Solirubrobacter pauli (DSM 14954, ATCC BAA-492, JCM 13025)

Name: Solirubrobacter pauli (DSM 14954, ATCC BAA-492, JCM 13025)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 14087

Type strain

Strain Designation B33D1

Culture col. no. DSM 14954 ATCC BAA-492 JCM 13025 B33D1 KCTC 9974 1 more

NCBI tax ID(s) 166793

Special Collections DSMZ JCM KCTC CIP

History <- W. B. Whitman, Univ. of Georgia, Athens, USA; B33D1 <- M. A. Furlong, Dept. Natural Sci., Clayton College and State Univ., USA 2003, R. Upchurch, Georgia Univ., Athens, USA: strain B33D1 KCTC 9974 <-- W. B. Whitman B33D1. CIP <- 2003, R. Upchurch, Georgia Univ., Athens, USA: strain B33D1

Links

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

Gram-positive motile rod-shaped genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 100956

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

@ref 20215

Last LPSN update 2026-02-09 11:21:19

Domain Bacteria

Phylum Actinomycetota

Class Thermoleophilia

Order Solirubrobacterales

Family Solirubrobacteraceae

Genus Solirubrobacter

Species Solirubrobacter pauli

Full scientific name Solirubrobacter pauli Singleton et al. 2003

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Motility
121638	positive	rod-shaped

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
5617	NUTRIENT AGAR (DSMZ Medium 1)	Medium recipe at MediaDive	Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
33200	MEDIUM 328- for nutrient agar		Distilled water make up to (1000.000 ml);Agar (15.000 g);Peptone (5.000g);Beef extract (3.000 g)
121638	CIP Medium 328	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
5617	positive	growth	28
33200	positive	growth	22
67770	positive	growth	28
121638	positive	growth	15-37
121638	negative	growth	10
121638	negative	growth	41
121638	negative	growth	45

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	99.6

Halophily

@ref	Salt	Growth	Tested relation	Concentration
121638	NaCl	positive	growth	0 %
121638	NaCl		growth	2 %
121638	NaCl		growth	4 %
121638	NaCl		growth	6 %
121638	NaCl		growth	8 %
121638	NaCl		growth	10 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68371	27613 ChEBI	amygdalin	-	builds acid from	from API 50CH acid
68371	18305 ChEBI	arbutin	-	builds acid from	from API 50CH acid
68371	17057 ChEBI	cellobiose	-	builds acid from	from API 50CH acid
121638	16947 ChEBI	citrate	-	carbon source
68371	17108 ChEBI	D-arabinose	-	builds acid from	from API 50CH acid
68371	18333 ChEBI	D-arabitol	-	builds acid from	from API 50CH acid
68371	15824 ChEBI	D-fructose	-	builds acid from	from API 50CH acid
68371	28847 ChEBI	D-fucose	-	builds acid from	from API 50CH acid
68371	12936 ChEBI	D-galactose	-	builds acid from	from API 50CH acid
68371	17634 ChEBI	D-glucose	-	builds acid from	from API 50CH acid
68371	62318 ChEBI	D-lyxose	-	builds acid from	from API 50CH acid
68371	16899 ChEBI	D-mannitol	-	builds acid from	from API 50CH acid
68371	16024 ChEBI	D-mannose	-	builds acid from	from API 50CH acid
68371	16988 ChEBI	D-ribose	-	builds acid from	from API 50CH acid
68371	17924 ChEBI	D-sorbitol	-	builds acid from	from API 50CH acid
68371	16443 ChEBI	D-tagatose	-	builds acid from	from API 50CH acid
68371	65327 ChEBI	D-xylose	-	builds acid from	from API 50CH acid
68371	17113 ChEBI	erythritol	-	builds acid from	from API 50CH acid
121638	4853 ChEBI	esculin	+	hydrolysis
68371	4853 ChEBI	esculin	+	builds acid from	from API 50CH acid
68371	16813 ChEBI	galactitol	-	builds acid from	from API 50CH acid
68371	28066 ChEBI	gentiobiose	-	builds acid from	from API 50CH acid
68371	24265 ChEBI	gluconate	-	builds acid from	from API 50CH acid
68371	17754 ChEBI	glycerol	-	builds acid from	from API 50CH acid
68371	28087 ChEBI	glycogen	-	builds acid from	from API 50CH acid
121638	606565 ChEBI	hippurate	-	hydrolysis
68371	15443 ChEBI	inulin	-	builds acid from	from API 50CH acid
68371	30849 ChEBI	L-arabinose	-	builds acid from	from API 50CH acid
68371	18403 ChEBI	L-arabitol	-	builds acid from	from API 50CH acid
68371	18287 ChEBI	L-fucose	-	builds acid from	from API 50CH acid
68371	62345 ChEBI	L-rhamnose	-	builds acid from	from API 50CH acid
68371	17266 ChEBI	L-sorbose	-	builds acid from	from API 50CH acid
68371	65328 ChEBI	L-xylose	-	builds acid from	from API 50CH acid
68371	17716 ChEBI	lactose	-	builds acid from	from API 50CH acid
68371	17306 ChEBI	maltose	-	builds acid from	from API 50CH acid
68371	6731 ChEBI	melezitose	-	builds acid from	from API 50CH acid
68371	28053 ChEBI	melibiose	-	builds acid from	from API 50CH acid
68371	320061 ChEBI	methyl alpha-D-glucopyranoside	-	builds acid from	from API 50CH acid
68371	43943 ChEBI	methyl alpha-D-mannoside	-	builds acid from	from API 50CH acid
68371	74863 ChEBI	methyl beta-D-xylopyranoside	-	builds acid from	from API 50CH acid
68371	17268 ChEBI	myo-inositol	-	builds acid from	from API 50CH acid
68371	59640 ChEBI	N-acetylglucosamine	-	builds acid from	from API 50CH acid
121638	17632 ChEBI	nitrate	-	reduction
121638	17632 ChEBI	nitrate	-	respiration
121638	16301 ChEBI	nitrite	-	reduction
68371		Potassium 2-ketogluconate	-	builds acid from	from API 50CH acid
68371		Potassium 5-ketogluconate	-	builds acid from	from API 50CH acid
68371	16634 ChEBI	raffinose	-	builds acid from	from API 50CH acid
68371	15963 ChEBI	ribitol	-	builds acid from	from API 50CH acid
68371	17814 ChEBI	salicin	-	builds acid from	from API 50CH acid
68371	28017 ChEBI	starch	-	builds acid from	from API 50CH acid
68371	17992 ChEBI	sucrose	-	builds acid from	from API 50CH acid
68371	27082 ChEBI	trehalose	-	builds acid from	from API 50CH acid
68371	32528 ChEBI	turanose	-	builds acid from	from API 50CH acid
68371	17151 ChEBI	xylitol	-	builds acid from	from API 50CH acid

Antibiotic resistance

@ref	Metabolite	Is sensitive	Is resistant
121638	0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)

Metabolite production

@ref	Chebi-ID	Metabolite	Production
121638	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test	Methylred-test
121638	15688 ChEBI	acetoin	-
121638	17234 ChEBI	glucose		-

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
121638	alcohol dehydrogenase	-	1.1.1.1
68382	alkaline phosphatase	+	3.1.3.1	from API zym
68382	alpha-chymotrypsin	-	3.4.21.1	from API zym
68382	alpha-fucosidase	-	3.2.1.51	from API zym
68382	alpha-galactosidase	-	3.2.1.22	from API zym
68382	alpha-glucosidase	+	3.2.1.20	from API zym
68382	alpha-mannosidase	-	3.2.1.24	from API zym
121638	amylase	+
68382	beta-galactosidase	+	3.2.1.23	from API zym
121638	beta-galactosidase	+	3.2.1.23
68382	beta-glucosidase	+	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
121638	caseinase	+	3.4.21.50
121638	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
121638	DNase	-
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
121638	gamma-glutamyltransferase	-	2.3.2.2
121638	gelatinase	-
121638	lecithinase	-
68382	leucine arylamidase	+	3.4.11.1	from API zym
121638	lipase	-
68382	lipase (C 14)	-		from API zym
121638	lysine decarboxylase	-	4.1.1.18
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
121638	ornithine decarboxylase	-	4.1.1.17
121638	oxidase	-
121638	phenylalanine ammonia-lyase	-	4.3.1.24
121638	protease	-
68382	trypsin	-	3.4.21.4	from API zym
121638	tryptophan deaminase	-
121638	tween esterase	-
121638	urease	-	3.5.1.5
68382	valine arylamidase	+		from API zym

API zym

@ref	Control	Alkaline phosphatase	Esterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	Lipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	Trypsin	alpha- Chymotrypsin	Acid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	alpha- Galactosidase	beta- Galactosidase	beta- Glucuronidase	alpha- Glucosidase	beta- Glucosidase	N-acetyl-beta- glucosaminidase	alpha- Mannosidase	alpha- Fucosidase
121638	-	+	+	+	-	+	+	-	-	-	+	+	-	+	-	+	+	-	-	-

API 50CHac

@ref	ControlQ	GLY	ERY	DARA	LARA	RIB	DXYL	LXYL	ADO	MDX	GAL	GLU	FRU	MNE	SBE	RHA	DUL	INO	MAN	SOR	MDM	MDG	NAG	AMY	ARB	ESC	SAL	CEL	MAL	LAC	MEL	SAC	TRE	INU	MLZ	RAF	AMD	GLYG	XLT	GEN	TUR	LYX	TAG	DFUC	LFUC	DARL	LARL	GNT	2KG	5KG
121638	not determinedn.d.	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Agriculture	-
#Environmental	#Terrestrial	#Soil
#Host	#Invertebrates (Other)	#Annelida

Isolation

@ref	Sample type	Host species	Geographic location	Country	Country ISO 3 Code	Continent	Isolation date
5617	burrow of the epigeic earthworm Lumbricus rubellus in an agricultural soil	Lumbricus rubellus	Georgia, Athens	USA	USA	North America
67770	Burrow of the epigeic earthworm Lumbricus rubellus in agricultural soil	Lumbricus rubellus	Athens, GA	USA	USA	North America
121638	Environment, Burrow of Lumbricus rubellus in agricultural soil		Athens, Georgia	United States of America	USA	North America	1996

Taxonmaps

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

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
5617	1	Risk group (German classification) According to TRBA 466
121638	1	Risk group (French classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	ASM363375v1 assembly for Solirubrobacter pauli DSM 14954	scaffold	GCA_003633755	166793.3	2737471645	166793	69.07

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
5617	Earthworm burrow bacterium B33D1 16S ribosomal RNA gene, partial sequence	AY039806	1366		166793

GC content

@ref	GC-content (mol%)	Method
67770	71.6-72	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Solirubrobacter pauli DSM 14954
NCBI: GCA_003633755

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	78.90	no
125439	motility	BacteriaNetⓘ	yes	58.50	no
125439	gram_stain	BacteriaNetⓘ	positive	89.10	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.60	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Solirubrobacter pauli strain DSM 14954
PATRIC: 166793.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	70.57	no
125438	anaerobic	anaerobicⓘ	no	86.74	no
125438	spore-forming	spore-formingⓘ	yes	51.21	no
125438	aerobic	aerobicⓘ	yes	85.61	no
125438	thermophilic	thermophileⓘ	no	95.00	yes
125438	flagellated	motile2+ⓘ	no	52.69	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Baekduia soli gen. nov., sp. nov., a novel bacterium isolated from the soil of Baekdu Mountain and proposal of a novel family name, Baekduiaceae fam. nov.	An DS, Siddiqi MZ, Kim KH, Yu HS, Im WT.	J Microbiol	10.1007/s12275-018-7107-6	2018
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;
#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 .
#121638	Collection of Institut Pasteur ; Curators of the CIP; CIP 108104
#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 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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Solirubrobacter pauli (DSM 14954, ATCC BAA-492, JCM 13025)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Halophily

Metabolite utilization

Antibiotic resistance

Metabolite production

Metabolite tests

Enzymes

API zym

API 50CHac

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_003633755

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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