DOI: 10.5061/dryad.2sr6316
title: Data from: Microbiome interactions shape host fitness

description: Gut bacteria can affect key aspects of host fitness, such as development,
 fecundity, and lifespan, while the host, in turn, shapes the gut
 microbiome. However, it is unclear to what extent individual species
 versus community interactions within the microbiome are linked to host
 fitness. Here, we combinatorially dissect the natural microbiome of
 Drosophila melanogaster and reveal that interactions between bacteria
 shape host fitness through life history tradeoffs. Empirically, we made
 germ-free flies colonized with each possible combination of the five core
 species of fly gut bacteria. We measured the resulting bacterial community
 abundances and fly fitness traits, including development, reproduction,
 and lifespan. The fly gut promoted bacterial diversity, which, in turn,
 accelerated development, reproduction, and aging: Flies that reproduced
 more died sooner. From these measurements, we calculated the impact of
 bacterial interactions on fly fitness by adapting the mathematics of
 genetic epistasis to the microbiome. Development and fecundity converged
 with higher diversity, suggesting minimal dependence on interactions.
 However, host lifespan and microbiome abundances were highly dependent on
 interactions between bacterial species. Higher-order interactions
 (involving three, four, and five species) occurred in 13–44% of possible
 cases depending on the trait, with the same interactions affecting
 multiple traits, a reflection of the life history tradeoff. Overall, we
 found these interactions were frequently context-dependent and often had
 the same magnitude as individual species themselves, indicating that the
 interactions can be as important as the individual species in gut
 microbiomes.
description: Development
 DataRaw development time
 data for Drosophila melanogaster raised with all possible combinations of
 the five gut bacterial species examined in this study.DevelopmentData.csvDaily Fecundity DataRaw daily fecundity data for Drosophila melanogaster raised with all possible combinations of the five gut bacterial species examined in this study.DailyFecundityData.csvSurvival DataRaw survival data for Drosophila melanogaster raised with all possible combinations of the five gut bacterial species examined in this study.SurvivalData.csvFly Gut CFU DataRaw bacterial load data for the guts of Drosophila melanogaster raised with all possible combinations of the five gut bacterial species examined in this study.FlygutCFUsData.csvDevelopment Time Data Under Different ConditionsDevelopment time data for Drosophila melanogaster under different experimental conditions and fed various combinations of five species of gut bacteria.DevelopmentData_CompareMethods.csvSurvival Data for Antibiotic TreatmentsFemale survival data for Drosophila melanogaster under different experimental conditions and fed various combinations of five species of gut bacteria.FemaleSurvivalData_AntibioticTreatments.csvFecundity Data for Antibiotic TreatmentsFecundity data for Drosophila melanogaster under different experimental conditions and fed various combinations of five species of gut bacteria.FecundityData_AntibioticTreatments.csvSummary of Bacteria TreatmentsReference table of the gut bacteria treatments used in this study. The 32 treatments listed include all possible combinations of the 5 species of gut bacteria examined in this study.TreatmentSummary.csv