10.5061/DRYAD.2SR6316
Gould, Alison L.
University of California, Berkeley
Zhang, Vivian
University of California, Berkeley
Lamberti, Lisa
Swiss Federal Institute of Technology in Zurich
Jones, Eric W.
University of California, Santa Barbara
Obadia, Benjamin
University of California, Berkeley
Korasidis, Nikolaos
Swiss Federal Institute of Technology in Zurich
Gavryushkin, Alex
Swiss Federal Institute of Technology in Zurich
Carlson, Jean M.
University of California, Santa Barbara
Beerenwinkel, Niko
Swiss Federal Institute of Technology in Zurich
Ludington, William B.
University of California, Berkeley
Data from: Microbiome interactions shape host fitness
Dryad
dataset
2018
Epistasis
fitness landscape
2018-12-04T16:53:44Z
2018-12-04T16:53:44Z
en
https://doi.org/10.1073/pnas.1809349115
234819 bytes
1
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
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.
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