From endosymbiosis to holobionts: Evaluating a conceptual legacy

In her influential 1967 paper, Lynn Margulis synthesized a range of data to support the idea of endosymbiosis. Building on the success of this work, she applied the same methodology to promote the role of symbiosis more generally in evolution. As part of this broader project, she coined the term ‘holobiont’ to refer to a unified entity of symbiont and host. This concept is now applied with great gusto in microbiome research, and often implies not just a physiological unit but also various senses of an evolving system. My analysis will track how Margulis came to propose the term, its current use in microbiome research, and how those applications link back to Margulis. I then evaluate what contemporary use says about Margulis's legacy for microbiome research. •Lynn Margulis had strong ideas about evolution and evolving entities.•‘Holobiont’ is a term coined by Margulis in 1990 to describe host-microbe units.•Contemporary microbiome researchers who use holobiont concepts subscribe to a broader range of Margulisian views.•Margulis's ideas about holism, homeostasis and autopoiesis contribute to holobiont accounts.•Analysing Margulis's legacy in this contemporary research reveals shared problems.