Gordonia namibiensis (DSM 44568, NCIMB 13800, NAM-BN063A)

Name: Gordonia namibiensis (DSM 44568, NCIMB 13800, NAM-BN063A)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 10604

Type strain

Strain Designation NAM-BN063A

Culture col. no. DSM 44568 NCIMB 13800 NAM-BN063A NBRC 108229 KCTC 9952 5 more

NCBI tax ID(s) 1208314 168480

Special Collections DSMZ CCUG JCM KCTC CIP

History <- M. Goodfellow, Univ. Newcastle; NAM-BN063A NCIMB 13800 <-- M. Goodfellow NAM-BN063A. CIP <- 2002, NCIMB <- M. Goodfellow, Newcastle Univ., Newcastle, UK: strain NAM-BN063A

Links

Gordonia namibiensis NAM-BN063A is an obligate aerobe, Gram-positive, rod-shaped bacterium that was isolated from soil.

Gram-positive rod-shaped obligate aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 43769

NBRC 108229,NCIMB 13800,DSM 44568,KCTC 9952,CCUG47264,JCM 12074,CIP 107614,BCRC 16392,CCRC 16392,CCUG 47264 A,CCUG 47264 B

@ref 20215

Last LPSN update 2026-02-09 11:20:18

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Mycobacteriales

Family Gordoniaceae

Genus Gordonia

Species Gordonia namibiensis

Full scientific name Gordonia namibiensis Brandão et al. 2002

BacDive ID	Other strains from **Gordonia namibiensis** (1)	Type strain
10605	G. namibiensis NAM-BN063B, DSM 44569, NCIMB 13801

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
121228	positive	rod-shaped
125438			91
125438	positive		90.781
125439	positive		99.4

Colony morphology

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
11764	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
33147	MEDIUM 72- for trypto casein soja agar		Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
121228	CIP Medium 72	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
11764	positive	growth	28
33147	positive	growth	30
67770	positive	growth	28
121228	positive	growth	25-45
121228	negative	growth	10

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
121228	obligate aerobe
125438	aerobe	91.311
125439	obligate aerobe	95.9

Halophily

@ref	Salt	Growth	Tested relation	Concentration
121228	NaCl	positive	growth	0-10 %

Observation

67770

Observationquinones: MK-9(H₂)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
121228	16947 ChEBI	citrate	-	carbon source
68379	17634 ChEBI	D-glucose	-	fermentation	from API Coryne
68379	16899 ChEBI	D-mannitol	-	fermentation	from API Coryne
68379	16988 ChEBI	D-ribose	-	fermentation	from API Coryne
68379	65327 ChEBI	D-xylose	-	fermentation	from API Coryne
68379	4853 ChEBI	esculin	-	hydrolysis	from API Coryne
121228	4853 ChEBI	esculin	-	hydrolysis
68379	5291 ChEBI	gelatin	-	hydrolysis	from API Coryne
68379	28087 ChEBI	glycogen	-	fermentation	from API Coryne
121228	606565 ChEBI	hippurate	-	hydrolysis
68379	17716 ChEBI	lactose	-	fermentation	from API Coryne
68379	17306 ChEBI	maltose	-	fermentation	from API Coryne
68379	17632 ChEBI	nitrate	-	reduction	from API Coryne
121228	17632 ChEBI	nitrate	-	reduction
121228	17632 ChEBI	nitrate	-	respiration
121228	16301 ChEBI	nitrite	-	reduction
68379	17992 ChEBI	sucrose	-	fermentation	from API Coryne
68379	16199 ChEBI	urea	-	hydrolysis	from API Coryne

Antibiotic resistance

@ref	Metabolite	Is sensitive	Is resistant
121228	0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)

Metabolite production

@ref	Chebi-ID	Metabolite	Production
121228	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test	Methylred-test
121228	15688 ChEBI	acetoin	-
121228	17234 ChEBI	glucose		-

Enzymes

@ref	Value	Activity	Ec
121228	alcohol dehydrogenase	-	1.1.1.1
68379	alkaline phosphatase	+	3.1.3.1	from API Coryne
68382	alpha-chymotrypsin	-	3.4.21.1	from API zym
68382	alpha-fucosidase	-	3.2.1.51	from API zym
68382	alpha-galactosidase	-	3.2.1.22	from API zym
68382	alpha-glucosidase	+	3.2.1.20	from API zym
68379	alpha-glucosidase	+	3.2.1.20	from API Coryne
68382	alpha-mannosidase	-	3.2.1.24	from API zym
121228	amylase	-
68382	beta-galactosidase	-	3.2.1.23	from API zym
121228	beta-galactosidase	-	3.2.1.23
68379	beta-galactosidase	-	3.2.1.23	from API Coryne
68379	beta-glucosidase	-	3.2.1.21	from API Coryne
68382	beta-glucuronidase	-	3.2.1.31	from API zym
68379	beta-glucuronidase	-	3.2.1.31	from API Coryne
121228	caseinase	-	3.4.21.50
121228	catalase	+	1.11.1.6
121228	DNase	-
121228	gamma-glutamyltransferase	+	2.3.2.2
121228	gelatinase	-
68379	gelatinase	-		from API Coryne
121228	lecithinase	-
68382	leucine arylamidase	+	3.4.11.1	from API zym
121228	lipase	-
68382	lipase (C 14)	-		from API zym
121228	lysine decarboxylase	-	4.1.1.18
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68379	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API Coryne
121228	ornithine decarboxylase	-	4.1.1.17
121228	oxidase	-
121228	phenylalanine ammonia-lyase	-	4.3.1.24
121228	protease	-
68379	pyrazinamidase	-	3.5.1.B15	from API Coryne
121228	tryptophan deaminase	-
121228	tween esterase	+
121228	urease	+	3.5.1.5
68379	urease	-	3.5.1.5	from API Coryne

API coryne

@ref	Reduction of nitrateNIT	PYZ	PYRA	PAL	beta GUR	beta GAL	alpha GLU	beta NAG	ESC	URE	GEL	Control fermentationControl	GLU	RIB	XYL	MAN	MAL	LAC	SAC	GLYG	CAT
11764	-	-	+/-	+	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	not determinedn.d.

API zym

@ref	Control	Alkaline phosphatase	Esterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	Lipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	Trypsin	alpha- Chymotrypsin	Acid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	alpha- Galactosidase	beta- Galactosidase	beta- Glucuronidase	alpha- Glucosidase	beta- Glucosidase	N-acetyl-beta- glucosaminidase	alpha- Mannosidase	alpha- Fucosidase
11764	-	+/-	-	+/-	-	+	-	-	-	-	+/-	-	-	-	-	+	-	-	-	-
121228	-	+	+	+	-	+	+	+	+	-	+	+	-	-	-	+	+	-	-	-

API biotype100

@ref	ControlQ	D-glucose as carbon sourceGLU	D-fructose as carbon sourceFRU	D-galactose as carbon sourceGAL	D-trehalose as carbon sourceTRE	D-mannose as carbon sourceMNE	L-sorbose as carbon sourceSBE	D-melibiose as carbon sourceMEL	sucrose as carbon sourceSAC	D-raffinose as carbon sourceRAF	maltotriose as carbon sourceMTE	maltose as carbon sourceMAL	lactose as carbon sourceLAC	lactulose as carbon sourceLTE	1-O-methyl-beta-galactopyranoside as carbon sourceMbGa	1-O-methyl-alpha-galactopyranoside as carbon sourceMaGa	D-cellobiose as carbon sourceCEL	gentiobiose as carbon sourceGEN	1-O-methyl-beta-D-glucopyranoside as carbon sourceMbGu	esculin as carbon sourceESC	D-ribose as carbon sourceRIB	L-arabinose as carbon sourceARA	D-xylose as carbon sourceXYL	palatinose as carbon sourcePLE	L-rhamnose as carbon sourceRHA	L-fucose as carbon sourceFUC	D-melezitose as carbon sourceMLZ	D-arabitol as carbon sourceDARL	L-arabitol as carbon sourceLARL	xylitol as carbon sourceXLT	dulcitol as carbon sourceDUL	D-tagatose as carbon sourceTAG	glycerol as carbon sourceGLY	myo-inositol as carbon sourceINO	D-mannitol as carbon sourceMAN	maltitol as carbon sourceMTL	D-turanose as carbon sourceTUR	D-sorbitol as carbon sourceSOR	adonitol as carbon sourceADO	hydroxyquinoline-beta-glucuronide as carbon sourceHBG	D-lyxose as carbon sourceLYX	i-erythritol as carbon sourceERY	1-O-methyl-alpha-D-glucoside as carbon sourceMDG	3-O-methyl-D-glucose as carbon source3MDG	D-saccharate as carbon sourceSAT	mucate as carbon sourceMUC	L-tartrate as carbon sourceLTAT	D-tartrate as carbon sourceDTAT	meso-tartrate as carbon sourceMTAT	D-malate as carbon sourceDMLT	L-malate as carbon sourceLMLT	cis-aconitate as carbon sourceCATE	trans-aconitate as carbon sourceTATE	tricarballylate as carbon sourceTTE	citrate as carbon sourceCIT	D-glucuronate as carbon sourceGRT	D-galacturonate as carbon sourceGAT	2-ketogluconate as carbon source2KG	5-ketogluconate as carbon source5KG	tryptophan as carbon sourceTRY	N-acetyl-D-glucosamine as carbon sourceNAG	D-gluconate as carbon sourceGNT	phenylacetate as carbon sourcePAC	protocatechuate as carbon sourcePAT	4-hydroxybenzoate as carbon sourcepOBE	quinate as carbon sourceQAT	gentisate as carbon sourceGTE	3-hydroxybenzoate as carbon sourcemOBE	benzoate as carbon sourceBAT	3-phenylpropionate as carbon sourcePPAT	m-coumarate as carbon sourceCMT	trigonelline as carbon sourceTGE	betaine as carbon sourceBET	putrescine as carbon sourcePCE	4-aminobutyrate as carbon sourceABT	histamine as carbon sourceHIN	DL-lactate as carbon sourceLAT	caprate as carbon sourceCAP	caprylate as carbon sourceCYT	L-histidine as carbon sourceHIS	succinate as carbon sourceSUC	fumarate as carbon sourceFUM	glutarate as carbon sourceGRE	DL-glycerate as carbon sourceGYT	5-aminovalerate as carbon sourceAVT	ethanolamine as carbon sourceETN	tryptamine as carbon sourceTTN	D-glucosamine as carbon sourceGLN	itaconate as carbon sourceITA	3-hydroxybutyrate as carbon source3OBU	L-aspartate as carbon sourceAPT	L-glutamate as carbon sourceGTT	L-proline as carbon sourcePRO	D-alanine as carbon sourceDALA	L-alanine as carbon sourceLALA	L-serine as carbon sourceSER	malonate as carbon sourceMNT	propionate as carbon sourcePROP	L-tyrosine as carbon sourceTYR	2-ketoglutarate as carbon source2KT
121228	not determinedn.d.	-	+	-	+	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	-	+	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	+	-	-	-	-	-	-	+	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-	+	+	+	-	-	+	-	-	-	+	-	-	-	-	-	-	-	+	-	+

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Soil

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Isolation date
11764	soil	Kalahari	Namibia	NAM	Africa
67770	Kalahari soil	Waterberg area of Central Namibia	Namibia	NAM	Africa
121228	Environment, Namibian soil	Kalahari	Namibia	NAM	Africa	1997

Taxonmaps

69479

Global distribution of 16S sequence AF380930 (>99% sequence identity) for Gordonia from Microbeatlas

Aquatic Samples	44
Soil Samples	28
Animal Samples	117
Plant Samples	7
Total Samples	196

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
11764	1	Risk group (German classification) According to TRBA 466
121228	1	Risk group (French classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	ASM29823v1 assembly for Gordonia namibiensis NBRC 108229	contig	GCA_000298235	1208314.3	2523231041	1208314	64.82

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
11764	Gordonia namibiensis NAM-BN063A 16S ribosomal RNA gene, partial sequence	AF380930	1484		1208314

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Gordonia namibiensis NBRC 108229
NCBI: GCA_000298235

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	65.70	no
125439	motility	BacteriaNetⓘ	no	88.00	no
125439	gram_stain	BacteriaNetⓘ	positive	99.40	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	95.90	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Gordonia namibiensis NBRC 108229
PATRIC: 1208314.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	90.78	no
125438	anaerobic	anaerobicⓘ	no	97.59	no
125438	spore-forming	spore-formingⓘ	no	59.72	no
125438	aerobic	aerobicⓘ	yes	91.31	yes
125438	thermophilic	thermophileⓘ	no	96.00	yes
125438	flagellated	motile2+ⓘ	no	91.00	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Focusing on Gordonia Infections: Distribution, Antimicrobial Susceptibilities and Phylogeny.	Pino-Rosa S, Medina-Pascual MJ, Carrasco G, Garrido N, Villalon P, Valiente M, Valdezate S.	Antibiotics (Basel)	10.3390/antibiotics12111568	2023
Genetics	Genomic analysis provides insights into the Gordonia sp. W3S5 taxonomy and sulfur metabolism-related genes.	Parveen S, Akhtar N, Akram J.	3 Biotech	10.1007/s13205-021-02850-4	2021
Biotechnology	Draft genome sequence and comparative genomic analysis of Halomonas salifodinae strain A2 isolated from the Zapotitlán Salinas Valley, Puebla, Mexico.	Leon-Lemus A, Martinez-Garcia M, Cabirol N, Campos JE, Monsalvo-Reyes A.	Extremophiles	10.1007/s00792-025-01397-z	2025
	Exploring Anastomosis of Hyphae and Mating-Type Compatibility of Pochonia chlamydosporia Isolates of the Meloidogyne, Heterodera and Globodera Biotypes.	Finetti-Sialer MM, Manzanilla-Lopez RH.	Pathogens	10.3390/pathogens11060619	2022
Genetics	Characterization and Genomic Analysis of a Highly Efficient Dibutyl Phthalate-Degrading Bacterium Gordonia sp. Strain QH-12.	Jin D, Kong X, Liu H, Wang X, Deng Y, Jia M, Yu X.	Int J Mol Sci	10.3390/ijms17071012	2016
	In silico genome analysis reveals the metabolic versatility and biotechnology potential of a halotorelant phthalic acid esters degrading Gordonia alkanivorans strain YC-RL2.	Nahurira R, Wang J, Yan Y, Jia Y, Fan S, Khokhar I, Eltoukhy A.	AMB Express	10.1186/s13568-019-0733-5	2019
Metabolism	Environmentally triggered genomic plasticity and capsular polysaccharide formation are involved in increased ethanol and acetic acid tolerance in Kozakia baliensis NBRC 16680.	Brandt JU, Born FL, Jakob F, Vogel RF.	BMC Microbiol	10.1186/s12866-017-1070-y	2017
Enzymology	Evolutionary Convergence of Pathway-Specific Enzyme Expression Stoichiometry.	Lalanne JB, Taggart JC, Guo MS, Herzel L, Schieler A, Li GW.	Cell	10.1016/j.cell.2018.03.007	2018
Phylogeny	Actinoallomurus oryzae sp. nov., an endophytic actinomycete isolated from roots of a Thai jasmine rice plant.	Indananda C, Thamchaipenet A, Matsumoto A, Inahashi Y, Duangmal K, Takahashi Y.	Int J Syst Evol Microbiol	10.1099/ijs.0.022509-0	2011
Phylogeny	Gordonia namibiensis sp. nov., a novel nitrile metabolising actinomycete recovered from an African sand.	Brandao PF, Maldonado LA, Ward AC, Bull AT, Goodfellow M	Syst Appl Microbiol	10.1078/0723-2020-00074	2001

References

#11764	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 44568
#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 )
#33147	; Curators of the CIP;
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#68379	Automatically annotated from API Coryne .
#68382	Automatically annotated from API zym .
#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 .
#121228	Collection of Institut Pasteur ; Curators of the CIP; CIP 107614
#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 )

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Gordonia namibiensis (DSM 44568, NCIMB 13800, NAM-BN063A)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Halophily

Observation

Metabolite utilization

Antibiotic resistance

Metabolite production

Metabolite tests

Enzymes

API coryne

API zym

API biotype100

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000298235

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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