Name: Siccirubricoccus deserti CGMCC 1.15936
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 158554

Type strain:

Species: Siccirubricoccus deserti

Culture col. no.: CGMCC 1.15936, KCTC 62088, SYSU D8009

Strain history: <- Wael Nabil Hozzein, King Saud Univ.

NCBI tax ID(s): 2013562 (species)

Section

Siccirubricoccus deserti CGMCC 1.15936 is an aerobe, Gram-negative, coccus-shaped bacterium that forms irregular colonies and was isolated from sand sample.

coccus-shaped
colony-forming
Gram-negative
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	*Rhodospirillales*
	Family	*Acetobacteraceae*
	Genus	*Siccirubricoccus*
	Species	**Siccirubricoccus deserti**
	Full Scientific Name (LPSN)	Siccirubricoccus deserti Yang et al. 2017

Information on morphological and physiological properties Morphology

[Ref.: #65248]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %100

[Ref.: #65248]	Cell length	0.6-0.9 µm

[Ref.: #65248]	Cell shape	coccus-shaped

[Ref.: #65248]	Motility	no

[Ref.: #65248]	Colony color	pink-red
[Ref.: #65248]	Colony shape	irregular
[Ref.: #65248]	Cultivation medium used	R2A agar

Information on culture and growth conditions Culture and growth conditions

[Ref.: #65248]

Culture medium

Reasoner's 2A agar (R2A)

[Ref.: #65248]

Culture medium growth

		Temperature
[Ref.: #65248]	growth	4-45 °C
[Ref.: #65248]	optimum	28-37 °C
[Ref.: #67771]	growth	37 °C

[Ref.: #65248]	Temperature range	mesophilic
[Ref.: #67771]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #65248]			optimum	7
[Ref.: #65248]			growth	4-8

Information on physiology and metabolism Physiology and metabolism

[Ref.: #65248]	Oxygen tolerance	aerobe
[Ref.: #67771]	Oxygen tolerance	aerobe

[Ref.: #65248]	Ability of spore formation	no
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.984

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #65248]		NaCl		growth	0-1.5	%(w/v)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #65248]	(S)-lactate ChEBI	-	assimilation
[Ref.: #65248]	2-hydroxybutyrate ChEBI	-	assimilation
[Ref.: #65248]	2-oxobutanoate ChEBI	-	assimilation
[Ref.: #65248]	2-oxoglutarate ChEBI	+	assimilation
[Ref.: #65248]	3-hydroxybutyrate ChEBI	-	assimilation
[Ref.: #65248]	3-O-methyl-D-glucose ChEBI	-	assimilation
[Ref.: #65248]	4-hydroxyphenylacetic acid ChEBI	+	assimilation
[Ref.: #65248]	acetate ChEBI	+	assimilation
[Ref.: #65248]	acetoacetate ChEBI	-	assimilation
[Ref.: #65248]	adipate ChEBI	+	builds acid from
[Ref.: #65248]	alpha-D-glucose ChEBI	+	assimilation
[Ref.: #65248]	bromosuccinate ChEBI	-	assimilation
[Ref.: #65248]	cellobiose ChEBI	+	assimilation
[Ref.: #65248]	cellulose ChEBI	-	hydrolysis
[Ref.: #65248]	citrate ChEBI	-	assimilation
[Ref.: #65248]	D-arabitol ChEBI	-	assimilation
[Ref.: #65248]	D-arabitol ChEBI	+	assimilation
[Ref.: #65248]	D-aspartate ChEBI	-	assimilation
[Ref.: #65248]	D-fructose 6-phosphate ChEBI	-	assimilation
[Ref.: #65248]	D-fucose ChEBI	-	assimilation
[Ref.: #65248]	D-galacturonic acid ChEBI	-	assimilation
[Ref.: #65248]	D-gluconate ChEBI	-	assimilation
[Ref.: #65248]	D-glucose 6-phosphate ChEBI	-	assimilation
[Ref.: #65248]	D-glucuronate ChEBI	-	assimilation
[Ref.: #65248]	D-malate ChEBI	+	assimilation
[Ref.: #65248]	D-mannitol ChEBI	+	assimilation
[Ref.: #65248]	D-mannose ChEBI	+	assimilation
[Ref.: #65248]	D-saccharate ChEBI	+	assimilation
[Ref.: #65248]	D-serine ChEBI	-	assimilation
[Ref.: #65248]	D-sorbitol ChEBI	+	assimilation
[Ref.: #65248]	D-trehalose ChEBI	+	assimilation
[Ref.: #65248]	dextrin ChEBI	-	assimilation
[Ref.: #65248]	esculin ChEBI	+	hydrolysis
[Ref.: #65248]	formate ChEBI	-	assimilation
[Ref.: #65248]	gamma-aminobutyric acid ChEBI	-	assimilation
[Ref.: #65248]	gelatin ChEBI	+	assimilation
[Ref.: #65248]	gelatin ChEBI	+	hydrolysis
[Ref.: #65248]	gentiobiose ChEBI	-	assimilation
[Ref.: #65248]	glucuronamide ChEBI	-	assimilation
[Ref.: #65248]	glycerol ChEBI	-	assimilation
[Ref.: #65248]	glycine-proline ChEBI	-	assimilation
[Ref.: #65248]	inosine ChEBI	+	assimilation
[Ref.: #65248]	L-alanine ChEBI	+	assimilation
[Ref.: #65248]	L-arginine ChEBI	-	assimilation
[Ref.: #65248]	L-aspartate ChEBI	-	assimilation
[Ref.: #65248]	L-fructose ChEBI	+	assimilation
[Ref.: #65248]	L-galactonic acid gamma-lactone ChEBI	-	assimilation
[Ref.: #65248]	L-glutamate ChEBI	-	assimilation
[Ref.: #65248]	L-histidine ChEBI	-	assimilation
[Ref.: #65248]	L-malate ChEBI	+	assimilation
[Ref.: #65248]	L-pyroglutamic acid ChEBI	-	assimilation
[Ref.: #65248]	L-rhamnose ChEBI	+	assimilation
[Ref.: #65248]	L-serine ChEBI	+	assimilation
[Ref.: #65248]	lactose ChEBI	-	assimilation
[Ref.: #65248]	maltose ChEBI	-	assimilation
[Ref.: #65248]	melibiose ChEBI	-	assimilation
[Ref.: #65248]	methyl beta-D-glucopyranoside ChEBI	-	assimilation
[Ref.: #65248]	methyl pyruvate ChEBI	-	assimilation
[Ref.: #65248]	milk	-	degradation
[Ref.: #65248]	myo-inositol ChEBI	+	assimilation
[Ref.: #65248]	N-acetyl-D-mannosamine ChEBI	-	assimilation
[Ref.: #65248]	N-acetylgalactosamine ChEBI	-	assimilation
[Ref.: #65248]	N-acetylglucosamine ChEBI	-	assimilation
[Ref.: #65248]	n-acetylneuraminate ChEBI	-	assimilation
[Ref.: #65248]	nitrate ChEBI	+	reduction
[Ref.: #65248]	pectin ChEBI	+	assimilation
[Ref.: #65248]	potassium gluconate ChEBI	+	builds acid from
[Ref.: #65248]	propionate ChEBI	-	assimilation
[Ref.: #65248]	quinate ChEBI	-	assimilation
[Ref.: #65248]	raffinose ChEBI	-	assimilation
[Ref.: #65248]	salicin ChEBI	-	assimilation
[Ref.: #65248]	stachyose ChEBI	-	assimilation
[Ref.: #65248]	starch ChEBI	-	hydrolysis
[Ref.: #65248]	sucrose ChEBI	-	assimilation
[Ref.: #65248]	turanose ChEBI	-	assimilation
[Ref.: #65248]	tween 20 ChEBI	+	hydrolysis
[Ref.: #65248]	tween 40 ChEBI	-	assimilation
[Ref.: #65248]	tween 40 ChEBI	-	hydrolysis
[Ref.: #65248]	tween 60 ChEBI	-	hydrolysis
[Ref.: #65248]	tween 80 ChEBI	-	hydrolysis
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #65248]		hydrogen sulfide ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #65248]	acid phosphatase	+	3.1.3.2
[Ref.: #65248]	alkaline phosphatase	+	3.1.3.1
[Ref.: #65248]	alpha-chymotrypsin	-	3.4.21.1
[Ref.: #65248]	alpha-galactosidase	-	3.2.1.22
[Ref.: #65248]	alpha-glucosidase	-	3.2.1.20
[Ref.: #65248]	alpha-mannosidase	+	3.2.1.24
[Ref.: #65248]	beta-D-fucosidase	-	3.2.1.38
[Ref.: #65248]	beta-galactosidase	-	3.2.1.23
[Ref.: #65248]	beta-glucosidase	+	3.2.1.21
[Ref.: #65248]	beta-glucuronidase	-	3.2.1.31
[Ref.: #65248]	catalase	+	1.11.1.6
[Ref.: #65248]	cystine arylamidase	-	3.4.11.3
[Ref.: #65248]	cytochrome oxidase	+	1.9.3.1
[Ref.: #65248]	esterase (C 4)	+
[Ref.: #65248]	esterase Lipase (C 8)	+
[Ref.: #65248]	leucine arylamidase	+	3.4.11.1
[Ref.: #65248]	lipase (C 14)	-
[Ref.: #65248]	N-acetyl-beta-glucosaminidase	-	3.2.1.52
[Ref.: #65248]	naphthol-AS-BI-phosphohydrolase	+
[Ref.: #65248]	trypsin	-	3.4.21.4
[Ref.: #65248]	valine arylamidase	+
	Only first 10 entries are displayed. Click here to see all.

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

[Ref.: #65248]	Sample type/isolated from	sand sample
[Ref.: #65248]	Geographic location (country and/or sea, region)	desert
[Ref.: #65248]	Country	Saudi Arabia
[Ref.: #65248]	Country ISO 3 Code	SAU
[Ref.: #65248]	Continent	Asia
[Ref.: #65248]	Geographic location	24.3161°/38.5106°
[Ref.: #65248]	Enrichment culture	R2A agar
[Ref.: #65248]	Enrichment culture duration	7 days
[Ref.: #65248]	Enrichment culture temperature	37 ̊C
[Ref.: #65248]	Isolation/enrichment procedure	Two grams of the sand sample were suspended into a conical flask containing 18 ml sterile water and several glass beads. The suspension was kept incubated in an orbital shaker (37°C, 200 r.p.m., 1 h). Following incubation, it was diluted 1000-fold with sterile water and 0.2 ml aliquots were spread on Reasoner's 2A (R2A; BD) agar plates adjusted to pH 7.0. The isolation plates were incubated at 37°C for 7 days.

[Ref.: #67771]	Sample type/isolated from	From desert
[Ref.: #67771]	Geographic location (country and/or sea, region)	Riyadh
[Ref.: #67771]	Country	Saudi Arabia
[Ref.: #67771]	Country ISO 3 Code	SAU
[Ref.: #67771]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental

#Terrestrial

#Sandy

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.: #65248]	16S rRNA gene sequence	KY882041		GenBank

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Siccirubricoccus deserti CGMCC 1.15936	GCA_014644195	scaffold	GenBank	2013562 tax ID	*
[Ref.: #66792]	Siccirubricoccus deserti strain CGMCC 1.15936	2013562.4	wgs	PATRIC	2013562 tax ID	*

[Ref.: #65248]

GC-content

71.6 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: Siccirubricoccus deserti CGMCC 1.15936 NCBI: GCA_014644195.1
[Ref.: #69481]	spore-forming	no	86	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Siccirubricoccus deserti CGMCC 1.15936 NCBI: GCA_014644195.1
[Ref.: #69480]	flagellated	no	92	no
[Ref.: #69480]	gram-positive	no	98.276	yes
[Ref.: #69480]	anaerobic	no	96.577	yes
[Ref.: #69480]	aerobic	yes	87.303	yes
[Ref.: #69480]	halophile	no	91.666	no
[Ref.: #69480]	spore-forming	no	92.544	yes
[Ref.: #69480]	glucose-util	yes	81.64	no
[Ref.: #69480]	thermophile	no	94.186	yes
[Ref.: #69480]	motile	no	55.358	no
[Ref.: #69480]	glucose-ferment	no	91.311	no

Availability in culture collections External links

[Ref.: #65248]

Culture collection no.

CGMCC 1.15936, KCTC 62088, SYSU D8009

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Siccirubricoccus phaeus sp. nov., isolated from oil reservoir water and emended description of the genus Siccirubricoccus.	Li FL, Zhang YX, Zhang YK, Chen WF, Li WJ, Wang L	Antonie Van Leeuwenhoek	10.1007/s10482-021-01516-8	2021	*
Phylogeny	Roseicella frigidaeris gen. nov., sp. nov., isolated from an air-conditioning system.	Khan SA, Jeong SE, Jung HS, Quan ZX, Jeon CO	Int J Syst Evol Microbiol	10.1099/ijsem.0.003322	2019	*
Phylogeny	Siccirubricoccus deserti gen. nov., sp. nov., a proteobacterium isolated from a desert sample.	Yang ZW, Salam N, Hua ZS, Liu BB, Han MX, Fang BZ, Wang D, Xiao M, Hozzein WN, Li WJ	Int J Syst Evol Microbiol	10.1099/ijsem.0.002397	2017	*
Phylogeny	Siccirubricoccus soli sp. nov., a novel bacterial species isolated from Jiaozi Mountain soil.	Zhu GX, Wu YJ, Cao YR, Fan BJ, Jiao Y, Hou XL, Liu ZC, Zhang Y, He JB, Liang LM	Antonie Van Leeuwenhoek	10.1007/s10482-022-01771-3	2022	*

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 )

#65248

Zi-Wen Yang, Nimaichand Salam, Zheng-Shuang Hua, Bing-Bing Liu, Ming-Xian Han, Bao-Zhu Fang, Dong Wang, Min Xiao, Wael N. Hozzein, Wen-Jun Li: Siccirubricoccus deserti gen. nov., sp. nov., a proteobacterium isolated from a desert sample. IJSEM 67: 4862 - 4867 2017 ( DOI 10.1099/ijsem.0.002397 , PubMed 28984236 )

#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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