The prevalence of autism spectrum disorder (ASD) has increased significantly over the past two decades, with recent U.S. estimates indicating that 1 in 31 children is affected. However, no FDA‑approved treatments exist for core ASD symptoms.  Many individuals with ASD experience gastrointestinal symptoms, which correlate with ASD severity and suggest a potential role of the gut–brain axis in ASD pathogenesis. Disruptions of co-diversifying (CD) - vertically transmitted taxa over generations having a congruent phylogeny with their human host - gut microbiota with humans provide a framework for studying and predicting ASD severity and microbiota transplant therapy (MTT) outcomes. Utilizing preprocessed fecal shotgun metagenomic sequencing data obtained from a longitudinal, double-blind, placebo-controlled, phase 2 MTT clinical trial involving 51 ASD patients and 46 neurotypical (NT) individuals and a recently published list of 36 globally present gut microbial species showing specificity to human ancestry (co-diversification), we report that the relative abundance of co-diversifying taxa is positively correlated with ASD severity ( rho = -0.31, p = 0.029),  ASD individuals have a statistically significant lower relative abundance of CD taxa compared to NT individuals (p = 0.026) as well as a statistically significant lower number of co-diversifying observed species than NT individuals (p = 0.0035). For future directions, in ASD subjects, we aim to investigate if engraftment of CD taxa correlates with ASD outcomes. Furthermore, we aim to build models integrating host and microbial genomic data to predict ASD occurrence and severity. These results would potentially inform gut-microbiome-based intervention strategies for ameliorating ASD symptoms.