Strain identifier

BacDive ID: 159751

Type strain: Yes

Species: Flavobacterium psychroterrae

Strain Designation: P3922

NCBI tax ID(s): 2133767 (species)

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General

@ref: 66678

BacDive-ID: 159751

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

description: Flavobacterium psychroterrae P3922 is an aerobe, mesophilic, Gram-positive bacterium that has a yellow pigmentation and was isolated from stone fragment.

NCBI tax id

  • NCBI tax id: 2133767
  • Matching level: species

doi: 10.13145/bacdive159751.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Flavobacteriia
  • order: Flavobacteriales
  • family: Flavobacteriaceae
  • genus: Flavobacterium
  • species: Flavobacterium psychroterrae
  • full scientific name: Flavobacterium psychroterrae Králová et al. 2018

@ref: 66678

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Flavobacteriaceae

genus: Flavobacterium

species: Flavobacterium psychroterrae

strain designation: P3922

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityflagellum arrangementconfidence
66678positive1.6-4.5 µm0.3-0.5 µmrod-shapedyesgliding
69480negative99.997

colony morphology

  • @ref: 66678
  • colony color: clear metallic sheen
  • medium used: Endo agar

pigmentation

  • @ref: 66678
  • production: yes
  • color: yellow
  • name: flexirubin-type

Culture and growth conditions

culture medium

@refnamegrowth
66678Endo agaryes
66678MacConkey agarno
66678Marine agar (MA)no
66678Nutrient agar (NA)yes
66678Reasoner's 2A agar (R2A)yes
66678tryptic soy agar (TSA)yes

culture temp

@refgrowthtypetemperaturerange
66678nogrowth35mesophilic
66678positivegrowth1-25

culture pH

  • @ref: 66678
  • ability: positive
  • type: growth
  • pH: 6-9
  • PH range: alkaliphile

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
66678aerobe
66678microaerophile

spore formation

@refspore formationconfidence
66678no
69480no99.997
69481no100

halophily

@refsaltgrowthtested relationconcentration
66678NaClpositivegrowth1 %(w/v)
66678NaClnogrowth2 %(w/v)

observation

@refobservation
66678Cells occur singly, occasionally in pairs or irregular clusters.
66678Gliding motility present on R2A agar but no motility is observed by the hanging-drop technique.
66678Filamentous structures up to 7.0 µm long can be formed.
66678Presence of a capsule is negative.
66678Glucose is not fermented to acid in OF test medium.

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6667815792malonate-assimilation
6667827856acetamide-assimilation
6667853258citric acid-assimilation
6667817234glucose+builds acid from
6667817306maltose+builds acid from
6667818222xylose+builds acid from
6667828757fructose+builds acid from
6667813705acetoacetate-carbon source
6667815740formate-carbon source
6667815748D-glucuronate-carbon source
6667815971L-histidine-carbon source
6667816467L-arginine-carbon source
6667816523D-serine-carbon source
6667816537galactarate-carbon source
6667816634raffinose-carbon source
6667816651(S)-lactate-carbon source
66678167632-oxobutanoate-carbon source
6667816865gamma-aminobutyric acid-carbon source
6667816899D-mannitol-carbon source
6667816977L-alanine-carbon source
6667817115L-serine-carbon source
6667817164stachyose-carbon source
6667817268myo-inositol-carbon source
6667817272propionate-carbon source
6667817309pectin-carbon source
6667817596inosine-carbon source
6667817716lactose-carbon source
6667817754glycerol-carbon source
6667817924D-sorbitol-carbon source
6667817992sucrose-carbon source
66678181014-hydroxyphenylacetic acid-carbon source
6667818183L-pyroglutamic acid-carbon source
6667818287L-fucose-carbon source
6667818333D-arabitol-carbon source
6667826490quinate-carbon source
6667828053melibiose-carbon source
6667828847D-fucose-carbon source
6667829990D-aspartate-carbon source
6667830612D-glucarate-carbon source
6667830796(R)-malic acid-carbon source
6667830797(S)-malic acid-carbon source
6667832323glucuronamide-carbon source
6667832528turanose-carbon source
6667835418n-acetylneuraminate-carbon source
66678370543-hydroxybutyrate-carbon source
6667848607lithium chloride-carbon source
6667851850methyl pyruvate-carbon source
6667853258citric acid-carbon source
6667863153N-acetyl-D-mannosamine-carbon source
6667864103sodium butyrate-carbon source
66678645522-hydroxybutyrate-carbon source
6667871321fusidate-carbon source
6667873706bromosuccinate-carbon source
66678739183-O-methyl-D-glucose-carbon source
6667874611methyl (R)-lactate-carbon source
6667875229sodium bromate-carbon source
6667875248potassium tellurite-carbon source
6667878697D-fructose 6-phosphate-carbon source
66678100147nalidixic acid-carbon source
66678161680aztreonam-carbon source
666781 % sodium lactate-carbon source
66678168102-oxoglutarate-carbon source
666785291gelatin+carbon source
6667812936D-galactose+carbon source
6667814314D-glucose 6-phosphate+carbon source
6667815824D-fructose+carbon source
6667816024D-mannose+carbon source
6667816411acetic acid+carbon source
6667816551D-trehalose+carbon source
6667817057cellobiose+carbon source
6667817306maltose+carbon source
6667817464L-galactonic acid gamma-lactone+carbon source
6667817814salicin+carbon source
6667817925alpha-D-glucose+carbon source
6667818024D-galacturonic acid+carbon source
6667823652dextrin+carbon source
6667828066gentiobiose+carbon source
6667828800N-acetylgalactosamine+carbon source
6667829985L-glutamate+carbon source
6667829991L-aspartate+carbon source
6667853423tween 40+carbon source
6667859640N-acetylglucosamine+carbon source
6667862345L-rhamnose+carbon source
6667870744glycine-proline+carbon source
66678320055methyl beta-D-glucopyranoside+carbon source
6667862968cellulose-degradation
6667818186tyrosine-hydrolysis
6667853426tween 80-hydrolysis
6667861995lecithin-hydrolysis
666784853esculin+hydrolysis
666785291gelatin+hydrolysis
6667816991dna+hydrolysis
6667828017starch+hydrolysis
66678casein+hydrolysis
6667816301nitrite-reduction
6667817632nitrate+reduction

antibiotic resistance

@refChEBImetaboliteis antibioticis resistantresistance conc.is sensitivesensitivity conc.
6667828971ampicillinyesyes10 µg (disc)
6667817698chloramphenicolyesyes30 µg (disc)
6667818208penicillin gyesyes10 µg (disc)
6667827902tetracyclineyesyes30 µg (disc)
6667873908vibriostatyesyes150 µg (disc)

metabolite production

  • @ref: 66678
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
66678alpha-fucosidase-3.2.1.51
66678alpha-galactosidase-3.2.1.22
66678alpha-mannosidase-3.2.1.24
66678arginine dihydrolase-3.5.3.6
66678beta-glucuronidase-3.2.1.31
66678cystine arylamidase-3.4.11.3
66678lysine decarboxylase-4.1.1.18
66678ornithine decarboxylase-4.1.1.17
66678trypsin-3.4.21.4
66678urease-3.5.1.5
66678acid phosphatase+3.1.3.2
66678alkaline phosphatase+3.1.3.1
66678alpha-galactosidase+3.2.1.22
66678beta-galactosidase+3.2.1.23
66678beta-glucosidase+3.2.1.21
66678catalase+1.11.1.6
66678esterase (C 4)+
66678esterase Lipase (C 8)+
66678leucine arylamidase+3.4.11.1
66678N-acetyl-beta-glucosaminidase+3.2.1.52
66678naphthol-AS-BI-phosphohydrolase+
66678valine arylamidase+

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    66678C16:1 iso H1
    66678C16:0 3OH2
    66678C16:0 iso2
    66678C17:1 w6c4
    66678C15:0 2OH1.1
    66678C16:01.6
    66678C16:1 w7c/ C16:1 w6c11.6
    66678C17:0 2OH2.4
    66678C15:0 3OH2.5
    66678C15:0 iso20.2
    66678C15:1 w6c3.6
    66678C16:0 10-methyl/ C17:1 iso w9c4.5
    66678C16:0 iso 3OH5.3
    66678C15:1 iso G7.7
    66678C15:0 iso 3OH8.1
    66678C15:0 anteiso8.2
    66678C17:0 iso 3OH9.6
  • type of FA analysis: whole cell analysis
  • incubation temperature: 20
  • incubation time: 2
  • software version: Sherlock 6.2
  • library/peak naming table: RTSBA6.21
  • system: MIS MIDI
  • cutoff value:

Isolation, sampling and environmental information

isolation

  • @ref: 66678
  • sample type: stone fragment
  • geographic location: fissure in Kom arek Wall, James Ross Island
  • country: Antarctica
  • origin.country: ATA
  • continent: Australia and Oceania
  • latitude: -63.8305
  • longitude: -57.8388
  • enrichment culture: R2A agar
  • enrichment culture duration: 5-7 days
  • enrichment culture temperature: 15
  • isolation procedure: 1 g stone fragments or soil samples in 5 ml sterile saline solution, subsequently 100 µl of this suspension was spread by L-loop on the surface of Reasoner's 2A agar plates and cultivated at 15°C for up to 5-7 days. Analogously, water samples were spread on R2A agar plates (150 µl) and cultivated at 15°C for up to 5 days.

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Geologic

Sequence information

16S sequences

  • @ref: 66678
  • description: Flavobacterium sp. P3922 16S ribosomal RNA gene, partial sequence
  • accession: MH100901
  • length: 1357
  • database: ena
  • NCBI tax ID: 2133767

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Flavobacterium psychroterrae CCM 8827GCA_018380615scaffoldncbi2133767
66792Flavobacterium psychroterrae strain CCM 88272133767.3wgspatric2133767

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedno95.207no
gram-positiveno98.039no
anaerobicno99.72yes
aerobicyes91.893no
halophileno96.333no
spore-formingno92.795yes
thermophileno99.862yes
glucose-utilyes89.086no
motileno87.341no
glucose-fermentno84.013no

External links

@ref: 66678

culture collection no.: LMG 30616, CCM 8827

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny30095387Flavobacterium chryseum sp. nov. and Flavobacterium psychroterrae sp. nov., novel environmental bacteria isolated from Antarctica.Kralova S, Svec P, Busse HJ, Stankova E, Vaczi P, Sedlacek IInt J Syst Evol Microbiol10.1099/ijsem.0.0029522018Antarctic Regions, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flavobacterium/*classification/genetics/isolation & purification, Nucleic Acid Hybridization, Phosphatidylethanolamines/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Spermidine/analogs & derivatives/chemistry, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny31483240Flavobacterium ranwuense sp. nov., isolated from glacier.Zhang GQ, Liu Q, Liu HC, Zhou YG, Xin YHInt J Syst Evol Microbiol10.1099/ijsem.0.0036872019Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flavobacterium/*classification/isolation & purification, Ice Cover/*microbiology, Nucleic Acid Hybridization, Phosphatidylethanolamines/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny31702532Flavobacterium psychrotolerans sp. nov., a psychrotolerant bacterium isolated from Renlongba glacier on the Tibetan Plateau.Yang LL, Liu Q, Liu HC, Zhou YG, Xin YHInt J Syst Evol Microbiol10.1099/ijsem.0.0038682020Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flavobacterium/*classification/isolation & purification, Ice Cover/*microbiology, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Tibet, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorstitledoi/urljournalpubmed
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
66678Stanislava Kralova, Pavel Svec, Hans-Jürgen Busse, Eva Stankova, Peter Vaczi, Ivo SedlacekFlavobacterium chryseum sp. nov. and Flavobacterium psychroterrae sp. nov., novel environmental bacteria isolated from Antarctica10.1099/ijsem.0.002952IJSEM 68: 3132-3139 201830095387
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
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1