Human gut and oral microbiome atlas in healh and diseases

SNIC 2022/6-274


SNIC Medium Storage

Principal Investigator:

Saeed Shoaie


Kungliga Tekniska högskolan

Start Date:


End Date:


Primary Classification:

10203: Bioinformatics (Computational Biology) (applications to be 10610)

Secondary Classification:

10610: Bioinformatics and Systems Biology (methods development to be 10203)

Tertiary Classification:

10606: Microbiology (medical to be 30109 and agricultural to be 40302)



We are investigating gut and oral microbiome samples, in different diseases. We are going to perform large mapping of data to the non-redundant gut gene catalog to retrieve the gene abundances. We then profile the metagenome species and obtain the strains and species level informration. The abundant species will be then associated to the symptoms profile of the individuals. We aim to obtain the predisposition gut metagenome markers with different diseases to reveal the vulnerability of individuals to the infection and severity of the disease and also developing oral and gut-related problems. Afterward we will map the gut metagenome data to the antibiotic resisatnce (CARD database) to reveal resistome profile of the patients and potential rejects to specific antibiotic if they ended up with severe infection conditions. In second project we will analyse liver diseases gut and oral metagenome data to reveal the similarity of the species between the oral and gut and how this could increase the progression of the disease. We will go through the same process as above with additional work on integration to blood chemistry and immune profile.