Name: Paenibacillus sediminis GT-H3
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 11660

Type strain:

Species: Paenibacillus sediminis

Strain Designation: GT-H3, GTH-3

Culture col. no.: DSM 23491, CIP 110613, LMG 25635

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

NCBI tax ID(s): 664909 (species)

SI-ID 405459

DSM 23491, CIP 110613

Special Collections

Section

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

Gram-positive
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 sediminis**
	Full Scientific Name (LPSN)	Paenibacillus sediminis Wang et al. 2012

Information on morphological and physiological properties Morphology

[Ref.: #30269]	Gram stain	positive
[Ref.: #122536]	Gram stain	negative

[Ref.: #30269]	Cell length	6 µm

[Ref.: #30269]	Cell width	0.5 µm

[Ref.: #30269]	Cell shape	rod-shaped
[Ref.: #122536]	Cell shape	rod-shaped

[Ref.: #30269]	Motility	no
[Ref.: #122536]	Motility	no

[Ref.: #30269]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #17237]

Culture medium

R2A MEDIUM (DSMZ Medium 830)

[Ref.: #17237]

Culture medium growth

[Ref.: #17237]

Culture medium link

Medium recipe at MediaDive

[Ref.: #17237]

Culture medium composition

expand / minimize

[Ref.: #122536]

Culture medium

CIP Medium 372

[Ref.: #122536]

Culture medium growth

[Ref.: #122536]

Culture medium link

Medium recipe provided by DSMZ

	Temperatures	Kind of temperature		Temperature
[Ref.: #17237]			growth	30 °C
[Ref.: #30269]			growth	04-55 °C

	pH	Kind of pH		pH
[Ref.: #30269]			growth	6.5-8.5

Information on physiology and metabolism Physiology and metabolism

[Ref.: #30269]

Oxygen tolerance

aerobe

[Ref.: #30269]	Ability of spore formation	yes
[Ref.: #69480]	Ability of spore formation	yes Confidence in %93.763
[Ref.: #69481]	Ability of spore formation	yes Confidence in %100

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #30269]		NaCl		growth	2	%

	Metabolite utilization	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #30269]		glucose ChEBI	+	carbon source
[Ref.: #30269]		maltose ChEBI	+	carbon source

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #30269]		catalase	+	1.11.1.6
[Ref.: #30269]		cytochrome oxidase	+	1.9.3.1

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

[Ref.: #17237]	Sample type/isolated from	tidal flat
[Ref.: #17237]	Geographic location (country and/or sea, region)	West Sea, adjacent to Ganghwa Island (37°42' 02'' N 126° 22' 38'' E),
[Ref.: #17237]	Country	Republic of Korea
[Ref.: #17237]	Country ISO 3 Code	KOR
[Ref.: #17237]	Continent	Asia
[Ref.: #17237]	Geographic location	37.7006°/126.3770°

[Ref.: #122536]	Sample type/isolated from	Tidal flat
[Ref.: #122536]	Geographic location (country and/or sea, region)	West sea
[Ref.: #122536]	Country	Republic of Korea
[Ref.: #122536]	Country ISO 3 Code	KOR
[Ref.: #122536]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental

#Terrestrial

#Tidal flat

What are isolation sources categories?

[Ref.: #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

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #17237]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #122536]	Biosafety level	1	Risk group (French classification)

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.: #17237]	Paenibacillus sediminis strain GTH-3 16S ribosomal RNA gene, partial sequence	GQ355277	1452	GenBank ENA	664909 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Paenibacillus sediminis DSM 23491	GCA_017873765	contig	GenBank ENA	664909 tax ID	*
[Ref.: #66792]	Paenibacillus sediminis strain DSM 23491	664909.3	wgs	PATRIC	664909 tax ID	*
[Ref.: #66792]	Paenibacillus sediminis DSM 23491	2913409695	draft	JGI IMG/M	664909 tax ID	*

[Ref.: #17237]	GC-content	45.9 mol%	high performance liquid chromatography (HPLC)
[Ref.: #30269]	GC-content	45.9 mol%

Data predicted using genome information as a basis Genome-based predictions

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Paenibacillus sediminis strain DSM 23491 PATRIC: 664909.3
[Ref.: #69481]	spore-forming	spore-formingⓘ	yes	100	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Paenibacillus sediminis strain DSM 23491 PATRIC: 664909.3
[Ref.: #69480]	gram-positive	gram-positiveⓘ	yes	68.881	no
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	89.016	yes
[Ref.: #69480]	spore-forming	spore-formingⓘ	yes	93.763	yes
[Ref.: #69480]	aerobic	aerobicⓘ	yes	65.359	no
[Ref.: #69480]	thermophilic	thermophileⓘ	no	79.687	no
[Ref.: #69480]	flagellated	motile2+ⓘ	yes	84.304	no

Availability in culture collections External links

[Ref.: #17237]

Culture collection no.

DSM 23491, CIP 110613, LMG 25635

[Ref.: #80884]

SI-ID 405459

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 )

#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 (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 )

#80884

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-ID405459.1 )

#122536 Collection of Institut Pasteur ; Curators of the CIP; CIP 110613

#26610

IJSEM 1284 2012 ( DOI 10.1099/ijs.0.032102-0 , PubMed 21784963 )

* These data were automatically processed and therefore are not curated

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Paenibacillus sediminis strain DSM 23491

Paenibacillus sediminis strain DSM 23491

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