Identification of Key Features Pivotal to the Characteristics and Functions of Gut Bacteria Taxa through Machine Learning Methods.

Abstract

Background: Gut bacteria critically influence digestion, facilitate the breakdown of complex food substances, aid in essential nutrient synthesis, and contribute to immune system balance. However, current knowledge regarding intestinal bacteria remains insufficient.

Objective: This study aims to discover essential differences for different intestinal bacteria.

Methods: This study was conducted by investigating a total of 1478 gut bacterial samples comprising 235 Actinobacteria, 447 Bacteroidetes, and 796 Firmicutes, by utilizing sophisticated machine learning algorithms. By building on the dataset provided by Chen et al., we engaged sophisticated machine learning techniques to further investigate and analyze the gut bacterial samples. Each sample in the dataset was described by 993 unique features associated with gut bacteria, including 342 features annotated by the Antibiotic Resistance Genes Database, Comprehensive Antibiotic Research Database, Kyoto Encyclopedia of Genes and Genomes, and Virulence Factors of Pathogenic Bacteria. We employed incremental feature selection methods within a computational framework to identify the optimal features for classification.

Results: Eleven feature ranking algorithms selected several key features as pivotal to the characteristics and functions of gut bacteria. These features appear to facilitate the identification of specific gut bacterial species. Additionally, we established quantitative rules for identifying Actinobacteria, Bacteroidetes, and Firmicutes.

Conclusion: This research underscores the significant potential of machine learning in studying gut microbes and enhances our understanding of the multifaceted roles of gut bacteria.