Name: Rhodococcus trifolii T8
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 23160

Type strain:

Species: Rhodococcus trifolii

Strain Designation: T8

Culture col. no.: DSM 45580, CCM 7905, LMG 26204, CCUG 60724

Strain history: <- P. Kämpfer, Universität Giessen; T8 <- S.A. Wellner

NCBI tax ID(s): 908250 (species)

SI-ID 375956

LMG 26204, CCM 7905, DSM 45580

Special Collections

Other strains from Rhodococcus trifolii

Section

When using BacDive for research please cite our paper

Rhodococcus trifolii T8 is an aerobe, mesophilic bacterium that builds an aerial mycelium and was isolated from leaf surface of Trifolium repens.

aerobe
mesophilic
16S sequence
Bacteria
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	09-12-2024 (DD-MM-YYYY)
	Domain	*Bacteria*
	Phylum	*Actinomycetota*
	Class	*Actinomycetes*
	Order	*Mycobacteriales*
	Family	*Nocardiaceae*
	Genus	*Rhodococcus*
	Species	**Rhodococcus trifolii**
	Full Scientific Name (LPSN)	Rhodococcus trifolii Kämpfer et al. 2013

Synonym

Rhodococcoides trifolii

Information on morphological and physiological properties Morphology

[Ref.: #125439]	Gram stain	positive Confidence in %94.6
[Ref.: #125438]	Gram stain	positive Confidence in %91.801

[Ref.: #69408]	Colony color	Bright red orange (2008)
[Ref.: #69408]	Cultivation medium used	ISP 5

[Ref.: #69408]	Colony color	Red orange (2001)
[Ref.: #69408]	Cultivation medium used	ISP 2

[Ref.: #69408]	Colony color	Red orange (2001), salmon orange (2012)
[Ref.: #69408]	Cultivation medium used	suter with tyrosine

[Ref.: #69408]	Colony color	Salmon orange (2012)
[Ref.: #69408]	Cultivation medium used	ISP 3

[Ref.: #69408]	Colony color	Salmon orange (2012)
[Ref.: #69408]	Cultivation medium used	ISP 4

[Ref.: #69408]	Colony color	Salmon orange (2012)
[Ref.: #69408]	Cultivation medium used	ISP 6

[Ref.: #69408]	Colony color	Salmon orange (2012), red orange (2001)
[Ref.: #69408]	Cultivation medium used	ISP 7

[Ref.: #69408]	Colony color	Yellow orange (2000)
[Ref.: #69408]	Cultivation medium used	suter without tyrosine

[Ref.: #62414]	Incubation period	2 days

[Ref.: #69408]	Pigment production	no
[Ref.: #69408]	Pigment name	Melanin
[Ref.: #69408]	Pigment production	no
[Ref.: #69408]	Pigment name	soluble pigment

[Ref.: #69408]	Multicellular complex forming ability	no
[Ref.: #69408]	Multicellular complex name	Aerial mycelium
[Ref.: #69408]	Medium Name (multicellularity)	ISP 2

[Ref.: #69408]	Multicellular complex forming ability	no
[Ref.: #69408]	Multicellular complex name	Aerial mycelium
[Ref.: #69408]	Medium Name (multicellularity)	ISP 3

[Ref.: #69408]	Multicellular complex forming ability	no
[Ref.: #69408]	Multicellular complex name	Aerial mycelium
[Ref.: #69408]	Medium Name (multicellularity)	ISP 4

[Ref.: #69408]	Multicellular complex forming ability	no
[Ref.: #69408]	Multicellular complex name	Aerial mycelium
[Ref.: #69408]	Medium Name (multicellularity)	ISP 5

[Ref.: #69408]	Multicellular complex forming ability	no
[Ref.: #69408]	Multicellular complex name	Aerial mycelium
[Ref.: #69408]	Medium Name (multicellularity)	ISP 6

[Ref.: #69408]	Multicellular complex forming ability	yes
[Ref.: #69408]	Multicellular complex name	Aerial mycelium
[Ref.: #69408]	Medium Name (multicellularity)	ISP 7

[Ref.: #69408]	Multicellular complex forming ability	no
[Ref.: #69408]	Multicellular complex name	Aerial mycelium
[Ref.: #69408]	Medium Name (multicellularity)	suter with tyrosine

[Ref.: #69408]	Multicellular complex forming ability	no
[Ref.: #69408]	Multicellular complex name	Aerial mycelium
[Ref.: #69408]	Medium Name (multicellularity)	suter without tyrosine

Multimedia content

[Ref.: #69408]

Caption:

Plates (65, ISP2, ISP3, ISP4, ISP5, ISP7)

[Ref.: #69408]

Intellectual property rights:

Helmholtz-Zentrum für Infektionsforschung GmbH

[Ref.: #69408]

Caption:

Plates (65, ISP2, ISP3, ISP4, ISP5, ISP7)

[Ref.: #69408]

Intellectual property rights:

Helmholtz-Zentrum für Infektionsforschung GmbH

Information on culture and growth conditions Culture and growth conditions

[Ref.: #19256]

Culture medium

TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)

[Ref.: #19256]

Culture medium growth

[Ref.: #19256]

Culture medium link

Medium recipe at MediaDive

[Ref.: #19256]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #19256]			growth	28 °C
[Ref.: #62414]			growth	30 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #62414]	Oxygen tolerance	aerobe
[Ref.: #125438]	Oxygen tolerance	aerobe Confidence in %90.322
[Ref.: #125439]	Oxygen tolerance	obligate aerobe Confidence in %98.6

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #69408]		NaCl		growth	0-5	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #69408]	arabinose ChEBI	+/-	growth
[Ref.: #69408]	cellulose ChEBI	-	growth
[Ref.: #68379]	D-glucose ChEBI	-	fermentation	* from API Coryne
[Ref.: #68379]	D-mannitol ChEBI	-	fermentation	* from API Coryne
[Ref.: #68379]	D-ribose ChEBI	-	fermentation	* from API Coryne
[Ref.: #68379]	D-xylose ChEBI	-	fermentation	* from API Coryne
[Ref.: #69408]	fructose ChEBI	+	growth
[Ref.: #68379]	gelatin ChEBI	-	hydrolysis	* from API Coryne
[Ref.: #69408]	glucose ChEBI	+	growth
[Ref.: #68379]	glycogen ChEBI	-	fermentation	* from API Coryne
[Ref.: #69408]	inositol ChEBI	+	growth
[Ref.: #68379]	lactose ChEBI	-	fermentation	* from API Coryne
[Ref.: #68379]	maltose ChEBI	-	fermentation	* from API Coryne
[Ref.: #69408]	mannose ChEBI	+	growth
[Ref.: #68379]	nitrate ChEBI	-	reduction	* from API Coryne
[Ref.: #69408]	raffinose ChEBI	-	growth
[Ref.: #69408]	rhamnose ChEBI	+	growth
[Ref.: #69408]	sucrose ChEBI	+/-	growth
[Ref.: #68379]	sucrose ChEBI	-	fermentation	* from API Coryne
[Ref.: #68379]	urea ChEBI	+	hydrolysis	* from API Coryne
[Ref.: #69408]	xylose ChEBI	-	growth
	Only first 10 entries are displayed. Click here to see all.

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #68379]	alkaline phosphatase	+	3.1.3.1	* from API Coryne, 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.: #68379]	alpha-glucosidase	-	3.2.1.20	* from API Coryne
[Ref.: #68382]	alpha-mannosidase	-	3.2.1.24	* from API zym
[Ref.: #68382]	beta-galactosidase	-	3.2.1.23	* from API zym, API Coryne
[Ref.: #68382]	beta-glucosidase	+	3.2.1.21	* from API zym
[Ref.: #68382]	beta-glucuronidase	-	3.2.1.31	* from API zym, API Coryne
[Ref.: #68382]	cystine arylamidase	+	3.4.11.3	* from API zym
[Ref.: #68382]	esterase lipase (C 8)	+		* from API zym
[Ref.: #68379]	gelatinase	-		* from API Coryne
[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, API Coryne
[Ref.: #68379]	pyrazinamidase	-	3.5.1.B15	* from API Coryne
[Ref.: #68379]	pyrrolidonyl arylamidase	-	3.4.19.3	* from API Coryne
[Ref.: #68379]	urease	+	3.5.1.5	* from API Coryne
[Ref.: #68382]	valine arylamidase	+		* from API zym
	Only first 10 entries are displayed. Click here to see all.

API® Coryne:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Reduction of nitrateNIT	PyrazinamidasePYZ	Pyrrolidonyl arylamidasePYRA	Alkaline phosphatasePAL	beta-Glucuronidasebeta GUR	beta-Galactosidasebeta GAL	alpha-Glucosidasealpha GLU	N-Acetyl-beta-Glucosidasebeta NAG	Esculin hydrolysis/beta-GlucosidaseESC	Urease/urea hydrolysisURE	Gelatinase/gelatin hydrolysisGEL	Control fermentationControl	Fermentation of D-glucoseGLU	Fermentation of D-riboseRIB	Fermentation of D-xyloseXYL	Fermentation of D-mannitolMAN	Fermentation of maltoseMAL	Fermentation of lactoseLAC	Fermentation of sucroseSAC	Fermentation of glycogenGLYG	CatalaseCAT
[Ref.: #69408]	3901	-	-	-	+	-	-	-	-	+/-	+	-	not determinedn.d.	-	-	-	-	-	-	-	-	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.: #69408]	6085	not determinedn.d.	+	+/-	+	+	+	+	+	+/-	+/-	+	+/-	-	-	-	+	+	-	-	-

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

[Ref.: #19256]	Sample type/isolated from	leaf surface of Trifolium repens
[Ref.: #19256]	Host species	Trifolium repens
[Ref.: #19256]	Geographic location (country and/or sea, region)	Thuringia, Hainich-Dün region
[Ref.: #19256]	Country	Germany
[Ref.: #19256]	Country ISO 3 Code	DEU
[Ref.: #19256]	Continent	Europe

[Ref.: #62414]	Sample type/isolated from	Leaf surface,Trifolium repens
[Ref.: #62414]	Sampling date	2008
[Ref.: #62414]	Geographic location (country and/or sea, region)	Thüringen,Hainich-Dün
[Ref.: #62414]	Country	Germany
[Ref.: #62414]	Country ISO 3 Code	DEU
[Ref.: #62414]	Continent	Europe
* marker position based on {}

Isolation sources categories

#Host	#Plants	#Herbaceous plants (Grass,Crops)
#Host Body-Site	#Plant	#Leaf (Phyllosphere)

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence FR714843 (>99% sequence identity) for Rhodococcus from Microbeatlas

Aquatic Samples	1647
Soil Samples	1910
Animal Samples	3413
Plant Samples	2369
Total Samples	9339

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

[Ref.: #19256]

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.: #19256]	Rhodococcus trifolii partial 16S rRNA gene, type strain T8T	FR714843	1364	GenBank ENA	908250 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Rhodococcus trifolii CCM 7905	GCA_014635345	contig	GenBank ENA	908250 tax ID	*
[Ref.: #66792]	Rhodococcus trifolii strain CCM 7905	908250.3	wgs	PATRIC	908250 tax ID	*

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

	Model	Trait	Prediction	Confidence in %	In training data
	Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Rhodococcus trifolii strain CCM 7905 PATRIC: 908250.3
[Ref.: #125438]	gram-positive	gram-positiveⓘ	yes	91.801	no
[Ref.: #125438]	anaerobic	anaerobicⓘ	no	96.573	yes
[Ref.: #125438]	aerobic	aerobicⓘ	yes	90.322	no
[Ref.: #125438]	spore-forming	spore-formingⓘ	no	53.661	no
[Ref.: #125438]	thermophile	thermophilicⓘ	no	95.067	yes
[Ref.: #125438]	motile2+	flagellatedⓘ	no	86.871	no

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Rhodococcus trifolii CCM 7905 NCBI: GCA_014635345
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	no	57.5
[Ref.: #125439]	BacteriaNet	motilityⓘ	no	75.8
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	positive	94.6
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	obligate aerobe	98.6

Availability in culture collections External links

[Ref.: #19256]

Culture collection no.

DSM 45580, CCM 7905, LMG 26204, CCUG 60724

[Ref.: #87394]

SI-ID 375956

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Rhodococcus cerastii sp. nov. and Rhodococcus trifolii sp. nov., two novel species isolated from leaf surfaces.	Kampfer P, Wellner S, Lohse K, Lodders N, Martin K	Int J Syst Evol Microbiol	10.1099/ijs.0.044958-0	2012	*

References

#19256

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 45580

#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 )

#62414 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 60724

#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) .

#68379

Automatically annotated from API Coryne .

#68382

Automatically annotated from API zym .

#69408

Wink, J.: Compendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig .

#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 .

#87394

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-ID375956.1 )

#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 .

* These data were automatically processed and therefore are not curated

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Rhodococcus trifolii strain CCM 7905

Rhodococcus trifolii CCM 7905

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