Name: Cellulomonas oligotrophica Kc5
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 2376

Type strain:

Species: Cellulomonas oligotrophica

Strain Designation: Kc5

Culture col. no.: DSM 24482, JCM 17534, NBRC 109435

Strain history: K. Hatayama Kc5.

NCBI tax ID(s): 931536 (species)

SI-ID 399478

DSM 24482

Section

Cellulomonas oligotrophica Kc5 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from soil at an urban area.

Gram-positive
motile
rod-shaped
aerobe
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	*Micrococcales*
	Family	*Cellulomonadaceae*
	Genus	*Cellulomonas*
	Species	**Cellulomonas oligotrophica**
	Full Scientific Name (LPSN)	Cellulomonas oligotrophica Hatayama et al. 2013

Information on morphological and physiological properties Morphology

[Ref.: #30542]	Gram stain	positive
[Ref.: #69480]	Gram stain	positive Confidence in %100

[Ref.: #30542]	Cell length	6 µm

[Ref.: #30542]	Cell width	2 µm

[Ref.: #30542]	Cell shape	rod-shaped

[Ref.: #30542]	Motility	yes

[Ref.: #30542]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #17686]

Culture medium

TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)

[Ref.: #17686]

Culture medium growth

[Ref.: #17686]

Culture medium link

Medium recipe at MediaDive

[Ref.: #17686]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #17686]	growth	28 °C
[Ref.: #30542]	growth	25 °C
[Ref.: #30542]	optimum	15-37 °C
[Ref.: #67770]	growth	25 °C

[Ref.: #17686]	Temperature range	mesophilic
[Ref.: #30542]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #30542]			optimum	9
[Ref.: #30542]			growth	06-11

Information on physiology and metabolism Physiology and metabolism

[Ref.: #30542]

Oxygen tolerance

aerobe

[Ref.: #30542]	Ability of spore formation	no
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.882

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #30542]		NaCl		growth	0-6	%
[Ref.: #30542]		NaCl		optimum	3	%

[Ref.: #67770]

Observation

quinones: MK-9(H₄), MK-9(H₂)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #30542]	acetate ChEBI	+	carbon source
[Ref.: #30542]	arabinose ChEBI	+	carbon source
[Ref.: #30542]	cellobiose ChEBI	+	carbon source
[Ref.: #30542]	fructose ChEBI	+	carbon source
[Ref.: #30542]	galactose ChEBI	+	carbon source
[Ref.: #30542]	glucose ChEBI	+	carbon source
[Ref.: #30542]	glycerol ChEBI	+	carbon source
[Ref.: #30542]	glycogen ChEBI	+	carbon source
[Ref.: #30542]	maltose ChEBI	+	carbon source
[Ref.: #30542]	mannitol ChEBI	+	carbon source
[Ref.: #30542]	mannose ChEBI	+	carbon source
[Ref.: #30542]	melibiose ChEBI	+	carbon source
[Ref.: #30542]	nitrate ChEBI	+	reduction
[Ref.: #30542]	salicin ChEBI	+	carbon source
[Ref.: #30542]	sorbitol ChEBI	+	carbon source
[Ref.: #30542]	sucrose ChEBI	+	carbon source
[Ref.: #30542]	trehalose ChEBI	+	carbon source
[Ref.: #30542]	xylose ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #30542]		catalase	+	1.11.1.6
[Ref.: #30542]		gelatinase	+

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

[Ref.: #17686]	Sample type/isolated from	soil at an urban area
[Ref.: #17686]	Geographic location (country and/or sea, region)	Kanagawa, Kawasaki
[Ref.: #17686]	Country	Japan
[Ref.: #17686]	Country ISO 3 Code	JPN
[Ref.: #17686]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Moist soil from an urban area
[Ref.: #67770]	Geographic location (country and/or sea, region)	Kawasaki, Kanagawa Pref.
[Ref.: #67770]	Country	Japan
[Ref.: #67770]	Country ISO 3 Code	JPN
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental

#Terrestrial

#Soil

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AB602499 (>99% sequence identity) for Cellulomonas oligotrophica from Microbeatlas

Aquatic Samples	14
Soil Samples	15
Animal Samples	4
Plant Samples
Total Samples	33

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

[Ref.: #17686]

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.: #17686]	Cellulomonas oligotrophica gene for 16S ribosomal RNA, partial sequence	AB602499	1443	ENA	931536 tax ID

Genome sequence information:

Only first 5 entries are displayed. Click here to see all.

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Cellulomonas oligotrophica DSM 24482	GCA_013409875	contig	GenBank	931536 tax ID
[Ref.: #67770]	Cellulomonas oligotrophica JCM 17534	GCA_006386485	scaffold	GenBank	931536 tax ID
[Ref.: #66792]	Cellulomonas oligotrophica NBRC 109435	GCA_016862735	contig	GenBank	931536 tax ID	*
[Ref.: #66792]	Cellulomonas oligotrophica strain DSM 24482	931536.4	wgs	PATRIC	931536 tax ID	*
[Ref.: #66792]	Cellulomonas oligotrophica strain JCM 17534	931536.3	wgs	PATRIC	931536 tax ID	*
[Ref.: #66792]	Cellulomonas oligotrophica strain NBRC 109435	931536.5	wgs	PATRIC	931536 tax ID	*

[Ref.: #17686]	GC-content	75.8 mol%	high performance liquid chromatography (HPLC)
[Ref.: #30542]	GC-content	75.8 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: Cellulomonas oligotrophica strain NBRC 109435 PATRIC: 931536.5
[Ref.: #69481]	spore-forming	yes	88	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Cellulomonas oligotrophica strain DSM 24482 PATRIC: 931536.4
[Ref.: #69480]	motile	yes	85.744	yes
[Ref.: #69480]	flagellated	no	90.655	no
[Ref.: #69480]	gram-positive	yes	93.308	yes
[Ref.: #69480]	anaerobic	no	98.894	no
[Ref.: #69480]	halophile	no	91.713	no
[Ref.: #69480]	spore-forming	no	80.413	yes
[Ref.: #69480]	glucose-util	yes	87.936	yes
[Ref.: #69480]	aerobic	yes	89.242	yes
[Ref.: #69480]	thermophile	no	99.402	no
[Ref.: #69480]	glucose-ferment	no	64.654	no

Availability in culture collections External links

[Ref.: #17686]

Culture collection no.

DSM 24482, JCM 17534, NBRC 109435

[Ref.: #71931]

SI-ID 399478

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Cellulomonas shaoxiangyii sp. nov., isolated from faeces of Tibetan antelope (Pantholops hodgsonii) on the Qinghai-Tibet Plateau.	Tian Z, Lu S, Jin D, Yang J, Pu J, Lai XH, Ren ZH, Wu XM, Li J, Wang S, Xu J	Int J Syst Evol Microbiol	10.1099/ijsem.0.003939	2020	*
Phylogeny	Cellulomonas telluris sp. nov., an endoglucanase-producing actinobacterium isolated from Badain Jaran desert sand.	Shi YL, Sun Y, Ruan ZY, Su J, Yu LY, Zhang YQ	Int J Syst Evol Microbiol	10.1099/ijsem.0.003806	2020	*
Phylogeny	Cellulomonas soli sp. nov. and Cellulomonas oligotrophica sp. nov., isolated from soil.	Hatayama K, Esaki K, Ide T	Int J Syst Evol Microbiol	10.1099/ijs.0.038364-0	2012	*

References

#17686

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 24482

#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 )

#30542

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 #26873 (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 )

#71931

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-ID399478.1 )

#26873

IJSEM 60 2013 ( DOI 10.1099/ijs.0.038364-0 , PubMed 22328604 )

* These data were automatically processed and therefore are not curated

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Cellulomonas oligotrophica strain NBRC 109435

Cellulomonas oligotrophica strain DSM 24482

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