Name: Pedobacter yulinensis YL28-9
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 159787

Type strain:

Species: Pedobacter yulinensis

Strain Designation: YL28-9

Culture col. no.: CGMCC 1.16050, KCTC 62104

Strain history: <- Wei Yahong, Northwest Agriculture and Forestry Univ.

NCBI tax ID(s): 2126353 (species)

Section

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

colony-forming
Gram-negative
rod-shaped
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	*Pedobacter*
	Species	**Pedobacter yulinensis**
	Full Scientific Name (LPSN)	Pedobacter yulinensis Wei et al. 2018

Information on morphological and physiological properties Morphology

[Ref.: #66791]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.985

[Ref.: #66791]	Cell length	0.9-1.2 µm

[Ref.: #66791]	Cell width	0.3-0.5 µm

[Ref.: #66791]	Cell shape	rod-shaped

[Ref.: #66791]	Motility	no

[Ref.: #66791]	Colony size	1-1.55 mm
[Ref.: #66791]	Colony color	orange
[Ref.: #66791]	Colony shape	circular
[Ref.: #66791]	Incubation period	2-3 days
[Ref.: #66791]	Cultivation medium used	Nutrient agar (NA)

[Ref.: #66791]	Pigment production	no
[Ref.: #66791]	Pigment name	Flexirubin-type

Information on culture and growth conditions Culture and growth conditions

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Culture medium

LB (Luria-Bertani) agar

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Culture medium growth

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Culture medium

MacConkey agar

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Culture medium growth

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Culture medium

Nutrient agar (NA)

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Culture medium growth

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Culture medium

Reasoner's 2A agar (R2A)

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Culture medium growth

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Culture medium

Trypticase soy agar

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Culture medium growth

		Temperature
[Ref.: #66791]	optimum	30 °C
[Ref.: #66791]	growth	15-42 °C
[Ref.: #67771]	growth	30 °C

[Ref.: #66791]	Temperature range	mesophilic
[Ref.: #67771]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #66791]			optimum	7
[Ref.: #66791]			growth	6-9

Information on physiology and metabolism Physiology and metabolism

[Ref.: #66791]	Oxygen tolerance	aerobe
[Ref.: #67771]	Oxygen tolerance	aerobe

[Ref.: #66791]	Ability of spore formation	no
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.96
[Ref.: #69481]	Ability of spore formation	no Confidence in %100

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #66791]		NaCl		growth	0-2	%(w/v)
[Ref.: #66791]		NaCl		optimum	0	%(w/v)

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

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #66791]	acetic acid ChEBI	-	carbon source
[Ref.: #66791]	adipate ChEBI	-	assimilation
[Ref.: #66791]	amygdalin ChEBI	+	builds acid from
[Ref.: #66791]	arbutin ChEBI	+	builds acid from
[Ref.: #66791]	beta-gentiobiose ChEBI	+	builds acid from
[Ref.: #66791]	butyrate ChEBI	-	assimilation
[Ref.: #66791]	carboxymethylcellulose ChEBI	-	hydrolysis
[Ref.: #66791]	casein	-	hydrolysis
[Ref.: #66791]	cellobiose ChEBI	+	builds acid from
[Ref.: #66791]	D-galactose ChEBI	+	builds acid from
[Ref.: #66791]	D-glucose ChEBI	+	assimilation
[Ref.: #66791]	D-glucose ChEBI	+	builds acid from
[Ref.: #66791]	D-mannitol ChEBI	-	assimilation
[Ref.: #66791]	D-mannose ChEBI	-	assimilation
[Ref.: #66791]	dna ChEBI	+	hydrolysis
[Ref.: #66791]	erythritol ChEBI	+	builds acid from
[Ref.: #66791]	esculin ChEBI	+	hydrolysis
[Ref.: #66791]	esculin ferric citrate	+	builds acid from
[Ref.: #66791]	gelatin ChEBI	-	hydrolysis
[Ref.: #66791]	gluconate ChEBI	-	assimilation
[Ref.: #66791]	glycerol ChEBI	-	builds acid from
[Ref.: #66791]	inosine ChEBI	-	carbon source
[Ref.: #66791]	L-arabinose ChEBI	-	assimilation
[Ref.: #66791]	L-phenylalanine ChEBI	+	carbon source
[Ref.: #66791]	L-tyrosine ChEBI	-	hydrolysis
[Ref.: #66791]	lactose ChEBI	+	builds acid from
[Ref.: #66791]	malate ChEBI	-	assimilation
[Ref.: #66791]	maltose ChEBI	+	assimilation
[Ref.: #66791]	maltose ChEBI	+	builds acid from
[Ref.: #66791]	mannose ChEBI	+	builds acid from
[Ref.: #66791]	melezitose ChEBI	+	builds acid from
[Ref.: #66791]	melibiose ChEBI	+	builds acid from
[Ref.: #66791]	methanol ChEBI	-	carbon source
[Ref.: #66791]	methyl alpha-D-glucopyranoside ChEBI	+	builds acid from
[Ref.: #66791]	N-acetylglucosamine ChEBI	+	assimilation
[Ref.: #66791]	nitrate ChEBI	+	reduction
[Ref.: #66791]	phenylacetate ChEBI	-	assimilation
[Ref.: #66791]	raffinose ChEBI	+	builds acid from
[Ref.: #66791]	salicin ChEBI	+	builds acid from
[Ref.: #66791]	sodium citrate ChEBI	-	assimilation
[Ref.: #66791]	starch ChEBI	+	builds acid from
[Ref.: #66791]	starch ChEBI	+	hydrolysis
[Ref.: #66791]	succinamate ChEBI	-	carbon source
[Ref.: #66791]	sucrose ChEBI	+	builds acid from
[Ref.: #66791]	trehalose ChEBI	+	builds acid from
[Ref.: #66791]	turanose ChEBI	+	builds acid from
[Ref.: #66791]	tween 20 ChEBI	+	hydrolysis
[Ref.: #66791]	tween 80 ChEBI	-	hydrolysis
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #66791]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #66791]	acid phosphatase	+	3.1.3.2
[Ref.: #66791]	alkaline phosphatase	+	3.1.3.1
[Ref.: #66791]	alpha-chymotrypsin	-	3.4.21.1
[Ref.: #66791]	alpha-fucosidase	+	3.2.1.51
[Ref.: #66791]	alpha-galactosidase	+	3.2.1.22
[Ref.: #66791]	alpha-glucosidase	+	3.2.1.20
[Ref.: #66791]	alpha-mannosidase	-	3.2.1.24
[Ref.: #66791]	arginine dihydrolase	+	3.5.3.6
[Ref.: #66791]	beta-galactosidase	+	3.2.1.23
[Ref.: #66791]	beta-glucosidase	+	3.2.1.21
[Ref.: #66791]	beta-glucuronidase	-	3.2.1.31
[Ref.: #66791]	catalase	+	1.11.1.6
[Ref.: #66791]	cystine arylamidase	-	3.4.11.3
[Ref.: #66791]	cytochrome oxidase	-	1.9.3.1
[Ref.: #66791]	esterase (C 4)	-
[Ref.: #66791]	esterase Lipase (C 8)	+
[Ref.: #66791]	leucine arylamidase	+	3.4.11.1
[Ref.: #66791]	lipase (C 14)	-
[Ref.: #66791]	N-acetyl-beta-glucosaminidase	+	3.2.1.52
[Ref.: #66791]	naphthol-AS-BI-phosphohydrolase	+
[Ref.: #66791]	protease	-
[Ref.: #66791]	trypsin	-	3.4.21.4
[Ref.: #66791]	urease	+	3.5.1.5
[Ref.: #66791]	valine arylamidase	+
	Only first 10 entries are displayed. Click here to see all.

Fatty acid profile

Metadata FA analysis

Reference

[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

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

[Ref.: #66791]	Sample type/isolated from	sandy soil in in the Mu Us in Yulin
[Ref.: #66791]	Geographic location (country and/or sea, region)	Shaanxi province
[Ref.: #66791]	Country	China
[Ref.: #66791]	Country ISO 3 Code	CHN
[Ref.: #66791]	Continent	Asia
[Ref.: #66791]	Geographic location	34.0000°/108.0000°
[Ref.: #66791]	Enrichment culture duration	5 days
[Ref.: #66791]	Enrichment culture temperature	30 ̊C
[Ref.: #66791]	Isolation/enrichment procedure	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).

[Ref.: #67771]	Sample type/isolated from	From soil
[Ref.: #67771]	Geographic location (country and/or sea, region)	Yulin city, Shaanxi Province
[Ref.: #67771]	Country	China
[Ref.: #67771]	Country ISO 3 Code	CHN
[Ref.: #67771]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Terrestrial	#Sandy
#Environmental	#Terrestrial	#Soil

What are isolation sources categories?

[Ref.: #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

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.: #66791]	Pedobacter sp. strain YL28-9 16S ribosomal RNA gene, partial sequence	KY120369	1484	ENA	2126353 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Pedobacter yulinensis YL28-9	GCA_003029735	scaffold	GenBank	2126353 tax ID	*
[Ref.: #66792]	Pedobacter yulinensis YL28-9	2855540664	draft	JGI IMG/M	2126353 tax ID	*

[Ref.: #66791]

GC-content

50.40 mol%

sequence analysis

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: Pedobacter yulinensis YL28-9 NCBI: GCA_003029735.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Pedobacter yulinensis YL28-9 NCBI: GCA_003029735.1
[Ref.: #69480]	flagellated	no	96.896	no
[Ref.: #69480]	gram-positive	no	97.178	yes
[Ref.: #69480]	anaerobic	no	99.212	yes
[Ref.: #69480]	halophile	no	96.149	yes
[Ref.: #69480]	spore-forming	no	93.728	yes
[Ref.: #69480]	glucose-util	yes	86.577	no
[Ref.: #69480]	aerobic	yes	88.933	no
[Ref.: #69480]	thermophile	no	98.914	yes
[Ref.: #69480]	motile	no	89.794	yes
[Ref.: #69480]	glucose-ferment	no	89.486	no

Availability in culture collections External links

[Ref.: #66791]

Culture collection no.

CGMCC 1.16050, KCTC 62104

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 .

#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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