Dorea formicigenerans

(aka Eubacterium formicgenerans)

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

Overview

  • Dorea formicigenerans, (aka Eubacterium formicgenerans), is a Gram-positive, non-spore-forming, strictly anaerobic, non-motile, rod-shaped bacterium. It has been detected in at least 28 gut microbiome compilation studies or metastudies. The DNA G+C content is 40-44%. Dorea formicigenerans is often a widespread coloniser of gut. (Holdeman1974; Taras2002; Blaut2011Bergey)



  • This organism has been recovered from human faeces (Ludwig2009). The risk classification (www.baua.de) for this organism is 1, i.e., low risk of infection and spread. Pathogenicity status unknown, or very unlikely to be pathogenic. Is a known gut commensal. Robust growth can have positive consequences for gut health.
    • GENERAL CHARACTERISTICS (Holdeman1974); (Taras2002); (Blaut2011Bergey);
    Character Response
  • 🧂
  • Salt tolerance:
  • doesn't tolerate 6.5% salt;
  • 🌡
  • Temperature tolerance:
  • grows weakly at 30℃; grows weakly at 45℃; Grows optimally at 37℃.
  • H+
  • Acid from carbohydrates usually produced:
  • fructose; galactose; glucose; lactose; maltose;
  • ⥅
  • Substrates assimilated or utilised:
  • glucose; maltose; pyruvate;
  • ±
  • Strain-dependent substrate utilisation:
  • arabinose;
  • Active enzymes:
  • β-galactosidase; α-glucosidase;
    • SPECIAL FEATURES (Holdeman1974); (Taras2002); (Blaut2011Bergey);
    Character Response
  • ✓
  • Metabolites produced:
  • formate; acetate; lactate; ethanol;
  • ✗
  • Metabolites not produced:
  • butyrate; indole;
  • ✗
  • Nitrate:
  • not reduced
  • ✗
  • NO3➔NO2:
  • not reduced
    • RESPONSE TO ANTIBIOTICS
    Class Active Resistant
  • Penicillins:
  • amoxicillin; ampicillin; azlocillin; aztreonam; bacampicillin; benzylpenicillin; cloxacillin; dicloxacillin; imipenem; meropenem; oxacillin; piperacillin; ticarcillin;
  • Cephalosporins:
  • cefaclor; cefazolin; cefdinir; cefepime; cefixime; cefmetazole; cefoperazone; cefotaxime; cefotetan; cefotiam; cefoxitin; ceftazidime; cefuroxime; cephalothin; moxalactam;
  • cefadroxil;
  • Macrolides:
  • azithromycin; clarithromycin; erythromycin; josamycin; roxithromycin; spiramycin;
  • Tetracyclines:
  • chlortetracycline; doxycycline; meclocycline; methacycline; minocycline; oxytetracycline; tetracycline;
  • Quinolines:
  • ciprofloxacin; clinafloxacin; enoxacin; gatifloxacin; moxifloxacin; sarafloxacin;
  • clavulanic-acid; nalidixic-acid; norfloxacin; ofloxacin; pefloxacin; pipemidic-acid; sparfloxacin;
  • Aminoglycosides:
  • amikacin; dihydrostreptomycin; gentamicin; kanamycin; neomycin; sisomicin; spectinomycin; streptomycin; tobramycin;
  • Polypep/ketides:
  • bacitracin; rifabutin; rifampicin; rifapentine;
  • Heterocycles:
  • chloramphenicol; fusidic-acid; metronidazole; nitrofurantoin;
  • isoniazid; sulfadiazine; sulfadimethoxine; sulfamethoxazole; sulfanilamide; trimethoprim;
  • Vancomycins:
  • vancomycin;
  • Miscellaneous antibiotics:
  • clindamycin; lincomycin; linezolid; colistin;
  • NOTES

    Formerly known as Eubacterium formicgenerans. This is a common inhabitant of the human gut.

    Fuel sources used:
    It can use simple sugars (including lactose) and protein for energy.

    Metabolites produced:
    Our genomic analysis indicates that most members of this species can produce the following metabolites: acetate, BCAAs, lactate, cobalamin, folate, biotin, riboflavin.

    Metabolites consumed:
    In addition, our genomic analysis indicates that most members of this species do not consume any reported metabolites.

    Emerging research:
    This species has been observed at decreased levels in individuals with colon cancer and chronic fatigue syndrome, indicating it likely plays a beneficial role in health.

  • References: [1] [2] [3] [4] [5]

  • Holdeman, L. V., & Moore, W. E. C. (1974). New genus, Coprococcus, twelve new species, and emended descriptions of four previously described species of bacteria from human feces. International Journal of Systematic Bacteriology, 24(2), 260–277.

    • Details

    GENERAL
    Lineage Physiology General Growth Tolerances Hydrol./digest./degr.
    Phylum:  Firmicutes Class:  Clostridia Order:  Eubacteriales Family:  Lachnospiraceae Genus:  Dorea Alt. name:  Eubacterium formicgenerans Gram stain:  + O2 Relation.:  strictly anaerobic Spore:  No spore Motility:  Sessile Morphology:  Rod
    Health:   Positive
    Source:  human faeces (Ludwig2009)
    DNA G+C(%):  40-44
    Opt. T:  37℃
    Lower T(℃):  30(w)
    High T(℃):  45(w)
    NaCl >6%:  6.5(neg)
    		Aesculin:  neg Urea:  neg Gelatin:  neg Starch:  neg Hippurate:  vr
    CARBOHYDRATE ACID FORMATION
    Monosaccharide O/F Oligosaccharide O/F Polysaccharide O/F Polyol O/F Other O/F
    Fructose:  + Galactose:  + Glucose:  + Mannose:  neg Rhamnose:  neg Sorbose:  neg Lactose:  + Maltose:  + Melezitose:  neg Melibiose:  neg Sucrose:  neg Trehalose:  neg Amygdalin:  neg Cellulose:  neg Dextrin:  neg Aesculin:  neg Glycogen:  neg Inulin:  neg Adonitol:  neg Dulcitol:  neg Glycerol:  neg Mannitol:  neg Salicin:  neg
    SUBSTRATE ASSIMILATION & UTILISATION
    Monosaccharide util/assim Oligosaccharide util/assim Other carboh. util/assim Amino acid util/assim Organic acid util/assim
    Arabinose:  d Glucose:  + Mannose:  neg Rhamnose:  neg Maltose:  + Melibiose:  neg Raffinose:  neg Trehalose:  neg Amygdalin:  neg Aesculin:  neg Gluconate:  neg Inositol:  neg Inulin:  neg Sorbitol:  neg Lactate:  neg Pyruvate:  +
    ENZYME ACTIVITY
    Enzymes: General Enzymes: Carbohydrate Enzymes: Protein Enzymes: Arylamidases Enzymes: Esters/fats
    Oxidase:  neg Catalase:  neg Urease:  neg Ac-β-glcamnd:  neg α-Fucosidase:  neg α-Galactosidase:  neg β-Galactosidase:  + α-Glucosidase:  + β-Glucosidase:  neg β-Glucuronidase:  neg ArgDH:  neg GluDC:  neg AlanineAA:  neg GluGluAA:  neg GlyAA:  neg LeuAA:  neg LeuGlyAA:  neg PyrrolidAA:  neg AlkalineP:  neg
    METABOLITES - PRODUCTION & USE
    Fuel Usable Metabolites Metabolites Released Special Products Compounds Produced

    		Formate:  + Acetate:  + Butyrate:  neg Lactate:  + Ethanol:  + Indole:  neg
    ANTIBIOTICS ℞
    Penicillins & Penems (μg/mL) Cephalosporins (μg/mL) Aminoglycosides (μg/mL) Macrolides (μg/mL) Quinolones (μg/mL)
    amoxicillin:  Sens
    ampicillin:  Sens
    azlocillin:  Sens
    aztreonam:  Sens
    bacampicillin:  Sens
    benzyl-pen:  Sens
    cloxacillin:  Sens
    dicloxacillin:  Sens
    oxacillin:  Sens
    piperacillin:  Sens
    ticarcillin:  Sens
    imipenem:  Sens
    meropenem:  Sens
    cefaclor:  Sens
    cefadroxil:  Res
    cefazolin:  Sens
    cefdinir:  Sens
    cefepime:  Sens
    cefixime:  Sens
    cefmetazole:  Sens
    cefoperazone:  Sens
    cefotaxime:  Sens
    cefotetan:  Sens
    cefotiam:  Sens
    cefoxitin:  Sens
    ceftazidime:  Sens
    cefuroxime:  Sens
    cephalothin:  Sens
    moxalactam:  Sens
    amikacin:  Res
    dihydrostrept:  Res
    gentamicin:  Res
    kanamycin:  Res
    neomycin:  Res
    sisomicin:  Res
    spectinomycin:  Res
    streptomycin:  Res
    tobramycin:  Res
    azithromycin:  Sens
    erythromycin:  Sens
    clarithromycin:  Sens
    roxithromycin:  Sens
    spiramycin:  Sens
    josamycin:  Sens
    linezolid:  Sens
    ciprofloxacin:  Sens
    clavulanate:  Res
    clinafloxacin:  Sens
    enoxacin:  Sens
    gatifloxacin:  Sens
    moxifloxacin:  Sens
    nalidixic-acid:  Res
    norfloxacin:  Res
    ofloxacin:  Res
    pefloxacin:  Res
    pipemidic_acid:  Res
    sarafloxacin:  Sens
    sparfloxacin:  Res
    Tetracyclines (μg/mL) Vancomycin Class (μg/mL) Polypep/ketides (μg/mL) Heterocycles (μg/mL) Other (μg/mL)
    doxycycline:  Sens
    chlortetracycline:  Sens
    meclocycline:  Sens
    methacycline:  Sens
    minocycline:  Sens
    oxytetracycline:  Sens
    tetracycline:  Sens
    vancomycin:  Sens
    bacitracin:  Sens
    rifabutin:  Sens
    rifampicin:  Sens
    rifapentine:  Sens
    chloramphenicol:  Sens
    isoniazid:  Res
    metronidazole:  Sens
    nitrofurantoin:  Sens
    sulfadiazine:  Res
    sulfadimethoxine:  Res
    sulfamethoxazole:  Res
    sulfanilamide:  Res
    trimethoprim:  Res
    clindamycin:  Sens
    lincomycin:  Sens
    colistin:  Sens
    fusidic-acid:  Sens

    References

    SPECIFIC REFERENCES FOR DOREA FORMICIGENERANS
  • Holdeman1974 - New Genus, Coprococcus, Twelve New Species, and Emended Descriptions of Four Previously Described Species of Bacteria from Human Feces.
  • Taras2002 - Reclassification of Eubacterium formicigenerans Holdeman and Moore 1974 as Dorea formicigenerans gen. nov., comb. nov., and description of Dorea longicatena sp. nov., isolated from human faeces.
  • Blaut2011Bergey - Bergey's manual of systematic bacteriology. Vol. 3, The Firmicutes. Family Lachnospiraceae, Genus VIII. Dorea
  • deGoffau2014 - Aberrant gut microbiota composition at the onset of type 1 diabetes in young children
  • Hu2019 - The Gut Microbiome Signatures Discriminate Healthy From Pulmonary Tuberculosis Patients
  • Jackson2016 - Signatures of early frailty in the gut microbiota
  • MayaLucas2019 - The gut microbiome of Mexican children affected by obesity
  • Shapiro2019 - Psoriatic patients have a distinct structural and functional fecal microbiota compared with controls
  • Sokol2017 - Fungal microbiota dysbiosis in IBD
  • Takeshita2016 - A Single Species of Clostridium Subcluster XIVa Decreased in Ulcerative Colitis Patients
  • Wang2019b - Alterations in the human gut microbiome associated with Helicobacter pylori infection
  • Weir2013 - Stool microbiome and metabolome differences between colorectal cancer patients and healthy adults
  • Yu2015 - Metagenomic analysis of faecal microbiome as a tool towards targeted non-invasive biomarkers for colorectal cancer
  • Zuo2020 - Alterations in Gut Microbiota of Patients With COVID-19 During Time of Hospitalization
  • Laue2020 - Prospective associations of the infant gut microbiome and microbial function with social behaviors related to autism at age 3 years
  • Luna2016 - Distinct Microbiome-Neuroimmune Signatures Correlate With Functional Abdominal Pain in Children With Autism Spectrum Disorder.
  • ...............................
    • GUT MICROBIOME COMPILATIONS AND METASTUDIES FOR DOREA FORMICIGENERANS
  • Byrd2020 - Stability and dynamics of the human gut microbiome and its association with systemic immune traits.
  • Chen2020 - Structural and Functional Characterization of the Gut Microbiota in Elderly Women With Migraine
  • Chen2020a - Featured Gut Microbiomes Associated With the Progression of Chronic Hepatitis B Disease
  • De2020 - Metagenomic analysis of gut microbiome and resistome of diarrheal fecal samples from Kolkata, India, reveals the core and variable microbiota including signatures of microbial dark matter.
  • Forster2019 - A human gut bacterial genome and culture collection for improved metagenomic analyses.
  • Hu2019 - The Gut Microbiome Signatures Discriminate Healthy From Pulmonary Tuberculosis Patients
  • Jeong2021 - The effect of taxonomic classification by full-length 16S rRNA sequencing with a synthetic long-read technology
  • Jie2017 - The gut microbiome in atherosclerotic cardiovascular disease
  • Lagier2016 - Culture of previously uncultured members of the human gut microbiota by culturomics.
  • LeChatelier2013 - Richness of human gut microbiome correlates with metabolic markers
  • Li2019b - Disordered intestinal microbes are associated with the activity of Systemic Lupus Erythematosus
  • McLaughlin2010 - The bacteriology of pouchitis: a molecular phylogenetic analysis using 16S rRNA gene cloning and sequencing.
  • Minerbi2019 - Altered microbiome composition in individuals with fibromyalgia
  • Moore1974 - Human fecal flora: the normal flora of 20 Japanese-Hawaiians.
  • Nielsen2014 - MetaHIT Consortium. Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes.
  • PerezBrocal2015 - Metagenomic Analysis of Crohn's Disease Patients Identifies Changes in the Virome and Microbiome Related to Disease Status and Therapy, and Detects Potential Interactions and Biomarkers
  • Qin2012 - Metagenome-wide association study of gut microbiota in type 2 diabetes
  • RajilicStojanovic2014 - The first 1000 cultured species of the human gastrointestinal microbiota.
  • Rothschild2018 - Environment dominates over host genetics in shaping human gut microbiota.
  • Salonen2014 - Impact of diet and individual variation on intestinal microbiota composition and fermentation products in obese men.
  • Tyakht2013 - Human gut microbiota community structures in urban and rural populations in Russia.
  • 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.
  • Wang2018 - A metagenome-wide association study of gut microbiota in asthma in UK adults
  • Wang2018a - Morphine induces changes in the gut microbiome and metabolome in a morphine dependence model.
  • Wang2020a - Aberrant gut microbiota alters host metabolome and impacts renal failure in humans and rodents
  • Yang2020 - Species-Level Analysis of Human Gut Microbiota With Metataxonomics.
  • Yang2020a - Establishing high-accuracy biomarkers for colorectal cancer by comparing fecal microbiomes in patients with healthy families
  • Zeller2014 - Potential of fecal microbiota for early-stage detection of colorectal cancer
  • Zou2019 - 1,520 reference genomes from cultivated human gut bacteria enable functional microbiome analyses.
  • Zupancic2012 - Analysis of the Gut Microbiota in the Old Order Amish and Its Relation to the Metabolic Syndrome.
  • ...............................
    • GENERAL REFERENCES FOR DOREA FORMICIGENERANS
  • Ludwig2009 - Revised road map to the phylum Firmicutes.
    • Added: February 08, 2021