Name: Nocardioides exalbidus RC825
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 11129

Type strain:

Species: Nocardioides exalbidus

Strain Designation: RC825

Culture col. no.: DSM 22017, CCTCC AA 206016, IAM 15416, JCM 23199

Strain history: IAM 15416 <-- B. Li et al. RC825.

NCBI tax ID(s): 402596 (species)

SI-ID 319384

IAM 15416, JCM 23199

Special Collections

DSMZ
JCM

Section

When using BacDive for research please cite our paper

Nocardioides exalbidus RC825 is an aerobe, mesophilic bacterium that was isolated from Lichen.

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	*Propionibacteriales*
	Family	*Nocardioidaceae*
	Genus	*Nocardioides*
	Species	**Nocardioides exalbidus**
	Full Scientific Name (LPSN)	Nocardioides exalbidus Li et al. 2007

Information on morphological and physiological properties Morphology

[Ref.: #125439]	Gram stain	positive Confidence in %99.1

Information on culture and growth conditions Culture and growth conditions

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Culture medium

TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)

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Culture medium growth

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Culture medium link

Medium recipe at MediaDive

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Culture medium composition

expand / minimize

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Culture medium

GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)

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Culture medium growth

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Culture medium link

Medium recipe at MediaDive

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Culture medium composition

expand / minimize

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Culture medium

R2A MEDIUM (DSMZ Medium 830)

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Culture medium growth

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Culture medium link

Medium recipe at MediaDive

[Ref.: #16105]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #16105]			growth	28 °C
[Ref.: #67770]			growth	28 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #125438]	Oxygen tolerance	aerobe Confidence in %90.432
[Ref.: #125439]	Oxygen tolerance	obligate aerobe Confidence in %97

[Ref.: #67770]

Observation

quinones: MK-8(H₄)

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	cellulose degradation	100	5 of 5
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	vitamin K metabolism	100	5 of 5
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	acetate fermentation	100	4 of 4
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	phenylacetate degradation (aerobic)	100	5 of 5
[Ref.: #66794]	octane oxidation	100	3 of 3
[Ref.: #66794]	cardiolipin biosynthesis	100	7 of 7
[Ref.: #66794]	kanosamine biosynthesis II	100	2 of 2
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	teichoic acid biosynthesis	100	1 of 1
[Ref.: #66794]	starch degradation	100	10 of 10
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	aerobactin biosynthesis	100	1 of 1
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	ceramide biosynthesis	100	1 of 1
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	molybdenum cofactor biosynthesis	100	9 of 9
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	phenylalanine metabolism	92.31	12 of 13
[Ref.: #66794]	Entner Doudoroff pathway	90	9 of 10
[Ref.: #66794]	threonine metabolism	90	9 of 10
[Ref.: #66794]	propionate fermentation	90	9 of 10
[Ref.: #66794]	NAD metabolism	88.89	16 of 18
[Ref.: #66794]	aspartate and asparagine metabolism	88.89	8 of 9
[Ref.: #66794]	valine metabolism	88.89	8 of 9
[Ref.: #66794]	serine metabolism	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	isoleucine metabolism	87.5	7 of 8
[Ref.: #66794]	reductive acetyl coenzyme A pathway	85.71	6 of 7
[Ref.: #66794]	heme metabolism	85.71	12 of 14
[Ref.: #66794]	glutamate and glutamine metabolism	85.71	24 of 28
[Ref.: #66794]	urea cycle	84.62	11 of 13
[Ref.: #66794]	glycolysis	82.35	14 of 17
[Ref.: #66794]	pentose phosphate pathway	81.82	9 of 11
[Ref.: #66794]	metabolism of disaccharids	81.82	9 of 11
[Ref.: #66794]	flavin biosynthesis	80	12 of 15
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	factor 420 biosynthesis	80	4 of 5
[Ref.: #66794]	ethylmalonyl-CoA pathway	80	4 of 5
[Ref.: #66794]	glycogen metabolism	80	4 of 5
[Ref.: #66794]	3-chlorocatechol degradation	80	4 of 5
[Ref.: #66794]	vitamin B12 metabolism	79.41	27 of 34
[Ref.: #66794]	purine metabolism	78.72	74 of 94
[Ref.: #66794]	tetrahydrofolate metabolism	78.57	11 of 14
[Ref.: #66794]	photosynthesis	78.57	11 of 14
[Ref.: #66794]	CO2 fixation in Crenarchaeota	77.78	7 of 9
[Ref.: #66794]	d-mannose degradation	77.78	7 of 9
[Ref.: #66794]	leucine metabolism	76.92	10 of 13
[Ref.: #66794]	sulfopterin metabolism	75	3 of 4
[Ref.: #66794]	gluconeogenesis	75	6 of 8
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	C4 and CAM-carbon fixation	75	6 of 8
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	pyrimidine metabolism	73.33	33 of 45
[Ref.: #66794]	alanine metabolism	72.41	21 of 29
[Ref.: #66794]	tyrosine metabolism	71.43	10 of 14
[Ref.: #66794]	glutathione metabolism	71.43	10 of 14
[Ref.: #66794]	ubiquinone biosynthesis	71.43	5 of 7
[Ref.: #66794]	citric acid cycle	71.43	10 of 14
[Ref.: #66794]	propanol degradation	71.43	5 of 7
[Ref.: #66794]	arginine metabolism	70.83	17 of 24
[Ref.: #66794]	isoprenoid biosynthesis	69.23	18 of 26
[Ref.: #66794]	degradation of sugar alcohols	68.75	11 of 16
[Ref.: #66794]	tryptophan metabolism	68.42	26 of 38
[Ref.: #66794]	oxidative phosphorylation	68.13	62 of 91
[Ref.: #66794]	lipid metabolism	67.74	21 of 31
[Ref.: #66794]	sulfoquinovose degradation	66.67	2 of 3
[Ref.: #66794]	enterobactin biosynthesis	66.67	2 of 3
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	methane metabolism	66.67	2 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	non-pathway related	65.79	25 of 38
[Ref.: #66794]	histidine metabolism	65.52	19 of 29
[Ref.: #66794]	lysine metabolism	64.29	27 of 42
[Ref.: #66794]	degradation of sugar acids	64	16 of 25
[Ref.: #66794]	d-xylose degradation	63.64	7 of 11
[Ref.: #66794]	proline metabolism	63.64	7 of 11
[Ref.: #66794]	ketogluconate metabolism	62.5	5 of 8
[Ref.: #66794]	cysteine metabolism	61.11	11 of 18
[Ref.: #66794]	metabolism of amino sugars and derivatives	60	3 of 5
[Ref.: #66794]	lipoate biosynthesis	60	3 of 5
[Ref.: #66794]	arachidonate biosynthesis	60	3 of 5
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	58.82	10 of 17
[Ref.: #66794]	cholesterol biosynthesis	54.55	6 of 11
[Ref.: #66794]	vitamin B6 metabolism	54.55	6 of 11
[Ref.: #66794]	sulfate reduction	53.85	7 of 13
[Ref.: #66794]	methionine metabolism	53.85	14 of 26
[Ref.: #66794]	polyamine pathway	52.17	12 of 23
[Ref.: #66794]	glycolate and glyoxylate degradation	50	3 of 6
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	myo-inositol biosynthesis	50	5 of 10
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	androgen and estrogen metabolism	50	8 of 16
[Ref.: #66794]	carotenoid biosynthesis	50	11 of 22
[Ref.: #66794]	phenol degradation	50	10 of 20
[Ref.: #66794]	carnitine metabolism	50	4 of 8
[Ref.: #66794]	toluene degradation	50	2 of 4
[Ref.: #66794]	lactate fermentation	50	2 of 4
[Ref.: #66794]	cyclohexanol degradation	50	2 of 4
[Ref.: #66794]	dTDPLrhamnose biosynthesis	50	4 of 8
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	coenzyme M biosynthesis	50	5 of 10
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	degradation of pentoses	46.43	13 of 28
[Ref.: #66794]	lipid A biosynthesis	44.44	4 of 9
[Ref.: #66794]	nitrate assimilation	44.44	4 of 9
[Ref.: #66794]	arachidonic acid metabolism	44.44	8 of 18
[Ref.: #66794]	aclacinomycin biosynthesis	42.86	3 of 7
[Ref.: #66794]	benzoyl-CoA degradation	42.86	3 of 7
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
[Ref.: #66794]	ascorbate metabolism	40.91	9 of 22
[Ref.: #66794]	elloramycin biosynthesis	40	2 of 5
[Ref.: #66794]	glycine betaine biosynthesis	40	2 of 5
[Ref.: #66794]	D-cycloserine biosynthesis	40	2 of 5
[Ref.: #66794]	degradation of hexoses	38.89	7 of 18
[Ref.: #66794]	vitamin B1 metabolism	38.46	5 of 13
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	38.46	5 of 13
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	36.36	4 of 11
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	4-hydroxymandelate degradation	33.33	3 of 9
[Ref.: #66794]	selenocysteine biosynthesis	33.33	2 of 6
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	allantoin degradation	33.33	3 of 9
[Ref.: #66794]	phenylpropanoid biosynthesis	30.77	4 of 13
[Ref.: #66794]	alginate biosynthesis	25	1 of 4
[Ref.: #66794]	CMP-KDO biosynthesis	25	1 of 4
[Ref.: #66794]	methanogenesis from CO2	25	3 of 12
[Ref.: #66794]	butanoate fermentation	25	1 of 4
[Ref.: #66794]	biotin biosynthesis	25	1 of 4
[Ref.: #66794]	catecholamine biosynthesis	25	1 of 4
		Only first 10 entries are displayed. Click here to see all.

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

[Ref.: #16105]	Sample type/isolated from	Lichen
[Ref.: #16105]	Geographic location (country and/or sea, region)	Izu-Oshima Island
[Ref.: #16105]	Country	Japan
[Ref.: #16105]	Country ISO 3 Code	JPN
[Ref.: #16105]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Lichen
[Ref.: #67770]	Geographic location (country and/or sea, region)	Izu-Oshima Island
[Ref.: #67770]	Country	Japan
[Ref.: #67770]	Country ISO 3 Code	JPN
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Host

#Other

#Lichen

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AB273624 (>99% sequence identity) for Nocardioides exalbidus from Microbeatlas

Aquatic Samples	29
Soil Samples	163
Animal Samples	82
Plant Samples	47
Total Samples	321

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

[Ref.: #16105]

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.: #16105]	Nocardioides exalbidus gene for 16S rRNA, partial sequence, strain: RC825	AB273624	1453	GenBank ENA	402596 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Nocardioides exalbidus DSM 22017	GCA_900105585	contig	GenBank ENA	402596 tax ID
[Ref.: #66792]	Nocardioides exalbidus strain DSM 22017	402596.4	wgs	PATRIC	402596 tax ID	*
[Ref.: #66792]	Nocardioides exalbidus DSM 22017	2639762616	draft	JGI IMG/M	402596 tax ID	*

[Ref.: #16105]	GC-content	74.0 mol%	high performance liquid chromatography (HPLC)
[Ref.: #67770]	GC-content	71.8 mol%	genome sequence analysis
[Ref.: #67770]	GC-content	74 mol%	high performance liquid chromatography (HPLC)

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: Nocardioides exalbidus strain DSM 22017 PATRIC: 402596.4
[Ref.: #125438]	gram-positive	gram-positiveⓘ	yes	87.287	no
[Ref.: #125438]	anaerobic	anaerobicⓘ	no	97.257	no
[Ref.: #125438]	spore-forming	spore-formingⓘ	no	53.914	no
[Ref.: #125438]	aerobic	aerobicⓘ	yes	90.432	no
[Ref.: #125438]	thermophile	thermophilicⓘ	no	97.986	no
[Ref.: #125438]	motile2+	flagellatedⓘ	no	78	no

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Nocardioides exalbidus DSM 22017 NCBI: GCA_900105585
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	no	86.7
[Ref.: #125439]	BacteriaNet	motilityⓘ	no	68.9
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	positive	99.1
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	obligate aerobe	97

Availability in culture collections External links

[Ref.: #16105]

Culture collection no.

DSM 22017, CCTCC AA 206016, IAM 15416, JCM 23199

[Ref.: #80378]

SI-ID 319384

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Nocardioides baculatus sp. nov., a novel actinomycete isolated from the rhizosphere of Tagetes patula.	Chhetri G, Kim I, Kang M, Kim J, So Y, Seo T	Int J Syst Evol Microbiol	10.1099/ijsem.0.005012	2021	*
Phylogeny	Nocardioides euryhalodurans sp. nov., Nocardioides seonyuensis sp. nov. and Nocardioides eburneiflavus sp. nov., isolated from soil.	Roh SG, Lee C, Kim MK, Kang HJ, Kim YS, Kim MJ, Malik A, Kim SB	Int J Syst Evol Microbiol	10.1099/ijsem.0.004095	2020	*
Phylogeny	Nocardioides cavernae sp. nov., an actinobacterium isolated from a karst cave.	Han MX, Fang BZ, Tian Y, Zhang WQ, Jiao JY, Liu L, Zhang ZT, Xiao M, Wei DQ, Li WJ	Int J Syst Evol Microbiol	10.1099/ijsem.0.001676	2017	*
Phylogeny	Nocardioides flavus sp. nov., isolated from marine sediment.	Wang S, Zhou Y, Zhang G	Int J Syst Evol Microbiol	10.1099/ijsem.0.001507	2016	*

References

#16105

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 22017

#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 )

#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) .

#66794

Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;

#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 .

#80378

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-ID319384.1 )

#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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Nocardioides exalbidus strain DSM 22017

Nocardioides exalbidus DSM 22017

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