Streptacidiphilus oryzae (DSM 45098, CGMCC 4.2012, CIP 109342)

Name: Streptacidiphilus oryzae (DSM 45098, CGMCC 4.2012, CIP 109342)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 14879

Type strain

Strain Designation TH49

Culture col. no. DSM 45098 CGMCC 4.2012 CIP 109342 JCM 13271 KCTC 19220 2 more

NCBI tax ID(s) 348818

Special Collections DSMZ JCM KCTC CIP Literature strains

Links

Streptacidiphilus oryzae TH49 is an aerobe, spore-forming, mesophilic prokaryote that was isolated from rice field soil sample.

spore-forming Gram-positive rod-shaped aerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 297340

CGMCC 4.2012,JCM 13271,CIP 109342,KCTC 19220,BCRC 16837,CCRC 16837,DSM 45098

@ref 20215

Last LPSN update 2025-12-16 09:50:28

Domain Bacillati

Phylum Actinomycetota

Class Actinomycetes

Order Kitasatosporales

Family Streptomycetaceae

Genus Streptacidiphilus

Species Streptacidiphilus oryzae

Full scientific name Streptacidiphilus oryzae Wang et al. 2006

Synonyms (1)

Phaeacidiphilus oryzae

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
31741	positive	1 µm	0.7 µm	rod-shaped
67771	positive
125439	positive				98.9

Pigmentation

31741

Productionyes

Multimedia

@ref:	12340
multimedia content:	DSM_45098.jpg
multimedia.multimedia content:	https://www.dsmz.de/microorganisms/photos/DSM_45098.jpg
caption:	Medium 987 28°C
intellectual property rights:	© Leibniz-Institut DSMZ
manual_annotation:	1

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
12340	ISP2 MEDIUM (DSMZ Medium 987)	Medium recipe at MediaDive	Name: ISP 2 MEDIUM (DSMZ Medium 987) Composition: Agar 20.0 g/l Malt extract 10.0 g/l Dextrose 4.0 g/l Yeast extract 4.0 g/l Distilled water
12340	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
12340	ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84)	Medium recipe at MediaDive	Name: ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84) Composition: Agar 20.0 g/l Rolled oats 20.0 g/l ZnSO4 x 7 H2O 0.001 g/l MnCl2 x 4 H2O 0.001 g/l FeSO4 x 7 H2O 0.001 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
12340	positive	growth	28	mesophilic
31741	positive	growth	28-37	mesophilic
31741	positive	optimum	30	mesophilic
67770	positive	growth	28	mesophilic
67771	positive	growth	28	mesophilic

Culture pH

@ref	Ability	Type	PH	PH range
31741	positive	optimum	05-06
31741	positive	growth	3-6.5	acidophile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
31741	aerobe
67771	aerobe
125439	obligate aerobe	98.2

Spore formation

@ref	Spore formation	Confidence
31741
125439		90.8

Observation

@ref	Observation
31741	aggregates in chains
67770	quinones: MK-9(H₆), MK-9(H₈)
67771	quinones: MK-9(H6), MK-9(H8)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
31741	16449 ChEBI	alanine	+	carbon source
31741	22599 ChEBI	arabinose	+	carbon source
31741	17057 ChEBI	cellobiose	+	carbon source
31741	28757 ChEBI	fructose	+	carbon source
31741	28260 ChEBI	galactose	+	carbon source
31741	17234 ChEBI	glucose	+	carbon source
31741	28087 ChEBI	glycogen	+	carbon source
31741	27570 ChEBI	histidine	+	carbon source
31741	18403 ChEBI	L-arabitol	+	carbon source
31741	17716 ChEBI	lactose	+	carbon source
31741	29864 ChEBI	mannitol	+	carbon source
31741	37684 ChEBI	mannose	+	carbon source
31741	17632 ChEBI	nitrate	+	reduction
31741	28044 ChEBI	phenylalanine	+	carbon source
31741	15361 ChEBI	pyruvate	+	carbon source
31741	16634 ChEBI	raffinose	+	carbon source
31741	26546 ChEBI	rhamnose	+	carbon source
31741	17814 ChEBI	salicin	+	carbon source
31741	26986 ChEBI	threonine	+	carbon source

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
12340	rice field soil sample	Nontaburi Province	Thailand	THA	Asia
67770	Rice-field soil	Nontaburi Province	Thailand	THA	Asia
67771	From Rice-field soil	Nontaburi Province	Thailand	THA	Asia

Taxonmaps

69479

Global distribution of 16S sequence DQ208700 (>99% sequence identity) for Streptacidiphilus oryzae subclade from Microbeatlas

Aquatic Samples	84
Soil Samples	524
Animal Samples	77
Plant Samples	54
Total Samples	739

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
12340	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	ASM74481v1 assembly for Phaeacidiphilus oryzae TH49	contig	GCA_000744815	1449353.3	2574179794	1449353	76.77

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
12340	Streptacidiphilus oryzae strain TH49 16S ribosomal RNA gene, partial sequence	DQ208700	1446		348818

GC content

@ref	GC-content (mol%)	Method
67770	73.4	genome sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Phaeacidiphilus oryzae TH49
NCBI: GCA_000744815

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	90.80	no
125439	motility	BacteriaNetⓘ	no	85.00	no
125439	gram_stain	BacteriaNetⓘ	positive	98.90	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	98.20	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Streptacidiphilus oryzae TH49
PATRIC: 1449353.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	89.78	yes
125438	anaerobic	anaerobicⓘ	no	94.28	yes
125438	spore-forming	spore-formingⓘ	yes	86.78	no
125438	aerobic	aerobicⓘ	yes	87.03	yes
125438	thermophilic	thermophileⓘ	no	97.00	yes
125438	flagellated	motile2+ⓘ	no	82.50	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Targeted Large-Scale Genome Mining and Candidate Prioritization for Natural Product Discovery.	Malit JJL, Leung HYC, Qian PY.	Mar Drugs	10.3390/md20060398	2022
Phylogeny	Streptacidiphilus oryzae sp. nov., an actinomycete isolated from rice-field soil in Thailand.	Wang L, Huang Y, Liu Z, Goodfellow M, Rodriguez C	Int J Syst Evol Microbiol	10.1099/ijs.0.64165-0	2006

References

#12340	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 45098
#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 )
#31741	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 #28016 (see below)
#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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Streptacidiphilus oryzae (DSM 45098, CGMCC 4.2012, CIP 109342)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Multimedia

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Observation

Metabolite utilization

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000744815

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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