Henry Lucas P, Bergelson Joy
Center for Genomics and Systems Biology, New York, NY, USA.
Department of Biology, New York University, New York, NY, USA.
Nat Microbiol. 2025 Sep;10(9):2111-2121. doi: 10.1038/s41564-025-02076-7. Epub 2025 Aug 5.
Microbiome engineering seeks to reshape microbial communities to improve ecosystem function. However, many efforts fail due to inadequate design principles, often resulting in a loss of key microorganisms and disruption of links between the engineered community and its intended function. In contrast, decades of research in macroecology have uncovered key principles governing the relationship between biodiversity and ecosystem function. Here we translate these ecological principles to microbiome engineering, focusing on three stages: microbiome design, colonization and maintenance. We propose new approaches that leverage underlying ecological dynamics-particularly niche dynamics-to optimize diversity and abundance to promote stability and functionality, especially in host-associated microbiomes. We also highlight key research priorities to apply macro-ecosystem insights to microbial systems. Improving microbiome engineering in this way holds promise for solving pressing challenges in medicine and agriculture, while providing understanding of ecological processes that maintain biodiversity across biological scales.
微生物群落工程旨在重塑微生物群落以改善生态系统功能。然而，由于设计原则不完善，许多努力都失败了，这往往导致关键微生物的丧失以及工程化群落与其预期功能之间联系的中断。相比之下，数十年来在宏观生态学领域的研究揭示了生物多样性与生态系统功能之间关系的关键原则。在此，我们将这些生态学原则应用于微生物群落工程，重点关注三个阶段：微生物群落设计、定殖和维持。我们提出了新的方法，这些方法利用潜在的生态动态——特别是生态位动态——来优化多样性和丰度，以促进稳定性和功能性，尤其是在与宿主相关的微生物群落中。我们还强调了将宏观生态系统见解应用于微生物系统的关键研究重点。以这种方式改进微生物群落工程有望解决医学和农业领域的紧迫挑战，同时增进我们对跨生物尺度维持生物多样性的生态过程的理解。
