Name: Nakamurella endophytica 2Q3S-4-2
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 132455

Type strain:

Species: Nakamurella endophytica

Strain Designation: 2Q3S-4-2

Culture col. no.: DSM 100722, CGMCC 4.7308, JCM 31778

Strain history: CGMCC 4.7308 <-- L. Tuo; Inst. of Med. Biotechnol., Chin. Acad. Med. Sci. & Peking Union Med. Coll., China; 2Q3S-4-2.

NCBI tax ID(s): 1748367 (species)

Section

Nakamurella endophytica 2Q3S-4-2 is an aerobe, Gram-positive, coccus-shaped bacterium that forms circular colonies and was isolated from surface-sterilized bark of Kandelia candel.

coccus-shaped
colony-forming
Gram-positive
aerobe
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	*Nakamurellales*
	Family	*Nakamurellaceae*
	Genus	*Nakamurella*
	Species	**Nakamurella endophytica**
	Full Scientific Name (LPSN)	Nakamurella endophytica Tuo et al. 2016

Information on morphological and physiological properties Morphology

[Ref.: #43733]	Gram stain	positive
[Ref.: #43733]	Cell length	0.8-1.2 µm
[Ref.: #43733]	Cell shape	coccus-shaped

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

[Ref.: #69480]	Motility	no Confidence in %96.278

[Ref.: #43733]	Colony color	Vivid orange-yellow
[Ref.: #43733]	Colony shape	circular
[Ref.: #43733]	Cultivation medium used	ISP2 agar

Information on culture and growth conditions Culture and growth conditions

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Culture medium

ISP 2 agar

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Culture medium growth

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Culture medium

ISP 3 agar

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Culture medium growth

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Culture medium

ISP2 agar

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Culture medium growth

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Culture medium

Reasoner's 2A agar (R2A)

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Culture medium growth

[Ref.: #24244]

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.: #24244]

Culture medium composition

expand / minimize

[Ref.: #43733]

Culture medium

ISP 4 agar

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Culture medium growth

[Ref.: #43733]

Culture medium

ISP 5 agar

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Culture medium growth

		Temperature
[Ref.: #24244]	growth	28 °C
[Ref.: #43733]	growth	20-37 °C
[Ref.: #43733]	optimum	28-30 °C
[Ref.: #67770]	growth	28 °C

[Ref.: #24244]	Temperature range	mesophilic
[Ref.: #43733]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #43733]			optimum	7
[Ref.: #43733]			growth	5-9

Information on physiology and metabolism Physiology and metabolism

[Ref.: #43733]

Oxygen tolerance

aerobe

[Ref.: #43733]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	yes Confidence in %98
[Ref.: #69480]	Ability of spore formation	no Confidence in %93.962

[Ref.: #43733]

Halophily / tolerance level

non-halophilic

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #43733]		NaCl		growth	0-2	%(w/v)
[Ref.: #43733]		NaCl		optimum	0	%(w/v)

[Ref.: #67770]

Observation

quinones: MK-8(H₄)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #43733]	(S)-lactate ChEBI	+	oxidation
[Ref.: #43733]	2-hydroxybutyrate ChEBI	-	oxidation
[Ref.: #43733]	2-oxobutanoate ChEBI	-	oxidation
[Ref.: #43733]	2-oxoglutarate ChEBI	-	oxidation
[Ref.: #43733]	3-O-methyl-D-glucose ChEBI	-	oxidation
[Ref.: #43733]	4-hydroxyphenylacetic acid ChEBI	-	oxidation
[Ref.: #43733]	5-dehydro-D-gluconate ChEBI	+/-	builds acid from
[Ref.: #43733]	acetate ChEBI	-	oxidation
[Ref.: #43733]	acetoacetate ChEBI	+	oxidation
[Ref.: #43733]	adipate ChEBI	-	assimilation
[Ref.: #43733]	alpha-D-glucose ChEBI	+	oxidation
[Ref.: #43733]	alpha-lactose ChEBI	+	oxidation
[Ref.: #43733]	beta-hydroxybutyrate ChEBI	-	oxidation
[Ref.: #43733]	bromosuccinate ChEBI	-	oxidation
[Ref.: #43733]	casein	+	hydrolysis
[Ref.: #43733]	cellobiose ChEBI	+	oxidation
[Ref.: #43733]	citrate ChEBI	-	oxidation
[Ref.: #43733]	D-alanine ChEBI	-	oxidation
[Ref.: #43733]	D-arabitol ChEBI	+	oxidation
[Ref.: #43733]	D-aspartate ChEBI	-	oxidation
[Ref.: #43733]	D-fructose ChEBI	+	oxidation
[Ref.: #43733]	D-fructose 6-phosphate ChEBI	+	oxidation
[Ref.: #43733]	D-fucose ChEBI	+	oxidation
[Ref.: #43733]	D-galactonic acid lactone ChEBI	+	oxidation
[Ref.: #43733]	D-galactose ChEBI	+	oxidation
[Ref.: #43733]	D-galacturonic acid ChEBI	+	oxidation
[Ref.: #43733]	D-gluconate ChEBI	+	oxidation
[Ref.: #43733]	D-glucose ChEBI	-	assimilation
[Ref.: #43733]	D-glucose 6-phosphate ChEBI	+	oxidation
[Ref.: #43733]	D-glucuronate ChEBI	+	oxidation
[Ref.: #43733]	D-lyxose ChEBI	+/-	builds acid from
[Ref.: #43733]	D-malate ChEBI	-	oxidation
[Ref.: #43733]	D-mannitol ChEBI	-	assimilation
[Ref.: #43733]	D-mannitol ChEBI	+	oxidation
[Ref.: #43733]	D-mannose ChEBI	-	assimilation
[Ref.: #43733]	D-mannose ChEBI	+	oxidation
[Ref.: #43733]	D-ribose ChEBI	+/-	builds acid from
[Ref.: #43733]	D-saccharate ChEBI	-	oxidation
[Ref.: #43733]	D-serine ChEBI	-	oxidation
[Ref.: #43733]	D-sorbitol ChEBI	+	oxidation
[Ref.: #43733]	D-tagatose ChEBI	+/-	builds acid from
[Ref.: #43733]	D-xylose ChEBI	+/-	builds acid from
[Ref.: #43733]	decanoate ChEBI	-	assimilation
[Ref.: #43733]	dextrin ChEBI	-	oxidation
[Ref.: #43733]	esculin ChEBI	+	builds acid from
[Ref.: #43733]	formate ChEBI	-	oxidation
[Ref.: #43733]	galactarate ChEBI	-	oxidation
[Ref.: #43733]	gamma-aminobutyric acid ChEBI	-	oxidation
[Ref.: #43733]	gelatin ChEBI	+	oxidation
[Ref.: #43733]	gentiobiose ChEBI	+	oxidation
[Ref.: #43733]	glucose ChEBI	-	fermentation
[Ref.: #43733]	glucuronamide ChEBI	+	oxidation
[Ref.: #43733]	glycerol ChEBI	+	oxidation
[Ref.: #43733]	glycine-proline ChEBI	-	oxidation
[Ref.: #43733]	inosine ChEBI	-	oxidation
[Ref.: #43733]	L-arabinose ChEBI	-	assimilation
[Ref.: #43733]	L-arginine ChEBI	-	oxidation
[Ref.: #43733]	L-aspartate ChEBI	-	oxidation
[Ref.: #43733]	L-fucose ChEBI	-	oxidation
[Ref.: #43733]	L-glutamate ChEBI	-	oxidation
[Ref.: #43733]	L-histidine ChEBI	-	oxidation
[Ref.: #43733]	L-malate ChEBI	-	oxidation
[Ref.: #43733]	L-pyroglutamic acid ChEBI	-	oxidation
[Ref.: #43733]	L-rhamnose ChEBI	+	oxidation
[Ref.: #43733]	L-rhamnose ChEBI	+/-	builds acid from
[Ref.: #43733]	L-serine ChEBI	-	oxidation
[Ref.: #43733]	malate ChEBI	-	assimilation
[Ref.: #43733]	maltose ChEBI	-	assimilation
[Ref.: #43733]	maltose ChEBI	+	oxidation
[Ref.: #43733]	melibiose ChEBI	-	oxidation
[Ref.: #43733]	methyl (R)-lactate ChEBI	-	oxidation
[Ref.: #43733]	methyl D-glucoside ChEBI	-	oxidation
[Ref.: #43733]	methyl pyruvate ChEBI	+	oxidation
[Ref.: #43733]	myo-inositol ChEBI	-	oxidation
[Ref.: #43733]	N-acetyl-beta-D-mannosamine ChEBI	+	oxidation
[Ref.: #43733]	N-acetylgalactosamine ChEBI	-	oxidation
[Ref.: #43733]	N-acetylglucosamine ChEBI	-	assimilation
[Ref.: #43733]	N-acetylglucosamine ChEBI	+	oxidation
[Ref.: #43733]	n-acetylneuraminate ChEBI	+	oxidation
[Ref.: #43733]	nitrate ChEBI	-	reduction
[Ref.: #43733]	pectin ChEBI	+	oxidation
[Ref.: #43733]	phenylacetate ChEBI	-	assimilation
[Ref.: #43733]	potassium gluconate ChEBI	-	assimilation
[Ref.: #43733]	propionate ChEBI	-	oxidation
[Ref.: #43733]	quinate ChEBI	-	oxidation
[Ref.: #43733]	raffinose ChEBI	-	oxidation
[Ref.: #43733]	salicin ChEBI	+	oxidation
[Ref.: #43733]	salicin ChEBI	+/-	builds acid from
[Ref.: #43733]	sodium citrate ChEBI	-	assimilation
[Ref.: #43733]	stachyose ChEBI	-	oxidation
[Ref.: #43733]	starch ChEBI	-	hydrolysis
[Ref.: #43733]	sucrose ChEBI	+	oxidation
[Ref.: #43733]	trehalose ChEBI	+	oxidation
[Ref.: #43733]	turanose ChEBI	+	oxidation
[Ref.: #43733]	tween 40 ChEBI	-	hydrolysis
[Ref.: #43733]	tween 40 ChEBI	+	oxidation
[Ref.: #43733]	tween 80 ChEBI	-	hydrolysis
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Antibiotic sensitivity	Antibiotic resistance
[Ref.: #43733]	1 % sodium lactate		yes
[Ref.: #43733]	aztreonam ChEBI		yes
[Ref.: #43733]	fusidate ChEBI	yes
[Ref.: #43733]	guanidinium chloride ChEBI		yes
[Ref.: #43733]	lincomycin ChEBI		yes
[Ref.: #43733]	lithium chloride ChEBI	yes
[Ref.: #43733]	minocycline ChEBI	yes
[Ref.: #43733]	nalidixic acid ChEBI		yes
[Ref.: #43733]	niaproof ChEBI	yes
[Ref.: #43733]	potassium tellurite ChEBI		yes
[Ref.: #43733]	rifamycin sv ChEBI	yes
[Ref.: #43733]	sodium bromate ChEBI	yes
[Ref.: #43733]	sodium butyrate ChEBI		yes
[Ref.: #43733]	tetrazolium blue ChEBI	yes
[Ref.: #43733]	tetrazolium violet ChEBI		yes
[Ref.: #43733]	troleandomycin ChEBI	yes
[Ref.: #43733]	vancomycin ChEBI		yes
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite
[Ref.: #43733]		hydrogen sulfide ChEBI

	Physiological tests	Metabolite	Methylred-test
[Ref.: #43733]		glucose ChEBI	-

	Enzyme	Enzyme activity	EC number
[Ref.: #43733]	acid phosphatase	+	3.1.3.2
[Ref.: #43733]	alkaline phosphatase	+	3.1.3.1
[Ref.: #43733]	alpha-chymotrypsin	-	3.4.21.1
[Ref.: #43733]	alpha-fucosidase	-	3.2.1.51
[Ref.: #43733]	alpha-galactosidase	-	3.2.1.22
[Ref.: #43733]	alpha-glucosidase	+	3.2.1.20
[Ref.: #43733]	alpha-mannosidase	-	3.2.1.24
[Ref.: #43733]	beta-galactosidase	-	3.2.1.23
[Ref.: #43733]	beta-glucosidase	+	3.2.1.21
[Ref.: #43733]	beta-glucuronidase	-	3.2.1.31
[Ref.: #43733]	catalase	+	1.11.1.6
[Ref.: #43733]	cystine arylamidase	-	3.4.11.3
[Ref.: #43733]	cytochrome oxidase	-	1.9.3.1
[Ref.: #43733]	esterase (C 4)	-
[Ref.: #43733]	esterase Lipase (C 8)	+
[Ref.: #43733]	leucine arylamidase	+	3.4.11.1
[Ref.: #43733]	lipase (C 14)	-
[Ref.: #43733]	N-acetyl-beta-glucosaminidase	-	3.2.1.52
[Ref.: #43733]	naphthol-AS-BI-phosphohydrolase	+
[Ref.: #43733]	trypsin	-	3.4.21.4
[Ref.: #43733]	urease	-	3.5.1.5
[Ref.: #43733]	valine arylamidase	+/-
	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.: #24244]	Sample type/isolated from	surface-sterilized bark of Kandelia candel
[Ref.: #24244]	Host species	Kandelia candel
[Ref.: #24244]	Geographic location (country and/or sea, region)	Macao, Cotai Ecological Zones
[Ref.: #24244]	Country	China
[Ref.: #24244]	Country ISO 3 Code	CHN
[Ref.: #24244]	Continent	Asia
[Ref.: #24244]	Geographic location	22.1333°/113.5500°

[Ref.: #43733]	Sample type/isolated from	Surface-sterilized bark of Kandelia candel collected from Cotai Ecological Zones
[Ref.: #43733]	Geographic location (country and/or sea, region)	Macao
[Ref.: #43733]	Country	China
[Ref.: #43733]	Country ISO 3 Code	CHN
[Ref.: #43733]	Continent	Asia
[Ref.: #43733]	Geographic location	22.1410°/113.5750°

[Ref.: #67770]	Sample type/isolated from	Surface-sterilized bark of Kandelia candel from Cotai Ecological Zones
[Ref.: #67770]	Host species	Kandelia candel
[Ref.: #67770]	Geographic location (country and/or sea, region)	Macao
[Ref.: #67770]	Country	China
[Ref.: #67770]	Country ISO 3 Code	CHN
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Host	#Plants	#Shrub (Scrub)
#Host	#Plants	#Tree
#Host Body-Site	#Plant	#Bark
#Host Body-Site	#Plant	#Sterilized plant part

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence KT971019 (>99% sequence identity) for Nakamurella endophytica subclade from Microbeatlas

Aquatic Samples	52
Soil Samples	599
Animal Samples	43
Plant Samples	115
Total Samples	809

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

[Ref.: #24244]

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.: #24244]	Nakamurella endophytica strain 2Q3S-4-2 16S ribosomal RNA gene, partial sequence	KT971019	1475	ENA	1748367 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Nakamurella endophytica CGMCC 4.7308	GCA_014646215	scaffold	GenBank	1748367 tax ID	*
[Ref.: #66792]	Nakamurella endophytica strain CGMCC 4.7308	1748367.3	wgs	PATRIC	1748367 tax ID	*

[Ref.: #24244]

GC-content

67.8 mol%

high performance liquid chromatography (HPLC)

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Nakamurella endophytica CGMCC 4.7308 NCBI: GCA_014646215.1
[Ref.: #69480]	anaerobic	no	97.681	yes
[Ref.: #69480]	gram-positive	yes	100	yes
[Ref.: #69480]	spore-forming	no	93.962	yes
[Ref.: #69480]	thermophile	no	96.634	no
[Ref.: #69480]	motile	no	96.278	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Nakamurella endophytica CGMCC 4.7308 NCBI: GCA_014646215.1
[Ref.: #69481]	spore-forming	yes	98	no

Availability in culture collections External links

[Ref.: #24244]

Culture collection no.

DSM 100722, CGMCC 4.7308, JCM 31778

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Nakamurella intestinalis sp. nov., isolated from the faeces of Pseudorhynchus japonicus.	Kim SJ, Cho H, Joa JH, Hamada M, Ahn JH, Weon HY, Kwon SW	Int J Syst Evol Microbiol	10.1099/ijsem.0.002059	2017	*
Phylogeny	Nakamurella endophytica sp. nov., a novel endophytic actinobacterium isolated from the bark of Kandelia candel.	Tuo L, Li FN, Pan Z, Lou I, Guo M, Ming-Yuen Lee S, Chen L, Hu L, Sun CH	Int J Syst Evol Microbiol	10.1099/ijsem.0.000923	2016	*

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 )

#24244

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 100722

#43733

Li Tuo, Fei-Na Li, Zhen Pan, Inchio Lou, Min Guo, Simon Ming-Yuen Lee, Li Chen, Lin Hu, Cheng-Hang Sun: Nakamurella endophytica sp. nov., a novel endophytic actinobacterium isolated from the bark of Kandelia candel. IJSEM 66: 1577 - 1582 2016 ( DOI 10.1099/ijsem.0.000923 , PubMed 26813967 )

#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 .

#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 )

* These data were automatically processed and therefore are not curated

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Nakamurella endophytica CGMCC 4.7308

Nakamurella endophytica CGMCC 4.7308

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