Solutions in microbiome engineering: prioritizing barriers to organism establishment

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Microbiome engineering is increasingly being employed as a solution to challenges in health, agriculture, and climate. Often manipulation involves inoculation of new microbes designed to improve function into a preexisting microbial community. Despite, increased efforts in microbiome engineering inoculants frequently fail to establish and/or confer long-lasting modifications on ecosystem function. We posit that one underlying cause of these shortfalls is the failure to consider barriers to organism establishment. This is a key challenge and focus of macroecology research, specifically invasion biology and restoration ecology. We adopt a framework from invasion biology that summarizes establishment barriers in three categories: (1) propagule pressure, (2) environmental filtering, and (3) biotic interactions factors. We suggest that biotic interactions is the most neglected factor in microbiome engineering research, and we recommend a number of actions to accelerate engineering solutions.




Albright, M. B. N., Louca, S., Winkler, D. E., Feeser, K. L., Haig, S. J., Whiteson, K. L., … Dunbar, J. (2021). Solutions in microbiome engineering: prioritizing barriers to organism establishment. ISME Journal. Springer Nature.

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