Drosophila lifespan enhancement by exogenous bacteria

Mitochondria, the gut microbiome and ROS

In this review, we discuss the connections between mitochondria and the gut microbiome provided by reactive oxygen species (ROS). We examine the mitochondrion as an endosymbiotic organelle that is a hub for energy production, signaling, and cell homeostasis. Maintaining a diverse gut microbiome is generally associated with organismal fitness, intestinal health and resistance to environmental stress. In contrast, gut microbiome imbalance, termed dysbiosis, is linked to a reduction in organismal well-being. ROS are essential signaling molecules but can be damaging when present in excess. Increasing ROS levels have been shown to influence human health, homeostasis of gut cells, and the gastrointestinal microbial community's biodiversity. Reciprocally, gut microbes can affect ROS levels, mitochondrial homeostasis, and host health. We propose that mechanistic understanding of the suite of bi-directional interactions between mitochondria and the gut microbiome will facilitate innovative interdisciplinary studies examining evolutionary divergence and provide novel treatments and therapeutics for disease. GLOSS: In this review, we focus on the nexus between mitochondria and the gut microbiome provided by reactive oxygen species (ROS). Mitochondria are a cell organelle that is derived from an ancestral alpha-proteobacteria. They generate around 80% of the adenosine triphosphate that an organism needs to function and release a range of signaling molecules essential for cellular homeostasis. The gut microbiome is a suite of microorganisms that are commensal, symbiotic and pathogenic to their host. ROS are one predominant group of essential signaling molecules that can be harmful in excess. We suggest that the mitochondria- microbiome nexus is a frontier of research that has cross-disciplinary benefits in understanding genetic divergence and human well-being.

The role of commensal microbes in the lifespan of Drosophila melanogaster

Commensal microbes have mutualistic relationships with their host and mainly live in the host intestine. There are many studies on the relationships between commensal microbes and host physiology. However, there are inconsistent results on the effects of commensal microbes on host lifespan. To clarify this controversy, we generated axenic flies by using two controlled methods – bleaching and antibiotic treatment – and investigated the relationship between the commensal microbes and host lifespan in Drosophila melanogaster. The removal of microbes by using bleaching and antibiotic treatments without detrimental effects increased fly lifespan. Furthermore, a strain of flies colonized with a high load of microbiota showed a greater effect on lifespan extension when the microbes were eliminated, suggesting that commensal bacteria abundance may be a critical determinant of host lifespan. Consistent with those observations, microbial flora of aged fly gut significantly decreased axenic fly lifespan via an increase in bacterial load rather than through a change of bacterial composition. Our elaborately controlled experiments showed that the elimination of commensal microbes without detrimental side effects increased fly lifespan, and that bacterial load was a significant determinant of lifespan. Furthermore, our results indicate the presence of a deterministic connection between commensal microbes and host lifespan.

Genetic Influences of the Microbiota on the Life Span of Drosophila melanogaster

To better understand how associated microorganisms ("microbiota") influence organismal aging, we focused on the model organism Drosophila melanogaster We conducted a metagenome-wide association (MGWA) as a screen to identify bacterial genes associated with variation in the D. melanogaster life span. The results of the MGWA predicted that bacterial cysteine and methionine metabolism genes influence fruit fly longevity. A mutant analysis, in which flies were inoculated with Escherichia coli strains bearing mutations in various methionine cycle genes, confirmed a role for some methionine cycle genes in extending or shortening fruit fly life span. Initially, we predicted these genes might influence longevity by mimicking or opposing methionine restriction, an established mechanism for life span extension in fruit flies. However, follow-up transcriptome sequencing (RNA-seq) and metabolomic experiments were generally inconsistent with this conclusion and instead implicated glucose and vitamin B₆ metabolism in these influences. We then tested if bacteria could influence life span through methionine restriction using a different set of bacterial strains. Flies reared with a bacterial strain that ectopically expressed bacterial transsulfuration genes and lowered the methionine content of the fly diet also extended female D. melanogaster life span. Taken together, the microbial influences shown here overlap with established host genetic mechanisms for aging and therefore suggest overlapping roles for host and microbial metabolism genes in organismal aging.IMPORTANCE Associated microorganisms ("microbiota") are intimately connected to the behavior and physiology of their animal hosts, and defining the mechanisms of these interactions is an urgent imperative. This study focuses on how microorganisms influence the life span of a model host, the fruit fly Drosophila melanogaster First, we performed a screen that suggested a strong influence of bacterial methionine metabolism on host life span. Follow-up analyses of gene expression and metabolite abundance identified stronger roles for vitamin B₆ and glucose than methionine metabolism among the tested mutants, possibly suggesting a more limited role for bacterial methionine metabolism genes in host life span effects. In a parallel set of experiments, we created a distinct bacterial strain that expressed life span-extending methionine metabolism genes and showed that this strain can extend fly life span. Therefore, this work identifies specific bacterial genes that influence host life span, including in ways that are consistent with the expectations of methionine restriction.

Novel Experimental Methods for the Investigation of Hermetia illucens (Diptera: Stratiomyidae) Larvae

Large-scale insect rearing for food and feed production can be improved by understanding diet digestion and host-microbe interactions. To examine these processes in black soldier fly (Hermetia illucens L.; Diptera: Stratiomyidae) larvae, two protocols were developed. Protocol 1 describes a method to produce viable, sterile black soldier fly larvae and a gentle method for diet sterilization. Sterile black soldier fly larvae can be used to study the diverse role of microbes in larval development. Nutrient requirements of sterile black soldier fly larvae are met only through diet. Viable sterile black soldier fly larvae were consistently generated using a four-step treatment with alternating immersions of eggs for 2 min each in ethanol (70%) and sodium hypochlorite (0.6%), over two cycles. A nonthermal method of diet sterilization, namely high-energy electron beam (HEEB) treatment, was introduced. Subsequently, growth of sterile black soldier fly larvae was observed on the HEEB-treated diets (40, 60, and 40% of replicates with poultry feed, liver pie, and an artificial diet, respectively) but not on autoclaved diets. In Protocol 2, we propose a novel method to collect frass from individual larvae. We then measured the metabolites in frass, using high-pressure liquid chromatography. Results on metabolites confirmed the influence of digestion. For instance, succinate increased from 1 to 2 and 7 μmol/g sample from diet to gut homogenate and frass, respectively. The collection method is a promising tool to estimate the diet and nutrient requirements of black soldier fly larvae, thus increasing the performance and reliability of black soldier fly larvae rearing. We discuss in detail the possible applications and limitations of our methods in black soldier fly larvae research.

Methionyl-tRNA Synthetase Regulates Lifespan in Drosophila

Methionyl-tRNA synthetase (MRS) is essential for translation. MRS mutants reduce global translation, which usually increases lifespan in various genetic models. However, we found that MRS inhibited Drosophila reduced lifespan despite of the reduced protein synthesis. Microarray analysis with MRS inhibited Drosophila revealed significant changes in inflammatory and immune response genes. Especially, the expression of anti-microbial peptides (AMPs) genes was reduced. When we measured the expression levels of AMP genes during aging, those were getting increased in the control flies but reduced in MRS inhibition flies agedependently. Interestingly, in the germ-free condition, the maximum lifespan was increased in MRS inhibition flies compared with that of the conventional condition. These findings suggest that the lifespan of MRS inhibition flies is reduced due to the down-regulated AMPs expression in Drosophila.

Drosophila-associated bacteria differentially shape the nutritional requirements of their host during juvenile growth

The interplay between nutrition and the microbial communities colonizing the gastrointestinal tract (i.e., gut microbiota) determines juvenile growth trajectory. Nutritional deficiencies trigger developmental delays, and an immature gut microbiota is a hallmark of pathologies related to childhood undernutrition. However, how host-associated bacteria modulate the impact of nutrition on juvenile growth remains elusive. Here, using gnotobiotic Drosophila melanogaster larvae independently associated with Acetobacter pomorum^WJL (Ap^WJL) and Lactobacillus plantarum^NC8 (Lp^NC8), 2 model Drosophila-associated bacteria, we performed a large-scale, systematic nutritional screen based on larval growth in 40 different and precisely controlled nutritional environments. We combined these results with genome-based metabolic network reconstruction to define the biosynthetic capacities of Drosophila germ-free (GF) larvae and its 2 bacterial partners. We first established that Ap^WJL and Lp^NC8 differentially fulfill the nutritional requirements of the ex-GF larvae and parsed such difference down to individual amino acids, vitamins, other micronutrients, and trace metals. We found that Drosophila-associated bacteria not only fortify the host’s diet with essential nutrients but, in specific instances, functionally compensate for host auxotrophies by either providing a metabolic intermediate or nutrient derivative to the host or by uptaking, concentrating, and delivering contaminant traces of micronutrients. Our systematic work reveals that beyond the molecular dialogue engaged between the host and its bacterial partners, Drosophila and its associated bacteria establish an integrated nutritional network relying on nutrient provision and utilization.

A study of gnotobiotic fruit flies shows that the animal is involved in an integrated nutritional network with its facultative commensal bacteria, centered around the utilization and sharing of nutrients.

Coinfection of the secondary symbionts, Hamiltonella defensa and Arsenophonus sp. contribute to the performance of the major aphid pest, Aphis gossypii (Hemiptera: Aphididae)

Bacterial endosymbionts play important roles in ecological traits of aphids. In this study, we characterize the bacterial endosymbionts of A. gossypii collected in Karaj, Iran and their role in the performance of the aphid. Our results indicated that beside Buchnera aphidicola, A. gossypii, also harbors both Hamiltonella defensa and Arsenophonus sp. Quantitative PCR (qPCR) results revealed that the populations of the endosymbionts increased throughout nymphal development up to adult emergence; thereafter, populations of Buchnera and Arsenophonus were diminished while the density of H. defensa constantly increased. Buchnera reduction caused prolonged development and no progeny production. Furthermore, secondary symbiont reduction led to reduction of the total life span and intrinsic rate of natural increase as well as appearance of the deformed dead offspring in comparison with the control insects. Reduction of the secondary symbionts did not affect parasitism rate of the aphid by the parasitic wasp Aphidius matricariae. Together these findings showed that H. defensa and Arsenophonus contributed to the fitness of A. gossypii by enhancing its performance, but not through parasitoid resistance.

Drosophila Sexual Attractiveness in Older Males Is Mediated by Their Microbiota

Age is well known to be a basis for female preference of males. However, the mechanisms underlying age-based choices are not well understood, with several competing theories and little consensus. The idea that the microbiota can affect host mate choice is gaining traction, and in this study we examine whether the male microbiota influences female preference for older individuals in the fruit fly Drosophila pseudoobscura. We find that an intact microbiota is a key component of attractiveness in older males. However, we found no evidence that this decrease in older male attractiveness was simply due to impaired microbiota generally reducing male quality. Instead, we suggest that the microbiota underlies an honest signal used by females to assess male age, and that impaired microbiota disrupt this signal. This suggests that age-based preferences may break down in environments where the microbiota is impaired, for example when individuals are exposed to naturally occurring antibiotics, extreme temperatures, or in animals reared in laboratories on antibiotic supplemented diet.

The microbiota influences the Drosophila melanogaster life history strategy

Organisms are locally adapted when members of a population have a fitness advantage in one location relative to conspecifics in other geographies. For example, across latitudinal gradients, some organisms may trade off between traits that maximize fitness components in one, but not both, of somatic maintenance or reproductive output. Latitudinal gradients in life history strategies are traditionally attributed to environmental selection on an animal's genotype, without any consideration of the possible impact of associated microorganisms ("microbiota") on life history traits. Here, we show in Drosophila melanogaster, a key model for studying local adaptation and life history strategy, that excluding the microbiota from definitions of local adaptation is a major shortfall. First, we reveal that an isogenic fly line reared with different bacteria varies the investment in early reproduction versus somatic maintenance. Next, we show that in wild fruit flies, the abundance of these same bacteria was correlated with the latitude and life history strategy of the flies, suggesting geographic specificity of the microbiota composition. Variation in microbiota composition of locally adapted D. melanogaster could be attributed to both the wild environment and host genetic selection. Finally, by eliminating or manipulating the microbiota of fly lines collected across a latitudinal gradient, we reveal that host genotype contributes to latitude-specific life history traits independent of the microbiota and that variation in the microbiota can suppress or reverse the differences between locally adapted fly lines. Together, these findings establish the microbiota composition of a model animal as an essential consideration in local adaptation.

Factors that affect the translation of dietary restriction into a longer life

Nutritional interventions, such as dietary or calorie restriction, are known to have a variety of health-promoting effects. The most impressive are the direct effects on life expectancy, which have been reproduced in many animal models. A variety of dietary restriction protocols have been described, which differ either in their macronutrient composition or in the time window for consumption. Mechanistically, the effects of dietary restriction are mediated mainly through signaling pathways that have central roles in the maintenance of cellular energy balance. Among these, target of rapamycin and insulin signaling appear to be the most important. Such nutritional interventions can have their effects in two different ways: either by direct interaction with the metabolism of the host organism, or by modulating the composition and performance of its endogenous microbiome. Various dietary restriction regimens have been identified that significantly alter the microbiome and thus profoundly modulate host metabolism. This review aims to discuss the mechanisms by which dietary restriction can affect life expectancy, and in particular the role of the microbiome.

Effect of gut microbes on olfactory behavior of Drosophila melanogaster larva

The symbiotic relationship between an animal and its gut microbiota is known to influence host neural function and behavior. The mechanisms by which gut microbiota influence brain function are not well understood. This study measures the impact of gut microbiota on olfactory behavior of Drosophila larvae and explores possible mechanisms by which gut microbiota communicate with neural circuits. The microbiota load in Drosophila larvae was altered by treating them with antibiotics or probiotics. Control larvae and larvae with altered microbiota loads were subjected to olfactory assays to analyze the chemotaxis response of larvae to odorants. Larvae treated with antibiotics had reduced microbiota load and exhibited reduced chemotaxis response toward odorants compared to control animals. This behavioral phenotype was partially rescued in larvae treated with probiotics that resulted in partial recovery of microbiota loads. Expression levels of several olfactory genes in larvae subjected to different treatments were analyzed. The results suggest that the expression of certain components of the GABA signaling pathway is sensitive to microbiota load. The study concludes that the microbiota influences homeostatic mechanisms in the host that control GABA production and GABA-receptor expression, which are known to impact host olfactory behavior. These results have implications for understanding the bidirectional communication between a host organism and its microbiota as well as for understanding the modulation of olfactory neuron function.

Species-specific transcriptional profiles of the gut and gut microbiome of Ceratitis quilicii and Ceratitis rosa sensu stricto

The fruit fly species, Ceratitis rosa sensu stricto and Ceratitis quilicii, are sibling species restricted to the lowland and highland regions, respectively. Until recently, these sibling species were considered as allopatric populations of C. rosa with distinct bionomics. We used deep Next Generation Sequencing (NGS) technology on intact guts of individuals from the two sibling species to compare their transcriptional profiles and simultaneously understand gut microbiome and host molecular processes and identify distinguishing genetic differences between the two species. Since the genomes of both species had not been published previously, the transcriptomes were assembled de novo into transcripts. Microbe-specific transcript orthologs were separated from the assembly by filtering searches of the transcripts against microbe databases using OrthoMCL. We then used differential expression analysis of host-specific transcripts (i.e. those remaining after the microbe-specific transcripts had been removed) and microbe-specific transcripts from the two-sibling species to identify defining species-specific transcripts that were present in only one fruit fly species or the other, but not in both. In C. quilicii females, bacterial transcripts of Pectobacterium spp., Enterobacterium buttiauxella, Enterobacter cloacae and Klebsiella variicola were upregulated compared to the C. rosa s.s. females. Comparison of expression levels of the host transcripts revealed a heavier investment by C. quilicii (compared with C. rosa s.s.) in: immunity; energy production; cell proliferation; insecticide resistance; reproduction and proliferation; and redox reactions that are usually associated with responses to stress and degradation of fruit metabolites.

Yeasts affect tolerance of Drosophila melanogaster to food substrate with high NaCl concentration

The ability of model animal species, such as Drosophila melanogaster, to adapt quickly to various adverse conditions has been shown in many experimental evolution studies. It is usually assumed by default that such adaptation is due to changes in the gene pool of the studied population of macroorganisms. At the same time, it is known that microbiome can influence biological processes in macroorganisms. In order to assess the possible impact of microbiome on adaptation, we performed an evolutionary experiment in which some D. melanogaster lines were reared on a food substrate with high NaCl concentration while the others were reared on the standard (favourable) substrate. We evaluated the reproductive efficiency of experimental lines on the high salt substrate three years after the experiment started. Our tests confirmed that the lines reared on the salty substrate became more tolerant to high NaCl concentration. Moreover, we found that pre-inoculation of the high salt medium with homogenized salt-tolerant flies tended to improve reproductive efficiency of naïve flies on this medium (compared to pre-inoculation with homogenized control flies). The analysis of yeast microbiome in fly homogenates revealed significant differences in number and species richness of yeasts between salt-tolerant and control lines. We also found that some individual yeast lines extracted from the salt-tolerant flies improved reproductive efficiency of naïve flies on salty substrate (compared to baker's yeast and no yeast controls), whereas the effect of the yeast lines extracted from the control flies tended to be smaller. The yeast Starmerella bacillaris extracted from the salt-tolerant flies showed the strongest positive effect. This yeast is abundant in all salt-tolerant lines, and very rare or absent in all control lines. The results are consistent with the hypothesis that some components of the yeast microbiome of D. melanogaster contribute to to flies' tolerance to food substrate with high NaCl concentration.

Symbiotic bacteria motivate the foraging decision and promote fecundity and survival of Bactrocera dorsalis (Diptera: Tephritidae)

Background

The gut bacteria of tephritid fruit flies play prominent roles in nutrition, reproduction, maintenance and ecological adaptations of the host. Here, we adopted an approach based on direct observation of symbiotic or axenic flies feeding on dishes seeded with drops of full diet (containing all amino acids) or full diet supplemented with bacteria at similar concentrations to explore the effects of intestinal bacteria on foraging decision and fitness of Bactrocera dorsalis.

Results

The results show that intestinal probiotics elicit beneficial foraging decision and enhance the female reproduction fitness and survival of B. dorsalis (symbiotic and axenic), yet preferences for probiotic diets were significantly higher in axenic flies to which they responded faster compared to full diet. Moreover, females fed diet supplemented with Pantoea dispersa and Enterobacter cloacae laid more eggs but had shorter lifespan while female fed Enterococcus faecalis and Klebsiella oxytoca enriched diets lived longer but had lower fecundity compared to the positive control. Conversely, flies fed sugar diet (negative control) were not able to produce eggs, but lived longer than those from the positive control.

Conclusions

These results suggest that intestinal bacteria can drive the foraging decision in a way which promotes the reproduction and survival of B. dorsalis. Our data highlight the potentials of gut bacterial isolates to control the foraging behavior of the fly and empower the sterile insect technique (SIT) program through the mass rearing.

Gut yeasts do not improve desiccation survival in Drosophila melanogaster

A healthy gut microbiota generally improves the performance of its insect host. Although the effects can be specific to the species composition of the microbial community, the role of gut microbiota in determining water balance has not been well explored. We used axenic and gnotobiotic (reared with a known microbiota) Drosophila melanogaster to test three hypotheses about the effects of gut yeasts on the water balance of adult flies: 1) that gut yeasts would improve desiccation survival in adult flies; 2) that larval yeasts would improve adult desiccation survival; 3) that the effects would be species-specific, such that yeasts closely associated with D. melanogaster in nature are more likely to be beneficial than those rarely found in association with D. melanogaster. We used Saccharomyces cerevisiae (often used in Drosophila cultures, but rarely associated with D. melanogaster in nature), Lachancea kluyveri (associated with some species of Drosophila, but not D. melanogaster), and Pichia kluyveri (associated with D. melanogaster in nature). Adult inoculation with yeasts had no effect on survival of desiccating conditions. Inoculation with P. kluyveri as larvae did not change desiccation survival in adults; however, rearing with L. kluyveri or S. cerevisiae reduced adult desiccation survival. We conclude that adult inoculation with gut yeasts has no impact on desiccation survival, but that rearing with yeasts can have either no or detrimental effect. The effects appear to be species-specific: P. kluyveri did not have a negative impact on desiccation tolerance, suggesting some level of co-adaptation with D. melanogaster. We note that S. cerevisiae may not be an appropriate species for studying the effects of gut yeasts on D. melanogaster.

The Nutritional Environment Influences the Impact of Microbes on Drosophila melanogaster Life Span

D. melanogaster ingests microorganisms growing within its rotting vegetation diet. Some of these microbes form associations with flies, while others pass through the gut with meals. Fly-microbe-diet interactions are dynamic, and changes to the fly culture medium can influence microbial growth in the overall environment. In turn, these alterations in microbial growth may not only impact the nutritional value of fly meals but also modulate behavior and health, at least in part due to direct contributions to fly nutrition. The interactive ecology between flies, microbes, and their environment can cause a specific microbe to be either beneficial or detrimental to fly life span, indicating that the environment should be considered a key influential factor in host-microbe interactions.

Microbes can extend Drosophila melanogaster life span by contributing to the nutritional value of malnourishing fly culture medium. The beneficial effect of microbes during malnutrition is dependent on their individual ability to proliferate in the fly environment and is mimicked by lifelong supplementation of equivalent levels of heat-killed microbes or dietary protein, suggesting that microbes can serve directly as a protein-rich food source. Here, we use nutritionally rich fly culture medium to demonstrate how changes in dietary composition influence monocolonized fly life span; microbes that extend fly life span on malnourishing diets can shorten life on rich diets. The mechanisms employed by microbes to affect host health likely differ on low- or high-nutrient diets. Our results demonstrate how Drosophila-associated microbes can positively or negatively influence fly life span depending on the nutritional environment. Although controlled laboratory environments allow focused investigations on the interaction between fly microbiota and nutrition, the relevance of these studies is not straightforward, because it is difficult to mimic the nutritional ecology of natural Drosophila-microbe interactions. As such, caution is needed in designing and interpreting fly-microbe experiments and before categorizing microbes into specific symbiotic roles based on results obtained from experiments testing limited conditions.

Drosophila melanogaster as an alternative model organism in nutrigenomics

Nutrigenomics explains the interaction between the genome, the proteome, the epigenome, the metabolome, and the microbiome with the nutritional environment of an organism. It is therefore situated at the interface between an organism's health, its diet, and the genome. The diet and/or specific dietary compounds are able to affect not only the gene expression patterns, but also the epigenetic mechanisms as well as the production of metabolites and the bacterial composition of the microbiota. Drosophila melanogaster provides a well-suited model organism to unravel these interactions in the context of nutrigenomics as it combines several advantages including an affordable maintenance, a short generation time, a high fecundity, a relatively short life expectancy, a well-characterized genome, and the availability of several mutant fly lines. Furthermore, it hosts a mammalian-like intestinal system with a clear microbiota and a fat body resembling the adipose tissue with liver-equivalent oenocytes, supporting the fly as an excellent model organism not only in nutrigenomics but also in nutritional research. Experimental approaches that are essentially needed in nutrigenomic research, including several sequencing technologies, have already been established in the fruit fly. However, studies investigating the interaction of a specific diet and/or dietary compounds in the fly are currently very limited. The present review provides an overview of the fly's morphology including the intestinal microbiome and antimicrobial peptides as modulators of the immune system. Additionally, it summarizes nutrigenomic approaches in the fruit fly helping to elucidate host-genome interactions with the nutritional environment in the model organism Drosophila melanogaster.

Dietary ursolic acid improves health span and life span in male Drosophila melanogaster

The health and life span of Drosophila melanogaster are partly determined by intestinal barrier integrity, metabolic rate as well as stress response and the expression of longevity-associated genes, depending on genetic and dietary factors. Ursolic acid (UA) is a naturally occurring triterpenoid exhibiting potential antimicrobial, anti-inflammatory, and antiobesity activity and counteracting age-related deficits in muscle strength. In this study, UA was dietarily administered to w1118 D. melanogaster which significantly elongated the health and life span of males. Spargel (srl) is the Drosophila orthologue of mammalian peroxisome proliferator-activated receptor-gamma coactivator 1 α(PGC1α), an important regulator of energy homeostasis and mitochondrial function. Our results indicate that the health-promoting effect of UA, demonstrated by a significant increase in climbing activity, occurs via an upregulation of srl expression leading to a metabolic shift in the fly without reducing fecundity or gut integrity. Moreover, UA affected the flies' microbiota in a manner that contributed to life span extension. Srl expression and microbiota both seem to be affected by UA, as we determined by using srl-mutant and axenic flies. © 2018 BioFactors, 45(2):169-186, 2019.

Microbiome interactions shape host fitness

All animals have associated microbial communities called microbiomes that influence the physiology and fitness of their host. It is unclear to what extent individual microbial species versus interactions between them influence the host. Here, we mapped all possible interactions between individual species of bacteria against Drosophila melanogaster fruit fly fitness traits. Our approach revealed that the same bacterial interactions that shape microbiome abundances also shape host fitness traits. The fitness traits of lifespan and fecundity showed a life history tradeoff, where equal total fitness can be gotten by either high fecundity over a short life or low fecundity over a long life. The microbiome interactions are as important as the individual species in shaping these fundamental aspects of fly physiology.

Gut bacteria can affect key aspects of host fitness, such as development, fecundity, and lifespan, while the host, in turn, shapes the gut microbiome. However, it is unclear to what extent individual species versus community interactions within the microbiome are linked to host fitness. Here, we combinatorially dissect the natural microbiome of Drosophila melanogaster and reveal that interactions between bacteria shape host fitness through life history tradeoffs. Empirically, we made germ-free flies colonized with each possible combination of the five core species of fly gut bacteria. We measured the resulting bacterial community abundances and fly fitness traits, including development, reproduction, and lifespan. The fly gut promoted bacterial diversity, which, in turn, accelerated development, reproduction, and aging: Flies that reproduced more died sooner. From these measurements, we calculated the impact of bacterial interactions on fly fitness by adapting the mathematics of genetic epistasis to the microbiome. Development and fecundity converged with higher diversity, suggesting minimal dependence on interactions. However, host lifespan and microbiome abundances were highly dependent on interactions between bacterial species. Higher-order interactions (involving three, four, and five species) occurred in 13–44% of possible cases depending on the trait, with the same interactions affecting multiple traits, a reflection of the life history tradeoff. Overall, we found these interactions were frequently context-dependent and often had the same magnitude as individual species themselves, indicating that the interactions can be as important as the individual species in gut microbiomes.

Effect of dietary additives on intestinal permeability in both Drosophila and a human cell co-culture

Increased intestinal barrier permeability has been correlated with aging and disease, including type 2 diabetes, Crohn's disease, celiac disease, multiple sclerosis and irritable bowel syndrome. The prevalence of these ailments has risen together with an increase in industrial food processing and food additive consumption. Additives, including sugar, metal oxide nanoparticles, surfactants and sodium chloride, have all been suggested to increase intestinal permeability. We used two complementary model systems to examine the effects of food additives on gut barrier function: a Drosophila in vivo model and an in vitro human cell co-culture model. Of the additives tested, intestinal permeability was increased most dramatically by high sugar. High sugar also increased feeding but reduced gut and overall animal size. We also examined how food additives affected the activity of a gut mucosal defense factor, intestinal alkaline phosphatase (IAP), which fluctuates with bacterial load and affects intestinal permeability. We found that high sugar reduced IAP activity in both models. Artificial manipulation of the microbiome influenced gut permeability in both models, revealing a complex relationship between the two. This study extends previous work in flies and humans showing that diet can play a role in the health of the gut barrier. Moreover, simple models can be used to study mechanisms underlying the effects of diet on gut permeability and function.This article has an associated First Person interview with the first author of the paper.

Darwinian selection of host and bacteria supports emergence of Lamarckian-like adaptation of the system as a whole

Background

The relatively fast selection of symbiotic bacteria within hosts and the potential transmission of these bacteria across generations of hosts raise the question of whether interactions between host and bacteria support emergent adaptive capabilities beyond those of germ-free hosts.

Results

To investigate possibilities for emergent adaptations that may distinguish composite host-microbiome systems from germ-free hosts, we introduce a population genetics model of a host-microbiome system with vertical transmission of bacteria. The host and its bacteria are jointly exposed to a toxic agent, creating a toxic stress that can be alleviated by selection of resistant individuals and by secretion of a detoxification agent (“detox”). We show that toxic exposure in one generation of hosts leads to selection of resistant bacteria, which in turn, increases the toxic tolerance of the host’s offspring. Prolonged exposure to toxin over many host generations promotes anadditional form of emergent adaptation due to selection of hosts based on detox produced by their bacterial community as a whole (as opposed to properties of individual bacteria).

Conclusions

These findings show that interactions between pure Darwinian selections of host and its bacteria can give rise to emergent adaptive capabilities, including Lamarckian-like adaptation of the host-microbiome system.

Reviewers

This article was reviewed by Eugene Koonin, Yuri Wolf and Philippe Huneman.

Electronic supplementary material

The online version of this article (10.1186/s13062-018-0224-7) contains supplementary material, which is available to authorized users.

Generation of axenic Aedes aegypti demonstrate live bacteria are not required for mosquito development

The mosquito gut microbiome plays an important role in mosquito development and fitness, providing a promising avenue for novel mosquito control strategies. Here we present a method for rearing axenic (bacteria free) Aedes aegypti mosquitoes, consisting of feeding sterilized larvae on agar plugs containing a high concentration of liver and yeast extract. This approach allows for the complete development to adulthood while maintaining sterility; however, axenic mosquito's exhibit delayed development time and stunted growth in comparison to their bacterially colonized cohorts. These data challenge the notion that live microorganisms are required for mosquito development, and suggest that the microbiota's main role is nutritional. Furthermore, we colonize axenic mosquitoes with simplified microbial communities ranging from a single bacterial species to a three-member community, demonstrating the ability to control the composition of the microbiota. This axenic system will allow the systematic manipulation of the mosquito microbiome for a deeper understanding of microbiota-host interactions.

Contradictory Results in Microbiome Science Exemplified by Recent Drosophila Research

The bacterium Lactobacillus plantarum is prevalent in animal guts and is widely regarded as beneficial and probiotic. D. Fast et al. (mBio 9:e01114-18, 2018, https://doi.org/10.1128/mBio.01114-18) make the surprising discovery that L. plantarum reduces the life span of Drosophila melanogaster and link this effect with the loss and weakened proliferation of stem cells in the Drosophila gut.

The bacterium Lactobacillus plantarum is prevalent in animal guts and is widely regarded as beneficial and probiotic. D. Fast et al. (mBio 9:e01114-18, 2018, https://doi.org/10.1128/mBio.01114-18) make the surprising discovery that L. plantarum reduces the life span of Drosophila melanogaster and link this effect with the loss and weakened proliferation of stem cells in the Drosophila gut. These results are apparently at odds with published evidence for beneficial effects of L. plantarum, especially promoting high developmental rates and stimulating stem cell proliferation in young Drosophila. The among-study discrepancies highlight the context dependence of many effects of gut microbes on host health, likely influenced by host age and genotype, variation among bacterial strains, and diet. The diversity of results offers an opportunity to elucidate a fundamental mechanism(s) and the circumstances that dictate whether gut bacteria have positive or negative effects on host health. These studies also reinforce the value of Drosophila as an emerging model system for probiotic science.

Lithocholic Acid Improves the Survival of Drosophila Melanogaster

SCOPE

Primary bile acids are produced in the liver, whereas secondary bile acids, such as lithocholic acid (LCA), are generated by gut bacteria from primary bile acids that escape the ileal absorption. Besides their well-known function as detergents in lipid digestion, bile acids are important signaling molecules mediating effects on the host's metabolism.

METHODS AND RESULTS

Fruit flies (Drosophila melanogaster) are supplemented with 50 μmol L^-1 LCA either for 30 days or throughout their lifetime. LCA supplementation results in a significant induction of the mean (+12 days), median (+10 days), and maximum lifespan (+ 11 days) in comparison to untreated control flies. This lifespan extension is accompanied by an induction of spargel (srl), the fly homolog of mammalian PPAR-γ co-activator 1α (PGC1α). In wild-type flies, the administration of antibiotics abrogates both the LCA-mediated lifespan induction as well as the upregulation of srl.

CONCLUSION

It is shown that the secondary bile acid LCA significantly induces the mean, the median, and the maximum survival in D. melanogaster. Our data suggest that besides an upregulation of the PGC1α-homolog srl, unidentified alterations in the structure or metabolism of the gut microbiota contribute to the longevity effect mediated by LCA.

Spatiotemporal dynamics and genome-wide association genome-wide association analysis of desiccation tolerance in Drosophila melanogaster

Water availability is a major environmental challenge to a variety of terrestrial organisms. In insects, desiccation tolerance varies predictably over spatial and temporal scales and is an important physiological determinant of fitness in natural populations. Here, we examine the dynamics of desiccation tolerance in North American populations of Drosophila melanogaster using: (a) natural populations sampled across latitudes and seasons; (b) experimental evolution in field mesocosms over seasonal time; (c) genome-wide associations to identify SNPs/genes associated with variation for desiccation tolerance; and (d) subsequent analysis of patterns of clinal/seasonal enrichment in existing pooled sequencing data of populations sampled in both North America and Australia. A cline in desiccation tolerance was observed, for which tolerance exhibited a positive association with latitude; tolerance also varied predictably with culture temperature, demonstrating a significant degree of thermal plasticity. Desiccation tolerance evolved rapidly in field mesocosms, although only males showed differences in desiccation tolerance between spring and autumn collections from natural populations. Water loss rates did not vary significantly among latitudinal or seasonal populations; however, changes in metabolic rates during prolonged exposure to dry conditions are consistent with increased tolerance in higher latitude populations. Genome-wide associations in a panel of inbred lines identified twenty-five SNPs in twenty-one loci associated with sex-averaged desiccation tolerance, but there is no robust signal of spatially varying selection on genes associated with desiccation tolerance. Together, our results suggest that desiccation tolerance is a complex and important fitness component that evolves rapidly and predictably in natural populations.

Unraveling the Molecular Mechanism of Immunosenescence in Drosophila

A common feature of the aging process is a decline in immune system performance. Extensive research has sought to elucidate how changes in adaptive immunity contribute to aging and to provide evidence showing that changes in innate immunity have an important role in the overall decline of net immune function. Drosophila is an emerging model used to address questions related to immunosenescence via research that integrates its capacity for genetic dissection of aging with groundbreaking molecular biology related to innate immunity. Herein, we review information on the immunosenescence of Drosophila and suggest its possible mechanisms that involve changes in insulin/IGF(insulin-like growth factor)-1 signaling, hormones such as juvenile hormone and 20-hydroxyecdysone, and feedback system degeneration. Lastly, the emerging role of microbiota on the regulation of immunity and aging in Drosophila is discussed.

Overexpression of antimicrobial peptides contributes to aging through cytotoxic effects in Drosophila tissues

The innate immune response tends to become hyperactive and proinflammatory in older organisms. We investigated connections between activity of the immune-related genes and aging using the Drosophila model. A hallmark of Drosophila immunity is the production of antimicrobial peptides (AMP), whose expression is triggered via activation of the Toll and Imd immune pathways and regulated by NF-ĸB-like transcription factors, Dif/Dorsal and Relish. It was previously shown that overexpression of the upstream component of the immune pathways shortens lifespan via activation of the Relish-dependent immune response. Here we show that direct overexpression of the Relish target AMP genes broadly at high levels or in the fat body induced apoptosis, elicited depolarization of the mitochondria and significantly shortened lifespan. Underexpression of Relish in the fat body beginning in the second half of lifespan prevented overactivation of AMPs and extended longevity. Unlike infection-induced responses, the age-related increase in AMPs does not require the upstream recognition/transduction module of the Imd pathway. It does however require downstream elements, including Relish and Ird5, a component of the downstream IKK complex. Together, these results established causal links between high-level production of antimicrobial peptides and longevity.

Monoassociation with Lactobacillus plantarum Disrupts Intestinal Homeostasis in Adult Drosophila melanogaster

Adult Drosophila melanogaster raised in the absence of symbiotic bacteria have fewer intestinal stem cell divisions and a longer life span than their conventionally reared counterparts. However, we do not know if increased stem cell divisions are essential for symbiont-dependent regulation of longevity. To determine if individual symbionts cause aging-dependent death in Drosophila, we examined the impacts of common symbionts on host longevity. We found that monoassociation of adult Drosophila with Lactobacillus plantarum, a widely reported fly symbiont and member of the probiotic Lactobacillus genus, curtails adult longevity relative to germfree counterparts. The effects of Lactobacillus plantarum on life span were independent of intestinal aging. Instead, we found that association with Lactobacillus plantarum causes an extensive intestinal pathology within the host, characterized by loss of stem cells, impaired epithelial renewal, and a gradual erosion of epithelial ultrastructure. Our study uncovers an unknown aspect of Lactobacillus plantarum-Drosophila interactions and establishes a simple model to characterize symbiont-dependent disruption of intestinal homeostasis.IMPORTANCE Under homeostatic conditions, gut bacteria provide molecular signals that support the organization and function of the host intestine. Sudden shifts in the composition or distribution of gut bacterial communities impact host receipt of bacterial cues and disrupt tightly regulated homeostatic networks. We used the Drosophila melanogaster model to determine the effects of prominent fly symbionts on host longevity and intestinal homeostasis. We found that monoassociation with Lactobacillus plantarum leads to a loss of intestinal progenitor cells, impaired epithelial renewal, and disruption of gut architecture as flies age. These observations uncover a novel phenotype caused by monoassociation of a germfree host with a common symbiont and establish a simple model to characterize symbiont-dependent loss of intestinal homeostasis.

Obesity and Aging in the Drosophila Model

Being overweight increases the risk of many metabolic disorders, but how it affects lifespan is not completely clear. Not all obese people become ill, and the exact mechanism that turns excessive fat storage into a health-threatening state remains unknown. Drosophila melanogaster has served as an excellent model for many diseases, including obesity, diabetes, and hyperglycemia-associated disorders, such as cardiomyopathy or nephropathy. Here, we review the connections between fat storage and aging in different types of fly obesity. Whereas obesity induced by high-fat or high-sugar diet is associated with hyperglycemia, cardiomyopathy, and in some cases, shortening of lifespan, there are also examples in which obesity correlates with longevity. Transgenic lines with downregulations of the insulin/insulin-like growth factor (IIS) and target of rapamycin (TOR) signaling pathways, flies reared under dietary restriction, and even certain longevity selection lines are obese, yet long-lived. The mechanisms that underlie the differential lifespans in distinct types of obesity remain to be elucidated, but fat turnover, inflammatory pathways, and dysregulations of glucose metabolism may play key roles. Altogether, Drosophila is an excellent model to study the physiology of adiposity in both health and disease.

Microbial Quantity Impacts Drosophila Nutrition, Development, and Lifespan

In Drosophila, microbial association can promote development or extend life. We tested the impact of microbial association during malnutrition and show that microbial quantity is a predictor of fly longevity. Although all tested microbes, when abundantly provided, can rescue lifespan on low-protein diet, the effect of a single inoculation seems linked to the ability of that microbial strain to thrive under experimental conditions. Microbes, dead or alive, phenocopy dietary protein, and the calculated dependence on microbial protein content is similar to the protein requirements determined from fly feeding studies, suggesting that microbes enhance host protein nutrition by serving as protein-rich food. Microbes that enhance larval growth are also associated with the ability to better thrive on fly culture medium. Our results suggest an unanticipated range of microbial species that promote fly development and longevity and highlight microbial quantity as an important determinant of effects on physiology and lifespan during undernutrition.

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Microbial association promotes fly longevity and development on low-protein diet

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A wide range of microbes can serve as a source of protein during undernutrition

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The extent of effects correlates with microbiota quantity and biomass

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The most impactful microbial species simply thrive on fly culture medium

Short-Term, Intermittent Fasting Induces Long-Lasting Gut Health and TOR-Independent Lifespan Extension

Intermittent fasting (IF) can improve function and health during aging in laboratory model organisms, but the mechanisms at work await elucidation. We subjected fruit flies (Drosophila melanogaster) to varying degrees of IF and found that just one month of a 2-day fed:5-day fasted IF regime at the beginning of adulthood was sufficient to extend lifespan. This long-lasting, beneficial effect of early IF was not due to reduced fecundity. Starvation resistance and resistance to oxidative and xenobiotic stress were increased after IF. Early-life IF also led to higher lipid content in 60-day-old flies, a potential explanation for increased longevity. Guts of flies 40 days post-IF showed a significant reduction in age-related pathologies and improved gut barrier function. Improved gut health was also associated with reduced relative bacterial abundance. Early IF thus induced profound long-term changes. Pharmacological and genetic epistasis analysis showed that IF acted independently of the TOR pathway because rapamycin and IF acted additively to extend lifespan, and global expression of a constitutively active S6K did not attenuate the IF-induced lifespan extension. We conclude that short-term IF during early life can induce long-lasting beneficial effects, with robust increase in lifespan in a TOR-independent manner, probably at least in part by preserving gut health.

Beyond immunity: The Imd pathway as a coordinator of host defense, organismal physiology and behavior

The humoral arm of host defense in Drosophila relies on two evolutionarily conserved NFκB signaling cascades, the Toll and the immune deficiency (Imd) pathways. The Imd signaling pathway senses and neutralizes Gram-negative bacteria. Its activity is tightly adjusted, allowing the host to simultaneously prevent infection by pathogenic bacteria and tolerate beneficial gut microbiota. Over-activation of Imd signaling is detrimental at least in part by causing gut dysbiosis that further exacerbates intestinal pathologies. Furthermore, it is increasingly recognized that the Imd pathway or its components also play non-immune roles. In this review, we summarize recent advances in Imd signal transduction, discuss the gut-microbiota interactions mediated by Imd signaling, and finally elaborate on its diverse physiological functions beyond immunity. Understanding the multifaceted physiological outputs of Imd activation will help integrate its immune role into the regulation of whole organismal physiology.

The Drosophila model for microbiome research

The gut microbiome is increasingly recognized to play an important role in shaping the health and fitness of animals, including humans. Drosophila is emerging as a valuable model for microbiome research, combining genetic and genomic resources with simple protocols to manipulate the microbiome, such that microbiologically sterile flies and flies bearing a standardized microbiota can readily be produced in large numbers. Studying Drosophila has the potential to increase our understanding of how the microbiome influences host traits, and allows opportunities for hypothesis testing of microbial impacts on human health. Drosophila is being used to investigate aspects of host-microbe interactions, including the metabolism, the immune system and behavior. Drosophila offers a valuable alternative to rodent and other mammalian models of microbiome research for fundamental discovery of microbiome function, enabling improved research cost effectiveness and benefits for animal welfare.

Dietary and developmental shifts in butterfly-associated bacterial communities

Bacterial communities associated with insects can substantially influence host ecology, evolution and behaviour. Host diet is a key factor that shapes bacterial communities, but the impact of dietary transitions across insect development is poorly understood. We analysed bacterial communities of 12 butterfly species across different developmental stages, using amplicon sequencing of the 16S rRNA gene. Butterfly larvae typically consume leaves of a single host plant, whereas adults are more generalist nectar feeders. Thus, we expected bacterial communities to vary substantially across butterfly development. Surprisingly, only few species showed significant dietary and developmental transitions in bacterial communities, suggesting weak impacts of dietary transitions across butterfly development. On the other hand, bacterial communities were strongly influenced by butterfly species and family identity, potentially due to dietary and physiological variation across the host phylogeny. Larvae of most butterfly species largely mirrored bacterial community composition of their diets, suggesting passive acquisition rather than active selection. Overall, our results suggest that although butterflies harbour distinct microbiomes across taxonomic groups and dietary guilds, the dramatic dietary shifts that occur during development do not impose strong selection to maintain distinct bacterial communities across all butterfly hosts.

Microbiota-Mediated Modulation of Organophosphate Insecticide Toxicity by Species-Dependent Interactions with Lactobacilli in a Drosophila melanogaster Insect Model

Despite the benefits to the global food supply and agricultural economies, pesticides are believed to pose a threat to the health of both humans and wildlife. Chlorpyrifos (CP), a commonly used organophosphate insecticide, has poor target specificity and causes acute neurotoxicity in a wide range of species via the suppression of acetylcholinesterase. This effect is exacerbated 10- to 100-fold by chlorpyrifos oxon (CPO), a principal metabolite of CP. Since many animal-associated symbiont microorganisms are known to hydrolyze CP into CPO, we used a Drosophila melanogaster insect model to investigate the hypothesis that indigenous and probiotic bacteria could affect CP metabolism and toxicity. Antibiotic-treated and germfree D. melanogaster insects lived significantly longer than their conventionally reared counterparts when exposed to 10 μM CP. Drosophila melanogaster gut-derived Lactobacillus plantarum, but not Acetobacterindonesiensis, was shown to metabolize CP. Liquid chromatography tandem-mass spectrometry confirmed that the L. plantarum isolate preferentially metabolized CP into CPO when grown in CP-spiked culture medium. Further experiments showed that monoassociating germfree D. melanogaster with the L. plantarum isolate could reestablish a conventional-like sensitivity to CP. Interestingly, supplementation with the human probiotic Lactobacillus rhamnosus GG (a strain that binds but does not metabolize CP) significantly increased the survival of the CP-exposed germfree D. melanogaster This suggests strain-specific differences in CP metabolism may exist among lactobacilli and emphasizes the need for further investigation. In summary, these results suggest that (i) CPO formation by the gut microbiota can have biologically relevant consequences for the host, and (ii) probiotic lactobacilli may be beneficial in reducing in vivo CP toxicity.IMPORTANCE An understudied area of research is how the microbiota (microorganisms living in/on an animal) affects the metabolism and toxic outcomes of environmental pollutants such as pesticides. This study focused specifically on how the microbial biotransformation of chlorpyrifos (CP; a common organophosphate insecticide) affected host exposure and toxicity parameters in a Drosophila melanogaster insect model. Our results demonstrate that the biotransformation of CP by the gut microbiota had biologically relevant and toxic consequences on host health and that certain probiotic lactobacilli may be beneficial in reducing CP toxicity. Since inadvertent pesticide exposure is suspected to negatively impact the health of off-target species, these findings may provide useful information for wildlife conservation and environmental sustainability planning. Furthermore, the results highlight the need to consider microbiota composition differences between beneficial and pest insects in future insecticide designs. More broadly, this study supports the use of beneficial microorganisms to modulate the microbiota-mediated biotransformation of xenobiotics.

A novel polyphenolic prebiotic and probiotic formulation have synergistic effects on the gut microbiota influencing Drosophila melanogaster physiology

The gut microbiota is a vast community of synergistic bacterial species providing health benefits to the host. Imbalances in the gut microbiota (dysbiosis) due to diet, antibiotic use, age and stress contribute to disease development including diabetes, obesity, colon cancer, inflammatory bowel disease, inflammaging and neurodegeneration. Fortunately, a probiotic regime with a diet rich in prebiotics may reverse dysbiosis promoting health and wellness in age. The current study designs, optimizes and tests a novel probiotic and synbiotic formulation consisting of three metabolically active probiotics Lactobacillus plantarum, Lactobacillus fermentum and Bifidobacteria infantis together with a novel polyphenol-rich prebiotic, Triphala. The prebiotic action of Triphala was characterized using in vitro batch cultures, Drosophila melanogaster and a simulated model of the human gastrointestinal tract (SHIME) where in each model, Triphala supported growth of beneficial bacteria while inhibiting pathogenic species. Neither Triphala at 0.5% w/v nor the individual probiotics at 5.0 × 10⁸ to 7.5 × 10⁹ CFU/ml demonstrated toxicity in Drosophila. Interestingly, motility was combinatorially enhanced by the probiotic and synbiotic formulations reflecting the beneficial variations in the gut microbiota. Altogether, the present study shows that probiotics and synbiotics in combination are more effective at modulating the gut microbiota and eliciting biological effects than their components.

Stable association of a Drosophila-derived microbiota with its animal partner and the nutritional environment throughout a fly population's life cycle

In the past years, the fruit fly Drosophila melanogaster has been extensively used to study the relationship between animals and their associated microbes. Compared to the one of wild populations, the microbiota of laboratory-reared flies is less diverse, and comprises fewer bacterial taxa; nevertheless, the main commensal bacteria found in fly microbiota always belong to the Acetobacteraceae and Lactobacillaceae families. The bacterial communities associated with the fly are environmentally acquired, and the partners engage in a perpetual re-association process. Adult flies constantly ingest and excrete microbes from and onto their feeding substrate, which are then transmitted to the next generation developing within this shared habitat. We wanted to analyze the potential changes in the bacterial community during its reciprocal transfer between the two compartments of the niche (i.e. the fly and the diet). To address this question, we used a diverse, wild-derived microbial community and analyzed its relationship with the fly population and the nutritive substrate in a given habitat. Here we show that the community was overall well maintained upon transmission to a new niche, to a new fly population and to their progeny, illustrating the stable association of a Drosophila-derived microbiota with its fly partner and the nutritional environment. These results highlight the preponderant role of the nutritional substrate in the dynamics of Drosophila/microbiota interactions, and the need to fully integrate this variable when performing such studies.

Physiological responses of insects to microbial fermentation products: Insights from the interactions between Drosophila and acetic acid

Acetic acid is a fermentation product of many microorganisms, including some that inhabit the food and guts of Drosophila. Here, we investigated the effect of dietary acetic acid on oviposition and larval performance of Drosophila. At all concentrations tested (0.34-3.4%), acetic acid promoted egg deposition by mated females in no-choice assays; and females preferred to oviposit on diet with acetic acid relative to acetic acid-free diet. However, acetic acid depressed larval performance, particularly extending the development time of both larvae colonized with the bacterium Acetobacter pomorum and axenic (microbe-free) larvae. The larvae may incur an energetic cost associated with dissipating the high acid load on acetic acid-supplemented diets. This effect was compounded by suppressed population growth of A. pomorum on the 3.4% acetic acid diet, such that the gnotobiotic Drosophila on this diet displayed traits characteristic of axenic Drosophila, specifically reduced developmental rate and elevated lipid content. It is concluded that acetic acid is deleterious to larval Drosophila, and hypothesized that acetic acid may function as a reliable cue for females to oviposit in substrates bearing microbial communities that promote larval nutrition.

A Metagenome-Wide Association Study and Arrayed Mutant Library Confirm Acetobacter Lipopolysaccharide Genes Are Necessary for Association with Drosophila melanogaster

A metagenome wide association (MGWA) study of bacterial host association determinants in Drosophila predicted that LPS biosynthesis genes are significantly associated with host colonization. We were unable to create site-directed mutants for each of the predicted genes in Acetobacter, so we created an arrayed transposon insertion library using Acetobacter fabarum DsW_054 isolated from Drosophila. Creation of the A. fabarum DsW_054 gene knock-out library was performed by combinatorial mapping and Illumina sequencing of random transposon insertion mutants. Transposon insertion locations for 6,418 mutants were successfully mapped, including hits within 63% of annotated genes in the A. fabarum DsW_054 genome. For 45/45 members of the library, insertion sites were verified by arbitrary PCR and Sanger sequencing. Mutants with insertions in four different LPS biosynthesis genes were selected from the library to validate the MGWA predictions. Insertion mutations in two genes biosynthetically upstream of Lipid-A formation, lpxC and lpxB, show significant differences in host association, whereas mutations in two genes encoding LPS biosynthesis functions downstream of Lipid-A biosynthesis had no effect. These results suggest an impact of bacterial cell surface molecules on the bacterial capacity for host association. Also, the transposon insertion mutant library will be a useful resource for ongoing research on the genetic basis for Acetobacter traits.

The impact of Rhodiola rosea on the gut microbial community of Drosophila melanogaster

Background

The root extract of Rhodiola rosea has historically been used in Europe and Asia as an adaptogen, and similar to ginseng and Shisandra, shown to display numerous health benefits in humans, such as decreasing fatigue and anxiety while improving mood, memory, and stamina. A similar extract in the Rhodiola family, Rhodiola crenulata, has previously been shown to confer positive effects on the gut homeostasis of the fruit fly, Drosophila melanogaster. Although, R. rosea has been shown to extend lifespan of many organisms such as fruit flies, worms and yeast, its anti-aging mechanism remains uncertain. Using D. melanogaster as our model system, the purpose of this work was to examine whether the anti-aging properties of R. rosea are due to its impact on the microbial composition of the fly gut.

Results

Rhodiola rosea treatment significantly increased the abundance of Acetobacter, while subsequently decreasing the abundance of Lactobacillales of the fly gut at 10 and 40 days of age. Additionally, supplementation of the extract decreased the total culturable bacterial load of the fly gut, while increasing the overall quantifiable bacterial load. The extract did not display any antimicrobial activity when disk diffusion tests were performed on bacteria belonging to Microbacterium, Bacillus, and Lactococcus.

Conclusions

Under standard and conventional rearing conditions, supplementation of R. rosea significantly alters the microbial community of the fly gut, but without any general antibacterial activity. Further studies should investigate whether R. rosea impacts the gut immunity across multiple animal models and ages.

Nutrient-Dependent Impact of Microbes on Drosophila suzukii Development

Drosophila suzukii Matsumura is an invasive species of vinegar fly that has become a prominent pest of berries and other soft-skinned fruits. Unlike most other Drosophila species, female D. suzukii flies lay their eggs in ripening and ripe fruits and larvae develop within the fruit. To understand how D. suzukii larvae utilize ripe and ripening fruits, which usually have low levels of protein, we investigated the microbiota of field-captured and laboratory-reared D. suzukii flies and further examined the combined influence of diet and microbes on host fitness. Field-captured flies were associated with diverse microbiota, which varied significantly with sampling location and season. In contrast, laboratory-reared flies possessed strikingly lower bacterial abundance and diversity. A comparison of conventionally reared (CR) and germ-free (GF) flies revealed that the microbiota of D. suzukii does not alter its development significantly but decreases its life span under conditions of a nutrient-sufficient diet. However, the microbiota is essential for D. suzukii development on strawberry-based or blueberry-based fruit diets. This developmental failure could be rescued by reassociation with single bacterial or fungal species or by the addition of a high quantity of heat-killed microbes. In addition, we found that proteins are limiting with respect to fly development on fruit-based diets and that GF flies show signs of protein starvation. Taken together, our study results demonstrate that the microbiota provides key proteins required for the development of D. suzukii reared on fresh fruit. Our work shows that the impact of microbes on fly fitness depends strongly on nutritional conditions.

Animals are commonly associated with specific microbes, which play important roles in host development and fitness. However, little information about the function of microbes has been available for the important invasive pest Drosophila suzukii, also known as Spotted wing drosophila. Our study results demonstrate that the abundance and structure of microbiota in D. suzukii are strongly affected by the environment, where microbes have variable roles depending on the nutritional situation. For instance, we found that the presence of microbes is deleterious for flies growing on a protein-rich diet and yet is beneficial for flies growing on a diet of protein-poor fruits. Additionally, germ-free flies must feed on microbes to obtain the necessary protein for larval development on strawberries and blueberries. Our report validates the complexity seen in host-microbe interactions and may provide information useful for D. suzukii pest control.