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

Section

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

coccus-shaped
Gram-positive
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	*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 %100

[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 %90.955

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

[Ref.: #16163]	Temperature range	mesophilic
[Ref.: #29774]	Temperature range	mesophilic
[Ref.: #37592]	Temperature range	mesophilic
[Ref.: #61765]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

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	no
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.997

[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
[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
[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
[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	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	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	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	no	73	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Gordonia humi strain DSM 45298 PATRIC: 686429.3
[Ref.: #69480]	gram-positive	yes	90.541	yes
[Ref.: #69480]	anaerobic	no	99.557	no
[Ref.: #69480]	halophile	no	87.534	no
[Ref.: #69480]	spore-forming	no	82.255	yes
[Ref.: #69480]	glucose-util	yes	90.301	no
[Ref.: #69480]	thermophile	no	99.394	yes
[Ref.: #69480]	flagellated	no	98.742	no
[Ref.: #69480]	aerobic	yes	95.068	no
[Ref.: #69480]	glucose-ferment	no	84.942	no
[Ref.: #69480]	motile	no	95.827	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

Change proposal

You found an error in BacDive? Please tell us about it!

Note that changes will be reviewed and judged. If your changes are legitimate, changes will occur within the next BacDive update. Only proposed changes supported by the according reference will be reviewed. The BacDive team reserves the right to reject proposed changes.

Search for species Gordonia humi in external resources:
SILVA
BRENDA
PANGAEA
StrainInfo
GBIF

Gordonia humi strain DSM 45298

Gordonia humi strain DSM 45298

Change proposal

Change proposal