Introduction

Question 1

The evolution of understanding about host microbe interactions

Answer 1

Age of ignorance: before the late 19th century
- The microbial world was unknown and unknowable
- Disease was a commonly observed phenomena but explained in different ways (The four humours/ body fluids, poor air - e.g. Malaria and swamps, divine/ magical intervention)

Age of the germ: late 19th century onwards
- Technological advancements lead to the acceptance of the germ theory
- Disproved spontaneous generation, improved microscopy, culturing, animal models of infection
- This lead to the germ revolution in understanding and combatting infectious disease (e.g. aseptic sugery, vaccines and antimicrobial agents)
- However, all advancements tended to be based around medicine (not all diseases are microbial, most microbes do not cause disease-> look longer for archae to be discovered, many diseases are incidental to microbial growth)

Age on the gene: mind 20th century onwards
- The study of microbiology and microbes was important for the founding of moelcular biology
- Key advancements: hereditary of DNA (Grithith experiment-> smooth/ virulent pneumococci HGT to Rough/ avirulent pneumococci killing mice), studies on phage, E.coli as a model organism.

Age of the genome: late 20th century onwards
- Nucleotide sequencing developed and was used to study the whole genome
- Reference genomes created for most major pathogens
- However, it remained expensive and time consuming.

Populations and communities of genomes: Start of the 21st century
- Rapid sequencing developed and unimaginable increase in capacity
- Has enabled populations to be studied at the genomic and environmental level,
o ‘Population Genomics’ (knowing all the genes within a population)
o ‘Metagenomics’
o The Microbiome

Even after all this knowledge had developed, pathogens and disease still have a major impact on life.
- Example: child mortality rate over the last 170 years has changed relatively little

Question 2

The developement of immunology

Answer 2

• Animal infection models led to the discovery of the immune system:
  o Cellular immunity
  o Humoral immunity
  o Large debates over whether immunity was cellular or humoral (it is a combination)
• In addition to improving fundamental understanding, this led to:
  o Serum therapy
  o Vaccines
  o Understanding autoimmunity

Question 3

War against pathogens?

Answer 3

• Viewing infectious disease as a ‘war’ disables understanding of, and combatting, them.
• The modern landscape of disease is much to do with the decision we make about running our society, growing crops, interacting with animals etc.

Question 4

The importance of microbes and the sea

Answer 4

• Virtually all of the diversity resides in the sea, yet we have only recently started to study it.
• Virtually all evolution of the immune system occured in the sea .

Example: Coral holobiont
- The Holobiont comprises:
o Coral animal host
o Many obligate intracellular algal symbionts (Symbiodiniaceae)
o Multiple others, including fungi, endolithic algae, archaea
- 1 billion people depend on coral

Question 5

The importance of microbes and soil

Answer 5

• Soil contains a highly diverse microbiome
• Major contributor to plant microbiota
• These are then transferred to animals/ humans/invertebrates.
• Some mammals eat soil to add to their microbiome (Gorillas)
• Most antimicrobials (and AMR) come from the soil due to the huge diversity of microbes resulting in selection pressures.

Question 6

The human microbiome

Answer 6

• Humans can be thought of as a ‘super organism’, the person and the microbes.
• The microbiota/human interface is the immune response.

Question 7

Advatages to microbiology due to molecular genetics

Answer 7

o Enable uncultured and uncultivable organisms to be studied. (Most things cannot be grown on agar plates/ in a lab, leading to bias and incomplete samples)

o Are scalable and cost-effective

o Can be quantitative (or at least semi-quantitative)

o Are potentially comprehensive/ complete.

THis allows an increasingly detailed understanding of the host microbe interactions.

Question 8

Overview

Answer 8

The history of microbiology
- The age of ignorance
- The age of the germ
- The age of the gene
- The age of the genome
- The age of populations and communities

This evolution in understanding allowed important advancements in:
- Molecular genetics, molecular biology and immunology

Key to understand the microbial world in different settings
- Sea
- Soil
- Humans (need to be careful microbial research doesn’t become to medical-> not all microbes cause disease)