30Isolation and culture of gut bacteria enable testing for microbial roles in disease and 31 may also lead to novel therapeutics. However, the diversity of human gut microbial 32 communities (microbiota) impedes comprehensive experimental studies of individual 33 bacterial taxa. Here, we combine advances in droplet microfluidics and high-throughput 34 DNA sequencing to develop a platform for isolating and assaying microbiota members 35 in picoliter droplets (MicDrop). MicDrop can be used to create millions of distinct 36 bacterial colonies in a single experiment while using off-the-shelf parts compact enough 37 to fit in an anaerobic chamber. In proof-of-concept experiments, we used the platform to 38 characterize inter-individual metabolic variation among hundreds of polysaccharide-39 degrading gut bacteria from nine stool donors. We also used MicDrop to test the 40 hypothesis that growth kinetics of individual gut bacterial taxa are associated with long-41 term community dynamics in an artificial gut. These demonstrations suggest the 42 MicDrop platform could support future diagnostic efforts to personalize microbiota-43 directed therapies, as well as to provide comprehensive new insights into the ecology of 44 human gut microbiota. 45

Background: Short-chain fatty acids (SCFAs) derived from gut bacteria are associated with protective roles in diseases ranging from obesity to colorectal cancers. Intake of microbially accessible dietary fibers (prebiotics) lead to varying effects on SCFA production in human studies, and gut microbial responses to nutritional interventions vary by individual. It is therefore possible that prebiotic therapies will require customizing to individuals. Results: Here, we explored prebiotic personalization by conducting a three-way crossover study of three prebiotic treatments in healthy adults. We found that within individuals, metabolic responses were correlated across the three prebiotics. Individual identity, rather than prebiotic choice, was also the major determinant of SCFA response. Across individuals, prebiotic response was inversely related to basal fecal SCFA concentration, which, in turn, was associated with habitual fiber intake. Experimental measures of gut microbial SCFA production for each participant also negatively correlated with fiber consumption, supporting a model in which individuals gut microbiota are limited in their overall capacity to produce fecal SCFAs from fiber. Conclusions: Our findings support developing personalized prebiotic regimens that focus on selecting individuals who stand to benefit, and that such individuals are likely to be deficient in fiber intake.