Strain identifier

BacDive ID: 18066

Type strain: Yes

Species: Parvimonas micra

Strain Designation: 3024A, 3119B

Strain history: CIP <- 1997, J.P. Carlier, Inst. Pasteur, Paris, France: strain 3119B <- A.R. Prévot: strain 3119B

NCBI tax ID(s): 411465 (strain), 33033 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 8839

BacDive-ID: 18066

DSM-Number: 20468

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-positive, coccus-shaped, human pathogen

description: Parvimonas micra 3024A is an anaerobe, mesophilic, Gram-positive human pathogen that was isolated from Human purulent pleurisy.

NCBI tax id

NCBI tax idMatching level
411465strain
33033species

strain history

@refhistory
8839<- VPI, 5464 <- A.R. Prévot, 3024A (Streptococcus micros)
67770DSM 20468 <-- VPI 5464 <-- A. R. Prévot.
120944CIP <- 1997, J.P. Carlier, Inst. Pasteur, Paris, France: strain 3119B <- A.R. Prévot: strain 3119B

doi: 10.13145/bacdive18066.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Clostridia
  • order: Eubacteriales
  • family: Peptoniphilaceae
  • genus: Parvimonas
  • species: Parvimonas micra
  • full scientific name: Parvimonas micra (Prévot 1933) Tindall and Euzéby 2006
  • synonyms

    @refsynonym
    20215Streptococcus micros
    20215Micromonas micra
    20215Peptostreptococcus micros
    20215Micromonas micros
    20215Diplococcus glycinophilus
    20215Peptococcus glycinophilus

@ref: 8839

domain: Bacteria

phylum: Firmicutes

class: Clostridia

order: Clostridiales

family: Peptoniphilaceae

genus: Parvimonas

species: Parvimonas micra

full scientific name: Parvimonas micra (Prévot 1933) Tindall and Euzéby 2006

strain designation: 3024A, 3119B

type strain: yes

Morphology

cell morphology

  • @ref: 120944
  • gram stain: positive
  • cell shape: coccus-shaped

colony morphology

@refincubation period
571652 days
120944

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8839COLUMBIA 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
8839FASTIDIOUS ANAEROBE BROTH (DSMZ Medium 1203a)yeshttps://mediadive.dsmz.de/medium/1203aName: FASTIDIOUS ANAEROBE BROTH (DSMZ Medium 1203a) Composition: Fastidious Anaerobe Basal Broth 35.4 g/l Distilled water
8839PYG MEDIUM (MODIFIED) (DSMZ Medium 104)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium104.pdf
40295MEDIUM 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)
120944CIP Medium 20yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=20

culture temp

@refgrowthtypetemperaturerange
8839positivegrowth37mesophilic
40295positivegrowth37mesophilic
57165positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
8839anaerobe
57165anaerobe

murein

  • @ref: 8839
  • murein short key: A22.01
  • type: A4ß' L-Orn-D-Asp

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6838016199urea-hydrolysis
6838029016arginine-hydrolysis
6838016024D-mannose-fermentation
6838016634raffinose-fermentation
6838017632nitrate-reduction
6838027897tryptophan-energy source

antibiotic resistance

  • @ref: 120944
  • ChEBI: 6909
  • metabolite: metronidazole
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

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

metabolite tests

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

enzymes

@refvalueactivityec
68380leucine arylamidase+3.4.11.1
68380alkaline phosphatase+3.1.3.1
68380tryptophan deaminase-4.1.99.1
68380alpha-fucosidase-3.2.1.51
68380N-acetyl-beta-glucosaminidase-3.2.1.52
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

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
8839----------------++/-+/-+/-+++++/-+/-+++
8839----------------+++-++++-++-+
8839----------------+-+-+/-++/-+/-+/-+/---+/-
8839----------------++/-+-++++-----
8839----------------+++-+++/-++++++
8839------------+---+++-++++-+++-
8839----------------++++++++++-+-

Isolation, sampling and environmental information

isolation

@refsample type
57165Human purulent pleurisy
67770Human purulent pleurisy
8839unknown source of isolation
120944Human, Purulent pleurisy

isolation source categories

Cat1Cat2Cat3
#Host#Human
#Infection#Patient
#Host Body-Site#Oral cavity and airways#Lung

taxonmaps

  • @ref: 69479
  • File name: preview.99_6422.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15784;96_1035;97_1209;98_4743;99_6422&stattab=map
  • Last taxonomy: Parvimonas micra subclade
  • 16S sequence: AY323523
  • Sequence Identity:
  • Total samples: 32922
  • soil counts: 202
  • aquatic counts: 468
  • animal counts: 32131
  • plant counts: 121

Safety information

risk assessment

@refpathogenicity humanpathogenicity animalbiosafety levelbiosafety level comment
8839yesyes2Risk group (German classification)
1209441Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Parvimonas micra ATCC 33270 16S ribosomal RNA gene, partial sequenceAF5422311414ena411465
20218Peptostreptococcus micros ATCC 33270 (Sm type) 16S rRNA gene, partial sequenceU60326323ena411465
20218Parvimonas micra strain CCUG 46357 clone 1 16S-23S ribosomal RNA intergenic spacer, partial sequenceGQ496451548ena33033
20218Parvimonas micra strain CCUG 46357 clone 2 16S-23S ribosomal RNA intergenic spacer, partial sequenceGQ496452297ena33033
20218Parvimonas micra gene for 16S ribosomal RNA, partial sequence, strain: JCM 12970AB7290721487ena33033
8839Parvimonas micra ATCC 33270 16S ribosomal RNA gene, partial sequenceAY3235231481ena411465

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Parvimonas micra NCTC11808GCA_900637905completencbi33033
66792Parvimonas micra ATCC 33270411465.10wgspatric411465
66792Parvimonas micra strain NCTC1180833033.18completepatric33033
66792Parvimonas micra ATCC 33270641380421draftimg411465
67770Parvimonas micra ATCC 33270GCA_000154405scaffoldncbi411465

GC content

@refGC-content
883927.5
6777027-29

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedno98.38no
gram-positiveyes90.915no
anaerobicyes96.373yes
aerobicno98.152yes
halophileno51.693no
spore-formingno86.532no
thermophileno98.104yes
glucose-utilyes76.119no
motileno90.641no
glucose-fermentyes59.283no

External links

@ref: 8839

culture collection no.: DSM 20468, ATCC 33270, CCUG 46357, CIP 105294, JCM 12970, NCTC 11808, VPI 5464, GIFU 7824

straininfo link

  • @ref: 87054
  • straininfo: 40421

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Pathogenicity2685068Serological studies of peptostreptococci using an indirect fluorescent antibody test.Collins ML, Falkler WA Jr, Hall ER, Graham MBJ Dent Res10.1177/002203458906801108011989Fluorescent Antibody Technique, Humans, Mouth Diseases/microbiology, Peptostreptococcus/*isolation & purificationEnzymology
Enzymology7773401Crystalline surface protein of Peptostreptococcus anaerobius.Kotiranta A, Haapasalo M, Lounatmaa K, Kari KMicrobiology (Reading)10.1099/13500872-141-5-10651995Bacterial Proteins/chemistry/isolation & purification/*ultrastructure, Blotting, Western, Cell Membrane/chemistry/ultrastructure, Electrophoresis, Gel, Two-Dimensional, Electrophoresis, Polyacrylamide Gel, Freeze Etching, Humans, Membrane Proteins/chemistry/isolation & purification/*ultrastructure, Microscopy, Electron, Peptostreptococcus/chemistry/isolation & purification/*ultrastructure, Species SpecificityPhylogeny
Pathogenicity11846852Antimicrobial effects of 2.94 microm Er:YAG laser radiation on root surfaces: an in vitro study.Folwaczny M, Mehl A, Aggstaller H, Hickel RJ Clin Periodontol10.1034/j.1600-051x.2002.290111.x2002Aggregatibacter actinomycetemcomitans/radiation effects, Analysis of Variance, Bacteria/*radiation effects, Colony Count, Microbial, Eikenella corrodens/radiation effects, Erbium, Escherichia coli/radiation effects, Humans, *Lasers, Peptostreptococcus/radiation effects, Staphylococcus aureus/radiation effects, Statistics, Nonparametric, Tooth Root/*microbiology
Metabolism17229113Hemin nutritional stress inhibits bacterial invasion of radicular dentine by two endodontic anaerobes.Love RMInt Endod J10.1111/j.1365-2591.2006.01186.x2007Bacteria, Anaerobic/*metabolism, Culture Media, Dental Pulp Cavity/*microbiology, Dentin/*microbiology, Hemin/*metabolism, Humans, Peptostreptococcus/metabolism, Prevotella intermedia/metabolismCultivation
Metabolism17949340Degradation of serine-containing oligopeptides by Peptostreptococcus micros ATCC 33270.Uematsu H, Hossain MZ, Alam T, Ikeda T, Kuvatanasuchati J, Hoshino EOral Microbiol Immunol10.1111/j.1399-302X.2007.00374.x2007Acetate Kinase, Acetates/metabolism, Acetyltransferases, Adenosine Triphosphate/biosynthesis, Ammonia/metabolism, Formate Dehydrogenases, Formates/metabolism, Humans, L-Serine Dehydratase/metabolism, Oligopeptides/*metabolism, Peptostreptococcus/enzymology/*metabolism, Phosphate Acetyltransferase, Pyruvate Synthase, Pyruvic Acid/metabolism, Serine/*metabolism, Tyrosine/metabolismEnzymology
Phylogeny19351562Collagenase production and hemolytic activity related to 16S rRNA variability among Parvimonas micra oral isolates.Ota-Tsuzuki C, Alves Mayer MPAnaerobe10.1016/j.anaerobe.2009.03.0082009Animals, *Biodiversity, Cluster Analysis, Collagenases/*biosynthesis, DNA Fingerprinting, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Elastin/metabolism, Erythrocytes/microbiology, Genotype, Gingiva/microbiology, Gram-Positive Bacteria/*classification/genetics/isolation & purification/*metabolism, Hemolysis, Humans, Periodontal Diseases/microbiology, Polymorphism, Restriction Fragment Length, RNA, Ribosomal, 16S/*genetics, RabbitsMetabolism
Enzymology22405584Antimicrobial activity of Streptococcus salivarius K12 on bacteria involved in oral malodour.Masdea L, Kulik EM, Hauser-Gerspach I, Ramseier AM, Filippi A, Waltimo TArch Oral Biol10.1016/j.archoralbio.2012.02.0112012Actinobacteria/*growth & development/isolation & purification, Administration, Oral, Bacterial Proteins/pharmacology, Bacteriocins/pharmacology, Eubacterium/growth & development/isolation & purification, Gram-Positive Bacteria/growth & development/isolation & purification, Halitosis/*microbiology/*prevention & control, Humans, In Vitro Techniques, Linear Models, Microbial Sensitivity Tests, Probiotics/*pharmacology, Streptococcus/*physiologyPhylogeny
Pathogenicity26759339In-vitro activity of sodium-hypochlorite gel on bacteria associated with periodontitis.Jurczyk K, Nietzsche S, Ender C, Sculean A, Eick SClin Oral Investig10.1007/s00784-016-1711-92016Anti-Infective Agents, Local/pharmacology, Biofilms/drug effects, Chlorhexidine/analogs & derivatives/pharmacology, Gels, In Vitro Techniques, Microbial Sensitivity Tests, Periodontal Diseases/*drug therapy/*microbiology, Sodium Hypochlorite/*pharmacology, Stem Cells
Pathogenicity28341746Leveraging sequence-based faecal microbial community survey data to identify a composite biomarker for colorectal cancer.Shah MS, DeSantis TZ, Weinmaier T, McMurdie PJ, Cope JL, Altrichter A, Yamal JM, Hollister EBGut10.1136/gutjnl-2016-3131892017Area Under Curve, Biomarkers, Tumor/*analysis, Colorectal Neoplasms/diagnosis/*microbiology, DNA, Bacterial/analysis, Feces/*microbiology, Gastrointestinal Microbiome/*genetics, Humans, RNA, Ribosomal, 16S, Sensitivity and Specificity, Surveys and QuestionnairesPhylogeny
Pathogenicity30024592The regulation of DLTA gene in bacterial growth and biofilm formation by Parvimonas micra.Liu K, Hou BXEur Rev Med Pharmacol Sci10.26355/eurrev_201807_153902018Biofilms/*growth & development, Dental Plaque/*microbiology, Humans, Lipopolysaccharides/*metabolism, Teichoic Acids/*metabolismMetabolism
Phylogeny34878380Parvimonas parva sp. nov., derived from a human genito-urinary lesion.Jansson MK, Hering S, Buhl MEJInt J Syst Evol Microbiol10.1099/ijsem.0.0051002021Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Firmicutes/*classification/isolation & purification, Humans, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Urogenital Diseases/*microbiologyPathogenicity
Pathogenicity35397605Antibacterial efficacy of peracetic acid in comparison with sodium hypochlorite or chlorhexidine against Enterococcus faecalis and Parvimonas micra.Briseno-Marroquin B, Callaway A, Shalamzari NG, Wolf TGBMC Oral Health10.1186/s12903-022-02148-82022Agar, Anti-Bacterial Agents/pharmacology/therapeutic use, Chlorhexidine/pharmacology/therapeutic use, Dental Pulp Cavity, *Enterococcus faecalis, Firmicutes, Humans, Peracetic Acid/pharmacology, Root Canal Irrigants/pharmacology/therapeutic use, *Sodium Hypochlorite/pharmacology/therapeutic use
Pathogenicity35416697Development of the First Tractable Genetic System for Parvimonas micra, a Ubiquitous Pathobiont in Human Dysbiotic Disease.Higashi DL, McGuire S, Abdelrahman YM, Zou Z, Qin H, Anderson D, Palmer EA, Kreth J, Merritt JMicrobiol Spectr10.1128/spectrum.00465-222022Carcinogenesis, *Firmicutes/genetics, *Gram-Positive Bacteria, Humans

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
8839Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20468)https://www.dsmz.de/collection/catalogue/details/culture/DSM-20468
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
40295Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/17297
57165Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 46357)https://www.ccug.se/strain?id=46357
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/
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
87054Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID40421.1StrainInfo: A central database for resolving microbial strain identifiers
120944Curators of the CIPCollection of Institut Pasteur (CIP 105294)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105294