Strain identifier

BacDive ID: 23439

Type strain: Yes

Species: Algoriphagus machipongonensis

Strain Designation: PR1

Strain history: <- R. Alegado, Univ. of California, Berkeley, USA; PR1 <- R. Zuzow

NCBI tax ID(s): 388413 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 19197

BacDive-ID: 23439

DSM-Number: 24695

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

description: Algoriphagus machipongonensis PR1 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from mud, co-isolated with the colonial choanoflagellate Salpingoeca rosetta .

NCBI tax id

  • NCBI tax id: 388413
  • Matching level: species

strain history

  • @ref: 19197
  • history: <- R. Alegado, Univ. of California, Berkeley, USA; PR1 <- R. Zuzow

doi: 10.13145/bacdive23439.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Cytophagia
  • order: Cytophagales
  • family: Cyclobacteriaceae
  • genus: Algoriphagus
  • species: Algoriphagus machipongonensis
  • full scientific name: Algoriphagus machipongonensis Alegado et al. 2013

@ref: 19197

domain: Bacteria

phylum: Bacteroidetes

class: Cytophagia

order: Cytophagales

family: Cyclobacteriaceae

genus: Algoriphagus

species: Algoriphagus machipongonensis

full scientific name: Algoriphagus machipongonensis Alegado et al. 2013

strain designation: PR1

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
30556negative2.5 µm0.5 µmrod-shapedno
69480no92.561
69480negative99.98

pigmentation

  • @ref: 30556
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 19197
  • name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/514
  • composition: 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

@refgrowthtypetemperaturerange
19197positivegrowth28mesophilic
30556positivegrowth10-40
30556positiveoptimum30mesophilic

culture pH

@refabilitytypepHPH range
30556positivegrowth05-09alkaliphile
30556positiveoptimum7.5

Physiology and metabolism

oxygen tolerance

  • @ref: 30556
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
30556no
69481no94
69480no99.928

halophily

@refsaltgrowthtested relationconcentration
30556NaClpositivegrowth0-10 %
30556NaClpositiveoptimum3 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3055628260galactose+carbon source
3055617754glycerol+carbon source
3055629864mannitol+carbon source
305564853esculin+hydrolysis

enzymes

@refvalueactivityec
30556acid phosphatase+3.1.3.2
30556alkaline phosphatase+3.1.3.1
30556catalase+1.11.1.6
30556cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

  • @ref: 19197
  • sample type: mud, co-isolated with the colonial choanoflagellate Salpingoeca rosetta (ATCC 50818)
  • host species: Salpingoeca rosetta
  • geographic location: Virginia, Hog Island
  • country: USA
  • origin.country: USA
  • continent: North America

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Mud (Sludge)
#Host#Other

Safety information

risk assessment

  • @ref: 19197
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Algoriphagus machipongonensis PR1GCA_000166275completencbi388413
66792Algoriphagus machipongonensis PR1640612202completeimg388413

GC content

@refGC-contentmethod
1919738.7sequence analysis
3055638.7

Genome-based predictions

predictions

  • trait: spore-forming
  • prediction: no
  • confidence: 94
  • training_data: no

External links

@ref: 19197

culture collection no.: DSM 24695, ATCC BAA 2233

straininfo link

  • @ref: 87592
  • straininfo: 404908

literature

  • topic: Phylogeny
  • Pubmed-ID: 22368173
  • title: Algoriphagus machipongonensis sp. nov., co-isolated with a colonial choanoflagellate.
  • authors: Alegado RA, Grabenstatter JD, Zuzow R, Morris A, Huang SY, Summons RE, King N
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.038646-0
  • year: 2012
  • mesh: Bacterial Typing Techniques, Bacteroidetes/*classification/genetics/isolation & purification, Base Composition, Choanoflagellata, DNA, Bacterial/genetics, Fatty Acids/analysis, Geologic Sediments/microbiology, Molecular Sequence Data, Phospholipids/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Virginia
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
19197Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 24695)https://www.dsmz.de/collection/catalogue/details/culture/DSM-24695
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
30556Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2688728776041
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updates33211880Nucleic Acids Res. 49: D498-D508 2020
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
87592Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID404908.1StrainInfo: A central database for resolving microbial strain identifiers