Drosophila Genotype Influences Commensal Bacterial Levels

Early, Angela M.; Shanmugarajah, Niroshan; Buchon, Nicolas; Clark, Andrew G.

doi:10.1371/journal.pone.0170332

Cited by 44 publications

(44 citation statements)

References 61 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The compositions of the gut microbiomes of flies held on the different diets were distinct, which is consistent with the observations of a relatively flexible microbiota in this species (27)(28)(29)(31)(32)(33). However, the mating preferences of the flies were not associated with these microbiome differences.…”

Section: Discussionsupporting

confidence: 87%

See 1 more Smart Citation

Gut microbiomes and reproductive isolation in Drosophila

Leftwich

Clarke

Hutchings

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

View full text Add to dashboard Cite

Experimental studies of the evolution of reproductive isolation (RI) in real time are a powerful way in which to reveal fundamental, early processes that initiate divergence. In a classic speciation experiment, populations of were subjected to divergent dietary selection and evolved significant positive assortative mating by diet. More recently, a direct role for the gut microbiome in determining this type of RI in has been proposed. Manipulation of the diet, and hence the gut microbiome, was reported to result in immediate assortative mating by diet, which could be eliminated by reducing gut microbes using antibiotics and recreated by adding back We suggest that the evolutionary significance of this result is unclear. For example, in, the microbiome is reported as flexible and largely environmentally determined. Therefore, microbiome-mediated RI would be transient and would break down under dietary variation. In the absence of evolutionary coassociation or recurrent exposure between host and microbiome, there are no advantages for the gut bacteria or host in effecting RI. To explore these puzzling effects and their mechanisms further, we repeated the tests for RI associated with diet-specific gut microbiomes in Despite observing replicable differences in the gut microbiomes of flies maintained on different diets, we found no evidence for diet-associated RI, for any role of gut bacteria, or for specifically. The results suggest that there is no general role for gut bacteria in driving the evolution of RI in this species and resolve an evolutionary riddle.

show abstract

Section: Discussionsupporting

confidence: 87%

“…For example, natural populations of D. melanogaster are reported to exhibit fairly flexible, environmentally acquired gut microbiomes (e.g., refs. [27][28][29][30][31][32][33]. Hence the composition of the gut bacterial community seems to depend largely on the ingested diet (32).…”

Section: Gut Microbiomes and Reproductive Isolation In Drosophilamentioning

confidence: 99%

Gut microbiomes and reproductive isolation in Drosophila

Leftwich

Clarke

Hutchings

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

View full text Add to dashboard Cite

show abstract

“…While the immune response in D. melanogaster has been well-studied, our research using dense time-course gene expression data reveals genome-wide dynamic expression patterns at higher temporal detail. Specifically, we reveal responses to immune challenge with divergent initiation and resolution dynamics, cyclic patterns of gene expression, and patterns of co-regulation and functional trade-offs, while also assigning putative gene functions to uncharacterized genes through temporal guilt-by-association.MATERIALS AND METHODSFly lines, injections, and sample collectionMale adult Drosophila of about 4 days old from an F1 cross from two Drosophila melanogaster Genetic Reference Panel (DGRP) lines: line 379, which has shown to have low bacterial resistance, and line 360, which has high bacterial resistance(101). Flies were kept on a 12:12 dark-light cycle.Flies were injected in the abdomen with 9.2 μl of commercial lipopolysaccharide (LPS) (Escherichia coli 055:B5 Sigma) derived from the outer membrane of Gram-negative bacteria.…”

mentioning

confidence: 99%

Dense time-course gene expression profiling of the Drosophila melanogaster innate immune response

Schlamp

Delbare

Early

et al. 2020

Preprint

Self Cite

View full text Add to dashboard Cite

BackgroundImmune responses need to be initiated rapidly, and maintained as needed, to prevent establishment and growth of infections. At the same time, resources need to be balanced with other physiological processes. On the level of transcription, studies have shown that this balancing act is reflected in tight control of the initiation kinetics and shutdown dynamics of specific immune genes. ResultsTo investigate expression dynamics and trade-offs after infection genome-wide and with high temporal resolution, we performed an RNA-seq time course on D. melanogaster with 20 time points post-LPS injection. A combination of methods, including spline fitting, cluster analysis, and Granger Causality inference, allowed detailed dissection of expression profiles, lead-lag interactions, and functional annotation of genes through guilt-by-association. We identified genes encoding antimicrobial peptides and co-expressed, less well characterized genes, as immediate-early response genes with a sustained up-regulation up to five days after stimulation. In contrast, stress response genes and additional immune genes, among which were Bomanins, demonstrated early and transient responses. We further observed a strong trade-off with metabolic genes, which strikingly recovered to pre-infection levels before the immune response was fully resolved. ConclusionsThis high-dimensional dataset enabled the comprehensive study of immune response dynamics through the parallel application of multiple temporal data analysis methods. Multivariate Granger causality analysis proved to be a valuable addition to classical time course analysis methods such as clustering, due to its ability to define directed networks of lead-lag patterns.

show abstract

“…A valuable alternative model to uncover the genetic and molecular mechanisms underlying variation in gut immunocompetence is Drosophila melanogaster given that this organism is by now widely used to study the biological processes mediating the response to enteric infection [24][25][26][27][28]. Moreover, previous work including ours has shown that gut immunocompetence is a highly variable and heritable trait, not only in human [29] and mouse [30], but also in Drosophila [31,32]. Consequently, population resources such as the Drosophila Genetic Reference Panel (DGRP) can be effectively used to study the molecular nature of enteric infectioninduced gene expression variation.…”

Section: Introductionmentioning

confidence: 89%

cis-regulatory variation modulates susceptibility to enteric infection in the Drosophila genetic reference panel

et al. 2020

View full text Add to dashboard Cite

Background: Resistance to enteric pathogens is a complex trait at the crossroads of multiple biological processes. We have previously shown in the Drosophila Genetic Reference Panel (DGRP) that resistance to infection is highly heritable, but our understanding of how the effects of genetic variants affect different molecular mechanisms to determine gut immunocompetence is still limited. Results: To address this, we perform a systems genetics analysis of the gut transcriptomes from 38 DGRP lines that were orally infected with Pseudomonas entomophila. We identify a large number of condition-specific, expression quantitative trait loci (local-eQTLs) with infection-specific ones located in regions enriched for FOX transcription factor motifs. By assessing the allelic imbalance in the transcriptomes of 19 F1 hybrid lines from a large round robin design, we independently attribute a robust cis-regulatory effect to only 10% of these detected local-eQTLs. However, additional analyses indicate that many local-eQTLs may act in trans instead. Comparison of the transcriptomes of DGRP lines that were either susceptible or resistant to Pseudomonas entomophila infection reveals nutcracker as the only differentially expressed gene. Interestingly, we find that nutcracker is linked to infection-specific eQTLs that correlate with its expression level and to enteric infection susceptibility. Further regulatory analysis reveals one particular eQTL that significantly decreases the binding affinity for the repressor Broad, driving differential allele-specific nutcracker expression. Conclusions: Our collective findings point to a large number of infection-specific cis-and transacting eQTLs in the DGRP, including one common non-coding variant that lowers enteric infection susceptibility.

show abstract

Drosophila Genotype Influences Commensal Bacterial Levels

Cited by 44 publications

References 61 publications

Gut microbiomes and reproductive isolation in Drosophila

Gut microbiomes and reproductive isolation in Drosophila

Dense time-course gene expression profiling of the Drosophila melanogaster innate immune response

cis-regulatory variation modulates susceptibility to enteric infection in the Drosophila genetic reference panel

Contact Info

Product

Resources

About