The Future is Now: Engineered Microbes at the Intersection of Gut Health and Disease

The gastrointestinal tract is home to trillions of microorganisms which exist in symbiosis with their eukaryotic host. These microbes interact with their host in diverse and profound ways through regulation of immune function, secretion of bioactive metabolites, potentiation of gut barrier function, and so forth. Recent advances in our understanding of the role of these microbes have enabled the rational design of engineered microbes to address questions related to human gut health and disease.

In this Research Topic, we seek to explore recent advances in the development of engineered microbes that address issues related to the gastrointestinal tract. Specifically, we look for work that builds on our understanding of how endogenous microorganisms regulate GI health and how this knowledge might be leveraged for the treatment of disease.

Contributors are highly encouraged to submit primary research articles which utilize engineered microbes to address questions related to gastrointestinal health and diseases. Specifically, research articles that describe a newly constructed strain, a novel approach for an existing microbe, or a novel biochemical pathway/mechanism targetable through engineered microbes are highly desirable. Review manuscripts will also be considered but are considered of lower priority than primary research.

We welcome articles addressing, but not limited to, the following themes:

-Scope and novelty: Advances in engineered microbes for GI health/disease with emphasis on new strains, innovative repurposing of commensals/probiotics, or newly engineered biochemical pathways/mechanisms.

-Mechanistic foundations: Leverage endogenous microbiota functions—immune modulation, epithelial barrier enhancement, metabolite production (SCFAs, bile acids), pathogen exclusion, and host signaling control.

-Engineering strategies: Synthetic sensing/response circuits, stable genome edits (including CRISPR effectors), secretion systems, spatial targeting (mucus/colon), and biocontainment (kill-switches, HGT mitigation).

-Functional payloads: Anti-inflammatories (e.g., IL-10 mimetics), antimicrobial peptides/quorum quenchers, metabolic modulators (butyrate/propionate, bile salt hydrolases), xenobiotic and toxin processing.

-Sensing and theranostics: In vivo reporters, memory systems, and biosensors for inflammation, metabolites, and pathogens enabling real-time monitoring plus intervention.

-Community and ecology: Engineered consortia, cross-feeding networks, ecological stability, and strategies to integrate with or reshape resident microbiomes.

-Translation and validation: Delivery/formulation (oral encapsulation, colon-targeting, prebiotics), in vitro gut models and gnotobiotic mice, -omics readouts, and translational biomarkers.

-Safety, standards, and submissions: Genetic containment, off-target assessment, regulatory considerations; rigorous characterization (genomes, plasmids, SOPs, stability); priority for primary research with construction/efficacy data, with reviews as secondary.

Article types and fees

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

• Brief Research Report
• Editorial
• FAIR² Data
• General Commentary
• Hypothesis and Theory
• Methods
• Mini Review
• Opinion
• Original Research
• ... View all formats

Articles that are accepted for publication by our external editors following rigorous peer review incur a publishing fee charged to Authors, institutions, or funders.

Article types

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

• Brief Research Report
• Editorial
• FAIR² Data
• General Commentary
• Hypothesis and Theory
• Methods
• Mini Review
• Opinion
• Original Research
• Perspective
• Review
• Systematic Review

Keywords: Gut microbiota, intestine, inflammatory bowel disease, metabolism, colorectal cancer, genome engineering, synthetic biology

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.