Porphyromonas somerae

Bacteria
General | Carbohydrate O/F | Substrate utilisation | Enzymes | Metabolites | Antibiotics

Overview

  • Porphyromonas somerae is a Gram-negative, non-spore-forming, strictly anaerobic, non-motile, rod-shaped bacterium. It has been detected in at least 8 gut microbiome compilation studies or metastudies. The DNA G+C content is 47.8%. Porphyromonas somerae is probably a common, although minor, coloniser of the gut. (Summanen2005; Summanen2010Bergey)



  • This organism has been recovered from human faeces and leg ulcer. The risk classification (www.baua.de) for this organism is 2, i.e., risk of individual infection, but low risk of spread. Is a rare opportunistic pathogen. A possible gut commensal.
    • GENERAL CHARACTERISTICS (Summanen2005); (Summanen2010Bergey);
    Character Response
  • Substrates hydrolysed or digested:
  • gelatin;
  • 🌡
  • Temperature tolerance:
  • Grows optimally at 37℃.
  • H+
  • Acid from carbohydrates usually produced:
  • mannose;
  • Active enzymes:
  • Ala arylamidase; alkaline phosphatase; acid phosphatase; N-Ac β-glucosaminidase; chymotrypsin; β-galactosidase; Glu-Glu arylamidase; Leu-Gly arylamidase; naphthol-ASBI-P;
    • SPECIAL FEATURES (Summanen2005); (Summanen2010Bergey);
    Character Response
  • ✓
  • Metabolites produced:
  • acetate; propionate; butyrate; isobutyrate (minor); succinate (minor); isovalerate;
  • ✗
  • Metabolites not produced:
  • indole;
  • ✓
  • ONPG test:
  • active
  • ✗
  • Nitrate:
  • not reduced
  • Pigments:
  • black
    • RESPONSE TO ANTIBIOTICS (Summanen2005); (Summanen2010Bergey); (Goldstein2018a); (Goldstein2013a); (Goldstein2013b); (Tyrrell2012); (Citron2011); (Goldstein2008); (Goldstein2006a); (Goldstein2006c);
    Class Active Resistant
  • Penicillins:
  • amoxicillin-clavulanic acid; ampicillin; ampicillin-sulbactam; doripenem; ertapenem; imipenem; meropenem; penicillin G; piperacillin-tazobactam;
  • Cephalosporins:
  • cefotaxime; cefoxitin;
  • Macrolides:
  • fidaxomicin;
  • Tetracyclines:
  • tigecycline;
  • Quinolines:
  • levofloxacin; moxifloxacin;
  • Heterocycles:
  • metronidazole;
  • Vancomycins:
  • vancomycin;
  • Miscellaneous antibiotics:
  • clindamycin; linezolid;
  • daptomycin;

  • Lagier, J.-C., Armougom, F., Million, M., Hugon, P., Pagnier, I., Robert, C., Bittar, F., Fournous, G., Gimenez, G., Maraninchi, M., Trape, J.-F., Koonin, E. V., La Scola, B., & Raoult, D. (2012). Microbial culturomics: paradigm shift in the human gut microbiome study. Clinical Microbiology and Infection: The Official Publication of the European Society of Clinical Microbiology and Infectious Diseases, 18(12), 1185–1193.

    • Details

    GENERAL
    Lineage Physiology General Growth Tolerances Hydrol./digest./degr.
    Phylum:  Bacteroidetes Class:  Bacteroidia Order:  Bacteroidales Family:  Porphyromonadaceae Genus:  Porphyromonas Gram stain:  neg O2 Relation.:  strictly anaerobic Spore:  No spore Motility:  Sessile Morphology:  Rod Pigment:  black
    Health:  Unknown
    Source:  human faeces and leg ulcer
    DNA G+C(%):  47.8
    Opt. T:  37℃
    		Aesculin:  neg Urea:  neg Gelatin:  +
    CARBOHYDRATE ACID FORMATION
    Monosaccharide O/F Oligosaccharide O/F Polysaccharide O/F Polyol O/F Other O/F
    Arabinose:  neg Glucose:  w Mannose:  + Rhamnose:  neg Xylose:  neg Cellubiose:  neg Lactose:  w Maltose:  w Melezitose:  neg Sucrose:  neg Trehalose:  neg Glycerol:  neg Mannitol:  neg Sorbitol:  neg Salicin:  neg
    SUBSTRATE ASSIMILATION & UTILISATION
    Monosaccharide util/assim Oligosaccharide util/assim Other carboh. util/assim Amino acid util/assim Organic acid util/assim
    Glucose:  w Lactose:  w Inositol:  w
    ENZYME ACTIVITY
    Enzymes: General Enzymes: Carbohydrate Enzymes: Protein Enzymes: Arylamidases Enzymes: Esters/fats
    Catalase:  neg Urease:  neg Ac-β-glcamnd:  + α-Fucosidase:  neg α-Galactosidase:  neg β-Galactosidase:  + α-Glucosidase:  vr β-Glucosidase:  neg β-Glucuronidase:  neg α-Mannosidase:  neg Xylosidase:  neg ArgDH:  neg Chymotrypsin:  + GluDC:  neg Trypsin:  neg AlanineAA:  + CystineAA:  neg GluGluAA:  + GlyAA:  neg LeuAA:  vr LeuGlyAA:  + PyrrolidAA:  neg ValAA:  vr AlkalineP:  + AcidP:  + Esterase(C4):  vr EstLip(C8):  vr Lipase:  neg
    METABOLITES - PRODUCTION & USE
    Fuel Usable Metabolites Metabolites Released Special Products Compounds Produced

    		Acetate:  + Propionate:  + Butyrate:  + Isobutyrate:  minor(+) Succinate:  minor(+) Isovalerate:  + Indole:  neg Pigment:  black
    ANTIBIOTICS ℞
    Penicillins & Penems (μg/mL) Cephalosporins (μg/mL) Aminoglycosides (μg/mL) Macrolides (μg/mL) Quinolones (μg/mL)
    amoxicillin:  Var
    Augmentin:  S(MIC50): 1, MIC90: 2, RNG: (0.125-4)
    ampicillin:  S(MIC50): 0.03, MIC90: 0.5, RNG: (0.03–2)
    amp-sulb:  S(MIC50): 0.06, MIC90: 1, RNG: (0.06–2)
    penicillin_G:  S(MIC50): 1, MIC90: 16, RNG: (0.25–>32)
    piper-taz:  S(MIC50): 0.015, MIC90: 0.015, RNG: (0.015–0.03)
    doripenem:  S(MIC50): 0.015, MIC90: 0.03, RNG: (0.015–0.06)
    ertapenem:  S(MIC50): 0.015, MIC90: 0.06, RNG: (0.015–0.125)
    imipenem:  S(MIC50): 0.03, MIC90: 0.06, RNG: (0.015–0.125)
    meropenem:  S(MIC50): 0.03, MIC90: 0.03, RNG: (0.03–0.125)
    cefepime:  Var(MIC50): 1, MIC90: 16, RNG: (0.25–16)
    cefotaxime:  S(MIC50): 0.06, MIC90: 2, RNG: (≤0.06–4)
    cefoxitin:  S(MIC50): 0.5, MIC90: 1, RNG: (0.25–2)
    ceftazidime:  Var(MIC50): 0.5, MIC90: 8, RNG: (0.25–32)
    fidaxomicin:  R(MIC50): 64, MIC90: 128, RNG: (0.03–128)
    linezolid:  S(MIC50): 1, MIC90: 2, RNG: (0.5–2)
    levofloxacin:  S(MIC50): 1, MIC90: 2, RNG: (0.25–16)
    moxifloxacin:  S(MIC50): 0.5, MIC90: 1, RNG: (0.03–16)
    Tetracyclines (μg/mL) Vancomycin Class (μg/mL) Polypep/ketides (μg/mL) Heterocycles (μg/mL) Other (μg/mL)
    doxycycline:  Var(MIC50): 8, MIC90: 8, RNG: (0.25–8)
    tigecycline:  S(MIC50): 0.06, MIC90: 0.06, RNG: (0.06–0.5)
    vancomycin:  S(MIC50): 4, MIC90: 8, RNG: (2–8)
    metronidazole:  S(MIC50): 0.125, MIC90: 0.5, RNG: (0.03–1)
    clindamycin:  S(MIC50): 0.06, MIC90: 1, RNG: (0.06–>128)
    daptomycin:  R(MIC50): >32, MIC90: >32, RNG: (>32)

    References

    SPECIFIC REFERENCES FOR PORPHYROMONAS SOMERAE
  • Summanen2005 - Porphyromonas somerae sp. nov., a Pathogen Isolated from Humans and Distinct from Porphyromonas levii.
  • Summanen2010Bergey - Bergey's manual of systematic bacteriology. Vol. 4, The Fusobacteria. Family Porphyromonadaceae, Genus I. Porphyromonas
  • Feng2015 - Gut microbiome development along the colorectal adenoma-carcinoma sequence
  • Kishikawa2020 - Metagenome-wide association study of gut microbiome revealed novel aetiology of rheumatoid arthritis in the Japanese population
  • Goldstein2018a - Comparative In Vitro Activities of Relebactam, Imipenem, the Combination of the Two, and Six Comparator Antimicrobial Agents against 432 Strains of Anaerobic Organisms, Including Imipenem-Resistant Strains.
  • Goldstein2013a - Comparative in vitro activities of SMT19969, a new antimicrobial agent, against Clostridium difficile and 350 gram-positive and gram-negative aerobic and anaerobic intestinal flora isolates.
  • Goldstein2013b - Comparative in vitro activities of GSK2251052, a novel boron-containing leucyl-tRNA synthetase inhibitor, against 916 anaerobic organisms.
  • Tyrrell2012 - In vitro activity of TD-1792, a multivalent glycopeptide-cephalosporin antibiotic, against 377 strains of anaerobic bacteria and 34 strains of Corynebacterium species.
  • Citron2011 - In vitro activity of ceftazidime-NXL104 against 396 strains of beta-lactamase-producing anaerobes.
  • Goldstein2008 - In vitro activities of doripenem and six comparator drugs against 423 aerobic and anaerobic bacterial isolates from infected diabetic foot wounds.
  • Goldstein2006a - In vitro activity of ceftobiprole against aerobic and anaerobic strains isolated from diabetic foot infections.
  • Goldstein2006c - Comparative in vitro susceptibilities of 396 unusual anaerobic strains to tigecycline and eight other antimicrobial agents.
  • ...............................
    • GUT MICROBIOME COMPILATIONS AND METASTUDIES FOR PORPHYROMONAS SOMERAE
  • Byrd2020 - Stability and dynamics of the human gut microbiome and its association with systemic immune traits.
  • Hu2019 - The Gut Microbiome Signatures Discriminate Healthy From Pulmonary Tuberculosis Patients
  • Jie2017 - The gut microbiome in atherosclerotic cardiovascular disease
  • Lagier2016 - Culture of previously uncultured members of the human gut microbiota by culturomics.
  • Pfleiderer2013 - Culturomics identified 11 new bacterial species from a single anorexia nervosa stool sample.
  • RajilicStojanovic2014 - The first 1000 cultured species of the human gastrointestinal microbiota.
  • Walker2011 - High-throughput clone library analysis of the mucosa-associated microbiota reveals dysbiosis and differences between inflamed and non-inflamed regions of the intestine in inflammatory bowel disease.
  • ...............................
    • Added: April 08, 2021