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Abstract

Methods and systems are provided for design, improvement, optimization, or personalization of microbiome therapeutics for various diseases. In one embodiment, a method comprises identifying a plurality of microbiome features associated with a disease, building a plurality of simulations by modeling the interactions between a plurality of microbial consortia with a plurality of microbiome samples; predicting one or more microbial consortia that improve the plurality of microbiome features associated with a disease from the plurality of simulations; and optimizing composition of one or more microbial consortia that further improve the plurality of microbiome features associated with a disease from the plurality of simulations or personalizing composition of a microbial consortia according to a patient's baseline microbiome to improve the plurality of microbiome features associated with a disease. In this way, effective microbial consortia for a variety of diseases may be reliably predicted in a high-throughput fashion.

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