Micro-eukaryotes in animal and plant microbiomes: Ecologies of disease?

Abstract Studies of animal and plant microbiomes are burgeoning, but the majority of these focus on bacteria and rarely include micro-eukaryotes other than fungi. However, there is growing evidence that micro-eukaryotes living on and in larger organisms (e.g. plants, animals, macroalgae) are diverse and in many cases abundant. We present here a new combination of ‘anti-metazoan’ primers: 574*f-Antimet_DB that should amplify a wide diversity of micro-eukaryotes including some groups that are difficult to amplify using other primer combinations. While many groups of micro-eukaryotic parasites are recognised, myriad other micro-eukaryotes are associated with hosts as previously unknown parasites (often genetically divergent so difficult to amplify using standard PCR primers), opportunistic parasites, commensals, and other ecto- and endo-symbionts, across the ‘symbiotic continuum. These fulfill a wide range of roles from pathogenesis to mutually beneficial symbioses, but mostly their roles are unknown and likely fall somewhere along this spectrum, although with the potential to switch the nature of their interactions with the host under different conditions. The composition and dynamics of host-associated microbial communities are also increasingly recognized as important moderators of host health. This ‘pathobiome’ approach to understanding disease is beginning to supercede a one-pathogen-one-disease paradigm, which cannot sufficiently explain many disease scenarios.