Memory is essential for behaviour, and it is supported in the brain by neuronal representations formed in the hippocampus and related structures. The gut microbiome can influence the brain and modify complex behaviours through interactions reported by the gut-brain-axis. Perturbations to the composition of the gut microbiome by environmental or genetic factors impact on mood and motivation and may affect memory. The strongest associations between gut microbiota, brain and memory originate from studies in germ-free mice, which are deprived of their microbiome from birth. The absence of microbes leads to a wide range of behavioural deficits including memory impairments. Conversely, ageing-associated memory decline in mice was shown to be reversed by state-of-the-art transplantation of faecal microbiota from young donor mice. However, the current focus on phenotypic consequences of microbiome interventions, and its potential for treatment leaves out of sight the identification of the underlying neuronal mechanisms mediating the effects. We hypothesise that specialised gut microbiome-responsive cell types and synaptic connections regulate the influence of the gut microbiome on hippocampal memory. Here, we aim to contrast neuronal networks in germ-free and conventional animals by (i) identifying constituent cell types; (ii) quantifying their spatial distribution; and (iii) determining their synaptic connectivity. We perform state-of-the-art multi-channel immunohistochemistry, high-resolution confocal microscopy and morphological quantification in the brainstem and in memory-related regions including hippocampus, prefrontal cortex, amygdala and dorsal striatum. Our results have started to reveal key biological organisational principles relevant to the understanding of the gut microbiota’s influence on the brain and memory.