TABLE 3.

Examples of student case study responses to the experimental design of metagenomics research

Excerpts from students’ case study writing in response to the following prompt: “Formulate a research question that can be investigated using next-generation sequencing methodology to evaluate the composition of the gut microbiota.” (See Appendix 1) *All sample data provided is from the upper level neuroscience course
Meets Expectations	How does the microbiome of individuals diagnosed with clinical depression differ from that of individuals who do not show symptoms of clinical depression? What type of gut microbiota is present within individuals with IBDs and dementia/Alzheimer’s disease, individuals with just IBDs, and individuals with dementia/ Alzheimer’s disease? In order to determine what type of gut microbiota is present within individuals with IBDs and dementia/Alzheimer’s disease, IBD, dementia/ Alzheimer’s disease, we can use 16 s ribosomal sequencing to determine this. How does the composition of one’s microbiome potentially predict their susceptibility of developing certain forms of epilepsy? As dementia rates have been shown to be influenced by various inflammatory bowel diseases (IBD), such as Crohn’s or Ulcerative Colitis, an exploratory treatment option includes exposing individuals with IBD to varying levels of an anti-nflammatory drug. This would occur as a double-blind longitudinal study to determine if rates of dementia remain high in these individuals compared to groups without the anti-inflammatory drug. With the methodology of 16 s ribosomal sequencing, varying levels of the different organisms within the microbiota of the IBD-gut could be observed throughout the timeline of the study. Therefore, negative effects from the anti-inflammatory drug on the microbiota could be monitored as well as the populations of bacteria thought to be having an association with dementia.
Needs Improvement Student Response Instructor Feedback	How does national cuisine and environment affect the microbiome, and what correlations can be seen in the microbiome of patients with a neurological disease across countries? This is a big research question exploring cuisine, environment, neurological disease and countries, making effective study not feasible. Adding specificity to have a more targeted research question is essential. We will attempt to use full shot-gun metagenomic sequencing to track which antibiotics affect which microbiota. We will be working with groups to find potential correlations between antibiotics used and bacteria populations present in the microbiome There is a disconnect here between the research question and experimental design. When looking at the fully sequenced genomes of bacteria of those diagnosed and living with major depressive disorder, are the sequenced genomes different than the average population of those living without major depressive disorder? In the study you’ve chosen, the authors conducted experiments to address this research question. What effect do various mutations of genes linked to IBD have on the susceptibility of Alzheimer’s development? This research question is not a microbiome research-related question.