Development Of Fruit Fly Research Articles

Body plan evolvability: The role of variability in gene regulatory networks.

Recent computational modeling of early fruit fly (Drosophila) development has characterized the degree to which gene regulation networks can be robust to natural variability. In the first few hours of development, broad spatial gradients of maternally derived transcription factors activate embryonic gap genes. These gap patterns determine the subsequent segmented insect body plan through pair-rule gene expression. Gap genes are expressed with greater spatial precision than the maternal patterns. Computational modeling of the gap-gap regulatory interactions provides a mechanistic understanding for this robustness to maternal variability in wild-type (WT) patterning. A long-standing question in evolutionary biology has been how a system which is robust, such as the developmental program creating any particular species' body plan, is also evolvable, i.e. how can a system evolve or speciate, if the WT form is strongly buffered and protected? In the present work, we use the WT model to explore the breakdown of such Waddington-type 'canalization'. What levels of variability will push the system out of the WT form; are there particular pathways in the gene regulatory mechanism which are more susceptible to losing the WT form; and when robustness is lost, what types of forms are most likely to occur (i.e. what forms lie near the WT)? Manipulating maternal effects in several different pathways, we find a common gap 'peak-to-step' pattern transition in the loss of WT.We discuss these results in terms of the evolvability of insect segmentation, and in terms of experimental perturbations and mutations which could test the model predictions. We conclude by discussing the prospects for using continuum models of pattern dynamics to investigate a wider range of evo-devo problems.

Airway specific deregulation of asthma-related serpins impairs tracheal architecture and oxygenation in D. melanogaster

Serine proteases are important regulators of airway epithelial homeostasis. Altered serum or cellular levels of two serpins, Scca1 and Spink5, have been described for airway diseases but their function beyond antiproteolytic activity is insufficiently understood. To close this gap, we generated fly lines with overexpression or knockdown for each gene in the airways. Overexpression of both fly homologues of Scca1 and Spink5 induced the growth of additional airway branches, with more variable results for the respective knockdowns. Dysregulation of Scca1 resulted in a general delay in fruit fly development, with increases in larval and pupal mortality following overexpression of this gene. In addition, the morphological changes in the airways were concomitant with lower tolerance to hypoxia. In conclusion, the observed structural changes of the airways evidently had a strong impact on the airway function in our model as they manifested in a lower physical fitness of the animals. We assume that this is due to insufficient tissue oxygenation. Future work will be directed at the identification of key molecular regulators following the airway-specific dysregulation of Scca1 and Spink5 expression.

Inheritance of H3K9 methylation regulates genome architecture in Drosophila early embryos

Constitutive heterochromatin is essential for transcriptional silencing and genome integrity. The establishment of constitutive heterochromatin in early embryos and its role in early fruitfly development are unknown. Lysine 9 trimethylation of histone H3 (H3K9me3) and recruitment of its epigenetic reader, heterochromatin protein 1a (HP1a), are hallmarks of constitutive heterochromatin. Here, we show that H3K9me3 is transmitted from the maternal germline to the next generation. Maternally inherited H3K9me3, and the histone methyltransferases (HMT) depositing it, are required for the organization of constitutive heterochromatin: early embryos lacking H3K9 methylation display de-condensation of pericentromeric regions, centromere-centromere de-clustering, mitotic defects, and nuclear shape irregularities, resulting in embryo lethality. Unexpectedly, quantitative CUT&Tag and 4D microscopy measurements of HP1a coupled with biophysical modeling revealed that H3K9me2/3 is largely dispensable for HP1a recruitment. Instead, the main function of H3K9me2/3 at this developmental stage is to drive HP1a clustering and subsequent heterochromatin compaction. Our results show that HP1a binding to constitutive heterochromatin in the absence of H3K9me2/3 is not sufficient to promote proper embryo development and heterochromatin formation. The loss of H3K9 HMTs and H3K9 methylation alters genome organization and hinders embryonic development.

NMR chemical shift assignment of Drosophila odorant binding protein 44a in complex with 8(Z)-eicosenoic acid

The odorant binding protein, OBP44a is one of the most abundant proteins expressed in the brain of the developing fruit fly Drosophila melanogaster. Its cellular function has not yet been determined. The OBP family of proteins is well established to recognize hydrophobic molecules. In this study, NMR is employed to structurally characterize OBP44a. NMR chemical shift perturbation measurements confirm that OBP44a binds to fatty acids. Complete assignments of the backbone chemical shifts and secondary chemical shift analysis demonstrate that the apo state of OBP44a is comprised of six α-helices. Upon binding 8(Z)-eicosenoic acid (8(Z)-C20:1), the OBP44a C-terminal region undergoes a conformational change, from unstructured to α-helical. In addition to C-terminal restructuring upon ligand binding, some hydrophobic residues show dramatic chemical shift changes. Surprisingly, several charged residues are also strongly affected by lipid binding. Some of these residues could represent key structural features that OBP44a relies on to perform its cellular function. The NMR chemical shift assignment is the first step towards characterizing the structure of OBP44a and how specific residues might play a role in lipid binding and release. This information will be important in deciphering the biological function of OBP44a during fly brain development.

Biochemical characterization of the Drosophila insulin receptor kinase and longevity-associated mutants.

Drosophila melanogaster (fruit fly) insulin receptor (D-IR) is highly homologous to the human counterpart. Like the human pathway, D-IR responds to numerous insulin-like peptides to activate cellular signals that regulate growth, development, and lipid metabolism in fruit flies. Allelic mutations in the D-IR kinase domain elevate life expectancy in fruit flies. We developed a robust heterologous expression system to express and purify wild-type and longevity-associated mutant D-IR kinase domains to investigate enzyme kinetics and substrate specificities. D-IR exhibits remarkable similarities to the human insulin receptor kinase domain but diverges in substrate preferences. We show that longevity-associated mutations reduce D-IR catalytic activity. Deletion of the unique kinase insert domain portion or mutations proximal to activating tyrosines do not influence kinase activity, suggesting their potential role in substrate recruitment and downstream signaling. Through biochemical investigations, this study enhances our comprehension of D-IR's role in Drosophila physiology, complementing genetic studies and expanding our knowledge on the catalytic functions of this conserved signaling pathway.

Synergist response of the Peach fruit fly, Bactrocera zonata (Saunders) to some ammonium based proteinaceous food bait attractants

BackgroundUnder the family Tephritidae, Bactrocera zonata (Saunders) is a serious pest, attacking fruits and vegetables causing large quantitative and qualitative damages throughout the world. Fruit flies require proteinaceous food for sexual maturation and egg development. Therefore, food bait attractants are frequently utilized for fruit fly detection, monitoring, mass trapping, and control. Using a Y-shape olfactometer (behavioral tests), we selected the best synthetic proteinaceous food bait attractants to volatiles identified by fruit fly antennae. The responses of B. zonata adults, male and female, to some ammonium compounds (ammonium acetate (AA), trimethylamine (TMA), and putrescine) that were mixed with certain food attractants were evaluated under laboratory conditions. Using flies ranging in age from 5 to 30 days, possible mixtures were discovered that might be useful in developing fruit fly attractants for both males and females. So, four base baits were developed by mixing protein hydrolysate with jaggery, papaya powder, kachri powder, potassium hydroxide (KOH), and guava pulp. Finally, thirty-two (32) synthetic blends were developed when the above four base baits were mixed with synthetic attractants.ResultsThe olfactometer bioassay indicated that protein hydrolysate and jaggery-based baits were effective in attracting both male and female flies throughout their adult lives when combined with AA + putrescine (Bait 6) and AA + TMA + putrescine (Bait 8). Similarly, protein hydrolysate + guava pulp-based baits combined with AA + putrescine (Bait 6) and AA + TMA + putrescine (Bait 8) was effective in attracting both male and female flies from 5 to 30 days of age. The pH of all 32 synthetic blends was measured and ranged from 4.77 to 11.35.ConclusionsAccording to our observation, the variation in pH may be due to differences in chemical composition between the attractants and food constituents. The pH of protein bait attractants may be an important factor in the attraction efficiency of B. zonata males and females.

A diabetes-like biochemical and behavioural phenotype of Drosophila induced by predator stress.

Predation can have both lethal and non-lethal effects on prey. The non-lethal effects of predation can instil changes in prey life history, behaviour, morphology and physiology, causing adaptive evolution. The chronic stress caused by sustained predation on prey is comparable to chronic stress conditions in humans. Conditions like anxiety, depression, and post-traumatic stress syndrome have also been implicated in the development of metabolic disorders such as obesity and diabetes. In this study, we found that predator stress induced during larval development in fruit flies Drosophila melanogaster impairs carbohydrate metabolism by systemic inhibition of Akt protein kinase, which is a central regulator of glucose uptake. However, Drosophila grown with predators survived better under direct spider predation in the adult phase. Administration of metformin and 5-hydroxytryptophan (5-HTP), a precursor of the neurotransmitter serotonin, reversed these effects. Our results demonstrate a direct link between predator stress and metabolic impairment, suggesting that a diabetes-like biochemical phenotype may be adaptive in terms of survival and reproductive success. We provide a novel animal model to explore the mechanisms responsible for the onset of these metabolic disorders, which are highly prevalent in human populations.

Population Dynamic and Distribution of Bactrocera carambolae and Bactrocera dorsalis in Orchard Habitat in Different Geographical Areas

Fruitflies, particularly Bactrocera carambolae and Bactrocera dorsalis, are significant pests that have the potential to diminish the quality and quantity of agricultural products. They may live in diverse habitats, particularly in agroecosystem habitats. Orchard habitats offer a source of food and development for fruit flies like B. carambolae and B. dorsalis not only in Java, notably Majalengka Regency, but also in Lombok Island and West Nusa Tenggara. Consequently, the purpose of there search is to observe (1) The population dynamic of B. carambolae and B. dorsalis in the orchard habitat. (2) Distribution of fruit flies B. carambolae and B. dorsalis trapping results in the orchard habitat. (3) Analyzing the factors affecting the presence of the fruit fly species B. carambolae and B. dorsalis in the orchard habitat. Fruitflies were sampled using the trap method between December 2021 and March 2022. In the orchard habitat on the mangosteen fruit commodity, the results indicated that B. carambolae and B. dorsalis had the largest population densities. Additionally, orchard locations on Lombok Island had the highest population density. Furthermore, fruitflies are more prevalent in perennial crops than in annual ones due to higher population density. Perennial crops are the ideal conditions for fruit fly development as compared to seasonal crops.

Population Dynamic and Distribution of Bactrocera carambolae and Bactrocera dorsalis in Orchard Habitat in Different Geographical Areas

Fruitflies, particularly Bactrocera carambolae and Bactrocera dorsalis, are significant pests that have the potential to diminish the quality and quantity of agricultural products. They may live in diverse habitats, particularly in agroecosystem habitats. Orchard habitats offer a source of food and development for fruit flies like B. carambolae and B. dorsalis not only in Java, notably Majalengka Regency, but also in Lombok Island and West Nusa Tenggara. Consequently, the purpose of there search is to observe (1) The population dynamic of B. carambolae and B. dorsalis in the orchard habitat. (2) Distribution of fruit flies B. carambolae and B. dorsalis trapping results in the orchard habitat. (3) Analyzing the factors affecting the presence of the fruit fly species B. carambolae and B. dorsalis in the orchard habitat. Fruitflies were sampled using the trap method between December 2021 and March 2022. In the orchard habitat on the mangosteen fruit commodity, the results indicated that B. carambolae and B. dorsalis had the largest population densities. Additionally, orchard locations on Lombok Island had the highest population density. Furthermore, fruitflies are more prevalent in perennial crops than in annual ones due to higher population density. Perennial crops are the ideal conditions for fruit fly development as compared to seasonal crops.

Effects of Diet Composition on the Life-History Traits of Bactrocera Dorsalis (Hendel) (Diptera: Tephritidae)

Nutrient acquisition at the larval stage has significant impacts on the development, body weight, and fecundity of fruit flies. In this study, we examined the effects of diet composition on the life-history traits of the oriental fruit fly Bactrocera dorsalis (Hendel) (Diptera: Tephritidae). We reared the flies on four larval diets, namely three artificial diets, which had the main ingredients of sugar, brewer’s yeast, and preservatives; and one fruit-based diet, which had the main contents of ground guava, brewer’s yeast, and preservatives. The three artificial diets had varied yeast-to-sugar ratios (Y:S) of 5:1 in the protein-rich diet, 1.67:1 in the standard diet, and 1:3 in the sugar-rich diet. Differences in development time, pupal weight, adult weight, and fecundity of B. dorsalis were investigated. It was found that the development times of fruit flies on the protein-rich and fruit-based diets were shorter than those on the sugar-rich and standard diets. Pupae and adults in the fruit-based and standard diets were heavier than those from the protein-rich and sugar-rich diets. There was a strong effect of diet on the per-day fecundity whereby the flies in the fruit-based diet had the highest per-day fecundity, while the lowest per-day fecundity was in the sugar-rich diet. The per-day fecundity of the fruit flies on the standard and sugar-rich diets increased gradually from day 1 to day 15, while it decreased in the protein-rich and fruit-based diets.

Endocytosis at extremes: Formation and internalization of giant clathrin-coated pits under elevated membrane tension.

Internalization of clathrin-coated vesicles from the plasma membrane constitutes the major endocytic route for receptors and their ligands. Dynamic and structural properties of endocytic clathrin coats are regulated by the mechanical properties of the plasma membrane. Here, we used conventional fluorescence imaging and multiple modes of structured illumination microscopy (SIM) to image formation of endocytic clathrin coats within live cells and tissues of developing fruit fly embryos. High resolution in both spatial and temporal domains allowed us to detect and characterize distinct classes of clathrin-coated structures. Aside from the clathrin pits and plaques detected in distinct embryonic tissues, we report, for the first time, formation of giant coated pits (GCPs) that can be up to two orders of magnitude larger than the canonical pits. In cultured cells, we show that GCP formation is induced by increased membrane tension. GCPs take longer to grow but their mechanism of curvature generation is the same as the canonical pits. We also demonstrate that GCPs split into smaller fragments during internalization. Considering the supporting roles played by actin filament dynamics under mechanically stringent conditions that slow down completion of clathrin coats, we suggest that local changes in the coat curvature driven by actin machinery can drive splitting and internalization of GCPs.

A Thermodynamic Model for Water Activity and Redox Potential in Evolution and Development.

Reactions involving water and oxygen are basic features of geological and biological processes. To understand how life interacts with its environment requires monitoring interactions with [Formula: see text] and [Formula: see text] not only at timescales relevant to organismal growth but also over billions of years of geobiological evolution. Chemical transformations intrinsic to evolution and development were characterized by analyzing data from recent phylostratigraphic and proteomic studies. This two-stage analysis involves obtaining chemical metrics (carbon oxidation state and stoichiometric hydration state) from the elemental compositions of proteins followed by modeling the relative stabilities of target proteins against a proteomic background to infer thermodynamic parameters [oxygen fugacity, water activity, and virtual redox potential (Eh)]. The main results of this study are a rise in carbon oxidation state of proteins spanning the time of the Great Oxidation Event, a rise in virtual redox potential that coincides with the likely emergence of aerobic metabolism, and a rise in carbon oxidation state of proteins inferred from the transcriptome in late stages of Bacillus subtilis biofilm growth. Furthermore, stoichiometric hydration state of expressed proteins decreases through stages of biofilm development, drops at the same time as a drop in organismal water content during fruit fly development, and is lower for proteins with more recent gene ages, all of which support the inference of higher hydration potentials at earlier time points. These results show how the evolutionary and developmental dynamics of major chemical variables can be deciphered through thermodynamic analysis of proteins as chemical entities.

Effect of various depths of pupation on adult emergence of interspecific hybrid of Bactrocera carambolae and Bactrocera dorsalis

The depth of the pupation is one of the important factors in the success of fruit flies to become imago. The objective of this study was to evaluate the effect of soil depth on survival, normality dan development time of adult interspecific hybrids of Bactrocera carambolae (Drew & Hancock) and B. dorsalis (Hendel). The experiments were carried out in a laboratory consisting of seven depths of pupation treatments (4 cm, 10 cm, 20 cm, 30 cm, 40 cm, 50 cm, and 60 cm) with four replications. Soil depth had a significant, negative effect on the survival of the emergence and development time of B. dorsalis and B. carambolae hybrids. The emergence rate was found to decrease with the increase in pupation depth. The higher survival of the emergence of the hybrid occurred at a depth of 4 cm (95% ± 1.91) and 10 cm (86% ± 2.58), while the lower survival occurred at a depth of 50 cm (12% ± 1.63) and 60 cm (5% ± 3.79). Normal imagoes were found in all soil depths except in 60 cm depth, where all imagoes had abnormal morphology. Means of development time ranged from 8.88 to 10.63 days. The depth of pupation influences the duration of pupae development. The means of development time at a depth of 4–40 cm was similar, but at a depth of 50 cm and 60 cm, a significantly longer time of development were observed. for more effective fruit fly control, this study suggests burying rotten fruit in the soil at a depth of 50 cm or more as a preventive measure for the development of fruit flies.

Coffea arabica and C. canephora as host plants for fruit flies (Tephritidae) and implications for commercial fruit crop pest management

Because of the economic importance of fruit flies throughout the world, increased knowledge of alternative hosts of these pests is essential for integrated pest management in economically valuable fruit crops grown in regions where other host plant species such as coffee are also commonly cultivated. Therefore, the objective of this study was to evaluate the suitability of the cultivated coffee species Coffea arabica L. and Coffea canephora Pierre ex A. Froehner as hosts of fruit fly species in the state of Espírito Santo, Brazil, where both coffee species are widely grown in close proximity to a variety of economically valuable, and fruit fly susceptible, commercial fruit crops. Mature fruits of both coffee species were collected from 681 farms in 54 municipalities of Espírito Santo to identify the fruit fly species infesting coffee fruits and determine fruit fly infestation levels. Field and laboratory experiments were also conducted to study the relationships between coffee species and fruit fly infestation and development. Field infestation of coffee fruits by fruit flies was higher in C. arabica than in C. canephora (‘Conilon’). A total of 136.7 fruit fly pupae per kg of C. arabica fruits were found, in comparison to 5.4 pupae per kg of C. canephora fruits, and 97.1% of the adult fruit flies reared from coffee fruits emerged from C. arabica fruits. Ceratitis capitata (Wied.) and Anastrepha fraterculus (Wied.) were the most common fruit fly species associated with fruits of both coffee species. The quantity of C. capitata reared from C. arabica fruits (55.2 adults kg−1) was 15.3 times higher than the quantity reared from C. canephora fruits. Coffea arabica was also a much better host for A. fraterculus than C. canephora based on the number of adults reared from fruits. Results of this study indicate that C. arabica is a potential reservoir host of fruit flies, and therefore may play a significant role in fruit fly pest survival when preferred host fruits are lacking in winter months. This is the first study that compares the two major cultivated coffee species as potential hosts and sources of fruit flies, and indicates that integrated pest management (IPM) should be utilized to inhibit dispersal of fruit flies from C. arabica to nearby areas where commercial fruit crops are grown.

Roles of matrix metalloproteinases in development, immunology, and ovulation in fruit Fly (Drosophila).

Matrix metalloproteinase (MMP), a protease enzyme, participates in proteolytic cleavage of extracellular matrix proteins from Drosophila and mammals. But, recent studies have revealed other physiologically important roles of MMP in Drosophila. MMP contributes to cardioblast movement and distribution of collagen proteins during cardiogenesis in developing Drosophila. Tissue remodeling, especially tracheal development is also maintained by MMP. MMP regulates certain immunological functions in Drosophila such as wound repairing, plasmatocyte assemblage at the injured site of the basement membrane and glial response to axon degeneration in Drosophila nervous system. But, the contribution of MMP to tumor formation and metastasis in Drosophila has made it an interesting topic among researchers. Ovulation and egg laying are also found to be affected positively by MMP in Drosophila.

Real-time single-cell characterization of the eukaryotic transcription cycle reveals correlations between RNA initiation, elongation, and cleavage.

The eukaryotic transcription cycle consists of three main steps: initiation, elongation, and cleavage of the nascent RNA transcript. Although each of these steps can be regulated as well as coupled with each other, their in vivo dissection has remained challenging because available experimental readouts lack sufficient spatiotemporal resolution to separate the contributions from each of these steps. Here, we describe a novel application of Bayesian inference techniques to simultaneously infer the effective parameters of the transcription cycle in real time and at the single-cell level using a two-color MS2/PP7 reporter gene and the developing fruit fly embryo as a case study. Our method enables detailed investigations into cell-to-cell variability in transcription-cycle parameters as well as single-cell correlations between these parameters. These measurements, combined with theoretical modeling, suggest a substantial variability in the elongation rate of individual RNA polymerase molecules. We further illustrate the power of this technique by uncovering a novel mechanistic connection between RNA polymerase density and nascent RNA cleavage efficiency. Thus, our approach makes it possible to shed light on the regulatory mechanisms in play during each step of the transcription cycle in individual, living cells at high spatiotemporal resolution.

Precise levels of the Drosophila adaptor protein Dreadlocks maintain the size and stability of germline ring canals.

ABSTRACTIntercellular bridges are essential for fertility in many organisms. The developing fruit fly egg has become the premier model system to study intercellular bridges. During oogenesis, the oocyte is connected to supporting nurse cells by relatively large intercellular bridges, or ring canals. Once formed, the ring canals undergo a 20-fold increase in diameter to support the movement of materials from the nurse cells to the oocyte. Here, we demonstrate a novel role for the conserved SH2/SH3 adaptor protein Dreadlocks (Dock) in regulating ring canal size and structural stability in the germline. Dock localizes at germline ring canals throughout oogenesis. Loss of Dock leads to a significant reduction in ring canal diameter, and overexpression of Dock causes dramatic defects in ring canal structure and nurse cell multinucleation. The SH2 domain of Dock is required for ring canal localization downstream of Src64 (also known as Src64B), and the function of one or more of the SH3 domains is necessary for the strong overexpression phenotype. Genetic interaction and localization studies suggest that Dock promotes WASp-mediated Arp2/3 activation in order to determine ring canal size and regulate growth.This article has an associated First Person interview with the first author of the paper.

Formation of a Morphogen Gradient - Acceleration by Quantum Walks

The establishment of graded concentration distributions of certain signalling molecules, called morphogens, is crucial for the successful embryonic development of multicellular organisms. The morphogen system that has been studied in the greatest detail is the Bicoid (Bcd) gradient established during the early embryonic development of fruit flies and provides the embryo cells with the necessary positional information for the proper implementation of the body plan of the organism. Both continuous as well as discrete-state classical random-walk models fail to provide a completely satisfactory explanation of the dynamics of Bcd gradient formation within the developmentally relevant timescales. By presuming the existence of an arbitrary chirality degree of freedom that characterizes each Bcd molecule, we here therefore develop a discrete-time quantum walk model of the process. Our approach is based on the recent suggestion that high temperatures and random interactions need not necessarily destroy many-body quantum coherence. In this way we are led to a system of non-classical master equations bearing an interference term that can be numerically solved on a computer. Our analysis predicts a large value of diffusion rate for the Bcd system in the very early nuclear division cycles that needs to be verified experimentally. Additionally, with the chirality and position degrees of freedom at our disposal entanglement shows up as a natural consequence in the system. Taking inspiration from a very recent demonstration of the existence of entanglement phenomenon in a hot, strongly-interacting atomic system, the discussion takes the point of view that the emergence of geometry in the embryo system is consequence of quantum entanglement that needs further understanding and analysis.

Proteome-Wide Analysis of ADAR-Mediated Messenger RNA Editing during Fruit Fly Ontogeny

Adenosine-to-inosine RNA editing is an enzymatic post-transcriptional modification which modulates immunity and neural transmission in multicellular organisms. In particular, it involves editing of mRNA codons with the resulting amino acid substitutions. We identified such sites for developmental proteomes of Drosophila melanogaster at the protein level using available data for 15 stages of fruit fly development from egg to imago and 14 time points of embryogenesis. In total, 40 sites were obtained, each belonging to a unique protein, including four sites related to embryogenesis. The interactome analysis has revealed that the majority of the editing-recoded proteins were associated with synaptic vesicle trafficking and actomyosin organization. Quantitation data analysis suggested the existence of a phase-specific RNA editing regulation with yet unknown mechanisms. These findings supported the transcriptome analysis results, which showed that a burst in the RNA editing occurs during insect metamorphosis from pupa to imago. Finally, targeted proteomic analysis was performed to quantify editing-recoded and genomically encoded versions of five proteins in brains of larvae, pupae, and imago insects, which showed a clear tendency toward an increase in the editing rate for each of them. These results will allow a better understanding of the protein role in physiological effects of RNA editing.

Effects of microbial evolution dominate those of experimental host-mediated indirect selection.

Microbes ubiquitously inhabit animals and plants, often affecting their host’s phenotype. As a result, even in a constant genetic background, the host’s phenotype may evolve through indirect selection on the microbiome. ‘Microbiome engineering’ offers a promising novel approach for attaining desired host traits but has been attempted only a few times. Building on the known role of the microbiome on development in fruit flies, we attempted to evolve earlier-eclosing flies by selecting on microbes in the growth media. We carried out parallel evolution experiments in no- and high-sugar diets by transferring media associated with fast-developing fly lines over the course of four selection cycles. In each cycle, we used sterile eggs from the same inbred population, and assayed mean fly eclosion times. Ultimately, flies eclosed seven to twelve hours earlier, depending on the diet, but microbiome engineering had no effect relative to a random-selection control treatment. 16S rRNA gene sequencing showed that the microbiome did evolve, particularly in the no sugar diet, with an increase in Shannon diversity over time. Thus, while microbiome evolution did affect host eclosion times, these effects were incidental. Instead, any experimentally enforced selection effects were swamped by uncontrolled microbial evolution, likely resulting in its adaptation to the media. These results imply that selection on host phenotypes must be strong enough to overcome other selection pressures simultaneously operating on the microbiome. The independent evolutionary trajectories of the host and the microbiome may limit the extent to which indirect selection on the microbiome can ultimately affect host phenotype. Random-selection lines accounting for independent microbial evolution are essential for experimental microbiome engineering studies.