How the microbiome keeps us healthy
Using metagenomics and host transcriptomics data to analyse the human signalling pathways affected by microorganisms.
The microbiome plays an important role in maintaining homeostatic functions in host systems, disrupting healthy microbiota could lead to the development of various disorders. Though differences in the microbiota between healthy and unhealthy phenotypes have been reported, the mechanistic role of the microbiota in modulating pro-homeostatic processes remains largely unexplored.
As a focused, gap-filling attempt to address this problem, the aim of the PhD project is to develop a bioinformatic pipeline to predict host-microbe interactions and analyze the effect of microbes on human signalling pathways based on -omics data using network biology approaches (in an industrial cooperation with the Unilever company). The outcome of the project will give an insight in to the effects of a healthy microbiome in the oral cavity and on the scalp for creating products for various applications.
Metadata gives information about microbes colonising a host system. To determine the microbiome of the scalp and oral cavity there are publicly available sources which gives information about the microbial community based on DNA (metagenomic data) or 16S rRNA (metataxonomic data). Based on the literature it is known that the microbial composition is diverse between healthy and unhealthy (gingivitis and dandruff) samples, therefore differences in the communities (first on species then on protein level) will be defined.
Host-microbe protein-protein interactions (PPIs) can help to understand crosstalks between the host system and its microbes. Considering the location, two subgroups of proteins (extracellular/membrane or intracellular/cytoplasmic proteins) are used therefore microbial and human protein location analysis will be carried out before the identification of host-microbe interactions.
Systems-level analysis of networks will help to identify new potential microbial regulators and understand the molecular background of gingivitis and dandruff. Finally, a semi-automatic algorithm will be implemented that allows the computational analysis of various other metagenomic and host-response datasets and makes the whole workflow reusable.
Dr. Janette Jones
Humans are colonized by many microorganisms both externally and internally. Microbes have a pre-homeostatic function which helps to maintain homeostasis in the human body. Changes in the composition of the community due to external (temperature, hygiene, etc.) or internal factors (aging, etc.) lead to dysbiosis, which means the disruption of the microbial equilibrium between commensal and pathogen species.
As a result, this state can cause various disorders in the host, such as inflammatory diseases. It is of great interest to understand how these microbes affect the human host system on a molecular level, as it can help to identify the key bacterial regulators which are responsible for interrupted homeostasis in the body.