MICR5831 Module 2 Tutorial 1

Why study the microbiome?

A person's microbiome may influence their susceptibility to infectious diseases and contribute to chronic illnesses

Differences in the microbiome between healthy individuals and those with disease

What does microbiome studies investigate

investigate the behaviour, interactions, and function of microbial communities within a specified environment

What are applications of microbiome studies

Novel therapeutics and prophylactics

Develop diagnostic biomarkers from the microbiome to identify diseases before they develop

Provide the overview of a microbiome study

study design, sample collection, DNA extraction, PCR amplification and library preparation, sequencing, analysis

What are some study design considerations

What is your research question?

Participant metadata – information catalogue containing details of all the samples used in an study

Selecting an appropriate sample size is a key step. In most cases, results with small sample sizes do not precisely represent general population-based outcomes

Choosing appropriate sample sizes based on statistical principles can certainly help to avoid biases and spurious interpretations

Controls – needed to identify whether a signal is real and not just a stochastic or spurious result

What are some commonly used bioinformatic pipelines

QIIME2

MOTHUR

R Software(DADA2, 

What is Denoising

a computational method for removing sequence errors from amplicon reads. It is a part of demultiplexing

What does QIME2 do

Uses DADA2 to:
Remove the primers and adapters
Denoise raw sequences to remove and/or correct “noisy” reads
Dereplicate sequences to reduce repetition and CPU requirements downstream

What is a feature table

a matrix of samples by observations

What are representative sequences

whole sequences that best characterise or summarise a set of sequences

What are reads

the DNA sequence from one fragment (a small section of DNA)

How do you pick sampling depth

Balancing act between sampling depth and number of samples

What happens when sampling depth is increased

Leads to increased detection of bacterial species and strains at lower abundance levels

What happens when there is a higher number of samples

Increases statistical power to prove that our experimental findings are true

How is assigning taxonomy done?

assigned using a reference database (SILVA, Ribosomal Database Project (RDP), Greengenes2)