Hierarchical multi-task deep learning-assisted construction of human gut microbiota reactive oxygen species-scavenging enzymes database

In the process of oxygen reduction, reactive oxygen species (ROS) are generated as intermediates, including superoxide anion (O2-), hydrogen peroxide (H2O2), and hydroxyl radicals (OH-). ROS can be destructive, and an imbalance between oxidants and antioxidants in the body can lead to pathological inflammation. Inappropriate ROS production can cause oxidative damage, disrupting the balance in the body and potentially leading to DNA damage in intestinal epithelial cells and beneficial bacteria. Microorganisms have evolved various enzymes to mitigate the harmful effects of ROS. Accurately predicting the types of ROS-scavenging enzymes (ROSes) is crucial for understanding the oxidative stress mechanisms and formulating strategies to combat diseases related to the "gut-organ axis." Currently, there are no available ROSes databases (DBs). In this study, we propose a systematic workflow comprising three modules and employ a hierarchical multi-task deep learning approach to collect, expand, and explore ROSes-related entries. Based on this, we have developed the human gut microbiota ROSes DB (http://39.101.72.186/), which includes 7,689 entries. This DB provides user-friendly browsing and search features to support various applications. With the assistance of ROSes DB, various communication-based microbial interactions can be explored, further enabling the construction and analysis of the evolutionary and complex networks of ROSes DB in human gut microbiota species.IMPORTANCEReactive oxygen species (ROS) is generated during the process of oxygen reduction, including superoxide anion, hydrogen peroxide, and hydroxyl radicals. ROS can potentially cause damage to cells and DNA, leading to pathological inflammation within the body. Microorganisms have evolved various enzymes to mitigate the harmful effects of ROS, thereby maintaining a balance of microorganisms within the host. The study highlights the current absence of a ROSes DB, emphasizing the crucial importance of accurately predicting the types of ROSes for understanding oxidative stress mechanisms and developing strategies for diseases related to the "gut-organ axis." This research proposes a systematic workflow and employs a multi-task deep learning approach to establish the human gut microbiota ROSes DB. This DB comprises 7,689 entries and serves as a valuable tool for researchers to delve into the role of ROSes in the human gut microbiota. Reactive oxygen species (ROS) is generated during the process of oxygen reduction, including superoxide anion, hydrogen peroxide, and hydroxyl radicals. ROS can potentially cause damage to cells and DNA, leading to pathological inflammation within the body. Microorganisms have evolved various enzymes to mitigate the harmful effects of ROS, thereby maintaining a balance of microorganisms within the host. The study highlights the current absence of a ROSes DB, emphasizing the crucial importance of accurately predicting the types of ROSes for understanding oxidative stress mechanisms and developing strategies for diseases related to the "gut-organ axis." This research proposes a systematic workflow and employs a multi-task deep learning approach to establish the human gut microbiota ROSes DB. This DB comprises 7,689 entries and serves as a valuable tool for researchers to delve into the role of ROSes in the human gut microbiota.