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

Strain history: CCM 7727 <-- P. Kämpfer CC-12301.

NCBI tax ID(s): 686429 (species)

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	07-12-2022 (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.: #29774]	Cell length	1.25 µm
[Ref.: #29774]	Cell width	1.25 µm
[Ref.: #29774]	Cell shape	coccus-shaped

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

[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

		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.: #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.: #29774]	proline ChEBI	+	carbon source
[Ref.: #29774]	sucrose ChEBI	+	carbon source

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #29774]		catalase	+	1.11.1.6
[Ref.: #29774]		cytochrome oxidase	+	1.9.3.1

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
* 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

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.: #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 Diaspora project based on: Gordonia humi strain DSM 45298 PATRIC: 686429.3
[Ref.: #69480]	gram-positive	yes	100	yes
[Ref.: #69480]	anaerobic	no	99.065	yes
[Ref.: #69480]	spore-forming	no	99.997	yes
[Ref.: #69480]	thermophile	no	99.574	yes
[Ref.: #69480]	motile	no	90.955	no

	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

Availability in culture collections External links

[Ref.: #16163]

Culture collection no.

DSM 45298, CCM 7727, CCUG 58853, JCM 17969

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 )

#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 )

#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;

#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 )

#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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