Microbial Signatures Associated with Gastrointestinal Function in a SERT Ala56 Knock-in Mouse Model

Background: The gut-microbiome-brain (GMB) axis plays a pivotal role in the manifestation of gastrointestinal (GI) and behavioral symptoms. The crosstalk between the enteric and central nervous systems is heavily influenced by the serotonin transporter (SERT), and specific enteric microbiota have been shown to modulate enteric serotonin (5-HT) production. The SERT Ala56 knock-in mouse model displays gastrointestinal (GI), brain, and behavioral phenotypes similar to those observed in autism spectrum disorder (ASD), and administration of a 5-HT₄ agonist, prucalopride has reversed the GI manifestations.

Objectives: 1) Characterize the enteric microbiome in a SERT Ala56 knock-in mouse model. 2) Determine whether treatment with prucalopride corrects gut dysbiosis. 3) Identify key organisms that are associated with changes in GI function.

Methods: Dams were given either prucalopride or vehicle (normal saline) throughout pregnancy and breastfeeding (E1-P21). Drug administration was stopped after 3 weeks to rule out acute drug effects. Five fecal pellets were collected from 9 male progeny per group (WT, SERTAla56+/-prucalopride) at 6-7 weeks of age. Bacterial DNA was extracted from fecal pellets, and next-generation sequencing targeting the V4 region of the 16S rRNA gene was performed on the Illumina MiSeq. With a minimum of 15,000 reads per sample, sequences were quality filtered, clustered into operational taxonomic units (OTUs), and taxonomic assignments were made. GI motility studies were done to measure in vivo total GI transit and colonic motility and in vitro colonic peristalsis. Integrative analysis of GI function and the microbiome was performed to identify factors influenced by microbial species.

Results: The microbial profile of the SERT Ala56 knock-in mice compared to wild type (WT) mice included increases in Prevotella sp. and Lactobacillus sp. and decreases in Bacteroides sp. and Odoribacter sp. Prucalopride treatment of SERT Ala56 mice during neurodevelopment, which prevented abnormalities in ENS anatomy and GI function, also caused microbial shifts that closely resembled WT mice. Integrative analysis also revealed a specific OTU, potentially identified as Clostridium clariflavum, that was found in increased abundance in mice that had the greatest improvements in total GI motility and the frequency of peristalsis.

Conclusions: Identification of a distinct microbial signature in the SERT Ala56 knock-in model, with parallel changes in GI improvements following prucalopride treatment, further solidifies an interaction between motility and the microbiome. This reversible mouse model effectively illustrates the interconnectivity of GI function and the enteric microbiome, with 5-HT playing a critical role. Future studies will include evaluation of behavior and CNS function.