Gut Microbiome Characteristics and Neurodevelopmental Functioning in Children With Autism Spectrum Disorder (GAIN-ASD)

Association Between Gut Microbiome Characteristics and Neurodevelopmental Functioning in Children With Autism Spectrum Disorder: A Multidomain Investigation of the Gut-Motor Axis

Autism Spectrum Disorder (ASD) is a neurodevelopmental condition that affects communication, behavior, sensory processing, and daily functioning. Recent research suggests that the gut microbiome, the community of microorganisms living in the gastrointestinal tract, may influence brain development and function through the gut-brain and gut-motor axes. Alterations in gut microbiome characteristics have been reported in children with ASD and may be associated with differences in neurodevelopmental outcomes.

This observational study aims to investigate the association between gut microbiome characteristics and neurodevelopmental functioning in children with ASD. The study will evaluate multiple domains of functioning, including motor performance, sensory processing, behavior, cognition, sleep, and participation in daily activities. Gut microbiome characteristics will be assessed using stool sample analysis, and neurodevelopmental outcomes will be measured using standardized assessments and validated questionnaires.

The findings of this study may improve understanding of the relationship between the gut microbiome and neurodevelopmental functioning in children with ASD and provide insights into the role of the gut-motor axis in shaping functional outcomes. This knowledge may support future research and contribute to the development of more personalized approaches to assessment and rehabilitation in ASD.

Study Overview

• Status: Not yet recruiting
• Conditions: Autism Spectrum Disorder

Detailed Description

Autism Spectrum Disorder (ASD) is a complex neurodevelopmental condition characterized by impairments in social communication, restricted and repetitive behaviors, sensory processing differences, and variable functional abilities across developmental domains. Increasing evidence suggests that the gut microbiome may play a role in neurodevelopment through bidirectional communication pathways linking the gastrointestinal system and the central nervous system. These interactions, commonly described as the gut-brain axis, have been implicated in behavioral, cognitive, sensory, and motor processes. More recently, the concept of the gut-motor axis has emerged, highlighting potential relationships between gut microbial composition and motor functioning.

Several studies have reported alterations in gut microbiome composition among children with ASD compared with typically developing peers. However, existing research has largely focused on autism symptom severity, behavioral manifestations, or gastrointestinal symptoms, while the association between gut microbiome characteristics and broader neurodevelopmental functioning remains insufficiently explored. Furthermore, few studies have examined multiple functional domains simultaneously within a rehabilitation framework.

The present study aims to investigate the association between gut microbiome characteristics and neurodevelopmental functioning in children with ASD. A multidomain assessment approach will be employed to evaluate neurodevelopmental outcomes encompassing motor performance, sensory processing, behavioral function, cognitive functioning, sleep, and participation in daily activities. Gut microbiome characteristics will be assessed through stool sample analysis using established microbiological methods. Neurodevelopmental outcomes will be evaluated using standardized assessments and validated caregiver-reported instruments.

By examining the relationship between gut microbiome characteristics and multidimensional functional outcomes, this study seeks to enhance understanding of the gut-motor axis in ASD and identify potential microbiome-related factors associated with neurodevelopmental functioning. The findings may contribute to the growing body of evidence on microbiome-neurodevelopment interactions and inform future translational and rehabilitation research in children with ASD.

• Study Type: Observational
• Enrollment (Estimated): 600

Contacts and Locations

• Study Contact: Name: Jeevarathinam Thirumalai, MPT; Phone Number: +91 6384577805; Email: jeevarathinamhope@gmail.com

Study Locations

• India
  • Tamil Nadu
    • Chennai, Tamil Nadu, India, 602 105
      • Saveetha Medical College and Hospital
      • Contact: Indra Sivakumar, PhD; Phone Number: +91 9444009042; Email: indras.smc@saveetha.com

Participation Criteria

Eligibility Criteria

• Ages Eligible for Study: Child
• Accepts Healthy Volunteers: No

• Sampling Method: Non-Probability Sample

Study Population

The study population will consist of children aged 3 to 12 years with a confirmed diagnosis of Autism Spectrum Disorder (ASD) who are receiving care at participating pediatric rehabilitation, developmental, neurology, psychiatry, and autism care centers. Eligible participants will undergo stool sample collection for gut microbiome analysis and multidomain neurodevelopmental assessment, including evaluation of autism severity, gross motor function, sensory processing, cognitive functioning, behavioral function, sleep, participation, quality of life, gastrointestinal symptoms, dietary intake, and anthropometric nutritional status. Written informed consent will be obtained from parents or legal guardians prior to participation.

Description

Inclusion Criteria:

• Children aged 3 to 12 years
• Clinical diagnosis of Autism Spectrum Disorder (ASD) according to DSM-5/ICD criteria and confirmed from medical records or specialist assessment
• Stable clinical status at the time of enrollment
• Parent/legal guardian willing to provide written informed consent
• Child able to undergo stool sample collection and neurodevelopmental assessments
• Parent/caregiver able to complete questionnaires and provide dietary and medical history

Exclusion Criteria:

• Use of systemic antibiotics, probiotics, prebiotics, synbiotics, or bowel-cleansing agents within the previous 4-12 weeks before stool collection
• Presence of acute gastrointestinal infection or acute febrile illness at the time of assessment
• Known chronic gastrointestinal disorders that may independently alter the gut microbiome, such as inflammatory bowel disease, celiac disease, short bowel syndrome, or chronic intestinal malabsorption
• Major neurological, genetic, or metabolic disorders other than ASD that may independently affect neurodevelopment
• Current use of medications known to significantly affect gut microbiota or bowel motility, if clinically relevant to your protocol
• Inability to provide stool sample or complete the required assessments
• Refusal of consent by parent/legal guardian

Study Plan

How is the study designed?

Number of groups / cohorts

2

Cohorts and Interventions

Group / Cohort
Children With Autism Spectrum Disorder; Children diagnosed with Autism Spectrum Disorder (ASD) who meet the study eligibility criteria. Participants will provide stool samples for gut microbiome analysis and undergo multidomain neurodevelopmental assessment.
Typically Developing Children; Age- and sex-matched typically developing children without a diagnosis of Autism Spectrum Disorder or other neurodevelopmental disorders. Participants will provide stool samples for gut microbiome analysis and undergo neurodevelopmental assessment for comparison with the ASD cohort.

What is the study measuring?

Primary Outcome Measures

Outcome Measure	Measure Description	Time Frame
ISAA Total Score	Autism severity will be assessed using the Indian Scale for Assessment of Autism (ISAA). The total score will be used to determine the severity of autism symptoms and examine associations with gut microbiome characteristics.	Baseline
Gut Microbiome Diversity and Composition	Gut microbiome characteristics will be assessed from stool samples using 16S rRNA gene sequencing. Primary microbiome outcomes will include alpha diversity indices (Shannon Diversity Index, Simpson Diversity Index, and Chao1 Richness Index), beta diversity measures, and the relative abundance of bacterial taxa. These measures will be used to characterize gut microbial diversity and composition in children with Autism Spectrum Disorder.	Baseline (single stool sample collected at study enrollment)

Secondary Outcome Measures

Outcome Measure	Measure Description	Time Frame
Gross Motor Function Measure-88 (GMFM-88) Total Score	Gross motor function will be assessed using the GMFM-88. Total scores and dimension scores will be used to evaluate motor performance and its association with gut microbiome characteristics.	Baseline
Gastrointestinal Symptom Severity Score	Gastrointestinal symptoms including constipation, diarrhea, abdominal pain, bloating, and stool consistency will be assessed using a structured gastrointestinal symptom questionnaire and Bristol Stool Form Scale.	Baseline
Strengths and Difficulties Questionnaire (SDQ) Total Difficulties Score	Behavioral functioning will be assessed using the SDQ. Higher scores indicate greater behavioral and emotional difficulties.	Baseline
PROMIS Sleep Disturbance Scale Score	Sleep disturbance will be assessed using the Patient-Reported Outcomes Measurement Information System (PROMIS) Sleep Disturbance Scale. The scale evaluates perceived sleep quality, sleep difficulties, sleep satisfaction, and sleep-related concerns. Higher scores indicate greater sleep disturbance. Associations between sleep disturbance and gut microbiome characteristics will be examined.	Baseline
Participation Questionnaire for Preschoolers With Autism (PPA) Score	Participation will be assessed using the Participation Questionnaire for Preschoolers With Autism (PPA). The questionnaire evaluates participation in home, preschool, community, play, and social activities. Higher scores indicate greater participation in everyday activities. Associations between participation outcomes and gut microbiome characteristics will be examined.	Baseline
Sensory Experiences Questionnaire (SEQ-2.1) Total Score	Sensory processing will be assessed using the Sensory Experiences Questionnaire (SEQ-2.1), a caregiver-reported measure designed to evaluate sensory experiences in children with Autism Spectrum Disorder. The questionnaire assesses sensory hyperreactivity, hyporeactivity, and sensory seeking behaviors across multiple sensory modalities. Higher scores indicate greater sensory processing difficulties.	Baseline
PROMIS Parent Proxy Cognitive Function Score	Cognitive functioning will be assessed using the Patient-Reported Outcomes Measurement Information System (PROMIS) Parent Proxy Cognitive Function measure. The instrument evaluates caregiver-reported difficulties related to attention, memory, concentration, learning, and thinking abilities in children. Higher scores indicate better perceived cognitive functioning. Associations between cognitive function and gut microbiome characteristics will be examined.	Baseline
Dietary Intake Score	Dietary intake will be assessed using parent proxy-reported 24-hour dietary recalls collected on 2-3 non-consecutive days, including at least one weekend day, using the multiple-pass recall method. Information on daily energy intake, macronutrient intake, dietary fiber intake, and consumption of key food groups will be recorded. A supplementary food frequency questionnaire will assess the habitual consumption of fruits and vegetables, whole grains, fermented foods, sugar-sweetened beverages, and ultra-processed foods. Composite healthy diet and unhealthy diet scores will be derived to characterize dietary patterns. Dietary intake variables will be used as covariates in analyses examining associations between gut microbiome characteristics and neurodevelopmental functioning in children with Autism Spectrum Disorder.	Baseline
Pediatric Quality of Life Inventory (PedsQL) Total Score	Quality of life will be assessed using the Pediatric Quality of Life Inventory (PedsQL). The instrument evaluates physical, emotional, social, and school functioning in children. Higher scores indicate better health-related quality of life. Associations between quality of life and gut microbiome characteristics will be examined in children with Autism Spectrum Disorder.	Baseline
Anthropometric Nutritional Status Score	Anthropometric nutritional status will be assessed using standardized measurements of height, weight, and body mass index (BMI). Age- and sex-specific z-scores for weight-for-age, height-for-age, BMI-for-age, and weight-for-height (where applicable) will be calculated according to World Health Organization (WHO) Child Growth Standards and Growth Reference charts. Nutritional status categories including undernutrition, normal nutritional status, overweight, and obesity will be determined. Associations between anthropometric nutritional status and gut microbiome characteristics will be examined in children with Autism Spectrum Disorder.	Baseline
Body Mass Index-for-Age (BMI-for-Age) Z-Score	Body mass index (BMI) will be calculated as weight (kg) divided by height squared (m²). BMI-for-age z-scores will be derived using WHO age- and sex-specific growth references. Higher or lower BMI-for-age z-scores will be used to evaluate nutritional status and their association with gut microbiome characteristics and neurodevelopmental functioning.	Baseline

Collaborators and Investigators

• Sponsor: Saveetha University

Publications and helpful links

General Publications

• Kang DW, Adams JB, Gregory AC, Borody T, Chittick L, Fasano A, Khoruts A, Geis E, Maldonado J, McDonough-Means S, Pollard EL, Roux S, Sadowsky MJ, Lipson KS, Sullivan MB, Caporaso JG, Krajmalnik-Brown R. Microbiota Transfer Therapy alters gut ecosystem and improves gastrointestinal and autism symptoms: an open-label study. Microbiome. 2017 Jan 23;5(1):10. doi: 10.1186/s40168-016-0225-7.
• Cryan JF, O'Riordan KJ, Cowan CSM, Sandhu KV, Bastiaanssen TFS, Boehme M, Codagnone MG, Cussotto S, Fulling C, Golubeva AV, Guzzetta KE, Jaggar M, Long-Smith CM, Lyte JM, Martin JA, Molinero-Perez A, Moloney G, Morelli E, Morillas E, O'Connor R, Cruz-Pereira JS, Peterson VL, Rea K, Ritz NL, Sherwin E, Spichak S, Teichman EM, van de Wouw M, Ventura-Silva AP, Wallace-Fitzsimons SE, Hyland N, Clarke G, Dinan TG. The Microbiota-Gut-Brain Axis. Physiol Rev. 2019 Oct 1;99(4):1877-2013. doi: 10.1152/physrev.00018.2018.
• Vuong HE, Hsiao EY. Emerging Roles for the Gut Microbiome in Autism Spectrum Disorder. Biol Psychiatry. 2017 Mar 1;81(5):411-423. doi: 10.1016/j.biopsych.2016.08.024. Epub 2016 Aug 26.
• Baranek GT, Watson LR, Boyd BA, Poe MD, David FJ, McGuire L. Hyporesponsiveness to social and nonsocial sensory stimuli in children with autism, children with developmental delays, and typically developing children. Dev Psychopathol. 2013 May;25(2):307-20. doi: 10.1017/S0954579412001071.

Study record dates

Study Major Dates

• Study Start (Estimated): July 1, 2026
• Primary Completion (Estimated): December 31, 2026
• Study Completion (Estimated): December 31, 2026

Study Registration Dates

• First Submitted: June 9, 2026
• First Submitted That Met QC Criteria: June 9, 2026
• First Posted (Actual): June 15, 2026

Study Record Updates

• Last Update Posted (Actual): June 15, 2026
• Last Update Submitted That Met QC Criteria: June 9, 2026
• Last Verified: June 1, 2026

More Information

Terms related to this study

• Keywords: Autism Spectrum Disorder; Gut Microbiome; Motor Performance; Gut-Brain Axis; Gut-Motor Axis
• Additional Relevant MeSH Terms: Mental Disorders; Neurodevelopmental Disorders; Child Development Disorders, Pervasive; Autism Spectrum Disorder
• Other Study ID Numbers: 079/06/2026/ISRB/FSR/SIBMS

Plan for Individual participant data (IPD)

• Plan to Share Individual Participant Data (IPD)?: UNDECIDED
• IPD Plan Description: Individual participant data (IPD) may be shared upon reasonable request following publication of the study findings, subject to institutional policies, ethical approval requirements, participant confidentiality protections, and applicable data-sharing agreements. A final decision regarding IPD sharing will be made after completion of the study and in accordance with institutional and regulatory guidelines.

Drug and device information, study documents

• Studies a U.S. FDA-regulated drug product: No
• Studies a U.S. FDA-regulated device product: No