Name: Kandeliimicrobium roseum XY-R6
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 159856

Type strain:

Species: Kandeliimicrobium roseum

Strain Designation: XY-R6

Culture col. no.: MCCC 1K01498, KCTC 52266, DSM 104294

Strain history: <- Ying Xu, College of Life Sciences Shenzhen Univ.

NCBI tax ID(s): 1737570 (species)

Section

Kandeliimicrobium roseum XY-R6 is an aerobe, mesophilic, Gram-negative bacterium that forms circular colonies and was isolated from rhizosphere soil sediment of the mangrove plant Kandelia candel.

colony-forming
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	*Rhodobacterales*
	Family	*Roseobacteraceae*
	Genus	*Kandeliimicrobium*
	Species	**Kandeliimicrobium roseum**
	Full Scientific Name (LPSN)	Kandeliimicrobium roseum Wang et al. 2018

Information on morphological and physiological properties Morphology

[Ref.: #66558]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.997

[Ref.: #66558]	Cell length	1.3-1.5 µm

[Ref.: #66558]	Cell width	0.6-0.8 µm

[Ref.: #66558]	Cell shape	rod-shaped

[Ref.: #66558]	Motility	no

[Ref.: #66558]	Colony size	0.4-0.7 mm
[Ref.: #66558]	Colony color	beige-pink
[Ref.: #66558]	Colony shape	circular
[Ref.: #66558]	Incubation period	2 days
[Ref.: #66558]	Cultivation medium used	Marine agar (MA)

Information on culture and growth conditions Culture and growth conditions

[Ref.: #66558]

Culture medium

Marine agar (MA)

[Ref.: #66558]

Culture medium growth

		Temperature
[Ref.: #66558]	optimum	28-34 °C
[Ref.: #66558]	growth	8-42 °C
[Ref.: #67771]	growth	30 °C

[Ref.: #66558]	Temperature range	mesophilic
[Ref.: #67771]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #66558]			optimum	6.5-8.0
[Ref.: #66558]			growth	5.0-9.5

Information on physiology and metabolism Physiology and metabolism

[Ref.: #67771]

Oxygen tolerance

aerobe

[Ref.: #69480]	Ability of spore formation	no Confidence in %99.992
[Ref.: #69481]	Ability of spore formation	no Confidence in %96

[Ref.: #66558]

Halophily / tolerance level

slightly halophilic

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #66558]		NaCl		growth	0-9.5	%(w/v)
[Ref.: #66558]		NaCl		optimum	1-4	%(w/v)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #66558]	(R)-amygdalin ChEBI	-	builds acid from
[Ref.: #66558]	(R)-malic acid ChEBI	-	carbon source
[Ref.: #66558]	(R)-malic acid ChEBI	-	energy source
[Ref.: #66558]	(S)-lactate ChEBI	+/-	carbon source
[Ref.: #66558]	(S)-lactate ChEBI	+/-	energy source
[Ref.: #66558]	(S)-malic acid ChEBI	-	carbon source
[Ref.: #66558]	(S)-malic acid ChEBI	-	energy source
[Ref.: #66558]	2-hydroxybutyrate ChEBI	-	carbon source
[Ref.: #66558]	2-hydroxybutyrate ChEBI	-	energy source
[Ref.: #66558]	2-oxobutanoate ChEBI	-	carbon source
[Ref.: #66558]	2-oxobutanoate ChEBI	-	energy source
[Ref.: #66558]	2-oxoglutarate ChEBI	+	carbon source
[Ref.: #66558]	2-oxoglutarate ChEBI	-	energy source
[Ref.: #66558]	3-hydroxybutyrate ChEBI	-	carbon source
[Ref.: #66558]	3-hydroxybutyrate ChEBI	-	energy source
[Ref.: #66558]	3-O-methyl-D-glucose ChEBI	-	carbon source
[Ref.: #66558]	3-O-methyl-D-glucose ChEBI	-	energy source
[Ref.: #66558]	4-hydroxyphenylacetic acid ChEBI	-	carbon source
[Ref.: #66558]	4-hydroxyphenylacetic acid ChEBI	-	energy source
[Ref.: #66558]	acetic acid ChEBI	-	carbon source
[Ref.: #66558]	acetic acid ChEBI	-	energy source
[Ref.: #66558]	acetoacetate ChEBI	+/-	carbon source
[Ref.: #66558]	acetoacetate ChEBI	+/-	energy source
[Ref.: #66558]	alpha-D-glucose ChEBI	+	carbon source
[Ref.: #66558]	alpha-D-glucose ChEBI	-	energy source
[Ref.: #66558]	alpha-D-glucose 6-phosphate ChEBI	-	carbon source
[Ref.: #66558]	alpha-D-glucose 6-phosphate ChEBI	-	energy source
[Ref.: #66558]	bromosuccinate ChEBI	-	carbon source
[Ref.: #66558]	bromosuccinate ChEBI	-	energy source
[Ref.: #66558]	cellobiose ChEBI	+	carbon source
[Ref.: #66558]	cellobiose ChEBI	-	energy source
[Ref.: #66558]	citric acid ChEBI	-	carbon source
[Ref.: #66558]	citric acid ChEBI	-	energy source
[Ref.: #66558]	D-arabitol ChEBI	+	carbon source
[Ref.: #66558]	D-arabitol ChEBI	-	energy source
[Ref.: #66558]	D-aspartate ChEBI	-	carbon source
[Ref.: #66558]	D-aspartate ChEBI	-	energy source
[Ref.: #66558]	D-fructose ChEBI	+	carbon source
[Ref.: #66558]	D-fructose ChEBI	-	energy source
[Ref.: #66558]	D-fucose ChEBI	+	carbon source
[Ref.: #66558]	D-fucose ChEBI	-	energy source
[Ref.: #66558]	D-galactose ChEBI	+	carbon source
[Ref.: #66558]	D-galactose ChEBI	-	energy source
[Ref.: #66558]	D-galacturonic acid ChEBI	+	carbon source
[Ref.: #66558]	D-galacturonic acid ChEBI	-	energy source
[Ref.: #66558]	D-glucarate ChEBI	-	carbon source
[Ref.: #66558]	D-glucarate ChEBI	-	energy source
[Ref.: #66558]	D-gluconate ChEBI	+/-	carbon source
[Ref.: #66558]	D-gluconate ChEBI	+/-	energy source
[Ref.: #66558]	D-glucose ChEBI	+	builds acid from
[Ref.: #66558]	D-glucuronate ChEBI	+	carbon source
[Ref.: #66558]	D-glucuronate ChEBI	-	energy source
[Ref.: #66558]	D-mannitol ChEBI	+	builds acid from
[Ref.: #66558]	D-mannitol ChEBI	+	carbon source
[Ref.: #66558]	D-mannitol ChEBI	-	energy source
[Ref.: #66558]	D-mannose ChEBI	+	carbon source
[Ref.: #66558]	D-mannose ChEBI	-	energy source
[Ref.: #66558]	D-serine ChEBI	-	carbon source
[Ref.: #66558]	D-serine ChEBI	-	energy source
[Ref.: #66558]	D-sorbitol ChEBI	-	builds acid from
[Ref.: #66558]	D-sorbitol ChEBI	+/-	carbon source
[Ref.: #66558]	D-sorbitol ChEBI	+/-	energy source
[Ref.: #66558]	dextrin ChEBI	+/-	carbon source
[Ref.: #66558]	dextrin ChEBI	+/-	energy source
[Ref.: #66558]	esculin ChEBI	+	hydrolysis
[Ref.: #66558]	formate ChEBI	+	carbon source
[Ref.: #66558]	formate ChEBI	-	energy source
[Ref.: #66558]	fusidate ChEBI	-	carbon source
[Ref.: #66558]	fusidate ChEBI	-	energy source
[Ref.: #66558]	galactarate ChEBI	-	carbon source
[Ref.: #66558]	galactarate ChEBI	-	energy source
[Ref.: #66558]	gamma-aminobutyric acid ChEBI	-	carbon source
[Ref.: #66558]	gamma-aminobutyric acid ChEBI	-	energy source
[Ref.: #66558]	gelatin ChEBI	+	hydrolysis
[Ref.: #66558]	gentiobiose ChEBI	+/-	carbon source
[Ref.: #66558]	gentiobiose ChEBI	+/-	energy source
[Ref.: #66558]	glucuronamide ChEBI	+	carbon source
[Ref.: #66558]	glucuronamide ChEBI	-	energy source
[Ref.: #66558]	glycerol ChEBI	+/-	carbon source
[Ref.: #66558]	glycerol ChEBI	+/-	energy source
[Ref.: #66558]	glycine-proline ChEBI	-	carbon source
[Ref.: #66558]	glycine-proline ChEBI	-	energy source
[Ref.: #66558]	guanidinium chloride ChEBI	-	carbon source
[Ref.: #66558]	guanidinium chloride ChEBI	-	energy source
[Ref.: #66558]	inosine ChEBI	+/-	carbon source
[Ref.: #66558]	inosine ChEBI	+/-	energy source
[Ref.: #66558]	L-alanine ChEBI	-	carbon source
[Ref.: #66558]	L-alanine ChEBI	-	energy source
[Ref.: #66558]	L-arabinose ChEBI	+	builds acid from
[Ref.: #66558]	L-arabinose ChEBI	+	carbon source
[Ref.: #66558]	L-arabinose ChEBI	-	energy source
[Ref.: #66558]	L-arginine ChEBI	+	hydrolysis
[Ref.: #66558]	L-aspartate ChEBI	-	carbon source
[Ref.: #66558]	L-aspartate ChEBI	-	energy source
[Ref.: #66558]	L-fucose ChEBI	+	carbon source
[Ref.: #66558]	L-fucose ChEBI	-	energy source
[Ref.: #66558]	L-galactonic acid gamma-lactone ChEBI	+/-	carbon source
[Ref.: #66558]	L-galactonic acid gamma-lactone ChEBI	+/-	energy source
[Ref.: #66558]	L-glutamate ChEBI	-	carbon source
[Ref.: #66558]	L-glutamate ChEBI	-	energy source
[Ref.: #66558]	L-histidine ChEBI	-	carbon source
[Ref.: #66558]	L-histidine ChEBI	-	energy source
[Ref.: #66558]	L-lysine ChEBI	-	hydrolysis
[Ref.: #66558]	L-ornithine ChEBI	-	hydrolysis
[Ref.: #66558]	L-pyroglutamic acid ChEBI	-	carbon source
[Ref.: #66558]	L-pyroglutamic acid ChEBI	-	energy source
[Ref.: #66558]	L-rhamnose ChEBI	+	builds acid from
[Ref.: #66558]	L-rhamnose ChEBI	+/-	carbon source
[Ref.: #66558]	L-rhamnose ChEBI	+/-	energy source
[Ref.: #66558]	L-serine ChEBI	+/-	carbon source
[Ref.: #66558]	L-serine ChEBI	+/-	energy source
[Ref.: #66558]	lactose ChEBI	-	carbon source
[Ref.: #66558]	lactose ChEBI	-	energy source
[Ref.: #66558]	maltose ChEBI	+/-	carbon source
[Ref.: #66558]	maltose ChEBI	+/-	energy source
[Ref.: #66558]	melibiose ChEBI	+	builds acid from
[Ref.: #66558]	melibiose ChEBI	+	carbon source
[Ref.: #66558]	melibiose ChEBI	-	energy source
[Ref.: #66558]	methyl (R)-lactate ChEBI	-	carbon source
[Ref.: #66558]	methyl (R)-lactate ChEBI	-	energy source
[Ref.: #66558]	methyl beta-D-glucopyranoside ChEBI	-	carbon source
[Ref.: #66558]	methyl beta-D-glucopyranoside ChEBI	-	energy source
[Ref.: #66558]	methyl pyruvate ChEBI	-	carbon source
[Ref.: #66558]	methyl pyruvate ChEBI	-	energy source
[Ref.: #66558]	myo-inositol ChEBI	-	builds acid from
[Ref.: #66558]	myo-inositol ChEBI	-	carbon source
[Ref.: #66558]	myo-inositol ChEBI	-	energy source
[Ref.: #66558]	N-acetyl-beta-D-mannosamine ChEBI	-	carbon source
[Ref.: #66558]	N-acetyl-beta-D-mannosamine ChEBI	-	energy source
[Ref.: #66558]	N-acetylgalactosamine ChEBI	-	carbon source
[Ref.: #66558]	N-acetylgalactosamine ChEBI	-	energy source
[Ref.: #66558]	N-acetylglucosamine ChEBI	-	carbon source
[Ref.: #66558]	N-acetylglucosamine ChEBI	-	energy source
[Ref.: #66558]	n-acetylneuraminate ChEBI	-	carbon source
[Ref.: #66558]	n-acetylneuraminate ChEBI	-	energy source
[Ref.: #66558]	nitrate ChEBI	-	reduction
[Ref.: #66558]	pectin ChEBI	+/-	carbon source
[Ref.: #66558]	pectin ChEBI	+/-	energy source
[Ref.: #66558]	propionate ChEBI	-	carbon source
[Ref.: #66558]	propionate ChEBI	-	energy source
[Ref.: #66558]	quinate ChEBI	-	carbon source
[Ref.: #66558]	quinate ChEBI	-	energy source
[Ref.: #66558]	raffinose ChEBI	-	carbon source
[Ref.: #66558]	raffinose ChEBI	-	energy source
[Ref.: #66558]	salicin ChEBI	+	carbon source
[Ref.: #66558]	salicin ChEBI	-	energy source
[Ref.: #66558]	sodium bromate ChEBI	-	carbon source
[Ref.: #66558]	sodium bromate ChEBI	-	energy source
[Ref.: #66558]	sodium butyrate ChEBI	-	carbon source
[Ref.: #66558]	sodium butyrate ChEBI	-	energy source
[Ref.: #66558]	sodium sulfate ChEBI	-	carbon source
[Ref.: #66558]	sodium sulfate ChEBI	-	energy source
[Ref.: #66558]	stachyose ChEBI	-	carbon source
[Ref.: #66558]	stachyose ChEBI	-	energy source
[Ref.: #66558]	sucrose ChEBI	+	carbon source
[Ref.: #66558]	sucrose ChEBI	-	energy source
[Ref.: #66558]	trehalose ChEBI	+	carbon source
[Ref.: #66558]	trehalose ChEBI	-	energy source
[Ref.: #66558]	turanose ChEBI	-	carbon source
[Ref.: #66558]	tween 20 ChEBI	+	hydrolysis
[Ref.: #66558]	tween 40 ChEBI	+	hydrolysis
[Ref.: #66558]	tween 60 ChEBI	+	hydrolysis
[Ref.: #66558]	tween 80 ChEBI	+	hydrolysis
[Ref.: #66558]	urea ChEBI	-	hydrolysis
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Antibiotic sensitivity	Concentration		Antibiotic resistance	Concentration
[Ref.: #66558]	Amikacin ChEBI	yes	30	µg (disc)
[Ref.: #66558]	ampicillin ChEBI	yes	30	µg (disc)
[Ref.: #66558]	chloramphenicol ChEBI	yes	30	µg (disc)
[Ref.: #66558]	ciprofloxacin ChEBI	yes	5	µg (disc)
[Ref.: #66558]	clindamycin ChEBI	yes	2	µg (disc)
[Ref.: #66558]	erythromycin ChEBI				yes	15	µg (disc)
[Ref.: #66558]	gentamicin ChEBI	yes	10	µg (disc)
[Ref.: #66558]	nalidixic acid ChEBI				yes	15	µg (disc)
[Ref.: #66558]	norfloxacin ChEBI	yes	10	µg (disc)
[Ref.: #66558]	novobiocin ChEBI	yes	30	µg (disc)
[Ref.: #66558]	penicillin g ChEBI	yes	20	Unit (disc)
[Ref.: #66558]	rifampicin ChEBI	yes	5	µg (disc)
[Ref.: #66558]	tetracycline ChEBI	yes	30	µg (disc)
[Ref.: #66558]	tobramycin ChEBI				yes	30	µg (disc)
[Ref.: #66558]	vancomycin ChEBI	yes	30	µg (disc)
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #66558]		hydrogen sulfide ChEBI	no
[Ref.: #66558]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #66558]	acid phosphatase	+	3.1.3.2
[Ref.: #66558]	alkaline phosphatase	+	3.1.3.1
[Ref.: #66558]	alpha-chymotrypsin	-	3.4.21.1
[Ref.: #66558]	alpha-fucosidase	-	3.2.1.51
[Ref.: #66558]	alpha-galactosidase	-	3.2.1.22
[Ref.: #66558]	alpha-glucosidase	+	3.2.1.20
[Ref.: #66558]	alpha-mannosidase	-	3.2.1.24
[Ref.: #66558]	beta-galactosidase	+	3.2.1.23
[Ref.: #66558]	beta-glucosidase	+	3.2.1.21
[Ref.: #66558]	beta-glucuronidase	-	3.2.1.31
[Ref.: #66558]	catalase	+	1.11.1.6
[Ref.: #66558]	cystine aminopeptidase	+/-	3.4.11.3
[Ref.: #66558]	cytochrome oxidase	-	1.9.3.1
[Ref.: #66558]	esterase (C 4)	+
[Ref.: #66558]	esterase Lipase (C 8)	+
[Ref.: #66558]	leucine aminopeptidase	+	3.4.1.1
[Ref.: #66558]	lipase (C 14)	+/-
[Ref.: #66558]	N-acetyl-beta-glucosaminidase	-	3.2.1.52
[Ref.: #66558]	naphthol-AS-BI-phosphohydrolase	-
[Ref.: #66558]	trypsin	-	3.4.21.4
[Ref.: #66558]	valine aminopeptidase	+
	Only first 10 entries are displayed. Click here to see all.

Fatty acid profile

Metadata FA analysis

Reference

[Ref.: #66558]

Fatty acid	Percentage
C18:1 w76c / C18:1 w7c	55.6
C19:0 cyclo w8c	21.6
C16:0	11.2
C16:1 iso I / C14:0 3OH	3
C18:1 w7c 11-methyl	2.9
C18:0	2
C10:0 3OH	0.6
C12:0	0.6

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

[Ref.: #66558]	Sample type/isolated from	rhizosphere soil sediment of the mangrove plant Kandelia candel
[Ref.: #66558]	Host species	Kandelia candel
[Ref.: #66558]	Sampling date	2016-06
[Ref.: #66558]	Geographic location (country and/or sea, region)	Mai Po Nature Reserve, Hong Kong
[Ref.: #66558]	Country	China
[Ref.: #66558]	Country ISO 3 Code	CHN
[Ref.: #66558]	Continent	Asia
[Ref.: #66558]	Geographic location	22.4900°/114.0500°
[Ref.: #66558]	Enrichment culture	MA
[Ref.: #66558]	Enrichment culture temperature	25 ̊C

[Ref.: #67771]	Sample type/isolated from	From kandelia root sediment
[Ref.: #67771]	Geographic location (country and/or sea, region)	Mai Po Inner Deep Bay Ramsar Site
[Ref.: #67771]	Country	China
[Ref.: #67771]	Country ISO 3 Code	CHN
[Ref.: #67771]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Mangrove
#Host Body-Site	#Plant	#Rhizosphere
#Host	#Plants	#Shrub (Scrub)
#Environmental	#Terrestrial	#Soil

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.: #66558]	Rhodobacteraceae bacterium XY-R6 16S ribosomal RNA gene, partial sequence	KT886061	1429	ENA	1737570 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Kandeliimicrobium roseum XY-R6	GCA_002869745	scaffold	GenBank	1737570 tax ID	*
[Ref.: #66792]	Kandeliimicrobium roseum XY-R6	2831393767	draft	JGI IMG/M	1737570 tax ID	*

[Ref.: #66558]

GC-content

69.30 mol%

high performance liquid chromatography (HPLC)

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: Kandeliimicrobium roseum XY-R6 NCBI: GCA_002869745.1
[Ref.: #69481]	spore-forming	no	96	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Kandeliimicrobium roseum XY-R6 NCBI: GCA_002869745.1
[Ref.: #69480]	flagellated	no	86.097	no
[Ref.: #69480]	gram-positive	no	98.766	no
[Ref.: #69480]	anaerobic	no	97.091	yes
[Ref.: #69480]	aerobic	yes	94.178	yes
[Ref.: #69480]	halophile	yes	54.314	no
[Ref.: #69480]	spore-forming	no	94.632	no
[Ref.: #69480]	glucose-util	yes	87.858	yes
[Ref.: #69480]	thermophile	no	97.327	no
[Ref.: #69480]	motile	no	61.431	yes
[Ref.: #69480]	glucose-ferment	no	88.77	no

Availability in culture collections External links

[Ref.: #66558]

Culture collection no.

MCCC 1K01498, KCTC 52266, DSM 104294

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Kandeliimicrobium roseum gen. nov., sp. nov., a new member of the family Rhodobacteraceae isolated from mangrove rhizosphere soil.	Wang KL, Song ZM, Rong CH, Hao LY, Lai QL, Li SF, Xu Y	Int J Syst Evol Microbiol	10.1099/ijsem.0.002773	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 )

#66558

Kai-Ling Wang, Zhi-Man Song, Cu-Huang Rong, Ling-Yun Hao, Qi-Liang Lai, Shuang-Fei Li and Ying Xu: Kandeliimicrobium roseum gen. nov., sp. nov., a new member of the family Rhodobacteraceae isolated from mangrove rhizosphere soil. IJSEM 68: 2158 - 2164 2018 ( DOI 10.1099/ijsem.0.002773 , PubMed 29762105 )

#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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