title: Host species and environmental effects on bacterial communities associated with Drosophila in the laboratory and in the natural environment.
abstract: The fruit fly Drosophila is a classic model organism to study adaptation as well as the relationship between genetic variation and phenotypes. Although associated bacterial communities might be important for many aspects of Drosophila biology, knowledge about their diversity, composition, and factors shaping them is limited. We used 454-based sequencing of a variable region of the bacterial 16S ribosomal RNA gene to characterize the bacterial communities associated with wild and laboratory Drosophila isolates. In order to specifically investigate effects of food source and host species on bacterial communities, we analyzed samples from wild Drosophila melanogaster and D. simulans collected from a variety of natural substrates, as well as from adults and larvae of nine laboratory-reared Drosophila species. We find no evidence for host species effects in lab-reared flies; instead, lab of origin and stochastic effects, which could influence studies of Drosophila phenotypes, are pronounced. In contrast, the natural Drosophila-associated microbiota appears to be predominantly shaped by food substrate with an additional but smaller effect of host species identity. We identify a core member of this natural microbiota that belongs to the genus Gluconobacter and is common to all wild-caught flies in this study, but absent from the laboratory. This makes it a strong candidate for being part of what could be a natural D. melanogaster and D. simulans core microbiome. Furthermore, we were able to identify candidate pathogens in natural fly isolates.
authors: Department of Biology, Stanford University, Stanford, California, USA. fabians@stanford.edu
authors: Fabian
authors: F
authors: Staubach
authors: John F
authors: JF
authors: Baines
authors: Sven
authors: S
authors: Künzel
authors: Elisabeth M
authors: EM
authors: Bik
authors: Dmitri A
authors: DA
authors: Petrov
mesh_terms: D000818:Animals; D001419:Bacteria / Q000145:classification / Q000235:genetics*; D044822:Biodiversity; D004330:Drosophila / Q000382:microbiology*; D004783:Environmental Microbiology; D054884:Host-Pathogen Interactions; D008297:Male; D054892:Metagenome; D064307:Microbiota; D010641:Phenotype; D012329:RNA, Bacterial; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D013045:Species Specificity
chemical_list: D012329:RNA, Bacterial; D012336:RNA, Ribosomal, 16S
references: Cell Host Microbe. 2008 Aug 14;4(2):147-58
references: 18692774
references: Obesity (Silver Spring). 2012 Apr;20(4):738-47
references: 21593810
references: PLoS Biol. 2010 Nov 16;8(11):e1000546
references: 21103409
references: Nature. 2012 May 09;486(7402):222-7
references: 22699611
references: Cell Metab. 2011 Sep 7;14(3):403-14
references: 21907145
references: Nat Rev Microbiol. 2007 May;5(5):355-62
references: 17384666
references: Science. 2011 Oct 7;334(6052):105-8
references: 21885731
references: Infect Immun. 2007 Apr;75(4):1565-76
references: 17220307
references: J Microbiol Methods. 2013 May;93(2):108-15
references: 23485423
references: Science. 2004 Mar 19;303(5665):1873-6
references: 15031506
references: Appl Microbiol. 1970 Jan;19(1):27-31
references: 4905947
references: Proc Biol Sci. 2010 Aug 7;277(1692):2311-9
references: 20356892
references: Science. 2011 Nov 4;334(6056):670-4
references: 22053049
references: Trends Ecol Evol. 2011 Jul;26(7):340-8
references: 21561679
references: Gut Microbes. 2012 Jul-Aug;3(4):307-21
references: 22572876
references: Environ Microbiol. 2009 Sep;11(9):2361-9
references: 19508335
references: Proc Biol Sci. 2012 Feb 22;279(1729):749-58
references: 21775330
references: Annu Rev Immunol. 2007;25:697-743
references: 17201680
references: Environ Microbiol. 2010 Jan;12(1):118-23
references: 19725865
references: Appl Microbiol Biotechnol. 2002 Nov;60(3):233-42
references: 12436304
references: Appl Environ Microbiol. 2007 Jun;73(11):3470-9
references: 17400769
references: Int J Syst Evol Microbiol. 2009 May;59(Pt 5):1108-11
references: 19406801
references: FEMS Microbiol Rev. 2003 Dec;27(5):663-93
references: 14638418
references: Science. 2008 Jun 20;320(5883):1647-51
references: 18497261
references: ISME J. 2012 Jul;6(7):1345-55
references: 22278669
references: Genetics. 2006 Nov;174(3):1539-54
references: 16888344
references: PLoS One. 2012;7(9):e41907
references: 23028430
references: Philos Trans R Soc Lond B Biol Sci. 2011 May 12;366(1569):1389-400
references: 21444313
references: Appl Environ Microbiol. 2009 Dec;75(23):7537-41
references: 19801464
references: Microb Ecol. 2012 Aug;64(2):416-30
references: 22438040
references: Appl Environ Microbiol. 2010 Nov;76(21):6963-70
references: 20851977
references: Cell. 2012 Dec 7;151(6):1345-57
references: 23217715
references: Genetics. 2000 Oct;156(2):699-709
references: 11014817
references: J Invertebr Pathol. 1969 Nov;14(3):365-74
references: 4904970
references: BMC Bioinformatics. 2008 Sep 19;9:386
references: 18803844
references: Science. 2012 Jun 8;336(6086):1262-7
references: 22674330
references: Science. 2011 May 20;332(6032):970-4
references: 21596990
references: Curr Biol. 2005 Mar 8;15(5):475-9
references: 15753044
references: Proc Natl Acad Sci U S A. 2003 Feb 18;100(4):1803-7
references: 12563031
references: Nucleic Acids Res. 2007;35(21):7188-96
references: 17947321
references: Cell Metab. 2007 Aug;6(2):144-52
references: 17681150
references: Cell Host Microbe. 2013 Jan 16;13(1):8-14
references: 23332152
references: Microbes Infect. 2011 Jul;13(7):673-83
references: 21354324
references: Semin Immunol. 2012 Feb;24(1):3-8
references: 22154556
references: Science. 2008 Feb 8;319(5864):777-82
references: 18218863
references: Nature. 2007 Nov 8;450(7167):203-18
references: 17994087
references: PLoS Genet. 2011 Sep;7(9):e1002272
references: 21966276
references: Environ Microbiol. 2011 Jul;13(7):1889-900
references: 21631690
references: Nature. 2011 May 12;473(7346):174-80
references: 21508958
references: EMBO Rep. 2006 Jul;7(7):688-93
references: 16819463
references: Lett Appl Microbiol. 2008 Jul;47(1):19-24
references: 18498317
references: Q Rev Biol. 2010 Jun;85(2):183-206
references: 20565040
references: Oecologia. 1996 Nov;108(3):552-561
references: 28307873
references: Bioinformatics. 2011 Aug 15;27(16):2194-200
references: 21700674
references: Proc Natl Acad Sci U S A. 2010 Nov 16;107(46):20051-6
references: 21041648