50 important research questions in microbial ecology

Rachael Antwis, Sarah Griffiths, Xavier Harrison, Paz Aranega-Bou, Andres Arce, Aimee Bettridge, Francesca Brailsford, Alexandre de Menezes, Andrew Devaynes, Kristian Forbes, Ellen Fry, Ian Goodhead, Erin Haskell, Chloe Heys, Chloe James, Sarah Johnston, Gillian Lewis, Zenobia Lewis, Michael Macey, Alan McCarthyJames MCDonald, Nasmille Mejia Florez, David O'Brien, Chloe Orland, Marco Pautasso, William Reid, Heather Robinson, Ken Wilson, William Sutherland

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Microbial ecology provides insights into the ecological and evolutionary dynamics of microbial communities underpinning every ecosystem on Earth. Microbial communities can now be investigated in unprecedented detail, although there is still a wealth of open questions to be tackled. Here we identify 50 research questions of fundamental importance to the science or application of microbial ecology, with the intention of summarising the field and bringing focus to new research avenues. Questions are categorised into seven themes: Host-Microbiome Interactions; Health and Infectious Diseases; Human Health and Food Security; Microbial Ecology in a Changing World; Environmental Processes; Functional Diversity; and Evolutionary Processes. Many questions recognise that microbes provide an extraordinary array of functional diversity that can be harnessed to solve real world problems. Our limited knowledge of spatial and temporal variation in microbial diversity and function is also reflected, as is the need to integrate micro- and macro-ecological concepts, and knowledge derived from studies with humans and diverse other organisms. Certain methods remain inadequate and currently limit progress in the field. Although not exhaustive, the questions presented are intended to stimulate discussion and provide focus for researchers, funders, and policy makers, informing the future research agenda in microbial ecology
Original languageEnglish
JournalFEMS Microbiology Ecology
Early online date3 Apr 2017
Publication statusE-pub ahead of print - 3 Apr 2017


  • environmental processes
  • evolutionaryprocesses
  • functional diversity
  • hostmicrobiomeinteractions
  • priority setting
  • research agenda


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