Strain identifier
BacDive ID: 133259
Type strain:
Species: Pontibacter aydingkolensis
Strain Designation: XAAS-1
Strain history: G. Osman; Inst. of Microbiol., Xinijang Acad. of Agric. Sci., China; XAAS-1.
NCBI tax ID(s): 1911536 (species)
General
@ref: 64833
BacDive-ID: 133259
DSM-Number: 103222
keywords: genome sequence, 16S sequence, Bacteria, aerobe, Gram-negative, rod-shaped, colony-forming
description: Pontibacter aydingkolensis XAAS-1 is an aerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from soil of a salt lake named Aydingkol.
NCBI tax id
- NCBI tax id: 1911536
- Matching level: species
strain history
@ref | history |
---|---|
64833 | <- G. Osman, Xinjiang Acd. Agri. Sci., China; XAAS-1 |
67770 | G. Osman; Inst. of Microbiol., Xinijang Acad. of Agric. Sci., China; XAAS-1. |
doi: 10.13145/bacdive133259.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacteroidota
- domain: Bacteria
- phylum: Bacteroidota
- class: Cytophagia
- order: Cytophagales
- family: Hymenobacteraceae
- genus: Pontibacter
- species: Pontibacter aydingkolensis
- full scientific name: Pontibacter aydingkolensis Osman et al. 2016
@ref: 64833
domain: Bacteria
phylum: Bacteroidetes
class: Cytophagia
order: Cytophagales
family: Hymenobacteraceae
genus: Pontibacter
species: Pontibacter aydingkolensis
full scientific name: Pontibacter aydingkolensis Osman et al. 2016
strain designation: XAAS-1
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | cell shape |
---|---|---|---|---|
25053 | negative | 0.8-1.2 µm | 0.3-0.4 µm | rod-shaped |
25053 | oval-shaped |
colony morphology
- @ref: 25053
- colony size: 1.0-2.0 mm
- colony color: light red
- colony shape: circular
- incubation period: 5 days
- medium used: 0.3 MB agar
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
25053 | 0.3 MB agar | yes | ||
64833 | BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) | yes | https://mediadive.dsmz.de/medium/514 | Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
25053 | positive | growth | 6-37 | |
25053 | positive | optimum | 28-30 | mesophilic |
64833 | positive | growth | 28 | mesophilic |
67770 | positive | growth | 28 | mesophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
25053 | positive | growth | 6.0-10.0 | alkaliphile |
25053 | positive | optimum | 7.0-8.0 |
Physiology and metabolism
oxygen tolerance
- @ref: 25053
- oxygen tolerance: aerobe
halophily
- @ref: 25053
- salt: NaCl
- growth: positive
- tested relation: growth
- concentration: 0-5.0 %(w/v)
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
25053 | 15588 | D-malate | - | respiration |
25053 | 15589 | L-malate | - | respiration |
25053 | 64552 | 2-hydroxybutyrate | - | respiration |
25053 | 16763 | 2-oxobutanoate | - | respiration |
25053 | 37054 | 3-hydroxybutyrate | - | respiration |
25053 | 73918 | 3-O-methyl-D-glucose | - | respiration |
25053 | 18101 | 4-hydroxyphenylacetic acid | - | respiration |
25053 | 17128 | adipate | - | assimilation |
25053 | 36219 | alpha-lactose | - | respiration |
25053 | 17925 | alpha-D-glucose | - | respiration |
25053 | 73706 | bromosuccinate | - | respiration |
25053 | 29990 | D-aspartate | - | respiration |
25053 | 12936 | D-galactose | - | respiration |
25053 | 17634 | D-glucose | - | assimilation |
25053 | 16899 | D-mannitol | - | respiration |
25053 | 16899 | D-mannitol | - | assimilation |
25053 | 16024 | D-mannose | - | respiration |
25053 | 16024 | D-mannose | - | assimilation |
25053 | 16523 | D-serine | - | respiration |
25053 | 17924 | D-sorbitol | - | respiration |
25053 | 27689 | decanoate | - | assimilation |
25053 | 23652 | dextrin | - | respiration |
25053 | 15740 | formate | - | respiration |
25053 | 16865 | gamma-aminobutyric acid | - | respiration |
25053 | 28066 | gentiobiose | - | respiration |
25053 | 17234 | glucose | - | builds acid from |
25053 | 17596 | inosine | - | respiration |
25053 | 16977 | L-alanine | - | respiration |
25053 | 30849 | L-arabinose | - | assimilation |
25053 | 17464 | L-galactonic acid gamma-lactone | - | respiration |
25053 | 25115 | malate | - | assimilation |
25053 | 17306 | maltose | - | respiration |
25053 | 17306 | maltose | - | assimilation |
25053 | 51850 | methyl pyruvate | - | respiration |
25053 | 506227 | N-acetylglucosamine | - | respiration |
25053 | 506227 | N-acetylglucosamine | - | assimilation |
25053 | 17632 | nitrate | - | reduction |
25053 | 32032 | potassium gluconate | - | assimilation |
25053 | 17272 | propionate | - | respiration |
25053 | 16634 | raffinose | - | respiration |
25053 | 17814 | salicin | - | respiration |
25053 | 53258 | sodium citrate | - | assimilation |
25053 | 27082 | trehalose | - | respiration |
25053 | 27897 | tryptophan | - | energy source |
25053 | 17521 | (-)-quinic acid | + | respiration |
25053 | 16651 | (S)-lactate | + | respiration |
25053 | 30916 | 2-oxoglutarate | + | respiration |
25053 | 30089 | acetate | + | respiration |
25053 | 13705 | acetoacetate | + | respiration |
25053 | casein | + | hydrolysis | |
25053 | 17057 | cellobiose | + | respiration |
25053 | 16947 | citrate | + | respiration |
25053 | 18333 | D-arabitol | + | respiration |
25053 | 15824 | D-fructose | + | respiration |
25053 | 78697 | D-fructose 6-phosphate | + | respiration |
25053 | 28847 | D-fucose | + | respiration |
25053 | 18024 | D-galacturonic acid | + | respiration |
25053 | 8391 | D-gluconate | + | respiration |
25053 | 14314 | D-glucose 6-phosphate | + | respiration |
25053 | 15748 | D-glucuronate | + | respiration |
25053 | 4853 | esculin | + | hydrolysis |
25053 | 16537 | galactarate | + | respiration |
25053 | 5291 | gelatin | + | hydrolysis |
25053 | 5291 | gelatin | + | respiration |
25053 | 32323 | glucuronamide | + | respiration |
25053 | 17754 | glycerol | + | respiration |
25053 | 70744 | glycyl-L-proline | + | respiration |
25053 | 17268 | myo-inositol | + | respiration |
25053 | 16467 | L-arginine | + | respiration |
25053 | 29991 | L-aspartate | + | respiration |
25053 | 18287 | L-fucose | + | respiration |
25053 | 29985 | L-glutamate | + | respiration |
25053 | 15971 | L-histidine | + | respiration |
25053 | 18183 | L-pyroglutamic acid | + | respiration |
25053 | 62345 | L-rhamnose | + | respiration |
25053 | 17115 | L-serine | + | respiration |
25053 | 28053 | melibiose | + | respiration |
25053 | 74611 | methyl (R)-lactate | + | respiration |
25053 | 320055 | methyl beta-D-glucopyranoside | + | respiration |
25053 | 63154 | N-acetyl-beta-D-mannosamine | + | respiration |
25053 | 506227 | N-acetylglucosamine | + | respiration |
25053 | 35418 | n-acetylneuraminate | + | respiration |
25053 | 17309 | pectin | + | respiration |
25053 | 17164 | stachyose | + | respiration |
25053 | 28017 | starch | + | hydrolysis |
25053 | 17992 | sucrose | + | respiration |
25053 | 32528 | turanose | + | respiration |
25053 | 53423 | tween 40 | + | respiration |
antibiotic resistance
@ref | ChEBI | metabolite | is antibiotic | is sensitive | is resistant |
---|---|---|---|---|---|
25053 | 27902 | tetracycline | yes | yes | |
25053 | 17076 | streptomycin | yes | yes | |
25053 | 28971 | ampicillin | yes | yes | |
25053 | 17334 | penicillin | yes | yes | |
25053 | 29007 | ceftriaxone | yes | yes | |
25053 | 6472 | lincomycin | yes | yes | |
25053 | 28077 | rifampicin | yes | yes | |
25053 | 3745 | clindamycin | yes | yes | |
25053 | 7507 | neomycin | yes | yes | |
25053 | 17698 | chloramphenicol | yes | yes | |
25053 | 48923 | erythromycin | yes | yes | |
25053 | 100246 | norfloxacin | yes | yes | |
25053 | 28001 | vancomycin | yes | yes | |
25053 | 31168 | acetylspiramycin | yes | yes | |
25053 | 204928 | cefotaxime | yes | yes | |
25053 | 7731 | ofloxacin | yes | yes | |
25053 | 6104 | kanamycin | yes | yes | |
25053 | 17833 | gentamicin | yes | yes | |
25053 | 28864 | tobramycin | yes | yes |
metabolite production
@ref | Chebi-ID | metabolite | production |
---|---|---|---|
25053 | 15688 | acetoin | no |
25053 | 35581 | indole | no |
metabolite tests
@ref | Chebi-ID | metabolite | voges-proskauer-test | indole test |
---|---|---|---|---|
25053 | 15688 | acetoin | - | |
25053 | 35581 | indole | - |
enzymes
@ref | value | activity | ec |
---|---|---|---|
25053 | acid phosphatase | + | 3.1.3.2 |
25053 | alkaline phosphatase | + | 3.1.3.1 |
25053 | alpha-chymotrypsin | + | 3.4.21.1 |
25053 | alpha-galactosidase | - | 3.2.1.22 |
25053 | alpha-glucosidase | - | 3.2.1.20 |
25053 | alpha-mannosidase | - | 3.2.1.24 |
25053 | arginine dihydrolase | - | 3.5.3.6 |
25053 | beta-D-fucosidase | - | 3.2.1.38 |
25053 | beta-galactosidase | - | 3.2.1.23 |
25053 | beta-glucosidase | - | 3.2.1.21 |
25053 | beta-glucuronidase | - | 3.2.1.31 |
25053 | catalase | + | 1.11.1.6 |
25053 | cystine arylamidase | + | 3.4.11.3 |
25053 | cytochrome oxidase | + | 1.9.3.1 |
25053 | esterase (C 4) | + | |
25053 | esterase lipase (C 8) | + | |
25053 | leucine arylamidase | + | 3.4.11.1 |
25053 | lipase (C 14) | - | |
25053 | lysine decarboxylase | - | 4.1.1.18 |
25053 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
25053 | naphthol-AS-BI-phosphohydrolase | + | |
25053 | ornithine decarboxylase | - | 4.1.1.17 |
25053 | trypsin | + | 3.4.21.4 |
25053 | tryptophan deaminase | - | 4.1.99.1 |
25053 | valine arylamidase | + |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent | latitude | longitude |
---|---|---|---|---|---|---|---|
25053 | soil of a salt lake named Aydingkol | Xinjiang Uyghur Autonomous Region | China | CHN | Asia | ||
64833 | soil of a salt lake | Xinjiang Uyghur Autonomous Region, Aydingkol Lake near Turpan City (89° 16' 22.7'' E 42° 38' 55.7'' N) | China | CHN | Asia | 42.6488 | 89.273 |
67770 | Soil of Aydingkol Lake near the Turpan City | Xinjiang | China | CHN | Asia |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Environmental | #Aquatic | #Lake (large) |
#Environmental | #Terrestrial | #Soil |
#Condition | #Saline |
Safety information
risk assessment
- @ref: 64833
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 64833
- description: Pontibacter sp. strain XAAS-1 16S ribosomal RNA gene, partial sequence
- accession: KX530203
- length: 1489
- database: ena
- NCBI tax ID: 1911536
Genome sequences
- @ref: 66792
- description: Pontibacter aydingkolensis DSM 103222
- accession: 2928185967
- assembly level: draft
- database: img
- NCBI tax ID: 1911536
GC content
- @ref: 64833
- GC-content: 52.1
- method: high performance liquid chromatography (HPLC)
External links
@ref: 64833
culture collection no.: CCTCC AB 2016134, JCM 31442, DSM 103222
straininfo link
- @ref: 91399
- straininfo: 401048
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 27902191 | Pontibacter aydingkolensis sp. nov., isolated from soil of a salt lake. | Osman G, Zhang T, Lou K, Gao Y, Chang W, Lin Q, Yang HM, Huo XD, Wang N | Int J Syst Evol Microbiol | 10.1099/ijsem.0.001551 | 2016 | Bacterial Typing Techniques, Base Composition, China, Cytophagaceae/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Lakes/*chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Salinity, Sequence Analysis, DNA, Sodium Chloride, Soil, *Soil Microbiology, Spermidine/analogs & derivatives/chemistry, Vitamin K 2/analogs & derivatives/chemistry | Transcriptome |
Phylogeny | 34694986 | Pontibacter cellulosilyticus sp. nov., a carboxymethyl cellulose-hydrolysing bacterium isolated from coastal water. | Kang M, Chhetri G, Kim J, Kim I, Seo T | Int J Syst Evol Microbiol | 10.1099/ijsem.0.005058 | 2021 | Bacterial Typing Techniques, Bacteroidetes/*classification/isolation & purification, Base Composition, *Carboxymethylcellulose Sodium/metabolism, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry | Transcriptome |
Reference
@id | authors | title | doi/url | journal | pubmed | catalogue |
---|---|---|---|---|---|---|
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 | |||
25053 | G. Z. Osman, T.,Lou, K.,Gao, Y.,Chang, W.,Lin, Q.,Yang, H. M.,Huo, X. D.,Wang, N. | Pontibacter aydingkolensis sp. nov., isolated from soil of a salt lake | 10.1099/ijsem.0.001551 | IJSEM 66: 5523-5528 2016 | 27902191 | |
64833 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-103222 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 103222) | |||
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 | |||
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
91399 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | StrainInfo: A central database for resolving microbial strain identifiers | 10.60712/SI-ID401048.1 |