Name: Arenibacter troitsensis R3674
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 5483

Type strain:

Species: Arenibacter troitsensis

Strain Designation: R3674

Culture col. no.: DSM 19835, JCM 11736, KMM 3674, NBRC 101532, CIP 108149

Strain history: CIP <- 2003, JCM <- 2002, M. Suzuki: strain R3674 <- KMM <- O.I. Nedashkovskaya

NCBI tax ID(s): 188872 (species)

SI-ID 99609

JCM 11736, CIP 108149, KCTC 12362, NBRC 101532, DSM 19835

Section

Arenibacter troitsensis R3674 is a mesophilic, Gram-negative bacterium that was isolated from bottom sediment sample.

Gram-negative
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	*Bacteroidota*
	Class	*Flavobacteriia*
	Order	*Flavobacteriales*
	Family	*Flavobacteriaceae*
	Genus	*Arenibacter*
	Species	**Arenibacter troitsensis**
	Full Scientific Name (LPSN)	Arenibacter troitsensis Nedashkovskaya et al. 2003

Information on morphological and physiological properties Morphology

[Ref.: #123587]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.989

[Ref.: #123587]	Cell shape	rod-shaped

[Ref.: #123587]	Motility	no

[Ref.: #123587]	Pigment production	no
[Ref.: #123587]	Pigment name	Flexirubin

Information on culture and growth conditions Culture and growth conditions

[Ref.: #8342]

Culture medium

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

[Ref.: #8342]

Culture medium growth

[Ref.: #8342]

Culture medium link

Medium recipe at MediaDive

[Ref.: #8342]

Culture medium composition

expand / minimize

[Ref.: #33895]

Culture medium

Marine agar (MA)

[Ref.: #33895]

Culture medium growth

[Ref.: #33895]

Culture medium composition

expand / minimize

[Ref.: #123587]

Culture medium

CIP Medium 13

[Ref.: #123587]

Culture medium growth

[Ref.: #123587]

Culture medium link

Medium recipe provided by DSMZ

	Kind of temperature		Temperature
[Ref.: #8342]		growth	28 °C
[Ref.: #33895]		growth	25 °C
[Ref.: #67770]		growth	25 °C
[Ref.: #123587]		growth	5-37 °C
[Ref.: #123587]	no	growth	41 °C
[Ref.: #123587]	no	growth	45 °C

[Ref.: #8342]	Temperature range	mesophilic
[Ref.: #33895]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic
[Ref.: #123587]	Temperature range	thermophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.997

	Salt	Tested relation		Salt conc.
[Ref.: #123587]	NaCl	no	growth	0	%
[Ref.: #123587]	NaCl	no	growth	2	%
[Ref.: #123587]	NaCl	no	growth	4	%
[Ref.: #123587]	NaCl	no	growth	6	%
[Ref.: #123587]	NaCl	no	growth	8	%
[Ref.: #123587]	NaCl	no	growth	10	%

[Ref.: #67770]

Observation

quinones: MK-6

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #123587]	esculin ChEBI	+	hydrolysis
[Ref.: #123587]	hippurate ChEBI	-	hydrolysis
[Ref.: #123587]	malonate ChEBI	-	assimilation
[Ref.: #123587]	nitrate ChEBI	-	reduction
[Ref.: #123587]	nitrate ChEBI	-	respiration
[Ref.: #123587]	nitrite ChEBI	-	reduction

	Metabolite production	Metabolite	Production
[Ref.: #123587]		indole ChEBI	no

	Physiological tests	Metabolite	Voges-Proskauer-test	Methylred-test
[Ref.: #123587]		acetoin ChEBI	-
[Ref.: #123587]		glucose ChEBI		-

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #123587]	alcohol dehydrogenase	-	1.1.1.1
[Ref.: #68382]	alkaline phosphatase	+	3.1.3.1	* from API zym
[Ref.: #68382]	alpha-chymotrypsin	-	3.4.21.1	* from API zym
[Ref.: #68382]	alpha-fucosidase	-	3.2.1.51	* from API zym
[Ref.: #68382]	alpha-galactosidase	+	3.2.1.22	* from API zym
[Ref.: #68382]	alpha-glucosidase	-	3.2.1.20	* from API zym
[Ref.: #68382]	alpha-mannosidase	-	3.2.1.24	* from API zym
[Ref.: #123587]	amylase	+
[Ref.: #123587]	beta-galactosidase	+	3.2.1.23
[Ref.: #68382]	beta-galactosidase	-	3.2.1.23	* from API zym
[Ref.: #68382]	beta-glucosidase	+	3.2.1.21	* from API zym
[Ref.: #68382]	beta-glucuronidase	-	3.2.1.31	* from API zym
[Ref.: #123587]	caseinase	+	3.4.21.50
[Ref.: #123587]	catalase	+	1.11.1.6
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #68382]	esterase (C 4)	+		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	+		* from API zym
[Ref.: #123587]	gamma-glutamyltransferase	+	2.3.2.2
[Ref.: #123587]	gelatinase	+/-
[Ref.: #123587]	lecithinase	-
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #123587]	lipase	-
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #123587]	lysine decarboxylase	-	4.1.1.18
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	+	3.2.1.52	* from API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #123587]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #123587]	oxidase	-
[Ref.: #123587]	phenylalanine ammonia-lyase	-	4.3.1.24
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #123587]	tryptophan deaminase	-
[Ref.: #123587]	tween esterase	+
[Ref.: #123587]	urease	-	3.5.1.5
[Ref.: #68382]	valine arylamidase	+		* from API zym
	Only first 10 entries are displayed. Click here to see all.

API® Biotype100:

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

	API ID	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
[Ref.: #123587]	2607	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.: #123587]	10929	-	+	+	+	-	+	+	-	-	-	+	+	+	-	-	-	+	+	-	-

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

[Ref.: #8342]	Sample type/isolated from	bottom sediment sample
[Ref.: #8342]	Geographic location (country and/or sea, region)	Sea of Japan, Gulf of Peter the Great, Troitsa Bay
[Ref.: #8342]	Country	Russia
[Ref.: #8342]	Country ISO 3 Code	RUS
[Ref.: #8342]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Bottom sediment from Troitsa Bay in the Gulf of Peter the Great
[Ref.: #67770]	Geographic location (country and/or sea, region)	Sea of Japan

[Ref.: #123587]	Sample type/isolated from	Environment, Marine bottom sediment
[Ref.: #123587]	Country	Japan
[Ref.: #123587]	Country ISO 3 Code	JPN
[Ref.: #123587]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental

#Terrestrial

#Sediment

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AB681469 (>99% sequence identity) for Arenibacter from Microbeatlas

Aquatic Samples	7063
Soil Samples	1235
Animal Samples	925
Plant Samples	168
Total Samples	9391

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

[Ref.: #8342]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #123587]	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.: #8342]	Arenibacter troitsensis gene for 16S rRNA, partial sequence	AB080771	1381	ENA	188872 tax ID
[Ref.: #20218]	Arenibacter troitsensis gene for 16S rRNA, partial sequence, strain: NBRC 101532	AB681469	1449	ENA	188872 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Arenibacter troitsensis DSM 19835	GCA_900177645	scaffold	GenBank	188872 tax ID	*
[Ref.: #66792]	Arenibacter troitsensis strain DSM 19835	188872.3	wgs	PATRIC	188872 tax ID	*
[Ref.: #66792]	Arenibacter troitsensis DSM 19835	2595699007	draft	JGI IMG/M	188872 tax ID	*

[Ref.: #8342]	GC-content	40.0 mol%
[Ref.: #67770]	GC-content	40 mol%	thermal denaturation, midpoint method (Tm)

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: Arenibacter troitsensis DSM 19835 NCBI: GCA_900177645.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Arenibacter troitsensis DSM 19835 NCBI: GCA_900177645.1
[Ref.: #69480]	motile	no	88.928	no
[Ref.: #69480]	flagellated	no	94.693	no
[Ref.: #69480]	gram-positive	no	97.782	no
[Ref.: #69480]	anaerobic	no	99.673	no
[Ref.: #69480]	aerobic	yes	92.987	no
[Ref.: #69480]	halophile	no	84.599	no
[Ref.: #69480]	spore-forming	no	96.76	no
[Ref.: #69480]	thermophile	no	99.45	yes
[Ref.: #69480]	glucose-util	yes	89.035	no
[Ref.: #69480]	glucose-ferment	no	89.467	no

Availability in culture collections External links

[Ref.: #8342]

Culture collection no.

DSM 19835, JCM 11736, KMM 3674, NBRC 101532, CIP 108149

[Ref.: #74970]

SI-ID 99609

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Arenibacter hampyeongensis sp. nov., a marine bacterium isolated from a tidal flat.	Jeong SH, Jin HM, Kim JM, Jeon CO	Int J Syst Evol Microbiol	10.1099/ijs.0.040683-0	2012	*
Phylogeny	Arenibacter troitsensis sp. nov., isolated from marine bottom sediment.	Nedashkovskaya OI, Suzuki M, Vysotskii MV, Mikhailov VV	Int J Syst Evol Microbiol	10.1099/ijs.0.02384-0	2003	*

References

#8342

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 19835

#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 )

#20218

Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )

#33895 ; Curators of the CIP;

#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;

#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 )

#74970

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-ID99609.1 )

#123587 Collection of Institut Pasteur ; Curators of the CIP; CIP 108149
* These data were automatically processed and therefore are not curated

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Arenibacter troitsensis DSM 19835

Arenibacter troitsensis DSM 19835

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