Like many areas of biology, human biology and medicine have benefited from rapid advances in molecular sequencing technology, which are now capable of characterizing microbiomes in unprecedented detail. Increasingly, the field is revealing a staggering taxonomic diversity of organisms in the human microbiome – many of which new to science.  More recently, medical researchers have identified functional roles of the microbiome in digestion, immunology and even behavior, which may be analogous to an ‘ecosystem function’ for human health. Plants also host and interact with a complex community of microbes, and for decades ecologists have struggled to understand the effects of plant-microbial associations on plant productivity, fitness and community structure. However, sequencing methods and analyses used in plant microbiome studies lag behind those now common in the medical field. Conversely, human microbiome studies address similar questions about microbial community structure and function that plant community ecologists have investigated since the 1950s. This session aims to bring together human biology and medical researchers, plant community ecologists, and microbial ecologists to foster communication, identify best practices, and propose promising new avenues of analysis. The session will emphasize next-generation sequencing and statistical methods for accurately reconstructing microbiome communities and inferring functional effects. A panel discussion will focus on how the approaches used in one field may be applied in the other.