Herbidospora daliensis (FIRDI 004, BCRC 16876, LMG 24336)

Name: Herbidospora daliensis (FIRDI 004, BCRC 16876, LMG 24336)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 133559

Type strain

Strain Designation 0385M-1

Culture col. no. FIRDI 004 BCRC 16876 LMG 24336 0385M-1 NBRC 106372 1 more

NCBI tax ID(s) 295585

Special Collections JCM Literature strains

History JCM <-- BCRC 16876 <-- M. Tseng 0385M-1.

Links

Herbidospora daliensis 0385M-1 is an aerobe, spore-forming, Gram-positive bacterium that was isolated from Sediment.

spore-forming Gram-positive aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 370197

NBRC 106372,BCRC 16876,LMG 24336,JCM 18061

@ref 20215

Last LPSN update 2026-05-29 08:38:07

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Streptosporangiales

Family Streptosporangiaceae

Genus Herbidospora

Species Herbidospora daliensis

Full scientific name Herbidospora daliensis Tseng et al. 2010

Morphology

Cell morphology

@ref	Gram stain	Confidence
29521	positive
125439	positive	97.073

Culture and growth conditions

Culture temp

@ref	Growth	Type	Temperature (°C)
29521	positive	growth	20-40
67770	positive	growth	28

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
29521	aerobe
125439	obligate aerobe	98.022

Spore formation

29521

Spore formationyes

Halophily

@ref	Salt	Growth	Tested relation	Concentration
29521	NaCl	positive	growth	<5 %

Observation

67770

Observationquinones: MK-10(H₄), MK-10(H₆), MK-9(H₄)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
29521	22599 ChEBI	arabinose	+	carbon source
29521	28757 ChEBI	fructose	+	carbon source
29521	28260 ChEBI	galactose	+	carbon source
29521	17234 ChEBI	glucose	+	carbon source
29521	17306 ChEBI	maltose	+	carbon source
29521	29864 ChEBI	mannitol	+	carbon source
29521	16634 ChEBI	raffinose	+	carbon source
29521	26546 ChEBI	rhamnose	+	carbon source
29521	17992 ChEBI	sucrose	+	carbon source

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Sediment
#Environmental	#Terrestrial	#Sediment

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
29521	Sediment
67770	Sediment from a river	Dali City	Taiwan, Province of China	TWN	Asia

Taxonmaps

69479

Global distribution of 16S sequence AY749433 (>99% sequence identity) for Herbidospora from Microbeatlas

Aquatic Samples	8
Soil Samples	35
Animal Samples	2
Plant Samples	304
Total Samples	349

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	ASM157058v1 assembly for Herbidospora daliensis NBRC 106372	scaffold	GCA_001570585	295585.3	2724679243	295585	64.69

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
29521	Herbidospora daliensis strain 0385M-1 16S ribosomal RNA gene, partial sequence	AY749433	1499		295585

GC content

@ref	GC-content (mol%)	Method
29521	70.7
67770	70.8	genome sequence analysis
67770	70.7	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: ASM157058v1 assembly for Herbidospora daliensis NBRC 106372
NCBI: GCA_001570585

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	gram_stain	BacteriaNetⓘ	positive	97.07	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	98.02	no
125439	motility	BacteriaNetⓘ	no	88.52	no
125439	spore_formation	BacteriaNetⓘ	yes	70.52	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Herbidospora daliensis strain NBRC 106372
PATRIC: 295585.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	88.75	no
125438	anaerobic	anaerobicⓘ	no	94.83	no
125438	spore-forming	spore-formingⓘ	yes	89.98	yes
125438	aerobic	aerobicⓘ	yes	87.80	no
125438	thermophilic	thermophileⓘ	no	93.00	yes
125438	flagellated	motile2+ⓘ	no	86.00	no

Literature

Topic	Title	Authors	Journal	DOI	Year
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	Herbidospora galbida sp. nov., a novel actinobacterium isolated from soil.	Han L, Yu M, Zhao J, Jiang H, Guo X, Shen G, Shen Y, Wang X, Xiang W	Int J Syst Evol Microbiol	10.1099/ijsem.0.003922	2020
Phylogeny	Herbidospora sakaeratensis sp. nov., isolated from soil, and reclassification of Streptosporangium claviforme as a later synonym of Herbidospora cretacea.	Boondaeng A, Suriyachadkun C, Ishida Y, Tamura T, Tokuyama S, Kitpreechavanich V	Int J Syst Evol Microbiol	10.1099/ijs.0.024315-0	2010
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

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 )
#25918	IJSEM 1168 2010 ( DOI 10.1099/ijs.0.014803-0 , PubMed 19667396 )
#29521	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 #25918
#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 .
#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 daliensis (FIRDI 004, BCRC 16876, LMG 24336)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Sequence information

Genome sequences

Genome browser: GCA_001570585

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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