Roseburia intestinalis

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

Overview

  • Roseburia intestinalis is a Gram-variable, strictly anaerobic, motile, rod-shaped - curved bacterium. It has been detected in at least 29 gut microbiome compilation studies or metastudies. The DNA G+C content is 42.6%. Roseburia intestinalis is often a widespread coloniser of gut. (Duncan2002b; Stanton2011Bergey)



  • 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 (Duncan2002b); (Stanton2011Bergey);
    Character Response
  • Substrates hydrolysed or digested:
  • aesculin;
  • H+
  • Acid from carbohydrates usually produced:
  • glucose; xylose; starch; xylan; raffinose; sucrose;
  • ⥅
  • Substrates assimilated or utilised:
  • L-arabinose; cellubiose; aesculin; fructose; glucose; maltose; raffinose; starch; sucrose; xylan; xylose; acetate;
  • Active enzymes:
  • α-galactosidase; β-galactosidase; α-glucosidase; β-glucosidase;
  • ±
  • Strain-dependent active enzymes:
  • N-Ac β-glucosaminidase;
    • SPECIAL FEATURES (Duncan2002b); (Stanton2011Bergey);
    Character Response
  • ✓
  • Metabolites produced:
  • formate; butyrate (major);
  • ✗
  • Metabolites not produced:
  • lactate; indole;
  • ✗
  • 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; gatifloxacin; moxifloxacin; sarafloxacin; sparfloxacin;
  • ciprofloxacin; clavulanic-acid; nalidixic-acid; norfloxacin; ofloxacin; pefloxacin; pipemidic-acid;
  • Aminoglycosides:
  • dihydrostreptomycin; gentamicin; sisomicin; spectinomycin;
  • kanamycin; neomycin; streptomycin;
  • 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

    This is a common and important member of the human gut microbiome. This organism can utilise xylan, a group of hemicelluloses, eg:

    (By Yikrazuul - Own work by uploader; PMID 15944805, Public Domain, https://commons.wikimedia.org/w/index.php?curid=7141810)

    Fuel sources used:
    It can use resistant starch, fibre, simple sugars and acetate for energy.

    Metabolites produced:
    Our genomic analysis indicates that most members of this species can produce the following metabolites: acetate, ammonia, B-glucuronidase, 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:
    This species has been observed at reduced levels in individuals with type 2 diabetes and children and adolescents with new-onset Crohn's disease.

  • Complementary studies have shown that Roseburia spp. play an important role in the control of gut inflammatory processes, amelioration of atherosclerosis and in the maturation of the immune system, primarily through the production of butyrate. [PMID: 30796211] A detailed investigation of the phenotypic and phylogenetic characteristics of the strain L1-82T (= DSM 14610T = NCIMB 13810T) revealed that they represent a novel species of anaerobic, low-G+C-content, butyrate-producing bacterium that shows net acetate utilization during growth on media containing carbohydrates and short-chain fatty acids. [PMID: 12361264]

    R. intestinalisis also a major xylanolytic bacterium in the colon, producing butyrate upon fermentation of xylan-rich substrates. [PMID: 20105245] The end-products of xylose fermentation by Roseburia sp. XB6B4 were butyrate, formate and lactate. In addition, Roseburia strain XB6B4 was shown to produce large amounts of H2 during xylose fermentation. [PMID: 17391327] Roseburia spp., together with Faecalibacterium prausnitzii and Eubacterium rectale, constitute a group of dominant butyrate-producing Firmicutes, estimated to account for 7̐24% of the total bacteria in the healthy human colon. R. intestinalis preferentially colonizes the mucin layer and this intimate association to the host may contribute to the local level of butyrate available for the colonic epithelial cells. This species appears to be a specialist able to grow only on a few glycans and has been recently shown to be a prominent xylan degrader in vitro and in the healthy human colon. [PMID: 30796211] Roseburia intestinalis XB6B4 draft genome 4,286,292 bp linear DNA Record removed. This RefSeq genome was suppressed because updated RefSeq validation criteria identified problems with the assembly or annotation. NC_021012.1 GI:479146200 

  • GutFeeling KnowledgeBase COMMENTS [Website]

    Roseburia spp., together with Faecalibacterium prausnitzii and Eubacterium rectale, constitute a group of dominant butyrate-producing Firmicutes, estimated to account for 7̐24% of the total bacteria in the healthy human colon. R. intestinalis preferentially colonizes the mucin layer and this intimate association to the host may contribute to the local level of butyrate available for the colonic epithelial cells. This species appears to be a specialist able to grow only on a few glycans and has been recently shown to be a prominent xylan degrader in vitro and in the healthy human colon. [PMID: 30796211]

  • Duncan, S. H., Hold, G. L., Barcenilla, A., Stewart, C. S., & Flint, H. J. (2002). Roseburia intestinalis sp. nov., a novel saccharolytic, butyrate-producing bacterium from human faeces. International Journal of Systematic and Evolutionary Microbiology, 52(Pt 5), 1615–1620.

    • Details

    GENERAL
    Lineage Physiology General Growth Tolerances Hydrol./digest./degr.
    Phylum:  Firmicutes Class:  Clostridia Order:  Eubacteriales Family:  Lachnospiraceae Genus:  Roseburia Gram stain:  vr O2 Relation.:  strictly anaerobic Motility:  Swimming Morphology:  Rod - curved
    Health:   Positive
    Source:  human faeces
    DNA G+C(%):  42.6
    		Aesculin:  + Urea:  neg
    CARBOHYDRATE ACID FORMATION
    Monosaccharide O/F Oligosaccharide O/F Polysaccharide O/F Polyol O/F Other O/F
    Glucose:  + Mannose:  neg Rhamnose:  neg Xylose:  + Melezitose:  neg Sucrose:  + Trehalose:  neg Inulin:  neg Starch:  + Xylan:  + Mannitol:  neg
    SUBSTRATE ASSIMILATION & UTILISATION
    Monosaccharide util/assim Oligosaccharide util/assim Other carboh. util/assim Amino acid util/assim Organic acid util/assim
    L-Arabinose:  + Fructose:  + Glucose:  + Rhamnose:  neg Ribose:  neg Xylose:  + Cellubiose:  + Maltose:  + Melezitose:  neg Melibiose:  w Raffinose:  + Sucrose:  + Trehalose:  neg Dulcitol:  neg Aesculin:  + Glycerol:  neg Inulin:  neg Mannitol:  neg Salicin:  neg Sorbitol:  neg Starch:  + Xylan:  + Acetate:  + Lactate:  neg
    ENZYME ACTIVITY
    Enzymes: General Enzymes: Carbohydrate Enzymes: Protein Enzymes: Arylamidases Enzymes: Esters/fats
    Catalase:  neg Urease:  neg Ac-β-glcamnd:  d α-Fucosidase:  neg α-Galactosidase:  + β-Galactosidase:  + α-Glucosidase:  + β-Glucosidase:  + 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:  + Butyrate:  Major(+) Lactate:  neg 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(0.375)
    piperacillin:  S(0.315)
    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(0.094)
    ceftazidime:  S(1)
    cefuroxime:  Sens
    cephalothin:  Sens
    moxalactam:  Sens
    amikacin:  Var(MIC50): 12), MIC90: Var(12
    dihydrostrept:  Sens
    gentamicin:  Sens
    kanamycin:  Res
    neomycin:  Res
    sisomicin:  Sens
    spectinomycin:  Sens
    streptomycin:  Res
    tobramycin:  Var(MIC50): 16), MIC90: Var(16
    azithromycin:  S(1)
    erythromycin:  S(4)
    clarithromycin:  S(0.5)
    roxithromycin:  Sens
    spiramycin:  S(0.064)
    josamycin:  Sens
    linezolid:  S(2)
    ciprofloxacin:  R(>32)
    clavulanate:  Res
    clinafloxacin:  Sens
    enoxacin:  Sens
    gatifloxacin:  S(3)
    moxifloxacin:  S(6)
    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(8)
    chlortetracycline:  Sens
    meclocycline:  Sens
    methacycline:  Sens
    minocycline:  Sens
    oxytetracycline:  Sens
    tetracycline:  Sens
    tigecycline:  S(<0.016)
    teicoplanin:  S(0.094)
    vancomycin:  S(0.25)
    bacitracin:  Sens
    rifabutin:  Sens
    rifampicin:  Sens
    rifapentine:  Sens
    chloramphenicol:  S(2)
    fosfomycin:  R(32)
    isoniazid:  Res
    metronidazole:  S(0.5)
    nitrofurantoin:  Sens
    sulfadiazine:  Res
    sulfadimethoxine:  Res
    sulfamethoxazole:  R(>1024)
    sulfanilamide:  Res
    trimethoprim:  R(>32)
    SXT:  R(>32)
    clindamycin:  S(<0.016)
    lincomycin:  Sens
    colistin:  S(6)
    fusidic-acid:  Sens

    References

    SPECIFIC REFERENCES FOR ROSEBURIA INTESTINALIS
  • Duncan2002b - Roseburia intestinalis sp. nov., a novel saccharolytic, butyrate-producing bacterium from human faeces.
  • Stanton2011Bergey - Bergey's manual of systematic bacteriology. Vol. 3, The Firmicutes. Family Lachnospiraceae, Genus XVI. Roseburia
  • Borgo2017 - Microbiota in anorexia nervosa: The triangle between bacterial species, metabolites and psychological tests
  • DeAngelis2013 - Fecal microbiota and metabolome of children with autism and pervasive developmental disorder not otherwise specified
  • Debyser2016 - Faecal proteomics: A tool to investigate dysbiosis and inflammation in patients with cystic fibrosis
  • Finegold2010 - Pyrosequencing study of fecal microflora of autistic and control children
  • Hayden2020 - Fecal dysbiosis in infants with cystic fibrosis is associated with early linear growth failure
  • Hoffman2014 - Escherichia coli dysbiosis correlates with gastrointestinal dysfunction in children with cystic fibrosis
  • Hu2019 - The Gut Microbiome Signatures Discriminate Healthy From Pulmonary Tuberculosis Patients
  • Jie2017 - The gut microbiome in atherosclerotic cardiovascular disease
  • Kinumaki2015 - Characterization of the gut microbiota of Kawasaki disease patients by metagenomic analysis
  • Li2012 - Molecular-phylogenetic characterization of the microbiota in ulcerated and non-ulcerated regions in the patients with Crohn's disease
  • Qin2012 - Metagenome-wide association study of gut microbiota in type 2 diabetes
  • Qin2014 - Alterations of the human gut microbiome in liver cirrhosis
  • Sjodin2019 - Temporal and long-term gut microbiota variation in allergic disease: A prospective study from infancy to school age
  • Takahashi2016 - Reduced Abundance of Butyrate-Producing Bacteria Species in the Fecal Microbial Community in Crohn's Disease
  • VichVila2018 - Gut microbiota composition and functional changes in inflammatory bowel disease and irritable bowel syndrome
  • VillanuevaMillan2019 - Characterization of gut microbiota composition in HIV-infected patients with metabolic syndrome
  • Yu2015 - Metagenomic analysis of faecal microbiome as a tool towards targeted non-invasive biomarkers for colorectal cancer
  • Luna2016 - Distinct Microbiome-Neuroimmune Signatures Correlate With Functional Abdominal Pain in Children With Autism Spectrum Disorder.
  • ...............................
    • GUT MICROBIOME COMPILATIONS AND METASTUDIES FOR ROSEBURIA INTESTINALIS
  • Browne2016 - Culturing of 'unculturable' human microbiota reveals novel taxa and extensive sporulation.
  • 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
  • Dubinkina2017 - Links of gut microbiota composition with alcohol dependence syndrome and alcoholic liver disease
  • 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
  • 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
  • McLaughlin2010 - The bacteriology of pouchitis: a molecular phylogenetic analysis using 16S rRNA gene cloning and sequencing.
  • Minerbi2019 - Altered microbiome composition in individuals with fibromyalgia
  • New2022 - Collective effects of human genomic variation on microbiome function.
  • Nielsen2014 - MetaHIT Consortium. Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes.
  • PerisBondia2011 - The active human gut microbiota differs from the total microbiota.
  • 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.
  • ...............................
    • GENERAL REFERENCES FOR ROSEBURIA INTESTINALIS
  • Ludwig2009 - Revised road map to the phylum Firmicutes.
    • Added: February 08, 2021