A novel strategy to investigate longitudinal changes within the gut microbiome: Insights from mouse models of sepsis and Alzheimer's disease

Sepsis is a life-threatening condition that is caused by the immune system’s inability to respond appropriately to an infection. How sepsis can change the gut microbiome in ways that alter the brain and behavior is not well understood. One project in my laboratory is to identify ways to prevent or mitigate the neurological impact of sepsis by understanding how gut microbial communities change in response to sepsis. To investigate this, we compared changes in the gut microbiome between wild type (WT) and Alzheimer’s disease transgenic (CVN-AD) mice who received a sepsis injury. WT and CVN-AD mice were subjected to the cecal ligation and puncture model of sepsis or a sham surgery. Fecal samples were collected from each mouse at baseline (day 0) and 6 days post-sepsis. Each fecal sample was processed in triplicate using Shoreline Biome’s StrainID kit, which features a 16S-23S amplicon product that includes the highly variable internal transcribed spacer (ITS) region. Pooled amplicons (~2500 bp) were sequenced on the PacBio Sequel platform, and reads were demultiplexed using SBAnalyzer software and mapped to the novel Athena database. Dramatic differences in gut microbiome profiles between day 0 and day 6 post-sepsis were observed in both WT and CVN-AD mice. First, a dramatic decrease of the commensal Muribaculum was observed in all septic mice. Second, a unique cluster of septic samples displayed a large increase in Clostridium with a proportional decrease in Muribaculum on day 6. Third, samples with a higher percentage of Lactobacillus at day 0 had a lower decrease in Muribaculum and increase in Clostridium on day 6. WT and CVN-AD mice showed the greatest differences in their abundance of the Lactobacillus strains: L. murinus L. johnsonii, and L. reuteri. These results show that the combination of the StrainID kit, PacBio Sequel, SBAnalyzer software, and Athena database provide an optimal strategy to uncover species- and strain-differences in microbial communities.

Learning Objectives:

1. Explain how sepsis can change the gut microbiome in ways that affect human health and behavior

2. Identify ways that Alzheimer’s disease-like pathology can modify gut microbiome responses during sepsis

3. Describe advantages of 16S-ITS-23S rRNA amplicon sequencing over standard short-read 16S rRNA sequencing