Paenibacillus sediminis (DSM 23491, CIP 110613, GT-H3)

Name: Paenibacillus sediminis (DSM 23491, CIP 110613, GT-H3)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 11660

Type strain

Strain Designation GT-H3, GTH-3

Culture col. no. DSM 23491 CIP 110613 GT-H3 LMG 25635 GTH-3

NCBI tax ID(s) 664909

Special Collections DSMZ CIP Literature strains

History <- S. T. Lee, KAIST; GTH-3 CIP <- 2013, DSMZ <- S.T. Lee, Inst. of Science and Technol. Yuseong-gu, Daejon, Republic of Korea: strain GTH-3

Links

Paenibacillus sediminis GT-H3 is an aerobe, spore-forming, Gram-positive bacterium that was isolated from tidal flat.

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

Name and taxonomic classification

SI-ID 405459

LMG 25635,DSM 23491,CIP 110613

@ref 20215

Last LPSN update 2026-02-09 11:20:37

Domain Bacteria

Phylum Bacillota

Class Bacilli

Order Caryophanales

Family Paenibacillaceae

Genus Paenibacillus

Species Paenibacillus sediminis

Full scientific name Paenibacillus sediminis Wang et al. 2012

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility
30269	positive	6 µm	0.5 µm	rod-shaped
122536	negative			rod-shaped

Pigmentation

30269

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
17237	R2A MEDIUM (DSMZ Medium 830)		Medium recipe at MediaDive	Name: R2A MEDIUM (DSMZ Medium 830; with strain-specific modifications) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l MnSO4 0.01 g/l Distilled water
122536	CIP Medium 372		Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
17237	positive	growth	30
30269	positive	growth	04-55

Culture pH

@ref	Ability	Type	PH	PH range
30269	positive	growth	6.5-8.5	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
30269	aerobe
125439	obligate aerobe	97.2

Spore formation

@ref	Spore formation	Confidence
30269
125439		92.8
125438		93.763

Halophily

@ref	Salt	Growth	Tested relation	Concentration
30269	NaCl	positive	growth	2 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
30269	17234 ChEBI	glucose	+	carbon source
30269	17306 ChEBI	maltose	+	carbon source

Enzymes

@ref	Value	Activity	Ec
30269	catalase	+	1.11.1.6
30269	cytochrome oxidase	+	1.9.3.1

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Tidal flat

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude
17237	tidal flat	West Sea, adjacent to Ganghwa Island (37°42' 02'' N 126° 22' 38'' E),	Republic of Korea	KOR	Asia	37.7006	126.377 37.7006/126.377
122536	Tidal flat	West sea	Republic of Korea	KOR	Asia

Taxonmaps

69479

Global distribution of 16S sequence GQ355277 (>99% sequence identity) for Paenibacillus sediminis subclade from Microbeatlas

Aquatic Samples	124
Soil Samples	649
Animal Samples	58
Plant Samples	158
Total Samples	989

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
17237	1	Risk group (German classification) According to TRBA 466
122536	1	Risk group (French classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM1787376v1 assembly for Paenibacillus sediminis DSM 23491	contig	GCA_017873765	664909.3	2913409695	664909	67.62

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
17237	Paenibacillus sediminis strain GTH-3 16S ribosomal RNA gene, partial sequence	GQ355277	1452		664909

GC content

@ref	GC-content (mol%)	Method
17237	45.9	high performance liquid chromatography (HPLC)
30269	45.9

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Paenibacillus sediminis DSM 23491
NCBI: GCA_017873765

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	92.80	no
125439	motility	BacteriaNetⓘ	yes	88.30	no
125439	gram_stain	BacteriaNetⓘ	variable	84.40	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	97.20	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Paenibacillus sediminis strain DSM 23491
PATRIC: 664909.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	68.88	no
125438	anaerobic	anaerobicⓘ	no	89.02	yes
125438	spore-forming	spore-formingⓘ	yes	93.76	yes
125438	aerobic	aerobicⓘ	yes	65.36	no
125438	thermophilic	thermophileⓘ	no	79.69	no
125438	flagellated	motile2+ⓘ	yes	84.30	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Paenibacillus sediminis sp. nov., a xylanolytic bacterium isolated from a tidal flat.	Wang L, Baek SH, Cui Y, Lee HG, Lee ST	Int J Syst Evol Microbiol	10.1099/ijs.0.032102-0	2011

References

#17237	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 23491
#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 )
#26610	IJSEM 1284 2012 ( DOI 10.1099/ijs.0.032102-0 , PubMed 21784963 )
#30269	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 #26610
#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 .
#122536	Collection of Institut Pasteur ; Curators of the CIP; CIP 110613
#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 sediminis (DSM 23491, CIP 110613, GT-H3)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Metabolite utilization

Enzymes

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_017873765

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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