Name: Sphingobacterium haloxyli 5JN-11
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 159833

Type strain:

Species: Sphingobacterium haloxyli

Strain Designation: 5JN-11

Culture col. no.: ACCC 60072, KCTC 62457

NCBI tax ID(s): 2100533 (species)

Special Collections

Section

When using BacDive for research please cite our paper

Sphingobacterium haloxyli 5JN-11 is a Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from the endophytic bacterial diversity of Haloxylon ammodendron.

colony-forming
Gram-negative
rod-shaped
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	*Bacteroidota*
	Class	*Sphingobacteriia*
	Order	*Sphingobacteriales*
	Family	*Sphingobacteriaceae*
	Genus	*Sphingobacterium*
	Species	**Sphingobacterium haloxyli**
	Full Scientific Name (LPSN)	Sphingobacterium haloxyli Liu et al. 2018

Information on morphological and physiological properties Morphology

[Ref.: #66702]	Gram stain	negative

[Ref.: #66702]	Cell length	0.6-1.1 µm

[Ref.: #66702]	Cell width	0.2-0.5 µm

[Ref.: #66702]	Cell shape	rod-shaped

[Ref.: #66702]	Motility	no

[Ref.: #66702]	Colony color	white
[Ref.: #66702]	Colony shape	circular
[Ref.: #66702]	Cultivation medium used	Trypticase Soy Agar (TSA)

Information on culture and growth conditions Culture and growth conditions

[Ref.: #66702]

Culture medium

tryptic soy agar (TSA)

[Ref.: #66702]

Culture medium growth

	Temperatures	Kind of temperature		Temperature
[Ref.: #66702]			growth	20-42 °C
[Ref.: #66702]			optimum	28-30 °C

	pH	Kind of pH		pH
[Ref.: #66702]			optimum	7.0-8.0
[Ref.: #66702]			growth	7.0-9.0

Information on physiology and metabolism Physiology and metabolism

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #66702]		NaCl		growth	0-6	%(w/v)
[Ref.: #66702]		NaCl		optimum	0-2	%(w/v)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #66702]	2,3-butanediol ChEBI	-	respiration
[Ref.: #66702]	2-hydroxybutyrate ChEBI	-	respiration
[Ref.: #66702]	2-oxobutanoate ChEBI	-	respiration
[Ref.: #66702]	2-oxoglutarate ChEBI	-	respiration
[Ref.: #66702]	2-oxopentanoate ChEBI	-	respiration
[Ref.: #66702]	3-hydroxybutyrate ChEBI	-	respiration
[Ref.: #66702]	4-hydroxy-L-proline ChEBI	-	respiration
[Ref.: #66702]	4-hydroxybutyrate ChEBI	-	respiration
[Ref.: #66702]	4-hydroxyphenylacetic acid ChEBI	-	respiration
[Ref.: #66702]	acetic acid ChEBI	+	respiration
[Ref.: #66702]	adipate ChEBI	-	assimilation
[Ref.: #66702]	alpha-cyclodextrin ChEBI	+	respiration
[Ref.: #66702]	alpha-D-glucose ChEBI	+	respiration
[Ref.: #66702]	bromosuccinate ChEBI	-	respiration
[Ref.: #66702]	casein	-	hydrolysis
[Ref.: #66702]	cellobiose ChEBI	+	respiration
[Ref.: #66702]	cis-aconitate ChEBI	-	respiration
[Ref.: #66702]	citric acid ChEBI	-	respiration
[Ref.: #66702]	D-alanine ChEBI	-	respiration
[Ref.: #66702]	D-arabitol ChEBI	-	respiration
[Ref.: #66702]	D-fructose ChEBI	+	respiration
[Ref.: #66702]	D-galactonic acid lactone ChEBI	-	respiration
[Ref.: #66702]	D-galactose ChEBI	+	respiration
[Ref.: #66702]	D-galacturonic acid ChEBI	-	respiration
[Ref.: #66702]	D-glucarate ChEBI	-	respiration
[Ref.: #66702]	D-gluconate ChEBI	-	respiration
[Ref.: #66702]	D-glucosaminic acid ChEBI	-	respiration
[Ref.: #66702]	D-glucose ChEBI	+	assimilation
[Ref.: #66702]	D-glucose 6-phosphate ChEBI	-	respiration
[Ref.: #66702]	D-glucuronate ChEBI	-	respiration
[Ref.: #66702]	D-mannitol ChEBI	-	assimilation
[Ref.: #66702]	D-mannitol ChEBI	+	respiration
[Ref.: #66702]	D-mannose ChEBI	+	assimilation
[Ref.: #66702]	D-mannose ChEBI	+	respiration
[Ref.: #66702]	D-psicose ChEBI	-	respiration
[Ref.: #66702]	D-serine ChEBI	-	respiration
[Ref.: #66702]	D-sorbitol ChEBI	-	respiration
[Ref.: #66702]	decanoate ChEBI	-	assimilation
[Ref.: #66702]	dextrin ChEBI	+	respiration
[Ref.: #66702]	DL-carnitine ChEBI	-	respiration
[Ref.: #66702]	erythritol ChEBI	-	respiration
[Ref.: #66702]	esculin ChEBI	+	hydrolysis
[Ref.: #66702]	ethanolamine ChEBI	-	respiration
[Ref.: #66702]	formate ChEBI	-	respiration
[Ref.: #66702]	gamma-aminobutyric acid ChEBI	-	respiration
[Ref.: #66702]	gelatin ChEBI	-	hydrolysis
[Ref.: #66702]	gentiobiose ChEBI	+	respiration
[Ref.: #66702]	glucose 1-phosphate ChEBI	-	respiration
[Ref.: #66702]	glucuronamide ChEBI	-	respiration
[Ref.: #66702]	glycerol ChEBI	-	respiration
[Ref.: #66702]	glycerol 1-phosphate ChEBI	-	respiration
[Ref.: #66702]	glycogen ChEBI	-	respiration
[Ref.: #66702]	glycyl L-aspartic acid ChEBI	-	respiration
[Ref.: #66702]	glycyl-L-glutamate ChEBI	-	respiration
[Ref.: #66702]	inosine ChEBI	-	respiration
[Ref.: #66702]	itaconate ChEBI	-	respiration
[Ref.: #66702]	L-alaninamide ChEBI	-	respiration
[Ref.: #66702]	L-alanine ChEBI	-	respiration
[Ref.: #66702]	L-alanylglycine ChEBI	-	respiration
[Ref.: #66702]	L-arabinose ChEBI	+	assimilation
[Ref.: #66702]	L-arabinose ChEBI	+	respiration
[Ref.: #66702]	L-asparagine ChEBI	+	respiration
[Ref.: #66702]	L-aspartate ChEBI	-	respiration
[Ref.: #66702]	L-fucose ChEBI	-	respiration
[Ref.: #66702]	L-glutamate ChEBI	-	respiration
[Ref.: #66702]	L-histidine ChEBI	-	respiration
[Ref.: #66702]	L-leucine ChEBI	-	respiration
[Ref.: #66702]	L-ornithine ChEBI	-	respiration
[Ref.: #66702]	L-phenylalanine ChEBI	-	respiration
[Ref.: #66702]	L-proline ChEBI	-	respiration
[Ref.: #66702]	L-pyroglutamic acid ChEBI	-	respiration
[Ref.: #66702]	L-rhamnose ChEBI	+	respiration
[Ref.: #66702]	L-serine ChEBI	-	respiration
[Ref.: #66702]	L-threonine ChEBI	+	respiration
[Ref.: #66702]	lactate ChEBI	-	respiration
[Ref.: #66702]	lactose ChEBI	-	respiration
[Ref.: #66702]	lactulose ChEBI	+	respiration
[Ref.: #66702]	malate ChEBI	-	assimilation
[Ref.: #66702]	malonate ChEBI	-	respiration
[Ref.: #66702]	maltose ChEBI	+	assimilation
[Ref.: #66702]	maltose ChEBI	+	respiration
[Ref.: #66702]	melibiose ChEBI	+	respiration
[Ref.: #66702]	methyl beta-D-glucopyranoside ChEBI	+	respiration
[Ref.: #66702]	methyl pyruvate ChEBI	-	respiration
[Ref.: #66702]	monomethyl succinate ChEBI	-	respiration
[Ref.: #66702]	myo-inositol ChEBI	-	respiration
[Ref.: #66702]	N-acetylgalactosamine ChEBI	+	respiration
[Ref.: #66702]	N-acetylglucosamine ChEBI	+	assimilation
[Ref.: #66702]	N-acetylglucosamine ChEBI	+	respiration
[Ref.: #66702]	nitrate ChEBI	-	reduction
[Ref.: #66702]	phenylacetate ChEBI	-	assimilation
[Ref.: #66702]	phenylethylamine ChEBI	-	respiration
[Ref.: #66702]	potassium gluconate ChEBI	-	assimilation
[Ref.: #66702]	propionate ChEBI	-	respiration
[Ref.: #66702]	putrescine ChEBI	-	respiration
[Ref.: #66702]	quinate ChEBI	-	respiration
[Ref.: #66702]	raffinose ChEBI	+	respiration
[Ref.: #66702]	ribitol ChEBI	+	respiration
[Ref.: #66702]	sebacic acid ChEBI	-	respiration
[Ref.: #66702]	sodium citrate ChEBI	-	assimilation
[Ref.: #66702]	starch ChEBI	-	hydrolysis
[Ref.: #66702]	succinamate ChEBI	-	respiration
[Ref.: #66702]	succinate ChEBI	-	respiration
[Ref.: #66702]	sucrose ChEBI	+	respiration
[Ref.: #66702]	thymidine ChEBI	-	respiration
[Ref.: #66702]	trehalose ChEBI	+	respiration
[Ref.: #66702]	turanose ChEBI	+	respiration
[Ref.: #66702]	tween 40 ChEBI	-	respiration
[Ref.: #66702]	tween 80 ChEBI	-	respiration
[Ref.: #66702]	uridine ChEBI	-	respiration
[Ref.: #66702]	urocanic acid ChEBI	-	respiration
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #66702]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #66702]	acid phosphatase	+	3.1.3.2
[Ref.: #66702]	alkaline phosphatase	+	3.1.3.1
[Ref.: #66702]	alpha-fucosidase	-	3.2.1.51
[Ref.: #66702]	alpha-galactosidase	-	3.2.1.22
[Ref.: #66702]	alpha-mannosidase	-	3.2.1.24
[Ref.: #66702]	arginine dihydrolase	-	3.5.3.6
[Ref.: #66702]	beta-galactosidase	-	3.2.1.23
[Ref.: #66702]	beta-glucosidase	-	3.2.1.21
[Ref.: #66702]	beta-glucuronidase	-	3.2.1.31
[Ref.: #66702]	catalase	+	1.11.1.6
[Ref.: #66702]	cytochrome oxidase	+	1.9.3.1
[Ref.: #66702]	esterase (C 4)	+
[Ref.: #66702]	esterase Lipase (C 8)	+
[Ref.: #66702]	leucine arylamidase	+	3.4.11.1
[Ref.: #66702]	naphthol-AS-BI-phosphohydrolase	+
[Ref.: #66702]	trypsin	+	3.4.21.4
[Ref.: #66702]	urease	+	3.5.1.5
[Ref.: #66702]	valine arylamidase	-
	Only first 10 entries are displayed. Click here to see all.

Fatty acid profile

Metadata FA analysis

Reference

[Ref.: #66702]

Fatty acid	Percentage
C16:1 w7c / C16:1 w6c	48.1
C15:0 ios	25.3
C17:0 iso 3OH	9.4
C16:0 iso	4.1
C16:0 10-methyl / iso-C17:1w9c	2.2
C15:0 iso 3OH	1.9
C16:0 3OH	1.5
C16:1 w5c	1.4
C17:1 iso / C17:1 anteiso	0.8

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

[Ref.: #66702]	Sample type/isolated from	the endophytic bacterial diversity of Haloxylon ammodendron
[Ref.: #66702]	Host species	Haloxylon ammodendron
[Ref.: #66702]	Geographic location (country and/or sea, region)	Kumtag desert in Xinjiang Uyghur autonomous region
[Ref.: #66702]	Country	China
[Ref.: #66702]	Country ISO 3 Code	CHN
[Ref.: #66702]	Continent	Asia
[Ref.: #66702]	Geographic location	40.0881°/94.6756°
[Ref.: #66702]	Isolation/enrichment procedure	The methods of surface-sterilization of stems, and the isolation and identification of strains were according to Liu et al.
* marker position based on {}

Isolation sources categories

#Host Body-Site	#Plant	#Endosphere
#Host	#Plants	#Shrub (Scrub)

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.: #66702]	Sphingobacterium haloxyli strain 5JN-11 16S ribosomal RNA gene, partial sequence	MG669350	1450	GenBank ENA	2100533 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Sphingobacterium haloxyli 5JN-11	GCA_002980525	contig	GenBank ENA	2100533 tax ID	*
[Ref.: #66792]	Sphingobacterium haloxyli 5JN-11	2849507829	draft	JGI IMG/M	2100533 tax ID	*

[Ref.: #66702]

GC-content

42.8 mol%

genome sequence analysis

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

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Sphingobacterium haloxyli 5JN-11 NCBI: GCA_002980525
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	no	87
[Ref.: #125439]	BacteriaNet	motilityⓘ	no	54.9
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	negative	88.2
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	obligate aerobe	85.2

Availability in culture collections External links

[Ref.: #66702]

Culture collection no.

ACCC 60072, KCTC 62457

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Sphingobacterium haloxyli sp. nov., an endophytic bacterium isolated from Haloxylon ammodendron stems in Kumtag desert.	Liu L, Hui N, Liang LX, Zhang XX, Li LB, Sun QW	Int J Syst Evol Microbiol	10.1099/ijsem.0.002982	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 )

#66702

Lei Liu, Nan Hui, Li-xiong Liang, Xiao-xia Zhang, Lu-bin Li, Qi-wu Sun: Sphingobacterium haloxyli sp. nov., an endophytic bacterium isolated from Haloxylon ammodendron stems in Kumtag desert. IJSEM 68: 3279 - 3284 2018 ( DOI 10.1099/ijsem.0.002982 , PubMed 30156529 )

#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) .

#125439

Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .

* These data were automatically processed and therefore are not curated

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