Name: Paenibacillus macquariensis subsp. defensor M4-2
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 11642

Type strain:

Species: Paenibacillus macquariensis subsp. defensor

Strain Designation: M4-2

Culture col. no.: DSM 23149, JCM 14954, NCIMB 14397, CIP 110021

Strain history: CIP <- 2009, JCM <- 2007, I. Yumoto, AIST, Saporo, Japan: strain M4-2

NCBI tax ID(s): 467974 (subspecies)

SI-ID 364169

JCM 14954, NCIMB 14397, CIP 110021, DSM 23149

Special Collections

Section

When using BacDive for research please cite our paper

Paenibacillus macquariensis subsp. defensor M4-2 is a facultative anaerobe, Gram-negative, motile bacterium that was isolated from boreal soil.

Gram-negative
motile
rod-shaped
facultative anaerobe
16S sequence
Bacteria
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	09-12-2024 (DD-MM-YYYY)
	Domain	*Bacteria*
	Phylum	*Bacillota*
	Class	*Bacilli*
	Order	*Caryophanales*
	Family	*Paenibacillaceae*
	Genus	*Paenibacillus*
	Species	**Paenibacillus macquariensis subsp. defensor**
	Full Scientific Name (LPSN)	Paenibacillus macquariensis subsp. defensor Hoshino et al. 2009

Information on morphological and physiological properties Morphology

[Ref.: #120739]	Gram stain	negative

[Ref.: #120739]	Cell shape	rod-shaped

[Ref.: #120739]	Motility	yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #16733]

Culture medium

CASO AGAR (MERCK 105458) (DSMZ Medium 220)

[Ref.: #16733]

Culture medium growth

[Ref.: #16733]

Culture medium link

Medium recipe at MediaDive

[Ref.: #16733]

Culture medium composition

expand / minimize

[Ref.: #37903]

Culture medium

MEDIUM 72- for trypto casein soja agar

[Ref.: #37903]

Culture medium growth

[Ref.: #37903]

Culture medium composition

expand / minimize

[Ref.: #120739]

Culture medium

CIP Medium 72

[Ref.: #120739]

Culture medium growth

[Ref.: #120739]

Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #16733]	growth	20-25 °C
[Ref.: #37903]	growth	30 °C
[Ref.: #67770]	growth	30 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #120739]

Oxygen tolerance

facultative anaerobe

[Ref.: #125438]

Ability of spore formation

yes Confidence in %95.851

[Ref.: #67770]

Observation

quinones: MK-7

	Metabolite utilization	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #120739]		nitrate ChEBI	-	reduction
[Ref.: #120739]		nitrite ChEBI	-	reduction

	Metabolite production	Metabolite	Production
[Ref.: #120739]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	-	3.1.3.2	* from API zym
[Ref.: #68382]	alkaline phosphatase	-	3.1.3.1	* from API zym
[Ref.: #68382]	alpha-chymotrypsin	-	3.4.21.1	* from API zym
[Ref.: #68382]	alpha-fucosidase	-	3.2.1.51	* from API zym
[Ref.: #68382]	alpha-galactosidase	-	3.2.1.22	* from API zym
[Ref.: #68382]	alpha-glucosidase	-	3.2.1.20	* from API zym
[Ref.: #68382]	alpha-mannosidase	-	3.2.1.24	* from API zym
[Ref.: #68382]	beta-galactosidase	+	3.2.1.23	* from API zym
[Ref.: #68382]	beta-glucosidase	+	3.2.1.21	* from API zym
[Ref.: #68382]	beta-glucuronidase	-	3.2.1.31	* from API zym
[Ref.: #120739]	catalase	+	1.11.1.6
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #68382]	esterase (C 4)	+		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	+		* from API zym
[Ref.: #68382]	leucine arylamidase	-	3.4.11.1	* from API zym
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #120739]	oxidase	+
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #120739]	urease	-	3.5.1.5
[Ref.: #68382]	valine arylamidase	-		* from API zym
	Only first 10 entries are displayed. Click here to see all.

API® zym:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Control	2-naphthyl phosphateAlkaline phosphatase	2-naphthyl butyrateEsterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	2-naphthyl myristateLipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	N-benzoyl-DL-arginine-2-naphthylamideTrypsin	N-glutaryl-phenylalanine-2-naphthylamidealpha- Chymotrypsin	2-naphthyl phosphateAcid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	6-Br-2-naphthyl-alphaD-galactpyranosidealpha- Galactosidase	2-naphthyl-betaD-galactpyranosidebeta- Galactosidase	Naphthol-AS-BI-betaD-glucuronidebeta- Glucuronidase	2-naphthyl-alphaD-glucopyranosidealpha- Glucosidase	6-Br-2-naphthyl-betaD-glucopyranosidebeta- Glucosidase	1-naphthyl-N-acetyl-betaD-glucosaminideN-acetyl-beta- glucosaminidase	6-Br-2-naphthyl-alphaD-mannopyranosidealpha- Mannosidase	2-naphthyl-alphaL-fucopyranosidealpha- Fucosidase
[Ref.: #120739]	12296	-	-	+	+	-	-	-	-	-	-	-	+	-	+	-	-	+	-	-	-

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

[Ref.: #16733]	Sample type/isolated from	boreal soil
[Ref.: #16733]	Geographic location (country and/or sea, region)	Russian Far East, Oblast Magadan, Magadan Nature Reserve, Koni Peninsula
[Ref.: #16733]	Country	Russia
[Ref.: #16733]	Country ISO 3 Code	RUS
[Ref.: #16733]	Continent	Europe

[Ref.: #67770]	Sample type/isolated from	Boreal soil collected from the Koni Peninsula
[Ref.: #67770]	Geographic location (country and/or sea, region)	Magadan Nature Reserve, Oblast Magadan, Russian Far East
[Ref.: #67770]	Country	Russia
[Ref.: #67770]	Country ISO 3 Code	RUS

[Ref.: #120739]	Sample type/isolated from	Environment, Boreal soil
[Ref.: #120739]	Geographic location (country and/or sea, region)	Far East
[Ref.: #120739]	Country	Russian Federation
[Ref.: #120739]	Country ISO 3 Code	RUS
[Ref.: #120739]	Continent	Europe
* marker position based on {}

Isolation sources categories

#Environmental

#Terrestrial

#Soil

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AB360546 (>99% sequence identity) for Paenibacillus from Microbeatlas

Aquatic Samples	100
Soil Samples	1259
Animal Samples	152
Plant Samples	220
Total Samples	1731

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

[Ref.: #16733]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #120739]	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.: #67770]	Paenibacillus macquariensis subsp. defensor genes for 16S rRNA, 16S-23S internal transcribed spacer, 23S rRNA, partial and complete sequence, strain: M4-2	AB468953	588	GenBank ENA	467974 tax ID
[Ref.: #16733]	Paenibacillus macquariensis subsp. defensor gene for 16S ribosomal RNA, strain: M4-2 (= JCM 14954, = NCIMB 14397)	AB360546	1550	GenBank ENA	467974 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Paenibacillus macquariensis subsp. defensor JCM 14954	GCA_001637215	contig	GenBank ENA	467974 tax ID
[Ref.: #66792]	Paenibacillus macquariensis subsp. defensor strain JCM 14954	467974.3	wgs	PATRIC	467974 tax ID	*
[Ref.: #66792]	Paenibacillus macquariensis defensor JCM 14954	2744054793	draft	JGI IMG/M	467974 tax ID	*

[Ref.: #16733]

GC-content

42.8 mol%

high performance liquid chromatography (HPLC)

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

	Model	Trait	Prediction	Confidence in %	In training data
	Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Paenibacillus macquariensis subsp. defensor strain JCM 14954 PATRIC: 467974.3
[Ref.: #125438]	gram-positive	gram-positiveⓘ	yes	56.757	no
[Ref.: #125438]	anaerobic	anaerobicⓘ	no	92.405	yes
[Ref.: #125438]	spore-forming	spore-formingⓘ	yes	95.851	no
[Ref.: #125438]	aerobic	aerobicⓘ	yes	53.389	no
[Ref.: #125438]	thermophile	thermophilicⓘ	no	93.37	yes
[Ref.: #125438]	motile2+	flagellatedⓘ	yes	81.331	no

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Paenibacillus macquariensis subsp. defensor JCM 14954 NCBI: GCA_001637215
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	yes	85.6
[Ref.: #125439]	BacteriaNet	motilityⓘ	yes	82.5
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	variable	76.9
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	obligate aerobe	89.5

Availability in culture collections External links

[Ref.: #16733]

Culture collection no.

DSM 23149, JCM 14954, NCIMB 14397, CIP 110021

[Ref.: #80866]

SI-ID 364169

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Paenibacillus crassostreae sp. nov., isolated from the Pacific oyster Crassostrea gigas.	Shin SK, Kim E, Yi H	Int J Syst Evol Microbiol	10.1099/ijsem.0.002444	2017	*
Phylogeny	Paenibacillus macquariensis subsp. defensor subsp. nov., isolated from boreal soil.	Hoshino T, Nakabayashi T, Hirota K, Matsuno T, Koiwa R, Fujiu S, Saito I, Tkachenko OB, Matsuyama H, Yumoto I	Int J Syst Evol Microbiol	10.1099/ijs.0.006304-0	2009	*

References

#16733

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 23149

#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 )

#37903 ; Curators of the CIP;

#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;

#68382

Automatically annotated from API zym .

#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 .

#80866

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-ID364169.1 )

#120739 Collection of Institut Pasteur ; Curators of the CIP; CIP 110021

#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 .

* These data were automatically processed and therefore are not curated

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Paenibacillus macquariensis subsp. defensor strain JCM 14954

Paenibacillus macquariensis subsp. defensor JCM 14954

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