Name: Iodobacter ciconiae H11R3
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 164502

Type strain:

Species: Iodobacter ciconiae

Strain Designation: H11R3

Culture col. no.: JCM 33283, KCTC 62666, DSM 109119

Strain history: <- J.-W. Bae; <- S. Y. Lee, Dept. Biology, Kyung Hee Univ., Seoul, Republic of Korea; H11R3

NCBI tax ID(s): 2496266 (species)

Special Collections

Section

When using BacDive for research please cite our paper

Iodobacter ciconiae H11R3 is a facultative anaerobe, psychrophilic, Gram-negative bacterium that forms circular colonies and was isolated from Feces from Oriental stork, Ciconia boyciana.

colony-forming
Gram-negative
rod-shaped
facultative anaerobe
psychrophilic
16S sequence
Bacteria
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	09-12-2024 (DD-MM-YYYY)
	Domain	*Bacteria*
	Phylum	*Pseudomonadota*
	Class	*Betaproteobacteria*
	Order	*Neisseriales*
	Family	*Chromobacteriaceae*
	Genus	*Iodobacter*
	Species	**Iodobacter ciconiae**
	Full Scientific Name (LPSN)	Iodobacter ciconiae Lee et al. 2019

Information on morphological and physiological properties Morphology

[Ref.: #68186]	Gram stain	negative
[Ref.: #125438]	Gram stain	negative Confidence in %96.75

[Ref.: #68186]	Cell length	2.0-2.2 µm

[Ref.: #68186]	Cell width	0.9-1.0 µm

[Ref.: #68186]	Cell shape	rod-shaped

[Ref.: #68186]	Motility	no

[Ref.: #68186]	Colony color	beige
[Ref.: #68186]	Colony shape	circular
[Ref.: #68186]	Incubation period	2 days
[Ref.: #68186]	Cultivation medium used	Trypticase Soy Agar (TSA)

[Ref.: #68186]	Pigment production	no
[Ref.: #68186]	Pigmentation color	violet
[Ref.: #68186]	Pigment name	violacein

Information on culture and growth conditions Culture and growth conditions

[Ref.: #125079]

Culture medium

R2A MEDIUM (DSMZ Medium 830)

[Ref.: #125079]

Culture medium growth

[Ref.: #125079]

Culture medium link

Medium recipe provided by DSMZ

[Ref.: #125079]

Culture medium

TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)

[Ref.: #125079]

Culture medium growth

[Ref.: #125079]

Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #67770]	growth	15 °C
[Ref.: #68186]	growth	4-30 °C
[Ref.: #68186]	optimum	15 °C
[Ref.: #125079]	growth	15 °C

	pH	Kind of pH		pH
[Ref.: #68186]			optimum	8
[Ref.: #68186]			growth	6-9

Information on physiology and metabolism Physiology and metabolism

[Ref.: #68186]

Oxygen tolerance

facultative anaerobe

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #68186]		NaCl		growth	0-1.5	%(w/v)
[Ref.: #68186]		NaCl		optimum	0.5	%(w/v)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68186]	2-hydroxybutyrate ChEBI	-	assimilation
[Ref.: #68186]	3-hydroxybutyrate ChEBI	-	assimilation
[Ref.: #68186]	acetic acid ChEBI	-	assimilation
[Ref.: #68186]	acetoacetate ChEBI	+	carbon source
[Ref.: #68186]	alpha-D-glucose ChEBI	+	carbon source
[Ref.: #68186]	bromosuccinate ChEBI	-	assimilation
[Ref.: #68186]	D-arabinose ChEBI	-	assimilation
[Ref.: #68186]	D-arabitol ChEBI	-	assimilation
[Ref.: #68186]	D-fructose ChEBI	+	builds acid from
[Ref.: #68186]	D-fructose ChEBI	-	assimilation
[Ref.: #68186]	D-fructose 6-phosphate ChEBI	-	assimilation
[Ref.: #68186]	D-gluconate ChEBI	+	carbon source
[Ref.: #68186]	D-glucose ChEBI	+	assimilation
[Ref.: #68186]	D-glucose ChEBI	+	builds acid from
[Ref.: #68186]	D-glucose 6-phosphate ChEBI	+	carbon source
[Ref.: #68186]	D-mannose ChEBI	-	builds acid from
[Ref.: #68186]	D-mannose ChEBI	-	assimilation
[Ref.: #68186]	D-ribose ChEBI	+	builds acid from
[Ref.: #68186]	D-saccharate ChEBI	-	assimilation
[Ref.: #68186]	dextrin ChEBI	-	assimilation
[Ref.: #68186]	esculin ChEBI	+	hydrolysis
[Ref.: #68186]	glycerol ChEBI	-	assimilation
[Ref.: #68186]	glycyl-L-proline ChEBI	-	assimilation
[Ref.: #68186]	inosine ChEBI	-	assimilation
[Ref.: #68186]	L-alanine ChEBI	-	assimilation
[Ref.: #68186]	L-arabinose ChEBI	-	builds acid from
[Ref.: #68186]	L-aspartate ChEBI	-	assimilation
[Ref.: #68186]	L-glutamate ChEBI	+	carbon source
[Ref.: #68186]	L-histidine ChEBI	-	assimilation
[Ref.: #68186]	L-lactate	+	carbon source
[Ref.: #68186]	L-serine ChEBI	-	assimilation
[Ref.: #68186]	maltose ChEBI	+	assimilation
[Ref.: #68186]	maltose ChEBI	+	builds acid from
[Ref.: #68186]	maltose ChEBI	+	carbon source
[Ref.: #68186]	melibiose ChEBI	-	assimilation
[Ref.: #68186]	methyl D-glucoside ChEBI	-	assimilation
[Ref.: #68186]	methyl pyruvate ChEBI	-	assimilation
[Ref.: #68186]	N-acetyl-beta-D-mannosamine ChEBI	+	carbon source
[Ref.: #68186]	n-acetyl-D-galactosamine ChEBI	+	carbon source
[Ref.: #68186]	N-acetyl-D-glucosamine ChEBI	+	carbon source
[Ref.: #68186]	N-acetylglucosamine ChEBI	+	assimilation
[Ref.: #68186]	N-acetylglucosamine ChEBI	+	builds acid from
[Ref.: #68186]	nitrate ChEBI	+	reduction
[Ref.: #68186]	pectin ChEBI	-	assimilation
[Ref.: #68186]	potassium gluconate ChEBI	+	assimilation
[Ref.: #68186]	potassium gluconate ChEBI	+	builds acid from
[Ref.: #68186]	sucrose ChEBI	+	builds acid from
[Ref.: #68186]	sucrose ChEBI	+	carbon source
[Ref.: #68186]	trehalose ChEBI	+	builds acid from
[Ref.: #68186]	trehalose ChEBI	+	carbon source
[Ref.: #68186]	turanose ChEBI	-	assimilation
[Ref.: #68186]	tween 40 ChEBI	-	assimilation
	Only first 10 entries are displayed. Click here to see all.

	Enzyme	Enzyme activity	EC number
[Ref.: #68186]	acid phosphatase	+	3.1.3.2
[Ref.: #68186]	alkaline phosphatase	+	3.1.3.1
[Ref.: #68186]	alpha-glucosidase	+	3.2.1.20
[Ref.: #68186]	arginine dihydrolase	-	3.5.3.6
[Ref.: #68186]	catalase	+	1.11.1.6
[Ref.: #68186]	cytochrome oxidase	+	1.9.3.1
[Ref.: #68186]	esterase Lipase (C 8)	+
[Ref.: #68186]	leucine arylamidase	+	3.4.11.1
[Ref.: #68186]	N-acetyl-beta-glucosaminidase	+	3.2.1.52
[Ref.: #68186]	naphthol-AS-BI-phosphohydrolase	+
[Ref.: #68186]	valine arylamidase	+
	Only first 10 entries are displayed. Click here to see all.

Fatty acid profile

Metadata FA analysis

Reference

[Ref.: #68186]

Fatty acid	Percentage
C16:1 w7c/C16:1 w6c	62.7
C16:0	20.8
C14:0	7.6
C12:0 3OH	2.6
C18:1 w7c/C18:1 w6c	2.4
C10:0 3OH	2
C12:0	0.6

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

[Ref.: #67770]	Sample type/isolated from	Feces from Oriental stork, Ciconia boyciana
[Ref.: #67770]	Host species	Ciconia boyciana
[Ref.: #67770]	Geographic location (country and/or sea, region)	Seoul Grand Park Zoo
[Ref.: #67770]	Country	Republic of Korea
[Ref.: #67770]	Country ISO 3 Code	KOR
[Ref.: #67770]	Continent	Asia

[Ref.: #68186]	Sample type/isolated from	fecal sample from Oriental stork, Ciconia boyciana
[Ref.: #68186]	Geographic location (country and/or sea, region)	Seoul Grand Park Zoo
[Ref.: #68186]	Country	Republic of Korea
[Ref.: #68186]	Country ISO 3 Code	KOR
[Ref.: #68186]	Continent	Asia
[Ref.: #68186]	Enrichment culture	R2A
[Ref.: #68186]	Enrichment culture temperature	10 ̊C

[Ref.: #125079]	Sample type/isolated from	Feces of oriental stork Ciconia boyciana
[Ref.: #125079]	Geographic location (country and/or sea, region)	Seoul Grand Park zoo, 102, Daegongwongwangjang-ro, Gwacheon-si, Gyeonggi-do,
[Ref.: #125079]	Country	Republic of Korea
[Ref.: #125079]	Country ISO 3 Code	KOR
[Ref.: #125079]	Continent	Asia
* marker position based on {}

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.: #68186]	Iodobacter ciconiae strain H11R3 16S ribosomal RNA gene, partial sequence	MK285606	1465	GenBank ENA	1915058 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Iodobacter ciconiae H11R3	GCA_003952345	complete	GenBank ENA	2496266 tax ID

[Ref.: #68186]

GC-content

48 mol%

genome sequence analysis

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

	Model	Trait	Prediction	Confidence in %	In training data
	Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Iodobacter ciconiae H11R3 NCBI: GCA_003952345.1
[Ref.: #125438]	gram-positive	gram-positiveⓘ	no	96.75	no
[Ref.: #125438]	anaerobic	anaerobicⓘ	no	96.285	yes
[Ref.: #125438]	aerobic	aerobicⓘ	no	55.301	yes
[Ref.: #125438]	spore-forming	spore-formingⓘ	no	85.102	no
[Ref.: #125438]	thermophile	thermophilicⓘ	no	97.5	no
[Ref.: #125438]	motile2+	flagellatedⓘ	yes	76.324	no

Availability in culture collections External links

[Ref.: #67770]

Culture collection no.

JCM 33283, KCTC 62666, DSM 109119

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Iodobacter ciconiae sp. nov., a bacterium isolated from feces of oriental stork, Ciconia boyciana.	Lee JY, Kang W, Kim PS, Lee SY, Shin NR, Sung H, Lee JY, Yun JH, Jeong YS, Han JE, Jung MJ, Hyun DW, Kim HS, Tak EJ, Kang MS, Lee KE, Lee BH, Bae JW	Int J Syst Evol Microbiol	10.1099/ijsem.0.003583	2019	*

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 )

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;

#68186

Jae-Yun Lee, Woorim Kang, Pil Soo Kim, So-Yeon Lee, Na-Ri Shin, Hojun Sung, June-Young Lee, Ji-Hyun Yun, Yun-Seok Jeong, Jeong Eun Han, Mi-Ja Jung, Dong-Wook Hyun, Hyun Sik Kim, Euon Jung Tak, Myung-Suk Kang, Ki-Eun Lee, Byoung-Hee Lee and Jin-Woo Bae: Iodobacter ciconiae sp. nov., a bacterium isolated from feces of oriental stork, Ciconia boyciana. IJSEM 69: 2948 - 2953 2019 ( DOI 10.1099/ijsem.0.003583 )

#125079

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 109119

#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 )

* These data were automatically processed and therefore are not curated

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