Finding disease-specific shifts in the human gut microbiome through correlation network-based modeling
Caroline Ting ([email protected]), Jana Reiser ([email protected]), Kailey Hua ([email protected]), Maxine Lui ([email protected])
Final project for 02-251 Great Ideas in Computational Biology (Spring 2024)
The gut microbiome has been shown to have great influence over the human digestive system and the immune system, as well as neuronal well-being, metabolism, and overall health. Studies have shown that the gut microbiome is capable of positively influencing human health, from protecting against pathogenic invasion to strengthening the immune system. Microbiota encode more genes than their human hosts, and thus control a variety of metabolic functions beyond the scope of our own systems. An alteration of the diversity and abundance of microorganisms in the gut microbiome has been implicated in a variety of diseases, most commonly irritable bowel syndrome (IBS) and inflammatory bowel disease (IBD), where IBD is a precursor to colorectal cancer (CRC). In this paper, we present a topological network analysis of the microbiome of patients suffering from IBS, IBD, and CRC. All of which are diseases that are increasing significantly in recent years and are associated with inflammation in the gastrointestinal tract (GIT). We analyze the biodiversity and interconnectedness of the microbiome of patients with IBS, IBD, and CRC to gain a better understanding of the resilience and stability of the microbiomes and the factors that lead to inflammation of the GIT. Possible applications of these analyses include microbiota-targeted therapeutic treatments for overgrown or missing bacteria, as well as tracking the severity of the disease progression. We also found the most significant bacteria present in patients with IBS, IBD, and CRC, which act as biomarkers for the diseases for non-invasive diagnosis.
The gut microbiome is defined as the class of microorganisms inhabiting the human digestive tract, and its imbalance has been linked with many digestive conditions. Extensive research has been conducted to study the relationship between the gut microbiome and gastrointestinal conditions. There is also ongoing research for gut microbiome-targeted therapeutics for treating many of these conditions, and to stabilize it to a healthy balance of microorganisms.
In current literature, studies have used network-based approaches to characterize the abundance and biodiversity of microbiota in different groups of patients. The ability to understand the differences between the gut microbiome of healthy individuals and diseased states will allow us to design more accurate microbiota-targeted therapeutics as well as gain a larger understanding of the affects of gastrointestinal conditions.
We focus on a network analysis of the connections between taxa in the gut microbiome of IBS and IBD, two common gastrointestinal conditions, and CRC, a cancer which is intimately associated with the gut microbiome, as it makes up much of the tumor's microenvironment. Our work shows the shifts in abundance and interconnectedness of the gut microbiome in these three disease classes, and can aid researchers in microbiota-based disease class annotation.
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