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Douglas AE. The Drosophila model for microbiome research. Lab Anim (NY) 2018; 47:157-164. [PMID: 29795158 DOI: 10.1038/s41684-018-0065-0] [Citation(s) in RCA: 102] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Accepted: 04/23/2018] [Indexed: 02/06/2023]
Abstract
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.
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Affiliation(s)
- Angela E Douglas
- Department of Entomology and Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA.
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A Metagenome-Wide Association Study and Arrayed Mutant Library Confirm Acetobacter Lipopolysaccharide Genes Are Necessary for Association with Drosophila melanogaster. G3-GENES GENOMES GENETICS 2018; 8:1119-1127. [PMID: 29487183 PMCID: PMC5873903 DOI: 10.1534/g3.117.300530] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
A metagenome wide association (MGWA) study of bacterial host association determinants in Drosophila predicted that LPS biosynthesis genes are significantly associated with host colonization. We were unable to create site-directed mutants for each of the predicted genes in Acetobacter, so we created an arrayed transposon insertion library using Acetobacter fabarum DsW_054 isolated from Drosophila. Creation of the A. fabarum DsW_054 gene knock-out library was performed by combinatorial mapping and Illumina sequencing of random transposon insertion mutants. Transposon insertion locations for 6,418 mutants were successfully mapped, including hits within 63% of annotated genes in the A. fabarum DsW_054 genome. For 45/45 members of the library, insertion sites were verified by arbitrary PCR and Sanger sequencing. Mutants with insertions in four different LPS biosynthesis genes were selected from the library to validate the MGWA predictions. Insertion mutations in two genes biosynthetically upstream of Lipid-A formation, lpxC and lpxB, show significant differences in host association, whereas mutations in two genes encoding LPS biosynthesis functions downstream of Lipid-A biosynthesis had no effect. These results suggest an impact of bacterial cell surface molecules on the bacterial capacity for host association. Also, the transposon insertion mutant library will be a useful resource for ongoing research on the genetic basis for Acetobacter traits.
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53
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Morimoto J, Simpson SJ, Ponton F. Direct and trans-generational effects of male and female gut microbiota in Drosophila melanogaster. Biol Lett 2017; 13:rsbl.2016.0966. [PMID: 28724687 PMCID: PMC5543016 DOI: 10.1098/rsbl.2016.0966] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2016] [Accepted: 06/12/2017] [Indexed: 02/03/2023] Open
Abstract
There is increasing evidence of the far-reaching effects of gut bacteria on physiological and behavioural traits, yet the fitness-related consequences of changes in the gut bacteria composition of sexually interacting individuals remain unknown. To address this question, we manipulated the gut microbiota of fruit flies, Drosophila melanogaster, by monoinfecting flies with either Acetobacter pomorum (AP) or Lactobacillus plantarum (LP). Re-inoculated individuals were paired in all treatment combinations. LP-infected males had longer mating duration and induced higher short-term offspring production in females compared with AP-infected males. Furthermore, females of either re-inoculation state mated with AP-infected males were more likely to have zero offspring after mating, suggesting a negative effect of AP on male fertility. Finally, we found that the effects of male and female gut bacteria interacted to modulate their daughters', but not sons' body mass, revealing a new trans-generational effect of parental gut microbiota. In conclusion, this study shows direct and trans-generational effects of the gut microbiota on mating and reproduction.
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Affiliation(s)
- Juliano Morimoto
- Department of Zoology, Edward Grey Institute, University of Oxford, South Parks Road, Oxford OX1 3PS, United Kingdom .,Charles Perkins Centre, University of Sydney, Camperdown, New South Wales 2006, Australia.,Programa de Pós-Graduação em Ecologia e Conservação, Federal University of Paraná, Curitiba 19031, CEP 81531-990, Brazil
| | - Stephen J Simpson
- Charles Perkins Centre, University of Sydney, Camperdown, New South Wales 2006, Australia.,School of Life and Environmental Sciences, University of Sydney, Sydney 2050, Australia
| | - Fleur Ponton
- Department of Biological Sciences, Macquarie University, North Ryde, New South Wales 2109, Australia
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54
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Starr AE, Deeke SA, Li L, Zhang X, Daoud R, Ryan J, Ning Z, Cheng K, Nguyen LVH, Abou-Samra E, Lavallée-Adam M, Figeys D. Proteomic and Metaproteomic Approaches to Understand Host–Microbe Interactions. Anal Chem 2017; 90:86-109. [DOI: 10.1021/acs.analchem.7b04340] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Amanda E. Starr
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Shelley A. Deeke
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Leyuan Li
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Xu Zhang
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Rachid Daoud
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - James Ryan
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Zhibin Ning
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Kai Cheng
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Linh V. H. Nguyen
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Elias Abou-Samra
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Mathieu Lavallée-Adam
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Daniel Figeys
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
- Molecular Architecture of Life Program, Canadian Institute for Advanced Research, Toronto, Ontario, M5G 1M1, Canada
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55
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Winans NJ, Walter A, Chouaia B, Chaston JM, Douglas AE, Newell PD. A genomic investigation of ecological differentiation between free-living and Drosophila-associated bacteria. Mol Ecol 2017; 26:4536-4550. [PMID: 28667798 DOI: 10.1111/mec.14232] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2017] [Revised: 05/31/2017] [Accepted: 06/08/2017] [Indexed: 12/27/2022]
Abstract
Various bacterial taxa have been identified both in association with animals and in the external environment, but the extent to which related bacteria from the two habitat types are ecologically and evolutionarily distinct is largely unknown. This study investigated the scale and pattern of genetic differentiation between bacteria of the family Acetobacteraceae isolated from the guts of Drosophila fruit flies, plant material and industrial fermentations. Genome-scale analysis of the phylogenetic relationships and predicted functions was conducted on 44 Acetobacteraceae isolates, including newly sequenced genomes from 18 isolates from wild and laboratory Drosophila. Isolates from the external environment and Drosophila could not be assigned to distinct phylogenetic groups, nor are their genomes enriched for any different sets of genes or category of predicted gene functions. In contrast, analysis of bacteria from laboratory Drosophila showed they were genetically distinct in their universal capacity to degrade uric acid (a major nitrogenous waste product of Drosophila) and absence of flagellar motility, while these traits vary among wild Drosophila isolates. Analysis of the competitive fitness of Acetobacter discordant for these traits revealed a significant fitness deficit for bacteria that cannot degrade uric acid in culture with Drosophila. We propose that, for wild populations, frequent cycling of Acetobacter between Drosophila and the external environment prevents genetic differentiation by maintaining selection for traits adaptive in both the gut and external habitats. However, laboratory isolates bear the signs of adaptation to persistent association with the Drosophila host under tightly defined environmental conditions.
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Affiliation(s)
- Nathan J Winans
- Department of Entomology, Cornell University, Ithaca, NY, USA
| | - Alec Walter
- Department of Biological Sciences, State University of New York at Oswego, Oswego, NY, USA
| | - Bessem Chouaia
- Department of Entomology, Cornell University, Ithaca, NY, USA
| | - John M Chaston
- Department of Entomology, Cornell University, Ithaca, NY, USA.,Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT, USA
| | - Angela E Douglas
- Department of Entomology, Cornell University, Ithaca, NY, USA.,Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Peter D Newell
- Department of Entomology, Cornell University, Ithaca, NY, USA.,Department of Biological Sciences, State University of New York at Oswego, Oswego, NY, USA
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56
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Trinder M, Daisley BA, Dube JS, Reid G. Drosophila melanogaster as a High-Throughput Model for Host-Microbiota Interactions. Front Microbiol 2017; 8:751. [PMID: 28503170 PMCID: PMC5408076 DOI: 10.3389/fmicb.2017.00751] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2017] [Accepted: 04/12/2017] [Indexed: 01/14/2023] Open
Abstract
Microbiota research often assumes that differences in abundance and identity of microorganisms have unique influences on host physiology. To test this concept mechanistically, germ-free mice are colonized with microbial communities to assess causation. Due to the cost, infrastructure challenges, and time-consuming nature of germ-free mouse models, an alternative approach is needed to investigate host–microbial interactions. Drosophila melanogaster (fruit flies) can be used as a high throughput in vivo screening model of host–microbiome interactions as they are affordable, convenient, and replicable. D. melanogaster were essential in discovering components of the innate immune response to pathogens. However, axenic D. melanogaster can easily be generated for microbiome studies without the need for ethical considerations. The simplified microbiota structure enables researchers to evaluate permutations of how each microbial species within the microbiota contribute to host phenotypes of interest. This enables the possibility of thorough strain-level analysis of host and microbial properties relevant to physiological outcomes. Moreover, a wide range of mutant D. melanogaster strains can be affordably obtained from public stock centers. Given this, D. melanogaster can be used to identify candidate mechanisms of host–microbe symbioses relevant to pathogen exclusion, innate immunity modulation, diet, xenobiotics, and probiotic/prebiotic properties in a high throughput manner. This perspective comments on the most promising areas of microbiota research that could immediately benefit from using the D. melanogaster model.
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Affiliation(s)
- Mark Trinder
- Centre for Human Microbiome and Probiotic Research, Lawson Health Research Institute, St. Joseph's Health Care London, LondonON, Canada.,Schulich School of Medicine and Dentistry, Department of Microbiology and Immunology, University of Western Ontario, LondonON, Canada
| | - Brendan A Daisley
- Centre for Human Microbiome and Probiotic Research, Lawson Health Research Institute, St. Joseph's Health Care London, LondonON, Canada.,Schulich School of Medicine and Dentistry, Department of Microbiology and Immunology, University of Western Ontario, LondonON, Canada
| | - Josh S Dube
- Centre for Human Microbiome and Probiotic Research, Lawson Health Research Institute, St. Joseph's Health Care London, LondonON, Canada.,Schulich School of Medicine and Dentistry, Department of Microbiology and Immunology, University of Western Ontario, LondonON, Canada
| | - Gregor Reid
- Centre for Human Microbiome and Probiotic Research, Lawson Health Research Institute, St. Joseph's Health Care London, LondonON, Canada.,Schulich School of Medicine and Dentistry, Department of Microbiology and Immunology, University of Western Ontario, LondonON, Canada.,Schulich School of Medicine and Dentistry, Department of Surgery, University of Western Ontario, LondonON, Canada
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