Qi Zhao ^1* Biswarup Sen ² Davida S Smyth ³ F L Consoli ⁴

• ¹ University of Science and Technology Liaoning, Anshan, China
• ² Tianjin University, Tianjin, Tianjin, China
• ³ Texas A&M University San Antonio, San Antonio, Texas, United States
• ⁴ University of São Paulo, São Paulo, Rio Grande do Sul, Brazil

Systems microbiology is a field that plays a pivotal role in deciphering the complexity of 19 microbial life. Studying microorganisms in their natural environments reveals the profound 20 ways these organisms contribute to various ecological processes. From nutrient cycling and 21 disease transmission to the synthesis of bioactive compounds, microorganisms play a vital role 22 in sustaining life on Earth. Beyond environmental science, this field holds immense value in 23 healthcare, contributing to the identification of novel pathogens, the development of antibiotics, 24 and a deeper understanding of how the human microbiome impacts health and disease. The 25 multidisciplinary nature of systems microbiology integrates tools and perspectives from 26 genetics, ecology, and bioinformatics, enabling researchers to unravel the complex 27 relationships within microbial communities. The insights gained from this field have far-28 reaching applications, offering solutions to challenges in agriculture, medicine, and 29 environmental conservation. As our understanding of microbial interactions deepens, the 30 significance of systems microbiology continues to grow, establishing it as a cornerstone of 31 modern scientific research and an essential tool for addressing global challenges. 32In this research topic, we aim to highlight key advancements and emerging trends in 33 systems microbiology, based on recent research conducted between 2022 and 2023. After 2 receiving 16 submissions, six high-quality articles were selected for publication following a 35 rigorous peer-review process. 36The issue is particularly notable for its significant contributions to our understanding of 37 the gut microbiome. For example, Huang et al. performed a comprehensive bibliometric 38 analysis using data from the Web of Science Core Collection to chart the evolution of research 39 on the gut microbiome. Their findings highlight the growing focus on gastrointestinal disorders, 40 particularly conditions like inflammatory bowel disease, ulcerative colitis, and Crohn's disease.3 expression network construction, these studies enhance our understanding of microbial systems 69 and their applications. The findings deepen our knowledge of the gut and oral microbiomes, 70 exploring their roles in health and disease, while also examining microbial diversity in 71 agricultural and pathogenic contexts. These contributions demonstrate how systems 72 microbiology connects basic research with practical applications, driving progress in 73 healthcare, agriculture, and environmental management. 74