Name: Rathayibacter caricis DSM 15933
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 7486

Type strain:

Species: Rathayibacter caricis

Culture col. no.: DSM 15933, UCM Ac-618, VKM Ac-1799, CIP 108056, JCM 13576

Strain history: CIP <- 2003, L. Evtushenko, VKM, Moscow, Russia

NCBI tax ID(s): 1328867 (strain), 110936 (species)

SI-ID 72229

VKM Ac-1799, DSM 15933, JCM 13576, CIP 108056

Section

Rathayibacter caricis DSM 15933 is an obligate aerobe, psychrophilic, Gram-positive bacterium that was isolated from phyllosphere of Carex sp..

Gram-positive
oval-shaped
obligate aerobe
psychrophilic
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	*Micrococcales*
	Family	*Microbacteriaceae*
	Genus	*Rathayibacter*
	Species	**Rathayibacter caricis**
	Full Scientific Name (LPSN)	Rathayibacter caricis Dorofeeva et al. 2002

Information on morphological and physiological properties Morphology

[Ref.: #117184]	Gram stain	positive

[Ref.: #117184]	Cell shape	oval-shaped

[Ref.: #117184]	Motility	no

Information on culture and growth conditions Culture and growth conditions

[Ref.: #6193]

Culture medium

TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)

[Ref.: #6193]

Culture medium growth

[Ref.: #6193]

Culture medium link

Medium recipe at MediaDive

[Ref.: #6193]

Culture medium composition

expand / minimize

[Ref.: #33879]

Culture medium

MEDIUM 263 - for Clavibacter, Rathayibacter ratayi, Nocardiodes plantarum

[Ref.: #33879]

Culture medium growth

[Ref.: #33879]

Culture medium composition

expand / minimize

[Ref.: #117184]

Culture medium

CIP Medium 111

[Ref.: #117184]

Culture medium growth

[Ref.: #117184]

Culture medium link

Medium recipe provided by DSMZ

	Kind of temperature		Temperature
[Ref.: #6193]		growth	24 °C
[Ref.: #33879]		growth	25 °C
[Ref.: #117184]		growth	10-30 °C
[Ref.: #117184]	no	growth	37 °C
[Ref.: #117184]	no	growth	41 °C

[Ref.: #6193]	Temperature range	psychrophilic
[Ref.: #33879]	Temperature range	mesophilic
[Ref.: #117184]	Temperature range	mesophilic
[Ref.: #117184]	Temperature range	thermophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #117184]

Oxygen tolerance

obligate aerobe

	Salt	Tested relation		Salt conc.
[Ref.: #117184]	NaCl		growth	0-4	%
[Ref.: #117184]	NaCl	no	growth	6	%
[Ref.: #117184]	NaCl	no	growth	8	%
[Ref.: #117184]	NaCl	no	growth	10	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #117184]	citrate ChEBI	-	carbon source
[Ref.: #68371]	D-arabinose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-arabitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-fucose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-lyxose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-mannitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-ribose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-sorbitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-tagatose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	erythritol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #117184]	esculin ChEBI	+	hydrolysis
[Ref.: #68371]	galactitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	gluconate ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	glycerol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	glycogen ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #117184]	hippurate ChEBI	-	hydrolysis
[Ref.: #68371]	inulin ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-arabitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-fucose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-sorbose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-xylose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	methyl alpha-D-glucopyranoside ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	methyl alpha-D-mannoside ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	methyl beta-D-xylopyranoside ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	N-acetylglucosamine ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #117184]	nitrate ChEBI	-	reduction
[Ref.: #117184]	nitrate ChEBI	-	respiration
[Ref.: #117184]	nitrite ChEBI	-	reduction
[Ref.: #68371]	Potassium 2-ketogluconate ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	Potassium 5-ketogluconate ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	ribitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #117184]	sodium thiosulfate ChEBI	-	builds gas from
[Ref.: #68371]	starch ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	xylitol ChEBI	-	builds acid from	* from API 50CH acid
	Only first 10 entries are displayed. Click here to see all.

	Antibiotica	Metabolite	Antibiotic sensitivity	Antibiotic resistance
[Ref.: #117184]		0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)	no	yes

	Metabolite production	Metabolite	Production
[Ref.: #117184]		indole ChEBI	no

	Physiological tests	Metabolite	Voges-Proskauer-test	Methylred-test
[Ref.: #117184]		acetoin ChEBI	-
[Ref.: #117184]		glucose ChEBI		-

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #117184]	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.: #117184]	amylase	+
[Ref.: #117184]	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.: #117184]	caseinase	-	3.4.21.50
[Ref.: #117184]	catalase	+	1.11.1.6
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #117184]	DNase	-
[Ref.: #68382]	esterase (C 4)	+		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	+		* from API zym
[Ref.: #117184]	gamma-glutamyltransferase	+	2.3.2.2
[Ref.: #117184]	gelatinase	-
[Ref.: #117184]	lecithinase	-
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #117184]	lipase	-
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #117184]	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.: #117184]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #117184]	oxidase	-
[Ref.: #117184]	phenylalanine ammonia-lyase	-	4.3.1.24
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #117184]	tryptophan deaminase	-
[Ref.: #117184]	tween esterase	-
[Ref.: #117184]	urease	-	3.5.1.5
[Ref.: #68382]	valine arylamidase	-		* from API zym
	Only first 10 entries are displayed. Click here to see all.

API® 50CH acid:

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

	API ID	ControlQ	Acid from glycerolGLY	Acid from erythritolERY	Acid from D-arabinoseDARA	Acid from L-arabinoseLARA	Acid from D-riboseRIB	Acid from D-xyloseDXYL	Acid from L-xyloseLXYL	Acid from D-adonitolADO	Acid from methyl beta-D-xylopyranosideMDX	Acid from D-galactoseGAL	Acid from D-glucoseGLU	Acid from D-fructoseFRU	Acid from D-mannoseMNE	Acid from L-sorboseSBE	Acid from L-rhamnoseRHA	Acid from dulcitolDUL	Acid from inositolINO	Acid from D-mannitolMAN	Acid from D-sorbitolSOR	Acid from methyl alpha-D-mannopyranosideMDM	Acid from methyl alpha-D-glucopyranosideMDG	Acid from N-acetyl-glucosamineNAG	Acid from amygdalinAMY	Acid from arbutinARB	Acid from esculinESC	Acid from salicinSAL	Acid from cellobioseCEL	Acid from maltoseMAL	Acid from lactoseLAC	Acid from melibioseMEL	Acid from sucroseSAC	Acid from trehaloseTRE	Acid from inulinINU	Acid from melezitoseMLZ	Acid from raffinoseRAF	Acid from starchAMD	Acid from glycogenGLYG	Acid from xylitolXLT	Acid from gentiobioseGEN	Acid from turanoseTUR	Acid from D-lyxoseLYX	Acid from D-tagatoseTAG	Acid from D-fucoseDFUC	Acid from L-fucoseLFUC	Acid from D-arabitolDARL	Acid from L-arabitolLARL	Acid from gluconateGNT	Acid from 2-Ketogluconate2KG	Acid from 5-Ketogluconate5KG
[Ref.: #117184]	11187	not determinedn.d.	-	-	-	+/-	-	+/-	-	-	-	+/-	+/-	+/-	+/-	-	+/-	-	+/-	-	-	-	-	-	+/-	+/-	+/-	+/-	+/-	+/-	+/-	+/-	+/-	+/-	-	+/-	+/-	-	-	-	+/-	+/-	-	-	-	-	-	-	-	-	-

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.: #117184]	2564	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.: #117184]	10853	-	+	+	+	-	+	-	-	-	-	+	-	+	+	-	+	+	-	-	-

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

[Ref.: #6193]	Sample type/isolated from	phyllosphere of Carex sp.
[Ref.: #6193]	Host species	Carex
[Ref.: #6193]	Geographic location (country and/or sea, region)	Belgorod region, Central Chernozem Nature Park
[Ref.: #6193]	Country	Russia
[Ref.: #6193]	Country ISO 3 Code	RUS
[Ref.: #6193]	Continent	Europe

[Ref.: #117184]	Sample type/isolated from	Environment, Phyllosphere of Carex sp.
[Ref.: #117184]	Geographic location (country and/or sea, region)	Belgorod
[Ref.: #117184]	Country	Russian Federation
[Ref.: #117184]	Country ISO 3 Code	RUS
[Ref.: #117184]	Continent	Europe
[Ref.: #117184]	Isolation date	1996
* marker position based on {}

Isolation sources categories

#Host	#Plants	#Herbaceous plants (Grass,Crops)
#Host Body-Site	#Plant	#Leaf (Phyllosphere)

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AF159364 (>99% sequence identity) for Rathayibacter from Microbeatlas

Aquatic Samples	191
Soil Samples	271
Animal Samples	671
Plant Samples	456
Total Samples	1589

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

[Ref.: #6193]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #117184]	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.: #6193]	Rathayibacter carexis 16S ribosomal RNA gene, partial sequence	AF159364	1496	ENA	110936 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Rathayibacter caricis DSM 15933	GCA_003044275	contig	GenBank	1328867 tax ID	*
[Ref.: #66792]	Rathayibacter caricis DSM 15933	1328867.3	wgs	PATRIC	1328867 tax ID	*
[Ref.: #66792]	Rathayibacter caricis DSM 15933	2791355017	draft	JGI IMG/M	1328867 tax ID	*

[Ref.: #6193]

GC-content

68 mol%

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Rathayibacter caricis DSM 15933 PATRIC: 1328867.3
[Ref.: #69480]	motile	no	90.831	no
[Ref.: #69480]	gram-positive	yes	93.857	no
[Ref.: #69480]	anaerobic	no	99.62	no
[Ref.: #69480]	halophile	no	83.598	no
[Ref.: #69480]	spore-forming	no	91.56	no
[Ref.: #69480]	glucose-util	yes	87.188	no
[Ref.: #69480]	aerobic	yes	93.688	no
[Ref.: #69480]	flagellated	no	97.751	no
[Ref.: #69480]	thermophile	no	99.44	yes
[Ref.: #69480]	glucose-ferment	no	91.111	no

Availability in culture collections External links

[Ref.: #6193]

Culture collection no.

DSM 15933, UCM Ac-618, VKM Ac-1799, CIP 108056, JCM 13576

[Ref.: #76932]

SI-ID 72229

Literature:

	Title	Authors	Journal	DOI	Year
Phylogeny	Rathayibacter caricis sp. nov. and Rathayibacter festucae sp. nov., isolated from the phyllosphere of Carex sp. and the leaf gall induced by the nematode Anguina graminis on Festuca rubra L., respectively.	Dorofeeva LV, Evtushenko LI, Krausova VI, Karpov AV, Subbotin SA, Tiedje JM	Int J Syst Evol Microbiol	10.1099/00207713-52-6-1917	2002	*
	D-rhamnan and teichuronic acid from the cell wall of Rathayibacter caricis VKM Ac-1799(T).	Shashkov AS, Potekhina NV, Tul'skaya EM, Dmitrenok AS, Senchenkova SN, Dorofeeva LV, Zaychikov VA, Evtushenko LI	Carbohydr Res	10.1016/j.carres.2021.108233	2021	*

References

#6193

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 15933

#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 )

#33879 ; 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) .

#68371

Automatically annotated from API 50CH acid .

#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) .

#76932

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-ID72229.1 )

#117184 Collection of Institut Pasteur ; Curators of the CIP; CIP 108056
* These data were automatically processed and therefore are not curated

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