Microbiome basics
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Microbiome = all microbes + their genomes + the environment they occupy.
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Humans have ~38 trillion microbial cells (more than human cells).
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Major phyla:
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Firmicutes (Gram+ anaerobes)
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Bacteroidetes (Gram– anaerobes)
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Proteobacteria (Gram– facultative rods)
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Actinobacteria (Gram+ bacilli)
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Normal flora by site
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Carrier state: colonization with potential pathogen (e.g., S. aureus).
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Body site |
Common flora |
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Skin |
Staph epidermidis, Corynebacterium, Propionibacterium |
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Mouth/Nasopharynx |
Strep mitis, Neisseria, anaerobes |
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Colon |
Bacteroides, Enterobacteriaceae, Enterococci, anaerobes |
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Vagina |
Lactobacillus, Strep, Corynebacterium, anaerobes |
Functions of the microbiome
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Nutrition:
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Fermentation → SCFAs (butyrate, acetate)
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Vitamin synthesis (e.g., B vitamins, K)
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Immune system bidirectional influence:
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Immune system maturation: evidence: Germ-free mice show impaired immunity (↓ IgA, ↓ dendritic cells)
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Colonization resistance: normal flora prevent pathogen overgrowth.
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Microbiota influence T-cell differentiation (Th1, Th2, Treg)
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Gut–immune–brain axis: Evidence: SCFAs affect CNS, mood, inflammation; dysbiosis linked to autism, depression, Parkinson’s
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Dysbiosis and disease
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Definite links:
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C. difficile infection
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Bacterial vaginosis
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Yeast infections
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Associated conditions:
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Obesity, IBD, diabetes, cardiovascular disease, depression
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Antibiotics and microbiome disruption
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Antibiotics can:
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Kill beneficial flora
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Reduce colonization resistance
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Promote overgrowth of pathogens (e.g., C. difficile)
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Antibiotic overuse:
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270 million prescriptions/year in US
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~30% unnecessary
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↑ resistance, ↑ adverse effects
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Antimicrobial stewardship principles
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4 D’s:
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Right Drug
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Right Dose
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De-escalation
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Right Duration
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Do:
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Get cultures
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Use narrow-spectrum agents
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Follow guidelines
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Don’t:
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Treat colonization
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Use antibiotics for viral infections
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Continue broad-spectrum unnecessarily
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USMLE tips
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Know normal flora by site.
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Understand colonization resistance and carrier state.
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Recognize SCFAs as key modulators/communicators between microbiome and host in immunity and metabolism.
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Link antibiotic use to dysbiosis and resistance.
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Apply stewardship principles in clinical scenarios.
Learning goals
- Explain virulence and how it relates to benign versus pathogenic microorganisms
- Name common bacterial species that are considered normal human flora for each of the following locations: skin, mouth, colon, and vagina, and describe how these organisms enhance host immunity
- Explain the impact of a distorted microbiome, related to antibiotic exposure or hospitalization, and identify diseases caused by dysbiosis
- Describe consequences of inappropriate antibiotic use and identify key strategies of antimicrobial stewardship
Required pre-class materials
Study materials
These materials are not required; they are supplementary to large-group session. They are intended as a curated guide to content focused on the learning objectives. There are both textbook and video resources for this session for students to use per their preference. For each reference, I have designated the learning goal addressed with a learning goal icon and and number.
Click the book icons below to go to the library resources listed.
This is considered by many to be “The Bible” of Internal Medicine. It presents the topic from a slightly different angle.
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The section on the microbiota and disease is most relevant.
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