Paenibacillus pinihumi (DSM 23905, JCM 16419, KACC 14199)

Name: Paenibacillus pinihumi (DSM 23905, JCM 16419, KACC 14199)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 11644

Type strain

Strain Designation S23

Culture col. no. DSM 23905 JCM 16419 KACC 14199 KCTC 13695 S23 1 more

NCBI tax ID(s) 1122924 669462

Special Collections DSMZ JCM KCTC

History DSMZ <- KCTC <- B.-C. Kim, KRIBB; S23 JCM <-- B.-C. Kim S23. KCTC <- KS Shin, KRIBB

Links

Paenibacillus pinihumi S23 is an aerobe, spore-forming, motile bacterium that was isolated from rhizosphere of Pinus densiflora.

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

Name and taxonomic classification

SI-ID 403095

KCTC 13695,JCM 16419,DSM 23905

@ref 20215

Last LPSN update 2026-05-29 08:27:36

Domain Bacteria

Phylum Bacillota

Class Bacilli

Order Caryophanales

Family Paenibacillaceae

Genus Paenibacillus

Species Paenibacillus pinihumi

Full scientific name Paenibacillus pinihumi Kim et al. 2010

Morphology

Cell morphology

@ref	Cell shape	Motility	Flagellum arrangement	Gram stain
67771	rod-shaped		peritrichous
67771				positive

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
17358	TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545)		Medium recipe at MediaDive	Name: TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545) Composition: Casein peptone 17.0 g/l NaCl 5.0 g/l Soy peptone 3.0 g/l D(+)-Glucose 2.5 g/l K2HPO4 2.5 g/l Distilled water
17358	CASO AGAR (MERCK 105458) (DSMZ Medium 220)		Medium recipe at MediaDive	Name: CASO AGAR (Merck 105458) (DSMZ Medium 220) Composition: Agar 15.0 g/l Casein peptone 15.0 g/l NaCl 5.0 g/l Soy peptone 5.0 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
17358	positive	growth	28
67770	positive	growth	25
67771	positive	growth	25-30

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
67771	aerobe
125439	facultative anaerobe	95.252

Spore formation

@ref	Type of spore	Confidence
67771	spore
125438		92.531
125439		92.602

Observation

@ref	Observation
67770	quinones: MK-7
67771	quinones: MK-7

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Plants	#Tree
#Host Body-Site	#Plant	#Rhizosphere

Isolation

@ref	Sample type	Host species	Country	Country ISO 3 Code	Continent
17358	rhizosphere of Pinus densiflora	Pinus densiflora	Republic of Korea	KOR	Asia
67770	Rhizosphere of a pine tree collected from Mt. Geyjok in Daejeon		Republic of Korea	KOR	Asia
67771	From rhizosphere soil of pine tree		Republic of Korea	KOR	Asia

Taxonmaps

69479

Global distribution of 16S sequence GQ423057 (>99% sequence identity) for Paenibacillus pinihumi subclade from Microbeatlas

Aquatic Samples	41
Soil Samples	195
Animal Samples	199
Plant Samples	192
Total Samples	627

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
17358	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	ASM42250v1 assembly for Paenibacillus pinihumi DSM 23905 = JCM 16419	scaffold	GCA_000422505	1122924.3	2524023129	1122924	67.89
67770	ASM131230v1 assembly for Paenibacillus pinihumi DSM 23905 = JCM 16419	contig	GCA_001312305	1122924.4	2728369719	1122924	6.86

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
17358	Paenibacillus pinihumi strain S23 16S ribosomal RNA gene, partial sequence	GQ423057	1474		1122924
124043	Paenibacillus pinihumi culture JCM:16419 16S ribosomal RNA gene, partial sequence.	PP095665	1406		669462

GC content

@ref	GC-content (mol%)	Method
67770	49.5	high performance liquid chromatography (HPLC)
67771	49.5

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM42250v1 assembly for Paenibacillus pinihumi DSM 23905 = JCM 16419
NCBI: GCA_000422505

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	facultative anaerobe	95.25	no
125439	gram_stain	BacteriaNetⓘ	variable	73.93	no
125439	spore_formation	BacteriaNetⓘ	yes	92.60	no
125439	motility	BacteriaNetⓘ	yes	85.06	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Paenibacillus pinihumi DSM 23905
PATRIC: 1122924.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	63.05	no
125438	anaerobic	anaerobicⓘ	no	96.01	no
125438	spore-forming	spore-formingⓘ	yes	92.53	yes
125438	aerobic	aerobicⓘ	yes	67.18	yes
125438	thermophilic	thermophileⓘ	no	95.58	yes
125438	flagellated	motile2+ⓘ	yes	87.00	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
	Complete Genome Sequences of Two Interactive Moderate Thermophiles, Paenibacillus napthalenovorans 32O-Y and Paenibacillus sp. 32O-W.	Butler RR, Wang J, Stark BC, Pombert JF.	Genome Announc	10.1128/genomea.01717-15	2016
Genetics	Distribution in microbial genomes of genes similar to lodA and goxA which encode a novel family of quinoproteins with amino acid oxidase activity.	Campillo-Brocal JC, Chacon-Verdu MD, Lucas-Elio P, Sanchez-Amat A.	BMC Genomics	10.1186/s12864-015-1455-y	2015
Phylogeny	Paenibacillus pinihumi sp. nov., a cellulolytic bacterium isolated from the rhizosphere of Pinus densiflora.	Kim BC, Lee KH, Kim MN, Kim EM, Rhee MS, Kwon OY, Shin KS	J Microbiol	10.1007/s12275-009-0270-z	2009

References

#17358	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 23905
#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 )
#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 .
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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 )

Rate our new design

Content

About us

Paenibacillus pinihumi (DSM 23905, JCM 16419, KACC 14199)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Observation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000422505

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

Help

Social Media