Nocardioides cavernae (DSM 29950, KCTC 39551, YIM A1136)

Name: Nocardioides cavernae (DSM 29950, KCTC 39551, YIM A1136)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 133079

Type strain

Culture col. no. DSM 29950 KCTC 39551 YIM A1136 JCM 30631

NCBI tax ID(s) 1921566

Special Collections DSMZ JCM KCTC Literature strains

History DSMZ <- W.-J. Li, Yunnan Institute of Microbiology, Kunming; YIM A1136 <- W. Zhang JCM <-- W.-J. Li; Yunnan Inst. of Microbiol., Yunnan Univ., China; YIM A1136.

Links

Nocardioides cavernae DSM 29950 is an aerobe, Gram-positive, rod-shaped bacterium that forms circular colonies and was isolated from soil, karst cave.

Gram-positive rod-shaped colony-forming aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 404125

KCTC 39551,DSM 29950

@ref 20215

Last LPSN update 2026-05-29 08:38:00

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Propionibacteriales

Family Nocardioidaceae

Genus Nocardioides

Species Nocardioides cavernae

Full scientific name Nocardioides cavernae Han et al. 2017

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
25227	positive	2.0-6.0 µm	0.2-0.5 µm	rod-shaped
125439	positive				98.35
125438	positive				90.739

Colony morphology

@ref	Colony color	Colony shape	Incubation period	Medium used
25227	opaque yellowish- white	circular	4 days	Reasoner’s 2A agar (R2A, Difco)

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
24867	TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)	Medium recipe at MediaDive	Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
25227	Reasoner’s 2A agar (R2A, Difco)
24867	R2A MEDIUM (DSMZ Medium 830)	Medium recipe at MediaDive	Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
24867	positive	growth	28
25227	positive	growth	4-35
25227	positive	optimum	28
67770	positive	growth	28

Culture pH

@ref	Ability	Type	PH
25227	positive	optimum	7
25227	positive	growth	6.0-8.0

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
25227	aerobe
125438	aerobe	91.6
125439	obligate aerobe	99.077

Spore formation

25227

Spore formationno

Halophily

@ref	Salt	Growth	Tested relation	Concentration
25227	NaCl	positive	growth	0.0-5.0 %(w/v)
25227	NaCl		optimum	0 %(w/v)

Observation

67770

Observationquinones: MK-8(H₄)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
25227	30916 ChEBI	2-oxoglutarate	+	oxidation
25227	30089 ChEBI	acetate	+	oxidation
25227	17128 ChEBI	adipate	-	assimilation
25227	17925 ChEBI	alpha-D-glucose	+	oxidation
25227	62968 ChEBI	cellulose	-	hydrolysis
25227	16947 ChEBI	citrate	+	oxidation
25227	8391 ChEBI	D-gluconate	+	oxidation
25227	17634 ChEBI	D-glucose	+	assimilation
25227	16899 ChEBI	D-mannitol	-	assimilation
25227	16024 ChEBI	D-mannose	-	assimilation
25227	27689 ChEBI	decanoate	+	assimilation
25227	4853 ChEBI	esculin	+	hydrolysis
25227	71321 ChEBI	fusidate	+	oxidation
25227	16537 ChEBI	galactarate	+	oxidation
25227	5291 ChEBI	gelatin	-	hydrolysis
25227	17234 ChEBI	glucose	-	fermentation
25227	17754 ChEBI	glycerol	+	oxidation
25227	30849 ChEBI	L-arabinose	-	assimilation
25227	29985 ChEBI	L-glutamate	+	oxidation
25227	15589 ChEBI	L-malate	+	oxidation
25227	17115 ChEBI	L-serine	+	oxidation
25227	24996 ChEBI	lactate	+	oxidation
25227	6472 ChEBI	lincomycin	+	oxidation
25227	25115 ChEBI	malate	+	assimilation
25227	17306 ChEBI	maltose	-	assimilation
25227	506227 ChEBI	N-acetylglucosamine	-	assimilation
25227	100147 ChEBI	nalidixic acid	+	hydrolysis
25227	75273 ChEBI	niaproof	+	oxidation
25227	17632 ChEBI	nitrate	-	reduction
25227	18401 ChEBI	phenylacetate	-	assimilation
25227	32032 ChEBI	potassium gluconate	+	assimilation
25227	75248 ChEBI	potassium tellurite	+	oxidation
25227	17272 ChEBI	propionate	+	oxidation
25227	26490 ChEBI	quinate	+	oxidation
25227	29673 ChEBI	rifamycin sv	+	oxidation
25227		skimmed milk	-	fermentation
25227	75229 ChEBI	sodium bromate	+	oxidation
25227	53258 ChEBI	sodium citrate	+	assimilation
25227	28017 ChEBI	starch	-	hydrolysis
25227	75198 ChEBI	tetrazolium blue	+	oxidation
25227	75193 ChEBI	tetrazolium violet	+	oxidation
25227	45735 ChEBI	troleandomycin	+	oxidation
25227	53424 ChEBI	tween 20	-	hydrolysis
25227	53423 ChEBI	tween 40	+	hydrolysis
25227	53425 ChEBI	tween 60	+	hydrolysis
25227	53426 ChEBI	tween 80	-	hydrolysis
25227	28001 ChEBI	vancomycin	+	oxidation

Metabolite production

@ref	Chebi-ID	Metabolite	Production
25227	16136 ChEBI	hydrogen sulfide
25227	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
25227	acid phosphatase	-	3.1.3.2
25227	alkaline phosphatase	-	3.1.3.1
25227	alpha-chymotrypsin	-	3.4.21.1
25227	alpha-galactosidase	-	3.2.1.22
25227	alpha-glucosidase	-	3.2.1.20
25227	alpha-mannosidase	-	3.2.1.24
25227	arginine dihydrolase	-	3.5.3.6
25227	beta-D-fucosidase	-	3.2.1.38
25227	beta-galactosidase	-	3.2.1.23
25227	beta-glucosidase	-	3.2.1.21
25227	beta-glucuronidase	-	3.2.1.31
25227	catalase	+	1.11.1.6
25227	cystine arylamidase	-	3.4.11.3
25227	cytochrome oxidase	-	1.9.3.1
25227	esterase (C 4)	+
25227	esterase Lipase (C 8)	+
25227	leucine arylamidase	+	3.4.11.1
25227	lipase (C 14)	-
25227	N-acetyl-beta-glucosaminidase	-	3.2.1.52
25227	naphthol-AS-BI-phosphohydrolase	+
25227	trypsin	-	3.4.21.4
25227	urease	-	3.5.1.5

Fatty acid profile

Metadata FA analysis

@ref

25227

Fatty acid	Percentage
C16:0	26.7
C18:1ω7c / C18:1ω6c	17.5
C16:1ω7c / C16:1ω6c	15.7
C17:0 cyclo	9.2
C12:0 2OH	8.8
C12:0 3OH	8.5
C10:0 3OH	6.2

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Geologic
#Environmental	#Terrestrial	#Soil

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude	Enrichment culture	Enrichment culture composition	Enrichment culture duration	Enrichment culture temperature	Isolation procedure
24867	soil, karst cave	Guizhou province, Xingyi county (25° 09' N 104° 46' E)	China	CHN	Asia	25.15	104.767 25.15/104.767
25227								Reasonerâ??s 2A agar (R2A, Difco)	supplemented with cycloheximide (50 mg/l) and nalidixic acid (20 mg/l)	2 weeks	28	standard dilution plate method
67770	Soil from a karst cave in Xingyi County	Guizhou Province, south-western China	China	CHN	Asia

Taxonmaps

69479

Global distribution of 16S sequence KX815990 (>99% sequence identity) for Nocardioides from Microbeatlas

Aquatic Samples	13
Soil Samples	110
Animal Samples	53
Plant Samples	14
Total Samples	190

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
24867	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM1690747v1 assembly for Nocardioides cavernae DSM 29950	contig	GCA_016907475	1921566.5	2893570996	1921566	78.75
66792	ASM1477967v1 assembly for Nocardioides cavernae KCTC 39551	contig	GCA_014779675	1921566.4		1921566	77.12

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
24867	Nocardioides cavernae strain YIM A1136 16S ribosomal RNA gene, partial sequence	KX815990	1507		1921566

GC content

@ref	GC-content (mol%)	Method
24867	71.4	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM1690747v1 assembly for Nocardioides cavernae DSM 29950
BV-BRC: 1921566.5

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.08	no
125439	gram_stain	BacteriaNetⓘ	positive	98.35	no
125439	motility	BacteriaNetⓘ	no	78.04	no
125439	spore_formation	BacteriaNetⓘ	no	84.72	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Nocardioides cavernae strain DSM 29950
PATRIC: 1921566.5

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	90.74	no
125438	anaerobic	anaerobicⓘ	no	98.16	no
125438	spore-forming	spore-formingⓘ	no	63.82	yes
125438	aerobic	aerobicⓘ	yes	91.60	no
125438	thermophilic	thermophileⓘ	no	97.77	yes
125438	flagellated	motile2+ⓘ	no	84.04	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
	Intra-abdominal nocardiosis and scedosporiosis in a dog: case report and literature review.	Lambert JR, Cheng AC, Lee LM, Raiford D, Zuber E, Kilbane E, Fish EJ, Krolak E, Hlusko KC, McMichael M, Wilkes RP, Wiederhold NP, Canete-Gibas CF, Barrantes Murillo DF.	J Vet Diagn Invest	10.1177/10406387241287799	2025
	Strong pairwise interactions do not drive interactions in a plant leaf associated microbial community.	Hohn F, Chaudhry V, Bagci C, Mahmoudi M, Klenk E, Berg L, Stincone P, Hughes CC, Petras D, Brotz-Oesterhelt H, Kemen E, Ziemert N.	ISME Commun	10.1093/ismeco/ycae117	2025
	Effect of intra- and inter-specific plant interactions on the rhizosphere microbiome of a single target plant at different densities.	Newberger DR, Deel HL, Manter DK, Vivanco JM.	PLoS One	10.1371/journal.pone.0316676	2025
	Pollution pressure drives microbial assemblages that improve the phytoremediation potential of heavy metals by Ricinus communis.	Rubio-Noguez D, Breton-Deval L, Salinas-Peralta I, Juarez K, Galicia L.	World J Microbiol Biotechnol	10.1007/s11274-024-04025-8	2024
Pathogenicity	Shell Disease Syndrome Is Associated with Reduced and Shifted Epibacterial Diversity on the Carapace of the Crustacean Cancer pagurus.	Bergen N, Kramer P, Romberg J, Wichels A, Gerlach G, Brinkhoff T.	Microbiol Spectr	10.1128/spectrum.03419-22	2022
	Elevated atmospheric CO₂ concentrations caused a shift of the metabolically active microbiome in vineyard soil.	Rosado-Porto D, Ratering S, Wohlfahrt Y, Schneider B, Glatt A, Schnell S.	BMC Microbiol	10.1186/s12866-023-02781-5	2023
	Indigenous oil-degrading bacteria more efficient in soil bioremediation than microbial consortium and active even in super oil-saturated soils.	Ali N, Khanafer M, Al-Awadhi H.	Front Microbiol	10.3389/fmicb.2022.950051	2022
	Wildland fire as an atmospheric source of viable microbial aerosols and biological ice nucleating particles.	Moore RA, Bomar C, Kobziar LN, Christner BC.	ISME J	10.1038/s41396-020-00788-8	2021
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 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

References

#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 )
#24867	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 29950
#25227	M. X. F. Han, B. Z.,Tian, Y.,Zhang, W. Q.,Jiao, J. Y.,Liu, L.,Zhang, Z. T.,Xiao, M.,Wei, D. Q.,Li, W. J.: Nocardioides cavernae sp. nov., an actinobacterium isolated from a karst cave. IJSEM 67: 633 - 639 2017 ( DOI 10.1099/ijsem.0.001676 , PubMed 27902315 )
#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;
#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 .
#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 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

Content

About us

Nocardioides cavernae (DSM 29950, KCTC 39551, YIM A1136)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Metabolite production

Enzymes

Fatty acid profile

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_016907475

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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