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Bacterial Genes of Metabolite Biomarkers of Autism Spectrum Disorders in Gut Microbiota of Young Children: Detection by Real-Time PCR and In Silico Analysis

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Abstract

Two different approaches, real-time PCR and in silico analysis, were used to study the abundance of bacterial genes encoding the enzymes producing biomarker metabolites in metagenomes of gut microbiota of children with autism spectrum disorders (ASD) and healthy children. As a result of the analysis of the published data, the following biomarker metabolites of ASD were chosen for the research: p-cresol, indole, propionic acid, and D-lactic acid. For the real-time PCR and the transcriptomic analysis, primer sequences were used specifically developed for conservative regions of the genes involved in production of these bacterial metabolites. Nucleotide sequences of the conservative regions were also united into a catalog and were searched in metagenomic assemblies as part of in silico analysis. Comparison of the results revealed a decrease in abundance of the genes in the metagenomes of children with ASD during both PCR and bioinformatics analyses. In addition, real-time PCR made it possible to detect a significant increase in abundance of the genes encoding p-hydroxyphenylacetate decarboxylase and D-lactate dehydrogenase in Bacteroides fragilis and Alistipes finegoldii species and methylmalonyl-CoA decarboxylase in B. fragilis, Alistipes shahii, and Eubacterium rectali species. A low level of the transcripts in total RNA was found in microbiota of a child with severe form of ASD.

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Funding

This study was supported by the Russian Science Foundation (project 17-15-01488).

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Correspondence to O. V. Averina.

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Statement of compliance with standards of research involving humans as subjects. All procedures carried out in a study with the participation of people comply with the ethical standards of the institutional and/or national research ethics committee and the 1964 Helsinki Declaration and its subsequent changes or comparable standards of ethics.

Informed voluntary consent was obtained from each of the participants in the study.

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Translated by A. Kashevarova

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Averina, O.V., Kovtun, A.S. & Danilenko, V.N. Bacterial Genes of Metabolite Biomarkers of Autism Spectrum Disorders in Gut Microbiota of Young Children: Detection by Real-Time PCR and In Silico Analysis. Russ J Genet 56, 1260–1268 (2020). https://doi.org/10.1134/S1022795420100026

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