🚀 Project Title:

🧬 Impact of Simple Sugar Intake on Gut Microbiome Composition

📅 Timeframe: September 2021 - December 2021
📍 Author: Jess Valiarovski
📚 Course: Foundations of Biology Laboratory: Computational Microbiology Research
🎓 Collaborators: Miguel Aguinaga, Ethan Chase, Olivia Yesker
🎓 Instructor: Joleen Khey

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🚀 Project Overview

This study examines how changes in simple sugar consumption affect microbial composition in the gut microbiome using computational and statistical analysis.

🔍 Hypothesis

✅ A diet high in simple sugars will decrease the alpha diversity of the gut microbiome.
✅ A diet high in simple sugars will increase the genus count of Prevotella.

Key Findings: ❌ No significant changes in alpha diversity or Prevotella count were observed when sugar intake increased.
🔬 These results suggest that Prevotella does not use simple sugars as a nutrient to maintain or expand its genus composition.

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📊 Methods & Data Processing

📝 Dataset Overview

• Source: Wu GD, et al. Linking long-term dietary patterns with gut microbial enterotypes. Science, 2011.
• DOI: 10.1126/science.1208344
• Participants: 98 healthy individuals
• Data Collection:
  • Short-term diet recorded from the “Recall” questionnaire
  • Long-term diet recorded from the Food Frequency Questionnaire (FRQ)
• Sample Type: Stool samples for microbial composition analysis

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🔬 Bioinformatics & Statistical Analysis

🧬 QIIME2 Pipeline Analysis (QIIME2)

✔ Bacterial 16S rDNA sequencing (via Roche 454 sequencing or shotgun metagenomics)
✔ Preprocessing:

• Reads truncated at 2000 for improved microbial representation
• Closed-reference filtering using the GreenGenes database for OTU classification
  ✔ Output Artifacts:
• OTU count table
• Taxonomy classification
• Shannon diversity index
  ✔ Converted to TSV format for further analysis in R

📊 R Studio Analysis (R Project)

✔ Extracted Shannon Index & Prevotella abundance from QIIME2 analysis
✔ Linear regression analysis to examine correlations between sugar intake and microbial diversity
✔ Three sugars analyzed:

• Fructose, Sucrose, Glucose vs. Shannon Index
  ✔ Data Visualization:
• Scatter plots to assess linear relationships
• ANOVA test to compare differences in alpha diversity across sugar types

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📌 Key Findings

🛠 Statistical Results

• No significant correlation between simple sugar intake and gut microbial alpha diversity.
• No significant change in Prevotella count when sugar intake increased.
• Contrary to hypothesis, Prevotella does not appear to metabolize simple sugars to maintain populations in the gut.

📈 Visualization Highlights

• Scatter plots showed no linear trend between sugar intake and microbial diversity.
• ANOVA results confirmed no significant differences in Shannon Index values across sugar types.

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🛠️ Technical Skills Demonstrated

✅ Bioinformatics Analysis: QIIME2, 16S rDNA sequencing
✅ Data Wrangling & Cleaning: pandas, numpy
✅ Statistical Modeling: Linear regression, ANOVA
✅ Data Visualization: ggplot2, scatter plots
✅ Reproducible Research: Pipeline from raw genetic data to hypothesis testing

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📎 References

Wu GD, et al. Linking long-term dietary patterns with gut microbial enterotypes. Science, 2011.
📄 DOI: 10.1126/science.1208344

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