The human gut microbiome vastly extends the set of metabolic reactions catalysed by our own cells, with far-reaching consequences for host health and disease. However, our knowledge of gut microbial metabolism relies on a handful of model organisms, limiting our ability to interpret and predict the metabolism of complex microbial communities. In this Perspective, we discuss emerging tools for analysing and modelling the metabolism of gut microorganisms and for linking microorganisms, pathways and metabolites at the ecosystem level, highlighting promising best practices for researchers. Continued progress in this area will also require infrastructure development to facilitate cross-disciplinary synthesis of scientific findings. Collectively, these efforts can enable a broader and deeper understanding of the workings of the gut ecosystem and open new possibilities for microbiome manipulation and therapy.

人类肠道微生物组极大地扩展了我们自身细胞催化的一系列代谢反应，对宿主健康和疾病产生深远影响。然而，我们对肠道微生物代谢的了解依赖于少数模型生物，限制了我们解释和预测复杂微生物群落代谢的能力。在本视角中，我们讨论了用于分析和建模肠道微生物代谢以及在生态系统水平上连接微生物、途径和代谢物的新兴工具，强调了研究人员有希望的最佳实践。这一领域的持续进步还需要基础设施的发展，以促进科学发现的跨学科综合。总的来说，这些努力可以使人们更广泛、更深入地了解肠道生态系统的运作，并为微生物组操纵和治疗开辟新的可能性。