Strain identifier
BacDive ID: 130750
Type strain: 
Species: Photobacterium sanctipauli
Strain history: <- CAIM <- A. P. B. Moreira et al., Institute of Biology, Federal University of Rio de Janeiro
NCBI tax ID(s): 1342794 (species)
version 9.3 (current version)
General
@ref: 21728
BacDive-ID: 130750
DSM-Number: 100436
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative
description: Photobacterium sanctipauli DSM 100436 is a mesophilic, Gram-negative bacterium that was isolated from bleached coral Madracis decactis.
NCBI tax id
- NCBI tax id: 1342794
- Matching level: species
strain history
- @ref: 21728
- history: <- CAIM <- A. P. B. Moreira et al., Institute of Biology, Federal University of Rio de Janeiro
doi: 10.13145/bacdive130750.20250331.9.3
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Gammaproteobacteria
- order: Vibrionales
- family: Vibrionaceae
- genus: Photobacterium
- species: Photobacterium sanctipauli
- full scientific name: Photobacterium sanctipauli Moreira et al. 2015
@ref: 21728
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Vibrionales, not validated
family: Vibrionaceae
genus: Photobacterium
species: Photobacterium sanctipauli
full scientific name: Photobacterium sanctipauli Moreira et al. 2015
type strain: yes
Morphology
cell morphology
| @ref | gram stain | confidence |
|---|---|---|
| 125438 | negative | 99.583 |
| 125439 | negative | 99.6 |
Culture and growth conditions
culture medium
- @ref: 21728
- 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: 21728
- growth: positive
- type: growth
- temperature: 28
Physiology and metabolism
spore formation
- @ref: 125439
- spore formation: no
- confidence: 99.6
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 68369 | 25115 | malate | - | assimilation |
| 68369 | 17128 | adipate | - | assimilation |
| 68369 | 27689 | decanoate | - | assimilation |
| 68369 | 24265 | gluconate | + | assimilation |
| 68369 | 17306 | maltose | - | assimilation |
| 68369 | 59640 | N-acetylglucosamine | - | assimilation |
| 68369 | 16899 | D-mannitol | + | assimilation |
| 68369 | 16024 | D-mannose | + | assimilation |
| 68369 | 30849 | L-arabinose | - | assimilation |
| 68369 | 17634 | D-glucose | + | assimilation |
| 68369 | 5291 | gelatin | - | hydrolysis |
| 68369 | 4853 | esculin | + | hydrolysis |
| 68369 | 16199 | urea | - | hydrolysis |
| 68369 | 29016 | arginine | + | hydrolysis |
| 68369 | 17634 | D-glucose | + | fermentation |
| 68369 | 27897 | tryptophan | - | energy source |
| 68369 | 17632 | nitrate | - | reduction |
metabolite production
- @ref: 68369
- Chebi-ID: 35581
- metabolite: indole
- production: no
metabolite tests
- @ref: 68369
- Chebi-ID: 35581
- metabolite: indole
- indole test: -
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 68369 | cytochrome oxidase | - | 1.9.3.1 |
| 68369 | gelatinase | - | |
| 68369 | beta-glucosidase | + | 3.2.1.21 |
| 68369 | urease | - | 3.5.1.5 |
| 68369 | arginine dihydrolase | + | 3.5.3.6 |
API 20NE
| @ref | NO3 | TRP | GLU_ Ferm | ADH Arg | URE | ESC | GEL | PNPG | GLU_ Assim | ARA | MNE | MAN | NAG | MAL | GNT | CAP | ADI | MLT | CIT | PAC | OX |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 21728 | - | - | + | + | - | + | - | + | + | - | + | + | - | - | + | - | - | - | - | - | - |
Isolation, sampling and environmental information
isolation
- @ref: 21728
- sample type: bleached coral Madracis decactis
- host species: Madracis decactis
- geographic location: St Peter and St Paul Archipelago, Mid-Atlantic Ridge
- country: Brazil
- origin.country: BRA
- continent: Middle and South America
- latitude: 0.9333
- longitude: -29.3667
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Marine |
| #Host | #Invertebrates (Other) | #Cnidaria (Corals) |
taxonmaps
- @ref: 69479
- File name: preview.99_60437.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_14;96_3204;97_33379;98_42899;99_60437&stattab=map
- Last taxonomy: Photobacterium sanctipauli subclade
- 16S sequence: KC751088
- Sequence Identity:
- Total samples: 140
- aquatic counts: 121
- animal counts: 19
Sequence information
16S sequences
- @ref: 21728
- description: Photobacterium sanctipauli strain A-394 16S ribosomal RNA gene, partial sequence
- accession: KC751088
- length: 1505
- database: nuccore
- NCBI tax ID: 1342794
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Photobacterium sanctipauli DSM 100436 | GCA_003026495 | contig | ncbi | 1342794 |
| 66792 | Photobacterium sanctipauli strain DSM 100436 | 1342794.7 | wgs | patric | 1342794 |
| 66792 | Photobacterium sanctipauli DSM 100436 | 2902482210 | draft | img | 1342794 |
Genome-based predictions
predictions
| @ref | model | trait | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 125438 | gram-positive | gram-positive | Positive reaction to Gram-staining | no | 99.583 | no |
| 125438 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 95.117 | no |
| 125438 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 86.794 | no |
| 125438 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | no | 54.134 | no |
| 125438 | thermophile | thermophilic | Ability to grow at temperatures above or equal to 45°C | no | 100 | yes |
| 125438 | motile2+ | flagellated | Ability to perform flagellated movement | yes | 87.283 | no |
| 125439 | BacteriaNet | spore_formation | Ability to form endo- or exospores | no | 99.6 | |
| 125439 | BacteriaNet | motility | Ability to perform movement | yes | 82.1 | |
| 125439 | BacteriaNet | gram_stain | Reaction to gram-staining | negative | 99.6 | |
| 125439 | BacteriaNet | oxygen_tolerance | Oxygenic conditions needed for growth | obligate aerobe | 86.9 |
External links
@ref: 21728
culture collection no.: DSM 100436, CAIM 1892, LMG 27910
straininfo link
- @ref: 89247
- straininfo: 403282
literature
- topic: Phylogeny
- Pubmed-ID: 25024905
- title: Photobacterium sanctipauli sp. nov. isolated from bleached Madracis decactis (Scleractinia) in the St Peter & St Paul Archipelago, Mid-Atlantic Ridge, Brazil.
- authors: Moreira AP, Duytschaever G, Chimetto Tonon LA, Froes AM, de Oliveira LS, Amado-Filho GM, Francini-Filho RB, De Vos P, Swings J, Thompson CC, Thompson FL
- journal: PeerJ
- DOI: 10.7717/peerj.427
- year: 2014
Reference
| @id | authors | title | doi/url | 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 | |
| 21728 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-100436 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 100436) | |
| 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 | |
| 68369 | Automatically annotated from API 20NE | |||
| 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/ | |
| 89247 | 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-ID403282.1 | |
| 125438 | Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann | Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets | 10.1101/2024.08.12.607695 | |
| 125439 | Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy | deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 | https://github.com/GenomeNet/deepG |