microbiomes

Question 1

biome defninition

Answer 1

The combined biotic and abiotic factors of a given environment

Question 2

microbiome definition

Answer 2

The collection of microorganisms (bacteria, archaea, eukaryotes, viruses), their genetic material + the surrounding environmental conditions

Question 3

microbiota definition

Answer 3

The microorganisms present in a defined environment

Question 4

Metagenome definition

Answer 4

The collection of genomes and genes from the members of a microbiota

Question 5

4 reasons to study microbial communities

Answer 5

1. Global biogeochemical cycles
2. Ecological function & resilience
3. Biotechnology & agriculture
4. Health and disease

Question 6

what are Early community studies

Answer 6

• Culture-based methods
• Selective media (i.e. sugars, pH, salt, antibiotics, inhibitors)
• Differential media (specific colours, growth patterns)
• Microscopic investigations - physical characteristics
  BUT the vast majority of microorganisms are non culturable on the plates
• viable but nonculturable species (VBNCs)
• biased representation of community composition

Question 7

methods to sequence complex communities to investigate WHO is there

Answer 7

• Microbiomes are highly complex & dynamic
  Multiple interactions:
• within & between species
• with the surrounding environment/host
• investigating WHO is there:
  >Metabarcoding = PCR amplicons (i.e. 16S rRNA)
  >Metagenomics = whole genomes

Question 8

methods to sequence complex communities to investigate Who is active, what are they doing & how might they be affecting the system?

Answer 8

Metatranscriptomics = transcriptomes (gene expression)
Metaproteomics = protein expression

Question 9

Host-specific factors in Host-associated microbiomes (our body)

Answer 9

genetics, immune system, age, hormones

Question 10

Environmental factors in Host-associated microbiomes (our body)

Answer 10

diet, stress, antibiotics, alcohol
*Many factors influence the amount / type of microbes we have in our body (incl early life experiences)

Question 11

explain Diet as a factor that influences the amount / type of microbes we have in our body

Answer 11

• Has largest, most direct effect on the gut microbiome
• Rapid response to dietary change
• Microbial metabolites positively and negatively influence host health (i.e. TMAO, SCFAs)

Question 12

what bacteria is associated with good gut health

Answer 12

Bifidobacterium & Lactobacillus
- Probiotics & prebiotics aim to increase ‘good bacteria’

Question 13

explain stress as a factor that influences the amount / type of microbes we have in our body

Answer 13

• Microbiota gut-brain communication (closely related)
• In a study, mild confinement stress :
  >increased cortisol (stress hormone)
  >Altered gut microbiome diversity & structure
  >Reduced probiotic taxa

Question 14

how could Harnessing microbiomes improve food security in agriculture

Answer 14

produce pathogen inhibitory compounds
- Improved health & disease resistance in animals + crops
- Improved feed efficiency
- Better quality & more nutritious meat/milk
- Reduced methane production
- Exploiting novel (more sustainable) food source

Question 15

how do Microbiomes influence/adapt host phenotypic plasticity

Answer 15

• Microbiomes can enhance invasion success e.g in red bark beetle microbiota detoxify pine defensive compounds so they can eat them
• Cold tolerant microbiota enhance host cold tolerance