Croceifilum oryzae (DSM 46876, CCUG 66446, JCM 30426)

Name: Croceifilum oryzae (DSM 46876, CCUG 66446, JCM 30426)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 131502

Type strain

Strain Designation ZYf1a3

Culture col. no. DSM 46876 CCUG 66446 JCM 30426 ZYf1a3

NCBI tax ID(s) 1553429

Special Collections DSMZ CCUG JCM

History <- K. Hatayama, Sagami Chemical Research, Japan; ZYf1a3 K. Hatayama; Sagami Chem. Res. Inst., Japan; ZYf1a3.

Links

Croceifilum oryzae ZYf1a3 is an aerobe, mesophilic prokaryote that was isolated from rice paddy soil.

aerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 402111

JCM 30426,DSM 46876,CCUG 66446

@ref 20215

Last LPSN update 2026-02-09 11:31:28

Domain Bacteria

Phylum Bacillota

Class Bacilli

Order Caryophanales

Family Thermoactinomycetaceae

Genus Croceifilum

Species Croceifilum oryzae

Full scientific name Croceifilum oryzae Hatayama and Kuno 2015

Morphology

Colony morphology

63332

Incubation period2-3 days

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
22729	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)	Range
22729	positive	growth	28	mesophilic
63332	positive	growth	30	mesophilic
67770	positive	growth	28	mesophilic

Physiology and metabolism

Oxygen tolerance

63332

Oxygen toleranceaerobe

Observation

67770

Observationquinones: MK-7

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	Sampling date	Geographic location	Country	Country ISO 3 Code	Continent
22729	rice paddy soil		Kanagawa, Zama	Japan	JPN	Asia
63332	Rice paddy soil	2013-03-20	Kanagawa,Zama	Japan	JPN	Asia
67770	Rice paddy soil			Japan	JPN	Asia

Taxonmaps

69479

Global distribution of 16S sequence LC005486 (>99% sequence identity) for Thermoactinomycetaceae from Microbeatlas

Aquatic Samples	962
Soil Samples	3183
Animal Samples	711
Plant Samples	893
Total Samples	5749

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
22729	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
124043	ASM3081431v1 assembly for Croceifilum oryzae DSM 46876	contig	GCA_030814315	1553429.3	2926658099	1553429	60.13

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
22729	Croceifilum oryzae gene for 16S ribosomal RNA, partial sequence, clone: ZYf1a3c1	LC005484	1428	1553429
67770	Croceifilum oryzae gene for 16S ribosomal RNA, partial sequence, clone: ZYf1a3c3	LC005485	1427	1553429
67770	Croceifilum oryzae gene for 16S ribosomal RNA, partial sequence, clone: ZYf1a3c5	LC005486	1428	1553429

GC content

@ref	GC-content (mol%)	Method
22729	42.5	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: Croceifilum oryzae DSM 46876
IMG: 2926658099

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	70.70	no
125439	motility	BacteriaNetⓘ	yes	50.80	no
125439	gram_stain	BacteriaNetⓘ	positive	76.70	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	79.30	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Croceifilum oryzae gen. nov., sp. nov., isolated from rice paddy soil.	Hatayama K, Kuno T	Int J Syst Evol Microbiol	10.1099/ijsem.0.000537	2015

References

#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 )
#22729	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 46876
#63332	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 66446
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#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 .
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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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Croceifilum oryzae (DSM 46876, CCUG 66446, JCM 30426)

Name and taxonomic classification

Morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Observation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_030814315

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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