Name: Nocardioides sonneratiae DSM 100390
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 140344

Type strain:

Species: Nocardioides sonneratiae

Culture col. no.: DSM 100390, KCTC 39565, NBRC 110251, BGMRC 0092

Strain history: <- Chenghai Gao, Guangxi Academy of Sciences

NCBI tax ID(s): 1962348 (species)

SI-ID 400348

DSM 100390

Special Collections

Section

Nocardioides sonneratiae DSM 100390 is an aerobe, Gram-positive, rod-shaped bacterium that forms circular colonies and was isolated from branch of Sonneratia apetala.

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

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

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Actinomycetota*
	Class	*Actinomycetes*
	Order	*Propionibacteriales*
	Family	*Nocardioidaceae*
	Genus	*Nocardioides*
	Species	**Nocardioides sonneratiae**
	Full Scientific Name (LPSN)	Nocardioides sonneratiae Li et al. 2017

Information on morphological and physiological properties Morphology

[Ref.: #43845]	Gram stain	positive

[Ref.: #43845]	Cell length	0.9-1.5 µm

[Ref.: #43845]	Cell width	0.3-0.4 µm

[Ref.: #43845]	Cell shape	rod-shaped

[Ref.: #43845]	Motility	no

[Ref.: #43845]	Colony size	1-2 mm
[Ref.: #43845]	Colony color	light ivory
[Ref.: #43845]	Colony shape	circular
[Ref.: #43845]	Incubation period	4 days
[Ref.: #43845]	Cultivation medium used	R2A agar

Information on culture and growth conditions Culture and growth conditions

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Culture medium

BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)

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Culture medium growth

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Culture medium link

Medium recipe provided by DSMZ

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Culture medium

ISP 2 agar

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Culture medium growth

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Culture medium

ISP 2 agar

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Culture medium growth

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Culture medium composition

expand / minimize

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Culture medium

ISP 4 agar

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Culture medium growth

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Culture medium

ISP 5 agar

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Culture medium growth

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Culture medium

ISP 7 agar

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Culture medium growth

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Culture medium

Nutrient agar (NA)

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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

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Culture medium

Reasoner's 2A agar (R2A)

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Culture medium growth

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Culture medium composition

expand / minimize

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Culture medium

Tryptic soy agar

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Culture medium growth

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Culture medium composition

expand / minimize

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Culture medium

MODIFIED BACTO MARINE BROTH (DSMZ Medium 514d)

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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

ISP 3 agar

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Culture medium growth

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Culture medium

Tryptic soy agar

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Culture medium growth

		Temperature
[Ref.: #42951]	growth	28 °C
[Ref.: #43845]	growth	15-32 °C
[Ref.: #43845]	optimum	28 °C
[Ref.: #67771]	growth	30 °C

	pH	Kind of pH		pH
[Ref.: #43845]			optimum	7.0-7.5
[Ref.: #43845]			growth	6.0-9.0

Information on physiology and metabolism Physiology and metabolism

[Ref.: #43845]	Oxygen tolerance	aerobe
[Ref.: #67771]	Oxygen tolerance	aerobe

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Ability of spore formation

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #43845]		NaCl		growth	0-8	%(w/v)
[Ref.: #43845]		NaCl		optimum	2	%(w/v)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #43845]	(+)-L-lyxitol ChEBI	-	carbon source
[Ref.: #43845]	(S)-lactate ChEBI	+	carbon source
[Ref.: #43845]	2-dehydro-D-gluconate ChEBI	+	carbon source
[Ref.: #43845]	2-hydroxybutyrate ChEBI	+	carbon source
[Ref.: #43845]	2-oxobutanoate ChEBI	+	carbon source
[Ref.: #43845]	2-oxoglutarate ChEBI	+	carbon source
[Ref.: #43845]	3-O-methyl-D-glucose ChEBI	+	carbon source
[Ref.: #43845]	5-dehydro-D-gluconate ChEBI	+	carbon source
[Ref.: #43845]	acetate ChEBI	-	growth
[Ref.: #43845]	acetate ChEBI	+	carbon source
[Ref.: #43845]	acetate ChEBI	+	degradation
[Ref.: #43845]	acetoacetate ChEBI	+	carbon source
[Ref.: #43845]	amygdalin ChEBI	-	carbon source
[Ref.: #43845]	arbutin ChEBI	+	carbon source
[Ref.: #43845]	beta-hydroxybutyrate ChEBI	+	carbon source
[Ref.: #43845]	bromosuccinate ChEBI	+	carbon source
[Ref.: #43845]	cellobiose ChEBI	+	carbon source
[Ref.: #43845]	cellulose ChEBI	-	hydrolysis
[Ref.: #43845]	citrate ChEBI	+	carbon source
[Ref.: #43845]	D-alanine ChEBI	+	carbon source
[Ref.: #43845]	D-arabinose ChEBI	-	carbon source
[Ref.: #43845]	D-arabitol ChEBI	-	carbon source
[Ref.: #43845]	D-arabitol ChEBI	+	carbon source
[Ref.: #43845]	D-aspartate ChEBI	+	carbon source
[Ref.: #43845]	D-fructose ChEBI	+	carbon source
[Ref.: #43845]	D-fucose ChEBI	+	carbon source
[Ref.: #43845]	D-galactonate ChEBI	+	carbon source
[Ref.: #43845]	D-galactose ChEBI	+	carbon source
[Ref.: #43845]	D-galacturonic acid ChEBI	+	carbon source
[Ref.: #43845]	D-glucarate ChEBI	+	carbon source
[Ref.: #43845]	D-gluconate ChEBI	+	carbon source
[Ref.: #43845]	D-glucose ChEBI	+	carbon source
[Ref.: #43845]	D-glucose 6-phosphate ChEBI	+	carbon source
[Ref.: #43845]	D-glucuronate ChEBI	+	carbon source
[Ref.: #43845]	D-malate ChEBI	+	carbon source
[Ref.: #43845]	D-mannitol ChEBI	-	carbon source
[Ref.: #43845]	D-mannose ChEBI	-	carbon source
[Ref.: #43845]	D-ribose ChEBI	-	carbon source
[Ref.: #43845]	D-serine ChEBI	+	carbon source
[Ref.: #43845]	D-sorbitol ChEBI	+	carbon source
[Ref.: #43845]	D-tagatose ChEBI	-	carbon source
[Ref.: #43845]	D-trehalose ChEBI	+	carbon source
[Ref.: #43845]	D-xylose ChEBI	-	carbon source
[Ref.: #43845]	D-xylose ChEBI	+	carbon source
[Ref.: #43845]	erythritol ChEBI	-	carbon source
[Ref.: #43845]	formate ChEBI	+	carbon source
[Ref.: #43845]	galactarate ChEBI	+	carbon source
[Ref.: #43845]	galactitol ChEBI	+	carbon source
[Ref.: #43845]	gamma-aminobutyric acid ChEBI	+	carbon source
[Ref.: #43845]	gamma-cyclodextrin ChEBI	+	carbon source
[Ref.: #43845]	gelatin ChEBI	-	hydrolysis
[Ref.: #43845]	gelatin ChEBI	+	carbon source
[Ref.: #43845]	gentiobiose ChEBI	+	carbon source
[Ref.: #43845]	glucuronamide ChEBI	+	carbon source
[Ref.: #43845]	glycerol ChEBI	+	carbon source
[Ref.: #43845]	glycine-proline ChEBI	+	carbon source
[Ref.: #43845]	glycogen ChEBI	-	carbon source
[Ref.: #43845]	inosine ChEBI	+	carbon source
[Ref.: #43845]	inulin ChEBI	+	carbon source
[Ref.: #43845]	L-arabinose ChEBI	-	carbon source
[Ref.: #43845]	L-arginine ChEBI	+	carbon source
[Ref.: #43845]	L-aspartate ChEBI	+	carbon source
[Ref.: #43845]	L-fucose ChEBI	+	carbon source
[Ref.: #43845]	L-glutamate ChEBI	+	carbon source
[Ref.: #43845]	L-histidine ChEBI	+	carbon source
[Ref.: #43845]	L-malate ChEBI	+	carbon source
[Ref.: #43845]	L-pyroglutamic acid ChEBI	+	carbon source
[Ref.: #43845]	L-rhamnose ChEBI	-	carbon source
[Ref.: #43845]	L-serine ChEBI	+	carbon source
[Ref.: #43845]	L-sorbose ChEBI	+	carbon source
[Ref.: #43845]	lactate ChEBI	+	carbon source
[Ref.: #43845]	lactose ChEBI	-	carbon source
[Ref.: #43845]	lithium chloride ChEBI	+	carbon source
[Ref.: #43845]	maltose ChEBI	-	carbon source
[Ref.: #43845]	melezitose ChEBI	+	carbon source
[Ref.: #43845]	melibiose ChEBI	+	carbon source
[Ref.: #43845]	methyl (R)-lactate ChEBI	+	carbon source
[Ref.: #43845]	methyl alpha-D-glucopyranoside ChEBI	+	carbon source
[Ref.: #43845]	methyl alpha-D-mannoside ChEBI	+	carbon source
[Ref.: #43845]	methyl beta-D-glucopyranoside ChEBI	+	carbon source
[Ref.: #43845]	methyl pyruvate ChEBI	+	carbon source
[Ref.: #43845]	myo-inositol ChEBI	+	carbon source
[Ref.: #43845]	N-acetyl-beta-D-mannosamine ChEBI	+	carbon source
[Ref.: #43845]	N-acetylgalactosamine ChEBI	+	carbon source
[Ref.: #43845]	N-acetylglucosamine ChEBI	+	carbon source
[Ref.: #43845]	n-acetylneuraminate ChEBI	+	carbon source
[Ref.: #43845]	pectin ChEBI	+	carbon source
[Ref.: #43845]	propionate ChEBI	+	carbon source
[Ref.: #43845]	quinate ChEBI	+	carbon source
[Ref.: #43845]	raffinose ChEBI	-	carbon source
[Ref.: #43845]	ribitol ChEBI	-	carbon source
[Ref.: #43845]	salicin ChEBI	-	carbon source
[Ref.: #43845]	stachyose ChEBI	+	carbon source
[Ref.: #43845]	starch ChEBI	-	hydrolysis
[Ref.: #43845]	sucrose ChEBI	-	carbon source
[Ref.: #43845]	turanose ChEBI	+	carbon source
[Ref.: #43845]	tween 20 ChEBI	-	hydrolysis
[Ref.: #43845]	tween 40 ChEBI	+	hydrolysis
[Ref.: #43845]	tween 80 ChEBI	+	hydrolysis
[Ref.: #43845]	xylitol ChEBI	-	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Antibiotic resistance
[Ref.: #43845]	fusidate ChEBI	yes
[Ref.: #43845]	guanidinium chloride ChEBI	yes
[Ref.: #43845]	lincomycin ChEBI	yes
[Ref.: #43845]	lithium chloride ChEBI	yes
[Ref.: #43845]	minocycline ChEBI	yes
[Ref.: #43845]	niaproof ChEBI	yes
[Ref.: #43845]	potassium tellurite ChEBI	yes
[Ref.: #43845]	rifamycin sv ChEBI	yes
[Ref.: #43845]	sodium bromate ChEBI	yes
[Ref.: #43845]	troleandomycin ChEBI	yes
[Ref.: #43845]	vancomycin ChEBI	yes
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #43845]		hydrogen sulfide ChEBI	yes

	Enzyme	Enzyme activity	EC number
[Ref.: #43845]	acid phosphatase	+	3.1.3.2
[Ref.: #43845]	alkaline phosphatase	+	3.1.3.1
[Ref.: #43845]	alpha-galactosidase	+	3.2.1.22
[Ref.: #43845]	alpha-glucosidase	+/-	3.2.1.20
[Ref.: #43845]	alpha-mannosidase	-	3.2.1.24
[Ref.: #43845]	beta-D-fucosidase	-	3.2.1.38
[Ref.: #43845]	beta-galactosidase	-	3.2.1.23
[Ref.: #43845]	beta-glucosidase	-	3.2.1.21
[Ref.: #43845]	beta-glucuronidase	-	3.2.1.31
[Ref.: #43845]	catalase	+	1.11.1.6
[Ref.: #43845]	chymotrypsin	-	3.4.4.5
[Ref.: #43845]	cystine arylamidase	-	3.4.11.3
[Ref.: #43845]	cytochrome oxidase	-	1.9.3.1
[Ref.: #43845]	esterase (C 4)	+
[Ref.: #43845]	esterase Lipase (C 8)	+
[Ref.: #43845]	leucine arylamidase	+/-	3.4.11.1
[Ref.: #43845]	lipase (C 14)	+/-
[Ref.: #43845]	N-acetyl-beta-glucosaminidase	+	3.2.1.52
[Ref.: #43845]	naphthol-AS-BI-phosphohydrolase	+
[Ref.: #43845]	trypsin	-	3.4.21.4
[Ref.: #43845]	urease	+	3.5.1.5
[Ref.: #43845]	valine arylamidase	+/-
	Only first 10 entries are displayed. Click here to see all.

Fatty acid profile

Metadata FA analysis

Reference

[Ref.: #43845]

Fatty acid	Percentage
C16:0 iso	46.5
C18:1ω9c	13.9
C17:1ω8c	8.9
10-methyl C17:0	5.8
C17:0 3OH	3.1
C16:0	3
C17:0	2.4
C17:0 iso	2.4
C15:0 iso	1.9

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

[Ref.: #42951]	Sample type/isolated from	branch of Sonneratia apetala
[Ref.: #42951]	Host species	Sonneratia apetala
[Ref.: #42951]	Geographic location (country and/or sea, region)	Guangxi province, Maowei Sea
[Ref.: #42951]	Country	China
[Ref.: #42951]	Country ISO 3 Code	CHN
[Ref.: #42951]	Continent	Asia
[Ref.: #42951]	Geographic location	21.7481°/108.6040°

[Ref.: #43845]	Sample type/isolated from	branch of Sonneratia apelata collected from Maowei Sea, Guangxi province, China
[Ref.: #43845]	Geographic location (country and/or sea, region)	Maowei Sea, Guangxi province
[Ref.: #43845]	Country	China
[Ref.: #43845]	Country ISO 3 Code	CHN
[Ref.: #43845]	Continent	Asia
[Ref.: #43845]	Geographic location	21.7481°/108.6040°
[Ref.: #43845]	Enrichment culture	M4 medium
[Ref.: #43845]	Enrichment culture composition	1.0 g/L L-aspartic acid, 5.0 g/L trehalose, 1.0 g/L KNO 3, 0.5 g/L K2HPO4, 0.1 g/L NH4NO3, MgSO4.7H2O, 0.5 g/L NaCl, 0.01 g/L FeSO4, 0.001 g/L MnCl2.H2O, 0.001 g/L ZnSO4.7H2O, 13.0 g/L agar, pH 7.2–7.4
[Ref.: #43845]	Enrichment culture duration	2 weeks
[Ref.: #43845]	Enrichment culture temperature	28 ̊C

[Ref.: #67771]	Sample type/isolated from	From Sonneratia apelata
[Ref.: #67771]	Country	China
[Ref.: #67771]	Country ISO 3 Code	CHN
[Ref.: #67771]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Host	#Plants	#Shrub (Scrub)
#Host	#Plants	#Tree
#Host Body-Site	#Plant	#Stem (Branch)

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence KY655023 (>99% sequence identity) for Nocardioides sonneratiae subclade from Microbeatlas

Aquatic Samples	4
Soil Samples	13
Animal Samples
Plant Samples	1
Total Samples	18

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

[Ref.: #42951]

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.: #42951]	Nocardioides sonneratiae strain BGMRC0092 16S ribosomal RNA gene, partial sequence	KY655023	1442	GenBank ENA	1962348 tax ID

[Ref.: #42951]

GC-content

69.3 mol%

high performance liquid chromatography (HPLC)

Availability in culture collections External links

[Ref.: #42951]

Culture collection no.

DSM 100390, KCTC 39565, NBRC 110251, BGMRC 0092

[Ref.: #96643]

SI-ID 400348

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Nocardioides sonneratiae sp. nov., an endophytic actinomycete isolated from a branch of Sonneratia apetala.	Li F, Tuo L, Su ZW, Wei XQ, Zhang XY, Gao CH, Huang RM	Int J Syst Evol Microbiol	10.1099/ijsem.0.001979	2017	*
Phylogeny	Nocardioides coralli sp. nov., an actinobacterium isolated from stony coral in the South China Sea.	Shi SB, Cui LQ, Zeng Q, Long LJ, Tian XP	Int J Syst Evol Microbiol	10.1099/ijsem.0.005342	2022	*

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 )

#42951

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 100390

#43845

Fei Li, Li Tuo, Zhi-wei Su, Xiao-qun Wei, Xiao-Yong Zhang, Cheng-Hai Gao, Ri-Ming Huang: Nocardioides sonneratiae sp. nov., an endophytic actinomycete isolated from a branch of Sonneratia apetala. IJSEM 67: 2592 - 2597 2017 ( DOI 10.1099/ijsem.0.001979 , PubMed 28771135 )

#67771 Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;

#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 .

#96643

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-ID400348.1 )

* These data were automatically processed and therefore are not curated

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