Streptomyces naganishii (DSM 40282, ATCC 23939, CBS 923.68)

Name: Streptomyces naganishii (DSM 40282, ATCC 23939, CBS 923.68)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 15419

Type strain

Strain Designation H-4871

Culture col. no. DSM 40282 ATCC 23939 CBS 923.68 IFO 12892 ISP 5282 9 more

NCBI tax ID(s) 1306179 285447

Special Collections DSMZ JCM JMRC

History DSMZ <- E.B. Shirling, ISP <- T. Yamaguchi, H-4871 JCM <-- KCC S-0190 <-- H. Yonehara <-- T. Yamaguchi H-4871.

Links

Streptomyces naganishii H-4871 is a bacterium that was isolated from soil.

genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 389333

ATCC 23939,IFO 12892,DSM 40282,JCM 4190,NRRL B-1816,JCM 4654,CBS 923.68,NBRC 12892,BCRC 15130,CCRC 15130

@ref 20215

Last LPSN update 2026-05-29 08:28:32

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Kitasatosporales

Family Streptomycetaceae

Genus Streptomyces

Species Streptomyces naganishii

Full scientific name Streptomyces naganishii Yamaguchi and Saburi 1955 (Approved Lists 1980)

Morphology

Cell morphology

@ref	Motility	Confidence	Gram stain
125439		92.181
125439		99.306	positive

Multimedia

@ref:	9433
multimedia content:	DSM_40282.jpg
multimedia.multimedia content:	https://www.dsmz.de/microorganisms/photos/DSM_40282.jpg
caption:	Medium 65 28°C
intellectual property rights:	© Leibniz-Institut DSMZ
manual_annotation:	1

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
9433	GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)		Medium recipe at MediaDive	Name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) Composition: Agar 18.0 g/l Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l CaCO3 2.0 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
9433	positive	growth	28
67770	positive	growth	28

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	98.291

Spore formation

@ref	Spore formation	Confidence
125438		91.382

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Soil

Isolation

@ref	Sample type	Country	Country ISO 3 Code	Continent
9433	soil	Japan	JPN	Asia

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
9433	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
66792	ASM1465057v1 assembly for Streptomyces naganishii JCM 4654	contig	GCA_014650575	1306179.6		1306179	62.84
66792	ASM131542v1 assembly for Streptomyces naganishii JCM 4654	contig	GCA_001315425	1306179.5	2734481987	1306179	0

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Streptomyces naganishii gene for 16S rRNA, partial sequence, strain: NBRC 12892	AB184224	1472	1306179
20218	Streptomyces naganishii strain NRRL B-1816T 16S ribosomal RNA gene, partial sequence	DQ442529	1501	1306179
124043	Streptomyces naganishii JCM 4654 16S ribosomal RNA gene, partial sequence.	MT760592	1389	1306179

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM1465057v1 assembly for Streptomyces naganishii JCM 4654
NCBI: GCA_014650575

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	98.29	no
125439	gram_stain	BacteriaNetⓘ	positive	99.31	no
125439	motility	BacteriaNetⓘ	no	92.18	no
125439	spore_formation	BacteriaNetⓘ	yes	87.92	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Streptomyces naganishii JCM 4654
PATRIC: 1306179.6

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	89.62	no
125438	anaerobic	anaerobicⓘ	no	90.98	no
125438	spore-forming	spore-formingⓘ	yes	91.38	no
125438	aerobic	aerobicⓘ	yes	86.94	no
125438	thermophilic	thermophileⓘ	no	97.00	yes
125438	flagellated	motile2+ⓘ	no	88.50	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Chemical probing of thiotetronate bio-assembly.	Havemann J, Yurkovich ME, Jenkins R, Harringer S, Tao W, Wen S, Sun Y, Leadlay PF, Tosin M.	Chem Commun (Camb)	10.1039/c6cc09933e	2017
Enzymology	Two acidic, thermophilic GH28 polygalacturonases from Talaromyces leycettanus JCM 12802 with application potentials for grape juice clarification.	Li Y, Wang Y, Tu T, Zhang D, Ma R, You S, Wang X, Yao B, Luo H, Xu B.	Food Chem	10.1016/j.foodchem.2017.06.037	2017
Pathogenicity	Potentials of Actinomycetes from Reserved Environments as Antibacterial Agents Against Drug-Resistant Clinical Bacterial Strains.	Ahmed RN, Daniel F, Gbala ID, Sanni A.	Ethiop J Health Sci	10.4314/ejhs.v30i2.13	2020
	Antibacterial activity and biosynthetic potential of Streptomyces sp. PBR19, isolated from forest rhizosphere soil of Assam.	Mazumdar R, Thakur D.	Braz J Microbiol	10.1007/s42770-024-01454-3	2024
Biotechnology	The Co-Inoculation Effect on Triticum aestivum Growth with Synthetic Microbial Communities (SynComs) and Their Potential in Agrobiotechnology	Mazylyte R, Kailiuviene J, Mazoniene E, Orola L, Kaziuniene J, Mazylyte K, Lastauskiene E, Gegeckas A.	Plants (Basel)		2024
Metabolism	Studies on the production of actinomycin-D by Streptomyces griseoruber--a novel source.	Praveen V, Tripathi CK.	Lett Appl Microbiol	10.1111/j.1472-765x.2009.02689.x	2009
	Insecticidal characteristics and structural identification of the potential active compounds from Streptomyces sp. KR0006: Strain improvement through mutagenesis.	Kim YS, Umurzokov M, Cho KM, Choi JS, Park KW.	PLoS One	10.1371/journal.pone.0274766	2022
	Plant growth-promoting properties of Streptomyces spp. isolates and their impact on mung bean plantlets' rhizosphere microbiome.	Nonthakaew N, Panbangred W, Songnuan W, Intra B.	Front Microbiol	10.3389/fmicb.2022.967415	2022
	Isolation, Characterization, and Efficacy of Actinobacteria Associated with Arbuscular Mycorrhizal Spores in Promoting Plant Growth of Chili (Capsicum flutescens L.).	Chaiya L, Kumla J, Suwannarach N, Kiatsiriroat T, Lumyong S.	Microorganisms	10.3390/microorganisms9061274	2021
	Complete integration of carbene-transfer chemistry into biosynthesis.	Huang J, Quest A, Cruz-Morales P, Deng K, Pereira JH, Van Cura D, Kakumanu R, Baidoo EEK, Dan Q, Chen Y, Petzold CJ, Northen TR, Adams PD, Clark DS, Balskus EP, Hartwig JF, Mukhopadhyay A, Keasling JD.	Nature	10.1038/s41586-023-06027-2	2023
	Community Structures and Antifungal Activity of Root-Associated Endophytic Actinobacteria in Healthy and Diseased Cucumber Plants and Streptomyces sp. HAAG3-15 as a Promising Biocontrol Agent.	Cao P, Li C, Wang H, Yu Z, Xu X, Wang X, Zhao J, Xiang W.	Microorganisms	10.3390/microorganisms8020236	2020
Metabolism	Production of anti-cancer agent using microbial biotransformation.	Roh C, Kang C.	Molecules	10.3390/molecules191016684	2014
	Endophytic actinobacteria of a halophytic desert plant Pteropyrum olivieri: promising growth enhancers of sunflower.	Zahra T, Hamedi J, Mahdigholi K.	3 Biotech	10.1007/s13205-020-02507-8	2020
	Biocontrol Potential of Endophytic Actinobacteria against Fusarium solani, the Causal Agent of Sudden Decline Syndrome on Date Palm in the UAE.	Alblooshi AA, Purayil GP, Saeed EE, Ramadan GA, Tariq S, Altaee AS, El-Tarabily KA, AbuQamar SF.	J Fungi (Basel)	10.3390/jof8010008	2021
Metabolism	The role of trace metal ions in aflatoxin B1 degradation by Flavobacterium aurantiacum.	D'Souza DH, Brackett RE.	J Food Prot	10.4315/0362-028x-61.12.1666	1998
	Diversity, Novelty, and Antimicrobial Activity of Endophytic Actinobacteria From Mangrove Plants in Beilun Estuary National Nature Reserve of Guangxi, China.	Jiang ZK, Tuo L, Huang DL, Osterman IA, Tyurin AP, Liu SW, Lukyanov DA, Sergiev PV, Dontsova OA, Korshun VA, Li FN, Sun CH.	Front Microbiol	10.3389/fmicb.2018.00868	2018
	Factors Affecting Aflatoxin B₁ Removal by Flavobacterium aurantiacum.	Line JE, Brackett RE.	J Food Prot	10.4315/0362-028x-58.1.91	1995
	Role of Toxin Concentration and Second Carbon Source in Microbial Transformation of Aflatoxin B₁ by Flavobacterium aurantiacum.	Line JE, Brackett RE.	J Food Prot	10.4315/0362-028x-58.9.1042	1995
Metabolism	Loop of Streptomyces Feruloyl Esterase Plays an Important Role in the Enzyme's Catalyzing the Release of Ferulic Acid from Biomass.	Uraji M, Tamura H, Mizohata E, Arima J, Wan K, Ogawa K, Inoue T, Hatanaka T.	Appl Environ Microbiol	10.1128/aem.02300-17	2018
Phylogeny	Phylogenetic relationships in the family Streptomycetaceae using multi-locus sequence analysis.	Labeda DP, Dunlap CA, Rong X, Huang Y, Doroghazi JR, Ju KS, Metcalf WW.	Antonie Van Leeuwenhoek	10.1007/s10482-016-0824-0	2017
Metabolism	Metabolomics of the bio-degradation process of aflatoxin B1 by actinomycetes at an initial pH of 6.0.	Eshelli M, Harvey L, Edrada-Ebel R, McNeil B.	Toxins (Basel)	10.3390/toxins7020439	2015
Metabolism	Structure elucidation of A58365A and A58365B, angiotensin converting enzyme inhibitors produced by Streptomyces chromofuscus.	Hunt AH, Mynderse JS, Samlaska SK, Fukuda DS, Maciak GM, Kirst HA, Occolowitz JL, Swartzendruber JK, Jones ND.	J Antibiot (Tokyo)	10.7164/antibiotics.41.771	1988
Metabolism	Isolation of A58365A and A58365B, angiotensin converting enzyme inhibitors produced by Streptomyces chromofuscus.	Mynderse JS, Samlaska SK, Fukuda DS, Du Bus RH, Baker PJ.	J Antibiot (Tokyo)	10.7164/antibiotics.38.1003	1985
	A genomics-led approach to deciphering the mechanism of thiotetronate antibiotic biosynthesis.	Tao W, Yurkovich ME, Wen S, Lebe KE, Samborskyy M, Liu Y, Yang A, Liu Y, Ju Y, Deng Z, Tosin M, Sun Y, Leadlay PF.	Chem Sci	10.1039/c5sc03059e	2016
Metabolism	Microbial transformations of natural antitumor agents XXII: Conversion of bouvardin to O-desmethylbouvardin and bouvardin catechol.	Petroski RJ, Bates RB, Linz GS, Rosazza JP.	J Pharm Sci	10.1002/jps.2600721114	1983
Metabolism	The industrial anaerobe Clostridium acetobutylicum uses polyketides to regulate cellular differentiation.	Herman NA, Kim SJ, Li JS, Cai W, Koshino H, Zhang W.	Nat Commun	10.1038/s41467-017-01809-5	2017
	Induction of ermSV by 16-membered-ring macrolide antibiotics.	Kamimiya S, Weisblum B.	Antimicrob Agents Chemother	10.1128/aac.41.3.530	1997
Pathogenicity	Aflatoxin B 1 uptake by Flavobacterium aurantiacum and resulting toxic effects.	Lillehoj EB, Ciegler A, Hall HH.	J Bacteriol	10.1128/jb.93.1.464-471.1967	1967
Genetics	Genomic insights into biosynthesis and adaptation in the bioactive marine bacterium Streptomyces albidoflavus VIP-1 from the Red Sea.	Sedeek AM, Elfeky H, Hanora AS, Solyman SM.	BMC Microbiol	10.1186/s12866-025-04109-x	2025
Genetics	Streptomyces spinosus sp. nov. and Streptomyces shenzhenensis subsp. oryzicola subsp. nov. endophytic actinobacteria isolated from Jasmine rice and their genome mining for potential as antibiotic producers and plant growth promoters.	Kaewkla O, Sukpanoa S, Suriyachadkun C, Chamroensaksi N, Chumroenphat T, Franco CMM.	Antonie Van Leeuwenhoek	10.1007/s10482-022-01741-9	2022
Phylogeny	Streptomyces mahasarakhamensis sp. nov., an Endophytic Actinobacterium Isolated from Jasmine Rice and its Potential as plant Growth Promoter.	Sukpanoa S, Kaewkla O, Suriyachadkun C, Papayrata C, Klankeo P, Franco CMM.	Curr Microbiol	10.1007/s00284-024-03747-0	2024
	Streptomyces argyrophyllae sp. nov., isolated from the rhizosphere soil of Cathaya argyrophylla.	Mo P, Zhou F, Luo X, Zhang Y, Deng A, Xie P, Wang Y.	Arch Microbiol	10.1007/s00203-023-03668-9	2023
Phylogeny	Description of Streptomyces siderophoricus sp. nov., a promising nocardamine-producing species isolated from the rhizosphere soil of Mangifera indica.	Duangupama T, Pittayakhajonwut P, Intaraudom C, Suriyachadkun C, Tadtong S, Kuncharoen N, He YW, Tanasupawat S, Thawai C.	J Antibiot (Tokyo)	10.1038/s41429-024-00763-x	2024
Phylogeny	Streptomyces endocoffeicus sp. nov., an endophytic actinomycete isolated from Coffea arabica (L.).	Nammali A, Intaraudom C, Pittayakhajonwut P, Suriyachadkun C, Tadtong S, Tanasupawat S, Thawai C.	Antonie Van Leeuwenhoek	10.1007/s10482-021-01648-x	2021
Phylogeny	Streptomyces mayonensis sp. nov., isolated from the volcanic soils of Mt. Mayon, Philippines.	Aguilar GM, Oliveros KMP, Rosana ARR, Opulencia RB, Raymundo AK.	Int J Syst Evol Microbiol	10.1099/ijsem.0.006900	2025
Phylogeny	Streptomyces fodineus sp. nov., an actinobacterium with antifungal activity isolated from mine area soil.	Kim MK, Kang HJ, Roh SG, Park JS, Kim SB.	Int J Syst Evol Microbiol	10.1099/ijsem.0.003353	2019
Phylogeny	Streptomyces xylanilyticus sp. nov., isolated from soil.	Moonmangmee D, Kanchanasin P, Phongsopitanun W, Tanasupawat S, Moonmangmee S.	Int J Syst Evol Microbiol	10.1099/ijsem.0.002282	2017
Enzymology	Streptomyces euryhalinus sp. nov., a new actinomycete isolated from a mangrove forest.	Biswas K, Choudhury JD, Mahansaria R, Saha M, Mukherjee J.	J Antibiot (Tokyo)	10.1038/ja.2017.3	2017
Enzymology	Leucobacter humi sp. nov., Isolated from Forest Soil.	Her J, Lee SS.	Curr Microbiol	10.1007/s00284-015-0820-z	2015
Phylogeny	Streptomyces xinjiangensis sp. nov., an actinomycete isolated from Lop Nur region.	Cheng C, Li YQ, Asem MD, Lu CY, Shi XH, Chu X, Zhang WQ, Di An D, Li WJ.	Arch Microbiol	10.1007/s00203-016-1234-4	2016
Metabolism	Streptomyces lactacystinicus sp. nov. and Streptomyces cyslabdanicus sp. nov., producing lactacystin and cyslabdan, respectively.	Take A, Matsumoto A, Omura S, Takahashi Y.	J Antibiot (Tokyo)	10.1038/ja.2014.162	2015
Phylogeny	Streptomyces seymenliensis sp. nov., isolated from soil.	Tatar D, Sahin N.	Antonie Van Leeuwenhoek	10.1007/s10482-014-0339-5	2015
Phylogeny	Streptomyces panaciradicis sp. nov., a beta-glucosidase-producing bacterium isolated from ginseng rhizoplane.	Lee HJ, Cho GY, Chung SH, Whang KS.	Int J Syst Evol Microbiol	10.1099/ijs.0.061705-0	2014
Phylogeny	Streptomyces araujoniae sp. nov.: an actinomycete isolated from a potato tubercle.	da Silva LJ, Taketani RG, de Melo IS, Goodfellow M, Zucchi TD.	Antonie Van Leeuwenhoek	10.1007/s10482-013-9901-9	2013
Phylogeny	Streptomyces erringtonii sp. nov. and Streptomyces kaempferi sp. nov., isolated from a hay meadow soil.	Santhanam R, Rong X, Huang Y, Goodfellow M.	Antonie Van Leeuwenhoek	10.1007/s10482-012-9788-x	2013
Phylogeny	Streptomyces chiangmaiensis sp. nov. and Streptomyces lannensis sp. nov., isolated from the South-East Asian stingless bee (Tetragonilla collina).	Promnuan Y, Kudo T, Ohkuma M, Chantawannakul P.	Int J Syst Evol Microbiol	10.1099/ijs.0.045930-0	2013
Phylogeny	Leucobacter denitrificans sp. nov., isolated from cow dung.	Weon HY, Anandham R, Tamura T, Hamada M, Kim SJ, Kim YS, Suzuki K, Kwon SW.	J Microbiol	10.1007/s12275-012-1324-1	2012
Phylogeny	Streptomyces ziwulingensis sp. nov., isolated from grassland soil.	Lin YB, Wang XY, Wang TT, An SS, Shi P, Wei GH.	Int J Syst Evol Microbiol	10.1099/ijs.0.043026-0	2013
Phylogeny	Streptomyces manipurensis sp. nov., a novel actinomycete isolated from a limestone deposit site in Manipur, India.	Nimaichand S, Zhu WY, Yang LL, Ming H, Nie GX, Tang SK, Ningthoujam DS, Li WJ.	Antonie Van Leeuwenhoek	10.1007/s10482-012-9720-4	2012
Phylogeny	Streptomyces coacervatus sp. nov., isolated from the intestinal tract of Armadillidium vulgare.	Shibazaki A, Omoto Y, Kudo T, Yaguchi T, Saito A, Ando A, Mikami Y, Gonoi T.	Int J Syst Evol Microbiol	10.1099/ijs.0.019091-0	2011
Phylogeny	Streptomyces zinciresistens sp. nov., a zinc-resistant actinomycete isolated from soil from a copper and zinc mine.	Lin YB, Wang XY, Li HF, Wang NN, Wang HX, Tang M, Wei GH.	Int J Syst Evol Microbiol	10.1099/ijs.0.024018-0	2011
Phylogeny	Streptomyces alni sp. nov., a daidzein-producing endophyte isolated from a root of Alnus nepalensis D. Don.	Liu N, Wang H, Liu M, Gu Q, Zheng W, Huang Y.	Int J Syst Evol Microbiol	10.1099/ijs.0.65769-0	2009
Phylogeny	Streptomyces triticagri sp. nov. and Streptomyces triticirhizae sp. nov., two novel Actinobacteria isolated from the rhizosphere soil of wheat (Triticum aestivum L.).	Han C, Yu Z, Zhao J, Shi H, Hu J, Yu B, Song J, Shen Y, Xiang W, Wang X	Int J Syst Evol Microbiol	10.1099/ijsem.0.003727	2020
Phylogeny	Streptomyces boninensis sp. nov., isolated from soil from a limestone cave in the Ogasawara Islands.	Take A, Inahashi Y, Omura S, Takahashi Y, Matsumoto A	Int J Syst Evol Microbiol	10.1099/ijsem.0.002753	2018

References

#9433	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 40282
#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 )
#20216	Curators of the JMRC: Jena Microbial Resource Collection (JMRC):
#20218	Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )
#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;
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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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About us

Streptomyces naganishii (DSM 40282, ATCC 23939, CBS 923.68)

Name and taxonomic classification

Morphology

Cell morphology

Multimedia

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_014650575

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

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