All Things Poop

Our gut microbiomes have long been known to be critical for immunity, nutrient processing, etc. More recently, research has suggested that gut bacteria play an important bidirectional role in brain development & function, and the modulation of stress response. Major Depressive Disorder (MDD) patients have altered microbial compositions and many metabolites which play a role in depression are byproducts of gut microbiota.

My lab is focusing on the effects of chronic social defeat on the microbiomes of mice (as a pre-clinical model). In short, the social defeat (SD) paradigm involves placing the subject mice into the same cages as aggressive mice, allowing them to fight, and then separating the mice using a divider while but keeping them in close proximity to each other for a day. After the process is repeated 10 times with different aggressive mice, the subjects present with anxiety and depressive symptoms.

The aim is to study changes in microbial richness and diversity, and differences in the relative abundances of gut bacteria at the family and phylum levels between depressed and healthy subjects. This is measured through fecal samples which are collected from the subjects’ cages before the paradigm (a baseline) and after SD. The mice are then treated with electroconvulsive shocks (ECS), and post-treatment samples are taken to examine whether reductions in symptoms are also accompanied by a stabilizing microbiome. Many people don’t realize that ECS is still used today to treat severe depression in humans!

The aggregate sequencing results from a pilot study by Kara McGaughey. Each color represents a bacterial phylum, and the shifts in the microbiomes of the depressed group are easily visible.

I’m involved with comparing two DNA extraction kits using the pre-SD fecal samples to choose the more suitable one for the rest of the experiment. I was initially surprised to learn that there is no ‘gold standard’ in DNA extraction and that the various kits in the market all detect varying species & proportions of bacteria. Although my project has ended up being more about microbiology than neuroscience, learning about the different bacterial DNA extraction and sequencing protocols is definitely cool. I’ve also learnt a ton about the measures used to assess the purity (microplate spectrophotometer), concentration (fluorometer) & quality (TapeStation) of extracted DNA. I’m really looking forward to seeing & comparing the sequencing results!

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