Integration of fungal and bacterial microbiome sequencing data

Abstract

The analysis of the bacterial microbiome has become routine, but the study of the fungal microbiome, or mycobiome, is still hindered by a lack of robust databases and bioinformatic pipelines. To address this challenge, we developed FunOMIC and its updated version, a pipeline with built-in taxonomic and functional databases for identifying fungi from the human microbiome using shotgun sequencing. The pipeline includes raw sequence quality control, removal of human and bacterial DNA, and comprehensive taxonomic and functional mycobiome profiling. We validated the pipeline using in silico-generated mock communities and over 2,600 real human metagenomic samples. Our findings show that shotgun sequencing combined with FunOMIC outperforms the commonly used internal transcribed spacer (ITS) sequencing in terms of accuracy and cost-effectiveness. We proposed the application of shotgun sequencing with a new enrichment protocol to provide a cost-effective approach to perform gut mycobiome profiling at the species level._x000D_ _x000D_ We also investigated the relationship between microbial diversity, composition, and functions with habitual diet composition. Our study showed that microbial diversity and composition were associated with specificdiet composition instead of driven by global dietary changes._x000D_ _x000D_ Furthermore, we proposed a web server called MycoDM, which provides searching of mycobial markers, online data analysis, and visualization platform to investigate the relationship of human gut mycobiome with various diseases using shotgun metagenomic data. This platform will help researchers study the role of the fungal community associated with disease, which is still unclear. But growing evidence suggests that mycobiome dysbiosis can be related to various conditions and human immune function and metabolism malfunction._x000D_ _x000D_ Our work provides a comprehensive description of the inter-kingdom interaction between bacteria and fungi integrating dietary data. We believe that our proposed workflow will be a valuable resource for mycobiome studies.

Date of Award	22 Jun 2023
Original language	English
Supervisor	Chaysavanh Manichanh (Director)