Notes on the Microbial World: Domains of Life, Fungi, Protozoa, and Viruses
Course Overview
This course will explore the microbial world, mainly focusing on bacteria and viruses, but also covering other important microbes and their impact on health.
We'll move quickly through chapters 3 and 4 after an introduction; chapter 2 is just a brief overview of basic biology.
It's a good idea to read chapter 3 in advance for more details.
The Three Domains of Life
Life is divided into three main groups (domains): Bacteria, Archaea, and Eukarya.
Humans are in the Eukarya domain.
Bacteria and Archaea are called prokaryotes; Eukarya are eukaryotes.
The key difference:
Prokaryotic cells do not have a nucleus.
Eukaryotic cells have a nucleus.
(A small exception: human red blood cells don't have a nucleus, but most eukaryotic cells do.)
Don't worry too much about specific genus and species names yet; focus on understanding the main groups.
Nucleus: A Key Feature
The nucleus is a membrane-covered part inside eukaryotic cells that holds the cell's genetic material (DNA) and chromosomes.
Prokaryotic cells don't have a nucleus. Their DNA is found in an area called the nucleoid, which isn't membrane-bound.
Having a nucleus is a defining characteristic of eukaryotic cells and allows for more complex structures like mitochondria and the endoplasmic reticulum.
Simply put: Bacteria and Archaea (two domains) are prokaryotic and lack a nucleus. Eukarya (the third domain) includes organisms with nuclei.
Microbes: Abundant and Important
Microbes, especially prokaryotes, are the most common living things on Earth, found in huge numbers and diverse environments like soil, water, and extreme places.
Their abundance highlights their importance in microbiology, health, and ecosystems.
We'll mostly discuss bacteria when talking about human health; Archaea, though interesting (often found in extreme environments), will be covered less.
Eukaryotic Microbes
Eukaryotic microbes include:
Fungi
Protists (like protozoa)
Algae (protists that perform photosynthesis)
(Animals and plants are also eukaryotes but are not the focus of this course on microbes.)
Examples show a yeast cell (fungus), an alga, and an amoeba (protozoan), demonstrating that eukaryotic cells are more complex than prokaryotes.
A key point: eukaryotic microbes have specialized compartments called organelles (like mitochondria, ER, and the nucleus) that prokaryotes don't.
Fungi (A Main Eukaryotic Group)
There are about known types of fungi.
Roughly types of fungi live on or inside the human body.
How fungi interact with us:
Commensal relationship: The microbe benefits, but the host (us) isn't harmed (and might or might not benefit). Think of it as 'sharing a meal' without causing trouble.
Pathogenic relationship: The microbe benefits by harming the host. This is a one-sided, damaging interaction.
Many fungi on the human body are commensals.
Some yeasts can be pathogenic, causing issues like candidiasis (thrush or more widespread infections).
Fungal spores are reproductive particles that float in the air. We inhale many every day, from to spores.
Usually, if your immune system is healthy, these don't cause disease, but they can trigger allergies or asthma in some people.
Candida (different species): This is a yeast that normally lives in small amounts in places like the mouth.
Too much Candida, or an imbalance, can lead to candidiasis (e.g., thrush in the mouth, or systemic infections).
Some Candida types are becoming harder to treat with antifungal drugs, which is a growing concern.
Yeast vs. Molds (types of fungi):
Yeast: Single-celled fungi that reproduce by 'budding' (they grow a smaller cell that eventually breaks off). Example: Saccharomyces cerevisiae (used for baking and brewing).
Molds: Multicellular fungi that form thread-like structures called hyphae. A network of hyphae is called a mycelium, which looks like fuzzy colonies as they release airborne spores.
A common mold example is Aspergillus.
Fungal Cell Walls: Yeast cell walls are typically made of chitin or cellulose. Chitin is also found in insect shells, and cellulose in plant cell walls.
Ecological Role: Fungi are crucial decomposers, breaking down dead organic material, which helps recycle nutrients in ecosystems.
In labs, it's common to see fungal colonies (yeasts and molds) when testing air samples.
Protozoa (Another Eukaryotic Microbe Group)
Protozoa are single-celled eukaryotic microbes found in water and sometimes on land. Some live in humans as commensals or parasites.
How they move (very diverse):
Flagella: Long, whip-like tails that move in waves (different from how bacterial flagella spin).
Cilia: Short, many hair-like structures that beat to push the organism along.
Pseudopods: "False feet" that extend and pull back, helping the cell move and capture food.
Dangerous protozoans to know:
Giardia (Giardia lamblia or Giardia intestinalis): An intestinal parasite that causes giardiasis, often from contaminated water. It can lead to severe stomach problems and dehydration.
Naegleria fowleri (commonly called the "brain-eating amoeba"): An amoeba that infects the brain, usually after entering through the nose from warm freshwater. It can cause a severe form of meningitis and can be deadly if not treated quickly.
How it's spread: Exposure often happens during swimming, water sports, or using a neti pot with tap water when it should be sterile or boiled water.
Detection and treatment: Diagnosed with molecular tests or by examining brain tissue. Fast treatment is essential because, if delayed, the death rate is very high.
Protozoan infections are a major concern, particularly those spread through water and food.
Good water safety and hygiene (like clean drinking water and proper neti pot use) are important for prevention.
Algae (Briefly)
Algae are eukaryotic organisms that use photosynthesis (like plants) to make their own food. They are often grouped with protists.
An example is a multicellular alga, showing another type of photosynthetic eukaryote.
We won't focus much on algae as pathogens, but they show how diverse eukaryotic microbes are.
Prokaryotes: Bacteria and Archaea
Most of this course will concentrate on bacteria. Archaea are interesting, often found in extreme environments (extremophiles), but will be discussed less.
Both Bacteria and Archaea are prokaryotes and are incredibly abundant and crucial for ecosystems.
How a prokaryotic cell is organized (different from eukaryotes):
No true nucleus; the DNA isn't enclosed in a membrane.
They have a nucleoid region where the chromosome is located (not a nucleus).
Their internal structure is simpler than eukaryotic cells.
Viruses are different. They are microbe-sized but much smaller than bacteria and can only be seen with an electron microscope. They infect all forms of life.
Viruses: On the Edge of "Life"
Viruses are generally not considered living because they can't produce energy or reproduce on their own outside of a host cell.
They are parasites, meaning they need another living cell to multiply.
Viruses are everywhere and infect all three domains of life.
They are typically much smaller than bacteria and need powerful electron microscopes to be seen.
We'll cover more about viruses later, focusing on their basic biology and how they interact with host cells.
Connections and Real-World Importance
Our bodies are home to many helpful fungi and bacteria (commensals) that live in different places and contribute to our health. When this balance is disturbed, it can lead to disease (e.g., candidiasis).
Dangerous organisms and infections are real concerns: for instance, fungi becoming resistant to antifungal drugs (like Candida), waterborne diseases (Giardia, Naegleria), and allergic reactions from airborne spores.
The idea of commensals versus pathogens is central to understanding how microbes affect health and disease.
Practically and ethically, we need to think about how we handle exposure to microbes (airborne spores, water safety, proper use of antibiotics/antifungals, infection control in hospitals and communities).
Quick Reference: Key Facts
Total fungal species known:
Fungal species on the human body:
Airborne fungal spores inhaled daily: from to
Major prokaryotic domains: Bacteria and Archaea (two out of three main life domains)
Nucleus: The membrane-bound part in eukaryotic cells holding DNA and chromosomes
Example of yeast: Saccharomyces cerevisiae
Fungal infection example: Candidiasis (like thrush in the mouth, or body-wide infections)
Protozoan examples:
Giardia (Giardia lamblia): causes giardiasis
Naegleria fowleri (brain-eating amoeba): causes brain infection
Broader Themes and Relevance
This lecture provides the foundation for understanding the great variety of microbes and the fundamental differences in cell structure, which will help us later understand how bacteria work and cause disease.
Many human illnesses come from fungal and protozoan pathogens, and getting exposed through air and water is a main way they spread.
The debate about whether viruses are "living" prompts deeper questions about what life truly is and how we classify organisms.
The focus on the balance between helpful microbes (commensals) and harmful ones (pathogens) highlights how crucial our body's microbial community is for our well-being and how we manage disease.