Traumatic Brain Injury in Mice Induces Acute Bacterial Dysbiosis Within the Fecal Microbiome

Abstract

The secondary injury cascade that is activated following traumatic brain injury (TBI) induces responses from multiple physiological systems, including the immune system. These responses are not limited to the area of brain injury; they can also alter peripheral organs such as the intestinal tract. Gut microbiota play a role in the regulation of immune cell populations and microglia activation, and microbiome dysbiosis is implicated in immune dysregulation and behavioral abnormalities. However, changes to the gut microbiome induced after acute TBI remains largely unexplored. In this study, we have investigated the impact of TBI on bacterial dysbiosis. To test the hypothesis that TBI results in changes in microbiome composition, we performed controlled cortical impact (CCI) or sham injury in male 9-weeks old C57BL/6J mice. Fresh stool pellets were collected at baseline and at 24 h post-CCI. 16S rRNA based microbiome analysis was performed to identify differential abundance in bacteria at the genus and species level. In all baseline vs. 24 h post-CCI samples, we evaluated species-level differential abundances via clustered and annotated operational taxonomic units (OTU). At a high-level view, we observed significant changes in two genera after TBI, Marvinbryantia, and Clostridiales. At the species-level, we found significant decreases in three species (Lactobacillus gasseri, Ruminococcus flavefaciens, and Eubacterium ventriosum), and significant increases in two additional species (Eubacterium sulci, and Marvinbryantia formatexigens). These results pinpoint critical changes in the genus-level and species-level microbiome composition in injured mice compared to baseline; highlighting a previously unreported acute dysbiosis in the microbiome after TBI.

Keywords: Lactobacillus; bacterial dysbiosis; brain damage; controlled cortical impact injury; gut microbes; gut-brain axis; microbiome; traumatic brain injury.

Figure 1

Family and Genus level changes before and after brain injury. (A) Box and whiskers plot shows the microbial community analysis using short-read (Illumina) sequencing comparing TBI and Sham animals at baseline levels and 24 h after brain injury (n = 8/group). The genus Lactobacillus relative abundance is noticeably decreased, by up to >2 log fold change (p > 0.05). The Marvinbryantia (p = 0.02) and Clostridiales genera (^*p < 0.05) both significantly increase after TBI. (B) Krona chart highlights the genus differential abundance in Sham mice, TBI-baseline and 24 h post-TBI mice. TBI-baseline and Sham exhibit similar compositions, while 24 h post-TBI Krona plot highlights a shift in the community composition.

Figure 2

Species-level changes after acute brain injury. (A) The legend indicates each detected bacterial species, ordered from highest relative abundance to lowest relative abundance (colors are repeated). Gray colored bars at the top of each column in the bar plot represents the highest relative abundance of any species: Barnesiella intestinihominis. (B) TBI causes a significant decrease in Lactobacilus gasseri (^****p < 0.0001), Ruminococcus flavefaciens (^*p < 0.05), and Eubacterium ventriosum (^*p < 0.05) compared to baseline levels; and a significant increase in Eubacterium sulci (^*p < 0.05), and Marvinbryantia formatexigens (^*p < 0.05). TBI also caused a decrease in L. gasseri (#p < 0.05) with the sham group (baseline and 24 h), (n = 8/group). (C) Krona chart highlights the relative differential abundance within the Lactobacillus family after injury, showing a near complete loss of L. gasseri, johnsonii, and taiwainensis bacteria, leaving L. rogosae as the lone representative in that genus after TBI.