Solirubrobacter soli (DSM 22325, JCM 14923, KCTC 12628)

Name: Solirubrobacter soli (DSM 22325, JCM 14923, KCTC 12628)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 14088

Type strain

Culture col. no. DSM 22325 JCM 14923 KCTC 12628 LMG 23485 Gsoil 355

NCBI tax ID(s) 1123262 363832

Special Collections DSMZ JCM KCTC Literature strains

History DSMZ <- LMG; LMG 23485 <- S.-T. Lee, KAIST <- W.-T. Im JCM <-- LMG 23485 <-- D.-C. Yang Gsoil 355. KCTC <- ST Lee, KAIST

Links

Solirubrobacter soli DSM 22325 is an aerobe, Gram-positive, rod-shaped bacterium that was isolated from soil from a ginseng field.

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

Name and taxonomic classification

SI-ID 309492

KCTC 12628,LMG 23485,JCM 14923,DSM 22325

@ref 20215

Last LPSN update 2026-05-29 08:28:12

Domain Bacteria

Phylum Actinomycetota

Class Thermoleophilia

Order Solirubrobacterales

Family Solirubrobacteraceae

Genus Solirubrobacter

Species Solirubrobacter soli

Full scientific name Solirubrobacter soli Kim et al. 2007

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell shape	Confidence
31958	positive	2 µm	rod-shaped
67771	positive
125439	positive			98.317

Colony morphology

16282

Incubation period8-14 days

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
16282	R2A MEDIUM (DSMZ Medium 830)		Medium recipe at MediaDive	Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
16282	positive	growth	28
31958	positive	growth	25-30
67770	positive	growth	28
67771	positive	growth	28

Culture pH

@ref	Ability	Type	PH	PH range
31958	positive	optimum	8
31958	positive	growth	5.0-11	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
31958	aerobe
67771	aerobe
125439	obligate aerobe	99.504

Spore formation

31958

Spore formationno

Halophily

@ref	Salt	Growth	Tested relation	Concentration
31958	NaCl	positive	growth	0.0-1.5 %
31958	NaCl	positive	optimum	0.75 %

Observation

67770

Observationquinones: MK-7(H₄)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
31958	17128 ChEBI	adipate	+	carbon source
31958	22599 ChEBI	arabinose	+	carbon source
31958	33984 ChEBI	fucose	+	carbon source
31958	24265 ChEBI	gluconate	+	carbon source
31958	17234 ChEBI	glucose	+	carbon source
31958	17306 ChEBI	maltose	+	carbon source
31958	28053 ChEBI	melibiose	+	carbon source
31958	17268 ChEBI	myo-inositol	+	carbon source
31958	506227 ChEBI	N-acetylglucosamine	+	carbon source
31958	26271 ChEBI	proline	+	carbon source
31958	26546 ChEBI	rhamnose	+	carbon source
31958	33942 ChEBI	ribose	+	carbon source
31958	17814 ChEBI	salicin	+	carbon source
31958	17992 ChEBI	sucrose	+	carbon source

Enzymes

@ref	Value	Activity	Ec
31958	acid phosphatase	+	3.1.3.2
31958	alkaline phosphatase	+	3.1.3.1
31958	catalase	+	1.11.1.6
31958	cytochrome oxidase	+	1.9.3.1
31958	gelatinase	+

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Agriculture	#Field
#Environmental	#Terrestrial	#Soil
#Host	#Plants	#Herbaceous plants (Grass,Crops)

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
16282	soil from a ginseng field	Daejeon	Republic of Korea	KOR	Asia
67770	Soil of a ginseng field		Republic of Korea	KOR	Asia
67771	From soil	KAIST	Republic of Korea	KOR	Asia

Taxonmaps

69479

Global distribution of 16S sequence AB245334 (>99% sequence identity) for Solirubrobacter soli subclade from Microbeatlas

Aquatic Samples	81
Soil Samples	998
Animal Samples	85
Plant Samples	226
Total Samples	1390

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
16282	1	Risk group (German 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	ASM42366v1 assembly for Solirubrobacter soli DSM 22325	scaffold	GCA_000423665	1123262.3	2524023148	1123262	56.31

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
16282	Solirubrobacter soli gene for 16S rRNA, partial sequence	AB245334	1495		363832

GC content

@ref	GC-content (mol%)	Method
16282	71.5	high performance liquid chromatography (HPLC)
31958	71.5

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM42366v1 assembly for Solirubrobacter soli DSM 22325
NCBI: GCA_000423665

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.50	no
125439	gram_stain	BacteriaNetⓘ	positive	98.32	no
125439	motility	BacteriaNetⓘ	no	80.76	no
125439	spore_formation	BacteriaNetⓘ	yes	48.12	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Solirubrobacter soli DSM 22325
PATRIC: 1123262.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	71.88	yes
125438	anaerobic	anaerobicⓘ	no	85.08	no
125438	spore-forming	spore-formingⓘ	yes	55.96	no
125438	aerobic	aerobicⓘ	yes	83.98	yes
125438	thermophilic	thermophileⓘ	no	94.11	yes
125438	flagellated	motile2+ⓘ	no	56.13	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Metagenomic data of microbiota in mangrove soil from Lukut River, Malaysia.	Yahaya N, Mohamed Rehan M, Hamdan NH, Nasaruddin SM.	Data Brief	10.1016/j.dib.2024.110155	2024
Genetics	Microbial community in buckwheat rhizosphere with different nitrogen application rates.	Wang D, Ren H.	PeerJ	10.7717/peerj.15514	2023
Genetics	Environmental distribution and genomic characteristics of Solirubrobacter, with proposal of two novel species.	Jiang ZM, Mou T, Sun Y, Su J, Yu LY, Zhang YQ.	Front Microbiol	10.3389/fmicb.2023.1267771	2023
Genetics	High-quality draft genome sequence of Gaiella occulta isolated from a 150 meter deep mineral water borehole and comparison with the genome sequences of other deep-branching lineages of the phylum Actinobacteria.	Severino R, Froufe HJC, Barroso C, Albuquerque L, Lobo-da-Cunha A, da Costa MS, Egas C.	Microbiologyopen	10.1002/mbo3.840	2019
Genetics	Testing the Two-Step Model of Plant Root Microbiome Acquisition Under Multiple Plant Species and Soil Sources.	Barajas HR, Martinez-Sanchez S, Romero MF, Alvarez CH, Servin-Gonzalez L, Peimbert M, Cruz-Ortega R, Garcia-Oliva F, Alcaraz LD.	Front Microbiol	10.3389/fmicb.2020.542742	2020
	Current Insights into the Role of Rhizosphere Bacteria in Disease Suppressive Soils.	Gomez Exposito R, de Bruijn I, Postma J, Raaijmakers JM.	Front Microbiol	10.3389/fmicb.2017.02529	2017
Phylogeny	Bacterial and archaeal communities in Lake Nyos (Cameroon, Central Africa).	Tiodjio RE, Sakatoku A, Nakamura A, Tanaka D, Fantong WY, Tchakam KB, Tanyileke G, Ohba T, Hell VJ, Kusakabe M, Nakamura S, Ueda A.	Sci Rep	10.1038/srep06151	2014
Enzymology	Specific microbial attachment to root knot nematodes in suppressive soil.	Adam M, Westphal A, Hallmann J, Heuer H.	Appl Environ Microbiol	10.1128/aem.03905-13	2014
	Cultivation-independent methods applied to the microbial prospection of oil and gas in soil from a sedimentary basin in Brazil.	Miqueletto PB, Andreote FD, Dias AC, Ferreira JC, Dos Santos Neto EV, de Oliveira VM.	AMB Express	10.1186/2191-0855-1-35	2011
Metabolism	Competing formate- and carbon dioxide-utilizing prokaryotes in an anoxic methane-emitting fen soil.	Hunger S, Schmidt O, Hilgarth M, Horn MA, Kolb S, Conrad R, Drake HL.	Appl Environ Microbiol	10.1128/aem.00282-11	2011
Phylogeny	Oleiagrimonas soli gen. nov., sp. nov., a genome-sequenced gammaproteobacterium isolated from an oilfield.	Fang T, Wang H, Huang Y, Zhou H, Dong P.	Int J Syst Evol Microbiol	10.1099/ijs.0.000158	2015
Phylogeny	Novosphingobium arabidopsis sp. nov., a DDT-resistant bacterium isolated from the rhizosphere of Arabidopsis thaliana.	Lin SY, Hameed A, Liu YC, Hsu YH, Lai WA, Huang HI, Young CC.	Int J Syst Evol Microbiol	10.1099/ijs.0.054460-0	2014
Phylogeny	Novosphingobium chloroacetimidivorans sp. nov., a chloroacetamide herbicide-degrading bacterium isolated from activated sludge.	Chen Q, Zhang J, Wang CH, Jiang J, Kwon SW, Sun LN, Shen WB, He J.	Int J Syst Evol Microbiol	10.1099/ijs.0.062950-0	2014
Enzymology	Burkholderia dabaoshanensis sp. nov., a heavy-metal-tolerant bacteria isolated from Dabaoshan mining area soil in China.	Zhu H, Guo J, Chen M, Feng G, Yao Q.	PLoS One	10.1371/journal.pone.0050225	2012
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

References

#16282	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 22325
#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 )
#28214	IJSEM 1453 2007 ( DOI 10.1099/ijs.0.64715-0 , PubMed 17625174 )
#31958	Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #28214
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#67771	Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;
#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 .
#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 soli (DSM 22325, JCM 14923, KCTC 12628)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Enzymes

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000423665

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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