Microbiome Engineering in Human Health and Agriculture

This review paper discusses how microbiome engineering can improve both human health and agriculture by deliberately designing and managing microbial communities rather than focusing on single "probiotic" strains. It explains how gut microbiomes can be engineered with diet, probiotics, fecal microbiota transplantation, and live biotherapeutic products to produce beneficial metabolites, control pathogens, and support therapy. On the agricultural side, it covers how soil, plant, and animal (especially rumen) microbiomes can be manipulated to enhance nutrient use, increase stress tolerance and disease resistance, and reduce methane emissions from livestock. The paper also points out why many microbiome-based products fail in real-world conditions and proposes ecological design principles and better measurement tools to create more reliable, context-aware microbiome interventions. This review paper discusses how microbiome engineering can enhance both human health and agriculture by deliberately designing and managing microbial communities rather than focusing solely on individual "probiotic" strains. It explains how gut microbiomes can be optimized through diet, probiotics, fecal microbiota transplantation, and live biotherapeutic products to produce beneficial metabolites, control pathogens, and support therapeutic efforts. On the agricultural side, the paper describes how the microbiomes of soil, plants, and animals—particularly in the rumen—can be manipulated to improve nutrient usage, increase stress tolerance and disease resistance, and reduce methane emissions from livestock. Additionally, the paper highlights why many microbiome-based products fail in real-world applications and proposes ecological design principles, as well as improved measurement tools, to create more reliable, context-aware microbiome interventions. This review paper discusses how microbiome engineering can enhance both human health and agriculture by deliberately designing and managing microbial communities rather than focusing solely on individual "probiotic" strains. It explains how gut microbiomes can be optimized through diet, probiotics, fecal microbiota transplantation, and live biotherapeutic products to produce beneficial metabolites, control pathogens, and support therapeutic efforts.