B.Sc. Thesis: Investigating the effects of Mycobacterium suricattae infection on the gut microbiome of wild meerkats (Suricata suricatta) applying High Throughput Sequencing technology

Author: Martin Geiger

Supervisors: Prof. Dr. Simone Sommer, Dr. Alice Risely

Year: 2020

Project Description

The purpose of this bachelor thesis was to investigate the effects of infection on the gut microbiome using TB and meerkats as model system. The Mycobacterium tuberculosis complex (MTBC) contains distinct lineages of zoonotic pathogens causing tuberculosis (TB) disease in humans and a variety of wild and domestic mammal species, including meerkats (Suricata suricatta). Meerkats are small carnivores inhabiting desert regions of southern Africa and are routinely affected by outbreaks of meerkat TB (Mycobacterium suricattae). TB infection may cause microbiome dysbiosis via two mechanisms:

1. infection induces a deterministic shift into an alternative stable state;

2. infection has stochastic effects on the microbiome, creating an unstable community configuration with greater dispersion (the “Anna Karenina principle”).

Lab methods that I applied to generate an Illumina MiSeq DNA Amplicon sequencing library:

• DNA extraction
• Polymerase chain reaction (PCR) amplification
• Gel electrophoresis
• Cleaning, capillary electrophoresis, concentration measurements, normalization
• Illumina paired-end sequencing

I analyzed 16S amplicon microbiome data from 362 samples collected from 58 individuals with known TB infection history. I found that M. suricattae infection is associated with negative effects on the physical condition of meerkats. However, no alterations in alpha or beta diversity of gut microbiome composition linked to TB infection or symptoms were detected.

Folder Structure

│projectdir
│
├── report            <- Thesis and presentation
│   ├── presentation  <- PDF of the final presentation
│   ├── thesis        <- PDF of the final thesis
│
├── src               <- R script for data analysis
│
├── README.md