Name: Deinococcus humi MK03
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 23889

Type strain:

Species: Deinococcus humi

Strain Designation: MK03

Culture col. no.: DSM 27939, JCM 17915, KCTC 13619

Strain history: <- MK Kim, Seoul Women's Univ.

NCBI tax ID(s): 662880 (species)

SI-ID 382386

JCM 17915, KCTC 13619, LMG 28476, DSM 27939

Section

Deinococcus humi MK03 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from soil from campus.

coccus-shaped
Gram-positive
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	*Deinococcota*
	Class	*Deinococci*
	Order	*Deinococcales*
	Family	*Deinococcaceae*
	Genus	*Deinococcus*
	Species	**Deinococcus humi**
	Full Scientific Name (LPSN)	Deinococcus humi Srinivasan et al. 2012

Information on morphological and physiological properties Morphology

[Ref.: #30489]	Gram stain	positive
[Ref.: #67771]	Gram stain	positive

[Ref.: #30489]	Cell width	0.95 µm

[Ref.: #30489]	Cell shape	coccus-shaped
[Ref.: #67771]	Cell shape	coccus-shaped

[Ref.: #30489]	Motility	no
[Ref.: #67771]	Motility	no

[Ref.: #30489]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #20525]

Culture medium

R2A MEDIUM (DSMZ Medium 830)

[Ref.: #20525]

Culture medium growth

[Ref.: #20525]

Culture medium link

Medium recipe at MediaDive

[Ref.: #20525]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #20525]	growth	28 °C
[Ref.: #30489]	growth	20-37 °C
[Ref.: #30489]	optimum	30 °C
[Ref.: #67770]	growth	30 °C
[Ref.: #67771]	growth	30 °C

[Ref.: #20525]	Temperature range	mesophilic
[Ref.: #30489]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic
[Ref.: #67771]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #30489]			optimum	7.25
[Ref.: #30489]			growth	5.5-9

Information on physiology and metabolism Physiology and metabolism

[Ref.: #30489]	Oxygen tolerance	aerobe
[Ref.: #67771]	Oxygen tolerance	aerobe

[Ref.: #30489]	Ability of spore formation	no
[Ref.: #67771]	Ability of spore formation	no

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #30489]		NaCl		growth	0-3	%

[Ref.: #67770]	Observation	quinones: MK-8
[Ref.: #67771]	Observation	quinones: MK-8

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #30489]	3-hydroxybenzoate ChEBI	+	carbon source
[Ref.: #30489]	4-hydroxybenzoate ChEBI	+	carbon source
[Ref.: #30489]	5-dehydro-D-gluconate ChEBI	+	carbon source
[Ref.: #30489]	alanine ChEBI	+	carbon source
[Ref.: #30489]	arabinose ChEBI	+	carbon source
[Ref.: #30489]	citrate ChEBI	+	carbon source
[Ref.: #30489]	decanoate ChEBI	+	carbon source
[Ref.: #30489]	lactate ChEBI	+	carbon source
[Ref.: #30489]	mannitol ChEBI	+	carbon source
[Ref.: #30489]	melibiose ChEBI	+	carbon source
[Ref.: #30489]	myo-inositol ChEBI	+	carbon source
[Ref.: #30489]	N-acetylglucosamine ChEBI	+	carbon source
[Ref.: #30489]	nitrate ChEBI	+	reduction
[Ref.: #30489]	sucrose ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Enzyme	Enzyme activity	EC number
[Ref.: #30489]	acid phosphatase	+	3.1.3.2
[Ref.: #30489]	catalase	+	1.11.1.6
[Ref.: #30489]	gelatinase	+

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

[Ref.: #20525]	Sample type/isolated from	soil from campus
[Ref.: #20525]	Geographic location (country and/or sea, region)	Seoul Women's University
[Ref.: #20525]	Country	Republic of Korea
[Ref.: #20525]	Country ISO 3 Code	KOR
[Ref.: #20525]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Soil from the campus of Seoul Women's University
[Ref.: #67770]	Geographic location (country and/or sea, region)	Seoul
[Ref.: #67770]	Country	Republic of Korea
[Ref.: #67770]	Country ISO 3 Code	KOR
[Ref.: #67770]	Continent	Asia

[Ref.: #67771]	Sample type/isolated from	From ginseng soil
[Ref.: #67771]	Country	Republic of Korea
[Ref.: #67771]	Country ISO 3 Code	KOR
[Ref.: #67771]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental

#Terrestrial

#Soil

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence MT760376 (>99% sequence identity) for Deinococcus humi subclade from Microbeatlas

Aquatic Samples	326
Soil Samples	736
Animal Samples	732
Plant Samples	386
Total Samples	2180

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

[Ref.: #20525]

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.: #20525]	Deinococcus humi strain MK03 16S ribosomal RNA gene, partial sequence	GQ339889	1469	ENA	662880 tax ID
[Ref.: #67771]	Deinococcus humi strain JCM 17915 16S ribosomal RNA gene, partial sequence	MT760376	1322	ENA	662880 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.: #66792]	Deinococcus humi DSM 27939	GCA_014201875	contig	GenBank	662880 tax ID	*
[Ref.: #66792]	Deinococcus humi JCM 17915	GCA_014647275	scaffold	GenBank	662880 tax ID	*
[Ref.: #66792]	Deinococcus humi strain DSM 27939	662880.4	wgs	PATRIC	662880 tax ID	*
[Ref.: #66792]	Deinococcus humi strain JCM 17915	662880.5	wgs	PATRIC	662880 tax ID	*
[Ref.: #66792]	Deinococcus humi DSM 27939	2861281385	draft	JGI IMG/M	662880 tax ID	*
[Ref.: #66792]	Deinococcus humi MK03	2597489808	draft	JGI IMG/M	662880 tax ID	*

[Ref.: #20525]	GC-content	64.5 mol%	high performance liquid chromatography (HPLC)
[Ref.: #30489]	GC-content	64.5 mol%

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Deinococcus humi JCM 17915 NCBI: GCA_014647275.1
[Ref.: #69480]	flagellated	no	94.015	yes
[Ref.: #69480]	gram-positive	yes	81.296	yes
[Ref.: #69480]	anaerobic	no	98.893	no
[Ref.: #69480]	aerobic	yes	93.13	yes
[Ref.: #69480]	halophile	no	90.727	no
[Ref.: #69480]	spore-forming	no	90.296	yes
[Ref.: #69480]	glucose-util	yes	85.552	no
[Ref.: #69480]	thermophile	no	97.769	no
[Ref.: #69480]	motile	no	88.275	no
[Ref.: #69480]	glucose-ferment	no	91.307	no

Availability in culture collections External links

[Ref.: #20525]

Culture collection no.

DSM 27939, JCM 17915, KCTC 13619

[Ref.: #87899]

SI-ID 382386

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Deinococcus humi sp. nov., isolated from soil.	Srinivasan S, Lee JJ, Lim S, Joe M, Kim MK	Int J Syst Evol Microbiol	10.1099/ijs.0.037234-0	2012	*

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 )

#20525

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 27939

#30489

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 #26822 (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;
#67771 Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;

#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) .

#87899

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-ID382386.1 )

#26822

IJSEM 2844 2012 ( DOI 10.1099/ijs.0.037234-0 , PubMed 22228662 )

* These data were automatically processed and therefore are not curated

Change proposal

You found an error in BacDive? Please tell us about it!

Note that changes will be reviewed and judged. If your changes are legitimate, changes will occur within the next BacDive update. Only proposed changes supported by the according reference will be reviewed. The BacDive team reserves the right to reject proposed changes.

Search for species Deinococcus humi in external resources:
SILVA
BRENDA
PANGAEA
StrainInfo
GBIF

Deinococcus humi JCM 17915

Change proposal

Change proposal