Numerous studies have shown that animal nutrition is tightly linked to gut microbiota, especially under nutritional stress. In Drosophila melanogaster, microbiota are known to promote juvenile growth, development, and survival on poor diets, mainly through enhanced digestion leading to changes in hormonal signaling. Here, we show that this reliance on microbiota is greatly reduced in replicated Drosophila populations that became genetically adapted to a poor larval diet in the course of over 170 generations of experimental evolution. Protein and polysaccharide digestion in these poor-diet-adapted populations became much less dependent on colonization with microbiota. This was accompanied by changes in expression levels of dFOXO transcription factor, a key regulator of cell growth and survival, and many of its targets. These evolutionary changes in the expression of dFOXO targets to a large degree mimic the response of the same genes to microbiota, suggesting that the evolutionary adaptation to poor diet acted on mechanisms that normally mediate the response to microbiota. Our study suggests that some metazoans have retained the evolutionary potential to adapt their physiology such that association with microbiota may become optional rather than essential.
Survival & developmental time
Time from egg to pupation and the proportion of larvae surviving to pupation. The values are means for each replicate bottle. The results are reported in Fig 1B,C in the paper.
Weight & Growth Rate
Data on dry weight and growth rate reported in Fig. 5A and Fig. S2. Data for germ-free females of Control populations CTL5 and CTL6 are missing due an insufficient number of flies surviving to adulthood.
Digestive enzymes RT-qPCR
The raw data (expressed as Ct-values) from RT-qPCR on genes for digestive proteases and amylases and maltases, measured in larvae of Control and Selected populations, developing at the poor diet at two stages, (early and late 3rd instar). Actin was used as the reference gene (column "Actin_Ct"). The data underlie the results presented in Fig. 2A,B and Fig. 3B,C in the paper.
The absorbance data from the protease activity assay (results presented in Fig. 2C). Protease activity was analyzed as log or the ratio of absorbance at 440 nm to 280 nm. Samples were taken at different time points during larval development, expressed as relative time during the 3rd larval instar. There were three technical replicates per sample, processed in three blocks.
The raw data from the amylase activity assay (results presented in Fig. 3A). The amylase activity was analyzed as the log-transformed ratio of the rate of reaction k (defined in the Methods of the paper) to absorbance at 280 nm.
Microbiota abundance by qPCR after experimental inoculation
The raw data from qPCR quantifying the abundance of Acetobarcter 16S ribosomal subunit genomic DNA relative to host genomic Actin DNA in larvae experimentally colonized with the dominant Acetobacter strain and in GF larvae. CT values are averaged over 3 biological replicates. The data underlie results reported in Fig. 4B and S1, orange and blue points.
Microbiota abundance in conventionally reared larvae
The raw data from qPCR quantifying the abundance of Acetobarcter 16S ribosomal subunit genomic DNA relative to host genomic Actin DNA in larvae experimentally conventionally reared under the same conditions as in the experimental evolution regimes (i.e., Selected larvae are raised on the poor diet but the Controls are raised on the standard diet). The data underlie results reported in Fig. 4B and S1, green points.