Herbidospora yilanensis (FIRDI 003, BCRC 16875, LMG 24337)

Name: Herbidospora yilanensis (FIRDI 003, BCRC 16875, LMG 24337)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 133560

Type strain

Strain Designation 0351M-12

Culture col. no. FIRDI 003 BCRC 16875 LMG 24337 0351M-12 NBRC 106371 1 more

NCBI tax ID(s) 354426

Special Collections JCM Literature strains

History BCRC 16875 <-- M. Tseng 0351M-12.

Links

Herbidospora yilanensis 0351M-12 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 376991

NBRC-106371,BCRC 16875,LMG 24337,JCM 18062

@ref 20215

Last LPSN update 2026-02-09 11:31:58

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Streptosporangiales

Family Streptosporangiaceae

Genus Herbidospora

Species Herbidospora yilanensis

Full scientific name Herbidospora yilanensis Tseng et al. 2010

Morphology

Cell morphology

@ref	Gram stain	Confidence
29521	positive
125439	positive	99.7
125439		90.6

Pigmentation

29521

Productionno

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
125438	aerobe	91.502
125439	obligate aerobe	93.4

Spore formation

29521

Spore formationyes

Halophily

@ref	Salt	Growth	Tested relation	Concentration
29521	NaCl	positive	growth	<1 %

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	28757 ChEBI	fructose	+	carbon source
29521	28260 ChEBI	galactose	+	carbon source
29521	17234 ChEBI	glucose	+	carbon source
29521	17754 ChEBI	glycerol	+	carbon source
29521	24996 ChEBI	lactate	+	carbon source
29521	17306 ChEBI	maltose	+	carbon source
29521	29864 ChEBI	mannitol	+	carbon source
29521	37684 ChEBI	mannose	+	carbon source
29521	28053 ChEBI	melibiose	+	carbon source
29521	17268 ChEBI	myo-inositol	+	carbon source
29521	16634 ChEBI	raffinose	+	carbon source
29521	26546 ChEBI	rhamnose	+	carbon source
29521	17814 ChEBI	salicin	+	carbon source
29521	30031 ChEBI	succinate	+	carbon source
29521	17992 ChEBI	sucrose	+	carbon source
29521	27082 ChEBI	trehalose	+	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 dry lake	Yilan County	Taiwan, Province of China	TWN	Asia

Taxonmaps

69479

Global distribution of 16S sequence DQ246623 (>99% sequence identity) for Herbidospora from Microbeatlas

Aquatic Samples	8
Soil Samples	294
Animal Samples	18
Plant Samples	30
Total Samples	350

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	ASM157056v1 assembly for Herbidospora yilanensis NBRC 106371	scaffold	GCA_001570565	354426.3	2724679242	354426	53.4

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
29521	Herbidospora yilanensis strain 0351M-12 16S ribosomal RNA gene, partial sequence	DQ246623	1517		354426

GC content

@ref	GC-content (mol%)	Method
29521	70.6
67770	70.6	high performance liquid chromatography (HPLC)
67770	70.7	genome sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Herbidospora yilanensis NBRC 106371
NCBI: GCA_001570565

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	82.60	no
125439	motility	BacteriaNetⓘ	no	90.60	no
125439	gram_stain	BacteriaNetⓘ	positive	99.70	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	93.40	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Herbidospora yilanensis strain NBRC 106371
PATRIC: 354426.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	88.31	yes
125438	anaerobic	anaerobicⓘ	no	94.84	yes
125438	spore-forming	spore-formingⓘ	yes	89.51	yes
125438	thermophilic	thermophileⓘ	no	94.50	yes
125438	aerobic	aerobicⓘ	yes	91.50	yes
125438	flagellated	motile2+ⓘ	no	85.50	yes

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 solisilvae sp. nov., a novel cellulose-degrading actinobacterium isolated from forest soil.	Yu M, Zhou R, Li J, Han L, Wang H, Zhang S, Zhao J, Wang X, Song J, Xiang W	Antonie Van Leeuwenhoek	10.1007/s10482-021-01542-6	2021
Phylogeny	Herbidospora soli sp. nov., isolated from soil.	Niemhom N, Thawai C	Int J Syst Evol Microbiol	10.1099/ijsem.0.002503	2017
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 yilanensis (FIRDI 003, BCRC 16875, LMG 24337)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

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_001570565

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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