Microscale Gut Microbiota Spatial Heterogeneity Correlates with neuroinflammation in an Alzheimer’s Disease Model

Abstract

Rising evidence implicates composition of the gut microbiota in neurodegenerative processes, yet little is known about correlations between microscale spatial organization of microbial communities along mucosa of the intestine and brain inflammation in Alzheimer's disease (AD). In our investigation, we applied a validated transgenic mouse model of AD and age-matched wild-type controls to evaluate whether microscale heterogeneities in gut microbiota — i.e., small-scaled, spatially-resolved variations in microbial community composition over adjacent mucosal microenvironments in the intestine — are correlated with markers of neuroinflammation. We applied high-resolution spatial sampling of mucosal surfaces in small intestine and colon coupled with 16S rRNA gene amplicon sequencing and spatial in situ fluorescent hybridization to map community structure at sub-millimeter scale. Concurrent analyses of central nervous system inflammation involved immunohistochemical quantification of microglia and astrocytic activation and measurement of pro-inflammatory cytokine levels in hippocampal tissue. Behaviorally, animals received a battery of cognitive tests in order to place molecular results in context. We found our AD-model mice demonstrated enhanced microscale patchiness and beta-diversity of mucosa-associated microbiotas compared to controls, specifically in proximal colon. Regions of high local heterogeneity correlated with enhanced hippocampal microglia activation and greater levels of inflammatory cytokines. Further, variability of spatial patterns in microbiotas explained greater variability in neuroinflammatory markers compared to bulk measures of fecal community composition. These results implicate that microscale spatial structure of microbes in the gut — not only compositional content — could play a role as a causal factor in, or reflector of, neuroinflammatory states in AD, providing a new direction for mechanistic research as well as spatially-directed microbiome interventions.