Strain identifier

BacDive ID: 159700

Type strain: Yes

Species: Paracoccus fontiphilus

Strain Designation: MVW-1

Strain history: <- Wen-Ming Chen, National Kaohsiung Marine Univ.

NCBI tax ID(s): 1815556 (species)

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General

@ref: 66563

BacDive-ID: 159700

keywords: genome sequence, 16S sequence, Bacteria, aerobe, chemoheterotroph, Gram-negative, rod-shaped, colony-forming

description: Paracoccus fontiphilus MVW-1 is an aerobe, chemoheterotroph, Gram-negative bacterium that forms circular colonies and was isolated from freshwater sample.

NCBI tax id

  • NCBI tax id: 1815556
  • Matching level: species

strain history

  • @ref: 67771
  • history: <- Wen-Ming Chen, National Kaohsiung Marine Univ.

doi: 10.13145/bacdive159700.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Rhodobacterales
  • family: Paracoccaceae
  • genus: Paracoccus
  • species: Paracoccus fontiphilus
  • full scientific name: Paracoccus fontiphilus Sheu et al. 2018

@ref: 66563

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Paracoccus

species: Paracoccus fontiphilus

strain designation: MVW-1

type strain: yes

Morphology

cell morphology

  • @ref: 66563
  • gram stain: negative
  • cell length: 1.8-2.2 µm
  • cell width: 0.7-0.9 µm
  • cell shape: rod-shaped
  • motility: no

colony morphology

  • @ref: 66563
  • colony size: 0.8-1 mm
  • colony color: light orange
  • colony shape: circular
  • incubation period: 2 days
  • medium used: R2A medium

pigmentation

@refproductionnamecolor
66563noflexirubin-type
66563yescaroteniod pigmentsmaximum absorption at 488 nm

Culture and growth conditions

culture medium

@refnamegrowth
66563LB (Luria-Bertani) agaryes
66563Marine agar (MA)yes
66563Nutrient agar (NA)yes
66563Reasoner's 2A agar (R2A)yes
66563tryptic soy agar (TSA)yes

culture temp

@refgrowthtypetemperaturerange
66563positivegrowth15-30
66563positiveoptimum20-25
67771positivegrowth25mesophilic

culture pH

@refabilitytypepHPH range
66563positiveoptimum6-7
66563positivegrowth6-9alkaliphile

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
66563aerobe
67771aerobe

nutrition type

  • @ref: 66563
  • type: chemoheterotroph

spore formation

  • @ref: 66563
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
66563NaClpositivegrowth0-8 %
66563NaClpositiveoptimum0-3 %

observation

  • @ref: 66563
  • observation: Positive for poly-b-hydroxy-butyrate accumulation

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6656317057cellobiose-aerobic growth
6656317634D-glucose-aerobic growth
6656353423tween 40-aerobic growth
6656363150D-rhamnose-aerobic growth
6656312936D-galactose+aerobic growth
6656315824D-fructose+aerobic growth
6656315963ribitol+aerobic growth
6656316024D-mannose+aerobic growth
6656316634raffinose+aerobic growth
6656316899D-mannitol+aerobic growth
6656317306maltose+aerobic growth
6656317924D-sorbitol+aerobic growth
6656317992sucrose+aerobic growth
6656323652dextrin+aerobic growth
6656327082trehalose+aerobic growth
6656353424tween 20+aerobic growth
6656353425tween 60+aerobic growth
6656353426tween 80+aerobic growth
6656327689decanoate-assimilation
6656337684mannose-assimilation
6656353258citric acid-assimilation
6656359640N-acetylglucosamine-assimilation
6656317128adipate+assimilation
6656317234glucose+assimilation
6656317306maltose+assimilation
6656318401phenylacetate+assimilation
6656322599arabinose+assimilation
6656324265gluconate+assimilation
6656325115malate+assimilation
6656329864mannitol+assimilation
665636731melezitose-builds acid from
6656315443inulin-builds acid from
6656315824D-fructose-builds acid from
6656315963ribitol-builds acid from
6656316443D-tagatose-builds acid from
6656316634raffinose-builds acid from
6656316813galactitol-builds acid from
6656316899D-mannitol-builds acid from
6656317151xylitol-builds acid from
6656317266L-sorbose-builds acid from
6656317268myo-inositol-builds acid from
6656317306maltose-builds acid from
6656317716lactose-builds acid from
6656317754glycerol-builds acid from
6656317814salicin-builds acid from
6656317924D-sorbitol-builds acid from
6656317992sucrose-builds acid from
6656318287L-fucose-builds acid from
6656318305arbutin-builds acid from
6656318333D-arabitol-builds acid from
6656318403L-arabitol-builds acid from
6656327082trehalose-builds acid from
6656327613amygdalin-builds acid from
6656328017starch-builds acid from
6656328087glycogen-builds acid from
6656332032potassium gluconate-builds acid from
6656332528turanose-builds acid from
6656343943methyl alpha-D-mannoside-builds acid from
6656359640N-acetylglucosamine-builds acid from
6656362318D-lyxose-builds acid from
6656365328L-xylose-builds acid from
6656374863methyl beta-D-xylopyranoside-builds acid from
66563320061methyl alpha-D-glucopyranoside-builds acid from
66563potassium 2-dehydro-D-gluconate-builds acid from
66563potassium 5-dehydro-D-gluconate-builds acid from
6656312936D-galactose+builds acid from
6656316024D-mannose+builds acid from
6656316988D-ribose+builds acid from
6656317057cellobiose+builds acid from
6656317108D-arabinose+builds acid from
6656317113erythritol+builds acid from
6656317634D-glucose+builds acid from
6656328053melibiose+builds acid from
6656328066gentiobiose+builds acid from
6656328847D-fucose+builds acid from
6656330849L-arabinose+builds acid from
6656362345L-rhamnose+builds acid from
6656365327D-xylose+builds acid from
66563esculin ferric citrate+builds acid from
6656317234glucose-fermentation
665634853esculin-hydrolysis
665635291gelatin-hydrolysis
6656316199urea-hydrolysis
6656317029chitin-hydrolysis
6656328017starch-hydrolysis
6656353424tween 20-hydrolysis
6656361995lecithin-hydrolysis
6656385146carboxymethylcellulose-hydrolysis
66563casein-hydrolysis
6656316991dna+hydrolysis
6656353423tween 40+hydrolysis
6656353425tween 60+hydrolysis
6656353426tween 80+hydrolysis
66563corn oil+hydrolysis
6656317632nitrate-reduction

antibiotic resistance

@refChEBImetaboliteis antibioticis sensitivesensitivity conc.is resistantresistance conc.group ID
6656328971ampicillinyesyes10 µg (disc)
6656317698chloramphenicolyesyes30 µg (disc)
6656317833gentamicinyesyes10 µg (disc)
665636104kanamycinyesyes30 µg (disc)
66563100147nalidixic acidyesyes30 µg (disc)
6656328368novobiocinyesyes30 µg (disc)
6656318208penicillin gyesyes10 Unit (disc)
6656328077rifampicinyesyes5 µg (disc)
6656317076streptomycinyesyes10 µg (disc)
6656327902tetracyclineyesyes30 µg (disc)
6656345924trimethoprimyesyes1.25 µg (disc)26
665639332sulfamethoxazoleyesyes23.75 µg (disc)26

metabolite production

@refChebi-IDmetaboliteproduction
6656330033Bacteriochlorophyll alphano
6656335581indoleno

enzymes

@refvalueactivityec
66563arginine dihydrolase-3.5.3.6
66563acid phosphatase+3.1.3.2
66563alkaline phosphatase+3.1.3.1
66563alpha-galactosidase+3.2.1.22
66563alpha-glucosidase+3.2.1.20
66563beta-galactosidase+3.2.1.23
66563catalase+1.11.1.6
66563cystine arylamidase+3.4.11.3
66563cytochrome oxidase+1.9.3.1
66563esterase (C 4)+
66563esterase Lipase (C 8)+
66563leucine arylamidase+3.4.11.1
66563naphthol-AS-BI-phosphohydrolase+
66563valine arylamidase+

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    66563C18:010
    66563C16:01.8
    66563C14:0 3OH and/or C16:1 iso I1.9
    66563C18:0 3OH1.9
    66563C10:0 3OH2.4
    66563C17:03.6
    66563C18:1 w7c75.9
  • type of FA analysis: whole cell analysis
  • incubation medium: R2A
  • agar/liquid: agar
  • incubation temperature: 25
  • incubation time: 3
  • software version: Sherlock 6.0
  • library/peak naming table: RTSBA6.00
  • system: MIS MIDI
  • cutoff value:

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitudeenrichment cultureenrichment culture durationenrichment culture temperatureisolation procedure
66563freshwater samplefreshwater spring in Maolin District of Kaohsiung CityTaiwanTWNAsia22.8919120.684R2A agar3 days25standard dilution plating method
67771From riverKaohsiung CityTaiwanTWNAsia

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Aquatic
  • Cat3: #Freshwater

taxonmaps

  • @ref: 69479
  • File name: preview.99_12196.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_1674;97_7440;98_9167;99_12196&stattab=map
  • Last taxonomy: Paracoccus
  • 16S sequence: LT223122
  • Sequence Identity:
  • Total samples: 391
  • soil counts: 17
  • aquatic counts: 32
  • animal counts: 59
  • plant counts: 283

Sequence information

16S sequences

  • @ref: 66563
  • description: Paracoccus sp. MVW-1 partial 16S rRNA gene, strain MVW-1
  • accession: LT223122
  • length: 1411
  • database: ena
  • NCBI tax ID: 1815556

Genome sequences

  • @ref: 66792
  • description: Paracoccus fontiphilus MVW-1
  • accession: GCA_017356265
  • assembly level: contig
  • database: ncbi
  • NCBI tax ID: 1815556

GC content

  • @ref: 66563
  • GC-content: 63.4
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedno87.39yes
gram-positiveno97.98yes
anaerobicno98.708yes
aerobicyes88.812yes
halophileno86.546no
spore-formingno96.624yes
thermophileno96.59no
glucose-utilyes92.966no
motileno74.442yes
glucose-fermentno89.552yes

External links

@ref: 66563

culture collection no.: BCRC 80974, LMG 29554, KCTC 52239

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny29722645Paracoccus fontiphilus sp. nov., isolated from a freshwater spring.Sheu SY, Hsieh TY, Young CC, Chen WMInt J Syst Evol Microbiol10.1099/ijsem.0.0027932018Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Fresh Water/*microbiology, Hydroxybutyrates, Natural Springs/microbiology, Nucleic Acid Hybridization, Paracoccus/*classification/genetics/isolation & purification, Phospholipids/chemistry, *Phylogeny, Pigmentation, Polyamines/chemistry, Polyesters, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Taiwan, Ubiquinone/analogs & derivatives/chemistryTranscriptome
Phylogeny33388938Paracoccus lichenicola sp. nov., Isolated from Lichen.Lang L, An DF, Jiang LQ, Li GD, Wang LS, Wang XY, Li QY, Jiang CL, Jiang YCurr Microbiol10.1007/s00284-020-02321-82021Bacterial Typing Techniques, China, DNA, Bacterial/genetics, Fatty Acids, *Lichens, *Paracoccus/genetics, Phospholipids, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNATranscriptome
Phylogeny34905098Paracoccus shandongensis sp. nov., Isolated from Activated Sludge.Gong XF, Wang F, Meng D, Liu YL, Gu PF, Fan XY, Huang ZS, Du ZJ, Li QCurr Microbiol10.1007/s00284-021-02705-42021Bacterial Typing Techniques, China, DNA, Bacterial/genetics, Fatty Acids/analysis, *Paracoccus/genetics, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *SewageTranscriptome

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
66563Shih-Yi Sheu, Tsai-Ying Hsieh, Chiu-Chung Young, Wen-Ming ChenParacoccus fontiphilus sp. nov., isolated from a freshwater spring10.1099/ijsem.0.002793IJSEM 68: 2054-2060 201829722645
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
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/