Smaragdicoccus niigatensis Hou_blue | Type strain | DSM 44881, CIP 109538, MBIC 06267, JCM 14666, IFM 10815, NBRC 103563 | BacDiveID:11054

Strain identifier

BacDive ID: 11054

Type strain:

Species: Smaragdicoccus niigatensis

Strain Designation: Hou_blue

Culture col. no.: DSM 44881, CIP 109538, MBIC 06267, JCM 14666, IFM 10815, NBRC 103563

Strain history: CIP <- 2007, DSMZ <- A. Katsuta, MBIC, Iwate, Japan: strain Hou_blue

NCBI tax ID(s): 1123258 (strain), 359359 (species)

SI-ID 297334

DSM 44881, NBRC 103563, JCM 14666, CIP 109538

Section

Smaragdicoccus niigatensis Hou_blue is a mesophilic, Gram-positive, coccus-shaped bacterium that was isolated from oil springs.

coccus-shaped
Gram-positive
mesophilic
16S sequence
Bacteria
genome sequence

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	*Mycobacteriales*
	Family	*Nocardiaceae*
	Genus	*Smaragdicoccus*
	Species	**Smaragdicoccus niigatensis**
	Full Scientific Name (LPSN)	Smaragdicoccus niigatensis Adachi et al. 2007

Information on morphological and physiological properties Morphology

[Ref.: #31777]	Gram stain	positive
[Ref.: #121303]	Gram stain	positive
[Ref.: #69480]	Gram stain	positive Confidence in %100

[Ref.: #31777]	Cell width	0.86 µm

[Ref.: #31777]	Cell shape	coccus-shaped
[Ref.: #121303]	Cell shape	coccus-shaped

[Ref.: #121303]	Motility	no

[Ref.: #19883]	Colony color	Olive green
[Ref.: #19883]	Incubation period	10-14 days
[Ref.: #19883]	Cultivation medium used	ISP 2

[Ref.: #19883]	Colony color	Olive green
[Ref.: #19883]	Incubation period	10-14 days
[Ref.: #19883]	Cultivation medium used	ISP 3

[Ref.: #19883]	Incubation period	10-14 days
[Ref.: #19883]	Cultivation medium used	ISP 4

[Ref.: #19883]	Incubation period	10-14 days
[Ref.: #19883]	Cultivation medium used	ISP 5

[Ref.: #19883]	Incubation period	10-14 days
[Ref.: #19883]	Cultivation medium used	ISP 6

[Ref.: #19883]	Incubation period	10-14 days
[Ref.: #19883]	Cultivation medium used	ISP 7

Pigment production

no

[Ref.: #19883]	Multicellular complex forming ability	no
[Ref.: #19883]	Medium Name (multicellularity)	ISP 2

[Ref.: #19883]	Multicellular complex forming ability	no
[Ref.: #19883]	Medium Name (multicellularity)	ISP 3

[Ref.: #19883]	Multicellular complex forming ability	no
[Ref.: #19883]	Medium Name (multicellularity)	ISP 4

[Ref.: #19883]	Multicellular complex forming ability	no
[Ref.: #19883]	Medium Name (multicellularity)	ISP 5

[Ref.: #19883]	Multicellular complex forming ability	no
[Ref.: #19883]	Medium Name (multicellularity)	ISP 6

[Ref.: #19883]	Multicellular complex forming ability	no
[Ref.: #19883]	Medium Name (multicellularity)	ISP 7

Multimedia content

Caption:

electron microscopic image

Intellectual property rights:

© HZI/Manfred Rohde

Caption:

electron microscopic image

Intellectual property rights:

© HZI/Manfred Rohde

Caption:

electron microscopic image

Intellectual property rights:

© HZI/Manfred Rohde

Caption:

electron microscopic image

Intellectual property rights:

© HZI/Manfred Rohde

Caption:

electron microscopic image

Intellectual property rights:

© HZI/Manfred Rohde

Information on culture and growth conditions Culture and growth conditions

Culture medium

COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)

Culture medium growth

Culture medium link

Medium recipe at MediaDive

Culture medium composition

expand / minimize

Culture medium

MIDDLEBROOK MEDIUM (DSMZ Medium 645)

Culture medium growth

Culture medium link

Medium recipe at MediaDive

Culture medium composition

expand / minimize

Culture medium

ISP 2

Culture medium growth

Culture medium composition

expand / minimize

Culture medium

ISP 3

Culture medium growth

Culture medium composition

expand / minimize

Culture medium

ISP 4

Culture medium growth

Culture medium composition

expand / minimize

Culture medium

ISP 5

Culture medium growth

Culture medium composition

expand / minimize

Culture medium

ISP 6

Culture medium growth

Culture medium composition

expand / minimize

Culture medium

ISP 7

Culture medium growth

Culture medium composition

expand / minimize

[Ref.: #121303]

Culture medium

CIP Medium 93

[Ref.: #121303]

Culture medium growth

[Ref.: #121303]

Culture medium link

Medium recipe provided by DSMZ

	Temperatures	Kind of temperature		Temperature
[Ref.: #12166]			growth	30 °C
[Ref.: #19883]			optimum	28 °C
[Ref.: #31777]			growth	04-37 °C
[Ref.: #31777]			optimum	20.5 °C
[Ref.: #67770]			growth	28 °C

[Ref.: #12166]	Temperature range	mesophilic
[Ref.: #19883]	Temperature range	mesophilic
[Ref.: #31777]	Temperature range	psychrophilic
[Ref.: #67770]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #31777]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.897

	Metabolite utilization	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68369]		adipate ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]		arginine ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #68369]		D-glucose ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]		D-glucose ChEBI	-	fermentation	* from API 20NE, API Coryne
[Ref.: #68369]		D-mannitol ChEBI	-	assimilation	* from API 20NE
[Ref.: #68379]		D-mannitol ChEBI	-	fermentation	* from API Coryne
[Ref.: #68369]		D-mannose ChEBI	-	assimilation	* from API 20NE
[Ref.: #68379]		D-ribose ChEBI	-	fermentation	* from API Coryne
[Ref.: #68379]		D-xylose ChEBI	-	fermentation	* from API Coryne
[Ref.: #68369]		decanoate ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]		esculin ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #31777]		fructose ChEBI	+	carbon source
[Ref.: #68369]		gelatin ChEBI	-	hydrolysis	* from API 20NE, API Coryne
[Ref.: #68369]		gluconate ChEBI	-	assimilation	* from API 20NE
[Ref.: #31777]		glucose ChEBI	+	carbon source
[Ref.: #68379]		glycogen ChEBI	-	fermentation	* from API Coryne
[Ref.: #68369]		L-arabinose ChEBI	-	assimilation	* from API 20NE
[Ref.: #68379]		lactose ChEBI	-	fermentation	* from API Coryne
[Ref.: #68369]		malate ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]		maltose ChEBI	-	assimilation	* from API 20NE
[Ref.: #68379]		maltose ChEBI	-	fermentation	* from API Coryne
[Ref.: #68369]		N-acetylglucosamine ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]		nitrate ChEBI	-	reduction	* from API 20NE, API Coryne
[Ref.: #31777]		sucrose ChEBI	+	carbon source
[Ref.: #68379]		sucrose ChEBI	-	fermentation	* from API Coryne
[Ref.: #68369]		tryptophan ChEBI	-	energy source	* from API 20NE
[Ref.: #68379]		urea ChEBI	+	hydrolysis	* from API Coryne
		Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #68369]		indole ChEBI	no	* from API 20NE

	Physiological tests	Metabolite	Indole test
[Ref.: #68369]		indole ChEBI	-	* from API 20NE

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #68379]		alkaline phosphatase	+	3.1.3.1	* from API Coryne
[Ref.: #68382]		alpha-fucosidase	-	3.2.1.51	* from API zym
[Ref.: #68379]		alpha-glucosidase	+	3.2.1.20	* from API Coryne
[Ref.: #68382]		alpha-mannosidase	-	3.2.1.24	* from API zym
[Ref.: #68369]		arginine dihydrolase	-	3.5.3.6	* from API 20NE
[Ref.: #68379]		beta-galactosidase	-	3.2.1.23	* from API Coryne, API zym
[Ref.: #68369]		beta-glucosidase	-	3.2.1.21	* from API 20NE
[Ref.: #68379]		beta-glucuronidase	-	3.2.1.31	* from API Coryne, API zym
[Ref.: #68382]		esterase (C 4)	+		* from API zym
[Ref.: #68382]		esterase lipase (C 8)	+		* from API zym
[Ref.: #68379]		gelatinase	-		* from API Coryne, API 20NE
[Ref.: #68382]		leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #68379]		N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API Coryne, API zym
[Ref.: #68379]		pyrazinamidase	-	3.5.1.B15	* from API Coryne
[Ref.: #68379]		pyrrolidonyl arylamidase	+	3.4.19.3	* from API Coryne
[Ref.: #68379]		urease	+	3.5.1.5	* from API Coryne
		Only first 10 entries are displayed. Click here to see all.

API® 20NE:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Reduction of nitratesNO3	Indole productionTRP	Fermentation of D-glucoseGLU_ Ferm	Arginine dihydrolaseADH (Arg)	Urease/urea hydrolysisURE	Esculin hydrolysis/beta-GlucosidaseESC	Gelatinase/gelatin hydrolysisGEL	beta-GalactosidasePNPG	Assimilation of D-glucoseGLU_ Assim	Assimilation of L-arabinoseARA	Assimilation of D-mannoseMNE	Assimilation of D-mannitolMAN	Assimilation of N-acetyl-glucosamineNAG	Assimilation of maltoseMAL	Assimilation of gluconateGNT	Assimilation of capric acidCAP	Assimilation adipic acidADI	Assimilation of malic acidMLT	Assimilation of citric acidCIT	Assimilation of phenyl-acetic acidPAC	Cytochrome oxidaseOX
[Ref.: #12166]	24887	-	-	-	-	+/-	-	-	-	-	-	-	-	+	-	-	-	-	+	-	-	not determinedn.d.

API® Coryne:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Reduction of nitrateNIT	PyrazinamidasePYZ	Pyrrolidonyl arylamidasePYRA	Alkaline phosphatasePAL	beta-Glucuronidasebeta GUR	beta-Galactosidasebeta GAL	alpha-Glucosidasealpha GLU	N-Acetyl-beta-Glucosidasebeta NAG	Esculin hydrolysis/beta-GlucosidaseESC	Urease/urea hydrolysisURE	Gelatinase/gelatin hydrolysisGEL	Control fermentationControl	Fermentation of D-glucoseGLU	Fermentation of D-riboseRIB	Fermentation of D-xyloseXYL	Fermentation of D-mannitolMAN	Fermentation of maltoseMAL	Fermentation of lactoseLAC	Fermentation of sucroseSAC	Fermentation of glycogenGLYG	CatalaseCAT
[Ref.: #19883]	362	-	-	+	+	-	-	+	-	+/-	+	-	not determinedn.d.	-	-	-	-	-	-	-	-	not determinedn.d.

API® zym:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Control	2-naphthyl phosphateAlkaline phosphatase	2-naphthyl butyrateEsterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	2-naphthyl myristateLipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	N-benzoyl-DL-arginine-2-naphthylamideTrypsin	N-glutaryl-phenylalanine-2-naphthylamidealpha- Chymotrypsin	2-naphthyl phosphateAcid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	6-Br-2-naphthyl-alphaD-galactpyranosidealpha- Galactosidase	2-naphthyl-betaD-galactpyranosidebeta- Galactosidase	Naphthol-AS-BI-betaD-glucuronidebeta- Glucuronidase	2-naphthyl-alphaD-glucopyranosidealpha- Glucosidase	6-Br-2-naphthyl-betaD-glucopyranosidebeta- Glucosidase	1-naphthyl-N-acetyl-betaD-glucosaminideN-acetyl-beta- glucosaminidase	6-Br-2-naphthyl-alphaD-mannopyranosidealpha- Mannosidase	2-naphthyl-alphaL-fucopyranosidealpha- Fucosidase
[Ref.: #19883]	695	not determinedn.d.	+	+	+	+	+	+	+	+	+	+	+	+	-	-	+	+	-	-	-
[Ref.: #12166]	14195	-	-	+	+	-	+	-	-	-	-	-	+/-	-	-	-	+/-	-	-	-	-

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

[Ref.: #12166]	Sample type/isolated from	oil springs
[Ref.: #12166]	Geographic location (country and/or sea, region)	Niigata
[Ref.: #12166]	Country	Japan
[Ref.: #12166]	Country ISO 3 Code	JPN
[Ref.: #12166]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Soil from an oil spring
[Ref.: #67770]	Geographic location (country and/or sea, region)	Nishiyama-cho, Niigata Pref.
[Ref.: #67770]	Country	Japan
[Ref.: #67770]	Country ISO 3 Code	JPN
[Ref.: #67770]	Continent	Asia

[Ref.: #121303]	Sample type/isolated from	Environment, Oil springs
[Ref.: #121303]	Country	Japan
[Ref.: #121303]	Country ISO 3 Code	JPN
[Ref.: #121303]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Engineered

#Industrial

#Oil reservoir

What are isolation sources categories?

Global distribution of 16S sequence AB243007 (>99% sequence identity) for Smaragdicoccus niigatensis subclade from Microbeatlas

Aquatic Samples	431
Soil Samples	1610
Animal Samples	230
Plant Samples	231
Total Samples	2502

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

[Ref.: #12166]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #19883]	Biosafety level	1	Risk group (German classification)
[Ref.: #121303]	Biosafety level	1	Risk group (French classification)

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.: #31777]	Smaragdicoccus niigatensis gene for 16S rRNA, partial sequence	AB243007	1478	GenBank	359359 tax ID

Genome sequence information:

Only first 5 entries are displayed. Click here to see all.

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Smaragdicoccus niigatensis DSM 44881 = NBRC 103563	GCA_000380645	contig	GenBank	1123258 tax ID
[Ref.: #67770]	Smaragdicoccus niigatensis DSM 44881 = NBRC 103563	GCA_001552795	contig	GenBank	1123258 tax ID
[Ref.: #66792]	Smaragdicoccus niigatensis DSM 44881	1123258.3	wgs	PATRIC	1123258 tax ID	*
[Ref.: #66792]	Smaragdicoccus niigatensis DSM 44881 = NBRC 103563	1123258.7	wgs	PATRIC	1123258 tax ID	*
[Ref.: #66792]	Smaragdicoccus niigatensis DSM 44881	2519103184	draft	JGI IMG/M	1123258 tax ID	*
[Ref.: #66792]	Smaragdicoccus niigatensis NBRC 103563	2731957600	draft	JGI IMG/M	1123258 tax ID	*

[Ref.: #31777]	GC-content	63.7 mol%
[Ref.: #67770]	GC-content	63.7 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 GenomeNet Sporulation v. 1 based on: Smaragdicoccus niigatensis DSM 44881 = NBRC 103563 PATRIC: 1123258.7
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Smaragdicoccus niigatensis DSM 44881 PATRIC: 1123258.3
[Ref.: #69480]	motile	no	95.856	no
[Ref.: #69480]	flagellated	no	98.557	no
[Ref.: #69480]	gram-positive	yes	86.394	yes
[Ref.: #69480]	anaerobic	no	99.142	no
[Ref.: #69480]	aerobic	yes	87.239	no
[Ref.: #69480]	halophile	no	96.603	no
[Ref.: #69480]	spore-forming	no	70.7	no
[Ref.: #69480]	thermophile	no	98.753	no
[Ref.: #69480]	glucose-util	yes	86.515	no
[Ref.: #69480]	glucose-ferment	no	91.026	no

Availability in culture collections External links

Culture collection no.

DSM 44881, CIP 109538, MBIC 06267, JCM 14666, IFM 10815, NBRC 103563

SI-ID 297334

*

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Smaragdicoccus niigatensis gen. nov., sp. nov., a novel member of the suborder Corynebacterineae.	Adachi K, Katsuta A, Matsuda S, Peng X, Misawa N, Shizuri Y, Kroppenstedt RM, Yokota A, Kasai H	Int J Syst Evol Microbiol	10.1099/ijs.0.64254-0	2007	*

References

#12166

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 44881

#19883

Wink, J.: Compendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig .

#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 )

#31777

Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #28050 (see below)

#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) .

#66793

Mukherjee et al.: GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life. 35: 676 - 683 2017 ( DOI 10.1038/nbt.3886 , PubMed 28604660 )

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

#68369

Automatically annotated from API 20NE .

#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 .

#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 )

#80303

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-ID297334.1 )

#121303 Collection of Institut Pasteur ; Curators of the CIP; CIP 109538

#28050

IJSEM 297 2007 ( DOI 10.1099/ijs.0.64254-0 , PubMed 17267967 )

* These data were automatically processed and therefore are not curated

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