scholarly journals Noninvasive Analysis of Microbiome Dynamics in the Fruit Fly Drosophila melanogaster

2013 ◽  
Vol 79 (22) ◽  
pp. 6984-6988 ◽  
Author(s):  
Christine Fink ◽  
Fabian Staubach ◽  
Sven Kuenzel ◽  
John F. Baines ◽  
Thomas Roeder
Keyword(s):  
Drosophila Melanogaster ◽  
Microbial Communities ◽  
Time Course ◽  
Bacterial Species ◽  
Single Point ◽  
Fruit Fly ◽  
Model Organisms ◽  
Full Potential ◽  
Content Type ◽  
Noninvasive Analysis

ABSTRACTThe diversity and structure of the intestinal microbial community has a strong influence on life history. To understand how hosts and microbes interact, model organisms with comparatively simple microbial communities, such as the fruit fly (Drosophila melanogaster), offer key advantages. However, studies of theDrosophilamicrobiome are limited to a single point in time, because flies are typically sacrificed for DNA extraction. In order to test whether noninvasive approaches, such as sampling of fly feces, could be a means to assess fly-associated communities over time on the same cohort of flies, we compared the microbial communities of fly feces, dissected fly intestines, and whole flies across three differentDrosophilastrains. Bacterial species identified in either whole flies or isolated intestines were reproducibly found in feces samples. Although the bacterial communities of feces and intestinal samples were not identical, they shared similarities and obviously the same origin. In contrast to material from whole flies and intestines, feces samples were not compromised byWolbachiaspp. infections, which are widespread in laboratory and wild strains. In a proof-of-principle experiment, we showed that simple nutritional interventions, such as a high-fat diet or short-term starvation, had drastic and long-lasting effects on the micobiome. Thus, the analysis of feces can supplement the toolbox for microbiome studies inDrosophila, unleashing the full potential of such studies in time course experiments where multiple samples from single populations are obtained during aging, development, or experimental manipulations.

scholarly journals The Host as the Driver of the Microbiota in the Gut and External Environment of Drosophila melanogaster

2015 ◽  
Vol 81 (18) ◽  
pp. 6232-6240 ◽  
Author(s):  
Adam C.-N. Wong ◽  
Yuan Luo ◽  
Xiangfeng Jing ◽  
Soeren Franzenburg ◽  
Alyssa Bost ◽  
...  
Keyword(s):  
Drosophila Melanogaster ◽  
Microbial Communities ◽  
External Environment ◽  
Fruit Fly ◽  
Free Food ◽  
Content Type ◽  
Continuous Contact ◽  
Independent Effects ◽  
Antagonistic Interactions ◽  
Coordinated Effects

ABSTRACTMost associations between animals and their gut microbiota are dynamic, involving sustained transfer of food-associated microbial cells into the gut and shedding of microorganisms into the external environment with feces, but the interacting effects of host and microbial factors on the composition of the internal and external microbial communities are poorly understood. This study on laboratory cultures of the fruit flyDrosophila melanogasterreared in continuous contact with their food revealed time-dependent changes of the microbial communities in the food that were strongly influenced by the presence and abundance ofDrosophila. When germfreeDrosophilaeggs were aseptically added to nonsterile food, the microbiota in the food and flies converged to a composition dramatically different from that in fly-free food, showing thatDrosophilahas microbiota-independent effects on the food microbiota. The microbiota in both the flies that developed from unmanipulated eggs (bearing microorganisms) and the associated food was dominated by the bacteria most abundant on the eggs, demonstrating effective vertical transmission via surface contamination of eggs. Food coinoculated with a four-species defined bacterial community ofAcetobacterandLactobacillusspecies revealed the progressive elimination ofLactobacillusfrom the food bearing few or noDrosophila, indicating the presence of antagonistic interactions betweenAcetobacterandLactobacillus. Drosophilaat high densities ameliorated theAcetobacter/Lactobacillusantagonism, enablingLactobacillusto persist. This study withDrosophilademonstrates how animals can have major, coordinated effects on the composition of microbial communities in the gut and immediate environment.

scholarly journals Impact of Substratum Surface on Microbial Community Structure and Treatment Performance in Biological Aerated Filters

2013 ◽  
Vol 80 (1) ◽  
pp. 177-183 ◽  
Author(s):  
Lavane Kim ◽  
Eulyn Pagaling ◽  
Yi Y. Zuo ◽  
Tao Yan
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Bacterial Species ◽  
Community Analysis ◽  
Microbial Community Analysis ◽  
Rrna Gene ◽  
Content Type ◽  
Property Change ◽  
And Control ◽  
Start Ups

ABSTRACTThe impact of substratum surface property change on biofilm community structure was investigated using laboratory biological aerated filter (BAF) reactors and molecular microbial community analysis. Two substratum surfaces that differed in surface properties were created via surface coating and used to develop biofilms in test (modified surface) and control (original surface) BAF reactors. Microbial community analysis by 16S rRNA gene-based PCR-denaturing gradient gel electrophoresis (DGGE) showed that the surface property change consistently resulted in distinct profiles of microbial populations during replicate reactor start-ups. Pyrosequencing of the bar-coded 16S rRNA gene amplicons surveyed more than 90% of the microbial diversity in the microbial communities and identified 72 unique bacterial species within 19 bacterial orders. Among the 19 orders of bacteria detected,BurkholderialesandRhodocyclalesof theBetaproteobacteriaclass were numerically dominant and accounted for 90.5 to 97.4% of the sequence reads, and their relative abundances in the test and control BAF reactors were different in consistent patterns during the two reactor start-ups. Three of the five dominant bacterial species also showed consistent relative abundance changes between the test and control BAF reactors. The different biofilm microbial communities led to different treatment efficiencies, with consistently higher total organic carbon (TOC) removal in the test reactor than in the control reactor. Further understanding of how surface properties affect biofilm microbial communities and functional performance would enable the rational design of new generations of substrata for the improvement of biofilm-based biological treatment processes.

scholarly journals Deterioration-Associated Microbiome of Stone Monuments: Structure, Variation, and Assembly

2018 ◽  
Vol 84 (7) ◽  
Author(s):  
Qiang Li ◽  
Bingjian Zhang ◽  
Xiaoru Yang ◽  
Qinya Ge
Keyword(s):  
Microbial Communities ◽  
Large Scale ◽  
Imaging Techniques ◽  
Bacterial Species ◽  
Species Abundance ◽  
Population Variation ◽  
Structure Variation ◽  
Content Type ◽  
Stone Monuments ◽  
Stone Deterioration

ABSTRACTResearch on the microbial communities that colonize stone monuments may provide a new understanding of stone biodeterioration and microbe-induced carbonate precipitation. This work investigated the seasonal variation of microbial communities in 2016 and 2017, as well as its effects on stone monuments. We determined the bacterial and fungal compositions of 12 samples from four well-separated geographic locations by using 16S rRNA and internal transcribed spacer gene amplicon sequencing.Cyanobacteriaand Ascomycota were the predominant bacterial and fungal phyla, respectively, and differences in species abundance among our 12 samples and 2 years showed no consistent temporal or spatial trends. Alpha diversity, estimated by Shannon and Simpson indices, revealed that an increase or decrease in bacterial diversity corresponded to a decrease or increase in the fungal community from 2016 to 2017. Large-scale association analysis identified potential bacteria and fungi correlated with stone deterioration. Functional prediction revealed specific pathways and microbiota associated with stone deterioration. Moreover, a culture-dependent technique was used to identify microbial isolates involved in biodeterioration and carbonatogenesis; 64% of 85 bacterial isolates caused precipitation of carbonates in biomineralization assays. Imaging techniques including scanning electron microscopy with energy-dispersive spectroscopy, X-ray diffraction, and fluorescence imaging identified CaCO3crystals as calcite and vaterite. Although CaCO3precipitation induced by bacteria often has esthetically deleterious impacts on stone monuments, this process may potentially serve as a novel, environmentally friendly bacterial self-inoculation approach to the conservation of stone.IMPORTANCEComprehensive analyses of the microbiomes associated with the deterioration of stone monuments may contribute to the understanding of mechanisms of deterioration, as well as to the identification of potentially beneficial or undesirable microbial communities and their genomic pathways. In our study, we demonstrated thatCyanobacteriawas the predominant bacterial phylum and exhibited an increase from 2016 to 2017, whileProteobacteriashowed a decreasing trend. Apart from esthetic deterioration caused by cyanobacteria and fungi, white plaque, which is composed mainly of CaCO3and is probably induced byCrossiellaandCyanobacteria, was also considered to be another threat to stone monuments. We showed that there was no significant correlation between microbial population variation and geographic location. Specific functional genes and pathways were also enriched in particular bacterial species. The CaCO3precipitation induced by an indigenous community of carbonatogenic bacteria also provides a self-inoculation approach for the conservation of stone.

scholarly journals Improved Production of a Heterologous Amylase in Saccharomyces cerevisiae by Inverse Metabolic Engineering

2014 ◽  
Vol 80 (17) ◽  
pp. 5542-5550 ◽  
Author(s):  
Zihe Liu ◽  
Lifang Liu ◽  
Tobias Österlund ◽  
Jin Hou ◽  
Mingtao Huang ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Metabolic Engineering ◽  
Secretory Pathway ◽  
Single Point ◽  
Point Mutations ◽  
Model Organisms ◽  
Cell Factory ◽  
Amylase Secretion ◽  
Content Type ◽  
Inverse Metabolic Engineering

ABSTRACTThe increasing demand for industrial enzymes and biopharmaceutical proteins relies on robust production hosts with high protein yield and productivity. Being one of the best-studied model organisms and capable of performing posttranslational modifications, the yeastSaccharomyces cerevisiaeis widely used as a cell factory for recombinant protein production. However, many recombinant proteins are produced at only 1% (or less) of the theoretical capacity due to the complexity of the secretory pathway, which has not been fully exploited. In this study, we applied the concept of inverse metabolic engineering to identify novel targets for improving protein secretion. Screening that combined UV-random mutagenesis and selection for growth on starch was performed to find mutant strains producing heterologous amylase 5-fold above the level produced by the reference strain. Genomic mutations that could be associated with higher amylase secretion were identified through whole-genome sequencing. Several single-point mutations, including an S196I point mutation in theVTA1gene coding for a protein involved in vacuolar sorting, were evaluated by introducing these to the starting strain. By applying this modification alone, the amylase secretion could be improved by 35%. As a complement to the identification of genomic variants, transcriptome analysis was also performed in order to understand on a global level the transcriptional changes associated with the improved amylase production caused by UV mutagenesis.

scholarly journals Chromatin Structure and Function in Mosquitoes

2020 ◽  
Vol 11 ◽  
Author(s):  
Óscar M. Lezcano ◽  
Miriam Sánchez-Polo ◽  
José L. Ruiz ◽  
Elena Gómez-Díaz
Keyword(s):  
Drosophila Melanogaster ◽  
Regulatory Networks ◽  
Genome Structure ◽  
Nuclear Architecture ◽  
Model Organism ◽  
Fruit Fly ◽  
Model Organisms ◽  
Epigenetic Mechanisms ◽  
West Nile Fever ◽  
And Function

The principles and function of chromatin and nuclear architecture have been extensively studied in model organisms, such as Drosophila melanogaster. However, little is known about the role of these epigenetic processes in transcriptional regulation in other insects including mosquitoes, which are major disease vectors and a worldwide threat for human health. Some of these life-threatening diseases are malaria, which is caused by protozoan parasites of the genus Plasmodium and transmitted by Anopheles mosquitoes; dengue fever, which is caused by an arbovirus mainly transmitted by Aedes aegypti; and West Nile fever, which is caused by an arbovirus transmitted by Culex spp. In this contribution, we review what is known about chromatin-associated mechanisms and the 3D genome structure in various mosquito vectors, including Anopheles, Aedes, and Culex spp. We also discuss the similarities between epigenetic mechanisms in mosquitoes and the model organism Drosophila melanogaster, and advocate that the field could benefit from the cross-application of state-of-the-art functional genomic technologies that are well-developed in the fruit fly. Uncovering the mosquito regulatory genome can lead to the discovery of unique regulatory networks associated with the parasitic life-style of these insects. It is also critical to understand the molecular interactions between the vectors and the pathogens that they transmit, which could hold the key to major breakthroughs on the fight against mosquito-borne diseases. Finally, it is clear that epigenetic mechanisms controlling mosquito environmental plasticity and evolvability are also of utmost importance, particularly in the current context of globalization and climate change.

scholarly journals Drosophila melanogaster: A Veritable Genetic Tool and in vivo Model for Human Alzheimer’s Disease

2019 ◽  
pp. 1-9
Author(s):  
Oluwatosin Imoleayo, Oyeniran
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Drosophila Melanogaster ◽  
Molecular Mechanisms ◽  
Fruit Fly ◽  
Human Diseases ◽  
Model Organisms ◽  
In Vivo Model ◽  
Brain Functions ◽  
Drosophila Models

The rise in the cases of neurodegenerative diseases, such as the familial forms of Alzheimer’s disease is worrisome and a burden to many societies in our ever-increasing world. Due to the complexity in the nature of the brain and spinal cord characterized by an extremely organized network of neuronal cells, there is a need to answer scientific inquiries in uncomplicated, though similar, systems. Drosophila melanogaster (fruit-fly) is a well-studied and easily managed genetic model organism used for discerning the molecular mechanisms of many human diseases. There are strong conservations of several basic biological, physiological and neurological features between D. melanogaster and mammals, as about 75% of all human disease-causing genes are considered to possess a functional homolog in the fruit-fly. The development of Drosophila models of several neurodegenerative disorders via developed transgenic technologies has presented spectacular similarities to human diseases. An advantage that the fruit-fly has over other model organisms, such as the mouse, is its comparatively brief lifespan, which allows complex inquiries about brain functions to be addressed more quickly. Furthermore, there have been steady increases in understanding the pathophysiological basis of many neurological disorders via genetic screenings with the aid of Drosophila models. This review presents a widespread summary of the fruit-fly models relevant to Alzheimer’s disease, and highlight important genetic modifiers that have been recognized using this model.

scholarly journals Microbiota Influences Fitness and Timing of Reproduction in the Fruit Fly Drosophila melanogaster

2021 ◽  
Author(s):  
Melinda K. Matthews ◽  
Jaanna Malcolm ◽  
John M. Chaston
Keyword(s):  
Drosophila Melanogaster ◽  
Life History ◽  
Microbial Communities ◽  
Life History Traits ◽  
Fruit Fly ◽  
Clear Definition ◽  
Animal Life ◽  
Timing Of Reproduction ◽  
The Past ◽  
Definition Of

The ability of associated microorganisms (“microbiota”) to influence animal life history traits has been recognized and investigated, especially in the past 2 decades. For many microbial communities, there is not always a clear definition of whether the microbiota or its members are beneficial, pathogenic, or relatively neutral to their hosts’ fitness.

scholarly journals Respiratory Kinetics of Marine Bacteria Exposed to Decreasing Oxygen Concentrations

2015 ◽  
Vol 82 (5) ◽  
pp. 1412-1422 ◽  
Author(s):  
Xianzhe Gong ◽  
Emilio Garcia-Robledo ◽  
Andreas Schramm ◽  
Niels Peter Revsbech
Keyword(s):  
Cell Size ◽  
Respiration Rate ◽  
Time Course ◽  
Bacterial Species ◽  
Content Type ◽  
Terminal Oxidases ◽  
Diffusion Limited ◽  
Wide Range ◽  
Dinoroseobacter Shibae ◽  
Kinetics Of

ABSTRACTDuring aerobic respiration, microorganisms consume oxygen (O2) through the use of different types of terminal oxidases which have a wide range of affinities for O2. TheKmvalues for O2of these enzymes have been determined to be in the range of 3 to 200 nmol liter−1. In this study, we examined the time course of development of aerobic respiratory kinetics of four marine bacterial species (Dinoroseobacter shibae,Roseobacter denitrificans,Idiomarina loihiensis, andMarinobacter daepoensis) during exposure to decreasing O2concentrations. The genomes of all four species have genes for both high-affinity and low-affinity terminal oxidases. The respiration rate of the bacteria was measured by the use of extremely sensitive optical trace O2sensors (range, 1 to 1,000 nmol liter−1). Three of the four isolates exhibited apparentKmvalues of 30 to 60 nmol liter−1when exposed to submicromolar O2concentrations, but a decrease to values below 10 nmol liter−1was observed when the respiration rate per cell was lowered and the cell size was decreased due to starvation. The fourth isolate did not reach a low respiration rate per cell during starvation and exhibited apparentKmvalues of about 20 nmol liter−1throughout the experiment. The results clearly demonstrate not only that enzyme kinetics may limit O2uptake but also that even individual cells may be diffusion limited and that this diffusion limitation is the most pronounced at high respiration rates. A decrease in cell size by starvation, due to limiting organic carbon, and thereby more efficient diffusion uptake may also contribute to lower apparentKmvalues.

scholarly journals A modified gas-trapping method for high-throughput metabolic experiments in Drosophila melanogaster

BioTechniques ◽  
2019 ◽  
Vol 67 (3) ◽  
pp. 123-125 ◽  
Author(s):  
Deanne Francis ◽  
James R Krycer ◽  
Gregory J Cooney ◽  
David E James
Keyword(s):  
Drosophila Melanogaster ◽  
High Throughput ◽  
Time Course ◽  
Genetic Manipulation ◽  
Cost Effective ◽  
Fruit Fly ◽  
Experimental Diet ◽  
Precise Control ◽  
Gas Trapping ◽  
Trapping Method

Metabolism is often studied in animal models, with the Drosophila melanogaster fruit fly model offering ease of genetic manipulation and high-throughput studies. Fly metabolism is typically studied using end-point assays that are simple but destructive, and do not provide information on the utilization of specific nutrients. To address these limitations, we adapted existing gas-trapping protocols to measure the oxidation of radiolabeled substrates (such as glucose) in multi-well plates. This protocol is cost effective, simple, and offers precise control over experimental diet and measurement time, thus being amenable to high-throughput studies. Furthermore, it is nondestructive, enabling time-course experiments and multiplexing with other parameters. Overall, this protocol is useful for merging fly genetics with metabolic studies to understand whole organism responses to different macronutrients.

scholarly journals Rest is Required to Learn an Appetitively-Reinforced Operant Task in Drosophila

2020 ◽  
Author(s):  
Timothy D. Wiggin ◽  
Yung-Yi Hsiao ◽  
Jeffrey B. Liu ◽  
Robert Huber ◽  
Leslie C. Griffith
Keyword(s):  
Drosophila Melanogaster ◽  
Operant Conditioning ◽  
Food Reward ◽  
Molecular Mechanisms ◽  
Genetic Model ◽  
Fruit Fly ◽  
Model Organisms ◽  
Neural Basis ◽  
Operant Task ◽  
Insight Into

ABSTRACTMaladaptive operant conditioning contributes to development of neuropsychiatric disorders. Candidate genes have been identified that contribute to this maladaptive plasticity, but the neural basis of operant conditioning in genetic model organisms remains poorly understood. The fruit fly Drosophila melanogaster is a versatile genetic model organism that readily forms operant associations with punishment stimuli. However, operant conditioning with a food reward has not been demonstrated in flies, limiting the types of neural circuits that can be studied. Here we present the first sucrose-reinforced operant conditioning paradigm for flies. Flies of both sexes walk along a Y-shaped track with reward locations at the terminus of each hallway. When flies turn in the reinforced direction at the center of the track, sucrose is presented at the end of the hallway. Only flies that rest during training show evidence of learning the reward contingency. Flies rewarded independently of their behavior do not form a learned association but have the same amount of rest as trained flies, showing that rest is not driven by learning. Optogenetically-induced rest does not promote learning, indicating that rest is not sufficient for learning the operant task. We validated the sensitivity of this assay to detect the effect of genetic manipulations by testing the classic learning mutant dunce. Dunce flies are learning impaired in the Y-Track task, indicating a likely role for cAMP in the operant coincidence detector. This novel training paradigm will provide valuable insight into the molecular mechanisms of disease and the link between sleep and learning.SIGNIFICANCE STATEMENTOperant conditioning and mental health are deeply intertwined: maladaptive conditioning contributes to many pathologies, while therapeutic operant conditioning is a frequently used tool in talk therapy. Unlike drug interventions which target molecules or mechanisms, it is not known how operant conditioning changes the brain to promote wellness or distress. To gain mechanistic insight into how this form of learning works, we developed a novel operant training task for the fruit fly Drosophila melanogaster. We made three key discoveries. First, flies are able to learn an operant task to find food reward. Second, rest during training is necessary for learning. Third, the dunce gene is necessary for both classical and operant conditioning in flies, indicating that they may share molecular mechanisms.

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