SOfIA 2022

Introduction

The microbiome is a collective term used to refer to the microorganisms (bacteria, archaea, viruses, and fungi) that reside within an ecosystem. These microorganisms make up ~16% of the Earth’s total biomass, while human make up a mere 0.01%. All animals on Earth account for just 0.5% and plants are the largest form of biomass at ~83%. Microorganisms go unnoticed since they are not visible to the human eye. They live on our skin, in our bodies, in soil, in water, and well just about on every surface on Earth. Under a microscope these organisms can have unique physical appearances, but for the majority of bacteria and archaea, they all look nearly identical. Don’t let appearance fool you, most bacteria are harmless (you even include them in your diet ex. yogurt and cheese), but some bacteria are harmful (ex. C. diff and H. pylori). In order to identify bacteria we must look at their DNA. During this SOfIA project we will use bacteria to make a variety of food items (yogurt, sourdough bread, pickles, etc.), isolate DNA from foods, soil, and water samples, and use DNA sequencing to identify the genus and species of bacteria present.

Participants

Brad Sturgeon, Co-Instructor, Chemistry Faculty (besturgeon@monmouthcollege.edu)

Laura Moore, Co-Instructor, Chemistry Faculty (lmoore@monmouthcollege.edu)

Whitehall, Eliza, Returning mentor, Senior Chemistry Major (EJWHITEHALL@monmouthcollege.edu)

Lovell, Annalyn L (allovell@monmouthcollege.edu)

Hemling, Mya Melissa (mhemling@monmouthcollege.edu)

Cronin, Kailey Grace (kgcronin@monmouthcollege.edu)

Kalnins, Riley L (rkalnins@monmouthcollege.edu)

Soutsos, Peter Demetrios (psoutsos@monmouthcollege.edu)

Program

Week 1

Monday, Aug 1st

1) Introductions

2) Discuss the Abstract Key Words and Ideas:

- The microbiome is a collective term used to refer to the microorganisms (bacteria, archaea, viruses, and fungi) that reside within an ecosystem.

• Microbiota - referring directly to the bacteria/microorganisms; example, the microbiota consists of many species of bacteria.
• Microbiome - What the bacteria do; example, the microbiome is responsible for the metabolic complexity.

- These microorganisms make up ~13% of the Earth’s total biomass, while human make up a mere 0.01%. All animals on Earth account for just 0.4% and plants are the largest form of biomass at ~82%.

The biomass distribution on Earth (PNAS, 2017)

- Microorganisms go unnoticed since they are not visible to the human eye. They live on our skin, in our bodies, in soil, in water, and well just about on every surface on Earth. Under a microscope these organisms can have unique physical appearances, but for the majority of bacteria and archaea, they all look nearly identical. Don’t let appearance fool you, most bacteria are harmless (you even include them in your diet ex. yogurt and cheese), but some bacteria are harmful (ex. C. diff and H. pylori).

- In order to identify bacteria we must look at their DNA.

- During this SOfIA project we will use bacteria to make a variety of food items (yogurt, sourdough bread, pickles, etc.), isolate DNA from foods, soil, and water samples, and use DNA sequencing to identify the genus and species of bacteria present.

3) NOVA Wonders: What's Living in You? (2018, 53 mins)

4) Lunch (12-1 pm)

5) NOVA Wonder program discussion

• Bot flies
• Face mites
• Bacteria (round, spiral, rod), fungi, viruses, microscopes
• H. pylori
• American Gut Project/Rob Knight
• Bacterial Diversity
• Poop donor/FMT (Fecal matter transplant)/C. difficile

6) Let's Make Some Bread

• Basic bread recipe

- flour - 3 cups = 460 g = 100 baker's %

- water - 1-1/3 cups = 305 g = 66 baker's %

- yeast - 1 tsp = 4 g = 0.8 baker's %

- salt - 1 tsp = 7 g = 1.5 baker's %

Tuesday, Aug 2nd

1) Evaluation of bread dough

- kneeding/glutan formation

- hydration

- How to Knead Bread Dough by Hand | Detailed Instructions

2) Discussion of bakers %

- Baker's Percentage & Dough Hydration Explained

3) Lunch

4) Yeast under the microscope.

Friday, Aug 5th

2:00 pm presentations

Week 3

Thursday, Aug 18th

Illinois State Fair - Volunteer Day 12 - 4:30 pm.

Leave CSB parking lot at 9 am

Arrive back home at ~ 8 pm

Resources

NOVA Wonders: What's Living in You? (2018, 53 mins)

Earth Microbiome Project (EMP)

Human Microbiome Project (HMP)