7.2 Alzheimer’s dataset
Our body requires our organs working in tandem and communicating with each other in order to function. One of the key relationships you may have heard of is the gut-brain axis, a bidirectional relationship between the gastrointestinal system and the central nervous system.
To explore this relationship within the specific context of a disease, we have a dataset from Gut microbiota is altered in patients with Alzheimer’s disease by Zhuang et al. (2018). This dataset was selected by a student from Clovis Community College and integrated into our curriculum! In this study researchers sequenced the gut microbiome from 43 patients with Alzheimer’s disease and 43 patients from age and sex matched controls. The metadata is more sparse than our other datasets, but a wealth of taxonomic information remains unanalyzed!
As computational methods and biological databases have advanced in the nearly decade since, we reanalyzed the raw data from this study with a more recent database (SILVA 138.2). As such, you may find that your results are drastically different from the original study, and its possible that changes in our understanding of microbiology and the processed data may lead us to draw different conclusions than the original authors.
7.2.0.1 Some questions to get you started
- How similar are microbiomes between healthy and AD individuals in composition and/or alpha diversity?
- Looking at other published research studies, are the microbial taxa associated with AD also found in this study?
- Select a microbial taxa of interest (perhaps from the idea above) and explore it at increasing levels of resolution up to the level of species. Looking at other published research studies, what functions are these taxa associated with? Do they have any relation to AD or other neurodegenerative diseases?