Microbiota Lecture Notes

Microbiota

Organism Definition

  • Hierarchy of Biological Organization:

    • Atom: The smallest chemical unit (e.g., carbon atom).
    • Molecule: A group of joined atoms (e.g., DNA).
    • Organelle: A membrane-bounded structure with a specific function within a cell (e.g., chloroplast).
    • Cell: The fundamental unit of life; can be unicellular or part of a multicellular organism (e.g., leaf cell).
    • Tissue: A collection of specialized cells functioning in a coordinated manner (multicellular life only) (e.g., epidermis of a leaf).
    • Organ: A structure consisting of tissues organized to carry out specific functions (multicellular life only) (e.g., leaf).
    • Organ System: Organs connected physically or chemically that function together (multicellular life only) (e.g., aboveground part of a plant).
    • Organism: A single living individual (e.g., one acacia tree).
    • Population: A group of the same species living in the same place and time (e.g., multiple acacia trees).
    • Community: All populations that occupy the same region (e.g., all populations in a savanna).
    • Ecosystem: The living and nonliving components of an area (e.g., the savanna).
    • Biosphere: The global ecosystem; the parts of the planet and its atmosphere where life is possible.

  • Microbial Perspective:

    • Organisms exist in communities with other organisms.
    • At a level more complex than a single cell, interacting microbial cells must be considered.
    • Examples: Coral bleaching (loss of microbes from corals), giant tube worms with intracellular microbes.
    • The human body, from a microbiological perspective, is a community.

Historical Context of Germ Theory and Microbiome

  • 19th Century:
    • Germ Theory: Diseases are caused by invisible microbes.
  • 20th Century:
    • Focus on vanquishing germs through sanitation, vaccination, and antibiotics.
  • 21st Century:
    • Recognition of the microbiome as an important part of human health.

Human Microbiota

  • Cellular Composition:
    • Human cells in the human body: 30,000,000,000,00030,000,000,000,000 (30 trillion).
    • Microbial cells in/on the human body: 39 trillion.
  • Definitions:
    • Microbiota: The collection of microbial cells in/on the human body.
    • Microbiome: The small biome (living and nonliving components) in/on the human body.
  • Location:
    • Microbiota are found in non-sterile sites, such as mucosa (mouth, skin, gut, nose).
    • Sterile sites should ideally be devoid of microbes.
  • Impact of Microbiota:
    • Cystic fibrosis: Death often results from lung infection due to microbes colonizing the mucus.

Factors Influencing Microbiota Composition

  • Adaptation:
    • Only microbes with the right adaptations can survive and reproduce in specific environments (e.g., acidic stomach).
    • Microbe populations vary with sex, age, diet, body region, geography, occupation, hygiene, and ethnicity.
    • Distinction between residents (long-term inhabitants) vs. transients (temporary inhabitants).
  • Competitive Exclusion:
    • A healthy population of microbes occupies space to prevent pathogens from colonizing.
    • Homeostasis is maintained by resident microbes.
    • Example: Staphylococcus epidermidis releases chemicals that inhibit pathogens like MRSA and Cutibacterium and stimulates skin keratinocytes to secrete chemicals that promote wound healing and limit inflammation.

Functions of the Microbiota

  • Competitive Exclusion:
    • Example: Lactobacillus releases acids to lower the pH, inhibiting pathogens like yeast and offering some protection against sexually transmitted infections.
  • Hygiene Hypothesis:
    • Exposure to microbes during immune system development trains it to recognize what is normal.
    • Lack of exposure may lead to allergies and asthma.

Human Milk and Infant Microbiota

  • Human Milk Oligosaccharides (HMOs):
    • Human breast milk is full of HMOs, which are complex carbohydrates that human infants cannot digest.
    • Bifidobacterium infantis is a bacterial species with enzymes that digest HMOs and dominates the gut microbiome of breast milk-fed infants.
    • Formula-fed babies often lack these bacteria.
    • Breast milk is composed to feed the baby’s gut microbiota.

Dysbiosis and Medical Conditions

  • Dysbiosis:
    • Many human medical conditions result from a disruption to the microbiota, leading to a community that has been disrupted.
    • Infection: One type of microbe out of balance and over-abundant.

Gut-Brain Axis

  • Two-way Communication:
    • Two-way biochemical signaling between the GI tract and the central nervous system.
    • Links the brain and the gut microbiota via nerves, endocrine system, and immune system.
    • Impacts anxiety, autism, depression, and memory deficit.

Antibiotics and Microbiome Disruption

  • Effects of Antibiotics:
    • Antibiotics kill bacteria with little specificity, disrupting the microbiome.
    • There is no guarantee the microbial ecosystem will automatically return to normal following antibiotic treatment.
    • Some microbes are opportunistic and adapted for establishing themselves in disrupted human ecosystems like vaginal yeast infection and C. difficile.

Clostridioides difficile (C. diff)

  • Characteristics:
    • C. difficile causes inflammation of the colon, leading to mild to severe diarrhea.
    • Approximately 500,000 people are infected each year, resulting in about 30,000 deaths (according to the CDC).
    • C. difficile is a common part of the human microbiota but present only in small quantities.
  • Treatment:
    • The best treatment is to replace the missing microbiota.

Fecal Microbiota Transplant (FMT)

  • Procedure:
    • Gut microbiota is taken from a healthy individual and transferred to another.
    • Also known as "Bacteriotherapy."
  • Application:
    • Has successfully cured patients infected with C. difficile.

Gut Microbiota and Short Chain Fatty Acids (SCFA)

  • SCFA Production:
    • Complex carbs that we consume feed our gut microbiota, which ferment the carbs to produce short chain fatty acids (SCFAs).
  • Benefits of SCFA:
    • Promote lower blood sugar levels.
    • Reduce the risk of colon cancer.
    • Balance the gut microbiota to lower inflammatory bowel disease (IBD) risk.

Optimizing Gut Health

  • Gradual Increase in Fiber:
    • Increase fiber intake gradually, and it may take a month for the microbiota to adjust.
  • Benefits:
    • Lower blood sugar.
    • Healthier gut lining.
    • Improved mental health.

Human vs. Microbial Genes

  • Genetic Composition:
    • Humans have about 30,000 genes.
    • Microbial genes outnumber human genes by 100 to 1 playing a role in us all of our life.
    • At best, humans are 10 percent human, but more likely about one percent human.

End of Semester Information

  • Chapters 15,16 – due by midnight.
  • Final exam is at May 2, either at 8:00 am or 10:00 am; 2/3 from Chapters 12-16 and microbiota and 1/3 from all other chapters.
  • Grades will be posted by May 2.
  • Absolute deadline to contact for grades is May 7.