Microbial Ecology

, Volume 76, Issue 4, pp 1102–1114 | Cite as

Gut Microbial Dysbiosis in Indian Children with Autism Spectrum Disorders

  • Joby Pulikkan
  • Abhijit Maji
  • Darshan Bharat Dhakan
  • Rituja Saxena
  • Binoop Mohan
  • Milu Maria Anto
  • Neeti Agarwal
  • Tony GraceEmail author
  • Vineet K. SharmaEmail author
Human Microbiome


Autism spectrum disorder (ASD) is a term associated with a group of neurodevelopmental disorders. The etiology of ASD is not yet completely understood; however, a disorder in the gut-brain axis is emerging as a prominent factor leading to autism. To identify the taxonomic composition and markers associated with ASD, we compared the fecal microbiota of 30 ASD children diagnosed using Childhood Autism Rating Scale (CARS) score, DSM-5 approved AIIMS-modified INCLEN Diagnostic Tool for Autism Spectrum Disorder (INDT-ASD), and Indian Scale for Assessment of Autism (ISAA) tool, with family-matched 24 healthy children from Indian population using next-generation sequencing (NGS) of 16S rRNA gene amplicon. Our study showed prominent dysbiosis in the gut microbiome of ASD children, with higher relative abundances of families Lactobacillaceae, Bifidobacteraceae, and Veillonellaceae, whereas the gut microbiome of healthy children was dominated by the family Prevotellaceae. Comparative meta-analysis with a publicly available dataset from the US population consisting of 20 ASD and 20 healthy control samples from children of similar age, revealed a significantly high abundance of genus Lactobacillus in ASD children from both the populations. The results reveal the microbial dysbiosis and an association of selected Lactobacillus species with the gut microbiome of ASD children.


Autism spectrum disorder (ASD) Gut microbial dysbiosis Indian children Gut-brain axis Gastrointestinal symptoms 



We thank MHRD, Government of India, Centre for Research on Environment and Sustainable Technologies (CREST) at IISER Bhopal for providing financial support. However, the views expressed in this manuscript are that of the authors alone and no approval of the same, explicit or implicit, by MHRD should be assumed. The sequencing and computational analysis were performed at the NGS Facility and HPC and computing facility, respectively, at IISER Bhopal. JP, AM, DBD, and RS received fellowships from the Central University of Kerala, Centre for Research on Environment and Sustainable Technologies (CREST, IISER Bhopal), UGC (University Grants Commission), and DST-INSPIRE, respectively.

Author Contributions

JP and BM collected the samples. DBD carried out the metagenomic data analysis and all computational and statistical analysis. RS and AM carried out the library preparation and sequencing work. AM, DBD, JP, RS, TG, and VKS drafted the manuscript. MMA and NA performed the diagnosis of all the cases. TG and VKS conceived the work and participated in the design of the study. All authors read and approved the final manuscript.


This work was supported by the intramural funding received from IISER Bhopal, Madhya Pradesh, India, and Central University of Kerala, Kerala, India.

Compliance with Ethical Standards

The protocols for sample collection, sequencing, and analysis as described in the “Materials and Methods” was conducted in accordance with the approved guidelines by the Institutional Ethical Committee of IISER Bhopal, India.

Competing Interests

The authors declare that they have no competing interests.

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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  • Joby Pulikkan
    • 1
  • Abhijit Maji
    • 2
  • Darshan Bharat Dhakan
    • 2
  • Rituja Saxena
    • 2
  • Binoop Mohan
    • 1
  • Milu Maria Anto
    • 3
  • Neeti Agarwal
    • 4
  • Tony Grace
    • 1
    • 5
    Email author
  • Vineet K. Sharma
    • 2
    Email author
  1. 1.Department of Genomic ScienceCentral University of KeralaKasaragodIndia
  2. 2.Metagenomics and Systems Biology Group, Department of Biological SciencesIndian Institute of Science Education and Research BhopalBhopalIndia
  3. 3.Department of PsychologyPrajyoti Niketan CollegePudukadIndia
  4. 4.Department of Paediatrics and NeurologyMahaveer Institute of Medical ScienceBhopalIndia
  5. 5.Division of BiologyKansas State UniversityManhattanUSA

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