Name: Paenibacillus sonchi X19-5
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 133511

Type strain:

Species: Paenibacillus sonchi

Strain Designation: X19-5

Culture col. no.: CCBAU 83901, LMG 24727

NCBI tax ID(s): 373687 (species)

SI-ID 358704

LMG 24727

Other strains from Paenibacillus sonchi

P. sonchi DSM 28159, CCGB 1313, CECT 7330, ...

Section

Paenibacillus sonchi X19-5 is an aerobe, spore-forming, Gram-positive bacterium that was isolated from soil.

Gram-positive
motile
rod-shaped
spore-forming
aerobe
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 sonchi**
	Full Scientific Name (LPSN)	Paenibacillus sonchi Hong et al. 2009

Synonym

Paenibacillus riograndensis

Information on morphological and physiological properties Morphology

[Ref.: #29242]	Gram stain	positive
[Ref.: #69480]	Gram stain	positive Confidence in %99.999

[Ref.: #29242]	Cell length	5 µm

[Ref.: #29242]	Cell width	0.5 µm

[Ref.: #29242]	Cell shape	rod-shaped

[Ref.: #29242]	Motility	yes
[Ref.: #69480]	Motility	yes Confidence in %95.416

Information on culture and growth conditions Culture and growth conditions

	Temperatures	Kind of temperature		Temperature
[Ref.: #29242]			growth	10-40 °C
[Ref.: #29242]			optimum	30 °C

[Ref.: #29242]

Temperature range

mesophilic

	pH	Kind of pH		pH
[Ref.: #29242]			optimum	7.1

Information on physiology and metabolism Physiology and metabolism

[Ref.: #29242]

Oxygen tolerance

aerobe

[Ref.: #29242]	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

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #29242]		NaCl		optimum	3	%

	Metabolite utilization	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #29242]		fructose ChEBI	+	carbon source

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

[Ref.: #29242]	Sample type/isolated from	soil
* marker position based on {}

Isolation sources categories

#Environmental

#Terrestrial

#Soil

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence DQ358736 (>99% sequence identity) for Paenibacillus from Microbeatlas

Aquatic Samples	22
Soil Samples	152
Animal Samples	13
Plant Samples	15
Total Samples	202

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.: #29242]	Paenibacillus sonchi strain X19-5 16S ribosomal RNA gene, partial sequence	DQ358736	1516	GenBank	1173684 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Paenibacillus sonchi LMG 24727	GCA_016772475	complete	GenBank	373687 tax ID	*
[Ref.: #66792]	Paenibacillus sonchi X19-5	GCA_000316285	contig	GenBank	1173684 tax ID	*
[Ref.: #66792]	Paenibacillus sonchi X19-5	1173684.3	wgs	PATRIC	1173684 tax ID	*
[Ref.: #66792]	Paenibacillus sonchi strain LMG 24727	373687.11	complete	PATRIC	373687 tax ID	*
[Ref.: #66792]	Paenibacillus sonchi X19-5	2548877040	draft	JGI IMG/M	1173684 tax ID	*

[Ref.: #29242]

GC-content

46.8 mol%

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 sonchi LMG 24727 NCBI: GCA_016772475.1
[Ref.: #69481]	spore-forming	yes	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Paenibacillus sonchi LMG 24727 NCBI: GCA_016772475.1
[Ref.: #69480]	flagellated	yes	83.29	no
[Ref.: #69480]	gram-positive	yes	88.724	yes
[Ref.: #69480]	anaerobic	no	94.5	no
[Ref.: #69480]	aerobic	yes	82.306	yes
[Ref.: #69480]	halophile	no	95.122	no
[Ref.: #69480]	spore-forming	yes	95.892	yes
[Ref.: #69480]	thermophile	no	99.91	yes
[Ref.: #69480]	glucose-util	yes	87.997	no
[Ref.: #69480]	motile	yes	89.318	no
[Ref.: #69480]	glucose-ferment	no	76.46	no

Availability in culture collections External links

[Ref.: #29242]

Culture collection no.

CCBAU 83901, LMG 24727

[Ref.: #91476]

SI-ID 358704

Literature:

Only first 10 entries are displayed. Click here to see all.

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Paenibacillus helianthi sp. nov., a nitrogen fixing species isolated from the rhizosphere of Helianthus annuus L.	Ambrosini A, Sant'Anna FH, Heinzmann J, de Carvalho Fernandes G, Bach E, Passaglia LMP	Antonie Van Leeuwenhoek	10.1007/s10482-018-1135-4	2018	*
Phylogeny	Paenibacillus sonchi sp. nov., a nitrogen-fixing species isolated from the rhizosphere of Sonchus oleraceus.	Hong YY, Ma YC, Zhou YG, Gao F, Liu HC, Chen SF	Int J Syst Evol Microbiol	10.1099/ijs.0.009308-0	2009	*
Genetics	Data on complete genome sequence and annotation of Paenibacillus sonchi LMG 24727(T).	Lee G, Kim MJ, Shin JH	Data Brief	10.1016/j.dib.2021.107271	2021	*
Phylogeny	Reclassification of Paenibacillus riograndensis as a Genomovar of Paenibacillus sonchi: Genome-Based Metrics Improve Bacterial Taxonomic Classification.	Sant'Anna FH, Ambrosini A, de Souza R, de Carvalho Fernandes G, Bach E, Balsanelli E, Baura V, Brito LF, Wendisch VF, de Oliveira Pedrosa F, de Souza EM, Passaglia LMP	Front Microbiol	10.3389/fmicb.2017.01849	2017	*
Phylogeny	Paenibacillus azotifigens sp. nov., a novel nitrogen-fixing bacterium isolated from paddy soil.	Siddiqi MZ, Choi GM, Choi KD, Im WT	Int J Syst Evol Microbiol	10.1099/ijsem.0.002269	2017	*
Phylogeny	Paenibacillus jilunlii sp. nov., a nitrogen-fixing species isolated from the rhizosphere of Begonia semperflorens.	Jin HJ, Zhou YG, Liu HC, Chen SF	Int J Syst Evol Microbiol	10.1099/ijs.0.025056-0	2010	*

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 )

#29242

Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #25662 (see below)

#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) .

#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 )

#91476

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-ID358704.1 )

#25662

IJSEM 2656 2009 ( DOI 10.1099/ijs.0.009308-0 , PubMed 19625436 )

* These data were automatically processed and therefore are not curated

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Paenibacillus sonchi LMG 24727

Paenibacillus sonchi LMG 24727

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