How to wrangle with marine microbes

M Hallett

Check out Les Stroud’s Youtube channel for classic Survivorman.
Today I will be stranded on a desert island in the fierce conditions of the south pacific ocean.
With nothing but my Arc’teryx jacket and a single RSTudio Cloud license;
I will seek to survive the incredible sunny days, really salty water, and relentless sand
… suriving on nothing more than microbes that I wrangled into my \({\tt tibble}\).
It might seem easy but a week without that special tea from Indonesia of questionable legality which my grad student keeps giving me, and you are dead.

Intro. to Metagenomics: more focus on human microbiomes whereas we are looking at marine microbiomes.
Other links to material for metagenomics computational biology. This sort of analysis comes later.
Today we are just focused on wrangling a metagenomics dataset into R.

Sampling the microbiome of a site.
- human: gut, mouth, etc.
- soil
- water: ocean, lakes, …
What is a microbiome?
- The collection of endogenous viruses, Bacteria, Archae, and single-celled Eukaryota living in a space or environment.
- They can be living in commensal, pathogenic or symbiotic relationsips with each other and their environment (host).
What are the fundamental questions?
- What taxa are present?
- What is the frequency of each taxa?
- What is the state of each organism (eg measured through transcriptomics)?
- What does each taxa contribute to the community or environment?
  - For example, a sample may have a lot of cyanobacteria because…
  - For example, a sample may have a lot of Vibrio spp because …
  - For example, a smaple may have a lot of protists because …

Computational Biology Western