Learning to fly, with microbes

It's summer and that means time for research and reading groups here at IU Bloomington.  Given the interest in Drosophila across the department, I thought it might be fun to start a fly microbiome reading group this summer. We've got a really dynamic and diverse group -- everyone from stock center folks to genomics gurus and graduate students working in flies.  If you're already working in the fly, and haven't thought about the effect of the microbial community - shame on you!; seriously, have you had your head in a hole for the last decade? Beyond ignoring Wolbachia infection and effects on host phenotypes (such as insulin signaling, oogenesis, and others), ignoring the entire microbial community is really not defendable any more. 

If you haven't been interested in the fly microbiome, because it's depauperate (what a nasty word, aye?) and generally inconstant, I hope to change your mind.

Here are some of the papers we've been reading lately:

Chandler JA, Morgan Lang J, Bhatnagar S, Eisen JA, Kopp A (2011) Bacterial Communities of Diverse Drosophila Species: Ecological Context of a Host–Microbe Model System. PLoS Genet 7(9): e1002272. doi:10.1371/journal.pgen.1002272

The introduction to the system - here they surveyed wild-caught flies and flies from a few labs for bacterial composition and found little correspondence in OTUs between wild and lab flies and a surprising about of difference in bacteria colonizing flies of the same stock from different labs.

Blum JE, Fischer CN, Miles J, Handelsman J. 2013. Frequent replenishment sustains the beneficial microbiome of Drosophila melanogaster. mBio 4(6):e00860-13. doi:10.1128/mBio.00860-13

This study focused on lab flies and looked at the ability of the bacterial community associated with the fly to grow in the fly food. They hypothesize that this may be the major way in which these microbes get to the next generation (at least in the lab).

Newell, P. D., & Douglas, A. E. (2014). Interspecies interactions determine the impact of the gut microbiota on nutrient allocation in Drosophila melanogaster. Applied and environmental microbiology, 80(2), 788-796.

Here they use a gnotobiotic system to show that microbes affect the host differently when grown together. Also who is there (which Lactobacillus or Acetobacter species) matters.

Today I'm reading up on some more of Angela Douglas' work, and checking out John Chaston's new(ish) pub:

Chaston JM, Dobson AJ, Newell PD, Douglas AE. 2016. Host genetic control of the microbiota mediates the Drosophila nutritional phenotype. Appl Environ Microbiol 82:671–679. doi:10.1128/AEM.03301-15.

Here, they leverage the Drosophila genetic reference panel - a panel of inbred, originally wild-caught, flies that have had their genome sequenced.  This allows you to correlate or associate particular alleles in the fly with phenotypes, in this case, nutritional indicies (such as triglyceride levels) and with microbiome composition.  They establish gnotobiotic flies for these DGRP stocks, allowing them to control for microbiome input, and look at the colonized flies after they eclose.  

It is immediately obvious that host genetic background has an effect. 

Figure 1. Bacterial communities and phenotypic traits of 79 Drosophila lines from DGRP. (A) Microbiota composition was assessed by pyrosequencing with OTUs called at 97% sequence identity (see also Data Set S1 in the supplemental material). (B to E) Nutritional indices (in micrograms per milligram [dry weight]), with data represented as means ± standard errors of the means (SEMs) (error bars). In each panel, Drosophila lines are ordered by the sum of Acetobacter andLactobacillus species (A) or by mean nutritional index value (B to E)

They found a big effect with one species (Acetobaceter tropicalis) and go on to test these differences using mono-associated flies - again, showing just how easy it is to test these hypotheses in the fly system. 

Next they performed their GWAS experiment; they associated particular alleles with these backgrounds and found that flies with SNPs in genes related to neural processes (such as paralytic, calnexin 14D, and dunce) were enriched in their association with community composition.  Interesting! They conclude that maybe there is a gut-brain axis link in fly.  I found this part to be cool because I immediately thought of Wolbachia colonization of the neural tissues -- is a Wolbachia colonization in these flies affecting microbiome composition and are these alleles altering Wolbachia titer which in turn could affect microbiome composition? Unfortunately, they did not look into this, at least in this pub; some of the DGRP is colonized by Wolbachia but they are all different strains, isolated from different females, and Chaston et al., chucked the Wolbachia reads from their 16S rRNA gene analyses when they made their amplicons.  Sigh. Even within the microbiome community, Wolbachia is ignored yet again!

Fear not, dear reader, several people in the Wolbachia community sure are interested to see how this prevalent endosymbiont might alter host microbial ecology.  I know that some interesting datasets are coming soon from both the Teixeira and Frydman labs - stay tuned!