micro; 1. Classification of Microbes and The Microbiome

Classification of Microbes and The Microbiome and Health Class

  • Year: 2025

  • Undergraduate Medicine Lecturer: Dr. Niall Stevens

  • Institution: RCSI Royal College of Surgeons in Ireland

  • Date: 15th October 2025

Learning Outcomes

  • Classify microorganisms into categories:

    1. Bacteria

    2. Viruses

    3. Fungi

    4. Protozoa

    5. Arthropods

  • Differentiate microorganisms based on phenotypic and genotypic characteristics

  • Define important terms related to the human microbiome such as colonised, transient, symbiosis, etc.

  • Discuss various microbial components of the human microbiome including bacteria, fungi, and viruses, and explain the development of the microbiome over time

  • Associate microorganisms with their typical anatomical sites of residence

  • Discuss the significance of the microbiome for human health and the complications that arise when it is disrupted

  • Describe methods for restoring the microbiome post-disruption

Overview of Clinical Microbiology

  • The RCSI Department of Clinical Microbiology was established in 1965.

  • Professor Ellen C. Moorhouse was the first female Clinical Sciences Professor and contributed significantly to the department.

  • The department's main theme is "Infection and Host Response."

  • Activities include teaching, research, public engagement, and national health policy involvement.

  • Renowned for producing leaders in Healthcare and its academic excellence.

What is Microbiology?

  • Microbiology is defined as the study of microscopic organisms.

  • Some microorganisms can be seen with the naked eye, but most require microscopic techniques for observation.

    • Metric units for measurement:

    • 1 cm = 10^-2 m

    • 1 mm = 10^-3 m

    • 1 µm = 10^-6 m

    • 1 nm = 10^-9 m

    • 1 Å = 10^-10 m

What is Clinical Microbiology?

  • Clinical Microbiology is applied microbiology specifically oriented to facilitate patient management.

  • Key topics include:

    • Infection and antimicrobial resistance, recognized as top threats globally by WHO

    • Importance of preventing infections

    • Biological diversity and the emergence of new pathogens like SARS-COV-2

    • Connections with other disciplines (e.g., Helicobacter pylori and peptic ulcer disease)

Themes in Clinical Microbiology Teaching

  • Focus on clinically relevant pathogens (e.g., Staphylococcus aureus, Candida albicans)

  • Emphasis on scientific concepts like bacterial pathogenicity and antibiotic resistance

  • Instruction on major infections by organ system with a focus on diagnosis and therapy

  • Involvement in infection prevention strategies:

    • Community vaccination initiatives

    • Healthcare-associated infection management through precautions

Professionalism in Clinical Microbiology

  • Becoming a physician involves cultivating values, behaviors, and attitudes to enhance professional relationships and public trust.

  • Two major components of professionalism in Clinical Microbiology:

    1. Infection Prevention & Control

    2. Antimicrobial stewardship

Learning Outcomes: Microbial Classification

  • Classification uses the binomial system (Genus and Species):

    • Examples:

    • Homo sapiens

    • Staphylococcus aureus

    • Candida albicans

    • Plasmodium falciparum

    • Species are defined as groups of similar or interbreeding organisms within a genus.

Characteristics of Microorganisms

Bacteria

  • Composed of a single chromosome (genome) and lack cell organelles.

Fungi & Protozoa

  • Contain:

    • Nucleus (chromosomes)

    • Mitochondria

    • Golgi apparatus

    • Endoplasmic reticulum

The Bacterial Cell Structure

  • Components include:

    • Single chromosome

    • Plasmids (extrachromosomal DNA)

    • Cytoplasm

    • Ribosomes

    • Cytoplasmic membrane

    • Cell wall

    • Flagellae

    • Pili/Fimbriae

Classification of Microbes

  • Microorganisms are classified based on:

    • Phenotype: Observable features (microscopic and macroscopic characteristics)

    • Genotype: Genetic makeup of the organism

Analysis of Microbial Characteristics

Phenotypic Analysis

  • Methods for differentiating strains or confirming isolate identities include:

    • Biotyping (biochemical tests)

    • Serotyping (surface antigens)

    • Antibiograms (antibiotic susceptibility tests)

    • Phage typing (susceptibility to bacteriophages)

Genotypic Analysis

  • Involves:

    • Proteotypical characterization (e.g., MALDI-TOF)

    • Genotypic characterization (e.g., PCR, Whole Genome Sequencing)

Fungi

  • Defined as eukaryotic organisms characterized by:

    • Presence of a nucleus, chromosomes, mitochondria, etc.

    • Greater biological similarity to human cells compared to bacteria

    • Limited treatment options due to difficulties developing selective chemotherapy that distinguishes between fungal and human cells

Viruses

  • Viruses are not classified as cells as they:

    • Cannot produce metabolic energy or replicate independently

    • Are obligate intracellular parasites

  • Structure includes:

    • Nucleic acid + capsid (nucleocapsid)

    • Optional envelope derived from the host cell

Parasites

  • Include protozoans, helminths, and arthropods.

    • Protozoa: Single-celled eukaryotes that can be free-living (in aquatic environments) or parasitic (ectoparasites or endoparasites).

    • Helminths: Parasitic worms categorized into:

    1. Nematodes (e.g., roundworm)

    2. Trematodes (e.g., flukes)

    3. Cestodes (e.g., tapeworms)

    • Arthropods: Invertebrate animals that typically act as vectors for infectious agents, such as mosquitoes harboring malaria and Ixodes species that cause Lyme disease.

Prions

  • Associated with spongiform encephalopathies, they are small hydrophobic glycoproteins closely related to human proteins.

  • Lack nucleic acids; their pathogenesis involves possible interactions leading to amyloid plaque formation.

  • Associated diseases include:

    • Creutzfeldt-Jakob disease (CJD)

    • Kuru

    • Scrapie

    • Bovine Spongiform Encephalopathy (BSE)

The Human Microbiome

  • Comprises the collective genomes of microbes inhabiting the human body.

  • Humans possess around ten times more microbial cells than human cells.

    • Emphasis is often placed on bacterial microbiomes, but the roles of fungi and viruses are also significant.

    • Human Virome: Consists of human viruses (e.g., enteroviruses) and bacteriophages.

    • Human Mycobiome: Refers to fungal microbiome components, with species such as Saccharomyces, Malassezia, and Candida being the most prevalent.

Development of the Microbiome

  • At birth, the body is sterile, but surfaces quickly accumulate microbes after delivery.

  • Factors influencing microbiome development include:

    • Mode of delivery (vaginal vs. Cesarean)

    • Feeding type (breastfeeding vs. bottle feeding)

    • Introduction of solid foods

    • Factors such as age, genetics, stress, antibiotic exposure, and immune status also play roles.

Benefits of Microbiome

  1. Nutritional Support:

    • Provision of nutrients and stimulation of immune responses

    • Prevention of pathogenic overgrowth through competition for resources and attachment sites.

  2. Host Immunity:

    • Induction of immune competency through exposure to microbial antigens that stimulate antibody production.

  3. Nutritional Benefits:

    • Production of vitamins (e.g., Vitamin K and B12) crucial for various metabolic processes.

  4. Digestion:

    • Degradation of complex carbohydrates, providing additional energy sources for the human host.

Disruption of the Microbiome

  • Disruption can result in an imbalance where pathogenic microbes may proliferate due to the natural barriers being compromised.

  • Conditions leading to disruption include mucosal breaches, impaired host defenses, malnutrition, cancer, diabetes, and extensive use of antibiotics.

  • C. difficile: A normal gut resident kept in check by flora; overgrowth can lead to infection, particularly after antibiotic treatments.

    • Prevalence: Common healthcare-associated infection (HAI) seen as a toxin-mediated disease resulting in diarrhea and potential recurrence of infections.

Restoring the Microbiome

  • Faecal Microbiota Transplant (FMT): A therapeutic strategy where screened donor stool is transferred to replace dysfunctional microbiomes, carried out through colonoscopy, enema, or pill form.

  • Emphasizes robust donor screening and testing procedures.

Common Infections from Microbiome Disruption

S. aureus

  • Colonizes approximately 30% of healthy individuals, known for causing skin infections.

  • Skin flora usually inhibits its pathogenicity but breaches allow for potential infection, particularly in wounds or during bloodstream infections.

Candida albicans

  • Normally resides in the oral cavity and vagina, kept at low levels by the microbiome; can proliferate and cause infections upon environmental changes.

Summary

  • The human microbiome is critical for health.

  • Unique anatomical sites support diverse microbial communities.

  • Disruptions to the microbiome can lead to infections from opportunistic pathogens such as C. difficile, underscoring its integral role in maintaining human health.