MACROquestions in coastal MICRObiome science

Two years, 108 questions, and 23 perspectives resulted in seven research themes that will hopefully stimulate research ideas and discussions around the espresso machine.

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The horizon scanning method1 has become a popular method to review a field of research by soliciting experts on what they think on a particular topic. Coupled with a literature review, our Nature Ecology and Evolution Perspectives paper “A horizon scan of priorities for coastal marine microbiome research” assessed the current state of the research and asked the experts what the burning research questions were in coastal marine microbiome research. Our aim was to create a comprehensive vision that may unify the strategy of research on coastal marine microbiomes.

The resulting 108 horizon scanning questions were discussed in a 1-day workshop in Melbourne, Australia in early July 2017. At the time, I had a sense of the gaps for seagrass microbiome research, and as is turned out, the research questions and challenges in the workshop were broadly applicable across most coastal marine ecosystems. It was also clear holobiont-based questions were at the forefront as they made up nearly half of the questions, particularly those concerning holobiont health, resilience and function.


We initially workshopped 108 questions to 10 themes. Over the next two years, the team of 23 collaborators discussed, debated and condensed the 10 themes down to seven. These top themes broadly encompass the microbiome, microbiome and host, and the relationships among microbiome, host and environment. For each theme we aimed to not only synthesise the literature, but also suggest ways forward on how we can progress the questions. We also identified methodological challenges ranging from sequencing and bioinformatics hurdles to the complexities of performing much-needed manipulative experiments and applying fundamental concepts to management and industry. 

Our paper was my first opportunity to work in such a large, international team environment. The process of collating, discussing and synthesising the ideas presented here with the experts from a diverse range of microbiome backgrounds was an incredible experience as an early career researcher. We hope that this perspectives could provide some inspiration and motivation for future local and international collaborations and science.

Word cloud of the 108 questions that formed the foundation of the seven themes.


  1. Sutherland, W. J. et al. Identification of 100 fundamental ecological questions. J. Ecol. 101, 58–67 (2013).


Go to the profile of Stacey Trevathan-Tackett

Stacey Trevathan-Tackett

Postdoctoral Research Fellow, Deakin University

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