Strain identifier

BacDive ID: 5629

Type strain: Yes

Species: Psychroflexus tropicus

Strain Designation: LA1, LA1T

Strain history: CIP <- 2004, S.P. Donachie, Honolulu, USA: strain LA1T

NCBI tax ID(s): 1123035 (strain), 197345 (species)

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General

@ref: 5957

BacDive-ID: 5629

DSM-Number: 15496

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

description: Psychroflexus tropicus LA1 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from lake water.

NCBI tax id

NCBI tax idMatching level
197345species
1123035strain

strain history

@refhistory
5957<- S. P. Donachie; LA1
367362004, S.P. Donachie, Honolulu, USA: strain LA1T
123594CIP <- 2004, S.P. Donachie, Honolulu, USA: strain LA1T

doi: 10.13145/bacdive5629.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Flavobacteriia
  • order: Flavobacteriales
  • family: Flavobacteriaceae
  • genus: Psychroflexus
  • species: Psychroflexus tropicus
  • full scientific name: Psychroflexus tropicus Donachie et al. 2004

@ref: 5957

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Flavobacteriaceae

genus: Psychroflexus

species: Psychroflexus tropicus

full scientific name: Psychroflexus tropicus Donachie et al. 2004 emend. Hahnke et al. 2016

strain designation: LA1, LA1T

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityflagellum arrangementconfidence
29948negative2.25 µm0.21 µmrod-shapedyesgliding
69480negative99.993
123594negativerod-shapedno

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5957BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)yeshttps://mediadive.dsmz.de/medium/514Name: 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
36736Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
123594CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
5957positivegrowth28mesophilic
29948positivegrowth04-43
29948positiveoptimum30mesophilic
36736positivegrowth30mesophilic
123594positivegrowth25-30mesophilic
123594nogrowth5psychrophilic
123594nogrowth10psychrophilic
123594nogrowth15psychrophilic
123594nogrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
29948aerobe
123594facultative anaerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.996

halophily

@refsaltgrowthtested relationconcentration
29948NaClpositivegrowth01-20 %
29948NaClpositiveoptimum8.75 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
29948581435-dehydro-D-gluconate+carbon source
2994821217L-alaninamide+carbon source
2994816449alanine+carbon source
2994818403L-arabitol+carbon source
2994822653asparagine+carbon source
2994835391aspartate+carbon source
2994828757fructose+carbon source
2994817234glucose+carbon source
2994829987glutamate+carbon source
2994817754glycerol+carbon source
2994825017leucine+carbon source
2994829864mannitol+carbon source
2994837684mannose+carbon source
2994818257ornithine+carbon source
2994826271proline+carbon source
2994817822serine+carbon source
2994830911sorbitol+carbon source
2994817992sucrose+carbon source
2994826986threonine+carbon source
2994827082trehalose+carbon source
2994817632nitrate+reduction
1235944853esculin-hydrolysis
123594606565hippurate+hydrolysis
12359417632nitrate+reduction
12359416301nitrite-reduction

metabolite production

  • @ref: 123594
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
29948acid phosphatase+3.1.3.2
29948alkaline phosphatase+3.1.3.1
29948catalase+1.11.1.6
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase-3.2.1.21
68382alpha-glucosidase+3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin+3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase+
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase+3.1.3.1
123594oxidase-
123594beta-galactosidase-3.2.1.23
123594alcohol dehydrogenase-1.1.1.1
123594gelatinase+/-
123594amylase-
123594DNase-
123594caseinase+3.4.21.50
123594catalase+1.11.1.6
123594tween esterase-
123594gamma-glutamyltransferase+2.3.2.2
123594lecithinase-
123594lipase-
123594lysine decarboxylase-4.1.1.18
123594ornithine decarboxylase-4.1.1.17
123594phenylalanine ammonia-lyase-4.3.1.24
123594tryptophan deaminase-
123594urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
123594-+++-++-+-++---+----

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
5957lake waterHawai, Lake LaysanUSAUSANorth America
123594Laysan hypersaline lagoonNorthwestern Hawaiian Islands, HawaiiUnited States of AmericaUSANorth America2000

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Aquatic
  • Cat3: #Lake (large)

taxonmaps

  • @ref: 69479
  • File name: preview.99_3769.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_423;96_1937;97_2329;98_2873;99_3769&stattab=map
  • Last taxonomy: Psychroflexus tropicus subclade
  • 16S sequence: AF513434
  • Sequence Identity:
  • Total samples: 58
  • soil counts: 6
  • aquatic counts: 51
  • animal counts: 1

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
59571Risk group (German classification)
1235941Risk group (French classification)

Sequence information

16S sequences

  • @ref: 5957
  • description: Psychroflexus tropicus strain LA1 16S ribosomal RNA gene, partial sequence
  • accession: AF513434
  • length: 1418
  • database: ena
  • NCBI tax ID: 197345

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Psychroflexus tropicus DSM 15496GCA_000378765scaffoldncbi1123035
66792Psychroflexus tropicus DSM 154961123035.3wgspatric1123035
66792Psychroflexus tropicus DSM 154962518645613draftimg1123035

GC content

@refGC-contentmethod
595735±0.8
2994835
595736.5sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno88.928no
flagellatedno95.954yes
gram-positiveno98.406no
anaerobicno99.095yes
aerobicyes91.445yes
halophileyes82.786yes
spore-formingno96.374no
thermophileno98.514no
glucose-utilyes84.35yes
glucose-fermentno89.906no

External links

@ref: 5957

culture collection no.: DSM 15496, ATCC BAA 734, CIP 108448

straininfo link

  • @ref: 75112
  • straininfo: 132028

literature

  • topic: Phylogeny
  • Pubmed-ID: 15143045
  • title: Psychroflexus tropicus sp. nov., an obligately halophilic Cytophaga-Flavobacterium-Bacteroides group bacterium from an Hawaiian hypersaline lake.
  • authors: Donachie SP, Bowman JP, Alam M
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.02733-0
  • year: 2004
  • mesh: Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/genetics, Fatty Acids/analysis, Flavobacteriaceae/*classification/genetics/isolation & purification/*metabolism, Fresh Water/microbiology, Hawaii, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sodium Chloride
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
5957Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15496)https://www.dsmz.de/collection/catalogue/details/culture/DSM-15496
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
29948Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2631728776041
36736Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6071
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)
68382Automatically annotated from API zym
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.https://microbeatlas.org/MicrobeAtlas 1.0 beta
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
75112Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID132028.1StrainInfo: A central database for resolving microbial strain identifiers
123594Curators of the CIPCollection of Institut Pasteur (CIP 108448)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108448