The dysbiosis of gut microbiota is associated with the pathogenesis of human diseases. However, observing shifts in the microbe abundance cannot fully reveal underlying perturbations. Examining the relationship alterations (RAs) in the microbiome between health and disease statuses provides additional hints about the pathogenesis of human diseases, but no methods were designed to detect and quantify the RAs between different conditions directly. Here, we present profile monitoring for microbial relationship alteration (PM2RA), an analysis framework to identify and quantify the microbial RAs. The performance of PM2RA was evaluated with synthetic data, and it showed higher specificity and sensitivity than the co-occurrence-based methods. Analyses of real microbial datasets showed that PM2RA was robust for quantifying microbial RAs across different datasets in several diseases. By applying PM2RA, we identified several novel or previously reported microbes implicated in multiple diseases. PM2RA is now implemented as a web-based application available at http://www.pm2ra-xingyinliulab.cn/.

The gut microbiota has been found to interact with the brain through the microbiota-gut-brain axis, regulating various physiological processes. In recent years, the impacts of the gut microbiota on neurodevelopment through this axis have been increasingly appreciated. The gut microbiota is commonly considered to regulate neurodevelopment through three pathways, the immune pathway, the neuronal pathway, and the endocrine/systemic pathway, with overlaps and crosstalks in between. Accumulating studies have identified the role of the microbiota-gut-brain axis in neurodevelopmental disorders including autism spectrum disorder, attention deficit hyperactivity disorder, and Rett Syndrome. Numerous researchers have examined the physiological and pathophysiological mechanisms influenced by the gut microbiota in neurodevelopmental disorders (NDDs). This review aims to provide a comprehensive overview of advancements in research pertaining to the microbiota-gut-brain axis in NDDs. Furthermore, we analyzed both the current state of research progress and discuss future perspectives in this field.
Humans ; Brain-Gut Axis ; Autism Spectrum Disorder/metabolism* ; Brain/metabolism* ; Gastrointestinal Microbiome ; Neurodevelopmental Disorders/metabolism*