Strain identifier

BacDive ID: 23884

Type strain: Yes

Species: Pontibacter akesuensis

Strain Designation: AKesu 4, ASK 1

Strain history: <- R Lai, Nanjing Agricultural Univ., China

NCBI tax ID(s): 388950 (species)

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General

@ref: 21095

BacDive-ID: 23884

DSM-Number: 18820

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, rod-shaped

description: Pontibacter akesuensis AKesu 4 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from desert soil.

NCBI tax id

  • NCBI tax id: 388950
  • Matching level: species

strain history

@refhistory
21095<- R. Lai, Nanjing Agric. Univ., China; AKS 1
67771<- R Lai, Nanjing Agricultural Univ., China

doi: 10.13145/bacdive23884.20230509.8.1

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 akesuensis
  • full scientific name: Pontibacter akesuensis Zhou et al. 2007

@ref: 21095

domain: Bacteria

phylum: Bacteroidetes

class: Cytophagia

order: Cytophagales

family: Hymenobacteraceae

genus: Pontibacter

species: Pontibacter akesuensis

full scientific name: Pontibacter akesuensis Zhou et al. 2007 emend. Zhang et al. 2013

strain designation: AKesu 4, ASK 1

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
31959negative1.5-1.6 µm0.7-0.75 µmrod-shapedno
67771rod-shapedno
67771negative

pigmentation

  • @ref: 31959
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 21095
  • name: LB (Luria-Bertani) MEDIUM (DSMZ Medium 381)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/381
  • composition: Name: LB (Luria-Bertani) MEDIUM (DSMZ Medium 381) Composition: Agar 20.0 g/l NaCl 10.0 g/l Tryptone 10.0 g/l Yeast extract 5.0 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
21095positivegrowth28mesophilic
31959positivegrowth04-36
31959positiveoptimum29mesophilic
67771positivegrowth28-30mesophilic

culture pH

@refabilitytypepHPH range
31959positivegrowth7-11alkaliphile
31959positiveoptimum7.8

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31959aerobe
67771aerobe

spore formation

@refspore formation
31959no
67771no

halophily

@refsaltgrowthtested relationconcentration
31959NaClpositivegrowth0-4 %
31959NaClpositiveoptimum2 %

observation

  • @ref: 67771
  • observation: quinones: MK-7

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3195930089acetate+carbon source
3195921217L-alaninamide+carbon source
3195916449alanine+carbon source
3195940585alpha-cyclodextrin+carbon source
31959286442-oxopentanoate+carbon source
3195922599arabinose+carbon source
3195918403L-arabitol+carbon source
3195922653asparagine+carbon source
3195935391aspartate+carbon source
3195917126DL-carnitine+carbon source
3195917057cellobiose+carbon source
3195923652dextrin+carbon source
3195928757fructose+carbon source
3195933984fucose+carbon source
3195928260galactose+carbon source
3195924175galacturonate+carbon source
3195924265gluconate+carbon source
3195917234glucose+carbon source
3195929987glutamate+carbon source
3195928087glycogen+carbon source
3195927570histidine+carbon source
31959182404-hydroxy-L-proline+carbon source
3195917596inosine+carbon source
3195917240itaconate+carbon source
3195925017leucine+carbon source
3195917306maltose+carbon source
3195928053melibiose+carbon source
3195937657methyl D-glucoside+carbon source
3195951850methyl pyruvate+carbon source
3195917268myo-inositol+carbon source
31959506227N-acetylglucosamine+carbon source
3195918257ornithine+carbon source
3195928044phenylalanine+carbon source
3195926271proline+carbon source
3195917272propionate+carbon source
3195917148putrescine+carbon source
3195926490quinate+carbon source
3195916634raffinose+carbon source
3195926546rhamnose+carbon source
3195917822serine+carbon source
3195930911sorbitol+carbon source
3195930031succinate+carbon source
3195917992sucrose+carbon source
3195926986threonine+carbon source
3195917748thymidine+carbon source
3195927082trehalose+carbon source
3195917151xylitol+carbon source
319594853esculin+hydrolysis

enzymes

@refvalueactivityec
31959alpha-galactosidase+3.2.1.22
31959gelatinase+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
21095desert soilAkesu, XinJiang ProvinceChinaCHNAsia
67771From desert soilXinjiang ProvinceChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Desert
#Environmental#Terrestrial#Soil
#Condition#Xerophilic

taxonmaps

  • @ref: 69479
  • File name: preview.99_3775.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_60;96_1940;97_2333;98_2878;99_3775&stattab=map
  • Last taxonomy: Pontibacter akesuensis
  • 16S sequence: DQ672723
  • Sequence Identity:
  • Total samples: 472
  • soil counts: 225
  • aquatic counts: 168
  • animal counts: 60
  • plant counts: 19

Safety information

risk assessment

  • @ref: 21095
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 21095
  • description: Pontibacter akesuensis strain AKS 1 16S ribosomal RNA gene, partial sequence
  • accession: DQ672723
  • length: 1408
  • database: ena
  • NCBI tax ID: 388950

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pontibacter akesuensis DSM 18820GCA_900116885contigncbi388950
66792Pontibacter akesuensis KCTC 12758GCA_014651555scaffoldncbi388950
66792Pontibacter akesuensis strain DSM 18820388950.6wgspatric388950
66792Pontibacter akesuensis strain KCTC 12758388950.7wgspatric388950
66792Pontibacter akesuensis DSM 188202622736541draftimg388950

GC content

  • @ref: 31959
  • GC-content: 51.4

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno90.223yes
flagellatedno96.351yes
gram-positiveno98.494no
anaerobicno99.105yes
aerobicyes90.333yes
halophileno77.946no
spore-formingno95.423yes
thermophileno97.632no
glucose-utilyes89.412yes
glucose-fermentno87.227no

External links

@ref: 21095

culture collection no.: DSM 18820, CCTCC AB 206086, KCTC 12758, AKS 1

straininfo link

  • @ref: 87894
  • straininfo: 405247

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17267972Pontibacter akesuensis sp. nov., isolated from a desert soil in China.Zhou Y, Wang X, Liu H, Zhang KY, Zhang YQ, Lai R, Li WJInt J Syst Evol Microbiol10.1099/ijs.0.64716-02007Base Composition, China, Cytophagaceae/*classification/cytology/*isolation & purification/physiology, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Desert Climate, Fatty Acids/analysis/chemistry, Genes, rRNA, Microscopy, Electron, Transmission, Molecular Sequence Data, Phylogeny, Quinones/analysis/chemistry, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, *Soil MicrobiologyGenetics
Genetics27795233Complete Genome Sequence of Pontibacter akesuensis Strain AKS 1T, Which Exhibits Robust Nutrient Metabolism in Harsh Environments.Wang Y, He K, Jiang Y, Shen J, Yu BGenome Announc10.1128/genomeA.00997-162016Metabolism
Phylogeny30141769Pontibacter silvestris sp. nov., isolated from the soil of a Populus euphratica forest and emended description of the genus Pontibacter.Osman G, Wang Z, Wang N, Shayimu G, Hou M, Guo W, Yang XInt J Syst Evol Microbiol10.1099/ijsem.0.0029722018Bacterial Typing Techniques, Bacteroidetes/*classification/genetics/isolation & purification, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Forests, Phosphatidylethanolamines/chemistry, *Phylogeny, Populus/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorstitledoi/urlcatalogueID_cross_referencepubmedjournal
20215Parte, 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 DSMZ10.1099/ijsem.0.004332
21095Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-18820Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18820)
31959Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172821528776041
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar SchomburgBRENDA, the ELIXIR core data resource in 2021: new developments and updates10.1093/nar/gkaa102533211880Nucleic Acids Res. 49: D498-D508 2020
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
69479João 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 betahttps://microbeatlas.org/
87894Reimer, 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 identifiers10.60712/SI-ID405247.1