Gut Microbial Dysbiosis in Indian Children with Autism Spectrum Disorders
- 487 Downloads
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.
KeywordsAutism 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.
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.
The authors declare that they have no competing interests.
- 1.Filipek PA, Accardo PJ, Baranek GT, Cook Jr EH, Dawson G, Gordon B, Gravel JS, Johnson CP, Kallen RJ, Levy SE, Minshew NJ, Ozonoff S, Prizant BM, Rapin I, Rogers SJ, Stone WL, Teplin S, Tuchman RF, Volkmar FR (1999) The screening and diagnosis of autistic spectrum disorders. J Autism Dev Disord 29:439–484CrossRefPubMedGoogle Scholar
- 3.de Bildt A, Sytema S, Ketelaars C, Kraijer D, Mulder E, Volkmar F, Minderaa R (2004) Interrelationship between Autism Diagnostic Observation Schedule-Generic (ADOS-G), Autism Diagnostic Interview-Revised (ADI-R), and the Diagnostic and Statistical Manual of Mental Disorders (DSM-IV-TR) classification in children and adolescents with mental retardation. J Autism Dev Disord 34:129–137CrossRefPubMedGoogle Scholar
- 9.Valicenti-McDermott M, McVICAR K, Rapin I, Wershil BK, Cohen H, Shinnar S (2006) Frequency of gastrointestinal symptoms in children with autistic spectrum disorders and association with family history of autoimmune disease. Journal of Developmental & Behavioral Pediatrics 27: S128-S136Google Scholar
- 12.Millward C, Ferriter M, Calver S, Connell-Jones G (2008) Gluten-and casein-free diets for autistic spectrum disorder. Cochrane Database Syst Rev 2Google Scholar
- 13.Saxena R, Sharma V (2016) A metagenomic insight into the human microbiome: its implications in health and disease https://doi.org/10.1016/B978-0-12-420196-5.00009-5
- 23.Bhute S, Pande P, Shetty SA, Shelar R, Mane S, Kumbhare SV, Gawali A, Makhani H, Navandar M, Dhotre D (2016) Molecular characterization and meta-analysis of gut microbial communities illustrate enrichment of Prevotella and Megasphaera in Indian subjects. Front Microbiol 7Google Scholar
- 33.Liaw A, Wiener M (2002) Classification and regression by randomForest. R News 2:18–22Google Scholar
- 34.Kursa MB, Rudnicki WR (2010) Feature selection with the Boruta package. JournalGoogle Scholar
- 44.Maji A, Misra R, Dhakan DB, Gupta V, Mahato NK, Saxena R, Mittal P, Thukral N, Sharma E, Singh A (2017) Gut microbiome contributes to impairment of immunity in pulmonary tuberculosis patients by alteration of butyrate and propionate producers. Environ Microbiol 20:402–419. https://doi.org/10.1111/1462-2920.14015 CrossRefPubMedGoogle Scholar
- 49.De Angelis M, Piccolo M, Vannini L, Siragusa S, De Giacomo A, Serrazzanetti DI, Cristofori F, Guerzoni ME, Gobbetti M, Francavilla R (2013) Fecal microbiota and metabolome of children with autism and pervasive developmental disorder not otherwise specified. PLoS One 8:e76993CrossRefPubMedPubMedCentralGoogle Scholar
- 55.Larsen N, Vogensen FK, van den Berg FW, Nielsen DS, Andreasen AS, Pedersen BK, Al-Soud WA, Sorensen SJ, Hansen LH, Jakobsen M (2010) Gut microbiota in human adults with type 2 diabetes differs from non-diabetic adults. PLoS One 5:e9085. https://doi.org/10.1371/journal.pone.0009085 CrossRefPubMedPubMedCentralGoogle Scholar
- 57.Kassinen A, Krogius-Kurikka L, Makivuokko H, Rinttila T, Paulin L, Corander J, Malinen E, Apajalahti J, Palva A (2007) The fecal microbiota of irritable bowel syndrome patients differs significantly from that of healthy subjects. Gastroenterology 133:24–33. https://doi.org/10.1053/j.gastro.2007.04.005 CrossRefPubMedGoogle Scholar
- 59.Belanche A, Doreau M, Edwards JE, Moorby JM, Pinloche E, Newbold CJ (2012) Shifts in the rumen microbiota due to the type of carbohydrate and level of protein ingested by dairy cattle are associated with changes in rumen fermentation. J Nutr 142:1684–1692. https://doi.org/10.3945/jn.112.159574 CrossRefPubMedGoogle Scholar
- 60.De Filippo C, Cavalieri D, Di Paola M, Ramazzotti M, Poullet JB, Massart S, Collini S, Pieraccini G, Lionetti P (2010) Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa. Proc Natl Acad Sci U S A 107:14691–14696. https://doi.org/10.1073/pnas.1005963107 CrossRefPubMedPubMedCentralGoogle Scholar
- 61.David LA, Maurice CF, Carmody RN, Gootenberg DB, Button JE, Wolfe BE, Ling AV, Devlin AS, Varma Y, Fischbach MA, Biddinger SB, Dutton RJ, Turnbaugh PJ (2014) Diet rapidly and reproducibly alters the human gut microbiome. Nature 505:559–563. https://doi.org/10.1038/nature12820 CrossRefPubMedGoogle Scholar
- 62.Ercolini D, Francavilla R, Vannini L, De Filippis F, Capriati T, Di Cagno R, Iacono G, De Angelis M, Gobbetti M (2015) From an imbalance to a new imbalance: Italian-style gluten-free diet alters the salivary microbiota and metabolome of African celiac children. Sci Rep 5:18571. https://doi.org/10.1038/srep18571 CrossRefPubMedPubMedCentralGoogle Scholar
- 67.Veckman V, Miettinen M, Pirhonen J, Sirén J, Matikainen S, Julkunen I (2004) Streptococcus pyogenes and Lactobacillus rhamnosus differentially induce maturation and production of Th1-type cytokines and chemokines in human monocyte-derived dendritic cells. J Leukoc Biol 75:764–771CrossRefPubMedGoogle Scholar
- 68.O'Hara AM, O'Regan P, Fanning A, O'Mahony C, MacSharry J, Lyons A, Bienenstock J, O'Mahony L, Shanahan F (2006) Functional modulation of human intestinal epithelial cell responses by Bifidobacterium infantis and Lactobacillus salivarius. Immunology 118:202–215CrossRefPubMedPubMedCentralGoogle Scholar
- 77.Martín R, Miquel S, Benevides L, Bridonneau C, Robert V, Hudault S, Chain F, Berteau O, Azevedo V, Chatel JM (2017) Functional characterization of novel Faecalibacterium prausnitzii strains isolated from healthy volunteers: a step forward in the use of F. prausnitzii as a next-generation probiotic. Front Microbiol 8:1226CrossRefPubMedPubMedCentralGoogle Scholar
- 78.Oberc A, Coombes BK (2015) Convergence of external Crohn’s disease risk factors on intestinal bacteria. Front Immunol 6Google Scholar