Systems microbiology is a field that plays a pivotal role in deciphering the complexity of microbial life. Studying microorganisms in their natural environments reveals the profound ways in which these organisms contribute to various ecological processes. From nutrient cycling and disease transmission to the synthesis of bioactive compounds, microorganisms play a vital role in sustaining life on Earth. Beyond environmental science, this field holds immense value in healthcare, contributing to the identification of novel pathogens, the development of antibiotics, and a deeper understanding of how the human microbiome impacts health and disease. The multidisciplinary nature of systems microbiology integrates tools and perspectives from genetics, ecology, and bioinformatics, enabling researchers to unravel the complex relationships within microbial communities. The insights gained from this field have far-reaching applications, offering solutions to challenges in agriculture, medicine, and environmental conservation. As our understanding of microbial interactions deepens, the significance of systems microbiology continues to grow, establishing it as a cornerstone of modern scientific research and an essential tool for addressing global challenges.
In this Research Topic, we aim to highlight key advancements and emerging trends in systems microbiology, drawing on recent research conducted between 2022 and 2023. After receiving 16 submissions, six high-quality articles were selected for publication following a rigorous peer-review process.
The Research Topic is particularly notable for its significant contributions to our understanding of the gut microbiome. For example, Huang et al. performed a comprehensive bibliometric analysis using data from the Web of Science Core Collection to chart the evolution of research on the gut microbiome. Their findings highlighted the growing focus on gastrointestinal disorders, particularly conditions such as inflammatory bowel disease, ulcerative colitis, and Crohn's disease. In addition, the impact of gut microbiota on extra-intestinal diseases is gaining recognition, with emerging links to conditions such as obesity, diabetes, cardiovascular diseases, and even neurodegenerative disorders such as Alzheimer's and Parkinson's disease. Lyu et al. employed two-sample Mendelian randomization to uncover microbiota types that influence infection risk. Their research identified 18 microbiota that confer protection against infections and 13 associated with increased susceptibility. Among these, the Ruminococcaceae and Lachnospiraceae families, known for their butyrate production, were found to have both beneficial and detrimental effects on health.
Another key theme explored in this Research Topic is the role of oral microbiota in human health. Bao et al. introduced a novel approach called oral_voting_transfer, designed to improve the classification of oral microbiota species. This model successfully classified organelle proteins across five microorganisms, including Streptococcus mutans and Staphylococcus aureus. In a related study, Su et al. provided an in-depth analysis of how oral microbiota contribute to cancer development, shedding light on their role in tumorigenic processes and highlighting their potential as biomarkers for early cancer detection and prevention.
Two additional papers further expanded on this Research Topic by exploring microbiome diversity in non-human contexts. Aoki et al. developed a pipeline for analyzing the genomic diversity of the rice rhizosphere microbiome at the single-cell level. This technique enabled them to sequence over 3,000 single-amplified genomes, providing valuable insights into microbial functions within the paddy ecosystem. On the other hand, Soberanes-Gutiérrez et al. constructed a gene co-expression network for Ustilago maydis, a pathogenic fungus. Their analysis identified 13 key modules and highlighted critical transcription factors related to its pathogenicity, including those involved in nucleic acid binding, winged helix DNA binding, and the Zn2/Cys6 DNA-binding protein families.
To conclude this editorial, the studies featured in this Research Topic highlight the importance of systems microbiology in addressing key challenges across various domains. Using methods such as bibliometric analysis, Mendelian randomization, single-cell sequencing, and gene co-expression network construction, these studies enhance our understanding of microbial systems and their applications. The findings deepen our knowledge of the gut and oral microbiomes, exploring their roles in health and disease, while also examining microbial diversity in agricultural and pathogenic contexts. These contributions demonstrate how systems microbiology connects basic research with practical applications, driving progress in healthcare, agriculture, and environmental management.
Statements
Author contributions
QZ: Conceptualization, Funding acquisition, Project administration, Writing – original draft. BS: Writing – review & editing. DS: Writing – review & editing. FC: Writing – review & editing.
Funding
The author(s) declare financial support was received for the research, authorship, and/or publication of this article. Qi Zhao appreciated the financial support provided by Natural Science Foundation of Liaoning Province (Grant No. 2023-MS-288) and Fundamental Research Funds for the Liaoning Universities (Grant No. LJ212410146026).
Acknowledgments
We express our sincere gratitude to all authors whose work contributed to this Research Topic and the reviewers for their invaluable feedback. We also extend our thanks to the editorial team at Frontiers in Microbiology for their exceptional support, which made the successful publication of this Research Topic possible.
Conflict of interest
The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.
The author(s) declared that they were an editorial board member of Frontiers, at the time of submission. This had no impact on the peer review process and the final decision.
Publisher’s note
All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article, or claim that may be made by its manufacturer, is not guaranteed or endorsed by the publisher.
Summary
Keywords
systems microbiology, gut microbiome, microorganism, oral microbiota, microbiome diversity
Citation
Zhao Q, Sen B, Smyth DS and Cônsoli FL (2025) Editorial: Insights in systems microbiology: 2022/2023. Front. Microbiol. 15:1538030. doi: 10.3389/fmicb.2024.1538030
Received
02 December 2024
Accepted
30 December 2024
Published
14 January 2025
Volume
15 - 2024
Edited by
George Tsiamis, University of Patras, Greece
Reviewed by
Vassiliki Karapapa, Municipality of Agrinio, Greece
Updates
Copyright
© 2025 Zhao, Sen, Smyth and Cônsoli.
This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
*Correspondence: Qi Zhao zhaoqi@lnu.edu.cn
Disclaimer
All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article or claim that may be made by its manufacturer is not guaranteed or endorsed by the publisher.