Microbiome

The microbiome – the collection of microbes in and on our body - plays an important role in human health. Changes in the microbiome composition have been implicated in several diseases. Does the presence of certain microbes associate with disease?

We addressed this question in the context of liver cirrhosis-induced cognitive impairment. Microbiome data presents unique challenges such as high-dimensionality, low sample numbers, and sparsity. We used traditional ML methods combined with model interpretation techniques and biological pathway analysis to drive novel insights into how certain microbes might explain disease symptoms.

Relevant publications

• K. V. Saboo, N. Petrakov, A. Shamsaddini, A. Fagan, E. A. Gavis, M. Sikaroodi, S. McGeorge, P. Gillevet, R. K. Iyer, J. S. Bajaj (2022). Stool microbiota are superior to saliva in distinguishing cirrhosis and hepatic encephalopathy using machine learning. Journal of Hepatology.

• K. V. Saboo*, A. Shamsaddini*, M. V. Iyer, C. Hu, A. Fagan, E. A. Gavis, M. B. White, M. Fuchs, D. M. Heuman, M. Sikaroodi, R. K. Iyer, P. M. Gillevet, J. S. Bajaj (2021). Sex is associated with differences in gut microbial composition and function in hepatic encephalopathy. Journal of Hepatology.