Tomitella cavernae (DSM 45788, JCM 18542, YIM C00895)

Name: Tomitella cavernae (DSM 45788, JCM 18542, YIM C00895)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 132177

Type strain

Culture col. no. DSM 45788 JCM 18542 YIM C00895

NCBI tax ID(s) 1387982

Special Collections DSMZ JCM

History DSMZ <- S.-K. Tang, Yunnan Univ., Yunnan Inst. Microbiol. (YIM), Kunming, China; YIM C00895 <- J. Cheng JCM <-- S.-K. Tang YIM C00895.

Links

Tomitella cavernae DSM 45788 is a bacterium that was isolated from cave soil.

genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 402878

JCM 18542,DSM 45788

@ref 20215

Last LPSN update 2026-05-29 08:37:47

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Mycobacteriales

Family Nocardiaceae

Genus Tomitella

Species Tomitella cavernae

Full scientific name Tomitella cavernae corrig. Cheng et al. 2014

Synonyms (1)

Tomitella cavernea

Morphology

Cell morphology

@ref	Motility	Confidence
125438		93

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
23966	TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)		Medium recipe at MediaDive	Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
23966	positive	growth	28
67770	positive	growth	28

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	aerobe	97.951

Observation

67770

Observationquinones: MK-9(H₂)

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Geologic
#Environmental	#Terrestrial	#Soil

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude
23966	cave soil	Yunnan province, Jiuxiang Scenic Region, Diehong Bridge Scenic Spot (25° 04.270' N 103° 22.791' E)	China	CHN	Asia	25.0712	103.38 25.0712/103.38
67770	Soil from Jiuxiang Scenic Region	Yunnan Province, south-west China	China	CHN	Asia

Taxonmaps

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

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
23966	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
124043	ASM3954390v1 assembly for Tomitella cavernea JCM 18542	contig	GCA_039543905			1387982	74.79
66792	ASM1659914v1 assembly for Tomitella cavernea JCM 18542	contig	GCA_016599145	1387982.3	2994277607	1387982	56.36

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
23966	Tomitella cavernea strain YIM C00895 16S ribosomal RNA gene, partial sequence	KF548053	1546		1387982

GC content

@ref	GC-content (mol%)	Method
23966	67.5	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: ASM3954390v1 assembly for Tomitella cavernea JCM 18542
NCBI: GCA_039543905

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	97.95	no
125439	gram_stain	BacteriaNetⓘ	positive	78.80	no
125439	motility	BacteriaNetⓘ	yes	46.67	no
125439	spore_formation	BacteriaNetⓘ	yes	46.53	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Tomitella cavernea strain JCM 18542
PATRIC: 1387982.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	89.08	no
125438	anaerobic	anaerobicⓘ	no	97.91	no
125438	spore-forming	spore-formingⓘ	no	58.23	no
125438	aerobic	aerobicⓘ	yes	84.57	no
125438	thermophilic	thermophileⓘ	no	93.92	yes
125438	flagellated	motile2+ⓘ	no	93.00	no

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 .
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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 )

Rate our new design

Content

About us

Tomitella cavernae (DSM 45788, JCM 18542, YIM C00895)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Observation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_039543905

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

Help

Social Media