Low-diversity bacterial community in the gut of the fruitfly Drosophila melanogaster

Environmental Microbiology

Volumn 13, Issue 7, 2011, Pages 1889-1900

  Wong, Chun Nin Adam ^a   Ng, Patrick ^b   Douglas, Angela E ^a  

^a Department of Obstetrics Gynecology   (United States)

^b Department of Computer Science and School of Operations Research and Information Engineering   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA; RNA 16S;

ACETOBACTER; ANIMAL; ARTICLE; CLASSIFICATION; DNA SEQUENCE; DROSOPHILA MELANOGASTER; ECOSYSTEM; GASTROINTESTINAL TRACT; GENETICS; LACTOBACILLUS; METAGENOME; MICROBIOLOGY; NUCLEOTIDE SEQUENCE;

ACETOBACTER; ANIMALS; BASE SEQUENCE; DNA, BACTERIAL; DROSOPHILA MELANOGASTER; ECOSYSTEM; GASTROINTESTINAL TRACT; LACTOBACILLUS; METAGENOME; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA;

ACETOBACTER; ACETOBACTER POMORUM; ACETOBACTER TROPICALIS; BACTERIA (MICROORGANISMS); DROSOPHILA MELANOGASTER; HEXAPODA; LACTOBACILLUS; LACTOBACILLUS BREVIS; LACTOBACILLUS FRUCTIVORANS; LACTOBACILLUS PLANTARUM; OTUS;

EID: 79959841282     PISSN: 14622912     EISSN: 14622920     Source Type: Journal    
DOI: 10.1111/j.1462-2920.2011.02511.x     Document Type: Article

References (46)

1. Ashelford, K.E., Chuzhanova, N.A., Fry, J.C., Jones, A.J., and Weightman, A.J. (2006) New screening software shows that most recent large 16S rRNA gene clone libraries contain chimeras. Appl Environ Microbiol 72: 5734-5741.
2. Baker, A.C., Starger, C.J., McClanahan, T.R., and Glynn, P.W. (2004) Coral reefs: corals' adaptive response to climate change. Nature 430: 741.
3. Bakula, M. (1969) The persistence of a microbial flora during postembryogenesis of Drosophila melanogaster. J Invertebr Pathol 14: 365-374.
4. Behar, A., Yuval, B., and Jurkevitch, E. (2008) Gut bacterial communities in the Mediterranean fruit fly (Ceratitis capitata) and their impact on host longevity. J Insect Physiol 54: 1377-1383.
5. Buchon, N., Broderick, N.A., Poidevin, M., Pradervand, S., and Lemaitre, B. (2009) Drosophila intestinal response to bacterial infection: activation of host defense and stem cell proliferation. Cell Host Microbe 5: 200-211.
6. Claesson, M.J., Cusack, S., O'Sullivan, O., Greene-Diniz, R., de Weerd, H., Flannery, E., etal. (2011) Microbes and Health Sackler Colloquium: composition, variability, and temporal stability of the intestinal microbiota of the elderly. Proc Natl Acad Sci USA 108: 4586-4591.
7. Connell, J.H. (1978) Diversity in tropical rain forests and coral reefs. Science 199: 1302-1310.
8. Corby-Harris, V., Pontaroli, A.C., Shimkets, L.J., Bennetzen, J.L., Habel, K.E., and Promislow, D.E. (2007) Geographical distribution and diversity of bacteria associated with natural populations of Drosophila melanogaster. Appl Environ Microbiol 73: 3470-3479.
9. Costello, E.K., Lauber, C.L., Hamady, M., Fierer, N., Gordon, J.I., and Knight, R. (2009) Bacterial community variation in human body habitats across space and time. Science 326: 1694-1697.
10. Cox, C.R., and Gilmore, M.S. (2007) Native microbial colonization of Drosophila melanogaster and its use as a model of Enterococcus faecalis pathogenesis. Infect Immun 75: 1565-1576.
11. Crotti, E., Rizzi, A., Chouaia, B., Ricci, I., Favia, G., Alma, A., etal. (2010) Acetic acid bacteria, newly emerged symbionts of insects. Appl Environ Microbiol 76: 6963-6970.
12. Denef, V.J., Kalnejais, L.H., Mueller, R.S., Wilmes, P., Baker, B.J., Thomas, B.C., etal. (2010) Proteogenomic basis for ecological divergence of closely related bacteria in natural acidophilic microbial communities. Proc Natl Acad Sci USA 107: 2383-2390.
13. Denison, R.F., and Kiers, E.T. (2004) Lifestyle alternatives for rhizobia: mutualism, parasitism, and forgoing symbiosis. FEMS Microbiol Lett 237: 187-193.
14. Dethlefsen, L., McFall-Ngai, M., and Relman, D.A. (2007) An ecological and evolutionary perspective on human-microbe mutualism and disease. Nature 449: 811-818.
15. Dillon, R.J., and Dillon, V.M. (2004) The gut bacteria of insects: nonpathogenic interactions. Annu Rev Entomol 49: 71-92.
16. Douglas, A.E. (2010) The Symbiotic Habit. Princeton, NJ, USA: Princeton University Press.
17. Drancourt, M., and Raoult, D. (2005) Sequence-based identification of new bacteria: a proposition for creation of an orphan bacterium repository. J Clin Microbiol 43: 4311-4315.
18. Drancourt, M., Berger, P., and Raoult, D. (2004) Systematic 16S rRNA gene sequencing of atypical clinical isolates identified 27 new bacterial species associated with humans. J Clin Microbiol 42: 2197-2202.
19. Dunn, A.K., and Stabb, E.V. (2005) Culture-independent characterization of the microbiota of the ant lion Myrmeleon mobilis (Neuroptera: Myrmeleontidae). Appl Environ Microbiol 71: 8784-8794.
20. Fierer, N., and Jackson, R.B. (2006) The diversity and biogeography of soil bacterial communities. Proc Natl Acad Sci USA 103: 626-631.
21. Garren, M., Raymundo, L., Guest, J., Harvell, C.D., and Azam, F. (2009) Resilience of coral-associated bacterial communities exposed to fish farm effluent. PLoS ONE 4: e7319.
22. Grime, J.P. (1977) Evidence for the existence of three primary strategies in plants and its relevance to ecological and evolutionary theory. Am Nat 111: 1169-1194.
23. Grunwald, S., Pilhofer, M., and Holl, W. (2010) Microbial associations in gut systems of wood- and bark-inhabiting longhorned beetles [Coleoptera: Cerambycidae]. Syst Appl Microbiol 33: 25-34.
24. Huse, S.M., Huber, J.A., Morrison, H.G., Sogin, M.L., and Welch, D.M. (2007) Accuracy and quality of massively parallel DNA pyrosequencing. Genome Biol 8: R143.
25. Janda, J.M., and Abbott, S.L. (2007) 16S rRNA gene sequencing for bacterial identification in the diagnostic laboratory: pluses, perils, and pitfalls. J Clin Microbiol 45: 2761-2764.
26. Kunin, V., and Hugenholtz, P. (2010) PyroTagger: a fast, accurate pipeline for analysis of rRNA amplicon pyrosequence data. Open J 1: 1-8.
27. Kunin, V., Engelbrektson, A., Ochman, H., and Hugenholtz, P. (2010) Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates. Environ Microbiol 12: 118-123.
28. Lehman, R.M., Lundgren, J.G., and Petzke, L.M. (2009) Bacterial communities associated with the digestive tract of the predatory ground beetle, Poecilus chalcites, and their modification by laboratory rearing and antibiotic treatment. Microb Ecol 57: 349-358.
29. Ley, R.E., Lozupone, C.A., Hamady, M., Knight, R., and Gordon, J.I. (2008) Worlds within worlds: evolution of the vertebrate gut microbiota. Nat Rev Microbiol 6: 776-788.
30. Livak, K.J., and Schmittgen, T.D. (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. Methods 25: 402-408.
31. Ljungh, A., and Wadstrom, T. (eds) (2009) Lactobacillus Molecular Biology: From Genomics to Probiotics. Norfolk, UK: Caister Academic Press.
32. Mandel, M.J., Wollenberg, M.S., Stabb, E.V., Visick, K.L., and Ruby, E.G. (2009) A single regulatory gene is sufficient to alter bacterial host range. Nature 458: 215-218.
33. Matsui, H., Kato, Y., Chikaraishi, T., Moritani, M., Ban-Tokuda, T., and Wakita, M. (2010) Microbial diversity in ostrich ceca as revealed by 16S ribosomal RNA gene clone library and detection of novel Fibrobacter species. Anaerobe 16: 83-93.
34. Morales-Jimenez, J., Zuniga, G., Villa-Tanaca, L., and Hernandez-Rodriguez, C. (2009) Bacterial community and nitrogen fixation in the red turpentine beetle, Dendroctonus valens LeConte (Coleoptera: Curculionidae: Scolytinae). Microb Ecol 58: 879-891.
35. Needleman, S.B., and Wunsch, C.D. (1970) A general method applicable to the search for similarities in the amino acid sequence of two proteins. J Mol Biol 48: 443-453.
36. Qin, J., Li, R., Raes, J., Arumugam, M., Burgdorf, K.S., Manichanh, C., etal. (2010) A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464: 59-65.
37. Ren, C., Webster, P., Finkel, S.E., and Tower, J. (2007) Increased internal and external bacterial load during Drosophila aging without life-span trade-off. Cell Metab 6: 144-152.
38. Robinson, C.J., Schloss, P., Ramos, Y., Raffa, K., and Handelsman, J. (2010) Robustness of the bacterial community in the cabbage white butterfly larval midgut. Microb Ecol 59: 199-211.
39. Roh, S.W., Nam, Y.D., Chang, H.W., Kim, K.H., Kim, M.S., Ryu, J.H., etal. (2008) Phylogenetic characterization of two novel commensal bacteria involved with innate immune homeostasis in Drosophila melanogaster. Appl Environ Microbiol 74: 6171-6177.
40. Ryu, J.H., Ha, E.-M., Oh, C.-T., Seol, J.-H., Brey, P.T., Jin, I., etal. (2006) An essential complementary role of NF-κB pathway to microbicidal oxidants in Drosophila gut immunity. EMBO J 25: 3693-3701.
41. Ryu, J.H., Kim, S.H., Lee, H.Y., Bai, J.Y., Nam, Y.D., Bae, J.W., etal. (2008) Innate immune homeostasis by the homeobox gene caudal and commensal-gut mutualism in Drosophila. Science 319: 777-782.
42. Scanlan, D.J., Ostrowski, M., Mazard, S., Dufresne, A., Garczarek, L., Hess, W.R., etal. (2009) Ecological genomics of marine picocyanobacteria. Microbiol Mol Biol Rev 73: 249-299.
43. Sharon, G., Segal, D., Fingo, J.M., Hefetz, A., Zilber-Rosenberg, I., and Rosenberg, E. (2010) Commensal bacteria play a role in mating preference of Drosophila melanogaster. Proc Natl Acad Sci USA 107: 20051-20056.
44. Venn, A.A., Loram, J.E., Trapido-Rosenthal, H.G., Joyce, D.A., and Douglas, A.E. (2008) Importance of time and place: patterns in abundance of symbiodinium clades a and b in the tropical sea anemone condylactis gigantea. Biol Bull 215: 243-252.
45. Wilson, M. (2005) Microbial Inhabitants of Humans. Cambridge, UK: Cambridge University Press.
46. Yamada, Y., and Yukphan, P. (2008) Genera and species in acetic acid bacteria. Int J Food Microbiol 125: 15-24.