Frontiers | Personalized Microbiome Interventions: Multi-Omics Approaches to Optimizing Gut Health

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Submission deadlines

1. Manuscript Submission Deadline 28 February 2027

2. This Research Topic is currently accepting articles

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Background

Research in microbiome science has increasingly highlighted the fundamental impact of the gut microbiota on human health, with implications ranging from metabolic regulation to immune function and even neurobehavioral outcomes. Historically, most studies have concentrated on broad correlations between microbial populations and host health or disease, classifying individuals based on generalized community structures or typical “healthy” signatures. However, substantial individual variability in genetics, environmental exposures, dietary patterns, and baseline microbial compositions limits the effectiveness of one-size-fits-all interventions. Recent debates focus on how best to harness high-throughput and multi-omics analytical strategies and bioinformatic platforms to move beyond descriptive findings and toward genuinely personalized approaches that can predict and modulate health outcomes at the level of the individual. This shift is particularly relevant for developing targeted, evidence-based strategies to improve gut health and prevent disease in human and animals.Addressing this challenge, emerging evidence highlights the potential of advanced omics technologies such as genomics, transcriptomics, proteomics and metabolomics to decode personalized interactions between hosts and their microbiomes. Recent studies reveal that interventions tailored to the host’s genetic background and baseline or longitudinal microbiome profiles can elicit more favorable health outcomes than generic therapies. Innovations in metagenomic sequencing, computational modeling, and systems biology are ushering in a new era of precision microbiome medicine, yet knowledge gaps persist regarding the mechanisms underpinning successful interventions, the identification of robust response biomarkers, and the scalability of these approaches to diverse populations. There is a critical need for research that moves from conceptual frameworks and pilot studies to the validation and deployment of scalable, individualized microbial therapies.This Research Topic aims to foster interdisciplinary work that elucidates how integrative multi-omics technologies and bioinformatic tools can be leveraged to develop, optimize, and evaluate personalized microbiome interventions for gut health. Key objectives include assessing how host-specific factors, such as genetics, dietary intake, and lifestyle, and baseline microbiome composition, shape the efficacy of targeted microbial therapies, engineered microbiome, and identifying biomarkers for therapy response, and exploring the clinical and public health implications of personalized interventions across various disease contexts. The ultimate goal is to translate current knowledge into actionable, evidence-based strategies that advance precision nutrition, preventive medicine, and microbiome-based therapeutic innovation.To gather further insights in the domain of personalized gut microbiome interventions using multi-omics approaches, this Research Topic welcomes original research articles, reviews, mini-reviews and all type of article accepted by the journal that address, but are not limited to, the following themes:o Development and validation of predictive models for individualized responses to microbiome-targeted interventionso Integration of host genomics, metagenomics, meta-transcriptomics, meta-proteomics, and metabolomics for personalized intervention designo Influence of diet, lifestyle, medications, and environment on microbiome intervention efficacyo Identification, validation, and functional characterization of microbial and host biomarkers for therapy personalizationo Clinical, translational, and mechanistic studies on personalized microbiome-based preventive or therapeutic strategies o Computational, bioinformatic, and AI-driven approaches for stratification, response prediction, and intervention optimization.o Bioethical, societal, and regulatory considerations in individualized microbiome modulationWe particularly encourage submissions that provide mechanistic insight, translational relevance, or clinically actionable frameworks for precision microbiome interventions.

Article types and fees

This Research Topic accepts the following article types, unless otherwise specified in the Research Topic description:

• Editorial
• FAIR² Data
• FAIR² DATA Direct Submission
• General Commentary
• Hypothesis and Theory
• Methods
• Mini Review
• Opinion
• Original Research

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Keywords:Personalized microbiome interventions, Gut health, Multi-omics approaches, Bioinformatics, Host-microbiome interactions, Microbial therapies, Precision medicine, Microbiome biomarkers, Diet-microbiome interactions, Multi-omics

Important note: All contributions to this Research Topic must be within the scope of the section and journal to which they are submitted, as defined in their mission statements. Frontiers reserves the right to guide an out-of-scope manuscript to a more suitable section or journal at any stage of peer review

Frontiers in Microbiology

• Microorganisms in Vertebrate Digestive Systems

Manuscripts can be submitted to this Research Topic

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