Bacterial Genes of Metabolite Biomarkers of Autism Spectrum Disorders in Gut Microbiota of Young Children: Detection by
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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 O. V. Averinaa, c, *, A. S. Kovtuna, b, and V. N. Danilenkoa a
Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119991 Russia Moscow Institute of Physics and Technology (State University), Dolgoprudny, Moscow oblast, 141701 Russia cPirogov Russian National Research Medical University, Moscow, 117997 Russia *e-mail: [email protected]
b
Received December 10, 2019; revised January 31, 2020; accepted February 4, 2020
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. Keywords: gut microbiota, autism spectrum disorders, biomarkers, metagenome DOI: 10.1134/S1022795420100026
Gut microbiota, consisting of all microorganisms of the human digestive tract, is in bidirectional communication with the human brain and its effect on the brain is mainly carried out through the effect of produced neuroactive metabolites [1]. Various clinical and experimental data indicate the effect of gut microbiota on a wide range of behavioral aspects, including social, emotional, and anxious behavior [2]. Significant changes in the dynamic interaction of the microbiota with the host during the critical periods of early childhood lead to a deep disturbance in the signaling between the gut and the brain and can lead to disturbances in the development of the brain [3–5]. Autism spectrum disorder (ASD) is one of the diseases resulting from disorders in the development of the brain of a child. It is characterized by certain abnormalities in verbal and nonverbal communication and social interactions. Today, ASD is a c
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