Name: Kordiimonas pumila N18
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 158811

Type strain:

Species: Kordiimonas pumila

Strain Designation: N18

Culture col. no.: MCCC 1K03436, KCTC 62164

Strain history: <- Zhao Ju, Zhejiang Univ.

NCBI tax ID(s): 2161677 (species)

Special Collections

Section

Kordiimonas pumila N18 is an obligate aerobe, Gram-negative, motile bacterium that forms circular colonies and was isolated from coastal sediment.

colony-forming
Gram-negative
motile
rod-shaped
obligate aerobe
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	*Kordiimonadales*
	Family	*Temperatibacteraceae*
	Genus	*Kordiimonas*
	Species	**Kordiimonas pumila**
	Full Scientific Name (LPSN)	Kordiimonas pumila Ju et al. 2018

Information on morphological and physiological properties Morphology

[Ref.: #65575]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %95.594

[Ref.: #65575]	Cell length	1.0-2.9 µm

[Ref.: #65575]	Cell width	0.4-0.7 µm

[Ref.: #65575]	Cell shape	rod-shaped

[Ref.: #65575]	Motility	yes

[Ref.: #65575]	Flagellum arrangement	polar

[Ref.: #65575]	Colony size	0.2-0.8 mm
[Ref.: #65575]	Colony shape	circular
[Ref.: #65575]	Incubation period	2 days
[Ref.: #65575]	Cultivation medium used	MA

Information on culture and growth conditions Culture and growth conditions

[Ref.: #65575]

Culture medium

Marine agar (MA)

[Ref.: #65575]

Culture medium growth

		Temperature
[Ref.: #65575]	growth	10-37 °C
[Ref.: #65575]	optimum	28 °C
[Ref.: #67771]	growth	28 °C

	pH	Kind of pH		pH
[Ref.: #65575]			optimum	7.0
[Ref.: #65575]			growth	6.0-8.0

Information on physiology and metabolism Physiology and metabolism

[Ref.: #65575]	Oxygen tolerance	obligate aerobe
[Ref.: #67771]	Oxygen tolerance	aerobe

[Ref.: #69480]	Ability of spore formation	no Confidence in %92.66
[Ref.: #69481]	Ability of spore formation	no Confidence in %100

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #65575]		NaCl		growth	1-4	%(w/v)
[Ref.: #65575]		NaCl		optimum	2.5	%(w/v)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #65575]	2-oxoglutarate ChEBI	+	carbon source
[Ref.: #65575]	2-oxoglutarate ChEBI	+	growth
[Ref.: #65575]	4-hydroxy-L-proline ChEBI	+	carbon source
[Ref.: #65575]	4-hydroxy-L-proline ChEBI	+	growth
[Ref.: #65575]	alpha-cyclodextrin ChEBI	+	carbon source
[Ref.: #65575]	alpha-cyclodextrin ChEBI	+	growth
[Ref.: #65575]	alpha-D-glucose ChEBI	+	carbon source
[Ref.: #65575]	alpha-D-glucose ChEBI	+	growth
[Ref.: #65575]	cellobiose ChEBI	+	carbon source
[Ref.: #65575]	cellobiose ChEBI	+	growth
[Ref.: #65575]	D-arabitol ChEBI	+	carbon source
[Ref.: #65575]	D-arabitol ChEBI	+	growth
[Ref.: #65575]	fumarate ChEBI	-	electron acceptor
[Ref.: #65575]	gentiobiose ChEBI	+	carbon source
[Ref.: #65575]	gentiobiose ChEBI	+	growth
[Ref.: #65575]	glycyl-l-glutamate ChEBI	+	carbon source
[Ref.: #65575]	glycyl-l-glutamate ChEBI	+	growth
[Ref.: #65575]	L-alanylglycine ChEBI	+	carbon source
[Ref.: #65575]	L-alanylglycine ChEBI	+	growth
[Ref.: #65575]	L-asparagine ChEBI	+	carbon source
[Ref.: #65575]	L-asparagine ChEBI	+	growth
[Ref.: #65575]	L-aspartate ChEBI	+	carbon source
[Ref.: #65575]	L-aspartate ChEBI	+	growth
[Ref.: #65575]	L-histidine ChEBI	+	carbon source
[Ref.: #65575]	L-histidine ChEBI	+	growth
[Ref.: #65575]	L-leucine ChEBI	+	carbon source
[Ref.: #65575]	L-leucine ChEBI	+	growth
[Ref.: #65575]	L-phenylalanine ChEBI	+	carbon source
[Ref.: #65575]	L-phenylalanine ChEBI	+	growth
[Ref.: #65575]	L-proline ChEBI	+	carbon source
[Ref.: #65575]	L-proline ChEBI	+	growth
[Ref.: #65575]	L-pyroglutamic acid ChEBI	+	carbon source
[Ref.: #65575]	L-pyroglutamic acid ChEBI	+	growth
[Ref.: #65575]	L-threonine ChEBI	+	carbon source
[Ref.: #65575]	L-threonine ChEBI	+	growth
[Ref.: #65575]	lactose ChEBI	+	carbon source
[Ref.: #65575]	lactose ChEBI	+	growth
[Ref.: #65575]	maltose ChEBI	+	carbon source
[Ref.: #65575]	maltose ChEBI	+	growth
[Ref.: #65575]	methyl D-glucoside ChEBI	+	carbon source
[Ref.: #65575]	methyl D-glucoside ChEBI	+	growth
[Ref.: #65575]	myo-inositol ChEBI	+	carbon source
[Ref.: #65575]	myo-inositol ChEBI	+	growth
[Ref.: #65575]	N-acetylgalactosamine ChEBI	+	carbon source
[Ref.: #65575]	N-acetylgalactosamine ChEBI	+	growth
[Ref.: #65575]	N-acetylglucosamine ChEBI	+	carbon source
[Ref.: #65575]	N-acetylglucosamine ChEBI	+	growth
[Ref.: #65575]	nitrate ChEBI	-	electron acceptor
[Ref.: #65575]	nitrate ChEBI	-	reduction
[Ref.: #65575]	nitrite ChEBI	-	electron acceptor
[Ref.: #65575]	nitrite ChEBI	-	reduction
[Ref.: #65575]	putrescine ChEBI	+	carbon source
[Ref.: #65575]	putrescine ChEBI	+	growth
[Ref.: #65575]	raffinose ChEBI	+	carbon source
[Ref.: #65575]	raffinose ChEBI	+	growth
[Ref.: #65575]	sucrose ChEBI	+	carbon source
[Ref.: #65575]	sucrose ChEBI	+	growth
[Ref.: #65575]	trehalose ChEBI	+	carbon source
[Ref.: #65575]	trehalose ChEBI	+	growth
[Ref.: #65575]	tween 20 ChEBI	+	hydrolysis
[Ref.: #65575]	tween 40 ChEBI	+/-	hydrolysis
[Ref.: #65575]	tween 80 ChEBI	+	hydrolysis
[Ref.: #65575]	uridine ChEBI	+	carbon source
[Ref.: #65575]	uridine ChEBI	+	growth
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #65575]		hydrogen sulfide ChEBI	yes

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #65575]		catalase	+	1.11.1.6
[Ref.: #65575]		cytochrome oxidase	+	1.9.3.1

Fatty acid profile

Metadata FA analysis

Reference

[Ref.: #65575]

Fatty acid	Percentage
iso-C15:0 2-OH / 16:1ω7c	28.5
C17:1 iso ω9c	24.2
C15:0 iso	13
C16:0	8.2
C17:0 iso	5.2
C18:1ω6c / iso-C18:1ω7c	4.4
C18:0	4
C17:1ω8c	3.3
C17:1ω6c	3.3
C15:1 iso F	1.3
iso-C15:1ω8c	1.1
C17:0	0.9
C16:1 iso H	0.8
C16:0 iso	0.7
C18:0 2OH	0.6
C14:0	0.5

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

[Ref.: #65575]	Sample type/isolated from	coastal sediment
[Ref.: #65575]	Sampling date	2016-01
[Ref.: #65575]	Geographic location (country and/or sea, region)	Zhoushan
[Ref.: #65575]	Country	China
[Ref.: #65575]	Country ISO 3 Code	CHN
[Ref.: #65575]	Continent	Asia
[Ref.: #65575]	Geographic location	29.9771°/122.3960°
[Ref.: #65575]	Enrichment culture	MA
[Ref.: #65575]	Enrichment culture duration	4 days
[Ref.: #65575]	Enrichment culture temperature	30 ̊C

[Ref.: #67771]	Sample type/isolated from	From the marine sediment of ZhouShan Island
[Ref.: #67771]	Country	China
[Ref.: #67771]	Country ISO 3 Code	CHN
[Ref.: #67771]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Sediment
#Environmental	#Terrestrial	#Coast

What are isolation sources categories?

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.: #65575]	Kordiimonas pumila strain N18 16S ribosomal RNA gene, partial sequence	MF099898		GenBank ENA

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Kordiimonas pumila N18	GCA_015240255	complete	GenBank ENA	2161677 tax ID	*

[Ref.: #65575]

GC-content

55.3 mol%

high performance liquid chromatography (HPLC)

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

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Kordiimonas pumila N18 NCBI: GCA_015240255.1
[Ref.: #69481]	spore-forming	spore-formingⓘ	no	100	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Kordiimonas pumila N18 NCBI: GCA_015240255.1
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	95.594	yes
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	92.115	no
[Ref.: #69480]	aerobic	aerobicⓘ	yes	80.348	no
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	92.66	no
[Ref.: #69480]	thermophilic	thermophileⓘ	no	93.945	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	yes	73.496	no

Availability in culture collections External links

[Ref.: #65575]

Culture collection no.

MCCC 1K03436, KCTC 62164

Literature:

Topic	Title	Authors	Journal	DOI	Year
Genetics	Complete genome sequence of Kordiimonas pumila N18(T) sheds light on biogeochemical roles of the genus Kordiimonas.	Geng N, Yang D, Hua J, Huang LJ, Dong H, Sun C, Xu L	Mar Genomics	10.1016/j.margen.2022.100930	2022	*
Phylogeny	Kordiimonas pumila sp. nov., isolated from coastal sediment.	Ju Z, Zhang R, Hou XJ, Han SB, Li Y, Sun C, Wu M, Xu L	Int J Syst Evol Microbiol	10.1099/ijsem.0.002740	2018	*

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 )

#65575

Zhao Ju, Ran Zhang, Xin-Jun Hou, Shuai-Bo Han, Yu Li, Cong Sun, Min Wu and Lin Xu: Kordiimonas pumila sp. nov., isolated from coastal sediment. IJSEM 68: 1742 - 1748 2018 ( DOI 10.1099/ijsem.0.002740 , PubMed 29620500 )

#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;

#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 )

* These data were automatically processed and therefore are not curated

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