Eubacterium limosum

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

Overview

  • Eubacterium limosum is a Gram-positive, non-spore-forming, strictly anaerobic, non-motile, rod-shaped bacterium. It has been detected in at least 18 gut microbiome compilation studies or metastudies. The DNA G+C content is 47%. Eubacterium limosum is a common gut coloniser. (Moore1965; Wade2011aBergeys)



  • This organism has been recovered from human faeces, rumen, sewage, mud, animals and clinical sources (rectal abscesses, blood and wounds). The risk classification (www.baua.de) for this organism is 2, i.e., risk of individual infection, but low risk of spread. It is an opportunistic pathogen. Is a known gut commensal.
    • QUIRKS
  • Homoacetogen. Able to use the following donors: CO, methanol, betaine, phenylmethylether.
    • GENERAL CHARACTERISTICS (Moore1965); (Wade2011aBergeys);
    Character Response
  • Substrates hydrolysed or digested:
  • aesculin; DNA; pectin;
  • ±
  • Strain-dependent hydrolysis or digestion:
  • gelatin; starch;
  • 🧂
  • Salt tolerance:
  • doesn't tolerate 6.5% salt;
  • pH
  • Acidity tolerance:
  • tolerates pH 5.0; tolerates pH 9.6;
  • 🌡
  • Temperature tolerance:
  • grows at 30℃; grows at 45℃; Grows optimally at 37℃.
  • H+
  • Acid from carbohydrates usually produced:
  • L-arabinose; fructose; glucose; ribose; pectin; adonitol; erythritol; mannitol;
  • ±
  • Strain-dependent acid from carbs:
  • galactose; xylose;
  • ⥅
  • Substrates assimilated or utilised:
  • adonitol; d_arabitol; erythritol; fructose; glucose; mannitol; methanol; ribose; isoleucine; valine; lactate; pyruvate; H2 consumed; CO2 consumed;
  • Active enzymes:
  • acid phosphatase; esterase C4; glutamic acid decarboxylase; Leu-Gly arylamidase;
    • SPECIAL FEATURES (Moore1965); (Wade2011aBergeys);
    Character Response
  • ✓
  • Metabolites produced:
  • acetate; butyrate; lactate; isobutyrate (trace); succinate (trace); isovalerate (trace); Hâ‚‚S (most strains); Hâ‚‚;
  • ✗
  • Metabolites not produced:
  • ammonia; indole;
  • ✓
  • Haemolysis:
  • present
  • ✗
  • Nitrate:
  • not reduced
    • RESPONSE TO ANTIBIOTICS (Goldstein2003); (Wade2011aBergeys); (Goldstein2018a); (Goldstein2013a); (Goldstein2013b); (Tyrrell2012); (Citron2012a); (Goldstein2006); (Goldstein2005); (Citron2003); (Citron2001); (Goldstein2000a); (Goldstein1991);
    Class Active Resistant
  • Penicillins:
  • amoxicillin-clavulanic acid; ampicillin; ampicillin-sulbactam; ertapenem; imipenem; meropenem; penicillin; piperacillin-tazobactam;
  • Cephalosporins:
  • cefoxitin;
  • ceftazidime;
  • Macrolides:
  • pristinamycin; quinupristin-dalfopristin;
  • azithromycin; erythromycin; roxithromycin;
  • Tetracyclines:
  • tigecycline;
  • Quinolines:
  • moxifloxacin;
  • Heterocycles:
  • chloramphenicol; metronidazole;
  • Vancomycins:
  • vancomycin; dalbavancin; teicoplanin;
  • Miscellaneous antibiotics:
  • clindamycin; pristinamycin;

  • N/A

  • Metabolic pathway analysis revealed that E. limosum KIST612 uses the Wood-Ljungdahl pathway to fix CO (or CO2) and converts it into acetyl coenzyme A (acetyl-CoA), like other syngas-utilizing acetogens such as Moorella thermoacetica, Clostridium ljungdahlii, and Clostridium carboxidivorans strain P7T. E. limosum KIST612 also contains 10 genes annotated as subunits of hydrogenases that may provide reducing equivalents for CO2 reduction to organic carbons. The genome of E. limosum KIST612 contains genes that encode key enzymes that convert acetyl-CoA into potential bioenergy-compatible acids/alcohols (acetate, butyrate, and ethanol). In addition to these genes, key genes for growing on syngas can be a platform of synthetic biology to construct carbon fixation pathways for the production of biofuels or chemicals from syngas. [PMID: 21036996]

  • GutFeeling KnowledgeBase COMMENTS [Website]

    Eubacterium limosum (strain KIST612) is an acetogenic Gram-positive bacterium frequently isolated from an anaerobic digester and has a high growth rate on synthesis gas (CO; carbon monoxide) using it as a sole energy source. This organism produces acetate as well as butyrate and ethanol as fermentation products from syngas. Therefore, E. limosum has been considered for a model strain for bioenergy production from syngas (obtained from biomass). (Adapted from : www.ncbi.nlm.nih.gov/genomeprj/52281). [UP000006873]

  • Moore, WEC & LV Holdeman (1974). Human fecal flora: the normal flora of 20 Japanese-Hawaiians. Appl. Microbiol. 27: 961-979.

    • Details

    GENERAL
    Lineage Physiology General Growth Tolerances Hydrol./digest./degr.
    Phylum:  Firmicutes Class:  Clostridia Order:  Eubacteriales Family:  Eubacteriaceae Genus:  Eubacterium Gram stain:  + O2 Relation.:  strictly anaerobic Spore:  No spore Motility:  Sessile Morphology:  Rod
    Health:  Unknown
    Source:  human faeces, rumen, sewage, mud, animals and clinical sources (rectal abscesses, blood and wounds)
    DNA G+C(%):  47
    Opt. T:  37℃
    Lower T(℃):  30(+)
    High T(℃):  45(+)
    NaCl >6%:  6.5(neg)
    pH 4.2-5.9:  5.0(+)
    pH >8:  9.6(+)
    		Aesculin:  + Urea:  neg Gelatin:  d Starch:  d Arginine:  neg DNA:  + Hippurate:  neg Milk:  neg Meat:  neg Pectin:  +
    CARBOHYDRATE ACID FORMATION
    Monosaccharide O/F Oligosaccharide O/F Polysaccharide O/F Polyol O/F Other O/F
    L-Arabinose:  d(+) Fructose:  + Galactose:  d(neg) Glucose:  + Mannose:  neg Rhamnose:  neg Ribose:  + Sorbose:  neg Xylose:  d Cellubiose:  neg Lactose:  neg Maltose:  neg Melezitose:  neg Melibiose:  neg Sucrose:  neg Trehalose:  neg Amygdalin:  neg Cellulose:  neg Dextrin:  neg Aesculin:  neg Glycogen:  neg Inulin:  neg Starch:  neg Pectin:  + Adonitol:  + Dulcitol:  neg Erythritol:  + Glycerol:  neg Inositol:  neg Mannitol:  + 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
    Arabinose:  neg Fructose:  + Galactose:  neg Glucose:  + Mannose:  neg Rhamnose:  neg Ribose:  + Cellubiose:  neg Lactose:  neg Maltose:  neg Melezitose:  neg Melibiose:  neg Raffinose:  neg Sucrose:  neg Trehalose:  neg Adonitol:  + D-Arabitol:  + Dextrin:  neg Dulcitol:  neg Erythritol:  + Aesculin:  neg Ethanol:  neg Gluconate:  neg Inositol:  neg Mannitol:  + Methanol:  + Pectin:  neg Propanol:  neg Salicin:  neg Starch:  neg Xylitol:  neg Ile:  + Val:  + Acetate:  neg Fumarate:  neg Lactate:  + Malate:  neg Pyruvate:  + Succinate:  neg
    ENZYME ACTIVITY
    Enzymes: General Enzymes: Carbohydrate Enzymes: Protein Enzymes: Arylamidases Enzymes: Esters/fats
    Catalase:  neg Urease:  neg Ac-β-glcamnd:  neg α-Fucosidase:  neg α-Galactosidase:  neg β-Galactosidase:  neg α-Glucosidase:  neg β-Glucuronidase:  neg α-Mannosidase:  neg ArgDH:  neg GluDC:  + AlanineAA:  neg GluGluAA:  neg GlyAA:  neg LeuAA:  neg LeuGlyAA:  + PyrrolidAA:  neg AlkalineP:  vr AcidP:  + Esterase(C4):  + EstLip(C8):  neg Lipase(C14):  neg
    METABOLITES - PRODUCTION & USE
    Fuel Usable Metabolites Metabolites Released Special Products Compounds Produced

    		Acetate:  + Butyrate:  + Lactate:  + Isobutyrate:  trace(+) Succinate:  trace(+) Isovalerate:  trace(+) H2S:  d(+) Ammonia:  neg H2:  + Indole:  neg
    ANTIBIOTICS ℞
    Penicillins & Penems (μg/mL) Cephalosporins (μg/mL) Aminoglycosides (μg/mL) Macrolides (μg/mL) Quinolones (μg/mL)
    Augmentin:  S(≤0.06/0.5)
    ampicillin:  S(MIC50): 0.03, MIC90: 0.06, RNG: (0.03-0.125)
    amp-sulb:  SensRNG: (0.25/0.25)RNG: (0.25-0.5)
    penicillin:  S(MIC50): 0.125, MIC90: 2, RNG: (≤0.03-2)
    piper-taz:  S(MIC50): ≤0.03, MIC90: 0.25, RNG: (≤0.03-2)
    tica-clav:  Var(MIC50): 1, MIC90: 32, RNG: (0.06–32)
    ertapenem:  S(0.06/0.5)
    imipenem:  S(MIC50): 0.03, MIC90: 0.06, RNG: (≤0.03-0.25)
    meropenem:  S(MIC50): 0.062, MIC90: 0.25, RNG: (0.06-0.5)
    cefoxitin:  S(MIC50): 1, MIC90: 2, RNG: (1-2)
    ceftazidime:  R(MIC50): 8, MIC90: 32, RNG: (0.25–32)
    azithromycin:  R(MIC50): 4, MIC90: >32, RNG: (0.06–>32)
    erythromycin:  R(MIC50): 4, MIC90: >32, RNG: (0.06–>32)
    fidaxomicin:  Var(MIC50): 2, MIC90: 128, RNG: (0.25–256)
    clarithromycin:  Var(MIC50): 0.5, MIC90: >32, RNG: (0.06–>32)
    pristinamycin:  S(MIC50): 0.12, MIC90: 1, RNG: (0.03–2)
    quin-dalf:  S(MIC50): 0.25, MIC90: 1, RNG: (0.125-2)
    roxithromycin:  R(MIC50): 8, MIC90: >32, RNG: (0.06–>32)
    telithromycin:  Var(MIC50): 0.06, MIC90: >32, RNG: (0.06–>32)
    linezolid:  Var(MIC50): 2, MIC90: 4RNG: (0.25-8
    ciprofloxacin:  Var(MIC50): 1, MIC90: 16, RNG: (0.12-16)
    levofloxacin:  Var(MIC50): 0.5, MIC90: 4, RNG: (0.12-4)
    moxifloxacin:  S(MIC50): 0.5, MIC90: 1, RNG: (0.06–8)
    ofloxacin:  Var(MIC50): 1, MIC90: 8, RNG: (0.12-8)
    Tetracyclines (μg/mL) Vancomycin Class (μg/mL) Polypep/ketides (μg/mL) Heterocycles (μg/mL) Other (μg/mL)
    tigecycline:  S(MIC50): 0.125, MIC90: 0.5, RNG: (0.125–0.5)
    dalbavancin:  S(MIC50): 0.25, MIC90: 1, RNG: (0.06-2)
    teicoplanin:  S(MIC50): 0.125, MIC90: 0.125, RNG: (0.06–0.25)
    vancomycin:  S(MIC50): 0.125, MIC90: 0.25, RNG: (0.06-0.25)
    bacitracin:  Var(MIC50): 4, MIC90: >128, RNG: (0.25–>128)
    chloramphenicol:  S(MIC50): 2, MIC90: 8, RNG: (0.25–8)
    metronidazole:  S(MIC50): 0.25, MIC90: 1, RNG: (0.02-1)
    clindamycin:  S(MIC50): 0.06, MIC90: 0.5, RNG: (0.02-1)
    daptomycin:  Var(MIC50): 0.5, MIC90: 16, RNG: (0.06->32)

    References

    SPECIFIC REFERENCES FOR EUBACTERIUM LIMOSUM
  • Goldstein2003 - In Vitro Activities of Daptomycin, Vancomycin, Quinupristin- Dalfopristin, Linezolid, and Five Other Antimicrobials against 307 Gram-Positive Anaerobic and 31 Corynebacterium Clinical Isolates.
  • Cato1981 - Designation of Eubacterium limosum (Eggerth) Prevot as the Type Species of Eubacterium Request for an Opinion.
  • Kanauchi2006 - Eubacterium limosum ameliorates experimental colitis and metabolite of microbe attenuates colonic inflammatory action with increase of mucosal integrity.
  • Moore1965 - Synonymy of Eubacterium limosum and Butyribacterium rettgeri: Butyribacterium limosum comb. nov.
  • Schwiertz2000 - Quantification of Different Eubacterium spp. in Human Fecal Samples with Species-Specific 16S rRNA-Targeted Oligonucleotide Probes.
  • Wade2011aBergeys - Bergey's manual of systematic bacteriology. Vol. 3, The Firmicutes. Family Eubacteriaceae, Genus I. Eubacterium
  • Schippa2013 - Cystic fibrosis transmembrane conductance regulator (CFTR) allelic variants relate to shifts in faecal microbiota of cystic fibrosis patients
  • Laue2020 - Prospective associations of the infant gut microbiome and microbial function with social behaviors related to autism at age 3 years
  • 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.
  • Citron2012a - Comparative in vitro activities of LFF571 against Clostridium difficile and 630 other intestinal strains of aerobic and anaerobic bacteria.
  • Goldstein2006 - In vitro activity of moxifloxacin against 923 anaerobes isolated from human intra-abdominal infections.
  • Goldstein2005 - Comparative in vitro activities of XRP 2868, pristinamycin, quinupristin-dalfopristin, vancomycin, daptomycin, linezolid, clarithromycin, telithromycin, clindamycin, and ampicillin against anaerobic gram-positive species, actinomycetes, and lactobacilli.
  • Citron2003 - In vitro activities of ramoplanin, teicoplanin, vancomycin, linezolid, bacitracin, and four other antimicrobials against intestinal anaerobic bacteria.
  • Citron2001 - Comparative in vitro activities of ABT-773 against 362 clinical isolates of anaerobic bacteria.
  • Goldstein2000a - Comparative In vitro activities of ertapenem (MK-0826) against 1,001 anaerobes isolated from human intra-abdominal infections.
  • Goldstein1991 - Goldstein EJ, Citron DM. Susceptibility of anaerobic bacteria isolated from intra-abdominal infections to ofloxacin and interaction of ofloxacin with metronidazole.
  • ...............................
    • GUT MICROBIOME COMPILATIONS AND METASTUDIES FOR EUBACTERIUM LIMOSUM
  • Benno1989 - Comparison of fecal microflora of elderly persons in rural and urban areas of Japan.
  • Byrd2020 - Stability and dynamics of the human gut microbiome and its association with systemic immune traits.
  • Dubinkina2017 - Links of gut microbiota composition with alcohol dependence syndrome and alcoholic liver disease
  • Finegold1974 - Effect of diet on human fecal flora: comparison of Japanese and American diets
  • Forster2019 - A human gut bacterial genome and culture collection for improved metagenomic analyses.
  • Hu2019 - The Gut Microbiome Signatures Discriminate Healthy From Pulmonary Tuberculosis Patients
  • King2019 - Baseline human gut microbiota profile in healthy people and standard reporting template.
  • Lagier2016 - Culture of previously uncultured members of the human gut microbiota by culturomics.
  • MacFarlane2004 - Chemotaxonomic analysis of bacterial populations colonizing the rectal mucosa in patients with ulcerative colitis.
  • Moore1974 - Human fecal flora: the normal flora of 20 Japanese-Hawaiians.
  • New2022 - Collective effects of human genomic variation on microbiome function.
  • Pfleiderer2013 - Culturomics identified 11 new bacterial species from a single anorexia nervosa stool sample.
  • Qin2012 - Metagenome-wide association study of gut microbiota in type 2 diabetes
  • RajilicStojanovic2014 - The first 1000 cultured species of the human gastrointestinal microbiota.
  • Salonen2014 - Impact of diet and individual variation on intestinal microbiota composition and fermentation products in obese men.
  • Woodmansey2004 - Comparison of compositions and metabolic activities of fecal microbiotas in young adults and in antibiotic-treated and non-antibiotic-treated elderly subjects.
  • Zeller2014 - Potential of fecal microbiota for early-stage detection of colorectal cancer
  • ...............................
    • GENERAL REFERENCES FOR EUBACTERIUM LIMOSUM
  • Ludwig2009 - Revised road map to the phylum Firmicutes.
    • Added: February 08, 2021