Assembly Rules of the Human Microbiome: From Colonization to Disease

The assembly of the human microbiome is not a random accumulation of microbes, but a highly orchestrated process governed by complex ecological rules. From the initial seeding at birth to the established stability of adulthood, microbial communities undergo dynamic succession driven by deterministic selection (e.g., host filtering, interspecies competition) and stochastic processes (e.g., dispersal, drift). While advances in metagenomics and longitudinal sampling have allowed us to catalog "who is there," understanding the mechanistic "rules" that dictate how these communities assemble, maintain resilience, and ultimately collapse into dysbiosis remains a critical frontier. The ability of pathogens to bypass colonization resistance or for commensals to turn into pathobiont highlights the fragility of these assembly rules under stress. However, translating ecological theories, such as niche exclusion and priority effects, into clinical interventions for restoring microbiome homeostasis remains a significant challenge.This Research Topic aims to illuminate the mechanisms and ecological dynamics shaping the human microbiome from colonization to potential disease states. Key objectives include resolving how community assembly in one anatomical niche (such as the gut) can influence distant sites (exemplified by the gut-lung axis), understanding the effectiveness of interventions like Fecal Microbiota Transplantation (FMT) in re-establishing healthy community structure, and dissecting the ecological interactions—such as competitive exclusion and metabolic cooperation—that underpin therapeutic outcomes. By fostering interdisciplinary research at the intersection of microbial ecology, host-microbiome interactions, and translational medicine, the goal is to establish a robust framework for restoring and maintaining microbiome homeostasis.This Research Topic is focused on the mechanistic, ecological, and translational aspects of human microbiome assembly and its disruption, with particular attention to the gut and its systemic impacts. It does not include studies limited to descriptive cataloguing or purely clinical outcomes without molecular or ecological context. To gather further insights into the assembly and intervention dynamics of the human microbiome, we welcome articles addressing, but not limited to, the following themes:1. Mechanisms of Community Succession: Studies on early-life microbiome development, identifying critical windows of opportunity for immune programming.2. Colonization Resistance and Pathogen Invasion: Mechanisms underpinning colonization resistance and the strategies pathogens use to invade or disrupt established communities.3. Resilience and Recovery: Analysis of microbiome re-assembly after perturbations (e.g., antibiotics, chemotherapy) and factors predicting a return to homeostasis vs. a shift to alternative stable states.4. Host-Microbe Cross-talk in Assembly: The role of host immunity, mucosal barriers, and metabolic products in filtering microbial colonizers.5. The Gut-Lung Axis: Investigations into the bidirectional communication between the gastrointestinal and respiratory microbiomes, focusing on how dysbiosis in one compartment affects the assembly and disease susceptibility of the other.6. Therapeutic Interventions for Microbiome Restoration: Clinical and mechanistic studies on the impact of Fecal Microbiota Transplantation (FMT), probiotics, and prebiotics in correcting microbiome disorders and treating infectious or inflammatory diseases. Topic editors: Dan Li, Dong Sun, You Xu Source: https://www.frontiersin.org/research-topics/77244/assembly-rules-of-the-human-microbiome-from-colonization-to-disease