Individual variation of natural D. melanogaster associated bacterial communities

Abstract

D. melanogaster has become an important model organism to study host-microbe interaction.However, we still know little about the natural microbial communities that are associated with D.melanogaster. Especially, information on inter-individual variation is still lacking because most studies so far have used pooled material from several flies. Here, we collected bacterial 16S rRNA gene community profiles from a set of 32 individuals from a single population and compare the variation to that of samples collected from different substrates and locations. While community differences were on average larger between samples collected from different substrates, there was still a surprising amount of variation of microbial communities between individual flies. The samples clustered into two groups suggesting that there are yet unknown factors that affect the composition of natural fly associated microbial communities and need research. Importance D. melanogaster is an important model organism in evolutionary biology and also for the study of host-microbe interaction. In order to connect these to aspects of D. melanogaster biology, it is crucial to better understand the natural D. melanogaster microbiota because only the natural microbiota can affect the evolution of the host. We present, to our knowledge, the first data set that captures inter-individual variation of D. melanogaster associated bacterial communities.Clustering of communities into two larger groups suggests that there are important drivers of these communities that we do not understand yet suggesting in return that more research on the natural microbiota of D. melanogaster is needed.

Common structuring principles of the Drosophila melanogaster microbiome on a continental scale and between host and substrate

“…This enrichment was mainly driven by OTU2 (C. intestini). OTU2 matches sequences from previous studies on fruit flies in the natural environment (BLAST results, Table S6) (Cox and Gilmore, 2007;Chandler et al, 2011;Wang and Staubach, 2018) and in the laboratory . In particular, it perfectly matches C. intestini strain A911 (Roh et al, 2008) that is favoured by the fly host and has a protective function.…”

“…intestini ). OTU2 matches sequences from previous studies on fruit flies in the natural environment (BLAST results, Table S6) (Cox and Gilmore, ; Chandler et al ., ; Wang and Staubach, ) and in the laboratory (Ryu et al ., ). In particular, it perfectly matches C .…”

“…While the effects of substrate on the fly microbiome are well described (Chandler et al, 2011;Staubach et al, 2013;Wang and Staubach, 2018), continental-scale effects of temperature on a host-associated microbiome has, to our knowledge, not been described before. Temperature affects environmental microbiomes on a global scale (Zhou et al, 2016;Thompson et al, 2017) and the effect in Drosophila might reflect the exposure of flies to different environmental microbiomes, supporting a model in which the environmental metacommunities differ and affect composition of the host-associated community (Adair and Douglas, 2017;Miller et al, 2018).…”

“…Instead, probabilistic processes contribute to gut colonization (Obadia et al ., ) and community structure in natural populations can be explained to a large extent by neutral ecological mechanisms (Adair et al ., ). As in mammals and other organisms, environmental factors, such as the time of collection (Adair et al ., ; Behrman et al ., ) or diet (Chandler et al ., ; Staubach et al ., ; Erkosar et al ., ; Wang and Staubach, ) have a strong effect on the Drosophila microbiome.…”

Drosophila melanogasterestablishes a species-specific mutualistic interaction with stable gut-colonizing bacteria

“…This approach also allowed us to isolate bacteria for further functional characterization. Moreover, gut bacteria of D. melanogaster previously identified through 16S rRNA gene sequencing [20,26,28,41-46] belong to genera that can also be identified by culture dependent techniques. However, it is possible that our approach missed gut bacteria that do not grow in the media or conditions that we used.…”