Abstract
The imbalance of human gut microbiota has been associated with colorectal cancer. In recent years, metagenomics research has provided a large amount of scientific data enabling us to study the dedicated roles of gut microbes in the onset and progression of cancer. We removed unrelated and redundant features during feature selection by mutual information. We then trained a random forest classifier on a large metagenomics dataset of colorectal cancer patients and healthy people assembled from published reports and extracted and analysed the information from the learned decision trees. We identified key microbial species associated with colorectal cancers. These microbes included Porphyromonas asaccharolytica, Peptostreptococcus stomatis, Fusobacterium, Parvimonas sp., Streptococcus vestibularis and Flavonifractor plautii. We obtained the optimal splitting abundance thresholds for these species to distinguish between healthy and colorectal cancer samples. This extracted consensus decision tree may be applied to the diagnosis of colorectal cancers.
Highlights
Many microbial communities cohabit the human body, among which microbiota in the gut is the richest with more than 1000 species [1]
When the random forest model is used to study the relationship between Colorectal cancer (CRC) and microbiota, it can lead to a high false-negative rate [17]
We proposed a mutual information criterion to filter out species with weak associations with CRC in order to improve the quality of input data and reduce the complexity of resulting classification models [29]
Summary
Many microbial communities cohabit the human body, among which microbiota in the gut is the richest with more than 1000 species [1]. Gut microbes participate in many important physiological processes, such as food digestion, metabolism and immune response. In the long-term process of natural evolution, a dynamic balance has always been struck among gut microbiota, host and environment. Composition and function of the microbiota lead to abnormal metabolites of gut microbes, causing, in turn, metabolic diseases, such as obesity [2] and diabetes [3], in addition to chronic gut infections, like inflammatory bowel disease [4], ulcerative colitis, and Crohn’s disease [5,6], and malignant digestive system tumors, such as colorectal [7,8] and gastric cancers [9]. Colorectal cancer (CRC) is the third most prevalent malignant tumor in the world. The fecal occult blood test (FOBT) [13] is another clinical tool for identifying colorectal cancer, which has the advantages of being both noninvasive and economical
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