Strain identifier
BacDive ID: 159787
Type strain:
Species: Pedobacter yulinensis
Strain Designation: YL28-9
Strain history: <- Wei Yahong, Northwest Agriculture and Forestry Univ.
NCBI tax ID(s): 2126353 (species)
General
@ref: 66791
BacDive-ID: 159787
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, rod-shaped, colony-forming
description: 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.
NCBI tax id
- NCBI tax id: 2126353
- Matching level: species
strain history
- @ref: 67771
- history: <- Wei Yahong, Northwest Agriculture and Forestry Univ.
doi: 10.13145/bacdive159787.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacteroidota
- domain: Bacteria
- phylum: Bacteroidota
- class: Sphingobacteriia
- order: Sphingobacteriales
- family: Sphingobacteriaceae
- genus: Pedobacter
- species: Pedobacter yulinensis
- full scientific name: Pedobacter yulinensis Wei et al. 2018
@ref: 66791
domain: Bacteria
phylum: Bacteroidetes
class: Sphingobacteriia
order: Sphingobacteriales
family: Sphingobacteriaceae
genus: Pedobacter
species: Pedobacter yulinensis
strain designation: YL28-9
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | cell shape | motility | confidence |
---|---|---|---|---|---|---|
66791 | negative | 0.9-1.2 µm | 0.3-0.5 µm | rod-shaped | no | |
69480 | negative | 99.985 |
colony morphology
- @ref: 66791
- colony size: 1-1.55 mm
- colony color: orange
- colony shape: circular
- incubation period: 2-3 days
- medium used: Nutrient agar (NA)
pigmentation
- @ref: 66791
- production: no
- name: Flexirubin-type
Culture and growth conditions
culture medium
@ref | name | growth |
---|---|---|
66791 | LB (Luria-Bertani) agar | yes |
66791 | MacConkey agar | yes |
66791 | Nutrient agar (NA) | yes |
66791 | Reasoner's 2A agar (R2A) | yes |
66791 | Trypticase soy agar | yes |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
66791 | positive | optimum | 30 | mesophilic |
66791 | positive | growth | 15-42 | |
67771 | positive | growth | 30 | mesophilic |
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 |
---|---|
66791 | aerobe |
67771 | aerobe |
spore formation
@ref | spore formation | confidence |
---|---|---|
66791 | no | |
69480 | no | 99.96 |
69481 | no | 100 |
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 | 16024 | D-mannose | - | assimilation |
66791 | 16899 | D-mannitol | - | assimilation |
66791 | 17128 | adipate | - | assimilation |
66791 | 17968 | butyrate | - | assimilation |
66791 | 18401 | phenylacetate | - | assimilation |
66791 | 24265 | gluconate | - | assimilation |
66791 | 25115 | malate | - | assimilation |
66791 | 30849 | L-arabinose | - | assimilation |
66791 | 53258 | sodium citrate | - | assimilation |
66791 | 17306 | maltose | + | assimilation |
66791 | 17634 | D-glucose | + | assimilation |
66791 | 59640 | N-acetylglucosamine | + | assimilation |
66791 | 17754 | glycerol | - | builds acid from |
66791 | 6731 | melezitose | + | builds acid from |
66791 | 12936 | D-galactose | + | builds acid from |
66791 | 16634 | raffinose | + | builds acid from |
66791 | 17057 | cellobiose | + | builds acid from |
66791 | 17113 | erythritol | + | builds acid from |
66791 | 17306 | maltose | + | builds acid from |
66791 | 17634 | D-glucose | + | builds acid from |
66791 | 17716 | lactose | + | builds acid from |
66791 | 17814 | salicin | + | builds acid from |
66791 | 17992 | sucrose | + | builds acid from |
66791 | 18305 | arbutin | + | builds acid from |
66791 | 27082 | trehalose | + | builds acid from |
66791 | 27613 | amygdalin | + | builds acid from |
66791 | 28017 | starch | + | builds acid from |
66791 | 28053 | melibiose | + | builds acid from |
66791 | 32528 | turanose | + | builds acid from |
66791 | 37684 | mannose | + | builds acid from |
66791 | 71422 | beta-gentiobiose | + | builds acid from |
66791 | 320061 | methyl alpha-D-glucopyranoside | + | builds acid from |
66791 | esculin ferric citrate | + | builds acid from | |
66791 | 16411 | acetic acid | - | carbon source |
66791 | 17596 | inosine | - | carbon source |
66791 | 17790 | methanol | - | carbon source |
66791 | 143136 | succinamate | - | carbon source |
66791 | 17295 | L-phenylalanine | + | carbon source |
66791 | 5291 | gelatin | - | hydrolysis |
66791 | 17895 | L-tyrosine | - | hydrolysis |
66791 | 53426 | tween 80 | - | hydrolysis |
66791 | 85146 | carboxymethylcellulose | - | hydrolysis |
66791 | casein | - | hydrolysis | |
66791 | 4853 | esculin | + | hydrolysis |
66791 | 16991 | dna | + | hydrolysis |
66791 | 28017 | starch | + | hydrolysis |
66791 | 53424 | tween 20 | + | hydrolysis |
66791 | 17632 | nitrate | + | reduction |
metabolite production
- @ref: 66791
- Chebi-ID: 35581
- metabolite: indole
- production: no
enzymes
@ref | value | activity | ec |
---|---|---|---|
66791 | alpha-chymotrypsin | - | 3.4.21.1 |
66791 | alpha-mannosidase | - | 3.2.1.24 |
66791 | beta-glucuronidase | - | 3.2.1.31 |
66791 | cystine arylamidase | - | 3.4.11.3 |
66791 | cytochrome oxidase | - | 1.9.3.1 |
66791 | esterase (C 4) | - | |
66791 | lipase (C 14) | - | |
66791 | protease | - | |
66791 | trypsin | - | 3.4.21.4 |
66791 | acid phosphatase | + | 3.1.3.2 |
66791 | alkaline phosphatase | + | 3.1.3.1 |
66791 | alpha-fucosidase | + | 3.2.1.51 |
66791 | alpha-galactosidase | + | 3.2.1.22 |
66791 | alpha-glucosidase | + | 3.2.1.20 |
66791 | arginine dihydrolase | + | 3.5.3.6 |
66791 | beta-galactosidase | + | 3.2.1.23 |
66791 | beta-glucosidase | + | 3.2.1.21 |
66791 | catalase | + | 1.11.1.6 |
66791 | esterase Lipase (C 8) | + | |
66791 | leucine arylamidase | + | 3.4.11.1 |
66791 | N-acetyl-beta-glucosaminidase | + | 3.2.1.52 |
66791 | naphthol-AS-BI-phosphohydrolase | + | |
66791 | urease | + | 3.5.1.5 |
66791 | valine arylamidase | + |
fatty acid profile
fatty acids
@ref fatty acid percentage 66791 C15:1 iso H and/or C13:0 3OH 1.1 66791 C14:0 anteiso 1.16 66791 C19:0 1.2 66791 C18:0 1.6 66791 C16:1 w7c and/or C16:1 w6c 26.2 66791 C15:0 anteiso 3.3 66791 C16:0 3.5 66791 C15:0 iso 3OH 3.6 66791 C15:0 iso 31.7 66791 C14:0 iso 4.8 66791 C17:1 iso w9c / C16:0 10-methyl 6.5 66791 C17:0 iso 3OH 6.7 - type of FA analysis: whole cell analysis
- incubation medium: Tryptic Soy Agar
- agar/liquid: agar
- incubation temperature: 30
- incubation time: 2
- software version: Sherlock 6.0
- library/peak naming table: TSBA6
- system: MIS MIDI
- instrument: GC (6890 N; Agilent)
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | 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 | 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 |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Environmental | #Terrestrial | #Sandy |
#Environmental | #Terrestrial | #Soil |
taxonmaps
- @ref: 69479
- File name: preview.99_127824.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_115;96_49892;97_64242;98_85680;99_127824&stattab=map
- Last taxonomy: Pedobacter yulinensis subclade
- 16S sequence: KY120369
- Sequence Identity:
- Total samples: 15
- soil counts: 5
- aquatic counts: 4
- animal counts: 4
- plant counts: 2
Sequence information
16S sequences
- @ref: 66791
- description: Pedobacter sp. strain YL28-9 16S ribosomal RNA gene, partial sequence
- accession: KY120369
- length: 1484
- database: ena
- NCBI tax ID: 2126353
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Pedobacter yulinensis YL28-9 | GCA_003029735 | scaffold | ncbi | 2126353 |
66792 | Pedobacter yulinensis YL28-9 | 2855540664 | draft | img | 2126353 |
GC content
- @ref: 66791
- GC-content: 50.40
- method: sequence analysis
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
flagellated | no | 96.896 | no |
gram-positive | no | 97.178 | yes |
anaerobic | no | 99.212 | yes |
halophile | no | 96.149 | yes |
spore-forming | no | 93.728 | yes |
glucose-util | yes | 86.577 | no |
aerobic | yes | 88.933 | no |
thermophile | no | 98.914 | yes |
motile | no | 89.794 | yes |
glucose-ferment | no | 89.486 | no |
External links
@ref: 66791
culture collection no.: CGMCC 1.16050, KCTC 62104
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 29927365 | 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 | Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Pedobacter/*classification/genetics/isolation & purification, Phosphatidylethanolamines/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistry | Transcriptome |
Phylogeny | 34576992 | 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 | Bacterial Typing Techniques, China, DNA, Bacterial/genetics, Desert Climate, Extracellular Polymeric Substance Matrix/*chemistry/genetics/metabolism, Extracellular Space/chemistry, Fatty Acids/analysis, Metals, Heavy/pharmacology, Nucleic Acid Hybridization, Pedobacter/cytology/drug effects/*isolation & purification/*physiology, Phylogeny, RNA, Ribosomal, 16S/genetics, Sinorhizobium meliloti/cytology/drug effects/*isolation & purification/*physiology, Soil Microbiology | Enzymology |
Reference
@id | authors | title | doi/url | journal | pubmed |
---|---|---|---|---|---|
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 | 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 | 10.1099/ijsem.0.002868 | IJSEM 68: 2523-2529 2018 | 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) | https://diaspora-project.de/progress.html#genomes | ||
67771 | Curators of the KCTC | https://kctc.kribb.re.kr/En/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 | https://microbeatlas.org/ | ||
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) | https://diaspora-project.de/progress.html#genomes | ||
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | Predictions based on the model GenomeNet Sporulation v. 1 | 10.21203/rs.3.rs-2527258/v1 |