Name: Pseudoclavibacter endophyticus DSM 29943
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 132433

Type strain:

Species: Pseudoclavibacter endophyticus

Culture col. no.: DSM 29943, CGMCC 1.15081, KCTC 39112, EGI 60007, JCM 30633

Strain history: <- Wenjun Li

NCBI tax ID(s): 1778590 (species)

Section

Pseudoclavibacter endophyticus DSM 29943 is an aerobe, Gram-positive, rod-shaped bacterium that forms circular colonies and was isolated from surface-sterilized healthy roots of Glycyrrhiza uralensis F..

colony-forming
Gram-positive
rod-shaped
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	*Micrococcales*
	Family	*Microbacteriaceae*
	Genus	*Pseudoclavibacter*
	Species	**Pseudoclavibacter endophyticus**
	Full Scientific Name (PNU)	Pseudoclavibacter endophyticus Li et al. 2016

Information on morphological and physiological properties Morphology

[Ref.: #43744]	Gram stain	positive
[Ref.: #43744]	Cell length	1.1-2.3 µm
[Ref.: #43744]	Cell width	0.4-0.6 µm
[Ref.: #43744]	Cell shape	rod-shaped
[Ref.: #43744]	Motility	no

[Ref.: #43744]	Colony color	White, opaque
[Ref.: #43744]	Colony shape	circular
[Ref.: #43744]	Incubation period	7 days
[Ref.: #43744]	Cultivation medium used	R2A agar

Information on culture and growth conditions Culture and growth conditions

[Ref.: #43744]

Culture medium

GYEA

[Ref.: #43744]

Culture medium growth

[Ref.: #43744]

Culture medium

LB (Luria-Bertani) MEDIUM

[Ref.: #43744]

Culture medium growth

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Culture medium

Reasoner's 2A agar (R2A)

[Ref.: #43744]

Culture medium growth

[Ref.: #43744]

Culture medium

Trypticase Soy Agar (TSA)

[Ref.: #43744]

Culture medium growth

[Ref.: #24222]

Culture medium

TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)

[Ref.: #24222]

Culture medium growth

[Ref.: #24222]

Culture medium link

Medium recipe provided by DSMZ

[Ref.: #24222]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #24222]	growth	28 °C
[Ref.: #43744]	growth	10-60 °C
[Ref.: #43744]	optimum	25-35 °C
[Ref.: #67770]	growth	28 °C
[Ref.: #67771]	growth	28 °C

[Ref.: #24222]	Temperature range	mesophilic
[Ref.: #43744]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic
[Ref.: #67771]	Temperature range	mesophilic

	pH	Kind of pH		pH	pH range
[Ref.: #43744]			optimum	8
[Ref.: #43744]			growth	7-9	alkaliphile

Information on physiology and metabolism Physiology and metabolism

[Ref.: #43744]	Oxygen tolerance	aerobe
[Ref.: #67771]	Oxygen tolerance	aerobe

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #43744]		NaCl		growth	0-11	%(w/v)
[Ref.: #43744]		NaCl		optimum	4	%(w/v)

[Ref.: #67770]

Observation

quinones: MK-9

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #43744]	(S)-lactate ChEBI	-	respiration
[Ref.: #43744]	2-hydroxybutyrate ChEBI	-	respiration
[Ref.: #43744]	2-oxobutanoate ChEBI	-	respiration
[Ref.: #43744]	2-oxoglutarate ChEBI	-	respiration
[Ref.: #43744]	4-hydroxyphenylacetic acid ChEBI	+	respiration
[Ref.: #43744]	acetate ChEBI	+	respiration
[Ref.: #43744]	acetoacetate ChEBI	+	respiration
[Ref.: #43744]	arabinose ChEBI	-	builds acid from
[Ref.: #43744]	beta-hydroxybutyrate ChEBI	+	respiration
[Ref.: #43744]	citrate ChEBI	-	respiration
[Ref.: #43744]	D-fructose ChEBI	-	builds acid from
[Ref.: #43744]	D-fructose ChEBI	+	respiration
[Ref.: #43744]	D-fructose 6-phosphate ChEBI	-	respiration
[Ref.: #43744]	D-gluconate ChEBI	-	respiration
[Ref.: #43744]	D-glucose 6-phosphate ChEBI	-	respiration
[Ref.: #43744]	D-malate ChEBI	-	respiration
[Ref.: #43744]	D-mannitol ChEBI	+	respiration
[Ref.: #43744]	D-mannose ChEBI	-	builds acid from
[Ref.: #43744]	D-xylose ChEBI	-	builds acid from
[Ref.: #43744]	esculin ChEBI	+	fermentation
[Ref.: #43744]	formate ChEBI	+	respiration
[Ref.: #43744]	gelatin ChEBI	-	hydrolysis
[Ref.: #43744]	glucose ChEBI	-	builds acid from
[Ref.: #43744]	glycerol ChEBI	-	builds acid from
[Ref.: #43744]	glycerol ChEBI	-	respiration
[Ref.: #43744]	L-aspartate ChEBI	+	respiration
[Ref.: #43744]	L-glutamate ChEBI	+	respiration
[Ref.: #43744]	L-malate ChEBI	-	respiration
[Ref.: #43744]	mannitol ChEBI	-	builds acid from
[Ref.: #43744]	melibiose ChEBI	-	builds acid from
[Ref.: #43744]	methyl pyruvate ChEBI	-	respiration
[Ref.: #43744]	myo-inositol ChEBI	-	builds acid from
[Ref.: #43744]	myo-inositol ChEBI	-	respiration
[Ref.: #43744]	N-acetylglucosamine ChEBI	-	builds acid from
[Ref.: #43744]	N-acetylglucosamine ChEBI	-	respiration
[Ref.: #43744]	pectin ChEBI	-	respiration
[Ref.: #43744]	propionate ChEBI	-	respiration
[Ref.: #43744]	rhamnose ChEBI	-	builds acid from
[Ref.: #43744]	sorbitol ChEBI	-	builds acid from
[Ref.: #43744]	sucrose ChEBI	-	builds acid from
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Antibiotic sensitivity
[Ref.: #43744]	1 % sodium lactate	yes
[Ref.: #43744]	aztreonam ChEBI	yes
[Ref.: #43744]	lincomycin ChEBI	yes
[Ref.: #43744]	nalidixic acid ChEBI	yes
[Ref.: #43744]	potassium tellurite ChEBI	yes
[Ref.: #43744]	sodium bromate ChEBI	yes
[Ref.: #43744]	sodium butyrate ChEBI	yes
[Ref.: #43744]	tetrazolium violet ChEBI	yes
[Ref.: #43744]	troleandomycin ChEBI	yes

	Metabolite production	Metabolite
[Ref.: #43744]		indole ChEBI

	Enzyme	Enzyme activity	EC number
[Ref.: #43744]	acid phosphatase	-	3.1.3.2
[Ref.: #43744]	alkaline phosphatase	-	3.1.3.1
[Ref.: #43744]	alpha-galactosidase	-	3.2.1.22
[Ref.: #43744]	alpha-glucosidase	-	3.2.1.20
[Ref.: #43744]	alpha-mannosidase	-	3.2.1.24
[Ref.: #43744]	beta-D-fucosidase	-	3.2.1.38
[Ref.: #43744]	beta-galactosidase	-	3.2.1.23
[Ref.: #43744]	beta-glucosidase	+	3.2.1.21
[Ref.: #43744]	beta-glucuronidase	-	3.2.1.31
[Ref.: #43744]	catalase	+	1.11.1.6
[Ref.: #43744]	chymotrypsin	+	3.4.4.5
[Ref.: #43744]	cystine arylamidase	+	3.4.11.3
[Ref.: #43744]	cytochrome oxidase	-	1.9.3.1
[Ref.: #43744]	esterase (C 4)	+
[Ref.: #43744]	esterase Lipase (C 8)	+
[Ref.: #43744]	gelatinase	-
[Ref.: #43744]	leucine arylamidase	+	3.4.11.1
[Ref.: #43744]	lipase (C 14)	-
[Ref.: #43744]	N-acetyl-beta-glucosaminidase	-	3.2.1.52
[Ref.: #43744]	naphthol-AS-BI-phosphohydrolase	+
[Ref.: #43744]	trypsin	-	3.4.21.4
[Ref.: #43744]	urease	-	3.5.1.5
[Ref.: #43744]	valine arylamidase	+
	Only first 10 entries are displayed. Click here to see all.

Fatty acid profile

Metadata FA analysis

Reference

[Ref.: #43744]

Fatty acid	Percentage
C18:1ω7c / C18:1ω6c	18.3
C17:0cyclo	13
C16:0	11.6
C12:0	10.9
C19:0ω8c-cyclo	9.3
C16:1ω7c / C16:1ω6c	8.2
C12:0 3OH	2.8
C10:0 3OH	1.1
C17:1ω8c	0.9
C17:0	0.8
C14:0	0.8
C18:0	0.6
C16:1ω5c	0.5
C18:1ω9c	0.4
C11:0 iso 3OH	0.3

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

[Ref.: #24222]	Sample type/isolated from	surface-sterilized healthy roots of Glycyrrhiza uralensis F.
[Ref.: #24222]	Host species	Glycyrrhiza uralensis
[Ref.: #24222]	Geographic location (country and/or sea, region)	Xinjiang Province, Yili County (43.39° N 83.84° E)
[Ref.: #24222]	Country	China
[Ref.: #24222]	Country ISO 3 Code	CHN
[Ref.: #24222]	Continent	Asia
[Ref.: #24222]	Geographic location	43.3900°/83.8400°

[Ref.: #43744]	Sample type/isolated from	Healthy root of Glycyrrhiza uralensis F. collected from Yili County
[Ref.: #43744]	Geographic location (country and/or sea, region)	Yili County, Xinjiang Province
[Ref.: #43744]	Country	China
[Ref.: #43744]	Country ISO 3 Code	CHN
[Ref.: #43744]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Healthy roots of Glycyrrhiza uralensis F. from Yili County
[Ref.: #67770]	Host species	Glycyrrhiza uralensis
[Ref.: #67770]	Geographic location (country and/or sea, region)	Xinjiang Province, north-west China
[Ref.: #67770]	Country	China
[Ref.: #67770]	Country ISO 3 Code	CHN
[Ref.: #67770]	Continent	Asia

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

Isolation sources categories

#Host Body-Site	#Plant	#Sterilized plant part
#Host	#Plants	#Herbaceous plants (Grass,Crops)
#Host Body-Site	#Plant	#Root (Rhizome)

What are isolation sources categories?

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

[Ref.: #24222]

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.: #24222]	Pseudoclavibacter endophyticus strain EGI 60007 16S ribosomal RNA gene, partial sequence	KP721484	1490	ENA	1778590 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Pseudoclavibacter endophyticus CGMCC 1.15081	GCA_014640595	contig	GenBank	1778590 tax ID	*
[Ref.: #66792]	Pseudoclavibacter endophyticus strain CGMCC 1.15081	1778590.4	wgs	PATRIC	1778590 tax ID	*
[Ref.: #67770]	Pseudoclavibacter endophyticus EGI 60007	GCA_008831085	contig	GenBank	1778590 tax ID
[Ref.: #66792]	Klebsiella pneumoniae 21072123	GCA_024160045	contig	PATRIC	573 tax ID	*

[Ref.: #24222]

GC-content

63.3 mol%

high performance liquid chromatography (HPLC)

Availability in culture collections External links

[Ref.: #24222]

Culture collection no.

DSM 29943, CGMCC 1.15081, KCTC 39112, EGI 60007, JCM 30633

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Pseudoclavibacter endophyticus sp. nov., isolated from roots of Glycyrrhiza uralensis.	Li YQ, Li L, Fu YS, Cui ZQ, Duan YQ, Salam N, Guo JW, Chen W, Li WJ	Int J Syst Evol Microbiol	10.1099/ijsem.0.000876	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 )

#24222

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 29943

#43744

Yan-Qiong Li, Li Li, Yu-Song Fu, Zhao-Qiong Cui, Yan-Qing Duan, Nimaichand Salam, Jian-Wei Guo, Wei Chen, Wen-Jun Li: Pseudoclavibacter endophyticus sp. nov., isolated from roots of Glycyrrhiza uralensis. IJSEM 66: 1287 - 1292 2016 ( DOI 10.1099/ijsem.0.000876 , PubMed 26739161 )

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

#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) .

* These data were automatically processed and therefore are not curated

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