Eubacterium rectale

(aka Agathobacter rectalis)

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

Overview

  • Eubacterium rectale, (aka Agathobacter rectalis), is a Gram-positive, spore-forming, strictly anaerobic, motile, rod-shaped - curved bacterium. It has been detected in at least 36 gut microbiome compilation studies or metastudies. The DNA G+C content is 41.5%. Eubacterium rectale is often a widespread coloniser of gut. (Browne2016; Wade2011Bergeys; Rosero2016)



  • This organism has been recovered from human faeces. 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 (Wade2011Bergeys); (Rosero2016);
    Character Response
  • Substrates hydrolysed or digested:
  • aesculin; starch;
  • 🧂
  • Salt tolerance:
  • doesn't tolerate 6.5% salt;
  • 💧
  • Bile tolerance:
  • Doesn't tolerate 20% bile
  • 🌡
  • Temperature tolerance:
  • grows at 25℃; grows at 45℃; Grows optimally at 37℃.
  • H+
  • Acid from carbohydrates usually produced:
  • L-arabinose; fructose; glucose; mannose; xylose; amygdalin; cellulose; glycogen; cellubiose; lactose; maltose; melezitose; melibiose; raffinose; sucrose; trehalose; mannitol; xylitol; N-Ac glucosamine;
  • ±
  • Strain-dependent acid from carbs:
  • salicin;
  • ⥅
  • Substrates assimilated or utilised:
  • melibiose; acetate; pyruvate;
  • Active enzymes:
  • α-galactosidase; β-galactosidase; α-glucosidase;
    • SPECIAL FEATURES (Wade2011Bergeys); (Rosero2016);
    Character Response
  • ✓
  • Metabolites produced:
  • formate (minor); acetate; butyrate (major); lactate; H₂;
  • ✗
  • Metabolites not produced:
  • propionate; H₂S; ammonia; indole;
  • ✗
  • VP test:
  • not active
  • ✗
  • Nitrate:
  • not reduced
    • RESPONSE TO ANTIBIOTICS
    Class Active Resistant
  • Penicillins:
  • amoxicillin; amoxicillin-clavulanic acid; ampicillin; azlocillin; bacampicillin; benzylpenicillin; cloxacillin; dicloxacillin; imipenem; meropenem; oxacillin; piperacillin; ticarcillin;
  • aztreonam;
  • 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; tigecycline;
  • Quinolines:
  • clinafloxacin; enoxacin; sarafloxacin; sparfloxacin;
  • ciprofloxacin; clavulanic-acid; moxifloxacin; nalidixic-acid; norfloxacin; ofloxacin; pefloxacin; pipemidic-acid;
  • Aminoglycosides:
  • spectinomycin;
  • amikacin; dihydrostreptomycin; gentamicin; kanamycin; neomycin; sisomicin; streptomycin; tobramycin;
  • Polypep/ketides:
  • bacitracin; rifabutin; rifampicin; rifapentine;
  • Heterocycles:
  • chloramphenicol; fusidic-acid; metronidazole; nitrofurantoin;
  • fosfomycin; isoniazid; sulfadiazine; sulfadimethoxine; sulfamethoxazole; sulfanilamide; trimethoprim; trimethoprim-sulfamethoxazole;
  • Vancomycins:
  • vancomycin; teicoplanin;
  • Miscellaneous antibiotics:
  • clindamycin; lincomycin; linezolid;
  • colistin;
  • NOTES

    Previously named Eubacterium rectale, this is a common member of the human gut.

    Fuel sources used:
    It can use resistant plant resistant starches after initial degradation by Ruminococcus bromii.

    Metabolites produced:
    Our genomic analysis indicates that most members of this species can produce the following metabolites: acetate, BCAAs, butyrate, 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:
    Low levels of this bacterium have been observed in Crohn's disease and ulcerative colitis.

  • N/A

  • E. rectale is one of the major species in the human colon that is responsible for butyrate formation. This is an important trait, as butyrate, which is one of the three major short chain fatty acids (SCFA) formed in the colon, is the preferred energy source for colonocytes and has a protective effect against colon disease. [PMID: 18599726]

  • GutFeeling KnowledgeBase COMMENTS [Website]

    Eubacterium rectale is one of the most abundant bacterial species recovered from human faeces. E. rectale(Hauduroy et al. 1937) appears in the ��List of Bacterial Names with Standing in Nomenclature̥, but it is noted that the originally proposed type strain, VPI 0989T, has been lost and its possible replacement by another strain (VPI 0990) from the same faecal sample has never been formally proposed. It is therefore proposed that strain A1-86 (=DSM 17629=NCIMB 14373), isolated from human adult faeces, be formally recognized as the neotype strain of Eubacterium rectale. [PMID: 18599726]

  • 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 Alt. name:  Agathobacter rectalis Gram stain:  + O2 Relation.:  strictly anaerobic Spore:  Endospore Motility:  Swimming Morphology:  Rod - curved
    Health:   Positive
    Source:  human faeces
    DNA G+C(%):  41.5
    Opt. T:  37℃
    Lower T(℃):  25(+)
    High T(℃):  45(+)
    NaCl >6%:  6.5(neg)
    Bile reaction(%):  20(neg)
    		Aesculin:  + Urea:  neg Gelatin:  neg Starch:  + Hippurate:  neg Milk:  neg Meat:  neg
    CARBOHYDRATE ACID FORMATION
    Monosaccharide O/F Oligosaccharide O/F Polysaccharide O/F Polyol O/F Other O/F
    L-Arabinose:  w(+) Fructose:  + Glucose:  + Mannose:  d(+) Rhamnose:  neg Ribose:  neg Xylose:  + Cellubiose:  w(+) Lactose:  d(+) Maltose:  + Melezitose:  + Melibiose:  + Sucrose:  + Trehalose:  d(+) Amygdalin:  d(+) Cellulose:  + Aesculin:  neg Glycogen:  d(+) Starch:  w Mannitol:  d(+) Sorbitol:  w Xylitol:  + NAc-α-GA:  + Salicin:  d
    SUBSTRATE ASSIMILATION & UTILISATION
    Monosaccharide util/assim Oligosaccharide util/assim Other carboh. util/assim Amino acid util/assim Organic acid util/assim
    Melibiose:  w(+) Acetate:  + Lactate:  neg Pyruvate:  +
    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:  + β-Galactosidase:  + α-Glucosidase:  + β-Glucosidase:  vr 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

    Resistant Starch

    Branched-Chain AA, Cobalamin, Folate, Biotin, Riboflavin, Acetate, Lactate, Butyrate

    		Formate:  minor(+) Acetate:  + Propionate:  neg Butyrate:  Major(+) Lactate:  + H2S:  neg Ammonia:  neg H2:  + Indole:  neg
    ANTIBIOTICS ℞
    Penicillins & Penems (μg/mL) Cephalosporins (μg/mL) Aminoglycosides (μg/mL) Macrolides (μg/mL) Quinolones (μg/mL)
    amoxicillin:  S(0.25)
    Augmentin:  S(0.064)
    ampicillin:  Sens
    azlocillin:  Sens
    aztreonam:  Res
    bacampicillin:  Sens
    benzyl-pen:  Sens
    cloxacillin:  Sens
    dicloxacillin:  Sens
    oxacillin:  S(2)
    piperacillin:  S(0.2)
    ticarcillin:  Sens
    imipenem:  Sens
    meropenem:  S(0.064)
    cefaclor:  Sens
    cefadroxil:  Res
    cefazolin:  Sens
    cefdinir:  Sens
    cefepime:  Sens
    cefixime:  Sens
    cefmetazole:  Sens
    cefoperazone:  Sens
    cefotaxime:  S(1)
    cefotetan:  Sens
    cefotiam:  Sens
    cefoxitin:  S(7)
    ceftazidime:  S(4)
    cefuroxime:  Sens
    cephalothin:  Sens
    moxalactam:  Sens
    amikacin:  R(48)
    dihydrostrept:  Res
    gentamicin:  Res
    kanamycin:  Res
    neomycin:  Res
    sisomicin:  Res
    spectinomycin:  Sens
    streptomycin:  Res
    tobramycin:  R(24)
    azithromycin:  S(0.094)
    erythromycin:  S(0.38)
    clarithromycin:  S(0.094)
    roxithromycin:  Sens
    spiramycin:  S(0.016)
    josamycin:  Sens
    linezolid:  S(1.5)
    ciprofloxacin:  R(>32)
    clavulanate:  Res
    clinafloxacin:  Sens
    enoxacin:  Sens
    gatifloxacin:  Var(MIC50): 4), MIC90: Var(4
    moxifloxacin:  R(>32)
    nalidixic-acid:  Res
    norfloxacin:  R(>256)
    ofloxacin:  R(>32)
    pefloxacin:  Res
    pipemidic_acid:  Res
    sarafloxacin:  Sens
    sparfloxacin:  Sens
    Tetracyclines (μg/mL) Vancomycin Class (μg/mL) Polypep/ketides (μg/mL) Heterocycles (μg/mL) Other (μg/mL)
    doxycycline:  S(0.094)
    chlortetracycline:  Sens
    meclocycline:  Sens
    methacycline:  Sens
    minocycline:  Sens
    oxytetracycline:  Sens
    tetracycline:  Sens
    tigecycline:  S(<0.016)
    teicoplanin:  S(0.064)
    vancomycin:  S(1)
    bacitracin:  Sens
    rifabutin:  Sens
    rifampicin:  Sens
    rifapentine:  Sens
    chloramphenicol:  S(3)
    fosfomycin:  R(>1024)
    isoniazid:  Res
    metronidazole:  S(1.5)
    nitrofurantoin:  Sens
    sulfadiazine:  Res
    sulfadimethoxine:  Res
    sulfamethoxazole:  R(>1024)
    sulfanilamide:  Res
    trimethoprim:  R(>32)
    SXT:  R(>32)
    clindamycin:  S(<0.016)
    lincomycin:  Sens
    colistin:  R(32)
    fusidic-acid:  Sens

    References

    SPECIFIC REFERENCES FOR EUBACTERIUM RECTALE
  • Browne2016 - Culturing of 'unculturable' human microbiota reveals novel taxa and extensive sporulation.
  • Zuo2016 - Whole-genome-based phylogeny supports the objections against the reclassification of Eubacterium rectale to Agathobacter rectalis.
  • Wade2011Bergeys - Bergey's manual of systematic bacteriology. Vol. 3, The Firmicutes. Family Eubacteriaceae, Genus I. Eubacterium
  • Salyers1977 - Fermentation of mucins and plant polysaccharides by anaerobic bacteria from the human colon
  • Bojovic2020 - Gut Microbiota Dysbiosis Associated With Altered Production of Short Chain Fatty Acids in Children With Neurodevelopmental Disorders
  • Gao2020 - Functional Microbiomics Reveals Alterations of the Gut Microbiome and Host Co-Metabolism in Patients With Alcoholic Hepatitis
  • Balamurugan2008 - Real-time polymerase chain reaction quantification of specific butyrate-producing bacteria, Desulfovibrio and Enterococcus faecalis in the feces of patients with colorectal cancer
  • Balamurugan2010 - Quantitative differences in intestinal Faecalibacterium prausnitzii in obese Indian children
  • Bedarf2017 - Functional implications of microbial and viral gut metagenome changes in early stage L-DOPA-naïve Parkinson's disease patients
  • Benjamin2012 - Smokers with active Crohn's disease have a clinically relevant dysbiosis of the gastrointestinal microbiota
  • Cattaneo2017 - Association of brain amyloidosis with pro-inflammatory gut bacterial taxa and peripheral inflammation markers in cognitively impaired elderly
  • Coretti2018 - Gut Microbiota Features in Young Children With Autism Spectrum Disorders
  • Debyser2016 - Faecal proteomics: A tool to investigate dysbiosis and inflammation in patients with cystic fibrosis
  • deGoffau2014 - Aberrant gut microbiota composition at the onset of type 1 diabetes in young children
  • Giongo2011 - Toward defining the autoimmune microbiome for type 1 diabetes
  • Hedin2015 - Siblings of patients with Crohn's disease exhibit a biologically relevant dysbiosis in mucosal microbial metacommunities
  • Hu2019 - The Gut Microbiome Signatures Discriminate Healthy From Pulmonary Tuberculosis Patients
  • Hu2020 - Characterizing the gut microbiota in patients with chronic kidney disease
  • Jiang2018 - Altered gut microbiota profile in patients with generalized anxiety disorder
  • Kamo2017 - Dysbiosis and compositional alterations with aging in the gut microbiota of patients with heart failure
  • Kang2010 - Dysbiosis of fecal microbiota in Crohn's disease patients as revealed by a custom phylogenetic microarray
  • Kim2018 - Imbalance of gut microbiome and intestinal epithelial barrier dysfunction in patients with high blood pressure
  • Knoll2017 - Gut microbiota differs between children with Inflammatory Bowel Disease and healthy siblings in taxonomic and functional composition: a metagenomic analysis
  • Liu2019b - Altered gut microbiota and short chain fatty acids in Chinese children with autism spectrum disorder
  • Lun2018 - Altered gut microbiota and microbial biomarkers associated with chronic kidney disease
  • Manor2016 - Metagenomic evidence for taxonomic dysbiosis and functional imbalance in the gastrointestinal tracts of children with cystic fibrosis
  • Miragoli2017 - Impact of cystic fibrosis disease on archaea and bacteria composition of gut microbiota
  • Miyake2015 - Dysbiosis in the Gut Microbiota of Patients with Multiple Sclerosis, with a Striking Depletion of Species Belonging to Clostridia XIVa and IV Clusters
  • Moore1995 - Intestinal floras of populations that have a high risk of colon cancer
  • Olbjorn2019 - Fecal microbiota profiles in treatment-naïve pediatric inflammatory bowel disease - associations with disease phenotype, treatment, and outcome
  • Qi2019 - Intestinal Microbiota Is Altered in Patients with Gastric Cancer from Shanxi Province, China
  • Qin2012 - Metagenome-wide association study of gut microbiota in type 2 diabetes
  • Qin2014 - Alterations of the human gut microbiome in liver cirrhosis
  • Tarallo2019 - Altered Fecal Small RNA Profiles in Colorectal Cancer Reflect Gut Microbiome Composition in Stool Samples
  • Vaahtovuo2008 - Fecal microbiota in early rheumatoid arthritis
  • VichVila2018 - Gut microbiota composition and functional changes in inflammatory bowel disease and irritable bowel syndrome
  • Wang2020a - Aberrant gut microbiota alters host metabolome and impacts renal failure in humans and rodents
  • Zeller2014 - Potential of fecal microbiota for early-stage detection of colorectal cancer
  • Zhang2018a - Gut microbiota dysbiosis in male patients with chronic traumatic complete spinal cord injury
  • Zhang2019b - Dysbiosis of gut microbiota is associated with serum lipid profiles in male patients with chronic traumatic cervical spinal cord injury
  • Zhu2018 - Dysbiosis signatures of gut microbiota in coronary artery disease
  • Zuo2020 - Alterations in Gut Microbiota of Patients With COVID-19 During Time of Hospitalization
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  • Mahowald2009 - Characterizing a model human gut microbiota composed of members of its two dominant bacterial phyla.
  • Rosero2016 - Reclassification of Eubacterium rectale (Hauduroy et al. 1937) Prevot 1938 in a new genus Agathobacter gen. nov. as Agathobacter rectalis comb. nov., and description of Agathobacter ruminis sp. nov., isolated from the rumen contents of sheep and cows.
  • ...............................
    • GUT MICROBIOME COMPILATIONS AND METASTUDIES FOR EUBACTERIUM RECTALE
  • Benno1984 - The intestinal microflora of infants: composition of fecal flora in breast-fed and bottle-fed infants.
  • Benno1986 - Comparison of the fecal microflora in rural Japanese and urban Canadians.
  • Benno1989 - Comparison of fecal microflora of elderly persons in rural and urban areas of Japan.
  • Browne2016 - Culturing of 'unculturable' human microbiota reveals novel taxa and extensive sporulation.
  • 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
  • Chung2016 - Modulation of the human gut microbiota by dietary fibres occurs at the species level.
  • Finegold1974 - Effect of diet on human fecal flora: comparison of Japanese and American diets
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  • 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
  • Karlsson2013 - Gut metagenome in European women with normal, impaired and diabetic glucose control
  • 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.
  • LeChatelier2013 - Richness of human gut microbiome correlates with metabolic markers
  • MacFarlane2004 - Chemotaxonomic analysis of bacterial populations colonizing the rectal mucosa in patients with ulcerative colitis.
  • Mangin2004 - Molecular inventory of faecal microflora in patients with Crohn's disease.
  • McLaughlin2010 - The bacteriology of pouchitis: a molecular phylogenetic analysis using 16S rRNA gene cloning and sequencing.
  • Moore1995 - Intestinal floras of populations that have a high risk of colon cancer
  • Nielsen2014 - MetaHIT Consortium. Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes.
  • 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.
  • Urban2020 - Altered Fecal Microbiome Years after Traumatic Brain Injury
  • 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
  • Woodmansey2004 - Comparison of compositions and metabolic activities of fecal microbiotas in young adults and in antibiotic-treated and non-antibiotic-treated elderly subjects.
  • 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.
  • ...............................
    • GENERAL REFERENCES FOR EUBACTERIUM RECTALE
  • Ludwig2009 - Revised road map to the phylum Firmicutes.
    • Added: February 08, 2021