Name: Rummeliibacillus pycnus 1446
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 18131

Type strain:

Species: Rummeliibacillus pycnus

Strain Designation: 1446

Culture col. no.: DSM 15030, JCM 11075, NBRC 101231, NRRL NRS-1691, CIP 107434, DSM 7260, KCTC 13923

Strain history: CIP <- 2002, JCM <- 2000, HSCC: strain 1446 <- NRRL <- J.R. Norris <- T. Gibson: strain 4, "Bacillus pycnoticus"

NCBI tax ID(s): 101070 (species)

SI-ID 48393

DSM 7260, JCM 11075, NRRL NRS-1691, DSM 15030, KCTC 1530, DSM 2367, KCTC 13923, CIP 107434, LMG 21634, NBRC 101231

Other strains from Rummeliibacillus pycnus

R. pycnus Gibson 10, DSM 2369, NRRL NRS-1693
R. pycnus Gibson 13, DSM 2370, NRRL NRS-1694
R. pycnus Gibson 14, DSM 2371, NRRL NRS-1695

Section

Rummeliibacillus pycnus 1446 is an obligate aerobe, spore-forming, mesophilic bacterium that was isolated from soil.

motile
spore-forming
mesophilic
obligate 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	*Caryophanaceae*
	Genus	*Rummeliibacillus*
	Species	**Rummeliibacillus pycnus**
	Full Scientific Name (LPSN)	Rummeliibacillus pycnus (Nakamura et al. 2002) Vaishampayan et al. 2009

Synonym

Bacillus pycnus

Information on morphological and physiological properties Morphology

[Ref.: #122080]	Gram stain	positive
[Ref.: #69480]	Gram stain	positive Confidence in %100

[Ref.: #122080]	Cell shape	rod-shaped

[Ref.: #122080]	Motility	yes
[Ref.: #69480]	Motility	yes Confidence in %95.224

Information on culture and growth conditions Culture and growth conditions

[Ref.: #5681]

Culture medium

NUTRIENT AGAR (DSMZ Medium 1)

[Ref.: #5681]

Culture medium growth

[Ref.: #5681]

Culture medium link

Medium recipe at MediaDive

[Ref.: #5681]

Culture medium composition

expand / minimize

[Ref.: #122080]

Culture medium

CIP Medium 72

[Ref.: #122080]

Culture medium growth

[Ref.: #122080]

Culture medium link

Medium recipe provided by DSMZ

	Kind of temperature		Temperature
[Ref.: #5681]		growth	30 °C
[Ref.: #67770]		growth	30 °C
[Ref.: #122080]		growth	22-45 °C
[Ref.: #122080]	no	growth	10 °C
[Ref.: #122080]	no	growth	55 °C

[Ref.: #5681]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic
[Ref.: #122080]	Temperature range	psychrophilic
[Ref.: #122080]	Temperature range	thermophilic

	pH	Kind of pH		pH
[Ref.: #122080]			growth	6

Information on physiology and metabolism Physiology and metabolism

[Ref.: #122080]

Oxygen tolerance

obligate aerobe

[Ref.: #122080]	Ability of spore formation	yes
[Ref.: #69481]	Ability of spore formation	yes Confidence in %99
[Ref.: #69480]	Ability of spore formation	yes Confidence in %100

	Salt	Tested relation		Salt conc.
[Ref.: #122080]	NaCl		growth	0-2	%
[Ref.: #122080]	NaCl	no	growth	4	%
[Ref.: #122080]	NaCl	no	growth	6	%
[Ref.: #122080]	NaCl	no	growth	8	%
[Ref.: #122080]	NaCl	no	growth	10	%

[Ref.: #67770]

Observation

quinones: MK-7

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #122080]	citrate ChEBI	-	carbon source
[Ref.: #122080]	esculin ChEBI	-	hydrolysis
[Ref.: #122080]	hippurate ChEBI	-	hydrolysis
[Ref.: #122080]	nitrate ChEBI	-	reduction
[Ref.: #122080]	nitrate ChEBI	-	respiration
[Ref.: #122080]	nitrite ChEBI	-	reduction

	Metabolite production	Metabolite	Production
[Ref.: #122080]		indole ChEBI	no

	Physiological tests	Metabolite	Voges-Proskauer-test	Methylred-test
[Ref.: #122080]		acetoin ChEBI	-
[Ref.: #122080]		glucose ChEBI		-

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #122080]	alcohol dehydrogenase	-	1.1.1.1
[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.: #122080]	amylase	-
[Ref.: #122080]	beta-galactosidase	-	3.2.1.23
[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.: #122080]	caseinase	-	3.4.21.50
[Ref.: #122080]	catalase	+	1.11.1.6
[Ref.: #68382]	cystine arylamidase	+	3.4.11.3	* from API zym
[Ref.: #122080]	DNase	-
[Ref.: #68382]	esterase (C 4)	+		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	+		* from API zym
[Ref.: #122080]	gamma-glutamyltransferase	-	2.3.2.2
[Ref.: #122080]	gelatinase	-
[Ref.: #122080]	lecithinase	-
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #122080]	lipase	-
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #122080]	lysine decarboxylase	-	4.1.1.18
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #122080]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #122080]	oxidase	+
[Ref.: #122080]	protease	-
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #122080]	tween esterase	-
[Ref.: #122080]	urease	-	3.5.1.5
[Ref.: #68382]	valine arylamidase	+		* from API zym
	Only first 10 entries are displayed. Click here to see all.

API® Biotype100:

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

	API ID	ControlQ	D-glucose as carbon sourceGLU	D-fructose as carbon sourceFRU	D-galactose as carbon sourceGAL	D-trehalose as carbon sourceTRE	D-mannose as carbon sourceMNE	L-sorbose as carbon sourceSBE	D-melibiose as carbon sourceMEL	sucrose as carbon sourceSAC	D-raffinose as carbon sourceRAF	maltotriose as carbon sourceMTE	maltose as carbon sourceMAL	lactose as carbon sourceLAC	lactulose as carbon sourceLTE	1-O-methyl-beta-galactopyranoside as carbon sourceMbGa	1-O-methyl-alpha-galactopyranoside as carbon sourceMaGa	D-cellobiose as carbon sourceCEL	gentiobiose as carbon sourceGEN	1-O-methyl-beta-D-glucopyranoside as carbon sourceMbGu	esculin as carbon sourceESC	D-ribose as carbon sourceRIB	L-arabinose as carbon sourceARA	D-xylose as carbon sourceXYL	palatinose as carbon sourcePLE	L-rhamnose as carbon sourceRHA	L-fucose as carbon sourceFUC	D-melezitose as carbon sourceMLZ	D-arabitol as carbon sourceDARL	L-arabitol as carbon sourceLARL	xylitol as carbon sourceXLT	dulcitol as carbon sourceDUL	D-tagatose as carbon sourceTAG	glycerol as carbon sourceGLY	myo-inositol as carbon sourceINO	D-mannitol as carbon sourceMAN	maltitol as carbon sourceMTL	D-turanose as carbon sourceTUR	D-sorbitol as carbon sourceSOR	adonitol as carbon sourceADO	hydroxyquinoline-beta-glucuronide as carbon sourceHBG	D-lyxose as carbon sourceLYX	i-erythritol as carbon sourceERY	1-O-methyl-alpha-D-glucoside as carbon sourceMDG	3-O-methyl-D-glucose as carbon source3MDG	D-saccharate as carbon sourceSAT	mucate as carbon sourceMUC	L-tartrate as carbon sourceLTAT	D-tartrate as carbon sourceDTAT	meso-tartrate as carbon sourceMTAT	D-malate as carbon sourceDMLT	L-malate as carbon sourceLMLT	cis-aconitate as carbon sourceCATE	trans-aconitate as carbon sourceTATE	tricarballylate as carbon sourceTTE	citrate as carbon sourceCIT	D-glucuronate as carbon sourceGRT	D-galacturonate as carbon sourceGAT	2-ketogluconate as carbon source2KG	5-ketogluconate as carbon source5KG	tryptophan as carbon sourceTRY	N-acetyl-D-glucosamine as carbon sourceNAG	D-gluconate as carbon sourceGNT	phenylacetate as carbon sourcePAC	protocatechuate as carbon sourcePAT	4-hydroxybenzoate as carbon sourcepOBE	quinate as carbon sourceQAT	gentisate as carbon sourceGTE	3-hydroxybenzoate as carbon sourcemOBE	benzoate as carbon sourceBAT	3-phenylpropionate as carbon sourcePPAT	m-coumarate as carbon sourceCMT	trigonelline as carbon sourceTGE	betaine as carbon sourceBET	putrescine as carbon sourcePCE	4-aminobutyrate as carbon sourceABT	histamine as carbon sourceHIN	DL-lactate as carbon sourceLAT	caprate as carbon sourceCAP	caprylate as carbon sourceCYT	L-histidine as carbon sourceHIS	succinate as carbon sourceSUC	fumarate as carbon sourceFUM	glutarate as carbon sourceGRE	DL-glycerate as carbon sourceGYT	5-aminovalerate as carbon sourceAVT	ethanolamine as carbon sourceETN	tryptamine as carbon sourceTTN	D-glucosamine as carbon sourceGLN	itaconate as carbon sourceITA	3-hydroxybutyrate as carbon source3OBU	L-aspartate as carbon sourceAPT	L-glutamate as carbon sourceGTT	L-proline as carbon sourcePRO	D-alanine as carbon sourceDALA	L-alanine as carbon sourceLALA	L-serine as carbon sourceSER	malonate as carbon sourceMNT	propionate as carbon sourcePROP	L-tyrosine as carbon sourceTYR	2-ketoglutarate as carbon source2KT
[Ref.: #122080]	2211	not determinedn.d.	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-	+	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	+	-	+	-	+	-	-	+	-	-	+	-	-	-	-	+	-	+	-	-	+	+	-	-	-	-

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.: #122080]	10349	-	-	+	+	-	+	+	+	-	+	+	+	-	-	-	-	-	-	-	-

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

[Ref.: #5681]	Sample type/isolated from	soil

[Ref.: #67770]	Sample type/isolated from	Soil

[Ref.: #122080]	Sample type/isolated from	Environment, Soil
* marker position based on {}

Isolation sources categories

#Environmental

#Terrestrial

#Soil

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AF169531 (>99% sequence identity) for Rummeliibacillus pycnus subclade from Microbeatlas

Aquatic Samples	238
Soil Samples	959
Animal Samples	461
Plant Samples	101
Total Samples	1759

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

[Ref.: #5681]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #122080]	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]	Bacillus sp. NRS-1691 16S ribosomal RNA gene, partial sequence	AF169531	1411	ENA	101070 tax ID
[Ref.: #5681]	Bacillus pycnus gene for 16S rRNA, partial sequence	AB271739	1475	ENA	101070 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Rummeliibacillus pycnus DSM 15030	GCA_002884495	scaffold	GenBank	101070 tax ID	*
[Ref.: #66792]	Rummeliibacillus pycnus strain DSM 15030	101070.3	wgs	PATRIC	101070 tax ID	*
[Ref.: #66792]	Rummeliibacillus pycnus DSM 15030	2890201742	draft	JGI IMG/M	101070 tax ID	*

[Ref.: #67770]

GC-content

35 mol%

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Rummeliibacillus pycnus DSM 15030 NCBI: GCA_002884495.1
[Ref.: #69481]	spore-forming	yes	99	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Rummeliibacillus pycnus DSM 15030 NCBI: GCA_002884495.1
[Ref.: #69480]	flagellated	yes	90.782	no
[Ref.: #69480]	gram-positive	yes	81.618	no
[Ref.: #69480]	anaerobic	no	97.6	no
[Ref.: #69480]	aerobic	yes	82.975	no
[Ref.: #69480]	halophile	no	92.115	no
[Ref.: #69480]	spore-forming	yes	96.862	no
[Ref.: #69480]	glucose-util	yes	84.344	no
[Ref.: #69480]	thermophile	no	99.287	no
[Ref.: #69480]	motile	yes	89.108	no
[Ref.: #69480]	glucose-ferment	no	90.147	no

Availability in culture collections External links

[Ref.: #5681]

Culture collection no.

DSM 15030, JCM 11075, NBRC 101231, NRRL NRS-1691, CIP 107434, DSM 7260, KCTC 13923

[Ref.: #87118]

SI-ID 48393

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Rummeliibacillus suwonensis sp. nov., isolated from soil collected in a mountain area of South Korea.	Her J, Kim J	J Microbiol	10.1007/s12275-013-3126-5	2013	*
Phylogeny	Description of Rummeliibacillus stabekisii gen. nov., sp. nov. and reclassification of Bacillus pycnus Nakamura et al. 2002 as Rummeliibacillus pycnus comb. nov.	Vaishampayan P, Miyashita M, Ohnishi A, Satomi M, Rooney A, La Duc MT, Venkateswaran K	Int J Syst Evol Microbiol	10.1099/ijs.0.006098-0	2009	*
Phylogeny	Proposal of Viridibacillus gen. nov. and reclassification of Bacillus arvi, Bacillus arenosi and Bacillus neidei as Viridibacillus arvi gen. nov., comb. nov., Viridibacillus arenosi comb. nov. and Viridibacillus neidei comb. nov.	Albert RA, Archambault J, Lempa M, Hurst B, Richardson C, Gruenloh S, Duran M, Worliczek HL, Huber BE, Rossello-Mora R, Schumann P, Busse HJ	Int J Syst Evol Microbiol	10.1099/ijs.0.65256-0	2007	*
Phylogeny	Bacillus pycnus sp. nov. and Bacillus neidei sp. nov., round-spored bacteria from soil.	Nakamura LK, Shida O, Takagi H, Komagata K	Int J Syst Evol Microbiol	10.1099/00207713-52-2-501	2002	*

References

#5681

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 15030

#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 )

#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 .

#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 )

#87118

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-ID48393.1 )

#122080 Collection of Institut Pasteur ; Curators of the CIP; CIP 107434
* These data were automatically processed and therefore are not curated

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Rummeliibacillus pycnus DSM 15030

Rummeliibacillus pycnus DSM 15030

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