Paenibacillus sonchi (CCBAU 83901, LMG 24727, X19-5)

Name: Paenibacillus sonchi (CCBAU 83901, LMG 24727, X19-5)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 133511

Type strain

Strain Designation X19-5

Culture col. no. CCBAU 83901 LMG 24727 X19-5

NCBI tax ID(s) 373687

Special Collections Literature strains

Links

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

spore-forming Gram-positive motile rod-shaped aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 358704

LMG 24727

@ref 20215

Last LPSN update 2026-02-09 11:31:58

Domain Bacteria

Phylum Bacillota

Class Bacilli

Order Caryophanales

Family Paenibacillaceae

Genus Paenibacillus

Species Paenibacillus sonchi

Full scientific name Paenibacillus sonchi Hong et al. 2009

Synonyms (1)

Paenibacillus riograndensis

BacDive ID	Other strains from **Paenibacillus sonchi** (1)	Type strain
24281	P. sonchi DSM 28159, CCGB 1313, CECT 7330, SBR 5, CIP ...

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility
29242	positive	5 µm	0.5 µm	rod-shaped

Culture and growth conditions

Culture temp

@ref	Growth	Type	Temperature (°C)
29242	positive	growth	10-40
29242	positive	optimum	30

Culture pH

@ref	Ability	Type	PH
29242	positive	optimum	7.1

Physiology and metabolism

Oxygen tolerance

29242

Oxygen toleranceaerobe

Spore formation

@ref	Spore formation	Confidence
29242
125438		91.613
125439		96

Halophily

@ref	Salt	Growth	Tested relation	Concentration
29242	NaCl	positive	optimum	3 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
29242	28757 ChEBI	fructose	+	carbon source

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Soil

Isolation

29242

Sample typesoil

Taxonmaps

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

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM1677247v1 assembly for Paenibacillus sonchi LMG 24727	complete	GCA_016772475	373687.11	8115005262	373687	91.25
66792	Paenibacillus sonchi X19-5T assembly for Paenibacillus sonchi X19-5	contig	GCA_000316285	1173684.3	2548877040	1173684

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
29242	Paenibacillus sonchi strain X19-5 16S ribosomal RNA gene, partial sequence	DQ358736	1516		1173684

GC content

29242

GC-content (mol%)46.8

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Paenibacillus sonchi strain LMG 24727
PATRIC: 373687.11

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	79.00	no
125439	gram_stain	BacteriaNetⓘ	variable	83.40	no
125439	motility	BacteriaNetⓘ	yes	89.50	no
125439	spore_formation	BacteriaNetⓘ	yes	96.00	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Paenibacillus sonchi LMG 24727
NCBI: GCA_016772475.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	69.31	yes
125438	anaerobic	anaerobicⓘ	no	89.22	yes
125438	aerobic	aerobicⓘ	yes	51.57	yes
125438	spore-forming	spore-formingⓘ	yes	91.61	yes
125438	thermophilic	thermophileⓘ	no	93.39	yes
125438	flagellated	motile2+ⓘ	yes	83.64	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Genomic Insights into the Distribution and Phylogeny of Glycopeptide Resistance Determinants within the Actinobacteria Phylum.	Andreo-Vidal A, Binda E, Fedorenko V, Marinelli F, Yushchuk O.	Antibiotics (Basel)	10.3390/antibiotics10121533	2021
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 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
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 )
#25662	IJSEM 2656 2009 ( DOI 10.1099/ijs.0.009308-0 , PubMed 19625436 )
#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
#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 .
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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Paenibacillus sonchi (CCBAU 83901, LMG 24727, X19-5)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Metabolite utilization

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Sequence information

Genome sequences

Genome browser: GCA_016772475

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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