Name: Paenibacillus silagei LOOC204
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 132640

Type strain:

Species: Paenibacillus silagei

Strain Designation: LOOC204

Culture col. no.: DSM 101953, JCM 30974, MAFF 516319

Strain history: M. Tohno; NARO Inst. of Livestock & Grassland Sci., Japan; LOOC204.

NCBI tax ID(s): 1670801 (species)

SI-ID 407444

DSM 101953

Special Collections

Section

Paenibacillus silagei LOOC204 is a facultative anaerobe, spore-forming, Gram-negative bacterium that forms circular colonies and was isolated from corn silage stored for three months in a tower silo.

colony-forming
Gram-negative
rod-shaped
spore-forming
facultative anaerobe
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 silagei**
	Full Scientific Name (LPSN)	Paenibacillus silagei Tohno et al. 2016

Information on morphological and physiological properties Morphology

[Ref.: #24922]	Gram stain	negative

[Ref.: #24922]	Cell length	3.0-10.0 µm

[Ref.: #24922]	Cell width	0.7-0.9 µm

[Ref.: #24922]	Cell shape	rod-shaped

[Ref.: #24922]	Motility	no

[Ref.: #24922]	Colony color	white
[Ref.: #24922]	Colony shape	circular
[Ref.: #24922]	Incubation period	2 days
[Ref.: #24922]	Cultivation medium used	TSA plates

Information on culture and growth conditions Culture and growth conditions

[Ref.: #24922]

Culture medium

TSA plates

[Ref.: #24922]

Culture medium growth

[Ref.: #24429]

Culture medium

CASO AGAR (MERCK 105458) (DSMZ Medium 220)

[Ref.: #24429]

Culture medium growth

[Ref.: #24429]

Culture medium link

Medium recipe at MediaDive

[Ref.: #24429]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #24429]	growth	30 °C
[Ref.: #24922]	growth	4.0-37.0 °C
[Ref.: #67770]	growth	28 °C

	pH	Kind of pH		pH
[Ref.: #24922]			growth	6.0-8.5

Information on physiology and metabolism Physiology and metabolism

[Ref.: #24922]

Oxygen tolerance

facultative anaerobe

[Ref.: #24922]	Spore description	ellipsoidal,sub-terminal,in swollen sporangia
[Ref.: #24922]	Type of spore	spore
[Ref.: #24922]	Ability of spore formation	yes
[Ref.: #69480]	Ability of spore formation	yes Confidence in %92.869
[Ref.: #69481]	Ability of spore formation	yes Confidence in %100

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #24922]		NaCl		growth	2	%

[Ref.: #67770]

Observation

quinones: MK-7

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #24922]	2-dehydro-D-gluconate ChEBI	-	builds acid from
[Ref.: #24922]	5-dehydro-D-gluconate ChEBI	-	builds acid from
[Ref.: #24922]	amygdalin ChEBI	+	builds acid from
[Ref.: #24922]	arbutin ChEBI	+	builds acid from
[Ref.: #24922]	cellobiose ChEBI	+	builds acid from
[Ref.: #24922]	D-arabinose ChEBI	-	builds acid from
[Ref.: #24922]	D-arabitol ChEBI	-	builds acid from
[Ref.: #24922]	D-fructose ChEBI	+	builds acid from
[Ref.: #24922]	D-fucose ChEBI	-	builds acid from
[Ref.: #24922]	D-galactose ChEBI	+	builds acid from
[Ref.: #24922]	D-glucose ChEBI	+	builds acid from
[Ref.: #24922]	D-lyxose ChEBI	-	builds acid from
[Ref.: #24922]	D-mannitol ChEBI	+	builds acid from
[Ref.: #24922]	D-mannose ChEBI	+	builds acid from
[Ref.: #24922]	D-ribose ChEBI	-	builds acid from
[Ref.: #24922]	D-sorbitol ChEBI	-	builds acid from
[Ref.: #24922]	D-tagatose ChEBI	-	builds acid from
[Ref.: #24922]	D-trehalose ChEBI	+	builds acid from
[Ref.: #24922]	D-xylose ChEBI	+	builds acid from
[Ref.: #24922]	erythritol ChEBI	-	builds acid from
[Ref.: #24922]	esculin ChEBI	+	builds acid from
[Ref.: #24922]	galactitol ChEBI	-	builds acid from
[Ref.: #24922]	gentiobiose ChEBI	+	builds acid from
[Ref.: #24922]	gluconate ChEBI	+	builds acid from
[Ref.: #24922]	glycerol ChEBI	+	builds acid from
[Ref.: #24922]	glycogen ChEBI	+	builds acid from
[Ref.: #24922]	inulin ChEBI	+	builds acid from
[Ref.: #24922]	L-arabinose ChEBI	+	builds acid from
[Ref.: #24922]	L-arabitol ChEBI	-	builds acid from
[Ref.: #24922]	L-fucose ChEBI	+	builds acid from
[Ref.: #24922]	L-rhamnose ChEBI	+	builds acid from
[Ref.: #24922]	L-sorbose ChEBI	-	builds acid from
[Ref.: #24922]	L-xylose ChEBI	-	builds acid from
[Ref.: #24922]	lactose ChEBI	+	builds acid from
[Ref.: #24922]	maltose ChEBI	+	builds acid from
[Ref.: #24922]	melezitose ChEBI	-	builds acid from
[Ref.: #24922]	melibiose ChEBI	+	builds acid from
[Ref.: #24922]	methyl alpha-D-glucopyranoside ChEBI	+	builds acid from
[Ref.: #24922]	methyl alpha-D-mannoside ChEBI	-	builds acid from
[Ref.: #24922]	methyl beta-D-xylopyranoside ChEBI	+	builds acid from
[Ref.: #24922]	myo-inositol ChEBI	-	builds acid from
[Ref.: #24922]	N-acetylglucosamine ChEBI	+	builds acid from
[Ref.: #24922]	raffinose ChEBI	+	builds acid from
[Ref.: #24922]	ribitol ChEBI	-	builds acid from
[Ref.: #24922]	salicin ChEBI	+	builds acid from
[Ref.: #24922]	starch ChEBI	+	builds acid from
[Ref.: #24922]	sucrose ChEBI	+	builds acid from
[Ref.: #24922]	turanose ChEBI	+	builds acid from
[Ref.: #24922]	xylitol ChEBI	+	builds acid from
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #24922]		acetoin ChEBI	no

	Physiological tests	Metabolite	Voges-Proskauer-test
[Ref.: #24922]		acetoin ChEBI	-

	Enzyme	Enzyme activity	EC number
[Ref.: #24922]	acid phosphatase	+	3.1.3.2
[Ref.: #24922]	alkaline phosphatase	-	3.1.3.1
[Ref.: #24922]	alpha-fucosidase	-	3.2.1.51
[Ref.: #24922]	alpha-galactosidase	+	3.2.1.22
[Ref.: #24922]	alpha-glucosidase	+	3.2.1.20
[Ref.: #24922]	alpha-mannosidase	-	3.2.1.24
[Ref.: #24922]	beta-galactosidase	+	3.2.1.23
[Ref.: #24922]	beta-glucosidase	+	3.2.1.21
[Ref.: #24922]	beta-glucuronidase	-	3.2.1.31
[Ref.: #24922]	catalase	+	1.11.1.6
[Ref.: #24922]	chymotrypsin	-	3.4.4.5
[Ref.: #24922]	cystine arylamidase	-	3.4.11.3
[Ref.: #24922]	esterase (C 4)	+
[Ref.: #24922]	esterase lipase (C 8)	+
[Ref.: #24922]	leucine arylamidase	-	3.4.11.1
[Ref.: #24922]	lipase (C 14)	-
[Ref.: #24922]	N-acetyl-beta-glucosaminidase	-	3.2.1.52
[Ref.: #24922]	naphthol-AS-BI-phosphohydrolase	-
[Ref.: #24922]	trypsin	-	3.4.21.4
[Ref.: #24922]	valine arylamidase	-
	Only first 10 entries are displayed. Click here to see all.

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

[Ref.: #24429]	Sample type/isolated from	corn silage stored for three months in a tower silo
[Ref.: #24429]	Geographic location (country and/or sea, region)	Hokkaido (43° 0' 26'' N 141° 24' 41'' E)
[Ref.: #24429]	Country	Japan
[Ref.: #24429]	Country ISO 3 Code	JPN
[Ref.: #24429]	Continent	Asia
[Ref.: #24429]	Geographic location	43.0072°/141.4110°

[Ref.: #24922]	Sample type/isolated from	corn silage which had been prepared and stored for three months in a tower silo
[Ref.: #24922]	Enrichment culture	M17 broth (Difco) agar plates
[Ref.: #24922]	Enrichment culture duration	14 days
[Ref.: #24922]	Enrichment culture temperature	4 ̊C

[Ref.: #67770]	Sample type/isolated from	Corn silage
[Ref.: #67770]	Geographic location (country and/or sea, region)	Hokkaido
[Ref.: #67770]	Country	Japan
[Ref.: #67770]	Country ISO 3 Code	JPN
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Engineered	#Built environment	-
#Host	#Plants	#Herbaceous plants (Grass,Crops)

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence LC061279 (>99% sequence identity) for Paenibacillus from Microbeatlas

Aquatic Samples	286
Soil Samples	546
Animal Samples	395
Plant Samples	269
Total Samples	1496

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

[Ref.: #24429]

Biosafety level

Risk group (German classification)
According to TRBA 466

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.: #24429]	Paenibacillus silagei gene for 16S ribosomal RNA, partial sequence	LC061279	1483	GenBank ENA	1670801 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Paenibacillus silagei DSM 101953	GCA_017874735	contig	GenBank ENA	1670801 tax ID	*
[Ref.: #66792]	Paenibacillus silagei strain DSM 101953	1670801.3	wgs	PATRIC	1670801 tax ID	*
[Ref.: #66792]	Paenibacillus silagei DSM 101953	2913566476	draft	JGI IMG/M	1670801 tax ID	*

[Ref.: #24429]	GC-content	52.2 mol%	high performance liquid chromatography (HPLC)
[Ref.: #67770]	GC-content	51.5-52.9 mol%	high performance liquid chromatography (HPLC)

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 silagei strain DSM 101953 PATRIC: 1670801.3
[Ref.: #69481]	spore-forming	spore-formingⓘ	yes	100	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Paenibacillus silagei strain DSM 101953 PATRIC: 1670801.3
[Ref.: #69480]	gram-positive	gram-positiveⓘ	yes	61.37	yes
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	96.063	yes
[Ref.: #69480]	spore-forming	spore-formingⓘ	yes	92.869	yes
[Ref.: #69480]	aerobic	aerobicⓘ	no	59.96	yes
[Ref.: #69480]	thermophilic	thermophileⓘ	no	95.972	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	yes	85.171	no

Availability in culture collections External links

[Ref.: #24429]

Culture collection no.

DSM 101953, JCM 30974, MAFF 516319

[Ref.: #90953]

SI-ID 407444

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Paenibacillus piscarius sp. nov., a novel nitrogen-fixing species isolated from the gut of the armored catfish Parotocinclus maculicauda.	da Silva MBF, Lemos EA, Vollu RE, Abreu F, Rosado AS, Seldin L	Antonie Van Leeuwenhoek	10.1007/s10482-021-01694-5	2022	*
Phylogeny	Paenibacillus silagei sp. nov. isolated from corn silage.	Tohno M, Sakamoto M, Ohkuma M, Tajima K	Int J Syst Evol Microbiol	10.1099/ijsem.0.001279	2016	*

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 )

#24429

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 101953

#24922

M. S. Tohno, Mitsuo,Ohkuma, Moriya,Tajima, Kiyoshi: Paenibacillus silagei sp. nov. isolated from corn silage. IJSEM 66: 3873 - 3877 2016 ( DOI 10.1099/ijsem.0.001279 , PubMed 27380964 )

#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 .

#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 )

#90953

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-ID407444.1 )

* These data were automatically processed and therefore are not curated

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Paenibacillus silagei strain DSM 101953

Paenibacillus silagei strain DSM 101953

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