Pedobacter yulinensis (CGMCC 1.16050, KCTC 62104, YL28-9)

Name: Pedobacter yulinensis (CGMCC 1.16050, KCTC 62104, YL28-9)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 159787

Type strain

Strain Designation YL28-9

Culture col. no. CGMCC 1.16050 KCTC 62104 YL28-9

NCBI tax ID(s) 2126353

Special Collections KCTC Literature strains

History KCTC <- Wei Yahong, Northwest Agriculture and Forestry Univ.

Links

Pedobacter yulinensis YL28-9 is an aerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from sandy soil in in the Mu Us in Yulin.

Gram-negative rod-shaped colony-forming aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 26369

KCTC 62104

@ref 20215

Last LPSN update 2026-05-29 08:44:16

Domain Bacteria

Phylum Bacteroidota

Class Sphingobacteriia

Order Sphingobacteriales

Family Sphingobacteriaceae

Genus Pedobacter

Species Pedobacter yulinensis

Full scientific name Pedobacter yulinensis Wei et al. 2018

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
66791	negative	0.9-1.2 µm	0.3-0.5 µm	rod-shaped
125439	negative				99.873
125438	negative				97.985

Colony morphology

@ref	Colony size	Colony color	Colony shape	Incubation period	Medium used
66791	1-1.55 mm	orange	circular	2-3 days	Nutrient agar (NA)

Pigmentation

@ref	Production	Name
66791		flexirubin type pigments

Culture and growth conditions

Culture medium

@ref	Name	Growth
66791	LB (Luria-Bertani) agar
66791	MacConkey agar
66791	Nutrient agar (NA)
66791	Reasoner's 2A agar (R2A)
66791	Trypticase soy agar

Culture temp

@ref	Growth	Type	Temperature (°C)
66791	positive	optimum	30
66791	positive	growth	15-42
67771	positive	growth	30

Culture pH

@ref	Ability	Type	PH	PH range
66791	positive	optimum	7
66791	positive	growth	6-9	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
66791	aerobe
67771	aerobe
125439	obligate aerobe	97.554

Spore formation

@ref	Spore formation	Confidence
66791
125439		99.928

Halophily

@ref	Salt	Growth	Tested relation	Concentration
66791	NaCl	positive	growth	0-2 %(w/v)
66791	NaCl	positive	optimum	0 %(w/v)

Observation

@ref	Observation
66791	The only respiratory quinone is MK-7.
66791	The polar lipids contain phosphatidylethanolamine as the major polar lipid as well as four unidentified aminolipids and five unidentified lipids.
66791	They do not contain glycolipids.

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
66791	16411 ChEBI	acetic acid	-	carbon source
66791	17128 ChEBI	adipate	-	assimilation
66791	27613 ChEBI	amygdalin	+	builds acid from
66791	18305 ChEBI	arbutin	+	builds acid from
66791	71422 ChEBI	beta-gentiobiose	+	builds acid from
66791	17968 ChEBI	butyrate	-	assimilation
66791	85146 ChEBI	carboxymethylcellulose	-	hydrolysis
66791		casein	-	hydrolysis
66791	17057 ChEBI	cellobiose	+	builds acid from
66791	12936 ChEBI	D-galactose	+	builds acid from
66791	17634 ChEBI	D-glucose	+	assimilation
66791	17634 ChEBI	D-glucose	+	builds acid from
66791	16899 ChEBI	D-mannitol	-	assimilation
66791	16024 ChEBI	D-mannose	-	assimilation
66791	16991 ChEBI	dna	+	hydrolysis
66791	17113 ChEBI	erythritol	+	builds acid from
66791	4853 ChEBI	esculin	+	hydrolysis
66791		esculin ferric citrate	+	builds acid from
66791	5291 ChEBI	gelatin	-	hydrolysis
66791	24265 ChEBI	gluconate	-	assimilation
66791	17754 ChEBI	glycerol	-	builds acid from
66791	17596 ChEBI	inosine	-	carbon source
66791	30849 ChEBI	L-arabinose	-	assimilation
66791	17295 ChEBI	L-phenylalanine	+	carbon source
66791	17895 ChEBI	L-tyrosine	-	hydrolysis
66791	17716 ChEBI	lactose	+	builds acid from
66791	25115 ChEBI	malate	-	assimilation
66791	17306 ChEBI	maltose	+	assimilation
66791	17306 ChEBI	maltose	+	builds acid from
66791	37684 ChEBI	mannose	+	builds acid from
66791	6731 ChEBI	melezitose	+	builds acid from
66791	28053 ChEBI	melibiose	+	builds acid from
66791	17790 ChEBI	methanol	-	carbon source
66791	320061 ChEBI	methyl alpha-D-glucopyranoside	+	builds acid from
66791	59640 ChEBI	N-acetylglucosamine	+	assimilation
66791	17632 ChEBI	nitrate	+	reduction
66791	18401 ChEBI	phenylacetate	-	assimilation
66791	16634 ChEBI	raffinose	+	builds acid from
66791	17814 ChEBI	salicin	+	builds acid from
66791	53258 ChEBI	sodium citrate	-	assimilation
66791	28017 ChEBI	starch	+	builds acid from
66791	28017 ChEBI	starch	+	hydrolysis
66791	143136 ChEBI	succinamate	-	carbon source
66791	17992 ChEBI	sucrose	+	builds acid from
66791	27082 ChEBI	trehalose	+	builds acid from
66791	32528 ChEBI	turanose	+	builds acid from
66791	53424 ChEBI	tween 20	+	hydrolysis
66791	53426 ChEBI	tween 80	-	hydrolysis

Metabolite production

@ref	Chebi-ID	Metabolite	Production
66791	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
66791	acid phosphatase	+	3.1.3.2
66791	alkaline phosphatase	+	3.1.3.1
66791	alpha-chymotrypsin	-	3.4.21.1
66791	alpha-fucosidase	+	3.2.1.51
66791	alpha-galactosidase	+	3.2.1.22
66791	alpha-glucosidase	+	3.2.1.20
66791	alpha-mannosidase	-	3.2.1.24
66791	arginine dihydrolase	+	3.5.3.6
66791	beta-galactosidase	+	3.2.1.23
66791	beta-glucosidase	+	3.2.1.21
66791	beta-glucuronidase	-	3.2.1.31
66791	catalase	+	1.11.1.6
66791	cystine arylamidase	-	3.4.11.3
66791	cytochrome oxidase	-	1.9.3.1
66791	esterase (C 4)	-
66791	esterase Lipase (C 8)	+
66791	leucine arylamidase	+	3.4.11.1
66791	lipase (C 14)	-
66791	N-acetyl-beta-glucosaminidase	+	3.2.1.52
66791	naphthol-AS-BI-phosphohydrolase	+
66791	protease	-
66791	trypsin	-	3.4.21.4
66791	urease	+	3.5.1.5
66791	valine arylamidase	+

Fatty acid profile

Metadata FA analysis

@ref

66791

Fatty acid	Percentage
C15:0 iso	31.7
C16:1 w7c and/or C16:1 w6c	26.2
C17:0 iso 3OH	6.7
C17:1 iso w9c / C16:0 10-methyl	6.5
C14:0 iso	4.8
C15:0 iso 3OH	3.6
C16:0	3.5
C15:0 anteiso	3.3
C18:0	1.6
C19:0	1.2
C14:0 anteiso	1.16
C15:1 iso H and/or C13:0 3OH	1.1

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Sandy
#Environmental	#Terrestrial	#Soil

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude	Enrichment culture duration	Enrichment culture temperature	Isolation procedure
66791	sandy soil in in the Mu Us in Yulin	Shaanxi province	China	CHN	Asia	34	108 34/108	5 days	30	A 5.0 g sample of sandy soil was suspended in 45 ml sterile 0.85 % (w/v) NaCl for 30 min at 30°C by vigorously shaking the flask. The soil suspensions were serially diluted (10 ^-1-10^-6) and 0.1 ml of each dilution was inoculated onto nutrient agar (NA; tryptone, 10 g l^-1; beef extract, 3 g l^-1;NaCl, 5 g l^-1; agar 18 g l^-1;pH 7.2-7.4).
67771	From soil	Yulin city, Shaanxi Province	China	CHN	Asia

Taxonmaps

69479

Global distribution of 16S sequence KY120369 (>99% sequence identity) for Pedobacter yulinensis subclade from Microbeatlas

Aquatic Samples	4
Soil Samples	5
Animal Samples	4
Plant Samples	2
Total Samples	15

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM302973v1 assembly for Pedobacter yulinensis YL28-9	scaffold	GCA_003029735	2126353.3	2855540664	2126353	75.6

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
66791	Pedobacter yulinensis strain YL28-9 16S ribosomal RNA gene, partial sequence	KY120369	1484		2126353

GC content

@ref	GC-content (mol%)	Method
66791	50.40	sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM302973v1 assembly for Pedobacter yulinensis YL28-9
NCBI: GCA_003029735

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	97.55	no
125439	motility	BacteriaNetⓘ	no	67.38	no
125439	gram_stain	BacteriaNetⓘ	negative	99.87	no
125439	spore_formation	BacteriaNetⓘ	no	99.93	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Pedobacter yulinensis YL28-9
NCBI: GCA_003029735.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	97.99	yes
125438	anaerobic	anaerobicⓘ	no	96.86	no
125438	aerobic	aerobicⓘ	yes	87.42	no
125438	spore-forming	spore-formingⓘ	no	85.44	yes
125438	thermophilic	thermophileⓘ	no	96.99	no
125438	flagellated	motile2+ⓘ	no	89.23	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Screening and Characterization of Two Extracellular Polysaccharide-Producing Bacteria from the Biocrust of the Mu Us Desert.	Xue Z, Zhao S, Bold N, Zhang J, Hu Z, Hu X, Gao Y, Chen S, Wei Y	Molecules	10.3390/molecules26185521	2021
Phylogeny	Pedobacter yulinensis sp. nov., isolated from sandy soil, and emended description of the genus Pedobacter.	Wei Y, Wang B, Zhang L, Zhang J, Chen S	Int J Syst Evol Microbiol	10.1099/ijsem.0.002868	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 )
#66791	Yahong Wei, Baodan Wang, Limei Zhang, Jianguo Zhang, Shaolin Chen: Pedobacter yulinensis sp. nov., isolated from sandy soil, and emended description of the genus Pedobacter. IJSEM 68: 2523 - 2529 2018 ( DOI 10.1099/ijsem.0.002868 , PubMed 29927365 )
#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 .
#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 )

Content

About us

Pedobacter yulinensis (CGMCC 1.16050, KCTC 62104, YL28-9)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Metabolite production

Enzymes

Fatty acid profile

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Sequence information

Genome sequences

Genome browser: GCA_003029735

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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