DOI: 10.5061/dryad.0vt4b8h7z
title: Data from: Microbial solutions to dietary stress: Experimental evolution reveals host-microbiome interplay in Drosophila melanogaster

description: Can the microbiome serve as a reservoir of adaptive potential for hosts?
 To address this question, we leveraged ~150 generations of experimental
 evolution in Drosophila melanogaster in a stressful, high-sugar (HS) diet.
 We performed a fully reciprocal transplant experiment using the control
 and HS bacteria. If the microbiome confers benefits to hosts, then
 transplant recipients should gain fitness benefits compared to controls.
 Interestingly, we found that such benefits exist, but their magnitude
 depends on evolutionary history—mismatches between fly evolution and
 microbiome reduced fecundity and potentially exerted fitness costs,
 especially in the stressful HS diet. The dominant HS bacteria
 (​​Acetobacter pasteurianus) uniquely encoded several genes to enable uric
 acid degradation, mediating the toxic effects of uric acid accumulation
 due to the HS diet for flies. Our study demonstrates that host genotype x
 microbiome x environment interactions have substantial effects on host
 phenotype, highlighting how host evolution and ecological context together
 shape the adaptive potential of the microbiome.
description: # Data from: Microbial solutions to dietary stress: Experimental evolution
 reveals host-microbiome interplay in Drosophila melanogaster
 [https://doi.org/10.5061/dryad.0vt4b8h7z](https://doi.org/10.5061/dryad.0vt4b8h7z) ## Description of the data and file structure data was collected following ~150 generations of adaptation to HS diet selection  fully reciprocal host x microbiome x diet transplant  ### Files and variables #### File: acetos\_uricacid\_210713b.csv **Description:** uric acid degradation by C or HS Acetobacter on fly food  ##### Variables * sample: sample ID * abs: absorbance value  * um.ua: conversion to micromolar uric acid  * treatment: full treatment code (diet x uric acid x microbe) * diet: C or HS diet  * ua: how much uric acid added (0 or 200) * microbe: sterile, C Aceto, or HS Aceto  #### File: 2536\_aceto\_ovidata.csv **Description:** egg lay data for recipients of microbiome transplant  ##### Variables * plate.no: egg lay plate number  * date: date of egg lay  * well: which well in 24-well plate  * ovi.plate treat: C or HS ovipostion media  * fly.treat: total treatment (fly, microbiome, diet manipulation) * fly.geno: control or high sugar fly genotype * fly.micro: sterile, control Acetobacter, or high sugar Acetobacter * fly.food: control or high sugar diet  * fly.ID: fly rearing tube  * egg.no: number of eggs produced by female  #### File: ancom\_donor\_flygeno.csv **Description:**  ##### Variables * ASV ID: differentially expressed ASV ID * clr: centered log transformed abundance of ASV * W: test stat * sig: significance for differentially abundant between C or HS fly  * taxonomy: taxonomic assignment of ASV #### File: chs\_nowolb\_donors\_obj\_sp\_SHARE.rds **Description:** phyloseq object for microbiome analysis. Please download the package "phyloseq" to use this Rds object.  #### File: CHScomp\_table.csv **Description:** RAST assignments for function between C and HS Acetobacter strains  ##### Variables * Presence: A= HS acetobacter, B= C Acetobacter, A&B = shared between both strains  * Category: broad scale functional assignment  * Subcategory: subcategory functional assignment * Subsystem: subsystem functional assignment * Role: specific function  * Organism A: annotation in HS Acetobacter * SS active A: present in HS Acetobacter  * Organism B: annotation in C Acetobacter SS active B: present in C Acetobacter #### File: chs\_fecund\_variance\_adds.csv **Description:** Marginal R2 values for each model to assess the relative contribution of host genotype, microbiome, and diet to fecundity. Models were zero-inflated poisson generalized mixed linear models. Marginal R2 was estimated using MuMIN r.squaredGLMM.  ##### Variables * Model = terms included in statistical model * delta r2 = marginal R2 calculated using delta method (only this data is plotted in the supplement) * lognormal r2 = marginal R2 calculated using lognormal method * trigamma r2 = marginal R2 calculated using trigamma method