Strain identifier
BacDive ID: 18066
Type strain:
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)
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 id | Matching level |
---|---|
411465 | strain |
33033 | species |
strain history
@ref | history |
---|---|
8839 | <- VPI, 5464 <- A.R. Prévot, 3024A (Streptococcus micros) |
67770 | DSM 20468 <-- VPI 5464 <-- A. R. Prévot. |
120944 | CIP <- 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
@ref synonym 20215 Streptococcus micros 20215 Micromonas micra 20215 Peptostreptococcus micros 20215 Micromonas micros 20215 Diplococcus glycinophilus 20215 Peptococcus 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
@ref | incubation period |
---|---|
57165 | 2 days |
120944 |
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
8839 | COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) | yes | https://mediadive.dsmz.de/medium/693 | Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base |
8839 | FASTIDIOUS ANAEROBE BROTH (DSMZ Medium 1203a) | yes | https://mediadive.dsmz.de/medium/1203a | Name: FASTIDIOUS ANAEROBE BROTH (DSMZ Medium 1203a) Composition: Fastidious Anaerobe Basal Broth 35.4 g/l Distilled water |
8839 | PYG MEDIUM (MODIFIED) (DSMZ Medium 104) | yes | https://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium104.pdf | |
40295 | MEDIUM 20 - for Anaerobic bacteria | yes | Agar (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) | |
120944 | CIP Medium 20 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=20 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
8839 | positive | growth | 37 | mesophilic |
40295 | positive | growth | 37 | mesophilic |
57165 | positive | growth | 37 | mesophilic |
67770 | positive | growth | 37 | mesophilic |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
8839 | anaerobe |
57165 | anaerobe |
murein
- @ref: 8839
- murein short key: A22.01
- type: A4ß' L-Orn-D-Asp
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
68380 | 16199 | urea | - | hydrolysis |
68380 | 29016 | arginine | - | hydrolysis |
68380 | 16024 | D-mannose | - | fermentation |
68380 | 16634 | raffinose | - | fermentation |
68380 | 17632 | nitrate | - | reduction |
68380 | 27897 | tryptophan | - | 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
@ref | value | activity | ec |
---|---|---|---|
68380 | leucine arylamidase | + | 3.4.11.1 |
68380 | alkaline phosphatase | + | 3.1.3.1 |
68380 | tryptophan deaminase | - | 4.1.99.1 |
68380 | alpha-fucosidase | - | 3.2.1.51 |
68380 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68380 | beta-glucuronidase | - | 3.2.1.31 |
68380 | alpha-arabinosidase | - | 3.2.1.55 |
68380 | beta-glucosidase | - | 3.2.1.21 |
68380 | alpha-glucosidase | - | 3.2.1.20 |
68380 | beta-Galactosidase 6-phosphate | - | |
68380 | beta-galactosidase | - | 3.2.1.23 |
68380 | alpha-galactosidase | - | 3.2.1.22 |
68380 | arginine dihydrolase | - | 3.5.3.6 |
68380 | urease | - | 3.5.1.5 |
API rID32A
@ref | URE | ADH Arg | alpha GAL | beta GAL | beta GP | alpha GLU | beta GLU | alpha ARA | beta GUR | beta NAG | MNE | RAF | GDC | alpha FUC | NIT | IND | PAL | ArgA | ProA | LGA | PheA | LeuA | PyrA | TyrA | AlaA | GlyA | HisA | GGA | SerA |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
8839 | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + | +/- | +/- | +/- | + | + | + | + | +/- | +/- | + | + | + |
8839 | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + | + | + | - | + | + | + | + | - | + | + | - | + |
8839 | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + | - | + | - | +/- | + | +/- | +/- | +/- | +/- | - | - | +/- |
8839 | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + | +/- | + | - | + | + | + | + | - | - | - | - | - |
8839 | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + | + | + | - | + | + | +/- | + | + | + | + | + | + |
8839 | - | - | - | - | - | - | - | - | - | - | - | - | + | - | - | - | + | + | + | - | + | + | + | + | - | + | + | + | - |
8839 | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + | + | + | + | + | + | + | + | + | + | - | + | - |
Isolation, sampling and environmental information
isolation
@ref | sample type |
---|---|
57165 | Human purulent pleurisy |
67770 | Human purulent pleurisy |
8839 | unknown source of isolation |
120944 | Human, Purulent pleurisy |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#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
@ref | pathogenicity human | pathogenicity animal | biosafety level | biosafety level comment |
---|---|---|---|---|
8839 | yes | yes | 2 | Risk group (German classification) |
120944 | 1 | Risk group (French classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Parvimonas micra ATCC 33270 16S ribosomal RNA gene, partial sequence | AF542231 | 1414 | ena | 411465 |
20218 | Peptostreptococcus micros ATCC 33270 (Sm type) 16S rRNA gene, partial sequence | U60326 | 323 | ena | 411465 |
20218 | Parvimonas micra strain CCUG 46357 clone 1 16S-23S ribosomal RNA intergenic spacer, partial sequence | GQ496451 | 548 | ena | 33033 |
20218 | Parvimonas micra strain CCUG 46357 clone 2 16S-23S ribosomal RNA intergenic spacer, partial sequence | GQ496452 | 297 | ena | 33033 |
20218 | Parvimonas micra gene for 16S ribosomal RNA, partial sequence, strain: JCM 12970 | AB729072 | 1487 | ena | 33033 |
8839 | Parvimonas micra ATCC 33270 16S ribosomal RNA gene, partial sequence | AY323523 | 1481 | ena | 411465 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Parvimonas micra NCTC11808 | GCA_900637905 | complete | ncbi | 33033 |
66792 | Parvimonas micra ATCC 33270 | 411465.10 | wgs | patric | 411465 |
66792 | Parvimonas micra strain NCTC11808 | 33033.18 | complete | patric | 33033 |
66792 | Parvimonas micra ATCC 33270 | 641380421 | draft | img | 411465 |
67770 | Parvimonas micra ATCC 33270 | GCA_000154405 | scaffold | ncbi | 411465 |
GC content
@ref | GC-content |
---|---|
8839 | 27.5 |
67770 | 27-29 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
flagellated | no | 98.38 | no |
gram-positive | yes | 90.915 | no |
anaerobic | yes | 96.373 | yes |
aerobic | no | 98.152 | yes |
halophile | no | 51.693 | no |
spore-forming | no | 86.532 | no |
thermophile | no | 98.104 | yes |
glucose-util | yes | 76.119 | no |
motile | no | 90.641 | no |
glucose-ferment | yes | 59.283 | no |
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
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Pathogenicity | 2685068 | Serological studies of peptostreptococci using an indirect fluorescent antibody test. | Collins ML, Falkler WA Jr, Hall ER, Graham MB | J Dent Res | 10.1177/00220345890680110801 | 1989 | Fluorescent Antibody Technique, Humans, Mouth Diseases/microbiology, Peptostreptococcus/*isolation & purification | Enzymology |
Enzymology | 7773401 | Crystalline surface protein of Peptostreptococcus anaerobius. | Kotiranta A, Haapasalo M, Lounatmaa K, Kari K | Microbiology (Reading) | 10.1099/13500872-141-5-1065 | 1995 | Bacterial 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 Specificity | Phylogeny |
Pathogenicity | 11846852 | Antimicrobial effects of 2.94 microm Er:YAG laser radiation on root surfaces: an in vitro study. | Folwaczny M, Mehl A, Aggstaller H, Hickel R | J Clin Periodontol | 10.1034/j.1600-051x.2002.290111.x | 2002 | Aggregatibacter 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 | |
Metabolism | 17229113 | Hemin nutritional stress inhibits bacterial invasion of radicular dentine by two endodontic anaerobes. | Love RM | Int Endod J | 10.1111/j.1365-2591.2006.01186.x | 2007 | Bacteria, Anaerobic/*metabolism, Culture Media, Dental Pulp Cavity/*microbiology, Dentin/*microbiology, Hemin/*metabolism, Humans, Peptostreptococcus/metabolism, Prevotella intermedia/metabolism | Cultivation |
Metabolism | 17949340 | Degradation of serine-containing oligopeptides by Peptostreptococcus micros ATCC 33270. | Uematsu H, Hossain MZ, Alam T, Ikeda T, Kuvatanasuchati J, Hoshino E | Oral Microbiol Immunol | 10.1111/j.1399-302X.2007.00374.x | 2007 | Acetate 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/metabolism | Enzymology |
Phylogeny | 19351562 | Collagenase production and hemolytic activity related to 16S rRNA variability among Parvimonas micra oral isolates. | Ota-Tsuzuki C, Alves Mayer MP | Anaerobe | 10.1016/j.anaerobe.2009.03.008 | 2009 | Animals, *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, Rabbits | Metabolism |
Enzymology | 22405584 | Antimicrobial activity of Streptococcus salivarius K12 on bacteria involved in oral malodour. | Masdea L, Kulik EM, Hauser-Gerspach I, Ramseier AM, Filippi A, Waltimo T | Arch Oral Biol | 10.1016/j.archoralbio.2012.02.011 | 2012 | Actinobacteria/*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/*physiology | Phylogeny |
Pathogenicity | 26759339 | In-vitro activity of sodium-hypochlorite gel on bacteria associated with periodontitis. | Jurczyk K, Nietzsche S, Ender C, Sculean A, Eick S | Clin Oral Investig | 10.1007/s00784-016-1711-9 | 2016 | Anti-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 | |
Pathogenicity | 28341746 | Leveraging 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 EB | Gut | 10.1136/gutjnl-2016-313189 | 2017 | Area 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 Questionnaires | Phylogeny |
Pathogenicity | 30024592 | The regulation of DLTA gene in bacterial growth and biofilm formation by Parvimonas micra. | Liu K, Hou BX | Eur Rev Med Pharmacol Sci | 10.26355/eurrev_201807_15390 | 2018 | Biofilms/*growth & development, Dental Plaque/*microbiology, Humans, Lipopolysaccharides/*metabolism, Teichoic Acids/*metabolism | Metabolism |
Phylogeny | 34878380 | Parvimonas parva sp. nov., derived from a human genito-urinary lesion. | Jansson MK, Hering S, Buhl MEJ | Int J Syst Evol Microbiol | 10.1099/ijsem.0.005100 | 2021 | Bacterial 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/*microbiology | Pathogenicity |
Pathogenicity | 35397605 | Antibacterial 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 TG | BMC Oral Health | 10.1186/s12903-022-02148-8 | 2022 | Agar, 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 | |
Pathogenicity | 35416697 | Development 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 J | Microbiol Spectr | 10.1128/spectrum.00465-22 | 2022 | Carcinogenesis, *Firmicutes/genetics, *Gram-Positive Bacteria, Humans |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
8839 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20468) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-20468 | |||
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | |
40295 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/17297 | ||||
57165 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 46357) | https://www.ccug.se/strain?id=46357 | |||
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
68380 | Automatically annotated from API rID32A | |||||
69479 | João 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 | |||
87054 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID40421.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
120944 | Curators of the CIP | Collection of Institut Pasteur (CIP 105294) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105294 |