Name: Sphingobacterium populi 7Y-4
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 140613

Type strain:

Species: Sphingobacterium populi

Strain Designation: 7Y-4

Culture col. no.: CFCC 11742, KCTC 42247

Strain history: <- Yong Li, Dongxiaoful, Haidian district, Beijing, China

NCBI tax ID(s): 1812824 (species)

Section

Sphingobacterium populi 7Y-4 is an aerobe, mesophilic, Gram-negative bacterium that forms circular colonies and was isolated from symptomatic bark tissue of a Populus x euramericana canker sample.

colony-forming
Gram-negative
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	*Bacteroidota*
	Class	*Sphingobacteriia*
	Order	*Sphingobacteriales*
	Family	*Sphingobacteriaceae*
	Genus	*Sphingobacterium*
	Species	**Sphingobacterium populi**
	Full Scientific Name (LPSN)	Sphingobacterium populi Li et al. 2016

Information on morphological and physiological properties Morphology

[Ref.: #43128]	Gram stain	negative
[Ref.: #67771]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.989

[Ref.: #43128]	Motility	no
[Ref.: #67771]	Motility	no
[Ref.: #69480]	Motility	no Confidence in %92.793

[Ref.: #67771]	Cell shape	rod-shaped

[Ref.: #43128]	Colony size	1-2 mm
[Ref.: #43128]	Colony color	pale yellow
[Ref.: #43128]	Colony shape	circular
[Ref.: #43128]	Incubation period	2 days
[Ref.: #43128]	Cultivation medium used	TSA

Information on culture and growth conditions Culture and growth conditions

[Ref.: #43128]

Culture medium

Trypticase Soy Agar (TSA)

[Ref.: #43128]

Culture medium growth

		Temperature
[Ref.: #43128]	optimum	28-30 °C
[Ref.: #43128]	growth	10-37 °C
[Ref.: #67771]	growth	28 °C

[Ref.: #43128]	Temperature range	mesophilic
[Ref.: #67771]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #43128]			optimum	6.0-8.0
[Ref.: #43128]			growth	5-10

Information on physiology and metabolism Physiology and metabolism

[Ref.: #43128]	Oxygen tolerance	aerobe
[Ref.: #67771]	Oxygen tolerance	aerobe

[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.999

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #43128]		NaCl		growth	0-3	%(w/v)

[Ref.: #67771]

Observation

quinones: MK-7

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #43128]	2,3-butanediol ChEBI	+	respiration
[Ref.: #43128]	2-oxopentanoate ChEBI	+	respiration
[Ref.: #43128]	4-hydroxybutyrate ChEBI	+	respiration
[Ref.: #43128]	acetate ChEBI	+	respiration
[Ref.: #43128]	alpha-cyclodextrin ChEBI	+	respiration
[Ref.: #43128]	alpha-D-glucose ChEBI	+	respiration
[Ref.: #43128]	alpha-lactose ChEBI	+	respiration
[Ref.: #43128]	amygdalin ChEBI	-	builds acid from
[Ref.: #43128]	arbutin ChEBI	-	builds acid from
[Ref.: #43128]	bromosuccinate ChEBI	+	respiration
[Ref.: #43128]	cellobiose ChEBI	-	builds acid from
[Ref.: #43128]	cellobiose ChEBI	+	respiration
[Ref.: #43128]	citrate ChEBI	-	assimilation
[Ref.: #43128]	D-arabinose ChEBI	-	builds acid from
[Ref.: #43128]	D-arabitol ChEBI	-	builds acid from
[Ref.: #43128]	D-fructose ChEBI	-	builds acid from
[Ref.: #43128]	D-fructose ChEBI	+	respiration
[Ref.: #43128]	D-fucose ChEBI	-	builds acid from
[Ref.: #43128]	D-galactose ChEBI	-	builds acid from
[Ref.: #43128]	D-galactose ChEBI	+	respiration
[Ref.: #43128]	D-glucose ChEBI	-	builds acid from
[Ref.: #43128]	D-glucose ChEBI	+	carbon source
[Ref.: #43128]	D-glucose 6-phosphate ChEBI	+	respiration
[Ref.: #43128]	D-lyxose ChEBI	-	builds acid from
[Ref.: #43128]	D-mannitol ChEBI	-	builds acid from
[Ref.: #43128]	D-mannitol ChEBI	+	carbon source
[Ref.: #43128]	D-mannose ChEBI	-	builds acid from
[Ref.: #43128]	D-mannose ChEBI	+	carbon source
[Ref.: #43128]	D-mannose ChEBI	+	respiration
[Ref.: #43128]	D-psicose ChEBI	+	respiration
[Ref.: #43128]	D-ribose ChEBI	-	builds acid from
[Ref.: #43128]	D-sorbitol ChEBI	-	builds acid from
[Ref.: #43128]	D-sorbitol ChEBI	+	respiration
[Ref.: #43128]	D-tagatose ChEBI	-	builds acid from
[Ref.: #43128]	D-xylose ChEBI	-	builds acid from
[Ref.: #43128]	dextrin ChEBI	+	respiration
[Ref.: #43128]	erythritol ChEBI	-	builds acid from
[Ref.: #43128]	erythritol ChEBI	+	respiration
[Ref.: #43128]	esculin ChEBI	+	hydrolysis
[Ref.: #43128]	esculin ferric citrate	+	builds acid from
[Ref.: #43128]	galactitol ChEBI	-	builds acid from
[Ref.: #43128]	gelatin ChEBI	-	hydrolysis
[Ref.: #43128]	gentiobiose ChEBI	-	builds acid from
[Ref.: #43128]	gentiobiose ChEBI	+	respiration
[Ref.: #43128]	glucose 1-phosphate ChEBI	+	respiration
[Ref.: #43128]	glycerol ChEBI	-	builds acid from
[Ref.: #43128]	glycerol ChEBI	+	respiration
[Ref.: #43128]	glycogen ChEBI	-	builds acid from
[Ref.: #43128]	glycogen ChEBI	+	respiration
[Ref.: #43128]	inulin ChEBI	-	builds acid from
[Ref.: #43128]	L-arabinose ChEBI	-	builds acid from
[Ref.: #43128]	L-arabinose ChEBI	+	respiration
[Ref.: #43128]	L-arabitol ChEBI	-	builds acid from
[Ref.: #43128]	L-asparagine ChEBI	+	respiration
[Ref.: #43128]	L-fucose ChEBI	-	builds acid from
[Ref.: #43128]	L-fucose ChEBI	+	respiration
[Ref.: #43128]	L-glutamate ChEBI	+	respiration
[Ref.: #43128]	L-leucine ChEBI	+	respiration
[Ref.: #43128]	L-rhamnose ChEBI	-	builds acid from
[Ref.: #43128]	L-serine ChEBI	+	respiration
[Ref.: #43128]	L-sorbose ChEBI	-	builds acid from
[Ref.: #43128]	L-threonine ChEBI	+	respiration
[Ref.: #43128]	L-xylose ChEBI	-	builds acid from
[Ref.: #43128]	lactose ChEBI	-	builds acid from
[Ref.: #43128]	lactulose ChEBI	+	respiration
[Ref.: #43128]	maltose ChEBI	-	builds acid from
[Ref.: #43128]	maltose ChEBI	+	respiration
[Ref.: #43128]	melezitose ChEBI	-	builds acid from
[Ref.: #43128]	melibiose ChEBI	-	builds acid from
[Ref.: #43128]	melibiose ChEBI	+	respiration
[Ref.: #43128]	methyl alpha-D-glucopyranoside	-	builds acid from
[Ref.: #43128]	methyl alpha-D-mannoside ChEBI	-	builds acid from
[Ref.: #43128]	methyl beta-D-glucopyranoside ChEBI	+	respiration
[Ref.: #43128]	methyl beta-D-xylopyranoside ChEBI	-	builds acid from
[Ref.: #43128]	methyl pyruvate ChEBI	+	respiration
[Ref.: #43128]	monomethyl succinate ChEBI	+	respiration
[Ref.: #43128]	myo-inositol ChEBI	-	builds acid from
[Ref.: #43128]	N-acetylglucosamine ChEBI	-	builds acid from
[Ref.: #43128]	N-acetylglucosamine ChEBI	+	respiration
[Ref.: #43128]	nitrate ChEBI	-	reduction
[Ref.: #43128]	potassium 2-dehydro-D-gluconate	-	builds acid from
[Ref.: #43128]	potassium 5-dehydro-D-gluconate	-	builds acid from
[Ref.: #43128]	potassium gluconate ChEBI	-	builds acid from
[Ref.: #43128]	raffinose ChEBI	-	builds acid from
[Ref.: #43128]	raffinose ChEBI	+	respiration
[Ref.: #43128]	ribitol ChEBI	-	builds acid from
[Ref.: #43128]	salicin ChEBI	-	builds acid from
[Ref.: #43128]	starch ChEBI	-	builds acid from
[Ref.: #43128]	sucrose ChEBI	-	builds acid from
[Ref.: #43128]	sucrose ChEBI	+	respiration
[Ref.: #43128]	trehalose ChEBI	-	builds acid from
[Ref.: #43128]	trehalose ChEBI	+	respiration
[Ref.: #43128]	turanose ChEBI	-	builds acid from
[Ref.: #43128]	turanose ChEBI	+	respiration
[Ref.: #43128]	tween 40 ChEBI	+	respiration
[Ref.: #43128]	uridine ChEBI	+	respiration
[Ref.: #43128]	xylitol ChEBI	-	builds acid from
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Production
[Ref.: #43128]	acetoin ChEBI	no
[Ref.: #43128]	hydrogen sulfide ChEBI	no
[Ref.: #43128]	indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #43128]	acid phosphatase	+/-	3.1.3.2
[Ref.: #43128]	alkaline phosphatase	+	3.1.3.1
[Ref.: #43128]	alpha-chymotrypsin	+	3.4.21.1
[Ref.: #43128]	alpha-fucosidase	+	3.2.1.51
[Ref.: #43128]	alpha-galactosidase	+	3.2.1.22
[Ref.: #43128]	alpha-glucosidase	+	3.2.1.20
[Ref.: #43128]	alpha-mannosidase	+	3.2.1.24
[Ref.: #43128]	arginine dihydrolase	-	3.5.3.6
[Ref.: #43128]	beta-galactosidase	+	3.2.1.23
[Ref.: #43128]	beta-glucosidase	+	3.2.1.21
[Ref.: #43128]	catalase	+	1.11.1.6
[Ref.: #43128]	cystine arylamidase	-	3.4.11.3
[Ref.: #43128]	cytochrome oxidase	+	1.9.3.1
[Ref.: #43128]	esterase (C 4)	+
[Ref.: #43128]	esterase Lipase (C 8)	+
[Ref.: #43128]	gelatinase	-
[Ref.: #43128]	leucine arylamidase	+	3.4.11.1
[Ref.: #43128]	lipase (C 14)	-
[Ref.: #43128]	lysine decarboxylase	-	4.1.1.18
[Ref.: #43128]	N-acetyl-beta-glucosaminidase	+	3.2.1.52
[Ref.: #43128]	naphthol-AS-BI-phosphohydrolase	+
[Ref.: #43128]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #43128]	trypsin	+	3.4.21.4
[Ref.: #43128]	tryptophan deaminase	-	4.1.99.1
[Ref.: #43128]	urease	+	3.5.1.5
[Ref.: #43128]	valine arylamidase	-
	Only first 10 entries are displayed. Click here to see all.

Fatty acid profile

Metadata FA analysis

Reference

[Ref.: #43128]

Fatty acid	Percentage
C16:1ω7c / C16:1ω6c	31.8
C15:0 iso	28.6
C17:0 iso 3OH	23.3
C16:0 3OH	4.9
C16:0	4.8
C16:0 2OH	2.1
C15:0 iso 3OH	1.9
C17:1 iso ω9c / C16:0 10-methyl	1.1
C18:0	0.8

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

[Ref.: #43128]	Sample type/isolated from	symptomatic bark tissue of a Populus x euramericana canker sample
[Ref.: #43128]	Geographic location (country and/or sea, region)	Qingfeng, Puyang City, Henan Province, China
[Ref.: #43128]	Country	China
[Ref.: #43128]	Country ISO 3 Code	CHN
[Ref.: #43128]	Continent	Asia
[Ref.: #43128]	Isolation date	2010-08

[Ref.: #67771]	Sample type/isolated from	From the symptomatic bark tissue of a `Populus Ã— euramericana`
[Ref.: #67771]	Geographic location (country and/or sea, region)	Qingfeng, Puyang City, Henan Province
[Ref.: #67771]	Country	China
[Ref.: #67771]	Country ISO 3 Code	CHN
[Ref.: #67771]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Host	#Plants	#Tree
#Host Body-Site	#Plant	#Bark

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence KT988032 (>99% sequence identity) for Sphingobacterium populi subclade from Microbeatlas

Aquatic Samples	882
Soil Samples	1360
Animal Samples	1742
Plant Samples	1005
Total Samples	4989

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.: #43128]	16S rRNA gene sequences	KT988032	1400	ENA	1812824 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Sphingobacterium sp. CFCC 11742	1775560.3	wgs	PATRIC	1775560 tax ID	*
[Ref.: #66792]	Sphingobacterium sp. CFCC 11742	2728369126	draft	JGI IMG/M	1775560 tax ID	*
[Ref.: #66792]	Sphingobacterium sp. CFCC 11742	GCA_001586775	contig	GenBank	1775560 tax ID	*

[Ref.: #43128]

GC-content

41.7 mol%

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: Sphingobacterium sp. CFCC 11742 PATRIC: 1775560.3
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Sphingobacterium sp. CFCC 11742 PATRIC: 1775560.3
[Ref.: #69480]	motile	no	91.581	yes
[Ref.: #69480]	gram-positive	no	97.19	yes
[Ref.: #69480]	anaerobic	no	98.421	yes
[Ref.: #69480]	aerobic	yes	83.849	no
[Ref.: #69480]	halophile	no	78.1	no
[Ref.: #69480]	spore-forming	no	95.288	no
[Ref.: #69480]	thermophile	no	99.169	no
[Ref.: #69480]	glucose-util	yes	91.928	yes
[Ref.: #69480]	flagellated	no	96.426	yes
[Ref.: #69480]	glucose-ferment	no	87.215	no

Availability in culture collections External links

[Ref.: #43128]

Culture collection no.

CFCC 11742, KCTC 42247

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Sphingobacterium corticibacter sp. nov., isolated from bark of Populus x euramericana.	Li Y, Guo LM, Chang JP, Yang XQ, Xie SJ, Liu H, Piao CG	Int J Syst Evol Microbiol	10.1099/ijsem.0.003148	2019	*
Phylogeny	Sphingobacterium corticis sp. nov., isolated from bark of Populus x euramericana.	Li Y, Xu GT, Chang JP, Guo LM, Yang XQ, Piao CG	Int J Syst Evol Microbiol	10.1099/ijsem.0.002210	2017	*
Phylogeny	Sphingobacterium populi sp. nov., isolated from bark of Populus x euramericana.	Li Y, Song LM, Guo MW, Wang LF, Liang WX	Int J Syst Evol Microbiol	10.1099/ijsem.0.001217	2016	*

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 )

#43128

Yong Li, Li-min Song, Min-wei Guo, Lai-fa Wang and Wen-xing Liang: Sphingobacterium populi sp. nov., isolated from bark of Populus x euramericana. IJSEM 66: 3456 - 3462 2016 ( DOI 10.1099/ijsem.0.001217 , PubMed 27263534 )

#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;

#69479

João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.: MicrobeAtlas 1.0 beta .

#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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Sphingobacterium sp. CFCC 11742

Sphingobacterium sp. CFCC 11742

Change proposal

Change proposal