A theoretical framework for controlling complex microbial communities

Marco Tulio Angulo (), Claude H. Moog and Yang-Yu Liu ()
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Marco Tulio Angulo: Universidad Nacional Autónoma de México
Claude H. Moog: Laboratoire des Sciences du Numérique de Nantes
Yang-Yu Liu: Brigham and Women’s Hospital and Harvard Medical School

Nature Communications, 2019, vol. 10, issue 1, 1-12

Abstract: Abstract Microbes form complex communities that perform critical roles for the integrity of their environment or the well-being of their hosts. Controlling these microbial communities can help us restore natural ecosystems and maintain healthy human microbiota. However, the lack of an efficient and systematic control framework has limited our ability to manipulate these microbial communities. Here we fill this gap by developing a control framework based on the new notion of structural accessibility. Our framework uses the ecological network of the community to identify minimum sets of its driver species, manipulation of which allows controlling the whole community. We numerically validate our control framework on large communities, and then we demonstrate its application for controlling the gut microbiota of gnotobiotic mice infected with Clostridium difficile and the core microbiota of the sea sponge Ircinia oros. Our results provide a systematic pipeline to efficiently drive complex microbial communities towards desired states.

Date: 2019
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DOI: 10.1038/s41467-019-08890-y

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