Phocaeicola dorei

(aka Bacteroides dorei)

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

Overview

  • Phocaeicola dorei, (aka Bacteroides dorei), is a Gram-negative, non-spore-forming, 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 43%. Phocaeicola dorei is often a widespread coloniser of gut. (Song2010Bergeys; Bakir2006b; Terekhov2018)



  • This organism has been recovered from human faeces (Alkhalil2017) and clinical sources (blood - CCUG). The risk classification (www.baua.de) for this organism is 1, i.e., low risk of infection and spread. Is a rare opportunistic pathogen. Is a known gut commensal. Robust growth can have mixed consequences for gut health.
    • GENERAL CHARACTERISTICS (Song2010Bergeys); (Bakir2006b);
    Character Response
  • 💧
  • Bile tolerance:
  • Grows in the presence of bile
  • 🌡
  • Temperature tolerance:
  • grows at 37℃; Grows optimally at 37℃.
  • H+
  • Acid from carbohydrates usually produced:
  • arabinose; glucose; mannose; rhamnose; xylose; lactose; maltose; raffinose; sucrose;
  • Active enzymes:
  • Ala arylamidase; alkaline phosphatase; arabinosidase; Arg arylamidase; N-Ac β-glucosaminidase; fucosidase; α-galactosidase; β-galactosidase; α-glucosidase; β-glucosidase; β-glucuronidase; glutamic acid decarboxylase; Glu-Glu arylamidase; Gly arylamidase; His arylamidase; Leu arylamidase; Leu-Gly arylamidase; Phe arylamidase; Ser arylamidase; Tyr arylamidase;
    • SPECIAL FEATURES (Song2010Bergeys); (Bakir2006b);
    Character Response
  • ✗
  • Metabolites not produced:
  • indole;
  • ✗
  • Nitrate:
  • not reduced
    • RESPONSE TO ANTIBIOTICS (Song2010Bergeys); (Goldstein2013b);
    Class Active Resistant
  • Penicillins:
  • meropenem; piperacillin-tazobactam;
  • amoxicillin; oxacillin;
  • Cephalosporins:
  • ceftazidime;
  • Macrolides:
  • clarithromycin; spiramycin;
  • erythromycin;
  • Quinolines:
  • gatifloxacin; moxifloxacin; ofloxacin;
  • norfloxacin;
  • Aminoglycosides:
  • tobramycin;
  • Heterocycles:
  • metronidazole;
  • sulfamethoxazole;
  • NOTES

    This is a common inhabitant of the gut and is closely related to Bacteroides vulgatus.

    Fuel sources used:
    It can use fibre, resistant starch, simple sugars (including lactose), a wide range of proteins and mucus as energy sources.

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

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

    Disease associations:
    High levels of this species have been associated with colon cancer and the development of type 1 diabetes in children.

    Emerging research:
    This species has been associated with diets high in red meat.

    • Details

    GENERAL
    Lineage Physiology General Growth Tolerances Hydrol./digest./degr.
    Phylum:  Bacteroidetes Class:  Bacteroidia Order:  Bacteroidales Family:  Bacteroidaceae Genus:  Phocaeicola Alt. name:  Bacteroides dorei Gram stain:  neg O2 Relation.:  anaerobic Spore:  No spore Motility:  Sessile Morphology:  Rod
    Health:  Mixed
    Source:  human faeces (Alkhalil2017) and clinical sources (blood - CCUG)
    DNA G+C(%):  43
    Opt. T:  37℃
    Mid T(℃):  37(+)
    Bile reaction(%):  +
    		Aesculin:  neg Urea:  neg Gelatin:  neg
    CARBOHYDRATE ACID FORMATION
    Monosaccharide O/F Oligosaccharide O/F Polysaccharide O/F Polyol O/F Other O/F
    Arabinose:  + Glucose:  + Mannose:  + Rhamnose:  + Xylose:  + Cellubiose:  neg Lactose:  + Maltose:  + Melezitose:  neg Sucrose:  + Trehalose:  neg Glycerol:  neg Mannitol:  neg Sorbitol:  neg Salicin:  neg
    ENZYME ACTIVITY
    Enzymes: General Enzymes: Carbohydrate Enzymes: Protein Enzymes: Arylamidases Enzymes: Esters/fats
    Urease:  neg G6PDH6PGDH:  nr α-Arab:  + Ac-β-glcamnd:  + α-Fucosidase:  + α-Galactosidase:  + β-Galactosidase:  + α-Glucosidase:  + β-Glucosidase:  + β-Glucuronidase:  + ArgDH:  neg GluDC:  + AlanineAA:  + ArgAA:  + GluGluAA:  + GlyAA:  + HisAA:  + LeuAA:  + LeuGlyAA:  + ProAA:  neg PheAA:  + PyrogluAA:  neg SerAA:  + TyrAA:  + AlkalineP:  +
    METABOLITES - PRODUCTION & USE
    Fuel Usable Metabolites Metabolites Released Special Products Compounds Produced

    Fibre, Resistant Starch, Mucus, Simple Sugars, Lactose, Protein

    None/Unknown

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

    LPS Antigen

    		 Indole:  neg
    ANTIBIOTICS ℞
    Penicillins & Penems (μg/mL) Cephalosporins (μg/mL) Aminoglycosides (μg/mL) Macrolides (μg/mL) Quinolones (μg/mL)
    amoxicillin:  R(128)
    amp-sulb:  Var(MIC50): 4, MIC90: 16, RNG: (1–32)
    oxacillin:  R(128)
    piperacillin:  Var(MIC50): 32), MIC90: Var(32
    piper-taz:  S(MIC50): 2, MIC90: 8, RNG: (0.06–16)
    meropenem:  S(MIC50): 0.5, MIC90: 1, RNG: (0.125–32)
    cefotaxime:  Var(MIC50): 4), MIC90: Var(4
    cefoxitin:  Var(MIC50): 16, MIC90: 64, RNG: (4–64)
    ceftazidime:  R(MIC50): >128, MIC90: >128, RNG: (16–>128)
    tobramycin:  R(>1024)
    azithromycin:  Var(MIC50): 6), MIC90: Var(6
    erythromycin:  R(24)
    clarithromycin:  S(2)
    spiramycin:  S(1)
    ciprofloxacin:  Var(MIC50): 4), MIC90: Var(4
    gatifloxacin:  S(0.19)
    moxifloxacin:  S(0.38)
    norfloxacin:  R(>256)
    ofloxacin:  S(2)
    Tetracyclines (μg/mL) Vancomycin Class (μg/mL) Polypep/ketides (μg/mL) Heterocycles (μg/mL) Other (μg/mL)
    doxycycline:  Var(MIC50): 3), MIC90: Var(3
    tigecycline:  Var(MIC50): 0.5, MIC90: 8, RNG: (0.125–32)
    metronidazole:  S(MIC50): 2, MIC90: 2, RNG: (0.5–2)
    sulfamethoxazole:  R(24)
    clindamycin:  Var(MIC50): 2, MIC90: >128, RNG: (0.06–>128)

    References

    SPECIFIC REFERENCES FOR PHOCAEICOLA DOREI
  • Wexler2007 - Bacteroides : the Good, the Bad, and the Nitty-Gritty.
  • Song2010Bergeys - Bacteroides. In Bergey's manual of systematic bacteriology: Vol. 4. The Bacteroidetes, Spirochaetes, Tenericutes (Mollicutes), Acidobacteria, Fibrobacteres, Fusobacteria, Dictyoglomi, Gemmatimonadetes, Lentisphaerae, Verrucomicrobia, Chlamydiae, and Planctomycetes
  • Feng2015 - Gut microbiome development along the colorectal adenoma-carcinoma sequence
  • DavisRichardson2014 - Bacteroides dorei dominates gut microbiome prior to autoimmunity in Finnish children at high risk for type 1 diabetes
  • Debyser2016 - Faecal proteomics: A tool to investigate dysbiosis and inflammation in patients with cystic fibrosis
  • 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
  • Huang2019a - Metagenome-wide association study of the alterations in the intestinal microbiome composition of ankylosing spondylitis patients and the effect of traditional and herbal treatment
  • Li2019c - Gut Microbiota Differs Between Parkinson's Disease Patients and Healthy Controls in Northeast China
  • Tarallo2019 - Altered Fecal Small RNA Profiles in Colorectal Cancer Reflect Gut Microbiome Composition in Stool Samples
  • Wang2019 - Differential composition of gut microbiota among healthy volunteers, morbidly obese patients and post-bariatric surgery patients
  • Wang2019b - Alterations in the human gut microbiome associated with Helicobacter pylori infection
  • Wang2019d - Gut Microbiota Dysbiosis Is Associated with Altered Bile Acid Metabolism in Infantile Cholestasis
  • Zhang2019c - Changes of intestinal bacterial microbiota in coronary heart disease complicated with nonalcoholic fatty liver disease
  • Goldstein2013b - Comparative in vitro activities of GSK2251052, a novel boron-containing leucyl-tRNA synthetase inhibitor, against 916 anaerobic organisms.
  • Bakir2006b - Bacteroides dorei sp. nov., isolated from human faeces.
  • Petrov2017 - Analysis of Gut Microbiota in Patients with Parkinson's Disease.
  • Terekhov2018 - Ultrahigh-throughput functional profiling of microbiota communities.
  • Coretti2018 - Gut Microbiota Features in Young Children With Autism Spectrum Disorders
  • ...............................
    • GUT MICROBIOME COMPILATIONS AND METASTUDIES FOR PHOCAEICOLA DOREI
  • Almeida2019 - A new genomic blueprint of the human gut microbiota.
  • 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.
  • RajilicStojanovic2014 - The first 1000 cultured species of the human gastrointestinal microbiota.
  • Rothschild2018 - Environment dominates over host genetics in shaping human gut microbiota.
  • 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
  • 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
  • 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 PHOCAEICOLA DOREI
  • CCUG - Culture Collection University of Gothenburg - Entire Collection
  • Song2010Bergeys - Bacteroides. In Bergey's manual of systematic bacteriology: Vol. 4. The Bacteroidetes, Spirochaetes, Tenericutes (Mollicutes), Acidobacteria, Fibrobacteres, Fusobacteria, Dictyoglomi, Gemmatimonadetes, Lentisphaerae, Verrucomicrobia, Chlamydiae, and Planctomycetes
  • Alkhalil2017 - Bacterial involvements in ulcerative colitis: molecular and microbiological studies
    • Added: February 08, 2021