Strain identifier

BacDive ID: 133123

Type strain: Yes

Species: Pedobacter lusitanus

Strain Designation: NL19

NCBI tax ID(s): 1503925 (species)

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General

@ref: 25303

BacDive-ID: 133123

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

description: Pedobacter lusitanus NL19 is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from sludge collected from a deactivated uranium; mine.

NCBI tax id

  • NCBI tax id: 1503925
  • Matching level: species

doi: 10.13145/bacdive133123.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Sphingobacteriia
  • order: Sphingobacteriales
  • family: Sphingobacteriaceae
  • genus: Pedobacter
  • species: Pedobacter lusitanus
  • full scientific name: Pedobacter lusitanus Covas et al. 2017

@ref: 25303

domain: Bacteria

phylum: Bacteroidetes

class: Sphingobacteriia

order: Sphingobacteriales

family: Sphingobacteriaceae

genus: Pedobacter

species: Pedobacter lusitanus

strain designation: NL19

type strain: yes

Morphology

cell morphology

  • @ref: 25303
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: no

colony morphology

@refcolony colormedium used
25303light yellowNA
25303light yellowTSA
25303light yellowMacConkey agar
25303pale white shinyR2A
25303pale white shinyminimal medium

Culture and growth conditions

culture medium

@refnamegrowth
25303Nutrient agar (NA)yes
25303Trypticase Soy Agar (TSA)yes
25303MacConkey agaryes
25303Reasoner's 2A agar (R2A)yes
25303minimal mediumyes
25303TSByes

culture temp

@refgrowthtypetemperature
25303positivegrowth4-30
25303positiveoptimum18-30

culture pH

  • @ref: 25303
  • ability: positive
  • type: optimum
  • pH: 6-8

Physiology and metabolism

oxygen tolerance

  • @ref: 25303
  • oxygen tolerance: aerobe

halophily

@refsalttested relationconcentration
25303NaClmaximum2 %(w/v)
25303NaCloptimum0.5 %(w/v)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2530317128adipate-assimilation
2530315963ribitol-fermentation
2530322599arabinose-fermentation
2530317108D-arabinose-assimilation
2530317634D-glucose-fermentation
2530327689decanoate-assimilation
2530317895L-tyrosine-hydrolysis
25303L-xanthine-hydrolysis
2530317716lactose-fermentation
2530325115malate-assimilation
2530317632nitrate-reduction
2530318401phenylacetate-assimilation
2530332032potassium gluconate-assimilation
2530353258sodium citrate-assimilation
2530330911sorbitol-fermentation
2530327613amygdalin+builds acid from
25303casein+hydrolysis
2530317057cellobiose+builds acid from
2530315824D-fructose+builds acid from
2530312936D-galactose+builds acid from
2530317634D-glucose+builds acid from
2530317634D-glucose+assimilation
2530316899D-mannitol+assimilation
2530316899D-mannitol+builds acid from
2530316024D-mannose+assimilation
2530316024D-mannose+builds acid from
253034853esculin+hydrolysis
25303esculin ferric citrate+builds acid from
253035291gelatin+hydrolysis
2530318287L-fucose+builds acid from
2530317716lactose+builds acid from
2530317306maltose+assimilation
2530317306maltose+builds acid from
2530328053melibiose+builds acid from
2530343943methyl alpha-D-mannoside+builds acid from
25303506227N-acetylglucosamine+assimilation
2530317814salicin+builds acid from
2530328017starch+hydrolysis
2530317992sucrose+builds acid from
2530327082trehalose+builds acid from
2530353424tween 20+hydrolysis
2530353426tween 80+hydrolysis

antibiotic resistance

@refChEBIgroup IDmetaboliteis antibioticis sensitivesensitivity conc.is resistantresistance conc.
253034592426trimethoprimyesyes25 µg
25303933226sulfamethoxazoleyesyes25 µg
25303267610amoxicillinyesyes30 µg
253034894710clavulanic acidyesyes30 µg
2530328971ampicillinyesyes10 µg
25303161680aztreonamyesyes30 µg
25303478164cefepimeyesyes30 µg
25303209807cefoxitinyesyes30 µg
253033515cefuroximeyesyes30 µg
25303100241ciprofloxacinyesyes5 µg
253033508ceftazidimeyesyes10 µg
25303colistin sulfateyesyes10 µg
2530317833gentamicinyesyes10 µg
253037528netilmycinyesyes10 µg
253038232piperacillinyesyes30 µg
25303823222piperacillinyesyes30 µg
25303942122tazobactamyesyes60 µg
2530317076streptomycinyesyes10 µg
253032637amikacinyesyes30 µg
2530317698chloramphenicolyesyes30 µg
2530327644chlortetracyclinyesyes30 µg
2530318208penicillin gyesyes10 µg
2530328001vancomycinyesyes30 µg
2530371415nitrofurantoinyesyes100 µg
253039587ticarcillinyesyes75 µg
2530328864tobramycinyesyes10 µg
25303471744imipenemyesyes10 µg

metabolite production

@refChebi-IDmetaboliteproduction
2530317997dinitrogenno
2530316136hydrogen sulfideno
2530335581indoleno

enzymes

@refvalueactivityec
25303acid phosphatase+3.1.3.2
25303alkaline phosphatase+3.1.3.1
25303alpha-chymotrypsin-3.4.21.1
25303alpha-fucosidase+3.2.1.51
25303alpha-galactosidase-3.2.1.22
25303alpha-glucosidase+3.2.1.20
25303alpha-mannosidase-3.2.1.24
25303arginine dihydrolase-3.5.3.6
25303beta-galactosidase+3.2.1.23
25303beta-glucosidase-3.2.1.21
25303beta-glucuronidase-3.2.1.31
25303catalase+1.11.1.6
25303cystine arylamidase-3.4.11.3
25303cytochrome oxidase+1.9.3.1
25303esterase (C 4)+
25303esterase Lipase (C 8)+
25303leucine arylamidase+3.4.11.1
25303lipase (C 14)-
25303N-acetyl-beta-glucosaminidase+3.2.1.52
25303naphthol-AS-BI-phosphohydrolase+
25303trypsin-3.4.21.4
25303urease-3.5.1.5
25303valine arylamidase+

fatty acid profile

  • fatty acids

    @reffatty acidpercentageSD
    25303C13:0 anteiso0.090.01
    25303C15:0 anteiso2.360.01
    25303C17:0 anteiso0.280.01
    25303C10:00.080.01
    25303C10:0 3OH0.110.01
    25303C10:10.150.01
    25303C12:0 2OH0.140.01
    25303C12:0 3OH0.270.01
    25303C14:00.770.01
    25303C14:0 2OH0.140.01
    25303C14:0 3OH0.130.01
    25303C14:1ω5c18.780.01
    25303C15:00.520.02
    25303C15:1ω5c0.050.01
    25303C16:04.010.01
    25303C16:1ω5t0.10.01
    25303C16:1ω7c46.880.02
    25303C17:00.180.01
    25303C18:00.080.01
    25303C18:1ω7c0.380.01
    25303C4:08.30.03
    25303C6:00.890.06
    25303C8:00.850.02
    25303Cyclo-C170.360.01
    25303C14:0 iso0.20.01
    25303C15:0 iso 3OH1.840.01
    25303C16:0 iso0.90.07
    25303C17:0 iso6.740.02
    25303C17:0 iso 2OH0.080.01
    25303C18:0 iso0.110.01
  • type of FA analysis: whole cell analysis
  • incubation medium: R2V
  • incubation temperature: 20
  • incubation time: 2
  • system: MIS MIDI

Isolation, sampling and environmental information

isolation

  • @ref: 25303
  • sample type: sludge collected from a deactivated uranium mine
  • geographic location: Quinta do Bispo, District of Viseu, Portugal
  • country: Portugal
  • origin.country: PRT
  • continent: Europe
  • latitude: 40
  • longitude: -7

isolation source categories

Cat1Cat2Cat3
#Engineered#Other#Mine
#Environmental#Terrestrial#Mud (Sludge)

taxonmaps

  • @ref: 69479
  • File name: preview.99_3734.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_115;96_319;97_355;98_401;99_3734&stattab=map
  • Last taxonomy: Pedobacter lusitanus
  • 16S sequence: KJ579161
  • Sequence Identity:
  • Total samples: 1719
  • soil counts: 606
  • aquatic counts: 200
  • animal counts: 282
  • plant counts: 631

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
2530316S rRNA gene sequencesKJ5791611520ena1503925
25303Pedobacter sp. NL19 clone 1 16S ribosomal RNA gene, partial sequence; tRNA-Ile and tRNA-Ala genes, complete sequence; and 23S ribosomal RNA gene, partial sequenceKT932318874ena1503925
25303Pedobacter sp. NL19 clone 2 16S ribosomal RNA gene, partial sequence; tRNA-Ile and tRNA-Ala genes, complete sequence; and 23S ribosomal RNA gene, partial sequenceKT932319928ena1503925

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pedobacter lusitanus NL19GCA_000832545contigncbi1503925
66792Pedobacter lusitanus NL192639762777draftimg1503925

GC content

  • @ref: 25303
  • GC-content: 40.8
  • method: high performance liquid chromatography (HPLC)

External links

@ref: 25303

culture collection no.: LMG 29220, CECT 9028

literature

  • topic: Phylogeny
  • Pubmed-ID: 28109203
  • title: Pedobacter lusitanus sp. nov., isolated from sludge of a deactivated uranium mine.
  • authors: Covas C, Caetano T, Cruz A, Santos T, Dias L, Klein G, Abdulmawjood A, Rodriguez-Alcala LM, Pimentel LL, Gomes A, Freitas AC, Garcia-Serrano A, Fontecha J, Mendo S
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.001814
  • year: 2017
  • mesh: Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, DNA, Ribosomal Spacer/genetics, Fatty Acids/chemistry, Genes, Bacterial, *Mining, Nucleic Acid Hybridization, Pedobacter/*classification/genetics/isolation & purification, Phospholipids/chemistry, *Phylogeny, Portugal, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sewage/*microbiology, Sphingolipids, *Uranium, Vitamin K 2/analogs & derivatives/chemistry
  • topic2: Transcriptome

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
25303C. C. Covas, T.,Cruz, A.,Santos, T.,Dias, L.,Klein, G.,Abdulmawjood, A.,Rodríguez-Alcalá, L. M.,Pimentel, L. L.,Gomes, A.,Freitas, A. C.,Garcia-Serrano, A.,Fontecha, J.,Mendo, S.Pedobacter lusitanus sp. nov., isolated from sludge of a deactivated uranium mine10.1099/ijsem.0.001814IJSEM 67: 1339-1348 201728109203
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
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/