The gut microbiome has emerged as a central player in human health and disease, with particular relevance to infectious diseases. As a complex and dynamic community of microorganisms, the gut microbiota interacts closely with both resident and invading pathogens, influencing the severity of infections, host defense mechanisms, and even the efficacy of treatment strategies. Growing evidence, driven by advances in high-throughput sequencing and animal modeling, highlights the microbiome’s capacity to influence the outcome of infections caused by enteric pathogens, including Vibrio cholerae and Shigella. Understanding these interactions is crucial, not only for unraveling basic mechanisms of pathogenesis and immunity but also for informing the development of microbiota-targeted interventions.

This article collection focuses on the multifaceted role of the gut microbiome in modulating infectious agents and diseases. Central themes include elucidating how microbiota composition drives differences in pathogen virulence, host inflammatory responses, and disease progression, as well as how host-microbe-pathogen interactions shape these processes. The collection will also spotlight contentious issues in the field, such as the extent to which the microbiome can alter disease trajectories and the prospects for microbiome-based therapies. Special emphasis will be placed on mechanistic insights derived from model organisms, as well as the application of next-generation sequencing to identify microbial genetic elements that impact pathogenesis. By bringing together original research and review articles, this collection aims to clarify the microbiome’s pivotal function in infectious diseases and inspire novel preventive and therapeutic approaches.

To gather further insights into this complex interplay, we welcome articles addressing, but not limited to, the following sub-themes:

• Original research on gut microbiome modulation of Vibrio cholerae, Shigella, and other microbial pathogenesis

• Mechanistic studies using murine and other models to dissect microbiome-pathogen-host interactions

• Reviews on the influence of gut microbial composition on infectious disease outcomes

• Investigations into specific microbial taxa or proteins or metabolites that inhibit or enhance pathogen virulence

• Research employing next-generation sequencing to elucidate key microbial genes or pathways within the microbiome that affect infection

• Studies on how gut microbiota shape host immune responses and inflammation during infection

• Articles examining the microbiome’s role in shaping host susceptibility or resistance to enteric pathogens

• Computational approaches for modeling microbe-pathogen-host dynamics in the gut

• Meta-analyses of clinical cohorts linking microbiome features with infectious disease severity

• Perspectives on controversies and challenges in developing microbiome-targeted therapies for infections

• Reports on the effects of antibiotics or probiotics on microbiome-pathogen equilibrium and disease modulation

• Research on gut microbiome biomarkers predictive of infectious disease risk and outcomes

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Gut Microbiome's Role in Infectious Disease: Modulating Pathogens and Host Responses