Abstract
Fecal sampling is a non-invasive method which raises the possibility to study the development and the changes in the microbial community throughout different time points of a fly population or throughout different treatments. This method allows precise manipulation to trigger the fly’s physiology by nutritional interventions, bacterial infections or other stressors. As in most other animals, the intestinal microbiota is essential for a healthy fly-life. Because Drosophila only harbors a relative simple bacterial community with a small variety of round about 8 to 10 different species, it is rather easy to build up the microbial community and to investigate microbial changes after treatment.Another positive effect using the fly’s feces is that bacteria that are not part of the intestinal microbiome, for example Wolbachia, can be excluded directly from the analysis because they are not excreted.Using this method, the generated datasets may reflect a good paradigm to study microbiome associated diseases in a simple fly model or furthermore, to test drugs in a high-throughput approach.
Keywords: Drosophila, Intestine, Microbiome, Fecal sampling, DNA isolation
Background
Until now, studies aiming to characterize the intestinal microbiome in the fruit fly Drosophila melanogaster used whole flies or dissected intestines as sources for bacterial DNA isolation. The main idea using feces sampling is to enable analyzing the dynamics of the intestinal microbiome in response to different treatments such as nutritional interventions or drug administration in the same cohort of flies. We were able to demonstrate that all general bacteria species, which are known to be important members of the Drosophila microbiome can be detected in fecal samples (Chandler et al., 2011; Wong et al., 2011; Matos and Leulier, 2014). Although whole fly samples are apparently the most convenient sources to generate microbiome data, several drawbacks are faced with this approach including contamination with surface bacteria or with intracellular bacteria such as Wolbachia spec (Saridaki and Bourtzis, 2010; Clark et al., 2005). Using feces as a source for microbiome data acquisition, these contaminations can be excluded almost completely, and, most importantly, the same cohorts of flies can be analyzed several times during the course of a complex experimental setup, thus unleashing the full potential of Drosophila genetics for microbiome studies.
Materials and Reagents
Note: For full name of the abbreviations in the text, please see Table S1 in Supplemental file.
Equipment
Software
Procedure
Data analysis
Note: For statistical analysis, you should provide at least three independent biological replicates for each treatment, it’s suggested that it is better to prepare five.
Notes
Recipes
Acknowledgments
We thank Britta Laubenstein, Christiane Sandberg and Katja Cloppenborg-Schmidt for their excellent technical support. This work was supported by the Deutsche Forschungsgemeinschaft as part of the CRC 1182 (Project C2) and the Cluster of Excellence Inflammation@Interfaces.
References
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