated from API zym .

#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 )

#96869

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-ID404484.1 )

* These data were automatically processed and therefore are not curated

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