Abstract
Microorganisms in the human body play a vital role in metabolism, immune defense, nutrient absorption, cancer control, and prevention of pathogen colonization. More and more biological and clinical studies have shown that the imbalance of microbial communities is closely related to the occurrence and development of various complex human diseases. Finding potential microbial-disease associations is critical for understanding the pathology of a few diseases and thus further improving disease diagnosis and prognosis. In this study, we proposed a novel computational model to predict disease-associated microbes. Specifically, we first constructed a heterogeneous interconnection network based on known microbe-disease associations deposited in a few databases, the similarity between diseases, and the similarity between microorganisms. We then predicted novel microbe-disease associations by a new method called the double-ended restart random walk model (DRWHMDA) implemented on the interconnection network. In addition, we performed case studies of colon cancer and asthma for further evaluation. The results indicate that 10 and 9 of the top 10 microorganisms predicted to be associated with colorectal cancer and asthma were validated by relevant literatures, respectively. Our method is expected to be effective in identifying disease-related microorganisms and will help to reveal the relationship between microorganisms and complex human diseases.
Highlights
Microorganisms include bacteria, archaea, protozoa, fungi, and viruses
In order to better reveal the association between microbial diseases, based on the known heterogeneous network consisting of microbial-disease association and Gaussian interaction contour kernel similarity, we propose a computational model based on a double-ended restart random walk to predict diseaserelated microorganisms
We can draw a receiver operating characteristic (ROC) curve composed of points corresponding to different thresholds and obtain the area (AUC) under the ROC curve
Summary
Microorganisms include bacteria, archaea, protozoa, fungi, and viruses. There are different types of microorganisms on the human body and in the cavity connected to the outside world, such as the oral cavity, respiratory tract, intestinal tract, and urogenital tract [1, 2]. Microbes play important roles in human health, metabolism, immune defense, nutrient absorption, cancer control, and prevention of colonization of pathogens [3]. Microorganisms of the human body are mainly distributed on the body surface, intestine, and oral cavity, and the types and numbers of microorganisms are different. The number of microorganisms in the intestine is about ten times that of the body’s own cells. The density of microorganisms isolated from the colon is the highest, and 60% of the dry weight of human feces is bacteria [4]
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