Strain identifier

BacDive ID: 12534

Type strain: Yes

Species: Prevotella melaninogenica

Strain Designation: B282

Strain history: CIP <- 1997, J. P. Carlier, inst. Pasteur, Paris, France: strain AIP 10205 <- ATCC <- LV. Holdeman: strain VPI 4196, Bacteroides melaninogenicus subsp. melaninogenicus <- S. Finegold: strain B282

NCBI tax ID(s): 553174 (strain), 28132 (species)

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General

@ref: 2979

BacDive-ID: 12534

DSM-Number: 7089

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

description: Prevotella melaninogenica B282 is an anaerobe, mesophilic human pathogen that was isolated from sputum.

NCBI tax id

NCBI tax idMatching level
553174strain
28132species

strain history

@refhistory
2979<- ATCC <- L.V. Holdeman, VPI 2381 <- S. Finegold, B282
67770ATCC 25845 <-- L. V. Holdeman VPI 2381 <-- S. Finegold B282.
120882CIP <- 1997, J. P. Carlier, inst. Pasteur, Paris, France: strain AIP 10205 <- ATCC <- LV. Holdeman: strain VPI 4196, Bacteroides melaninogenicus subsp. melaninogenicus <- S. Finegold: strain B282

doi: 10.13145/bacdive12534.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Bacteroidia
  • order: Bacteroidales
  • family: Prevotellaceae
  • genus: Prevotella
  • species: Prevotella melaninogenica
  • full scientific name: Prevotella melaninogenica (Oliver and Wherry 1921) Shah and Collins 1990

  • synonyms

    @refsynonym
    20215Bacterium melaninogenicum
    20215Bacteroides melaninogenicus

@ref: 2979

domain: Bacteria

phylum: Bacteroidetes

class: Bacteroidia

order: Bacteroidales

family: Prevotellaceae

genus: Prevotella

species: Prevotella melaninogenica

full scientific name: Prevotella melaninogenica (Oliver and Wherry 1921) Shah and Collins 1990 emend. Wu et al. 1992 emend. Hahnke et al. 2016

strain designation: B282

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no93.927
6948099.999negative
120882nonegativerod-shaped

colony morphology

  • @ref: 2979
  • incubation period: 2-3 days

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
2979COLUMBIA 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
2979PYG MEDIUM (MODIFIED) (DSMZ Medium 104)yeshttps://mediadive.dsmz.de/medium/104Name: PYG MEDIUM (modified) (DSMZ Medium 104) Composition: Yeast extract 10.0 g/l Peptone 5.0 g/l Trypticase peptone 5.0 g/l Beef extract 5.0 g/l Glucose 5.0 g/l L-Cysteine HCl x H2O 0.5 g/l NaHCO3 0.4 g/l NaCl 0.08 g/l K2HPO4 0.04 g/l KH2PO4 0.04 g/l MgSO4 x 7 H2O 0.02 g/l CaCl2 x 2 H2O 0.01 g/l Hemin 0.005 g/l Ethanol 0.0038 g/l Resazurin 0.001 g/l Tween 80 Vitamin K1 NaOH Distilled water
40310MEDIUM 20 - for Anaerobic bacteriayesAgar (15.000 g);Glucose (5.000 g);Yeast extract (20.000 g);Tryptone (30.000 g);Cysteine hydrochloride (0.500 g);distilled water (1000.000 ml);Hemin solution -M00149 (25.000 ml)
120882CIP Medium 20yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=20

culture temp

@refgrowthtypetemperaturerange
2979positivegrowth37mesophilic
40310positivegrowth37mesophilic
44814positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
2979anaerobe
44814anaerobe
69480anaerobe99.364
120882anaerobe

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
6836727897tryptophan-energy source
12088217632nitrate-reduction
12088216301nitrite-reduction
6838016199urea-hydrolysis
6838029016arginine-hydrolysis
6838029985L-glutamate-degradation
6838017632nitrate-reduction
6838027897tryptophan-energy source

metabolite production

@refChebi-IDmetaboliteproduction
6836735581indoleno
12088235581indoleno
6838035581indoleno

metabolite tests

@refChebi-IDmetaboliteindole test
6838035581indole-
6836735581indole-

enzymes

@refvalueactivityec
68380serine arylamidase-
68380glutamyl-glutamate arylamidase+
68380glycin arylamidase-
68380alanine arylamidase+3.4.11.2
68380tyrosine arylamidase-
68380pyrrolidonyl arylamidase-3.4.19.3
68380leucine arylamidase-3.4.11.1
68380phenylalanine arylamidase-
68380leucyl glycin arylamidase+3.4.11.1
68380proline-arylamidase-3.4.11.5
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
68380arginine dihydrolase-3.5.3.6
68380urease-3.5.1.5
68367beta-glucosidase-3.2.1.21
68367gelatinase-
68367urease-3.5.1.5
120882oxidase-
120882catalase-1.11.1.6
120882urease-3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)-
68382esterase lipase (C 8)-
68382lipase (C 14)-
68382leucine arylamidase-3.4.11.1
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase+3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase+3.2.1.20
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase+3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
120882-+--------++-+-+-+-+

API 20A

@refINDUREGLUMANLACSACMALSALXYLARAGELESCGLYCELMNEMLZRAFSORRHATRE
2979--+-+++-------+-+---

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
2979--+/-+++---+---+--++-+----+-++-
2979--++++---+/--+-+--++-+----+--+-
2979--++++---+-+-+--++-+----+--+-
2979--++++---+++-+--++-+----+--+-

Isolation, sampling and environmental information

isolation

@refsample type
2979sputum
44814Sputum
67770Sputum
120882Sputum

isolation source categories

  • Cat1: #Host Body Product
  • Cat2: #Fluids
  • Cat3: #Sputum

taxonmaps

  • @ref: 69479
  • File name: preview.99_2177.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_44;96_87;97_173;98_1700;99_2177&stattab=map
  • Last taxonomy: Prevotella melaninogenica
  • 16S sequence: AY323525
  • Sequence Identity:
  • Total samples: 36993
  • soil counts: 254
  • aquatic counts: 495
  • animal counts: 36074
  • plant counts: 170

Safety information

risk assessment

@refpathogenicity humanpathogenicity animalbiosafety levelbiosafety level comment
2979yesyes2Risk group (German classification)
1208822Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Prevotella melaninogenica gene for 16S ribosomal RNA, partial sequence, strain: JCM 6325AB5476931480ena553174
20218Prevotella melaninogenica strain ATCC 25845 16S-23S ribosomal RNA intergenic spacer, partial sequenceAY546491523ena553174
20218Prevotella melaninogenica ATCC 25845 16S ribosomal RNA gene, complete sequenceL164691478ena28132
2979Prevotella melaninogenica 16S ribosomal RNA gene, partial sequenceAY3235251506ena553174
67770Prevotella melaninogenica ATCC 43982 16S ribosomal RNA gene, complete sequenceL164701473ena28132

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Prevotella melaninogenica ATCC 25845GCA_000144405completencbi553174
66792Prevotella melaninogenica ATCC 25845553174.6completepatric553174
66792Prevotella melaninogenica ATCC 25845648028051completeimg553174
66792Prevotella melaninogenica strain FDAARGOS_156628132.361completepatric28132
66792Prevotella melaninogenica strain FDAARGOS_156628132.350completepatric28132

GC content

  • @ref: 2979
  • GC-content: 41.0
  • method: sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno92.768no
flagellatedno96.592no
gram-positiveno97.246no
anaerobicyes97.802yes
aerobicno98.314yes
halophileno81.06no
spore-formingno95.745no
thermophileno98.277yes
glucose-utilyes88.482no
glucose-fermentyes58.937no

External links

@ref: 2979

culture collection no.: DSM 7089, ATCC 25845, JCM 6325, CCUG 4944 B, VPI 4196, BCRC 10622, CIP 105346, KCTC 3689, NCTC 12963, VPI 15087, AIP 10205

straininfo link

  • @ref: 81751
  • straininfo: 45775

literature

topicPubmed-IDtitleauthorsjournalyearmeshtopic2DOI
Metabolism9345789Fermentation product analysis in the identification of black-pigmented bacteria from periodontitis.Takada K, Hirasawa MMicrobios1997Antibodies, Bacterial/analysis/immunology, Antigens, Bacterial/analysis/immunology, Bacteriological Techniques, Chromatography, Gas, Culture Media/*analysis/metabolism, Electrophoresis, Polyacrylamide Gel, Fatty Acids/*analysis/metabolism, Fermentation, Gram-Negative Anaerobic Bacteria/growth & development/immunology/*metabolism, Humans, Immunodiffusion, Periodontitis/*microbiologyEnzymology
Pathogenicity10023261Inflammatory cytokine production and specific antibody responses against possible causative bacteria in patients with multilesional periapical periodontitis.Matsushita K, Tajima T, Tomita K, Abeyama K, Maruyama I, Takada H, Nagaoka SJ Endod1998Aggregatibacter actinomycetemcomitans/immunology, Antibodies, Bacterial/analysis/blood, Cytokines/*biosynthesis/blood/immunology, Fusobacterium nucleatum/immunology, Humans, Immunoglobulin A/blood, Immunoglobulin A, Secretory/analysis, Inflammation Mediators/blood/immunology/*metabolism, Periapical Periodontitis/*immunology/*microbiology, Porphyromonas/immunology, Prevotella/immunology, Saliva/immunologyBiotechnology10.1016/S0099-2399(98)80009-5
Pathogenicity10530260An evaluation of the action of different root canal irrigants on facultative aerobic-anaerobic, obligate anaerobic, and microaerophilic bacteria.D'Arcangelo C, Varvara G, De Fazio PJ Endod1999Anti-Infective Agents, Local/administration & dosage/*pharmacology, Bacteria, Anaerobic/*drug effects, Cetrimonium, Cetrimonium Compounds/administration & dosage/pharmacology, Chlorhexidine/administration & dosage/pharmacology, Colony Count, Microbial, Dose-Response Relationship, Drug, Edetic Acid/administration & dosage/pharmacology, Root Canal Irrigants/administration & dosage/*pharmacology, Sodium Hypochlorite/administration & dosage/pharmacology10.1016/S0099-2399(06)81170-2
Pathogenicity16369381Serum antibodies to oral anaerobic bacteria in patients with rheumatoid arthritis.Ogrendik M, Kokino S, Ozdemir F, Bird PS, Hamlet SMedGenMed2005Antibodies, Bacterial/*blood, Arthritis, Rheumatoid/*immunology/*microbiology, Australia, Bacteria, Anaerobic/*immunology, Female, Humans, Immunoglobulin G/*blood, Male, Middle Aged, Periodontitis/*immunology/*microbiology, Turkey505458
Phylogeny19931406The identification of genes specific to Prevotella intermedia and Prevotella nigrescens using genomic subtractive hybridization.Masakiyo Y, Yoshida A, Shintani Y, Takahashi Y, Ansai T, Takehara TAnaerobe2009Acyltransferases/*genetics, DNA Transposable Elements/genetics, Genes, Bacterial, Nucleic Acid Hybridization/methods, Periodontitis/microbiology, Prevotella intermedia/*genetics/pathogenicity, Prevotella nigrescens/enzymology/*genetics, Site-Specific DNA-Methyltransferase (Adenine-Specific)/genetics, Species Specificity, Virulence/geneticsEnzymology10.1016/j.anaerobe.2009.11.003
Phylogeny23793857Prevotella jejuni sp. nov., isolated from the small intestine of a child with coeliac disease.Hedberg ME, Israelsson A, Moore ERB, Svensson-Stadler L, Wai SN, Pietz G, Sandstrom O, Hernell O, Hammarstrom ML, Hammarstrom SInt J Syst Evol Microbiol2013Acetic Acid/metabolism, Bacterial Typing Techniques, Base Composition, Celiac Disease/*microbiology, Cell Line, Tumor, Child, DNA, Bacterial/genetics, DNA-Directed RNA Polymerases/genetics, Epithelial Cells/microbiology, Fatty Acids/chemistry, Female, Humans, Intestine, Small/cytology/*microbiology, Molecular Sequence Data, *Phylogeny, Prevotella/*classification/genetics/isolation & purification, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Succinic Acid/metabolism, SwedenMetabolism10.1099/ijs.0.052647-0

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
2979Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 7089)https://www.dsmz.de/collection/catalogue/details/culture/DSM-7089
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
40310Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/17355
44814Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 4944 B)https://www.ccug.se/strain?id=4944
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68367Automatically annotated from API 20A
68380Automatically annotated from API rID32A
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
81751Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID45775.1StrainInfo: A central database for resolving microbial strain identifiers
120882Curators of the CIPCollection of Institut Pasteur (CIP 105346)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105346