Name: Solirubrobacter pauli B33D1
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 14087

Type strain:

Species: Solirubrobacter pauli

Strain Designation: B33D1

Culture col. no.: DSM 14954, ATCC BAA-492, JCM 13025, CIP 108104, KCTC 9974

Strain history: CIP <- 2003, R. Upchurch, Georgia Univ., Athens, USA: strain B33D1

NCBI tax ID(s): 166793 (species)

SI-ID 100956

ATCC BAA-492, DSM 14954, JCM 13025, CIP 108104, KCTC 9974

Section

Solirubrobacter pauli B33D1 is a spore-forming, mesophilic, Gram-positive bacterium that was isolated from burrow of the epigeic earthworm Lumbricus rubellus in an agricultural soil.

Gram-positive
spore-forming
mesophilic
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	*Actinomycetota*
	Class	*Thermoleophilia*
	Order	*Solirubrobacterales*
	Family	*Solirubrobacteraceae*
	Genus	*Solirubrobacter*
	Species	**Solirubrobacter pauli**
	Full Scientific Name (LPSN)	Solirubrobacter pauli Singleton et al. 2003

Information on morphological and physiological properties Morphology

[Ref.: #121638]	Gram stain	positive
[Ref.: #69480]	Gram stain	positive Confidence in %99.691

[Ref.: #121638]	Cell shape	rod-shaped

[Ref.: #121638]	Motility	yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #5617]

Culture medium

NUTRIENT AGAR (DSMZ Medium 1)

[Ref.: #5617]

Culture medium growth

[Ref.: #5617]

Culture medium link

Medium recipe at MediaDive

[Ref.: #5617]

Culture medium composition

expand / minimize

[Ref.: #33200]

Culture medium

MEDIUM 328- for nutrient agar

[Ref.: #33200]

Culture medium growth

[Ref.: #33200]

Culture medium composition

expand / minimize

[Ref.: #121638]

Culture medium

CIP Medium 328

[Ref.: #121638]

Culture medium growth

[Ref.: #121638]

Culture medium link

Medium recipe provided by DSMZ

	Kind of temperature		Temperature
[Ref.: #5617]		growth	28 °C
[Ref.: #33200]		growth	22 °C
[Ref.: #67770]		growth	28 °C
[Ref.: #121638]		growth	15-37 °C
[Ref.: #121638]	no	growth	10 °C
[Ref.: #121638]	no	growth	41 °C
[Ref.: #121638]	no	growth	45 °C

[Ref.: #5617]	Temperature range	mesophilic
[Ref.: #33200]	Temperature range	psychrophilic
[Ref.: #67770]	Temperature range	mesophilic
[Ref.: #121638]	Temperature range	psychrophilic
[Ref.: #121638]	Temperature range	thermophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #69481]	Ability of spore formation	yes Confidence in %90
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.469

	Salt	Tested relation		Salt conc.
[Ref.: #121638]	NaCl		growth	0	%
[Ref.: #121638]	NaCl	no	growth	2	%
[Ref.: #121638]	NaCl	no	growth	4	%
[Ref.: #121638]	NaCl	no	growth	6	%
[Ref.: #121638]	NaCl	no	growth	8	%
[Ref.: #121638]	NaCl	no	growth	10	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68371]	amygdalin ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	arbutin ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	cellobiose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #121638]	citrate ChEBI	-	carbon source
[Ref.: #68371]	D-arabinose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-arabitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-fructose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-fucose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-galactose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-glucose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-lyxose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-mannitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-mannose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-ribose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-sorbitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-tagatose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-xylose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	erythritol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #121638]	esculin ChEBI	+	hydrolysis
[Ref.: #68371]	esculin ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	galactitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	gentiobiose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	gluconate ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	glycerol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	glycogen ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #121638]	hippurate ChEBI	-	hydrolysis
[Ref.: #68371]	inulin ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-arabinose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-arabitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-fucose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-rhamnose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-sorbose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-xylose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	lactose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	maltose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	melezitose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	melibiose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	methyl alpha-D-glucopyranoside ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	methyl alpha-D-mannoside ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	methyl beta-D-xylopyranoside ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	myo-inositol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	N-acetylglucosamine ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #121638]	nitrate ChEBI	-	reduction
[Ref.: #121638]	nitrate ChEBI	-	respiration
[Ref.: #121638]	nitrite ChEBI	-	reduction
[Ref.: #68371]	Potassium 2-ketogluconate ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	Potassium 5-ketogluconate ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	raffinose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	ribitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	salicin ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	starch ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	sucrose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	trehalose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	turanose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	xylitol ChEBI	-	builds acid from	* from API 50CH acid
	Only first 10 entries are displayed. Click here to see all.

	Antibiotica	Metabolite	Antibiotic sensitivity	Antibiotic resistance
[Ref.: #121638]		0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)	no	yes

	Metabolite production	Metabolite	Production
[Ref.: #121638]		indole ChEBI	no

	Physiological tests	Metabolite	Voges-Proskauer-test	Methylred-test
[Ref.: #121638]		acetoin ChEBI	-
[Ref.: #121638]		glucose ChEBI		-

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #121638]	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.: #121638]	amylase	+
[Ref.: #121638]	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.: #121638]	caseinase	+	3.4.21.50
[Ref.: #121638]	catalase	+	1.11.1.6
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #121638]	DNase	-
[Ref.: #68382]	esterase (C 4)	+		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	+		* from API zym
[Ref.: #121638]	gamma-glutamyltransferase	-	2.3.2.2
[Ref.: #121638]	gelatinase	-
[Ref.: #121638]	lecithinase	-
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #121638]	lipase	-
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #121638]	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.: #121638]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #121638]	oxidase	-
[Ref.: #121638]	phenylalanine ammonia-lyase	-	4.3.1.24
[Ref.: #121638]	protease	-
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #121638]	tryptophan deaminase	-
[Ref.: #121638]	tween esterase	-
[Ref.: #121638]	urease	-	3.5.1.5
[Ref.: #68382]	valine arylamidase	+		* from API zym
	Only first 10 entries are displayed. Click here to see all.

API® 50CH acid:

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

	API ID	ControlQ	Acid from glycerolGLY	Acid from erythritolERY	Acid from D-arabinoseDARA	Acid from L-arabinoseLARA	Acid from D-riboseRIB	Acid from D-xyloseDXYL	Acid from L-xyloseLXYL	Acid from D-adonitolADO	Acid from methyl beta-D-xylopyranosideMDX	Acid from D-galactoseGAL	Acid from D-glucoseGLU	Acid from D-fructoseFRU	Acid from D-mannoseMNE	Acid from L-sorboseSBE	Acid from L-rhamnoseRHA	Acid from dulcitolDUL	Acid from inositolINO	Acid from D-mannitolMAN	Acid from D-sorbitolSOR	Acid from methyl alpha-D-mannopyranosideMDM	Acid from methyl alpha-D-glucopyranosideMDG	Acid from N-acetyl-glucosamineNAG	Acid from amygdalinAMY	Acid from arbutinARB	Acid from esculinESC	Acid from salicinSAL	Acid from cellobioseCEL	Acid from maltoseMAL	Acid from lactoseLAC	Acid from melibioseMEL	Acid from sucroseSAC	Acid from trehaloseTRE	Acid from inulinINU	Acid from melezitoseMLZ	Acid from raffinoseRAF	Acid from starchAMD	Acid from glycogenGLYG	Acid from xylitolXLT	Acid from gentiobioseGEN	Acid from turanoseTUR	Acid from D-lyxoseLYX	Acid from D-tagatoseTAG	Acid from D-fucoseDFUC	Acid from L-fucoseLFUC	Acid from D-arabitolDARL	Acid from L-arabitolLARL	Acid from gluconateGNT	Acid from 2-Ketogluconate2KG	Acid from 5-Ketogluconate5KG
[Ref.: #121638]	11197	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.: #121638]	10887	-	+	+	+	-	+	+	-	-	-	+	+	-	+	-	+	+	-	-	-

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

[Ref.: #5617]	Sample type/isolated from	burrow of the epigeic earthworm Lumbricus rubellus in an agricultural soil
[Ref.: #5617]	Host species	Lumbricus rubellus
[Ref.: #5617]	Geographic location (country and/or sea, region)	Georgia, Athens
[Ref.: #5617]	Country	USA
[Ref.: #5617]	Country ISO 3 Code	USA
[Ref.: #5617]	Continent	North America

[Ref.: #67770]	Sample type/isolated from	Burrow of the epigeic earthworm Lumbricus rubellus in agricultural soil
[Ref.: #67770]	Host species	Lumbricus rubellus
[Ref.: #67770]	Geographic location (country and/or sea, region)	Athens, GA
[Ref.: #67770]	Country	USA
[Ref.: #67770]	Country ISO 3 Code	USA
[Ref.: #67770]	Continent	North America

[Ref.: #121638]	Sample type/isolated from	Environment, Burrow of Lumbricus rubellus in agricultural soil
[Ref.: #121638]	Geographic location (country and/or sea, region)	Athens, Georgia
[Ref.: #121638]	Country	United States of America
[Ref.: #121638]	Country ISO 3 Code	USA
[Ref.: #121638]	Continent	North America
[Ref.: #121638]	Isolation date	1996
* marker position based on {}

Isolation sources categories

#Engineered	#Agriculture	-
#Environmental	#Terrestrial	#Soil
#Host	#Invertebrates (Other)	#Annelida

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AY039806 (>99% sequence identity) for Solirubrobacter pauli subclade from Microbeatlas

Aquatic Samples	22
Soil Samples	566
Animal Samples	52
Plant Samples	177
Total Samples	817

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

[Ref.: #5617]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #121638]	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.: #5617]	Earthworm burrow bacterium B33D1 16S ribosomal RNA gene, partial sequence	AY039806	1366	ENA	166793 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Solirubrobacter pauli DSM 14954	GCA_003633755	scaffold	GenBank	166793 tax ID
[Ref.: #66792]	Solirubrobacter pauli strain DSM 14954	166793.3	wgs	PATRIC	166793 tax ID	*
[Ref.: #66792]	Solirubrobacter pauli DSM 14954	2737471645	draft	JGI IMG/M	166793 tax ID	*

[Ref.: #67770]

GC-content

71.6-72 mol%

high performance liquid chromatography (HPLC)

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: Solirubrobacter pauli DSM 14954 NCBI: GCA_003633755.1
[Ref.: #69481]	spore-forming	yes	90	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Solirubrobacter pauli strain DSM 14954 PATRIC: 166793.3
[Ref.: #69480]	motile	yes	70.887	no
[Ref.: #69480]	gram-positive	yes	83.404	no
[Ref.: #69480]	anaerobic	no	97.941	no
[Ref.: #69480]	aerobic	yes	86.488	no
[Ref.: #69480]	halophile	no	94.815	no
[Ref.: #69480]	spore-forming	no	82.562	no
[Ref.: #69480]	thermophile	no	98.101	yes
[Ref.: #69480]	glucose-util	yes	86.95	no
[Ref.: #69480]	flagellated	no	88.122	no
[Ref.: #69480]	glucose-ferment	no	86.471	no

Availability in culture collections External links

[Ref.: #5617]

Culture collection no.

DSM 14954, ATCC BAA-492, JCM 13025, CIP 108104, KCTC 9974

[Ref.: #83255]

SI-ID 100956

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Solirubrobacter taibaiensis sp. nov., isolated from a stem of Phytolacca acinosa Roxb.	Zhang L, Zhu L, Si M, Li C, Zhao L, Wei Y, Shen X	Antonie Van Leeuwenhoek	10.1007/s10482-014-0194-4	2014	*
Phylogeny	Solirubrobacter phytolaccae sp. nov., an endophytic bacterium isolated from roots of Phytolacca acinosa Roxb.	Wei L, Ouyang S, Wang Y, Shen X, Zhang L	Int J Syst Evol Microbiol	10.1099/ijs.0.057554-0	2013	*
Phylogeny	Solirubrobacter ginsenosidimutans sp. nov., isolated from soil of a ginseng field.	An DS, Wang L, Kim MS, Bae HM, Lee ST, Im WT	Int J Syst Evol Microbiol	10.1099/ijs.0.028431-0	2010	*
Phylogeny	Solirubrobacter soli sp. nov., isolated from soil of a ginseng field.	Kim MK, Na JR, Lee TH, Im WT, Soung NK, Yang DC	Int J Syst Evol Microbiol	10.1099/ijs.0.64715-0	2007	*
Phylogeny	Solirubrobacter pauli gen. nov., sp. nov., a mesophilic bacterium within the Rubrobacteridae related to common soil clones.	Singleton DR, Furlong MA, Peacock AD, White DC, Coleman DC, Whitman WB	Int J Syst Evol Microbiol	10.1099/ijs.0.02438-0	2003	*

References

#5617

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 14954

#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 )

#33200 ; 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;

#68371

Automatically annotated from API 50CH acid .

#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 )

#83255

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-ID100956.1 )

#121638 Collection of Institut Pasteur ; Curators of the CIP; CIP 108104
* These data were automatically processed and therefore are not curated

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Solirubrobacter pauli DSM 14954

Solirubrobacter pauli strain DSM 14954

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