Sphingobacterium populi (CFCC 11742, KCTC 42247, 7Y-4)

Name: Sphingobacterium populi (CFCC 11742, KCTC 42247, 7Y-4)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 140613

Type strain

Strain Designation 7Y-4

Culture col. no. CFCC 11742 KCTC 42247 7Y-4

NCBI tax ID(s) 1812824

Special Collections KCTC Literature strains

Links

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

Gram-negative colony-forming aerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 26625

KCTC 42247

@ref 20215

Last LPSN update 2025-12-16 10:03:38

Domain Pseudomonadati

Phylum Bacteroidota

Class Sphingobacteriia

Order Sphingobacteriales

Family Sphingobacteriaceae

Genus Sphingobacterium

Species Sphingobacterium populi

Full scientific name Sphingobacterium populi Li et al. 2016

Morphology

Cell morphology

@ref	Gram stain	Motility
43128	negative
67771
67771	negative
125438	negative
125439	negative

Colony morphology

@ref	Colony size	Colony color	Colony shape	Incubation period	Medium used
43128	1-2 mm	pale yellow	circular	2 days	TSA

Culture and growth conditions

Culture medium

@ref	Name	Growth
43128	Trypticase Soy Agar (TSA)

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
43128	positive	optimum	28-30	mesophilic
43128	positive	growth	10-37
67771	positive	growth	28	mesophilic

Culture pH

@ref	Ability	Type	PH
43128	positive	optimum	6.0-8.0
43128	positive	growth	5-10

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
43128	aerobe
67771	aerobe
125439	obligate aerobe

Spore formation

@ref	Spore formation	Confidence
125439		99.4

Halophily

@ref	Salt	Growth	Tested relation	Concentration
43128	NaCl	positive	growth	0-3 %(w/v)

Observation

67771

Observationquinones: MK-7

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
43128	62064 ChEBI	2,3-butanediol	+	respiration
43128	28644 ChEBI	2-oxopentanoate	+	respiration
43128	16724 ChEBI	4-hydroxybutyrate	+	respiration
43128	30089 ChEBI	acetate	+	respiration
43128	40585 ChEBI	alpha-cyclodextrin	+	respiration
43128	17925 ChEBI	alpha-D-glucose	+	respiration
43128	36219 ChEBI	alpha-lactose	+	respiration
43128	27613 ChEBI	amygdalin	-	builds acid from
43128	18305 ChEBI	arbutin	-	builds acid from
43128	73706 ChEBI	bromosuccinate	+	respiration
43128	17057 ChEBI	cellobiose	-	builds acid from
43128	17057 ChEBI	cellobiose	+	respiration
43128	16947 ChEBI	citrate	-	assimilation
43128	17108 ChEBI	D-arabinose	-	builds acid from
43128	18333 ChEBI	D-arabitol	-	builds acid from
43128	15824 ChEBI	D-fructose	-	builds acid from
43128	15824 ChEBI	D-fructose	+	respiration
43128	28847 ChEBI	D-fucose	-	builds acid from
43128	12936 ChEBI	D-galactose	-	builds acid from
43128	12936 ChEBI	D-galactose	+	respiration
43128	17634 ChEBI	D-glucose	-	builds acid from
43128	17634 ChEBI	D-glucose	+	carbon source
43128	14314 ChEBI	D-glucose 6-phosphate	+	respiration
43128	62318 ChEBI	D-lyxose	-	builds acid from
43128	16899 ChEBI	D-mannitol	-	builds acid from
43128	16899 ChEBI	D-mannitol	+	carbon source
43128	16024 ChEBI	D-mannose	-	builds acid from
43128	16024 ChEBI	D-mannose	+	carbon source
43128	16024 ChEBI	D-mannose	+	respiration
43128	27605 ChEBI	D-psicose	+	respiration
43128	16988 ChEBI	D-ribose	-	builds acid from
43128	17924 ChEBI	D-sorbitol	-	builds acid from
43128	17924 ChEBI	D-sorbitol	+	respiration
43128	16443 ChEBI	D-tagatose	-	builds acid from
43128	65327 ChEBI	D-xylose	-	builds acid from
43128	23652 ChEBI	dextrin	+	respiration
43128	17113 ChEBI	erythritol	-	builds acid from
43128	17113 ChEBI	erythritol	+	respiration
43128	4853 ChEBI	esculin	+	hydrolysis
43128		esculin ferric citrate	+	builds acid from
43128	16813 ChEBI	galactitol	-	builds acid from
43128	5291 ChEBI	gelatin	-	hydrolysis
43128	28066 ChEBI	gentiobiose	-	builds acid from
43128	28066 ChEBI	gentiobiose	+	respiration
43128	29042 ChEBI	glucose 1-phosphate	+	respiration
43128	17754 ChEBI	glycerol	-	builds acid from
43128	17754 ChEBI	glycerol	+	respiration
43128	28087 ChEBI	glycogen	-	builds acid from
43128	28087 ChEBI	glycogen	+	respiration
43128	15443 ChEBI	inulin	-	builds acid from
43128	30849 ChEBI	L-arabinose	-	builds acid from
43128	30849 ChEBI	L-arabinose	+	respiration
43128	18403 ChEBI	L-arabitol	-	builds acid from
43128	17196 ChEBI	L-asparagine	+	respiration
43128	18287 ChEBI	L-fucose	-	builds acid from
43128	18287 ChEBI	L-fucose	+	respiration
43128	29985 ChEBI	L-glutamate	+	respiration
43128	15603 ChEBI	L-leucine	+	respiration
43128	62345 ChEBI	L-rhamnose	-	builds acid from
43128	17115 ChEBI	L-serine	+	respiration
43128	17266 ChEBI	L-sorbose	-	builds acid from
43128	16857 ChEBI	L-threonine	+	respiration
43128	65328 ChEBI	L-xylose	-	builds acid from
43128	17716 ChEBI	lactose	-	builds acid from
43128	6359 ChEBI	lactulose	+	respiration
43128	17306 ChEBI	maltose	-	builds acid from
43128	17306 ChEBI	maltose	+	respiration
43128	6731 ChEBI	melezitose	-	builds acid from
43128	28053 ChEBI	melibiose	-	builds acid from
43128	28053 ChEBI	melibiose	+	respiration
43128		methyl alpha-D-glucopyranoside	-	builds acid from
43128	43943 ChEBI	methyl alpha-D-mannoside	-	builds acid from
43128	320055 ChEBI	methyl beta-D-glucopyranoside	+	respiration
43128	74863 ChEBI	methyl beta-D-xylopyranoside	-	builds acid from
43128	51850 ChEBI	methyl pyruvate	+	respiration
43128	75146 ChEBI	monomethyl succinate	+	respiration
43128	17268 ChEBI	myo-inositol	-	builds acid from
43128	506227 ChEBI	N-acetylglucosamine	-	builds acid from
43128	506227 ChEBI	N-acetylglucosamine	+	respiration
43128	17632 ChEBI	nitrate	-	reduction
43128		potassium 2-dehydro-D-gluconate	-	builds acid from
43128		potassium 5-dehydro-D-gluconate	-	builds acid from
43128	32032 ChEBI	potassium gluconate	-	builds acid from
43128	16634 ChEBI	raffinose	-	builds acid from
43128	16634 ChEBI	raffinose	+	respiration
43128	15963 ChEBI	ribitol	-	builds acid from
43128	17814 ChEBI	salicin	-	builds acid from
43128	28017 ChEBI	starch	-	builds acid from
43128	17992 ChEBI	sucrose	-	builds acid from
43128	17992 ChEBI	sucrose	+	respiration
43128	27082 ChEBI	trehalose	-	builds acid from
43128	27082 ChEBI	trehalose	+	respiration
43128	32528 ChEBI	turanose	-	builds acid from
43128	32528 ChEBI	turanose	+	respiration
43128	53423 ChEBI	tween 40	+	respiration
43128	16704 ChEBI	uridine	+	respiration
43128	17151 ChEBI	xylitol	-	builds acid from

Metabolite production

@ref	Chebi-ID	Metabolite
43128	15688 ChEBI	acetoin
43128	16136 ChEBI	hydrogen sulfide
43128	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
43128	acid phosphatase	+/-	3.1.3.2
43128	alkaline phosphatase	+	3.1.3.1
43128	alpha-chymotrypsin	+	3.4.21.1
43128	alpha-fucosidase	+	3.2.1.51
43128	alpha-galactosidase	+	3.2.1.22
43128	alpha-glucosidase	+	3.2.1.20
43128	alpha-mannosidase	+	3.2.1.24
43128	arginine dihydrolase	-	3.5.3.6
43128	beta-galactosidase	+	3.2.1.23
43128	beta-glucosidase	+	3.2.1.21
43128	catalase	+	1.11.1.6
43128	cystine arylamidase	-	3.4.11.3
43128	cytochrome oxidase	+	1.9.3.1
43128	esterase (C 4)	+
43128	esterase Lipase (C 8)	+
43128	gelatinase	-
43128	leucine arylamidase	+	3.4.11.1
43128	lipase (C 14)	-
43128	lysine decarboxylase	-	4.1.1.18
43128	N-acetyl-beta-glucosaminidase	+	3.2.1.52
43128	naphthol-AS-BI-phosphohydrolase	+
43128	ornithine decarboxylase	-	4.1.1.17
43128	trypsin	+	3.4.21.4
43128	tryptophan deaminase	-	4.1.99.1
43128	urease	+	3.5.1.5
43128	valine arylamidase	-

Fatty acid profile

Metadata FA analysis

@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

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Plants	#Tree
#Host Body-Site	#Plant	#Bark

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Isolation date
43128	symptomatic bark tissue of a Populus x euramericana canker sample	Qingfeng, Puyang City, Henan Province, China	China	CHN	Asia	2010-08
67771	From the symptomatic bark tissue of a `Populus Ã— euramericana`	Qingfeng, Puyang City, Henan Province	China	CHN	Asia

Taxonmaps

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

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM158677v1 assembly for Sphingobacterium sp. CFCC 11742	contig	GCA_001586775	1775560.3	2728369126	1775560	60.77
124043	ASM4268482v1 assembly for Sphingobacterium populi KCTC 42247	scaffold	GCA_042684825			1812824	57.44

Genome browser: GCA_001586775

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
43128	Sphingobacterium populi strain 7Y-4 16S ribosomal RNA gene, partial sequence	KT988032	1400		1812824

GC content

43128

GC-content (mol%)41.7

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Sphingobacterium sp. CFCC 11742
NCBI: GCA_001586775

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	99.40	no
125439	motility	BacteriaNetⓘ	no	66.10	no
125439	gram_stain	BacteriaNetⓘ	negative	99.80	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	92.10	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Sphingobacterium sp. CFCC 11742
PATRIC: 1775560.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	96.57	yes
125438	anaerobic	anaerobicⓘ	no	95.67	yes
125438	spore-forming	spore-formingⓘ	no	89.48	no
125438	aerobic	aerobicⓘ	yes	85.90	yes
125438	thermophilic	thermophileⓘ	no	97.50	yes
125438	flagellated	motile2+ⓘ	no	85.00	yes

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 .
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#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 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

Rate our new design

Content

About us

Sphingobacterium populi (CFCC 11742, KCTC 42247, 7Y-4)

Name and taxonomic classification