Strain identifier
BacDive ID: 23439
Type strain:
Species: Algoriphagus machipongonensis
Strain Designation: PR1
Strain history: <- R. Alegado, Univ. of California, Berkeley, USA; PR1 <- R. Zuzow
NCBI tax ID(s): 388413 (species)
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
@ref | gram stain | cell length | cell width | cell shape | motility | confidence |
---|---|---|---|---|---|---|
30556 | negative | 2.5 µm | 0.5 µm | rod-shaped | no | |
69480 | no | 92.561 | ||||
69480 | negative | 99.98 |
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
@ref | growth | type | temperature | range |
---|---|---|---|---|
19197 | positive | growth | 28 | mesophilic |
30556 | positive | growth | 10-40 | |
30556 | positive | optimum | 30 | mesophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
30556 | positive | growth | 05-09 | alkaliphile |
30556 | positive | optimum | 7.5 |
Physiology and metabolism
oxygen tolerance
- @ref: 30556
- oxygen tolerance: aerobe
spore formation
@ref | spore formation | confidence |
---|---|---|
30556 | no | |
69481 | no | 94 |
69480 | no | 99.928 |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
30556 | NaCl | positive | growth | 0-10 % |
30556 | NaCl | positive | optimum | 3 % |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
30556 | 28260 | galactose | + | carbon source |
30556 | 17754 | glycerol | + | carbon source |
30556 | 29864 | mannitol | + | carbon source |
30556 | 4853 | esculin | + | hydrolysis |
enzymes
@ref | value | activity | ec |
---|---|---|---|
30556 | acid phosphatase | + | 3.1.3.2 |
30556 | alkaline phosphatase | + | 3.1.3.1 |
30556 | catalase | + | 1.11.1.6 |
30556 | cytochrome 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
Cat1 | Cat2 | Cat3 |
---|---|---|
#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
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Algoriphagus machipongonensis PR1 | GCA_000166275 | complete | ncbi | 388413 |
66792 | Algoriphagus machipongonensis PR1 | 640612202 | complete | img | 388413 |
GC content
@ref | GC-content | method |
---|---|---|
19197 | 38.7 | sequence analysis |
30556 | 38.7 |
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
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed | journal |
---|---|---|---|---|---|---|---|
19197 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 24695) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-24695 | ||||
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | ||||
30556 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | 10.1128/mSphere.00237-17 | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 26887 | 28776041 | ||
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | ||||
66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | 33211880 | Nucleic Acids Res. 49: D498-D508 2020 | ||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | 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 | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | ||||
87592 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID404908.1 | StrainInfo: A central database for resolving microbial strain identifiers |