An exploration into the role of the infant gut microbiome in Foetal Alcohol Spectrum Disorders (FASD) Natasha Kitchin, Jacqueline S. Womersley, Andrea Engelbrecht, Anna-Susan Marais, Marlene M. de Vries, Philip A. May, Soraya Seedat and Sian M. J. Hemmings The prevalence of Foetal Alcohol Spectrum Disorders (FASD) in the Western Cape of South Africa is estimated to be between 20% and 28%, significantly higher than the global prevalence of 0.77%. Alcohol consumption compromises the integrity of the intestinal barrier thereby allowing bacteria to enter the bloodstream, and in doing so, be transported to the foetus. An altered maternal gut microbiome may influence foetal bacterial colonisation which may subsequently alter the functioning of the infant’s gut microbiota resulting in increased risk of developing a neurodevelopmental disorder. This study therefore aimed to compare the gut microbial composition of infants with and without FASD. Stool samples were collected from 211 infants (102 with FASD and 109 without FASD). 16S rRNA sequencing was performed on microbial DNA extracted from the stool samples. The dada2 pipeline was used to pre-process the fastq sequencing files, create an amplicon sequence variant table, and assign taxonomy. Differential compositional analyses were performed using PhyloSeq, while R was used to calculate diversity measures and compute the statistical analyses of microbial composition. There were no significant differences in alpha- or beta-diversity between infants diagnosed with FASD and those without FASD, however both delivery mode and Bristol Stool Scale influenced beta diversity. The infant gut microbiota was dominated by gram-negative anaerobes such as Prevotella and Bacteroides as well as Faecalibacterium to a lesser extent, with significant representations of gram-positive anaerobes such as Bifidobacterium and facultative microorganisms such as Eshcerichia/Shigella. Bifidobacterium was found to be significantly higher in infants diagnosed with FASD. A lower relative abundance of Bifidobacteria has been observed in children with Autism Spectrum Disorder (ASD), making this finding unexpected. Additionally, Prevotella was significantly higher in infants diagnosed with FASD. Although some articles have found a lower abundance of Prevotella in children with ASD, articles from other low- and middle-income countries have found higher levels of Prevotella in children with ASD. Of the less abundant genera, Rothia, Lactobacillus, Megasphaera, Catenibacterium and Holdemanella were found to be significantly higher in infants with FASD, while Pseudoflavonifracter, Morganella, Hungatella and Eisenbergiella were found to be significantly higher in infants without FASD. Although further studies are required, these findings are promising for microbe-based therapeutic interventions to reduce the extent of neurocognitive deficits and the debilitating symptoms associated with FASD.