Foundations of Microbiology: Classification, Microbiota, and Atomic Structure

Classification of Microbes

Major Groups of Microbes

Microbes are classified based on their cell type, structure, and physiological characteristics. The main groups include bacteria, archaea, protozoa, fungi, helminths, and viruses.

• Bacteria: Unicellular, prokaryotic organisms; pathogenic and nonpathogenic species exist.

• Archaea: Unicellular, prokaryotic; often found in extreme environments; not known to cause disease.

• Protozoa: Unicellular, eukaryotic; motile and aquatic; some are pathogenic.

• Fungi: Unicellular (yeasts) or multicellular (molds); eukaryotic; decomposers and some are pathogenic.

• Helminths: Multicellular, eukaryotic worms; some are parasitic.

• Viruses: Noncellular; consist of DNA or RNA; require host cells to replicate.

Microbe	Cell Type	Notes
Bacteria	Prokaryote	Unicellular, pathogenic and nonpathogenic
Archaea	Prokaryote	Unicellular, extremophiles, not known to cause disease
Protozoa	Eukaryote	Unicellular, motile, aquatic, some pathogenic
Fungi	Eukaryote	Unicellular (yeasts), multicellular (molds), decomposers, some pathogenic
Helminths	Eukaryote	Multicellular, parasitic worms
Viruses	Noncellular	DNA or RNA, require host cell, not living

Additional info: Endosymbiotic theory proposes that eukaryotic cells evolved from prokaryotic ancestors.

Origins of Life and Disease

Spontaneous Generation vs. Biogenesis

Historically, two main theories explained the origin of life:

• Spontaneous Generation: The idea that life arises from nonliving matter.

• Biogenesis: Life emerges only from existing life.

Pasteur's Experiment: Used swan-necked flasks to show that microbes do not appear spontaneously but come from pre-existing life. Boiled broth remained sterile until exposed to air.

Koch's Postulates of Disease

Koch's postulates are criteria used to establish a causative relationship between a microbe and a disease:

1. The same organism must be present in every case of the disease.

2. The organism must be isolated from the diseased host and grown as a pure culture.

3. The cultured organism should cause disease when introduced into a healthy host.

4. The organism must be re-isolated from the experimentally infected host.

Taxonomy and Classification

Taxonomy: Principles and Rankings

Taxonomy is the study of how organisms are grouped based on physical and physiological characteristics. The hierarchical system includes eight main ranks:

• Domain: Groups organisms by cell type (Bacteria, Archaea, Eukarya).

• Kingdom: Groups by relatedness (e.g., Animalia, Plantae, Fungi, Protista).

• Phylum → Class → Order → Family → Genus → Species (most precise).

Mnemonic: "Delightful King Philip Came Over For Great Spaghetti" helps remember the order.

• Strains: Genetic variants within a species.

• Binomial Nomenclature: Developed by Linnaeus; uses genus and species names (e.g., Escherichia coli).

Microbial Relationships and Microbiota

Types of Microbial Relationships

Microbes interact with hosts in various ways:

• Parasitism: Microbe harms the host.

• Mutualism: Both microbe and host benefit.

• Commensalism: Microbe benefits; host is unaffected.

Example: Humans and their microbiota exhibit mutualism.

Normal Microbiota

The human body hosts diverse microbial communities:

• Skin: ~1,000 species

• Mouth: ~600 species

• Urogenital tract: ~60 species

• Intestine: ~10,000 species

Disruptions (e.g., antibiotics, diet, hormones) can alter microbiota composition. Transient microbiota are temporary and can be removed by hygiene.

Biofilms

Biofilms are communities of microbes attached to surfaces, encased in a protective matrix.

1. Attachment: Cells adhere to a surface and begin to replicate.

2. Growth: Sticky matrix (biofilm) encourages adhesion and makes the film hard to penetrate.

3. Detachment: Free-floating cells can be released from the biofilm.

Applications: Microbes in biofilms are used in bioremediation and food production (e.g., cheese).

Functions and Benefits of Microbiota

Microbiota play essential roles in human health:

• Train the immune system

• Produce vitamins

• Digest foods and regulate allergic reactions

• Regulate moods and brain function

• Defend against microbial pathogens

Colonization begins at birth and expands in response to environmental and physiological changes.

Additional info: To be considered the same species, organisms must share at least 70% DNA sequence identity and 97% of a specific rRNA sequence.

Atomic Structure and Chemical Bonds

Structure of Atoms

Atoms are the basic units of matter, composed of protons, neutrons, and electrons.

• Electron: Negative charge, negligible mass

• Proton: Positive charge, 1 atomic mass unit

• Neutron: Neutral charge, 1 atomic mass unit

Each atom has a nucleus (protons and neutrons) surrounded by a cloud of electrons.

Atomic Number, Mass, and Isotopes

• Atomic number: Number of protons

• Atomic mass: Sum of protons and neutrons

• Isotopes: Elements with varying numbers of neutrons

Radioactive isotopes are unstable and release energy; they are used in medical diagnostics and cancer treatment.

Ions and Molecules

• Ions: Atoms with an imbalance of protons and electrons; can be positive (cation) or negative (anion).

• Molecules: Formed when two or more atoms bond together.

• Compounds: Molecules made of more than one type of element.

Chemical Bonds

• Ionic Bonds: Electrons are lost by one atom and gained by another; bound by electrostatic forces (e.g., NaCl).

• Covalent Bonds: Electrons are shared between atoms.

Additional info: Chemical bonds are essential for forming molecules and compounds necessary for life.