Name: Gordonia humi CC-12301
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 10622

Type strain:

Species: Gordonia humi

Strain Designation: CC-12301

Culture col. no.: DSM 45298, CCM 7727, CCUG 58853, JCM 17969, CIP 110237

Strain history: CIP <- 2011, P. Kämpfer, Inst. Angewandte Mikrobiol., Giessen Univ., Germany: strain CC-12301

NCBI tax ID(s): 686429 (species)

SI-ID 376096

CCM 7727, DSM 45298, JCM 17969, CIP 110237, CCUG 58853

Special Collections

Section

Gordonia humi CC-12301 is an aerobe, Gram-positive, coccus-shaped bacterium that was isolated from soil attached to a spawn used for growing Agaricus brasiliensis.

coccus-shaped
Gram-positive
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 humi**
	Full Scientific Name (LPSN)	Gordonia humi Kämpfer et al. 2011

Information on morphological and physiological properties Morphology

[Ref.: #29774]	Gram stain	positive
[Ref.: #119983]	Gram stain	positive
[Ref.: #69480]	Gram stain	positive Confidence in %91.413

[Ref.: #29774]	Cell length	1.25 µm

[Ref.: #29774]	Cell width	1.25 µm

[Ref.: #29774]	Cell shape	coccus-shaped
[Ref.: #119983]	Cell shape	rod-shaped

[Ref.: #119983]	Motility	no
[Ref.: #69480]	Motility	no Confidence in %95

Information on culture and growth conditions Culture and growth conditions

[Ref.: #16163]

Culture medium

TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)

[Ref.: #16163]

Culture medium growth

[Ref.: #16163]

Culture medium link

Medium recipe at MediaDive

[Ref.: #16163]

Culture medium composition

expand / minimize

[Ref.: #37592]

Culture medium

MEDIUM 72- for trypto casein soja agar

[Ref.: #37592]

Culture medium growth

[Ref.: #37592]

Culture medium composition

expand / minimize

[Ref.: #119983]

Culture medium

CIP Medium 72

[Ref.: #119983]

Culture medium growth

[Ref.: #119983]

Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #16163]	growth	28 °C
[Ref.: #29774]	optimum	27.5 °C
[Ref.: #37592]	growth	30 °C
[Ref.: #61765]	growth	37 °C
[Ref.: #67770]	growth	28 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #29774]	Oxygen tolerance	aerobe
[Ref.: #61765]	Oxygen tolerance	microaerophile
[Ref.: #119983]	Oxygen tolerance	obligate aerobe

[Ref.: #29774]

Ability of spore formation

[Ref.: #67770]

Observation

quinones: MK-9(H₂)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #29774]	3-hydroxybenzoate ChEBI	+	carbon source
[Ref.: #29774]	citrate ChEBI	+	carbon source
[Ref.: #29774]	N-acetylglucosamine ChEBI	+	carbon source
[Ref.: #119983]	nitrate ChEBI	+	reduction
[Ref.: #119983]	nitrite ChEBI	-	reduction
[Ref.: #29774]	proline ChEBI	+	carbon source
[Ref.: #29774]	sucrose ChEBI	+	carbon source

	Metabolite production	Metabolite	Production
[Ref.: #119983]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[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.: #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.: #29774]	catalase	+	1.11.1.6
[Ref.: #119983]	catalase	+	1.11.1.6
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #29774]	cytochrome oxidase	+	1.9.3.1
[Ref.: #68382]	esterase (C 4)	+		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	+		* from API zym
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #119983]	oxidase	+
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #119983]	urease	+	3.5.1.5
[Ref.: #68382]	valine arylamidase	-		* from API zym
	Only first 10 entries are displayed. Click here to see all.

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.: #119983]	12455	-	-	+	+	-	+	-	-	-	-	+	+	-	-	-	+	-	-	-	-

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

[Ref.: #16163]	Sample type/isolated from	soil attached to a spawn used for growing Agaricus brasiliensis
[Ref.: #16163]	Host species	Agaricus brasiliensis
[Ref.: #16163]	Country	Taiwan, Province of China
[Ref.: #16163]	Country ISO 3 Code	TWN
[Ref.: #16163]	Continent	Asia

[Ref.: #61765]	Sample type/isolated from	Soil
[Ref.: #61765]	Sampling date	2008
[Ref.: #61765]	Country	Taiwan, Province of China
[Ref.: #61765]	Country ISO 3 Code	TWN
[Ref.: #61765]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Soil attached to a spawn used for growing the edible mushroom Agaricus brasiliensis
[Ref.: #67770]	Host species	Agaricus brasiliensis

[Ref.: #119983]	Sample type/isolated from	Environment, Soil, hot spring of Green Island Lutao
[Ref.: #119983]	Country	Taiwan, Province of China
[Ref.: #119983]	Country ISO 3 Code	TWN
[Ref.: #119983]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Terrestrial	#Soil
#Host	#Fungi	-

What are isolation sources categories?

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

[Ref.: #16163]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #119983]	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.: #16163]	Gordonia humi partial 16S rRNA gene, type strain CC-12301T	FN561544	1438	GenBank ENA	686429 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Gordonia humi DSM 45298	GCA_014197435	contig	GenBank ENA	686429 tax ID	*
[Ref.: #66792]	Gordonia humi strain DSM 45298	686429.3	wgs	PATRIC	686429 tax ID	*
[Ref.: #66792]	Gordonia humi DSM 45298	2834003814	draft	JGI IMG/M	686429 tax ID	*

[Ref.: #29774]

GC-content

67 mol%

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

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Gordonia humi strain DSM 45298 PATRIC: 686429.3
[Ref.: #69481]	spore-forming	spore-formingⓘ	no	73	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Gordonia humi strain DSM 45298 PATRIC: 686429.3
[Ref.: #69480]	gram-positive	gram-positiveⓘ	yes	91.413	no
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	96.787	yes
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	57.105	yes
[Ref.: #69480]	aerobic	aerobicⓘ	yes	89.508	no
[Ref.: #69480]	thermophilic	thermophileⓘ	no	96.994	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	no	95	no

Availability in culture collections External links

[Ref.: #16163]

Culture collection no.

DSM 45298, CCM 7727, CCUG 58853, JCM 17969, CIP 110237

[Ref.: #79894]

SI-ID 376096

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Gordonia crocea sp. nov. and Gordonia spumicola sp. nov. isolated from sludge of a wastewater treatment plant.	Tamura T, Saito S, Hamada M, Kang Y, Hoshino Y, Gonoi T, Mikami Y, Yaguchi T	Int J Syst Evol Microbiol	10.1099/ijsem.0.004225	2020	*
Phylogeny	Gordonia humi sp. nov., isolated from soil.	Kampfer P, Young CC, Chu JN, Frischmann A, Busse HJ, Arun AB, Shen FT, Rekha PD	Int J Syst Evol Microbiol	10.1099/ijs.0.020545-0	2010	*

References

#16163

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 45298

#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 )

#29774

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 #26154 (see below)

#37592 ; Curators of the CIP;
#61765 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 58853

#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;

#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 )

#79894

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-ID376096.1 )

#119983 Collection of Institut Pasteur ; Curators of the CIP; CIP 110237

#26154

IJSEM 65 2013 ( DOI 10.1099/ijs.0.020545-0 , PubMed 20154330 )

* These data were automatically processed and therefore are not curated

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Gordonia humi strain DSM 45298

Gordonia humi strain DSM 45298

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