Evaluation of the genetic influence on the infant gut microbiome through 16S rRNA sequence data analysis of triplets

• Ano de defesa: 2022
• Autor(a) principal: Palmeira, Ondina Fonseca de Jesus
• Tipo de documento: Dissertação
• Tipo de acesso: Acesso aberto
• Idioma: eng
• Instituição de defesa: Biblioteca Digitais de Teses e Dissertações da USP
• Palavras-chave em Português: 16S; ASVs; Bebês trigêmeos dicoriônicos; Bioinformatic pipelines; Dichorionic triplet babies; Genética do hospedeiro; Herdabilidade; Heritability; Host genetics; Microbioma; Microbiome; Microbiota; Pipelines de bioinformática; Veillonella and Bacteroides; Veillonella e Bacteroides
• Link de acesso: https://www.teses.usp.br/teses/disponiveis/95/95131/tde-26052022-165736/

Studies have shown that the human microbiome plays an important role in physiology, from food digestion to mental diseases. Since the gut microbiota composes the greatest amount of microbial cells and genes outnumbering even our own cell and gene counts, it is expected that the gut microbiome would affect many biological functions, thus becoming key to maintaining homeostasis in the various biological processes. The structure of the gut microbiota is shaped by many factors, including the environment and host genetics. Understanding how these factors determine the gut microbiome during its development and establishment at the early stages of human life is crucial to infer commensal and pathological microbiome composition. The purpose of this study is to investigate how much host genetics and the environment influence the development and establishment of the gut microbiota profiles. For this purpose, five sets of dichorionic triplet babies (two monozygotic twins and one dizygotic twin) are followed during their first 3 years of life. By using Next-Generation Sequencing data (NGS) and Bioinformatic tools, such as specific pipelines for 16S amplicons, we will compare the triplets gut microbiomes regarding presence and absence and relative abundances. We will also try to identify structure patterns, compare results with the literature and integrate the information on the genera associated or not with host genetics. All samples presented enough reads to identify all taxa up to the genus level. Phylogenetic alpha diversity increased in samples at later time points indicating time as a determinant factor. Monozygotic twins were significant more similar in beta diversity when compared to their dizygotic co-twins (DZs). Consistent with the literature, Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria and Verrucomicrobia were the dominant phyla in all sets. Analysis of relative abundance of Amplicon Sequence Variants (ASVs) by Correspondence Analysis (CA) showed that monozygotic twins (MZs) are more similar at time points 9, 11 and 13 months. Heritability test and CA results, as well as shared ASVs, revealed that ASVs of the genera Veillonella and Bacteroides are more similar in MZs.