Cite this strain

Paenibacillus sp. (JCM 16163)

Name: Paenibacillus sp. (JCM 16163)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 161737

Type strain

Culture col. no. JCM 16163

NCBI tax ID(s) 206394

Special Collections JCM

Links

JCM 16163 is a mesophilic prokaryote that was isolated from Soil.

mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 131600

JCM 16163

@ref 20215

Last LPSN update 2025-12-16 10:08:48

Domain Bacillati

Phylum Bacillota

Class Bacilli

Order Caryophanales

Family Paenibacillaceae

Genus Paenibacillus

Full scientific name Paenibacillus Ash et al. 1994

Synonyms (1)

"Aerobacillus"

Morphology

Cell morphology

@ref	Motility	Confidence
125439		90.7

Culture and growth conditions

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
67770	positive	growth	37	mesophilic

Physiology and metabolism

Spore formation

@ref	Spore formation	Confidence
125439		96.2

Isolation, sampling and environmental information

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
67770	Soil	Ukima Park, Itabashi-ku, Tokyo	Japan	JPN	Asia

Taxonmaps

69479

Global distribution of 16S sequence AB091334 (>99% sequence identity) for Paenibacillus naphthalenovorans subclade from Microbeatlas

Aquatic Samples	379
Soil Samples	723
Animal Samples	515
Plant Samples	157
Total Samples	1774

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID
66792	ASM131258v1 assembly for Paenibacillus sp. YK5 JCM 16163	contig	GCA_001312585	206394.3	2734481908	206394

Genome browser: GCA_001312585

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
67770	Paenibacillus sp. YK5 gene for 16S rRNA, partial sequence	AB091334	1514		206394

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Paenibacillus sp. YK5 JCM 16163
NCBI: GCA_001312585

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	96.20	no
125439	motility	BacteriaNetⓘ	yes	90.70	no
125439	gram_stain	BacteriaNetⓘ	variable	82.70	no
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	81.60	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Paenibacillus sp. YK5 strain JCM 16163
PATRIC: 206394.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	59.61	no
125438	anaerobic	anaerobicⓘ	no	95.61	no
125438	spore-forming	spore-formingⓘ	yes	88.00	no
125438	aerobic	aerobicⓘ	yes	76.68	no
125438	thermophilic	thermophileⓘ	no	81.69	no
125438	flagellated	motile2+ⓘ	yes	82.85	no

Literature

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 )
#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;
#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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