Strain identifier

BacDive ID: 12508

Type strain: Yes

Species: Porphyromonas levii

Strain Designation: LEV

Strain history: CCUG 34320 <-- NCTC 11028 <-- M. Lev strain LEV 1.

NCBI tax ID(s): 1122973 (strain), 28114 (species)

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General

@ref: 16711

BacDive-ID: 12508

DSM-Number: 23370

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-negative, human pathogen

description: Porphyromonas levii LEV is an anaerobe, mesophilic, Gram-negative human pathogen that was isolated from bovine rumen.

NCBI tax id

NCBI tax idMatching level
1122973strain
28114species

strain history

@refhistory
16711<- CCUG; CCUG 34320 <- R. J. Owen, NCTC; NCTC 11028 <- M. Lev, Albert Einstein College of Medicine; New York;
67770CCUG 34320 <-- NCTC 11028 <-- M. Lev strain LEV 1.

doi: 10.13145/bacdive12508.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Bacteroidia
  • order: Bacteroidales
  • family: Porphyromonadaceae
  • genus: Porphyromonas
  • species: Porphyromonas levii
  • full scientific name: Porphyromonas levii (Johnson and Holdeman 1983 ex Holdeman et al. 1977) Shah et al. 1995

  • synonyms

    • @ref: 20215
    • synonym: Bacteroides levii

@ref: 16711

domain: Bacteria

phylum: Bacteroidetes

class: Bacteroidia

order: Bacteroidales

family: Porphyromonadaceae

genus: Porphyromonas

species: Porphyromonas levii

full scientific name: Porphyromonas levii (Johnson and Holdeman 1983) Shah et al. 1995 emend. Hahnke et al. 2016

strain designation: LEV

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • gram stain: negative
  • confidence: 99.998

colony morphology

  • @ref: 16711
  • type of hemolysis: gamma
  • incubation period: 1-2 days

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
16711COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)yeshttps://mediadive.dsmz.de/medium/693Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base
16711CHOPPED MEAT MEDIUM (DSMZ Medium 78)yeshttps://mediadive.dsmz.de/medium/78Name: CHOPPED MEAT MEDIUM (DSMZ Medium 78; with strain-specific modifications) Composition: Ground beef 500.0 g/l Casitone 30.0 g/l Agar 15.0 g/l Ethanol 9.5 g/l (optional) Yeast extract 5.0 g/l K2HPO4 5.0 g/l L-Cysteine HCl 0.5 g/l Haemin 0.005 g/l Resazurin 0.001 g/l Vitamin K3 0.0005 g/l (optional) Vitamin K1 (optional) NaOH (optional) Distilled water

culture temp

@refgrowthtypetemperaturerange
16711positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
16711anaerobe
69480anaerobe99.622

spore formation

@refspore formationconfidence
69481no100
69480no99.999

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836727082trehalose-builds acid from
6836762345L-rhamnose-builds acid from
6836730911sorbitol-builds acid from
6836716634raffinose-builds acid from
683676731melezitose-builds acid from
6836716024D-mannose-builds acid from
6836717057cellobiose-builds acid from
6836717754glycerol-builds acid from
683674853esculin-hydrolysis
683675291gelatin+hydrolysis
6836730849L-arabinose-builds acid from
6836765327D-xylose-builds acid from
6836717814salicin-builds acid from
6836717306maltose-builds acid from
6836717992sucrose-builds acid from
6836717716lactose-builds acid from
6836716899D-mannitol-builds acid from
6836717634D-glucose-builds acid from
6836716199urea-hydrolysis
6838016199urea-hydrolysis
6838029016arginine-hydrolysis
6838016024D-mannose-fermentation
6838016634raffinose-fermentation
6838029985L-glutamate-degradation
6838017632nitrate-reduction
6838027897tryptophan-energy source

metabolite production

  • @ref: 68380
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 68380
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
16711catalase-1.11.1.6
16711cytochrome-c oxidase-1.9.3.1
68380serine arylamidase-
68380glutamyl-glutamate arylamidase+
68380histidine arylamidase-
68380alanine arylamidase+3.4.11.2
68380pyrrolidonyl arylamidase-3.4.19.3
68380leucine arylamidase-3.4.11.1
68380leucyl glycin arylamidase+3.4.11.1
68380L-arginine arylamidase-
68380alkaline phosphatase+3.1.3.1
68380tryptophan deaminase-4.1.99.1
68380alpha-fucosidase-3.2.1.51
68380glutamate decarboxylase-4.1.1.15
68380beta-glucuronidase-3.2.1.31
68380alpha-arabinosidase-3.2.1.55
68380beta-glucosidase-3.2.1.21
68380alpha-glucosidase-3.2.1.20
68380beta-Galactosidase 6-phosphate-
68380beta-galactosidase+3.2.1.23
68380alpha-galactosidase-3.2.1.22
68380arginine dihydrolase-3.5.3.6
68380urease-3.5.1.5
68367beta-glucosidase-3.2.1.21
68367gelatinase+
68367urease-3.5.1.5

API 20A

@refUREGLUMANLACSACMALSALXYLARAGELESCGLYCELMNEMLZRAFSORRHATRE
16711---------+---------

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
16711---+------------+-+/-++/---+/-++/--+-
16711---+-----+------+--+----+--+-

Isolation, sampling and environmental information

isolation

@refsample type
16711bovine rumen
67770Bovine rumen

isolation source categories

Cat1Cat2Cat3
#Host#Mammals#Bovinae (Cow, Cattle)
#Host Body-Site#Organ#Rumen

taxonmaps

  • @ref: 69479
  • File name: preview.99_63835.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15883;96_27800;97_34998;98_45168;99_63835&stattab=map
  • Last taxonomy: Porphyromonas levii subclade
  • 16S sequence: FJ792536
  • Sequence Identity:
  • Total samples: 8580
  • soil counts: 894
  • aquatic counts: 607
  • animal counts: 6931
  • plant counts: 148

Safety information

risk assessment

  • @ref: 16711
  • pathogenicity human: yes
  • pathogenicity animal: yes
  • biosafety level: 2
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Porphyromonas levii gene for 16S ribosomal RNA, partial sequence, strain: JCM 13866AB5476641495ena1122973
20218Porphyromonas levii strain ATCC 29147 16S-23S ribosomal RNA intergenic spacer, partial sequenceAY546480852ena1122973
20218Porphyromonas levii strain ATCC 29147 16S ribosomal RNA gene, partial sequenceFJ7925361375ena1122973
16711Porphyromonas levii ATCC 29147 16S ribosomal RNA gene, complete sequenceL164931476ena28114

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Porphyromonas levii DSM 233701122973.3wgspatric1122973
66792Porphyromonas levii DSM 233702515154110draftimg1122973
67770Porphyromonas levii DSM 23370GCA_000379925scaffoldncbi1122973

GC content

@refGC-contentmethod
1671146
1671145.7sequence analysis
6777045-46thermal denaturation, midpoint method (Tm)
6777046-48

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno91.444no
flagellatedno97.088no
gram-positiveno96.581no
anaerobicyes99.052no
aerobicno97.577no
halophileno88.255no
spore-formingno96.593no
thermophileno97.745no
glucose-utilyes78.963no
glucose-fermentno53.05no

External links

@ref: 16711

culture collection no.: DSM 23370, ATCC 29147, CCUG 34320, JCM 13866, NCTC 11028, ACM 5042, CCUG 21027, HAMBI 467, VPI 10450, VPI 3300

straininfo link

  • @ref: 81727
  • straininfo: 40353

literature

  • topic: Phylogeny
  • Pubmed-ID: 16145091
  • title: Porphyromonas somerae sp. nov., a pathogen isolated from humans and distinct from porphyromonas levii.
  • authors: Summanen PH, Durmaz B, Vaisanen ML, Liu C, Molitoris D, Eerola E, Helander IM, Finegold SM
  • journal: J Clin Microbiol
  • DOI: 10.1128/JCM.43.9.4455-4459.2005
  • year: 2005
  • mesh: Animals, Bacterial Typing Techniques, Bacteroidaceae Infections/*microbiology, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Humans, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Porphyromonas/*classification/genetics/*isolation & purification/metabolism, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA
  • topic2: Pathogenicity

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
16711Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23370)https://www.dsmz.de/collection/catalogue/details/culture/DSM-23370
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68367Automatically annotated from API 20A
68380Automatically annotated from API rID32A
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
81727Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID40353.1StrainInfo: A central database for resolving microbial strain identifiers