Microbe-dependent and nonspecific effects of procedures to eliminate the resident microbiota from Drosophila melanogaster

Is Drosophila Larval Competition Involved in Incipient Speciation?

Geographical, ethological, temporal and ecological barriers can affect interbreeding between populations deriving from an ancestral population, this progressively leading to speciation. A rare case of incipient speciation currently occurs between Drosophila melanogaster populations sampled in Zimbabwe (Z) and all other populations (M). This phenomenon was initially characterized by Z females refusing to mate with M males. Despite the fact that Z and M flies produce different amounts of cuticular pheromones, their manipulation and that of other sensory signals exchanged during courtship behavior only marginally rescued the behavioral isolation. To further explore the putative mechanisms involved in this phenomenon, we first assessed the fecundity in matings between Z and M flies. Then, we measured the reproduction and survival in adults resulting of co-cultured Z and M larvae. In these two experiments, Z flies rarely emerged. Z and M larvae produced different amounts of food-derived metabolites which were altered in co-culture condition. This maybe related to the different bacteria composition in the gut and body of Z and M flies. However, the mating behavior of co-cultured flies did not change and their cuticular pheromone profile was slightly altered. Thus, the Z/M larval competition could reinforce the barriers induced by gametic and behavioral isolation processes on this incipient speciation phenomenon.

Procedures for the Detection of Wolbachia-Conferred Antiviral Protection in Drosophila melanogaster

Spread of Wolbachia infections in host populations may be enhanced by Wolbachia-conferred protection from viral pathogens. Wolbachia-infected Drosophila melanogaster survive the pathogenic effects of positive-sense single-stranded RNA virus infections at a higher rate than the flies without Wolbachia. The protection can occur with or without detectable reduction in virus titer. For the comparisons to be meaningful, Wolbachia-harboring and Wolbachia-free insects need to be genetically matched, and original populations of gut microbiota need to be restored after the removal of Wolbachia using antibiotics. Here, I describe the procedures needed to detect Wolbachia-conferred antiviral protection against Drosophila C virus measured as the difference in survival and viral titer between flies with and without Wolbachia.

Microbial degradation of plant toxins

Plants produce a variety of secondary metabolites in response to biotic and abiotic stresses. Although they have many functions, a subclass of toxic secondary metabolites mainly serve plants as deterring agents against herbivores, insects, or pathogens. Microorganisms present in divergent ecological niches, such as soil, water, or insect and rumen gut systems have been found capable of detoxifying these metabolites. As a result of detoxification, microbes gain growth nutrients and benefit their herbivory host via detoxifying symbiosis. Here, we review current knowledge on microbial degradation of toxic alkaloids, glucosinolates, terpenes, and polyphenols with an emphasis on the genes and enzymes involved in breakdown pathways. We highlight that the insect-associated microbes might find application in biotechnology and become targets for an alternative microbial pest control strategy.

The immunostimulatory role of an Enterococcus-dominated gut microbiota in host protection against bacterial and fungal pathogens in Galleria mellonella larvae

Understanding the intricate interplay between the gut microbiota and the immune response in insects is crucial, given its diverse impact on the pathogenesis of various microbial species. The microbiota's modulation of the host immune system is one such mechanism, although its complete impact on immune responses remains elusive. This study investigated the tripartite interaction between the gut microbiota, pathogens, and the host's response in Galleria mellonella larvae reared under axenic (sterile) and conventional (non-sterile) conditions. The influence of the microbiota on host fitness during infections was evaluated via two different routes: oral infection induced by Bacillus thuringiensis subsp. galleriae (Btg), and topical infection induced by Metarhizium robertsii (Mr). We observed that larvae without a microbiota can successfully fulfill their life cycle, albeit with more variation in their developmental time. We subsequently performed survival assays on final-instar larvae, using the median lethal dose (LD50) of Btg and Mr. Our findings indicated that axenic larvae were more vulnerable to an oral infection of Btg; specifically, a dose that was calculated to be half-lethal for the conventional group resulted in a 90%-100% mortality rate in the axenic group. Through a dual-analysis experimental design, we could identify the status of the gut microbiota using 16S rRNA sequencing and assess the level of immune-related gene expression in the same group of larvae at basal conditions and during infection. This analysis revealed that the microbiota of our conventionally reared population was dominated entirely by four Enterococcus species, and these species potentially stimulated the immune response in the gut, due to the increased basal expression of two antimicrobial peptides (AMPs)-gallerimycin and gloverin-in the conventional larvae compared with the axenic larvae. Furthermore, Enterococcus mundtii, isolated from the gut of conventional larvae, showed inhibition activity against Btg in vitro. Lastly, other immune effectors, namely, phenoloxidase activity in the hemolymph and total reactive oxygen/nitrogen species (ROS/RNS) in the gut, were tested to further investigate the extent of the stimulation of the microbiota on the immune response. These findings highlight the immune-modulatory role of the Enterococcus-dominated gut microbiota, an increasingly reported microbiota assemblage of laboratory populations of Lepidoptera, and its influence on the host's response to oral and topical infections.

Role of gut symbionts of insect pests: A novel target for insect-pest control

Insects possess beneficial and nuisance values in the context of the agricultural sector and human life around them. An ensemble of gut symbionts assists insects to adapt to diverse and extreme environments and to occupy every available niche on earth. Microbial symbiosis helps host insects by supplementing necessary diet elements, providing protection from predators and parasitoids through camouflage, modulation of signaling pathway to attain homeostasis and to trigger immunity against pathogens, hijacking plant pathways to circumvent plant defence, acquiring the capability to degrade chemical pesticides, and degradation of harmful pesticides. Therefore, a microbial protection strategy can lead to overpopulation of insect pests, which can drastically reduce crop yield. Some studies have demonstrated increased insect mortality via the destruction of insect gut symbionts; through the use of antibiotics. The review summarizes various roles played by the gut microbiota of insect pests and some studies that have been conducted on pest control by targeting the symbionts. Manipulation or exploitation of the gut symbionts alters the growth and population of the host insects and is consequently a potential target for the development of better pest control strategies. Methods such as modulation of gut symbionts via CRISPR/Cas9, RNAi and the combining of IIT and SIT to increase the insect mortality are further discussed. In the ongoing insect pest management scenario, gut symbionts are proving to be the reliable, eco-friendly and novel approach in the integrated pest management.

Selective Elimination of Wolbachia from the Leafhopper Yamatotettix flavovittatus Matsumura

Wolbachia infections affect the reproductive system and various biological traits of the host insect. There is a high frequency of Wolbachia infection in the leafhopper Yamatotettix flavovittatus Matsumura. To investigate the potential roles of Wolbachia in the host, it is important to generate a non-Wolbachia-infected line. The efficacy of antibiotics in eliminating Wolbachia from Y. flavovittatus remains unknown. This leafhopper harbors the mutualistic bacterium Candidatus Sulcia muelleri, which has an important function in the biological traits. The presence of Ca. S. muelleri raises a major concern regarding the use of antibiotics. We selectively eliminated Wolbachia, considering the influence of antibiotics on leafhopper survival and Ca. S. muelleri prevalence. The effect of artificial diets containing different doses of tetracycline and rifampicin on survival was optimized; high dose (0.5 mg/ml) of antibiotics induces a high mortality. A concentration of 0.2 mg/ml was chosen for the subsequent experiments. Antibiotic treatments significantly reduced the Wolbachia infection, and the Wolbachia density in the treated leafhoppers sharply declined. Wolbachia recurred in tetracycline-treated offspring, regardless of antibiotic exposure. However, Wolbachia is unable to be transmitted and restored in rifampicin-treated offspring. The dose and treatment duration had no significant effect on the infection and density of Ca. S. muelleri in the antibiotic-treated offspring. In conclusion, Wolbachia in Y. flavovittatus was stably eliminated using rifampicin, and the Wolbachia-free line was generated at least two generations after treatment. This report provides additional experimental procedures for removing Wolbachia from insects, particularly in host species with the coexistence of Ca. S. muelleri.

Microbiome-by-ethanol interactions impact Drosophila melanogaster fitness, physiology, and behavior

The gut microbiota can affect how animals respond to ingested toxins, such as ethanol, which is prevalent in the diets of diverse animals and often leads to negative health outcomes in humans. Ethanol is a complex dietary factor because it acts as a toxin, behavioral manipulator, and nutritional source, with both direct effects on the host as well as indirect ones through the microbiome. Here, we developed a model for chronic, non-intoxicating ethanol ingestion in the adult fruit fly, Drosophila melanogaster, and paired this with the tractability of the fly gut microbiota, which can be experimentally removed. We linked numerous physiological, behavioral, and transcriptional variables to fly fitness, including a combination of intestinal barrier integrity, stored triglyceride levels, feeding behavior, and the immunodeficiency pathway. Our results reveal a complex tradeoff between lifespan and fecundity that is microbiome-dependent and modulated by dietary ethanol and feeding behavior.

Interspecies microbiome transplantation recapitulates microbial acquisition in mosquitoes

BACKGROUND

Mosquitoes harbor microbial communities that play important roles in their growth, survival, reproduction, and ability to transmit human pathogens. Microbiome transplantation approaches are often used to study host-microbe interactions and identify microbial taxa and assemblages associated with health or disease. However, no such approaches have been developed to manipulate the microbiota of mosquitoes.

RESULTS

Here, we developed an approach to transfer entire microbial communities between mosquito cohorts. We undertook transfers between (Culex quinquefasciatus to Aedes aegypti) and within (Ae. aegypti to Ae. aegypti) species to validate the approach and determine the number of mosquitoes required to prepare donor microbiota. After the transfer, we monitored mosquito development and microbiota dynamics throughout the life cycle. Typical holometabolous lifestyle-related microbiota structures were observed, with higher dynamics of microbial structures in larval stages, including the larval water, and less diversity in adults. Microbiota diversity in recipient adults was also more similar to the microbiota diversity in donor adults.

CONCLUSIONS

This study provides the first evidence for successful microbiome transplantation in mosquitoes. Our results highlight the value of such methods for studying mosquito-microbe interactions and lay the foundation for future studies to elucidate the factors underlying microbiota acquisition, assembly, and function in mosquitoes under controlled conditions. Video Abstract.

Antibiotics reduce bacterial load in Exaiptasia diaphana, but biofilms hinder its development as a gnotobiotic coral model

Coral reefs are declining due to anthropogenic disturbances, including climate change. Therefore, improving our understanding of coral ecosystems is vital, and the influence of bacteria on coral health has attracted particular interest. However, a gnotobiotic coral model that could enhance studies of coral–bacteria interactions is absent. To address this gap, we tested the ability of treatment with seven antibiotics for 3 weeks to deplete bacteria in Exaiptasia diaphana, a sea anemone widely used as a coral model. Digital droplet PCR (ddPCR) targeting anemone Ef1-α and bacterial 16S rRNA genes was used to quantify bacterial load, which was found to decrease six-fold. However, metabarcoding of bacterial 16S rRNA genes showed that alpha and beta diversity of the anemone-associated bacterial communities increased significantly. Therefore, gnotobiotic E. diaphana with simplified, uniform bacterial communities were not generated, with biofilm formation in the culture vessels most likely impeding efforts to eliminate bacteria. Despite this outcome, our work will inform future efforts to create a much needed gnotobiotic coral model.

Bugs on Drugs: A Drosophila melanogaster Gut Model to Study In Vivo Antibiotic Tolerance of E. coli

With an antibiotic crisis upon us, we need to boost antibiotic development and improve antibiotics’ efficacy. Crucial is knowing how to efficiently kill bacteria, especially in more complex in vivo conditions. Indeed, many bacteria harbor antibiotic-tolerant persisters, variants that survive exposure to our most potent antibiotics and catalyze resistance development. However, persistence is often only studied in vitro as we lack flexible in vivo models. Here, I explored the potential of using Drosophila melanogaster as a model for antimicrobial research, combining methods in Drosophila with microbiology techniques: assessing fly development and feeding, generating germ-free or bacteria-associated Drosophila and in situ microscopy. Adult flies tolerate antibiotics at high doses, although germ-free larvae show impaired development. Orally presented E. coli associates with Drosophila and mostly resides in the crop. E. coli shows an overall high antibiotic tolerance in vivo potentially resulting from heterogeneity in growth rates. The hipA7 high-persistence mutant displays an increased antibiotic survival while the expected low persistence of ΔrelAΔspoT and ΔrpoS mutants cannot be confirmed in vivo. In conclusion, a Drosophila model for in vivo antibiotic tolerance research shows high potential and offers a flexible system to test findings from in vitro assays in a broader, more complex condition.

Functional characterization of cultivable gut bacterial communities associated with rugose spiralling whitefly, Aleurodicus rugioperculatus Martin

Gut symbiotic bacteria provide protection and nutrition to the host insect. A high reproductive rate and dispersal ability of the rugose spiralling whitefly help this polyphagous species to develop and thrive on many horticultural crops. In this study, we isolated the cultivable gut bacteria associated with rugose spiralling whitefly and demonstrated their role in the host insect. We also studied the influence of antibiotics on the rugose spiralling whitefly oviposition. A total of 70 gut bacteria were isolated from the second nymphal stage of rugose spiralling whitefly reared on coconut, banana, and sapota using seven growth media. From the 70 isolates, chitinase, siderophore (51), protease (44), and Glutathione-S-Transferase producers (16) were recorded. The activities of chitinase, siderophore, protease, and Glutathione-S-Transferase in the gut bacterial isolates of rugose spiralling whitefly ranged from 0.07 to 3.96 µmol^-1 min^-1 mL^-1, 10.01 to 76.93%, 2.10 to 83.40%, and 5.21 to 24.48 nmol^-1 min^-1 mL^-1 μg^-1 protein, respectively. The16S rRNA gene sequence analysis revealed that bacterial genera associated with the gut of rugose spiralling whitefly included Bacillus, Exiguobacterium, Acinetobacter, Lysinibacillus, Arthrobacter, and Pseudomonas. Based on the susceptibility of the gut bacteria to antibiotics, 11antibiotic treatments were administered to the host plant leaves infested with the nymphal stages. The antibiotics were evaluated for their effect on rugose spiralling whitefly oviposition. Among the antibiotic treatments, carbenicillin (100 µg mL^-1) + ciprofloxacin (5 µg mL^-1) significantly reduced the oviposition (13 eggs spiral^-1) and egg hatchability (61.54%) of rugose spiralling whitefly. Disruption of chitinase, siderophore, protease, and detoxification enzyme producers and elimination of these symbionts through antibiotics altered the host insect physiology and indirectly affected whitefly oviposition. In conclusion, gut bacteria-based management strategies might be used as insecticides for the effective control of whiteflies.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s13205-021-03081-3.

An integrated host-microbiome response to atrazine exposure mediates toxicity in Drosophila

The gut microbiome produces vitamins, nutrients, and neurotransmitters, and helps to modulate the host immune system-and also plays a major role in the metabolism of many exogenous compounds, including drugs and chemical toxicants. However, the extent to which specific microbial species or communities modulate hazard upon exposure to chemicals remains largely opaque. Focusing on the effects of collateral dietary exposure to the widely used herbicide atrazine, we applied integrated omics and phenotypic screening to assess the role of the gut microbiome in modulating host resilience in Drosophila melanogaster. Transcriptional and metabolic responses to these compounds are sex-specific and depend strongly on the presence of the commensal microbiome. Sequencing the genomes of all abundant microbes in the fly gut revealed an enzymatic pathway responsible for atrazine detoxification unique to Acetobacter tropicalis. We find that Acetobacter tropicalis alone, in gnotobiotic animals, is sufficient to rescue increased atrazine toxicity to wild-type, conventionally reared levels. This work points toward the derivation of biotic strategies to improve host resilience to environmental chemical exposures, and illustrates the power of integrative omics to identify pathways responsible for adverse health outcomes.

Effects of symbiotic population impairment on microbiome composition and longevity of Bactrocera dorsalis

In order to understand the role of symbionts for their insect hosts, it is customary to treat them with antibiotics or to sterilize eggs (treatments), resulting in aposymbiotic and axenic insects, respectively. Such axenic insects can then be compared with untreated controls. Fruit flies often bear complex communities which are greatly reduced by such treatments. However, the bacterial community is not completely eliminated. Here, we examine the effect of these procedures on the structure of the remaining bacterial communities in Bactrocera dorsalis (Diptera: Tephritidae) and on the insect longevity. The antibiotics (Norfloxacin and Ceftazedime) were administered to 1-day-old adult flies through sugar meal for 7 days, and eggs were surface sterilized and dechorionated to produce axenic lines. The flies were starved of protein before they were offered full diets or diets containing non-essential amino acids only. Antibiotic and egg disinfection treatments resulted in a significant reduction of the vast majority of gut bacterial populations, especially Proteobacteria, Firmicutes and Bacteroidetes. On the other hand, antibiotic allowed the persistence of Actinobacteria, Cyanobacteria and Acidobacteria populations. In untreated control flies, longevity was extended irrespective of diet quality in comparison to treated flies. Conversely, when gut bacteria were largely reduced (aposymbiotic and axenic flies), longevity was reduced in the non-essential amino acids diet treatment versus slightly improved in the presence of a protein diet. We discuss these results in an ecological-life-history perspective.

Sex-specific effects of the microbiota on adult carbohydrate intake and body composition in a polyphagous fly

The microbiota influences hosts' health and fitness. However, the extent to which the microbiota affects host' foraging decisions and related life history traits remains to be fully understood. Our study explored the effects of microbiota manipulation on foraging preference and phenotypic traits of larval and adult stages of the polyphagous fruit fly Bactrocera tryoni, one of the main horticultural pests in Australia. We generated three treatments: control (non-treated microbiota), axenic (removed microbiota), and reinoculation (individuals which had their microbiota removed then re-introduced). Our results confirmed that axenic larvae and immature (i.e., newly emerged 0 day-old, sexually-immature) adults were lighter than control and reinoculated individuals. Interestingly, we found a sex-specific effect of the microbiota manipulation on carbohydrate intake and body composition of 10 day-old mature adults. Axenic males ate less carbohydrate, and had lower body weight and total body fat relative to control and reinoculated males. Conversely, axenic females ate more carbohydrate than control and reinoculated ones, although body weight and lipid reserves were similar across treatments. Axenic females produced fewer eggs than control and reinoculated females. Our findings corroborate the far-reaching effects of microbiota in insects found in previous studies and show, for the first time, a sex-specific effect of microbiota on feeding behaviour in flies. Our results underscore the dynamic relationship between the microbiota and the host with the reinoculation of microbes restoring some traits that were affected in axenic individuals.

Sex-Dependent Effects of the Microbiome on Foraging and Locomotion in Drosophila suzukii

There is growing evidence that symbiotic microbes can influence multiple nutrition-related behaviors of their hosts, including locomotion, feeding, and foraging. However, how the microbiome affects nutrition-related behavior is largely unknown. Here, we demonstrate clear sexual dimorphism in how the microbiome affects foraging behavior of a frugivorous fruit fly, Drosophila suzukii. Female flies deprived of their microbiome (axenic) were consistently less active in foraging on fruits than their conventional counterparts, even though they were more susceptible to starvation and starvation-induced locomotion was notably more elevated in axenic than conventional females. Such behavioral change was not observed in male flies. The lag of axenic female flies but not male flies to forage on fruits is associated with lower oviposition by axenic flies, and mirrored by reduced food seeking observed in virgin females when compared to mated, gravid females. In contrast to foraging intensity being highly dependent on the microbiome, conventional and axenic flies of both sexes showed relatively consistent and similar fruit preferences in foraging and oviposition, with raspberries being preferred among the fruits tested. Collectively, this work highlights a clear sex-specific effect of the microbiome on foraging and locomotion behaviors in flies, an important first step toward identifying specific mechanisms that may drive the modulation of insect behavior by interactions between the host, the microbiome, and food.

Influence of inoculated gut bacteria on the development of Bactrocera dorsalis and on its susceptibility to the entomopathogenic fungus, Metarhizium anisopliae

Background

Symbiotic interactions between insects and bacteria have been associated with a vast variety of physiological, ecological and evolutionary consequences for the host. A wide range of bacterial communities have been found in association with the oriental fruit fly, Bactrocera dorsalis (Hendel) (Diptera: Tephritidae), an important pest of cultivated fruit in most regions of the world. We evaluated the diversity of gut bacteria in B. dorsalis specimens from several populations in Kenya and investigated the roles of individual bacterial isolates in the development of axenic (germ-free) B. dorsalis fly lines and their responses to the entomopathogenic fungus, Metarhizium anisopliae.

Results

We sequenced 16S rRNA to evaluate microbiomes and coupled this with bacterial culturing. Bacterial isolates were mono-associated with axenic B. dorsalis embryos. The shortest embryonic development period was recorded in flies with an intact gut microbiome while the longest period was recorded in axenic fly lines. Similarly, larval development was shortest in flies with an intact gut microbiome, in addition to flies inoculated with Providencia alcalifaciens. Adult B. dorsalis flies emerging from embryos that had been mono-associated with a strain of Lactococcus lactis had decreased survival when challenged with a standard dosage of M. anisopliae ICIPE69 conidia. However, there were no differences in survival between the germ-free lines and flies with an intact microbiome.

Conclusions

These findings will contribute to the selection of probiotics used in artificial diets for B. dorsalis rearing and the development of improved integrated pest management strategies based on entomopathogenic fungi.

Supplementary information

Supplementary information accompanies this paper at 10.1186/s12866-020-02015-y.

Selective and stable elimination of endosymbionts from multiple-infected whitefly Bemisia tabaci by feeding on a cotton plant cultured in antibiotic solutions

The maternally heritable endosymbiont provides many ecosystem functions. Antibiotic elimination of a specific symbiont and establishment of experimental host lines lacking certain symbionts enable the roles of a given symbiont to be explored. The whitefly Bemisia tabaci (Gennadius) in China harbors obligate symbiont Portiera infecting each individual, as well as facultative symbionts, such as Hamiltonella, Rickettsia and Cardinium, with co-infections occurring relatively frequently. So far no studies have evaluated the selectivity and efficacy of a specific symbiont elimination using antibiotics in whiteflies co-infected with different symbionts. Furthermore, no success has been achieved in establishing certain symbiont-free B. tabaci lines. In this study, we treated Hamiltonella-infected B. tabaci line, Hamiltonella-Rickettsia-co-infected line and Hamiltonella-Cardinium co-infected line by feeding B. tabaci adults with cotton plants cultured in water containing rifampicin, ampicillin or a mixture of them, aiming to selectively curing symbiont infections and establishing stable symbiont-free lines. We found ampicillin selectively eliminated Cardinium without affecting Portiera, Hamiltonella and Rickettsia, although they coexisted in the same host body. Meanwhile, all of the symbionts considered in our study can be removed by rifampicin. The reduction of facultative symbionts occurred at a much quicker pace than obligate symbiont Portiera during rifampicin treatment. Also, we measured the stability of symbiont elimination in whitefly successive generations and established Rickettsia-infected and Cardinium-infected lines which are absent in natural populations. Our results provide new protocols for selective elimination of symbionts co-existing in a host and establishment of different symbiont-infected host lines.

Effect of gut microbiota on α-amanitin tolerance in Drosophila tripunctata

The bacterial gut microbiota of many animals is known to be important for many physiological functions including detoxification. The selective pressures imposed on insects by exposure to toxins may also be selective pressures on their symbiotic bacteria, who thus may contribute to the mechanism of toxin tolerance for the insect. Amatoxins are a class of cyclopeptide mushroom toxins that primarily act by binding to RNA polymerase II and inhibiting transcription. Several species of mycophagous Drosophila are tolerant to amatoxins found in mushrooms of the genus Amanita, despite these toxins being lethal to most other known eukaryotes. These species can tolerate amatoxins in natural concentrations to utilize toxic mushrooms as larval hosts, but the mechanism by which these species are tolerant remains unknown. Previous data have shown that a local population of D. tripunctata exhibits significant genetic variation in toxin tolerance. This study assesses the potential role of the microbiome in α-amanitin tolerance in six wild-derived strains of Drosophila tripunctata. Normal and antibiotic-treated samples of six strains were reared on diets with and without α-amanitin, and then scored for survival from the larval stage to adulthood and for development time to pupation. Our results show that a substantial reduction in bacterial load does not influence toxin tolerance in this system, while confirming genotype and toxin-specific effects on survival are independent of the microbiome composition. Thus, we conclude that this adaptation to exploit toxic mushrooms as a host is likely intrinsic to the fly's genome and not a property of their microbiome.

Parental Microbiota Modulates Offspring Development, Body Mass and Fecundity in a Polyphagous Fruit Fly

The commensal microbiota is a key modulator of animal fitness, but little is known about the extent to which the parental microbiota influences fitness-related traits of future generations. We addressed this gap by manipulating the parental microbiota of a polyphagous fruit fly (Bactrocera tryoni) and measuring offspring developmental traits, body composition, and fecundity. We generated three parental microbiota treatments where parents had a microbiota that was non-manipulated (control), removed (axenic), or removed-and-reintroduced (reinoculation). We found that the percentage of egg hatching, of pupal production, and body weight of larvae and adult females were lower in offspring of axenic parents compared to that of non-axenic parents. The percentage of partially emerged adults was higher, and fecundity of adult females was lower in offspring of axenic parents relative to offspring of control and reinoculated parents. There was no significant effect of parental microbiota manipulation on offspring developmental time or lipid reserve. Our results reveal transgenerational effects of the parental commensal microbiota on different aspects of offspring life-history traits, thereby providing a better understanding of the long-lasting effects of host-microbe interactions.

Legacy of a Butterfly's Parental Microbiome in Offspring Performance

An insect's phenotype can be influenced by the experiences of the parental generation. However, the effects of the parental symbiotic microbiome and host plant use on the offspring are unclear. We addressed this gap of knowledge by studying Pieris brassicae, a multivoltine butterfly species feeding on different brassicaceous plants across generations. We investigated how disturbance of the parental bacterial community by antibiotic treatment affects F1 larval traits. We tested the effects depending on whether F1 larvae are feeding on the same plant species as their parents or on a different one. The parental treatment alone had no impact on the biomass of F1 larvae feeding on the parental plant species. However, the parental treatment had a detrimental effect on F1 larval biomass when F1 larvae had a different host plant than their parents. This effect was linked to higher larval prophenoloxidase activity and greater downregulation of the major allergen gene (MA), a glucosinolate detoxification gene of P. brassicae Bacterial abundance in untreated adult parents was high, while it was very low in F1 larvae from either parental type, and thus unlikely to directly influence larval traits. Our results suggest that transgenerational effects of the parental microbiome on the offspring's phenotype become evident when the offspring is exposed to a transgenerational host plant shift.IMPORTANCE Resident bacterial communities are almost absent in larvae of butterflies and thus are unlikely to affect their host. In contrast, adult butterflies contain conspicuous amounts of bacteria. While the host plant and immune state of adult parental butterflies are known to affect offspring traits, it has been unclear whether also the parental microbiome imposes direct effects on the offspring. Here, we show that disturbance of the bacterial community in parental butterflies by an antibiotic treatment has a detrimental effect on those offspring larvae feeding on a different host plant than their parents. Hence, the study indicates that disturbance of an insect's parental microbiome by an antibiotic treatment shapes how the offspring individuals can adjust themselves to a novel host plant.

An infection of Enterobacter ludwigii affects development and causes age-dependent neurodegeneration in Drosophila melanogaster

The effects of teeth-blackening bacteria Enterobacter ludwigii on the physiological system were investigated using the model organism Drosophila melanogaster. The bacteria were mixed with the fly food, and its effect was checked on the growth, development and behaviour of Drosophila. Microbes generate reactive oxygen species (ROS) within the haemolymph of the larvae once it enters into the body. The increased amount of ROS was evidenced by the NBT assay and using 2',7'-dichlorofluorescin diacetate dye, which indicates the mitochondrial ROS. The increased amount of ROS resulted in a number of abnormal nuclei within the gut. Besides that larvae walking became sluggish in comparison with wild type although the larvae crawling path did not change much. Flies hatched from the infectious larvae have the posterior scutellar bristle absent from the thorax and abnormal mechanosensory hairs in the eye, and they undergo time-dependent neurodegeneration as evidenced by the geotrophic and phototrophic assays. To decipher the mechanism of neurodegeneration, flies were checked for the presence of four important bioamines: tyramine, cadaverine, putrescine and histamine. Out of these four, histamine was found to be absent in infected flies. Histamine is a key molecule required for the functioning of the photoreceptor as well as mechanoreceptors. The mechanism via which mouth infectious bacteria E. ludwigii can affect the development and cause age-dependent neurodegeneration is explained in this paper.

Drosophila and its gut microbes: a model for drug-microbiome interactions

Drosophila is an excellent system to investigate how the presence and composition of the gut microbiome influences the efficacy of therapeutic drugs and downstream consequences for host health. These opportunities derive from two key attributes of Drosophila. First, Drosophila is amenable for microbiome research, with simple, standardized methods to produce large numbers of microbiologically-sterile flies and flies with a standardized gut microbiome, thereby facilitating experimental reproducibility. Second, Drosophila is a well-established genetic model that is increasingly used to elucidate the molecular and physiological basis of lesions associated with human disease alleles; this provides the opportunity to link microbiome/drug interactions to previously-described processes shaping health and disease. In this way, Drosophila can fast-track understanding of fundamental biology to generate precise hypotheses for testing in mammalian systems. Drosophila is particularly well-suited to investigate the incidence of microbiome/drug interactions mediated by different mechanisms, including microbial drug metabolism (to active, inactive or toxic derivatives), microbial production of compounds that inhibit drug efficacy, and off-target effects of the drug on the microbiome, resulting in dysbiosis and host ill-health. Drosophila can also be used to investigate how interactions between the microbiome and host genotype may shape responses to therapeutic drugs, informing the reliability of precision medicine based exclusively on human genomic markers.

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.

The multilevel antibiotic-induced perturbations to biological systems: Early-life exposure induces long-lasting damages to muscle structure and mitochondrial metabolism in flies

Antibiotics have been increasingly used over the past decades for human medicine, food-animal agriculture, aquaculture, and plant production. A significant part of the active molecules of antibiotics can be released into the environment, in turn affecting ecosystem functioning and biogeochemical processes. At lower organizational scales, these substances affect bacterial symbionts of insects, with negative consequences on growth and development of juveniles, and population dynamics. Yet, the multiple alterations of cellular physiology and metabolic processes have remained insufficiently explored in insects. We evaluated the effects of five antibiotics with different mode of action, i.e. ampicillin, cefradine, chloramphenicol, cycloheximide, and tetracycline, on the survival and ultrastructural organization of the flight muscles of newly emerged blow flies Chrysomya albiceps. Then, we examined the effects of different concentrations of antibiotics on mitochondrial protein content, efficiency of oxidative phosphorylation, and activity of transaminases (Glutamate oxaloacetate transaminase and glutamate pyruvate transaminase) and described the cellular metabolic perturbations of flies treated with antibiotics. All antibiotics affected the survival of the insects and decreased the total mitochondrial protein content in a dose-dependent manner. Ultrastructural organization of flight muscles in treated flies differs dramatically compared to the control groups and severe pathological damages/structures disorganization of mitochondria appeared. The activities of mitochondrial transaminases significantly increased with increased antibiotic concentrations. The oxidation rate of pyruvate + proline from isolated mitochondria of the flight muscles of 1-day-old flies was significantly reduced at high doses of antibiotics. In parallel, the level of several metabolites, including TCA cycle intermediates, was reduced in antibiotics-treated flies. Overall, antibiotics provoked a system-wide alteration of the structure and physiology of flight muscles of the blow fly Ch. albiceps, and may have fitness consequences at the organism level. Environmental antibiotic pollution is likely to have unwanted cascading ecological effects of insect population dynamics and community structure.

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.

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.

The effect of gut microbiota elimination in Drosophila melanogaster: A how-to guide for host-microbiota studies

In recent years, there has been a surge in interest in the effects of the microbiota on the host. Increasingly, we are coming to understand the importance of the gut microbiota in modulating host physiology, ecology, behavior, and evolution. One method utilized to evaluate the effect of the microbiota is to suppress or eliminate it, and compare the effect on the host with that of untreated individuals. In this study, we evaluate some of these commonly used methods in the model organism, Drosophila melanogaster. We test the efficacy of a low‐dose streptomycin diet, egg dechorionation, and an axenic or sterile diet, in the removal of gut bacteria within this species in a fully factorial design. We further determine potential side effects of these methods on host physiology by performing a series of standard physiological assays. Our results showed that individuals from all treatments took significantly longer to develop, and weighed less, compared to normal flies. Males and females that had undergone egg dechorionation weighed significantly less than streptomycin reared individuals. Similarly, axenic female flies, but not males, were much less active when analyzed in a locomotion assay. All methods decreased the egg to adult survival, with egg dechorionation inducing significantly higher mortality. We conclude that low‐dose streptomycin added to the dietary media is more effective at removing the gut bacteria than egg dechorionation and has somewhat less detrimental effects to host physiology. More importantly, this method is the most practical and reliable for use in behavioral research. Our study raises the important issue that the efficacy of and impacts on the host of these methods require investigation in a case‐by‐case manner, rather than assuming homogeneity across species and laboratories.

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.

Aerobic function in mitochondria persists beyond death by heat stress in insects

The critical thermal maximum (CT_max) of insects can be determined using flow-through thermolimit respirometry. It has been demonstrated that respiratory patterns cease and insects do not recover once the CT_max temperature has been reached. However, if high temperatures are maintained following the CT_max, researchers have observed a curious phenomenon whereby the insect body releases a large burst of carbon dioxide at a rate and magnitude that often exceed that of the live insect. This carbon dioxide release has been termed the post-mortal peak (PMP). We demonstrate here that the PMP is observed only at high temperatures, is oxygen-dependent, is prevented by cyanide exposure, and is associated with concomitant consumption of oxygen. We conclude that the PMP derives from highly active, aerobic metabolism in the mitochondria. The insect tracheal system contains air-filled tubes that reach deep into the tissues and allow mitochondria access to oxygen even upon organismal death. This unique condition permits the investigation of mitochondrial function during thermal failure in a manner that cannot be achieved using vertebrate organisms or in vitro preparations.

Gut Microbiota Modifies Olfactory-Guided Microbial Preferences and Foraging Decisions in Drosophila

The gut microbiota affects a wide spectrum of host physiological traits, including development [1-5], germline [6], immunity [7-9], nutrition [4, 10, 11], and longevity [12, 13]. Association with microbes also influences fitness-related behaviors such as mating [14] and social interactions [15, 16]. Although the gut microbiota is evidently important for host wellbeing, how hosts become associated with particular assemblages of microbes from the environment remains unclear. Here, we present evidence that the gut microbiota can modify microbial and nutritional preferences of Drosophila melanogaster. By experimentally manipulating the gut microbiota of flies subjected to behavioral and chemosensory assays, we found that fly-microbe attractions are shaped by the identity of the host microbiota. Conventional flies exhibit preference for their associated Lactobacillus, a behavior also present in axenic flies as adults and marginally as larvae. By contrast, fly preference for Acetobacter is primed by early-life exposure and can override the innate preference. These microbial preferences are largely olfactory guided and have profound impact on host foraging, as flies continuously trade off between acquiring beneficial microbes and balancing nutrients from food. Our study shows a role of animal microbiota in shaping host fitness-related behavior through their chemosensory responses, opening a research theme on the interrelationships between the microbiota, host sensory perception, and behavior.

Maternally-transmitted microbiota affects odor emission and preference in Drosophila larva

Experimental studies show that early sensory experience often affects subsequent sensory preference, suggesting that the heterogeneity of sensory cues in nature could induce significant inter-individual behavioral variation, potentially contributing to maintain intraspecific diversity. To test this hypothesis, we explored the behavioral effect induced by variation in the levels of a self-produced chemical, acetoin, and its link with intraspecific diversity. Acetoin is a pheromone-like substance produced by gut-associated microorganisms in Drosophila. Using wild-type Drosophila melanogaster populations producing variable acetoin levels, we (i) characterized factors involved in this variation and (ii) manipulated some of these factors to affect acetoin responses in larvae. We found that increased and decreased variations in acetoin levels were caused by microorganisms associated with the outside and inside of the egg, respectively. Wild-type larvae preferred acetoin-rich food only when they both produced and were exposed to substantial amounts of acetoin. The removal of the outside of the egg or the genetic alteration of olfaction abolished this preference. In contrast, larvae exposed to high doses of synthetic acetoin were repulsed by acetoin. The similar effects obtained with freshly caught wild-type lines suggest that this acetoin "production-preference" link underlies the diversity of acetoin-producing microorganisms among natural D. melanogaster populations.

Microbial influence on Drosophila biology

Commensal bacteria profoundly affect the biology of their animal partners. Drosophila melanogaster has been broadly used to study microbiota effects on invertebrates, whose findings are frequently applicable to translational studies. The beneficial role of commensal microbes on Drosophila biology is extensively described, ranging from growth to metabolism, immunity and even behaviour. However, the mechanisms underlying these effects are not well understood. Studies continue to discover new layers of complexity in the host-bacteria partnership that constantly changes depending on a plethora of different variables. This review discusses the latest advances in understanding the molecular bases of microbiota impact on Drosophila physiology and behaviour, emphasizing its broad influence and the intricate interdependence of the two partners in shaping their biology.

Immediate perception of a reward is distinct from the reward's long-term salience

Reward perception guides all aspects of animal behavior. However, the relationship between the perceived value of a reward, the latent value of a reward, and the behavioral response remains unclear. Here we report that, given a choice between two sweet and chemically similar sugars—L- and D-arabinose—Drosophila melanogaster prefers D- over L- arabinose, but forms long-term memories of L-arabinose more reliably. Behavioral assays indicate that L-arabinose-generated memories require sugar receptor Gr43a, and calcium imaging and electrophysiological recordings indicate that L- and D-arabinose differentially activate Gr43a-expressing neurons. We posit that the immediate valence of a reward is not always predictive of the long-term reinforcement value of that reward, and that a subset of sugar-sensing neurons may generate distinct representations of similar sugars, allowing for rapid assessment of the salient features of various sugar rewards and generation of reward-specific behaviors. However, how sensory neurons communicate information about L-arabinose quality and concentration—features relevant for long-term memory—remains unknown.

DOI:http://dx.doi.org/10.7554/eLife.22283.001

We often remember experiences that are rewarding in some way. However, not every rewarding experience is stored in memory, and the particular experiences we remember are not always those we would expect to remember. Why is it that some experiences generate long-term memories whereas others do not?

Fruit flies feed on a variety of different sugars present in rotting fruits. Although the flies find all of these sugars attractive, they form memories of some sugars more readily than others. This distinction is particularly striking in the case of two sugars with similar structures: D-arabinose and L-arabinose. Flies typically prefer D-arabinose over L-arabinose, but are more likely to remember an encounter with L-arabinose than D-arabinose.

McGinnis et al. have used fruit flies to explore how the rewarding properties of an experience affect how likely it is to be stored in memory. The experiments show that D-arabinose and L-arabinose generate different patterns of activity in the fly brain, and identify a subset of taste neurons that support the formation of memories specifically about L-arabinose. These neurons enable flies to associate features of their environment – such as odors – with the presence of this one particular sugar. Such memories may help the flies to find a similar food source again in the future. Artificially activating these neurons is also sufficient to trigger the formation of a memory, even in the absence of L-arabinose itself.

Taken as a whole, this work demonstrates that the immediate appeal of a reward can be separated from its ability to generate a long-term memory. The fact that activation of taste neurons can trigger memory formation explains how flies can quickly form long-term memories about desirable food sources. Looking ahead, further work will be required to understand the mechanisms that determine what animals like at any given moment, and what they remember over time.

DOI:http://dx.doi.org/10.7554/eLife.22283.002

Stable Host Gene Expression in the Gut of Adult Drosophila melanogaster with Different Bacterial Mono-Associations

There is growing evidence that the microbes found in the digestive tracts of animals influence host biology, but we still do not understand how they accomplish this. Here, we evaluated how different microbial species commonly associated with laboratory-reared Drosophila melanogaster impact host biology at the level of gene expression in the dissected adult gut and in the entire adult organism. We observed that guts from animals associated from the embryonic stage with either zero, one or three bacterial species demonstrated indistinguishable transcriptional profiles. Additionally, we found that the gut transcriptional profiles of animals reared in the presence of the yeast Saccharomyces cerevisiae alone or in combination with bacteria could recapitulate those of conventionally-reared animals. In contrast, we found whole body transcriptional profiles of conventionally-reared animals were distinct from all of the treatments tested. Our data suggest that adult flies are insensitive to the ingestion of the bacteria found in their gut, but that prior to adulthood, different microbes impact the host in ways that lead to global transcriptional differences observable across the whole adult body.

Gut microbiota in Drosophila melanogaster interacts with Wolbachia but does not contribute to Wolbachia-mediated antiviral protection

Animals experience near constant infection with microorganisms. A significant proportion of these microbiota reside in the alimentary tract. There is a growing appreciation for the roles gut microbiota play in host biology. The gut microbiota of insects, for example, have been shown to help the host overcome pathogen infection either through direct competition or indirectly by stimulating host immunity. These defenses may also be supplemented by coinfecting maternally inherited microbes such as Wolbachia. The presence of Wolbachia in a host can delay and/or reduce death caused by RNA viruses. Whether the gut microbiota of the host interacts with Wolbachia, or vice versa, the precise role of Wolbachia in antiviral protection is not known. In this study, we used 16S rDNA sequencing to characterise changes in gut microbiota composition in Drosophila melanogaster associated with Wolbachia infection and antibiotic treatment. We subsequently tested whether changes in gut composition via antibiotic treatment altered Wolbachia-mediated antiviral properties. We found that both antibiotics and Wolbachia significantly reduced the biodiversity of the gut microbiota without changing the total microbial load. We also showed that changing the gut microbiota composition with antibiotic treatment enhanced Wolbachia density but did not confer greater antiviral protection against Drosophila C virus to the host. We concluded there are significant interactions between Wolbachia and gut microbiota, but changing gut microbiota composition is not likely to be a means through which Wolbachia conveys antiviral protection to its host.

Mosquitoes host communities of bacteria that are essential for development but vary greatly between local habitats

Mosquitoes are insects of interest because several species vector disease-causing pathogens to humans and other vertebrates. We previously reported that mosquitoes from long-term laboratory cultures require living bacteria in their gut to develop, but development does not depend on particular species of bacteria. Here, we focused on three distinct but interrelated areas of study to better understand the role of bacteria in mosquito development by studying field and laboratory populations of Aedes aegypti, Aedes albopictus and Culex quinquefasciatus from the southeastern United States. Sequence analysis of bacterial 16S rRNA gene amplicons showed that bacterial community composition differed substantially in larvae from different collection sites, whereas larvae from the same site shared similarities. Although previously unknown to be infected by Wolbachia, results also indicated that Ae. aegypti from one field site hosted a dual infection. Regardless of collection site or factors like Wolbachia infection, however, each mosquito species required living bacteria in their digestive tract to develop. Results also identified several concerns in using antibiotics to eliminate the bacterial community in larvae in order to study its developmental consequences. Altogether, our results indicate that several mosquito species require living bacteria for development. We also hypothesize these species do not rely on particular bacteria because larvae do not reliably encounter the same bacteria in the aquatic habitats they develop in.

Rearing the Fruit Fly Drosophila melanogaster Under Axenic and Gnotobiotic Conditions

The influence of microbes on myriad animal traits and behaviors has been increasingly recognized in recent years. The fruit fly Drosophila melanogaster is a model for understanding microbial interactions with animal hosts, facilitated by approaches to rear large sample sizes of Drosophila under microorganism-free (axenic) conditions, or with defined microbial communities (gnotobiotic). This work outlines a method for collection of Drosophila embryos, hypochlorite dechorionation and sterilization, and transfer to sterile diet. Sterilized embryos are transferred to sterile diet in 50 ml centrifuge tubes, and developing larvae and adults remain free of any exogenous microbes until the vials are opened. Alternatively, flies with a defined microbiota can be reared by inoculating sterile diet and embryos with microbial species of interest. We describe the introduction of 4 bacterial species to establish a representative gnotobiotic microbiota in Drosophila. Finally, we describe approaches for confirming bacterial community composition, including testing if axenic Drosophila remain bacteria-free into adulthood.

Impact of gut microbiota on the fly's germ line

Unlike vertically transmitted endosymbionts, which have broad effects on their host's germ line, the extracellular gut microbiota is transmitted horizontally and is not known to influence the germ line. Here we provide evidence supporting the influence of these gut bacteria on the germ line of Drosophila melanogaster. Removal of the gut bacteria represses oogenesis, expedites maternal-to-zygotic-transition in the offspring and unmasks hidden phenotypic variation in mutants. We further show that the main impact on oogenesis is linked to the lack of gut Acetobacter species, and we identify the Drosophila Aldehyde dehydrogenase (Aldh) gene as an apparent mediator of repressed oogenesis in Acetobacter-depleted flies. The finding of interactions between the gut microbiota and the germ line has implications for reproduction, developmental robustness and adaptation.

The gut microbiota can play various roles in the host's physiology, but is not known to influence the germ line. Here, Elgart et al. show that certain extracellular gut bacteria can affect oogenesis and embryo development in the fruit fly.

Temporal changes of symbiont density and host fitness after rifampicin treatment in a whitefly of the Bemisia tabaci species complex

Microbial symbionts are essential or important partners to phloem-feeding insects. Antibiotics have been used to selectively eliminate symbionts from their host insects and establish host lines with or without certain symbionts for investigating functions of the symbionts. In this study, using the antibiotic rifampicin we attempted to selectively eliminate certain symbionts from a population of the Middle East-Asia Minor 1 whitefly of the Bemisia tabaci species complex, which harbors the primary symbiont "Candidatus Portiera aleyrodidarum" and two secondary symbionts "Candidatus Hamiltonella defensa" and Rickettsia. Neither the primary nor the secondary symbionts were completely depleted in the adults (F0) that fed for 48 h on a diet treated with rifampicin at concentrations of 1-100 μg/mL. However, both the primary and secondary symbionts were nearly completely depleted in the offspring (F1) of the rifampicin-treated adults. Although the F1 adults produced some eggs (F2), most of the eggs failed to hatch and none of them reached the second instar, and consequently the rifampicin-treated whitefly colony vanished at the F2 generation. Interestingly, quantitative polymerase chain reaction assays showed that in the rifampicin-treated whiteflies, the density of the primary symbiont was reduced at an obviously slower pace than the secondary symbionts. Mating experiments between rifampicin-treated and untreated adults demonstrated that the negative effects of rifampicin on host fitness were expressed when the females were treated by the antibiotic, and whether males were treated or not by the antibiotic had little contribution to the negative effects. These observations indicate that with this whitefly population it is not feasible to selectively eliminate the secondary symbionts using rifampicin without affecting the primary symbiont and establish host lines for experimental studies. However, the extinction of the whitefly colony at the second generation after rifampicin treatment indicates the potential of the antibiotic as a control agent of the whitefly pest.

The impacts of Wolbachia and the microbiome on mate choice in Drosophila melanogaster

Symbionts and parasites can manipulate their hosts' reproduction to their own benefit, profoundly influencing patterns of mate choice and evolution of the host population. Wolbachia is one of the most widespread symbionts among arthropods, and one that alters its hosts' reproduction in diverse and dramatic ways. While we are beginning to appreciate how Wolbachia's extreme manipulations of host reproduction can influence species diversification and reproductive isolation, we understand little about how symbionts and Wolbachia, in particular, may affect intrapopulation processes of mate choice. We hypothesized that the maternally transmitted Wolbachia would increase the attractiveness of its female hosts to further its own spread. We therefore tested the effects of Wolbachia removal and microbiome disruption on female attractiveness and male mate choice among ten isofemale lines of Drosophila melanogaster. We found variable effects of general microbiome disruption on female attractiveness, with indications that bacteria interact with hosts in a line-specific manner to affect female attractiveness. However, we found no evidence that Wolbachia influence female attractiveness or male mate choice among these lines. Although the endosymbiont Wolbachia can greatly alter the reproduction of their hosts in many species, there is no indication that they alter mate choice behaviours in D. melanogaster.

Uncovering effects of antibiotics on the host and microbiota using transkingdom gene networks

OBJECTIVE

Despite widespread use of antibiotics for the treatment of life-threatening infections and for research on the role of commensal microbiota, our understanding of their effects on the host is still very limited.

DESIGN

Using a popular mouse model of microbiota depletion by a cocktail of antibiotics, we analysed the effects of antibiotics by combining intestinal transcriptome together with metagenomic analysis of the gut microbiota. In order to identify specific microbes and microbial genes that influence the host phenotype in antibiotic-treated mice, we developed and applied analysis of the transkingdom network.

RESULTS

We found that most antibiotic-induced alterations in the gut can be explained by three factors: depletion of the microbiota; direct effects of antibiotics on host tissues and the effects of remaining antibiotic-resistant microbes. Normal microbiota depletion mostly led to downregulation of different aspects of immunity. The two other factors (antibiotic direct effects on host tissues and antibiotic-resistant microbes) primarily inhibited mitochondrial gene expression and amounts of active mitochondria, increasing epithelial cell death. By reconstructing and analysing the transkingdom network, we discovered that these toxic effects were mediated by virulence/quorum sensing in antibiotic-resistant bacteria, a finding further validated using in vitro experiments.

CONCLUSIONS

In addition to revealing mechanisms of antibiotic-induced alterations, this study also describes a new bioinformatics approach that predicts microbial components that regulate host functions and establishes a comprehensive resource on what, why and how antibiotics affect the gut in a widely used mouse model of microbiota depletion by antibiotics.

Differential temporal changes of primary and secondary bacterial symbionts and whitefly host fitness following antibiotic treatments

Where multiple symbionts coexist in the same host, the selective elimination of a specific symbiont may enable the roles of a given symbiont to be investigated. We treated the Mediterranean species of the whitefly Bemisia tabaci complex by oral delivery of the antibiotic rifampicin, and then examined the temporal changes of its primary symbiont "Candidatus Portiera aleyrodidarum" and secondary symbiont "Ca. Hamiltonella defensa" as well as host fitness for three generations. In adults treated with rifampicin (F0), the secondary symbiont was rapidly reduced, approaching complete disappearance as adults aged. In contrast, the primary symbiont was little affected until later in the adult life. In the offspring of these adults (F1), both symbionts were significantly reduced and barely detectable when the hosts reached the adult stage. The F1 adults laid few eggs (F2), all of which failed to hatch. Mating experiments illustrated that the negative effects of rifampicin on host fitness were exerted via female hosts but not males. This study provides the first evidence of differential temporal reductions of primary and secondary symbionts in whiteflies following an antibiotic treatment. Studies that disrupt functions of bacterial symbionts must consider their temporal changes.

Host genetic determinants of microbiota-dependent nutrition revealed by genome-wide analysis of Drosophila melanogaster

Animals bear communities of gut microorganisms with substantial effects on animal nutrition, but the host genetic basis of these effects is unknown. Here, we use Drosophila to demonstrate substantial among-genotype variation in the effects of eliminating the gut microbiota on five host nutritional indices (weight, and protein, lipid, glucose and glycogen contents); this includes variation in both the magnitude and direction of microbiota-dependent effects. Genome-wide associations to identify the genetic basis of the microbiota-dependent variation reveal polymorphisms in largely non-overlapping sets of genes associated with variation in the nutritional traits, including strong representation of conserved genes functioning in signaling. Key genes identified by the GWA study are validated by loss-of-function mutations that altered microbiota-dependent nutritional effects. We conclude that the microbiota interacts with the animal at multiple points in the signaling and regulatory networks that determine animal nutrition. These interactions with the microbiota are likely conserved across animals, including humans.

Environmental disruption of host-microbe co-adaptation as a potential driving force in evolution

The microbiome is known to have a profound effect on the development, physiology and health of its host. Whether and how it also contributes to evolutionary diversification of the host is, however, unclear. Here we hypothesize that disruption of the microbiome by new stressful environments interferes with host-microbe co-adaptation, contributes to host destabilization, and can drive irreversible changes in the host prior to its genetic adaptation. This hypothesis is based on three presumptions: (1) the microbiome consists of heritable partners which contribute to the stability (canalization) of host development and physiology in frequently encountered environments, (2) upon encountering a stressful new environment, the microbiome adapts much faster than the host, and (3) this differential response disrupts cooperation, contributes to host destabilization and promotes reciprocal changes in the host and its microbiome. This dynamic imbalance relaxes as the host and its microbiome establish a new equilibrium state in which they are adapted to one another and to the altered environment. Over long time in this new environment, the changes in the microbiome contribute to the canalization of the altered state. This scenario supports stability of the adapted patterns, while promoting variability which may be beneficial in new stressful conditions, thus allowing the organism to balance stability and flexibility based on contextual demand. Additionally, interaction between heritable microbial and epigenetic/physiological changes can promote new outcomes which persist over a wide range of timescales. A sufficiently persistent stress can further induce irreversible changes in the microbiome which may permanently alter the organism prior to genetic changes in the host. Epigenetic and microbial changes therefore provide a potential infrastructure for causal links between immediate responses to new environments and longer-term establishment of evolutionary adaptations.