Herbidospora cretacea (DSM 44071, IAM 14284, IFO 15474)

Name: Herbidospora cretacea (DSM 44071, IAM 14284, IFO 15474)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 16507

Type strain

Strain Designation K-319

Culture col. no. DSM 44071 IAM 14284 IFO 15474 JCM 8553 NBRC 15474 10 more

NCBI tax ID(s) 28444

Special Collections DSMZ JCM KCTC JMRC

History DSMZ <- IMET <- JCM, K-319 JCM <-- T. Kudo K-319.

Links

Herbidospora cretacea K-319 is a bacterium that was isolated from soil collected in Saitama.

genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 46177

ATCC 51904,JCM 8553,IFO 15474,NCIMB 13372,DSM 44071,IAM 14284,VKM Ac-1997,KCTC 9335,NBRC 15474,BCRC 16356,CCRC 16356,IAM 142840

@ref 20215

Last LPSN update 2026-05-29 08:28:47

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Streptosporangiales

Family Streptosporangiaceae

Genus Herbidospora

Species Herbidospora cretacea

Full scientific name Herbidospora cretacea Kudo et al. 1993

Synonyms (2)

Streptosporangium claviforme
Herbidospora osyris

BacDive ID	Other strains from **Herbidospora cretacea** (9)	Type strain
16508	H. cretacea D1, DSM 44127, IPV 2852, NBRC 15623, NCB ...
16509	H. cretacea DSM 45214, BCC 49353, CCTCC AA 208019, JCM ...
165810	H. cretacea JCM 8548
165811	H. cretacea JCM 8549, NRRL B-16917
165812	H. cretacea JCM 8550
165813	H. cretacea JCM 8551
165814	H. cretacea JCM 8552
165815	H. cretacea JCM 8554
165816	H. cretacea JCM 8555

Morphology

Cell morphology

@ref	Gram stain	Confidence
125438	positive	90.508
125439	positive	98.836

Multimedia

@ref:	11470
multimedia content:	DSM_44071-1.jpg
multimedia.multimedia content:	https://www.dsmz.de/microorganisms/photos/DSM_44071-1.jpg
intellectual property rights:	© Leibniz-Institut DSMZ
manual_annotation:	1

@ref:	11470
multimedia content:	DSM_44071.jpg
multimedia.multimedia content:	https://www.dsmz.de/microorganisms/photos/DSM_44071.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
11470	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
11470	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)
11470	positive	growth	28
67770	positive	growth	28

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	97.218

Spore formation

@ref	Spore formation	Confidence
125438		91.475

Observation

67770

Observationquinones: MK-10(III,IX-H₄), MK-10(H₂), MK-10(H₆)

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Soil

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
11470	soil collected in Saitama	Saitama	Japan	JPN	Asia
67770	Soil	Saitama Pref.	Japan	JPN	Asia

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
11470	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	ASM157060v1 assembly for Herbidospora cretacea NBRC 15474	scaffold	GCA_001570605	28444.4	2724679244	28444	61.26

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
11470	Herbidospora cretacea gene for 16S ribosomal RNA, partial sequence	D85485	1475		28444

GC content

@ref	GC-content (mol%)	Method
67770	70.7	genome sequence analysis
67770	70	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: ASM157060v1 assembly for Herbidospora cretacea NBRC 15474
NCBI: GCA_001570605

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	gram_stain	BacteriaNetⓘ	positive	98.84	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	97.22	no
125439	motility	BacteriaNetⓘ	no	89.30	no
125439	spore_formation	BacteriaNetⓘ	yes	69.99	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Herbidospora cretacea strain NBRC 15474
PATRIC: 28444.4

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	90.51	no
125438	anaerobic	anaerobicⓘ	no	95.90	no
125438	spore-forming	spore-formingⓘ	yes	91.48	no
125438	aerobic	aerobicⓘ	yes	89.45	no
125438	thermophilic	thermophileⓘ	no	95.50	yes
125438	flagellated	motile2+ⓘ	no	88.00	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Computational Identification of Repeat-Containing Proteins and Systems.	Altae-Tran H, Gao L, Strecker J, Macrae RK, Zhang F.	QRB Discov	10.1017/qrd.2020.14	2020
Phylogeny	Genome-based analysis of non-ribosomal peptide synthetase and type-I polyketide synthase gene clusters in all type strains of the genus Herbidospora.	Komaki H, Ichikawa N, Oguchi A, Hamada M, Tamura T, Fujita N	BMC Res Notes	10.1186/s13104-015-1526-9	2015
Phylogeny	Cell wall teichoic acids of actinomycetes of three genera of the order actinomycetales.	Streshinskaya GM, Shashkov AS, Usov AI, Evtushenko LI, Naumova IB	Biochemistry (Mosc)	10.1023/a:1016348724308	2002
Phylogeny	Herbidospora gen. nov., a new genus of the family Streptosporangiaceae Goodfellow et al. 1990.	Kudo T, Itoh T, Miyadoh S, Shomura T, Seino A	Int J Syst Bacteriol	10.1099/00207713-43-2-319	1993
Phylogeny	Herbidospora yilanensis sp. nov. and Herbidospora daliensis sp. nov., from sediment.	Tseng M, Yang SF, Yuan GF	Int J Syst Evol Microbiol	10.1099/ijs.0.014803-0	2009
Phylogeny	Herbidospora osyris sp. nov., isolated from surface-sterilized tissue of Osyris wightiana Wall. ex Wight.	Li J, Zhao GZ, Qin S, Zhu WY, Xu LH, Li WJ	Int J Syst Evol Microbiol	10.1099/ijs.0.010579-0	2009

References

#11470	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 44071
#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):
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#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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Herbidospora cretacea (DSM 44071, IAM 14284, IFO 15474)

Name and taxonomic classification

Morphology

Cell morphology

Multimedia

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Observation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_001570605

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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