Name: Paenibacillus sinopodophylli TEGR-3
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 133264

Type strain:

Species: Paenibacillus sinopodophylli

Strain Designation: TEGR-3

Culture col. no.: CCTCC AB 2016047, KCTC 33807

NCBI tax ID(s): 1837342 (species)

Section

Paenibacillus sinopodophylli TEGR-3 is a spore-forming, mesophilic, Gram-positive bacterium that was isolated from surface-sterilized roots of; Sinopodophyllum hexandrum.

Gram-positive
motile
rod-shaped
spore-forming
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	*Bacillota*
	Class	*Bacilli*
	Order	*Caryophanales*
	Family	*Paenibacillaceae*
	Genus	*Paenibacillus*
	Species	**Paenibacillus sinopodophylli**
	Full Scientific Name (LPSN)	Paenibacillus sinopodophylli Chen et al. 2016

Information on morphological and physiological properties Morphology

[Ref.: #25129]	Gram stain	positive
[Ref.: #69480]	Gram stain	positive Confidence in %100

[Ref.: #25129]	Cell length	2.0-3.1 µm

[Ref.: #25129]	Cell width	0.6-0.9 µm

[Ref.: #25129]	Cell shape	rod-shaped

[Ref.: #25129]	Motility	yes
[Ref.: #69480]	Motility	yes Confidence in %95.374

[Ref.: #25129]	Colony size	1.0-2.0 mm
[Ref.: #25129]	Colony color	white
[Ref.: #25129]	Incubation period	2 days
[Ref.: #25129]	Cultivation medium used	R2A agar

Information on culture and growth conditions Culture and growth conditions

[Ref.: #25129]

Culture medium

Reasoner's 2A agar (R2A)

[Ref.: #25129]

Culture medium growth

	Temperatures	Kind of temperature		Temperature
[Ref.: #25129]		no	growth	33 °C

[Ref.: #25129]

Temperature range

mesophilic

	pH	Kind of pH		pH
[Ref.: #25129]		no	growth	5.5

Information on physiology and metabolism Physiology and metabolism

[Ref.: #25129]	Spore description	Ellipsoidal subterminal or paracentral are formed in swollen sporangia
[Ref.: #25129]	Type of spore	endospore
[Ref.: #25129]	Ability of spore formation	yes
[Ref.: #69481]	Ability of spore formation	yes Confidence in %100
[Ref.: #69480]	Ability of spore formation	yes Confidence in %100

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #25129]	2-dehydro-D-gluconate ChEBI	-	builds acid from
[Ref.: #25129]	4-nitrophenyl beta-D-galactopyranoside hydrolysate	+	hydrolysis
[Ref.: #25129]	5-dehydro-D-gluconate ChEBI	-	builds acid from
[Ref.: #25129]	adipate ChEBI	-	assimilation
[Ref.: #25129]	amygdalin ChEBI	+	builds acid from
[Ref.: #25129]	arbutin ChEBI	+	builds acid from
[Ref.: #25129]	carboxymethylcellulose ChEBI	+	hydrolysis
[Ref.: #25129]	casein	-	hydrolysis
[Ref.: #25129]	cellobiose ChEBI	+	builds acid from
[Ref.: #25129]	citrate ChEBI	-	carbon source
[Ref.: #25129]	D-arabinose ChEBI	-	builds acid from
[Ref.: #25129]	D-arabitol ChEBI	-	builds acid from
[Ref.: #25129]	D-fructose ChEBI	+	builds acid from
[Ref.: #25129]	D-fucose ChEBI	-	builds acid from
[Ref.: #25129]	D-galactose ChEBI	+	builds acid from
[Ref.: #25129]	D-glucose ChEBI	-	builds gas from
[Ref.: #25129]	D-glucose ChEBI	+	assimilation
[Ref.: #25129]	D-glucose ChEBI	+	builds acid from
[Ref.: #25129]	D-lyxose ChEBI	-	builds acid from
[Ref.: #25129]	D-mannitol ChEBI	-	assimilation
[Ref.: #25129]	D-mannitol ChEBI	-	builds acid from
[Ref.: #25129]	D-mannose ChEBI	-	assimilation
[Ref.: #25129]	D-mannose ChEBI	+	builds acid from
[Ref.: #25129]	D-ribose ChEBI	-	builds acid from
[Ref.: #25129]	D-sorbitol ChEBI	-	builds acid from
[Ref.: #25129]	D-tagatose ChEBI	-	builds acid from
[Ref.: #25129]	D-xylose ChEBI	+	builds acid from
[Ref.: #25129]	decanoate ChEBI	-	assimilation
[Ref.: #25129]	erythritol ChEBI	-	builds acid from
[Ref.: #25129]	esculin ChEBI	+	hydrolysis
[Ref.: #25129]	esculin ChEBI	+	builds acid from
[Ref.: #25129]	galactitol ChEBI	-	builds acid from
[Ref.: #25129]	gelatin ChEBI	-	hydrolysis
[Ref.: #25129]	gentiobiose ChEBI	+	builds acid from
[Ref.: #25129]	glucose ChEBI	-	fermentation
[Ref.: #25129]	glycerol ChEBI	-	builds acid from
[Ref.: #25129]	glycogen ChEBI	+	builds acid from
[Ref.: #25129]	inulin ChEBI	-	builds acid from
[Ref.: #25129]	L-arabinose ChEBI	+	assimilation
[Ref.: #25129]	L-arabinose ChEBI	+	builds acid from
[Ref.: #25129]	L-arabitol ChEBI	-	builds acid from
[Ref.: #25129]	L-fucose ChEBI	-	builds acid from
[Ref.: #25129]	L-rhamnose ChEBI	+	builds acid from
[Ref.: #25129]	L-sorbose ChEBI	+	builds acid from
[Ref.: #25129]	L-xylose ChEBI	-	builds acid from
[Ref.: #25129]	lactose ChEBI	+	builds acid from
[Ref.: #25129]	malate ChEBI	-	assimilation
[Ref.: #25129]	maltose ChEBI	+	assimilation
[Ref.: #25129]	maltose ChEBI	+	builds acid from
[Ref.: #25129]	melezitose ChEBI	+	builds acid from
[Ref.: #25129]	melibiose ChEBI	+	builds acid from
[Ref.: #25129]	methyl alpha-D-glucopyranoside ChEBI	+	builds acid from
[Ref.: #25129]	methyl alpha-D-mannoside ChEBI	-	builds acid from
[Ref.: #25129]	methyl beta-D-xylopyranoside ChEBI	+	builds acid from
[Ref.: #25129]	myo-inositol ChEBI	+	builds acid from
[Ref.: #25129]	N-acetylglucosamine ChEBI	-	assimilation
[Ref.: #25129]	N-acetylglucosamine ChEBI	-	builds acid from
[Ref.: #25129]	nitrate ChEBI	-	reduction
[Ref.: #25129]	phenylacetate ChEBI	-	assimilation
[Ref.: #25129]	potassium gluconate ChEBI	-	assimilation
[Ref.: #25129]	potassium gluconate ChEBI	-	builds acid from
[Ref.: #25129]	raffinose ChEBI	+	builds acid from
[Ref.: #25129]	ribitol ChEBI	-	builds acid from
[Ref.: #25129]	salicin ChEBI	+	builds acid from
[Ref.: #25129]	sodium citrate ChEBI	-	assimilation
[Ref.: #25129]	starch ChEBI	+	hydrolysis
[Ref.: #25129]	starch ChEBI	+	builds acid from
[Ref.: #25129]	sucrose ChEBI	+	builds acid from
[Ref.: #25129]	trehalose ChEBI	+	builds acid from
[Ref.: #25129]	tryptophan ChEBI	-	energy source
[Ref.: #25129]	turanose ChEBI	+	builds acid from
[Ref.: #25129]	tyrosine ChEBI	-	hydrolysis
[Ref.: #25129]	xylitol ChEBI	-	builds acid from
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #25129]		acetoin ChEBI	no
[Ref.: #25129]		indole ChEBI	no

	Metabolite	Voges-Proskauer-test	Methylred-test	Indole test
[Ref.: #25129]	acetoin ChEBI	-
[Ref.: #25129]	glucose ChEBI		-
[Ref.: #25129]	indole ChEBI			-

	Enzyme	Enzyme activity	EC number
[Ref.: #25129]	6-phospho-beta-galactosidase	+	3.2.1.85
[Ref.: #25129]	acid phosphatase	+	3.1.3.2
[Ref.: #25129]	alkaline phosphatase	+	3.1.3.1
[Ref.: #25129]	alpha-chymotrypsin	-	3.4.21.1
[Ref.: #25129]	alpha-fucosidase	-	3.2.1.51
[Ref.: #25129]	alpha-galactosidase	+	3.2.1.22
[Ref.: #25129]	alpha-glucosidase	+	3.2.1.20
[Ref.: #25129]	alpha-mannosidase	-	3.2.1.24
[Ref.: #25129]	arginine dihydrolase	-	3.5.3.6
[Ref.: #25129]	beta-glucosidase	+	3.2.1.21
[Ref.: #25129]	beta-glucuronidase	-	3.2.1.31
[Ref.: #25129]	catalase	+	1.11.1.6
[Ref.: #25129]	cystine arylamidase	-	3.4.11.3
[Ref.: #25129]	cytochrome oxidase	-	1.9.3.1
[Ref.: #25129]	esterase (C 4)	+
[Ref.: #25129]	esterase lipase (C 8)	+
[Ref.: #25129]	leucine arylamidase	+	3.4.11.1
[Ref.: #25129]	leucine arylamidase	-	3.4.11.1
[Ref.: #25129]	lipase (C 14)	-
[Ref.: #25129]	N-acetyl-beta-glucosaminidase	-	3.2.1.52
[Ref.: #25129]	naphthol-AS-BI-phosphohydrolase	+
[Ref.: #25129]	trypsin	+	3.4.21.4
[Ref.: #25129]	tryptophan deaminase	-	4.1.99.1
[Ref.: #25129]	urease	-	3.5.1.5
	Only first 10 entries are displayed. Click here to see all.

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

[Ref.: #25129]	Sample type/isolated from	surface-sterilized roots of Sinopodophyllum hexandrum
[Ref.: #25129]	Geographic location (country and/or sea, region)	Taibai Mountain in Shaanxi Province, elevation of 3767m
[Ref.: #25129]	Country	China
[Ref.: #25129]	Country ISO 3 Code	CHN
[Ref.: #25129]	Continent	Asia
[Ref.: #25129]	Geographic location	34.0000°/107.0000°
[Ref.: #25129]	Isolation date	2014-06
* marker position based on {}

Isolation sources categories

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

What are isolation sources categories?

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.: #25129]	Paenibacillus sp. TEGR-3 16S ribosomal RNA gene, partial sequence	KX009022	1478	GenBank	1837342 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Paenibacillus sinopodophylli CCTCC AB 2016047	GCA_005930355	scaffold	GenBank	1837342 tax ID	*
[Ref.: #66792]	Paenibacillus sinopodophylli strain CCTCC AB 2016047	1837342.3	wgs	PATRIC	1837342 tax ID	*
[Ref.: #66792]	Paenibacillus sinopodophylli CCTCC AB 2016047	2925334634	draft	JGI IMG/M	1837342 tax ID	*

[Ref.: #25129]

GC-content

45.2 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: Paenibacillus sinopodophylli CCTCC AB 2016047 NCBI: GCA_005930355.1
[Ref.: #69481]	spore-forming	yes	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Paenibacillus sinopodophylli CCTCC AB 2016047 NCBI: GCA_005930355.1
[Ref.: #69480]	motile	yes	88.086	yes
[Ref.: #69480]	flagellated	yes	86.579	no
[Ref.: #69480]	gram-positive	yes	86.01	no
[Ref.: #69480]	anaerobic	no	99.194	no
[Ref.: #69480]	aerobic	yes	83.558	no
[Ref.: #69480]	halophile	no	93.828	no
[Ref.: #69480]	spore-forming	yes	94.021	yes
[Ref.: #69480]	thermophile	no	99.609	no
[Ref.: #69480]	glucose-util	yes	89.462	yes
[Ref.: #69480]	glucose-ferment	no	89.598	yes

Availability in culture collections External links

[Ref.: #25129]

Culture collection no.

CCTCC AB 2016047, KCTC 33807

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Paenibacillus paridis sp. nov., an endophytic bacterial species isolated from the root of Paris polyphylla Smith var. yunnanensis.	Wang M, Jiang XW, Tang SK, Zhi XY, Yang LL	Int J Syst Evol Microbiol	10.1099/ijsem.0.003997	2020	*
Phylogeny	Paenibacillus sinopodophylli sp. nov., a siderophore-producing endophytic bacterium isolated from roots of Sinopodophyllum hexandrum (Royle) Ying.	Chen C, Xin K, Li M, Li X, Cheng J, Zhang L, Shen X	Int J Syst Evol Microbiol	10.1099/ijsem.0.001458	2016	*
Phylogeny	Paenibacillus luteus sp. nov., isolated from soil.	Zhang Y, Zhuang J, Pang H, Wang Y, Li Y, Zhang J	Int J Syst Evol Microbiol	10.1099/ijsem.0.003475	2019	*

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 )

#25129

C. X. Chen, K.,Li, M.,Li, X.,Cheng, J.,Zhang, L.,Shen, X.: Paenibacillus sinopodophylli sp. nov., a siderophore-producing endophytic bacterium isolated from roots of Sinopodophyllum hexandrum (Royle) Ying. IJSEM 66: 4993 - 4999 2016 ( DOI 10.1099/ijsem.0.001458 , PubMed 27565539 )

#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) .

#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 )

* These data were automatically processed and therefore are not curated

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Paenibacillus sinopodophylli CCTCC AB 2016047

Paenibacillus sinopodophylli CCTCC AB 2016047

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