Name: Kaistia granuli Ko04
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 13564

Type strain:

Species: Kaistia granuli

Strain Designation: Ko04

Culture col. no.: DSM 23481, KCTC 12575, LMG 23410

Strain history: <- ST Lee, KAIST

NCBI tax ID(s): 1122132 (strain), 363259 (species)

SI-ID 289785

LMG 23410, KCTC 12575, DSM 23481

Section

Kaistia granuli Ko04 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from sludge.

Gram-negative
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	*Pseudomonadota*
	Class	*Alphaproteobacteria*
	Order	*Hyphomicrobiales*
	Family	*Kaistiaceae*
	Genus	*Kaistia*
	Species	**Kaistia granuli**
	Full Scientific Name (LPSN)	Kaistia granuli Lee et al. 2007

Information on morphological and physiological properties Morphology

[Ref.: #32136]	Gram stain	negative
[Ref.: #67771]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.977

[Ref.: #32136]	Cell length	1.2 µm

[Ref.: #32136]	Cell width	0.5 µm

[Ref.: #32136]	Cell shape	rod-shaped

[Ref.: #32136]	Motility	no

[Ref.: #32136]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #17223]

Culture medium

R2A MEDIUM (DSMZ Medium 830)

[Ref.: #17223]

Culture medium growth

[Ref.: #17223]

Culture medium link

Medium recipe at MediaDive

[Ref.: #17223]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #17223]	growth	28 °C
[Ref.: #32136]	growth	18-30 °C
[Ref.: #32136]	optimum	24 °C
[Ref.: #67771]	growth	30 °C

[Ref.: #17223]	Temperature range	mesophilic
[Ref.: #32136]	Temperature range	psychrophilic
[Ref.: #67771]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #32136]			optimum	6.75
[Ref.: #32136]			growth	5.0-8.0

Information on physiology and metabolism Physiology and metabolism

[Ref.: #32136]	Oxygen tolerance	aerobe
[Ref.: #67771]	Oxygen tolerance	aerobe

[Ref.: #32136]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.991

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #32136]		NaCl		growth	0-2	%
[Ref.: #32136]		NaCl		optimum	1	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #32136]	arabinose ChEBI	+	carbon source
[Ref.: #32136]	fucose ChEBI	+	carbon source
[Ref.: #32136]	glucose ChEBI	+	carbon source
[Ref.: #32136]	maltose ChEBI	+	carbon source
[Ref.: #32136]	mannitol ChEBI	+	carbon source
[Ref.: #32136]	mannose ChEBI	+	carbon source
[Ref.: #32136]	melibiose ChEBI	+	carbon source
[Ref.: #32136]	N-acetylglucosamine ChEBI	+	carbon source
[Ref.: #32136]	nitrate ChEBI	+	reduction
[Ref.: #32136]	rhamnose ChEBI	+	carbon source
[Ref.: #32136]	ribose ChEBI	+	carbon source
[Ref.: #32136]	salicin ChEBI	+	carbon source
[Ref.: #32136]	sorbitol ChEBI	+	carbon source
[Ref.: #32136]	sucrose ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Enzyme	Enzyme activity	EC number
[Ref.: #32136]	acid phosphatase	+	3.1.3.2
[Ref.: #32136]	alpha-galactosidase	+	3.2.1.22
[Ref.: #32136]	catalase	+	1.11.1.6
[Ref.: #32136]	cytochrome oxidase	+	1.9.3.1
[Ref.: #32136]	urease	+	3.5.1.5

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

[Ref.: #17223]	Sample type/isolated from	sludge
[Ref.: #17223]	Geographic location (country and/or sea, region)	wastewater treatment plant, Gongju
[Ref.: #17223]	Country	Republic of Korea
[Ref.: #17223]	Country ISO 3 Code	KOR
[Ref.: #17223]	Continent	Asia

[Ref.: #67771]	Sample type/isolated from	From sludge
[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

#Mud (Sludge)

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AB244762 (>99% sequence identity) for Kaistia from Microbeatlas

Aquatic Samples	825
Soil Samples	656
Animal Samples	306
Plant Samples	131
Total Samples	1918

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

[Ref.: #17223]

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.: #17223]	Kaistia granuli gene for 16S rRNA, partial sequence	AB244762	1429	ENA	363259 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Kaistia granuli DSM 23481 Ko04	GCA_000380505	contig	GenBank	1122132 tax ID	*
[Ref.: #66792]	Kaistia granuli DSM 23481 strain Ko04	1122132.6	wgs	PATRIC	1122132 tax ID	*
[Ref.: #66792]	Kaistia granuli DSM 23481	2521172615	draft	JGI IMG/M	1122132 tax ID	*

[Ref.: #17223]	GC-content	67.8 mol%	high performance liquid chromatography (HPLC)
[Ref.: #32136]	GC-content	67.8 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: Kaistia granuli DSM 23481 strain Ko04 PATRIC: 1122132.6
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Kaistia granuli DSM 23481 strain Ko04 PATRIC: 1122132.6
[Ref.: #69480]	motile	no	86.569	yes
[Ref.: #69480]	flagellated	no	95.39	yes
[Ref.: #69480]	gram-positive	no	97.691	yes
[Ref.: #69480]	anaerobic	no	99.139	no
[Ref.: #69480]	halophile	no	91.107	yes
[Ref.: #69480]	spore-forming	no	96.737	yes
[Ref.: #69480]	thermophile	no	98.326	yes
[Ref.: #69480]	glucose-util	yes	91.708	yes
[Ref.: #69480]	aerobic	yes	91.012	no
[Ref.: #69480]	glucose-ferment	no	91.263	no

Availability in culture collections External links

[Ref.: #17223]

Culture collection no.

DSM 23481, KCTC 12575, LMG 23410

[Ref.: #82752]

SI-ID 289785

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Kaistia defluvii sp. nov., isolated from river sediment.	Jin L, Kim KK, Lee HG, Ahn CY, Oh HM	Int J Syst Evol Microbiol	10.1099/ijs.0.038687-0	2012	*
Phylogeny	Kaistia geumhonensis sp. nov. and Kaistia dalseonensis sp. nov., two members of the class Alphaproteobacteria.	Jin L, Kim KK, Baek SH, Lee ST	Int J Syst Evol Microbiol	10.1099/ijs.0.028894-0	2010	*
Phylogeny	Kaistia granuli sp. nov., isolated from anaerobic granules in an upflow anaerobic sludge blanket reactor.	Lee HW, Yu HS, Liu QM, Jung HM, An DS, Im WT, Jin FX, Lee ST	Int J Syst Evol Microbiol	10.1099/ijs.0.65023-0	2007	*

References

#17223

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 23481

#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 )

#32136

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 #28380 (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) .

#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) .

#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 )

#82752

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-ID289785.1 )

#28380

IJSEM 2280 2007 ( DOI 10.1099/ijs.0.65023-0 , PubMed 17911297 )

* These data were automatically processed and therefore are not curated

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Kaistia granuli DSM 23481 strain Ko04

Kaistia granuli DSM 23481 strain Ko04

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