Birth by caesarean section (CS) is an increasingly common obstetrical procedure, improving both mother and infant outcomes. The long-term outcomes of this procedure for the offspring have been recognized following the emerging evidence of elevated risk of metabolic and neurological dysfunction in those born by CS, including increased risk of diagnosis anxiety or depression. The mechanism linking CS birth to mood disorders is unknown, but is thought to stem from the altered microbial exposure during birthing, which may impact offspring development. The abnormal microbiota during critical developmental windows may prime these systems for dysfunction. Prebiotic fibers promote a favourable microbiota composition, potentially attenuating abnormal microbiota development, and reducing the risk of negative health outcomes. The objective of this thesis was to examine the effect of prebiotic supplementation in early life on rat pups born by CS, to assess if it is able to rescue the unfavorable microbiota profile stemming from CS birth and reduce the risk of developing anxiety-like behaviour. Sprague Dawley rats born by CS (n=40) and VB (n=45) either divided into a control group fed regular rat chow or a oligofructose supplemented diet (5% OFS from p21-p42, 10% OFS from p42 – p115). At 11 weeks of age rats were subjected to behavioural testing to assess anxiety-like behaviour (elevated plus maze and open field test), sociability (three chamber sociability test), cognition (novel object recognition) and anhedonia (sucrose preference test). Gut microbiota composition (16S rRNA sequencing), various metabolic outcomes (glucose tolerance, body composition, and serum analytes) and amygdala gene expression (RT-qPCR). CS birth resulted in increased anxiety-like behavior in males in the EPM, differences in gut microbiota (diversity and abundance), reduced glucose tolerance, altered serum metabolite concentration, and altered amygdala gene expression. All of these metrics other than gene expression were improved with OFS supplementation. There were no differences in depressive-like behaviour (anhedonia), cognition, or social behaviour. Overall, birth by CS led to a variety of developmental alterations, many of which was preventable to OFS supplementation. This provides further evidence regarding the developmental abnormalities following CS birth, and the potential use of prebiotic supplementation to reduce these abnormalities.