Name: Tomitella cavernae DSM 45788
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 132177

Type strain:

Species: Tomitella cavernae

Culture col. no.: DSM 45788, JCM 18542, YIM C00895

Strain history: S.-K. Tang YIM C00895.

NCBI tax ID(s): 1387982 (species)

SI-ID 402878

DSM 45788

Section

Tomitella cavernae DSM 45788 is a spore-forming, mesophilic bacterium that was isolated from cave soil.

spore-forming
mesophilic
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	*Mycobacteriales*
	Family	*Nocardiaceae*
	Genus	*Tomitella*
	Species	**Tomitella cavernae**
	Full Scientific Name (LPSN)	Tomitella cavernae corrig. Cheng et al. 2014

Synonym

Tomitella cavernea

Information on morphological and physiological properties Morphology

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

[Ref.: #69480]	Motility	no Confidence in %93.346

Information on culture and growth conditions Culture and growth conditions

[Ref.: #23966]

Culture medium

TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)

[Ref.: #23966]

Culture medium growth

[Ref.: #23966]

Culture medium link

Medium recipe at MediaDive

[Ref.: #23966]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #23966]			growth	28 °C
[Ref.: #67770]			growth	28 °C

[Ref.: #23966]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #69481]	Ability of spore formation	yes Confidence in %97
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.974

[Ref.: #67770]

Observation

quinones: MK-9(H₂)

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

[Ref.: #23966]	Sample type/isolated from	cave soil
[Ref.: #23966]	Geographic location (country and/or sea, region)	Yunnan province, Jiuxiang Scenic Region, Diehong Bridge Scenic Spot (25° 04.270' N 103° 22.791' E)
[Ref.: #23966]	Country	China
[Ref.: #23966]	Country ISO 3 Code	CHN
[Ref.: #23966]	Continent	Asia
[Ref.: #23966]	Geographic location	25.0712°/103.3800°

[Ref.: #67770]	Sample type/isolated from	Soil from Jiuxiang Scenic Region
[Ref.: #67770]	Geographic location (country and/or sea, region)	Yunnan Province, south-west China
[Ref.: #67770]	Country	China
[Ref.: #67770]	Country ISO 3 Code	CHN
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Terrestrial	#Geologic
#Environmental	#Terrestrial	#Soil

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence KF548053 (>99% sequence identity) for Tomitella cavernea subclade from Microbeatlas

Aquatic Samples	554
Soil Samples	1311
Animal Samples	1675
Plant Samples	222
Total Samples	3762

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #23966]

Biosafety level

Risk group (German classification)
According to TRBA 466

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.: #23966]	Tomitella cavernea strain YIM C00895 16S ribosomal RNA gene, partial sequence	KF548053	1546	ENA	1387982 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Tomitella cavernea JCM 18542	GCA_016599145	contig	GenBank	1387982 tax ID	*
[Ref.: #66792]	Tomitella cavernea strain JCM 18542	1387982.3	wgs	PATRIC	1387982 tax ID	*

[Ref.: #23966]

GC-content

67.5 mol%

high performance liquid chromatography (HPLC)

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: Tomitella cavernea strain JCM 18542 PATRIC: 1387982.3
[Ref.: #69481]	spore-forming	yes	97	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Tomitella cavernea strain JCM 18542 PATRIC: 1387982.3
[Ref.: #69480]	motile	no	92.64	no
[Ref.: #69480]	gram-positive	yes	89.164	no
[Ref.: #69480]	anaerobic	no	99.327	no
[Ref.: #69480]	halophile	no	64.681	no
[Ref.: #69480]	spore-forming	no	84.52	no
[Ref.: #69480]	thermophile	no	94.586	yes
[Ref.: #69480]	glucose-util	yes	90.61	no
[Ref.: #69480]	aerobic	yes	91.36	no
[Ref.: #69480]	flagellated	no	98.546	no
[Ref.: #69480]	glucose-ferment	no	86.356	no

Availability in culture collections External links

[Ref.: #23966]

Culture collection no.

DSM 45788, JCM 18542, YIM C00895

[Ref.: #90532]

SI-ID 402878

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Tomitella cavernea sp. nov., an actinomycete isolated from soil.	Cheng J, Wang HF, Li L, Chen W, Duan YQ, Duan BL, Lu XH, Ding YB, Li WJ	Int J Syst Evol Microbiol	10.1099/ijs.0.060202-0	2014	*

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 )

#23966

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 45788

#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 )

#90532

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-ID402878.1 )

* These data were automatically processed and therefore are not curated

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Tomitella cavernea strain JCM 18542

Tomitella cavernea strain JCM 18542

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