A Systematic Review of Mixed Studies Exploring the Effects of Probiotics on Gut-Microbiome to Modulate Therapy in Children With Autism Spectrum Disorder

Best practices for developing microbiome-based disease diagnostic classifiers through machine learning

The human gut microbiome, crucial in various diseases, can be utilized to develop diagnostic models through machine learning (ML). The specific tools and parameters used in model construction such as data preprocessing, batch effect removal and modeling algorithms can impact model performance and generalizability. To establish an generally applicable workflow, we divided the ML process into three above-mentioned steps and optimized each sequentially using 83 gut microbiome cohorts across 20 diseases. We tested a total of 156 tool-parameter-algorithm combinations and benchmarked them according to internal- and external- AUCs. At the data preprocessing step, we identified four data preprocessing methods that performed well for regression-type algorithms and one method that excelled for non-regression-type algorithms. At the batch effect removal step, we identified the "ComBat" function from the sva R package as an effective batch effect removal method and compared the performance of various algorithms. Finally, at the ML algorithm selection step, we found that Ridge and Random Forest ranked the best. Our optimized work flow performed similarly comparing with previous exhaustive methods for disease-specific optimizations, thus is generally applicable and can provide a comprehensive guideline for constructing diagnostic models for a range of diseases, potentially serving as a powerful tool for future medical diagnostics.

Progress in Probiotic Science: Prospects of Functional Probiotic-Based Foods and Beverages

This comprehensive review explores the evolving role of probiotic-based foods and beverages, highlighting their potential as functional and "future foods" that could significantly enhance nutrition, health, and overall well-being. These products are gaining prominence for their benefits in gut health, immune support, and holistic wellness. However, their future success depends on addressing critical safety concerns and navigating administrative complexities. Ensuring that these products "do more good than harm" involves rigorous evaluations of probiotic strains, particularly those sourced from the human gastrointestinal tract. Lactic acid bacteria (LABs) serve as versatile and effective functional starter cultures for the development of probiotic foods and beverages. The review emphasizes the role of LABs as functional starter cultures and the development of precision probiotics in advancing these products. Establishing standardized guidelines and transparent practices is essential, requiring collaboration among regulatory bodies, industry stakeholders, and the scientific community. The review underscores the importance of innovation in developing "friendly bacteria," "super probiotics," precision fermentation, and effective safety assessments. The prospects of functional probiotic-based foods and beverages rely on refining these elements and adapting to emerging scientific advancements. Ultimately, empowering consumers with accurate information, fostering innovation, and maintaining stringent safety standards will shape the future of these products as trusted and beneficial components of a health-conscious society. Probiotic-based foods and beverages, often infused with LABs, a "friendly bacteria," are emerging as "super probiotics" and "future foods" designed to "do more good than harm" for overall health.

Effect of nutritional supplements on gut microbiome in individuals with neurodevelopmental disorders: a systematic review and narrative synthesis

BACKGROUND

Neurodevelopmental disorders (NDDs) encompass a range of disruptive conditions with varying prevalence rates and multiple contributing factors. Recent studies have suggested a potential connection between NDDs and the gut-brain axis. Furthermore, there is evidence indicating that nutritional supplements might have an impact on gastrointestinal (GI) and behavioral symptoms. This study aimed to explore the effects of nutritional supplements on the gut microbiota and behavioral symptoms in individuals with NDDs.

METHODS

A systematic search of databases such as PubMed, Scopus, Web of Science, Embase, and APA PsycINFO was conducted, utilizing relevant keywords until February 2025. In addition, the search for gray literature was carried out on Google Scholar and ProQuest. The risk of bias was assessed using the ROBINS-I tool for non-randomized studies and the RoB-1 tool for randomized controlled trials. Due to the heterogeneity of the studies, a Synthesis without Meta-analysis (SWiM) approach was employed.

RESULTS

The overall findings from the studies indicated positive effects of supplementation in reducing the Gastrointestinal Severity Index (GIS) score and alleviating GI symptoms. Supplementation with probiotics and vitamins increased good microbiomes (GM) and decrease in bad microbiomes (BM) among individuals with autism spectrum disorder (ASD). Moreover, the Firmicutes to Bacteroidetes ratio (F/R ratio) exhibited significant changes after supplementation. Additionally, improvements were observed in various assessment scores, including ATEC, ABC, CARS, and PGI-2.

CONCLUSIONS

Nutritional supplementation in individuals with NDDs can have a positive influence by modulating the microbiome, reducing dysbiosis, and enhancing gut barrier integrity. Shifting in the F/R ratio can be considered as the reason for improving gastrointestinal and behavioral symptoms by influencing neurotransmitter activity and neuroinflammation. Targeting the gut-brain axis with interventions that focus on gut microbiota offers a promising adjunct therapy for the management of NDD. Registration of the review protocol. PROSPERO registration no. CRD42023460449.

Critical Appraisal of Systematic Reviews Assessing Gut Microbiota and Effect of Probiotic Supplementation in Children with ASD-An Umbrella Review

Given the significance of gut microbiota in autism spectrum disorder (ASD), we aimed to assess the quality of systematic reviews (SRs) of studies assessing gut microbiota and effects of probiotic supplementation in children with ASD. PubMed, EMBASE, PsycINFO, Medline, and Cochrane databases were searched from inception to November 2024. We included SRs of randomised or non-randomized studies reporting on gut microbiota or effects of probiotics in children with ASD. A total of 48 SRs (probiotics: 21, gut microbiota: 27) were included. The median (IQR) number of studies and participants was 7 (5) and 328 (362), respectively, for SRs of probiotic intervention studies and 18 (18) and 1083 (1201), respectively, for SRs of gut microbiota studies in children with ASD. The quality of included SRs was low (probiotics: 12, gut microbiota: 14) to critically low (probiotics: 9, gut microbiota: 13) due to lack of reporting of critical items including prior registration, deviation from protocol, and risk of bias assessment of included studies. Assuring robust methodology and reporting of future studies is important for generating robust evidence in this field.

Microbiota in Autism Spectrum Disorder: A Systematic Review

Autism spectrum disorder (ASD) is a complex neurodevelopmental condition characterized by several core symptoms: restricted interests, communication difficulties, and impaired social interactions. Many ASD children experience gastrointestinal functional disorders, impacting their well-being. Emerging evidence suggests that a gut microbiota imbalance may exacerbate core and gastrointestinal symptoms. Our review assesses the gut microbiota in children with ASD and interventions targeting microbiota modulation. The analysis of forty-four studies (meta-analyses, reviews, original research) reveals insights into the gut microbiota-ASD relationship. While specific microbiota alterations are mixed, some trends emerge. ASD children exhibit increased Firmicutes (36-81%) and Pseudomonadota (78%) and decreased Bacteroidetes (56%). The Bacteroidetes to Firmicutes ratio tends to be lower (56%) compared to children without ASD, which correlates with behavioral and gastrointestinal abnormalities. Probiotics, particularly Lactobacillus, Bifidobacterium, and Streptococcus strains, show promise in alleviating behavioral and gastrointestinal symptoms (66%). Microbiota transfer therapy (MTT) seems to have lasting benefits for the microbiota and symptoms in one longitudinal study. Prebiotics can potentially help with gastrointestinal and behavioral issues, needing further research for conclusive efficacy due to different interventions being used. This review highlights the gut microbiota-ASD interplay, offering potential therapeutic avenues for the gut-brain axis. However, study heterogeneity, small sample sizes, and methodological variations emphasize the need for comprehensive, standardized research. Future investigations may unveil complex mechanisms linking the gut microbiota to ASD, ultimately enhancing the quality of life for affected individuals.

The gut microbiome in children with mood, anxiety, and neurodevelopmental disorders: An umbrella review

Research on the gut microbiome and mental health among children and adolescents is growing. This umbrella review provides a high-level overview of current evidence syntheses to amalgamate current research and inform future directions. Searches were conducted across seven databases for peer-reviewed pediatric (<18 years) review literature. Studies reporting gut microbiome composition and/or biotic supplementation on depression, bipolar disorder, anxiety, attention deficit hyperactivity disorder, autism spectrum disorder (ASD), or obsessive-compulsive disorder (OCD) were included. Deduplication and screening took place in Covidence. A sensitivity analysis was conducted to assess the degree of primary study overlap. Among the 39 included review studies, 23 (59%) were observational and 16 (41%) were interventional. Most reviews (92%) focused on ASD. Over half (56%) of the observational and interventional reviews scored low or critically low for methodological quality. A higher abundance of Clostridium clusters and a lower abundance of Bifidobacterium were consistently observed in ASD studies. Biotic supplementation was associated with ASD symptom improvement. Gut microbiome-mental health evidence syntheses in child and youth depression, anxiety, bipolar disorder, and OCD are lacking. Preliminary evidence suggests an association between specific microbiota and ASD symptoms, with some evidence supporting a role for probiotic supplementation ASD therapy.