Name: Herbidospora yilanensis 0351M-12
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 133560

Type strain:

Species: Herbidospora yilanensis

Strain Designation: 0351M-12

Culture col. no.: FIRDI 003, BCRC 16875, LMG 24337, JCM 18062, NBRC 106371

Strain history: BCRC 16875 <-- M. Tseng 0351M-12.

NCBI tax ID(s): 354426 (species)

SI-ID 376991

BCRC 16875, LMG 24337, JCM 18062

Section

Herbidospora yilanensis 0351M-12 is an aerobe, spore-forming, Gram-positive bacterium that was isolated from Sediment.

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

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Actinomycetota*
	Class	*Actinomycetes*
	Order	*Streptosporangiales*
	Family	*Streptosporangiaceae*
	Genus	*Herbidospora*
	Species	**Herbidospora yilanensis**
	Full Scientific Name (LPSN)	Herbidospora yilanensis Tseng et al. 2010

Information on morphological and physiological properties Morphology

[Ref.: #29521]	Gram stain	positive
[Ref.: #69480]	Gram stain	positive Confidence in %100

[Ref.: #29521]	Motility	no

[Ref.: #29521]

Pigment production

Information on culture and growth conditions Culture and growth conditions

	Temperatures	Kind of temperature		Temperature
[Ref.: #29521]			growth	20-40 °C
[Ref.: #67770]			growth	28 °C

[Ref.: #67770]

Temperature range

mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #29521]

Oxygen tolerance

aerobe

[Ref.: #29521]	Ability of spore formation	yes
[Ref.: #69481]	Ability of spore formation	yes Confidence in %100
[Ref.: #69480]	Ability of spore formation	yes Confidence in %100

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #29521]		NaCl		growth	<1	%

[Ref.: #67770]

Observation

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

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #29521]	fructose ChEBI	+	carbon source
[Ref.: #29521]	galactose ChEBI	+	carbon source
[Ref.: #29521]	glucose ChEBI	+	carbon source
[Ref.: #29521]	glycerol ChEBI	+	carbon source
[Ref.: #29521]	lactate ChEBI	+	carbon source
[Ref.: #29521]	maltose ChEBI	+	carbon source
[Ref.: #29521]	mannitol ChEBI	+	carbon source
[Ref.: #29521]	mannose ChEBI	+	carbon source
[Ref.: #29521]	melibiose ChEBI	+	carbon source
[Ref.: #29521]	myo-inositol ChEBI	+	carbon source
[Ref.: #29521]	raffinose ChEBI	+	carbon source
[Ref.: #29521]	rhamnose ChEBI	+	carbon source
[Ref.: #29521]	salicin ChEBI	+	carbon source
[Ref.: #29521]	succinate ChEBI	+	carbon source
[Ref.: #29521]	sucrose ChEBI	+	carbon source
[Ref.: #29521]	trehalose ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #29521]	Sample type/isolated from	Sediment

[Ref.: #67770]	Sample type/isolated from	Sediment from a dry lake
[Ref.: #67770]	Geographic location (country and/or sea, region)	Yilan County
[Ref.: #67770]	Country	Taiwan
[Ref.: #67770]	Country ISO 3 Code	TWN
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Sediment
#Environmental	#Terrestrial	#Sediment

What are isolation sources categories?

[Ref.: #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

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #29521]	Herbidospora yilanensis strain 0351M-12 16S ribosomal RNA gene, partial sequence	DQ246623	1517	GenBank	354426 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Herbidospora yilanensis NBRC 106371	GCA_001570565	scaffold	GenBank	354426 tax ID
[Ref.: #66792]	Herbidospora yilanensis strain NBRC 106371	354426.3	wgs	PATRIC	354426 tax ID	*
[Ref.: #66792]	Herbidospora yilanensis NBRC 106371	2724679242	draft	JGI IMG/M	354426 tax ID	*

[Ref.: #29521]	GC-content	70.6 mol%
[Ref.: #67770]	GC-content	70.6 mol%	high performance liquid chromatography (HPLC)
[Ref.: #67770]	GC-content	70.7 mol%	genome sequence analysis

Data predicted using genome information as a basis Genome-based predictions

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Herbidospora yilanensis NBRC 106371 NCBI: GCA_001570565.1
[Ref.: #69481]	spore-forming	yes	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Herbidospora yilanensis strain NBRC 106371 PATRIC: 354426.3
[Ref.: #69480]	gram-positive	yes	89.04	no
[Ref.: #69480]	anaerobic	no	99.038	no
[Ref.: #69480]	halophile	no	94.346	yes
[Ref.: #69480]	spore-forming	yes	95.049	yes
[Ref.: #69480]	glucose-util	yes	88.373	no
[Ref.: #69480]	motile	no	91.036	no
[Ref.: #69480]	flagellated	no	98.182	no
[Ref.: #69480]	thermophile	no	98.453	yes
[Ref.: #69480]	aerobic	yes	92.25	yes
[Ref.: #69480]	glucose-ferment	no	93.089	no

Availability in culture collections External links

[Ref.: #29521]

Culture collection no.

FIRDI 003, BCRC 16875, LMG 24337, JCM 18062, NBRC 106371

[Ref.: #91505]

SI-ID 376991

Literature:

Topic	Title	Authors	Journal	DOI	Year
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	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 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 )

#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 (see below)

#66792

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#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 .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#91505

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID376991.1 )

#25918

IJSEM 1168 2010 ( DOI 10.1099/ijs.0.014803-0 , PubMed 19667396 )

* These data were automatically processed and therefore are not curated

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Herbidospora yilanensis NBRC 106371

Herbidospora yilanensis strain NBRC 106371

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