Name: Pseudogracilibacillus endophyticus DT7-02
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 158768

Type strain:

Species: Pseudogracilibacillus endophyticus

Strain Designation: DT7-02

Culture col. no.: KCTC 33854, JCM 31192

Strain history: <- Seung Bum Kim, Chungnam National Univ.

NCBI tax ID(s): 1534102 (species)

Section

Pseudogracilibacillus endophyticus DT7-02 is an aerobe, spore-forming, Gram-positive bacterium that forms circular colonies and was isolated from inner root of evening primrose .

colony-forming
Gram-positive
motile
rod-shaped
spore-forming
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	*Bacillota*
	Class	*Bacilli*
	Order	*Caryophanales*
	Family	*Bacillaceae*
	Genus	*Pseudogracilibacillus*
	Species	**Pseudogracilibacillus endophyticus**
	Full Scientific Name (LPSN)	Pseudogracilibacillus endophyticus Park et al. 2018

Information on morphological and physiological properties Morphology

[Ref.: #65523]	Gram stain	positive
[Ref.: #67771]	Gram stain	positive

[Ref.: #65523]	Cell length	1.8-2.6 µm

[Ref.: #65523]	Cell width	0.7 µm

[Ref.: #65523]	Cell shape	rod-shaped
[Ref.: #67771]	Cell shape	rod-shaped

[Ref.: #65523]	Motility	yes
[Ref.: #67771]	Motility	yes

[Ref.: #65523]	Colony color	pinkish-yellow
[Ref.: #65523]	Colony shape	circular
[Ref.: #65523]	Incubation period	3 days
[Ref.: #65523]	Cultivation medium used	TSA

Information on culture and growth conditions Culture and growth conditions

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Culture medium

TSB

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Culture medium growth

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Culture medium

PYE

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Culture medium growth

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Culture medium

Trypticase Soy Agar (TSA)

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Culture medium growth

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Culture medium composition

expand / minimize

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Culture medium

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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

		Temperature
[Ref.: #65523]	growth	20-44 °C
[Ref.: #65523]	optimum	40 °C
[Ref.: #67770]	growth	40 °C
[Ref.: #67771]	growth	40 °C

[Ref.: #65523]	Temperature range	thermophilic
[Ref.: #67770]	Temperature range	thermophilic
[Ref.: #67771]	Temperature range	thermophilic

	pH	Kind of pH		pH
[Ref.: #65523]			optimum	8-9
[Ref.: #65523]			growth	7-10

Information on physiology and metabolism Physiology and metabolism

[Ref.: #65523]	Oxygen tolerance	aerobe
[Ref.: #67771]	Oxygen tolerance	aerobe

[Ref.: #65523]	Spore description	spherical
[Ref.: #65523]	Ability of spore formation	yes
[Ref.: #67771]	Type of spore	endospore
[Ref.: #67771]	Ability of spore formation	yes

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Halophily / tolerance level

moderately halophilic

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #65523]		NaCl		growth	0-8	%(w/v)
[Ref.: #65523]		NaCl		optimum	4	%(w/v)

[Ref.: #67770]	Observation	quinones: MK-7
[Ref.: #67771]	Observation	quinones: MK-7

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #65523]	adipate ChEBI	-	assimilation
[Ref.: #65523]	amygdalin ChEBI	-	builds acid from
[Ref.: #65523]	arbutin ChEBI	-	builds acid from
[Ref.: #65523]	cellobiose ChEBI	-	builds acid from
[Ref.: #65523]	D-arabinose ChEBI	+	builds acid from
[Ref.: #65523]	D-arabitol ChEBI	-	builds acid from
[Ref.: #65523]	D-fructose ChEBI	+	builds acid from
[Ref.: #65523]	D-fucose ChEBI	-	builds acid from
[Ref.: #65523]	D-galactose ChEBI	+	builds acid from
[Ref.: #65523]	D-glucose ChEBI	-	assimilation
[Ref.: #65523]	D-glucose ChEBI	-	builds acid from
[Ref.: #65523]	D-lyxose ChEBI	+	builds acid from
[Ref.: #65523]	D-mannitol ChEBI	-	assimilation
[Ref.: #65523]	D-mannitol ChEBI	-	builds acid from
[Ref.: #65523]	D-mannose ChEBI	-	assimilation
[Ref.: #65523]	D-mannose ChEBI	-	builds acid from
[Ref.: #65523]	D-ribose ChEBI	+	builds acid from
[Ref.: #65523]	D-sorbitol ChEBI	-	builds acid from
[Ref.: #65523]	D-tagatose ChEBI	+	builds acid from
[Ref.: #65523]	D-trehalose ChEBI	-	builds acid from
[Ref.: #65523]	D-xylose ChEBI	+	builds acid from
[Ref.: #65523]	decanoate ChEBI	-	assimilation
[Ref.: #65523]	erythritol ChEBI	-	builds acid from
[Ref.: #65523]	esculin ChEBI	+	hydrolysis
[Ref.: #65523]	esculin ferric citrate	+	builds acid from
[Ref.: #65523]	galactitol ChEBI	-	builds acid from
[Ref.: #65523]	gelatin ChEBI	-	hydrolysis
[Ref.: #65523]	gentiobiose ChEBI	-	builds acid from
[Ref.: #65523]	glucose ChEBI	-	fermentation
[Ref.: #65523]	glycerol ChEBI	+	builds acid from
[Ref.: #65523]	glycogen ChEBI	-	builds acid from
[Ref.: #65523]	inulin ChEBI	-	builds acid from
[Ref.: #65523]	L-arabinose ChEBI	-	assimilation
[Ref.: #65523]	L-arabinose ChEBI	+	builds acid from
[Ref.: #65523]	L-arabitol ChEBI	-	builds acid from
[Ref.: #65523]	L-fucose ChEBI	-	builds acid from
[Ref.: #65523]	L-rhamnose ChEBI	-	builds acid from
[Ref.: #65523]	L-sorbose ChEBI	+	builds acid from
[Ref.: #65523]	L-xylose ChEBI	+	builds acid from
[Ref.: #65523]	lactose ChEBI	-	builds acid from
[Ref.: #65523]	malate ChEBI	-	assimilation
[Ref.: #65523]	maltose ChEBI	-	assimilation
[Ref.: #65523]	maltose ChEBI	-	builds acid from
[Ref.: #65523]	melezitose ChEBI	-	builds acid from
[Ref.: #65523]	melibiose ChEBI	-	builds acid from
[Ref.: #65523]	methyl alpha-D-glucopyranoside ChEBI	-	builds acid from
[Ref.: #65523]	methyl alpha-D-mannoside ChEBI	-	builds acid from
[Ref.: #65523]	methyl beta-D-xylopyranoside ChEBI	-	builds acid from
[Ref.: #65523]	myo-inositol ChEBI	-	builds acid from
[Ref.: #65523]	N-acetylglucosamine ChEBI	-	assimilation
[Ref.: #65523]	N-acetylglucosamine ChEBI	-	builds acid from
[Ref.: #65523]	nitrate ChEBI	+	reduction
[Ref.: #65523]	phenylacetate ChEBI	-	assimilation
[Ref.: #65523]	potassium 2-dehydro-D-gluconate	+	builds acid from
[Ref.: #65523]	potassium 5-dehydro-D-gluconate	+	builds acid from
[Ref.: #65523]	potassium gluconate ChEBI	-	assimilation
[Ref.: #65523]	potassium gluconate ChEBI	-	builds acid from
[Ref.: #65523]	raffinose ChEBI	-	builds acid from
[Ref.: #65523]	ribitol ChEBI	-	builds acid from
[Ref.: #65523]	salicin ChEBI	-	builds acid from
[Ref.: #65523]	sodium citrate ChEBI	-	assimilation
[Ref.: #65523]	starch ChEBI	-	builds acid from
[Ref.: #65523]	sucrose ChEBI	-	builds acid from
[Ref.: #65523]	turanose ChEBI	+	builds acid from
[Ref.: #65523]	xylitol ChEBI	-	builds acid from
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #65523]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #65523]	acid phosphatase	-	3.1.3.2
[Ref.: #65523]	alkaline phosphatase	-	3.1.3.1
[Ref.: #65523]	alpha-chymotrypsin	+	3.4.21.1
[Ref.: #65523]	alpha-fucosidase	-	3.2.1.51
[Ref.: #65523]	alpha-galactosidase	-	3.2.1.22
[Ref.: #65523]	alpha-glucosidase	-	3.2.1.20
[Ref.: #65523]	alpha-mannosidase	-	3.2.1.24
[Ref.: #65523]	arginine dihydrolase	-	3.5.3.6
[Ref.: #65523]	beta-galactosidase	-	3.2.1.23
[Ref.: #65523]	beta-glucosidase	-	3.2.1.21
[Ref.: #65523]	beta-glucuronidase	-	3.2.1.31
[Ref.: #65523]	catalase	+	1.11.1.6
[Ref.: #65523]	cystine arylamidase	-	3.4.11.3
[Ref.: #65523]	cytochrome oxidase	+	1.9.3.1
[Ref.: #65523]	esterase (C 4)	+
[Ref.: #65523]	esterase Lipase (C 8)	+
[Ref.: #65523]	leucine arylamidase	+	3.4.11.1
[Ref.: #65523]	lipase (C 14)	-
[Ref.: #65523]	N-acetyl-beta-glucosaminidase	+	3.2.1.52
[Ref.: #65523]	naphthol-AS-BI-phosphohydrolase	+
[Ref.: #65523]	trypsin	+	3.4.21.4
[Ref.: #65523]	urease	-	3.5.1.5
[Ref.: #65523]	valine arylamidase	+
	Only first 10 entries are displayed. Click here to see all.

Fatty acid profile

Metadata FA analysis

Reference

[Ref.: #65523]

Fatty acid	Percentage
C15:0 anteiso	47.7
C17:0 anteiso	24.8
C16:0 iso	15.7
C16:0	2.5
C14:0 iso	2.1
C15:0 iso	1.7

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

[Ref.: #65523]	Sample type/isolated from	inner root of evening primrose (Oenothera biennis)
[Ref.: #65523]	Enrichment culture	TSA
[Ref.: #65523]	Enrichment culture temperature	30 ̊C

[Ref.: #67770]	Sample type/isolated from	Surface-sterilized root of Oenothera biennis (evening primrose)
[Ref.: #67770]	Host species	Oenothera biennis
[Ref.: #67770]	Geographic location (country and/or sea, region)	Daejeon
[Ref.: #67770]	Country	Republic of Korea
[Ref.: #67770]	Country ISO 3 Code	KOR
[Ref.: #67770]	Continent	Asia

[Ref.: #67771]	Sample type/isolated from	From plant root
[Ref.: #67771]	Geographic location (country and/or sea, region)	Daecheongho Lake
[Ref.: #67771]	Country	Republic of Korea
[Ref.: #67771]	Country ISO 3 Code	KOR
[Ref.: #67771]	Continent	Asia
* marker position based on {}

Isolation sources categories

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

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence KM253061 (>99% sequence identity) for Pseudogracilibacillus endophyticus from Microbeatlas

Aquatic Samples	15
Soil Samples	108
Animal Samples	26
Plant Samples	2
Total Samples	151

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.: #65523]	16S rRNA gene sequence	KM253061		GenBank

[Ref.: #65523]	GC-content	35.1 mol%	Thermal denaturation, fluorometry
[Ref.: #67770]	GC-content	35.1 mol%	thermal denaturation, midpoint method (Tm)
[Ref.: #67771]	GC-content	35.1 mol%

Availability in culture collections External links

[Ref.: #65523]

Culture collection no.

KCTC 33854, JCM 31192

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Pseudogracilibacillus endophyticus sp. nov., a moderately thermophilic and halophilic species isolated from plant root.	Park J, Kim MK, Yun BR, Han JH, Kim SB	Int J Syst Evol Microbiol	10.1099/ijsem.0.002475	2017	*

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 )

#65523

Jisun Park, Min-Kyeong Kim, Bo-Ram Yun, Ji-Hye Han and Seung Bum Kim: Pseudogracilibacillus endophyticus sp. nov., a moderately thermophilic and halophilic species isolated from plant root. IJSEM 68: 165 - 169 2018 ( DOI 10.1099/ijsem.0.002475 , PubMed 29125459 )

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

* These data were automatically processed and therefore are not curated

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