Name: Thermogemmatispora onikobensis ONI-1
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 140666

Type strain:

Species: Thermogemmatispora onikobensis

Strain Designation: ONI-1, ON1-1

Culture col. no.: KCTC 19768, JCM 16817, NBRC 111776

Strain history: <- Y Aiba <- Tokyo Univ.

NCBI tax ID(s): 732234 (species)

Section

Thermogemmatispora onikobensis ONI-1 is an aerobe, spore-forming, thermophilic bacterium that was isolated from fallen leaves on geothermal soils at Onikobe hot springs.

Gram-positive
ovoid-shaped
spore-forming
aerobe
thermophilic
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	*Chloroflexota*
	Class	*Ktedonobacteria*
	Order	*Thermogemmatisporales*
	Family	*Thermogemmatisporaceae*
	Genus	*Thermogemmatispora*
	Species	**Thermogemmatispora onikobensis**
	Full Scientific Name (LPSN)	Thermogemmatispora onikobensis Yabe et al. 2011

Information on morphological and physiological properties Morphology

[Ref.: #43387]	Gram stain	positive
[Ref.: #67771]	Gram stain	positive
[Ref.: #69480]	Gram stain	positive Confidence in %99.592

[Ref.: #43387]	Cell length	1-2 µm

[Ref.: #43387]	Cell width	0.5-1.5 µm

[Ref.: #43387]	Cell shape	ovoid-shaped
[Ref.: #67771]	Cell shape	filament-shaped

[Ref.: #43387]	Motility	no
[Ref.: #67771]	Motility	no
[Ref.: #69480]	Motility	no Confidence in %95.601

[Ref.: #43387]	Colony color	white
[Ref.: #43387]	Incubation period	14 days
[Ref.: #43387]	Cultivation medium used	FS1V medium

Information on culture and growth conditions Culture and growth conditions

[Ref.: #43387]

Culture medium

FS1V medium

[Ref.: #43387]

Culture medium growth

		Temperature
[Ref.: #43387]	optimum	60-65 °C
[Ref.: #43387]	growth	50-74 °C
[Ref.: #67770]	growth	60 °C
[Ref.: #67771]	growth	60-65 °C

[Ref.: #43387]	Temperature range	thermophilic
[Ref.: #67770]	Temperature range	thermophilic
[Ref.: #67771]	Temperature range	thermophilic
[Ref.: #69480]	Temperature range	thermophilic Confidence in %99.118

	pH	Kind of pH		pH
[Ref.: #43387]			optimum	7
[Ref.: #43387]			growth	4.6-8

Information on physiology and metabolism Physiology and metabolism

[Ref.: #43387]	Oxygen tolerance	aerobe
[Ref.: #67771]	Oxygen tolerance	aerobe

[Ref.: #43387]	Type of spore	spore
[Ref.: #43387]	Ability of spore formation	yes
[Ref.: #67771]	Type of spore	spore
[Ref.: #67771]	Ability of spore formation	yes
[Ref.: #69481]	Ability of spore formation	yes Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.388

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #43387]		NaCl		growth	1	%
[Ref.: #43387]		NaCl	no	growth	2	%

[Ref.: #67770]	Observation	quinones: MK-9(H₂)
[Ref.: #67771]	Observation	quinones: MK-9(H2)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #43387]	casein	-	hydrolysis
[Ref.: #43387]	cellulose ChEBI	+	hydrolysis
[Ref.: #43387]	chitin ChEBI	+	hydrolysis
[Ref.: #43387]	D-fructose ChEBI	-	assimilation
[Ref.: #43387]	D-glucose ChEBI	+	assimilation
[Ref.: #43387]	D-glucose ChEBI	+	carbon source
[Ref.: #43387]	D-mannitol ChEBI	+	assimilation
[Ref.: #43387]	D-mannitol ChEBI	+	carbon source
[Ref.: #43387]	D-xylose ChEBI	+	assimilation
[Ref.: #43387]	D-xylose ChEBI	+	carbon source
[Ref.: #43387]	gelatin ChEBI	+	hydrolysis
[Ref.: #43387]	L-arabinose ChEBI	-	assimilation
[Ref.: #43387]	L-rhamnose ChEBI	+	assimilation
[Ref.: #43387]	L-rhamnose ChEBI	+	carbon source
[Ref.: #43387]	myo-inositol ChEBI	-	assimilation
[Ref.: #43387]	raffinose ChEBI	-	assimilation
[Ref.: #43387]	starch ChEBI	-	hydrolysis
[Ref.: #43387]	sucrose ChEBI	+	assimilation
[Ref.: #43387]	sucrose ChEBI	+	carbon source
[Ref.: #43387]	xylan ChEBI	+	hydrolysis
	Only first 10 entries are displayed. Click here to see all.

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #43387]		catalase	+	1.11.1.6

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

[Ref.: #43387]	Sample type/isolated from	fallen leaves on geothermal soils at Onikobe hot springs
[Ref.: #43387]	Geographic location (country and/or sea, region)	Jigokudani in Onikobe Hot Springs, Miyagi Prefecture
[Ref.: #43387]	Country	Japan
[Ref.: #43387]	Country ISO 3 Code	JPN
[Ref.: #43387]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Fallen leaves on geothermal soil at Onikobe hot springs
[Ref.: #67770]	Geographic location (country and/or sea, region)	Miyagi Pref.
[Ref.: #67770]	Country	Japan
[Ref.: #67770]	Country ISO 3 Code	JPN
[Ref.: #67770]	Continent	Asia

[Ref.: #67771]	Sample type/isolated from	From fallen leaves on geothermal soil, Onikobe hot springs
[Ref.: #67771]	Geographic location (country and/or sea, region)	Miyagi
[Ref.: #67771]	Country	Japan
[Ref.: #67771]	Country ISO 3 Code	JPN
[Ref.: #67771]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Thermal spring
#Condition	#Thermophilic (>45°C)	-
#Host Body-Site	#Plant	#Leaf (Phyllosphere)

What are isolation sources categories?

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.: #43387]	16S rRNA gene sequence	AB547912		GenBank

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Thermogemmatispora onikobensis NBRC 111776	GCA_001748285	contig	GenBank	732234 tax ID
[Ref.: #66792]	Thermogemmatispora onikobensis strain NBRC 111776	732234.3	wgs	PATRIC	732234 tax ID	*
[Ref.: #66792]	Thermogemmatispora onikobensis NBRC 111776	2832587005	draft	JGI IMG/M	732234 tax ID	*

[Ref.: #43387]	GC-content	60.2 mol%	high performance liquid chromatography (HPLC)
[Ref.: #67771]	GC-content	60.2 mol%

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: Thermogemmatispora onikobensis strain NBRC 111776 PATRIC: 732234.3
[Ref.: #69481]	spore-forming	yes	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Thermogemmatispora onikobensis strain NBRC 111776 PATRIC: 732234.3
[Ref.: #69480]	motile	no	91.265	yes
[Ref.: #69480]	flagellated	no	96.764	yes
[Ref.: #69480]	gram-positive	yes	72.454	no
[Ref.: #69480]	anaerobic	no	96.143	yes
[Ref.: #69480]	aerobic	yes	76.687	yes
[Ref.: #69480]	halophile	no	92.907	yes
[Ref.: #69480]	spore-forming	yes	51.75	yes
[Ref.: #69480]	thermophile	yes	99.155	no
[Ref.: #69480]	glucose-util	yes	84.645	yes
[Ref.: #69480]	glucose-ferment	no	86.66	no

Availability in culture collections External links

[Ref.: #43387]

Culture collection no.

KCTC 19768, JCM 16817, NBRC 111776

Literature:

Topic	Title	Authors	Journal	DOI	Year
Genetics	Draft Genome Sequence of Thermogemmatispora onikobensis NBRC 111776T, an Aerial Mycelium- and Spore-Forming Thermophilic Bacterium Belonging to the Class Ktedonobacteria.	Komaki H, Hosoyama A, Yabe S, Yokota A, Uchino Y, Takano H	Genome Announc	10.1128/genomeA.01156-16	2016	*
Phylogeny	Description of Thermogemmatispora carboxidivorans sp. nov., a carbon-monoxide-oxidizing member of the class Ktedonobacteria isolated from a geothermally heated biofilm, and analysis of carbon monoxide oxidation by members of the class Ktedonobacteria.	King CE, King GM	Int J Syst Evol Microbiol	10.1099/ijs.0.059675-0	2014	*
Phylogeny	Thermogemmatispora onikobensis gen. nov., sp. nov. and Thermogemmatispora foliorum sp. nov., isolated from fallen leaves on geothermal soils, and description of Thermogemmatisporaceae fam. nov. and Thermogemmatisporales ord. nov. within the class Ktedonobacteria.	Yabe S, Aiba Y, Sakai Y, Hazaka M, Yokota A	Int J Syst Evol Microbiol	10.1099/ijs.0.024877-0	2010	*

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 )

#43387

Shuhei Yabe, Yoshifumi Aiba, Yasuteru Sakai, Masaru Hazaka, Akira Yokota: Thermogemmatispora onikobensis gen. nov., sp. nov. and Thermogemmatispora foliorum sp. nov., isolated from fallen leaves on geothermal soils, and description of Thermogemmatisporaceae fam. nov. and Thermogemmatisporales ord. nov. within the class Ktedonobacteria. IJSEM 61: 903 - 910 2011 ( DOI 10.1099/ijs.0.024877-0 , PubMed 20495028 )

#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;
#67771 Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;

#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 )

* These data were automatically processed and therefore are not curated

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Thermogemmatispora onikobensis strain NBRC 111776

Thermogemmatispora onikobensis strain NBRC 111776

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