Lessons from Digestive-Tract Symbioses Between Bacteria and Invertebrates

Literature Cited

1. Abubucker S, Segata N, Goll J, Schubert AM, Izard J. 1.  et al. 2012. Metabolic reconstruction for metagenomic data and its application to the human microbiome. PLOS Comput. Biol. 8:e1002358 [Google Scholar]
2. Aksoy E, Telleria EL, Echodu R, Wu Y, Okedi LM. 2.  et al. 2014. Analysis of multiple tsetse fly populations in Uganda reveals limited diversity and species-specific gut microbiota. Appl. Environ. Microbiol. 80:4301–12 [Google Scholar]
3. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 3.  1990. Basic local alignment search tool. J. Mol. Biol. 215:403–10 [Google Scholar]
4. Anderson KE, Sheehan TH, Mott BM, Maes P, Snyder L. 4.  et al. 2013. Microbial ecology of the hive and pollination landscape: bacterial associates from floral nectar, the alimentary tract and stored food of honey bees (Apis mellifera). PLOS ONE 8:e83125 [Google Scholar]
5. Barquist L, Boinett CJ, Cain AK. 5.  2013. Approaches to querying bacterial genomes with transposon-insertion sequencing. RNA Biol. 10:1161–69 [Google Scholar]
6. Bauer S, Tholen A, Overmann J, Brune A. 6.  2000. Characterization of abundance and diversity of lactic acid bacteria in the hindgut of wood- and soil-feeding termites by molecular and culture-dependent techniques. Arch. Microbiol. 173:126–37 [Google Scholar]
7. Benjamino J, Graf J. 7.  2016. Characterization of the core and caste-specific microbiota in the termite, Reticulitermes flavipes. Front. Microbiol. 7:717 [Google Scholar]
8. Bhasin A, Chaston JM, Goodrich-Blair H. 8.  2012. Mutational analyses reveal overall topology and functional regions of NilB, a bacterial outer membrane protein required for host association in a model of animal-microbe mutualism. J. Bacteriol. 194:1763–76 [Google Scholar]
9. Bomar L, Graf J. 9.  2012. Investigation into the physiologies of Aeromonas veronii in vitro and inside the digestive tract of the medicinal leech using RNA-seq. Biol. Bull. 223:155–66 [Google Scholar]
10. Bomar L, Maltz M, Colston S, Graf J. 10.  2011. Directed culturing of microorganisms using metatranscriptomics. mBio 2:e00012–11 [Google Scholar]
11. Bomar L, Stephens WZ, Nelson MC, Velle K, Guillemin K, Graf J. 11.  2013. Draft genome sequence of Aeromonas veronii Hm21, a symbiotic isolate from the medicinal leech digestive tract. Genome Announc. 1:e00800–13 [Google Scholar]
12. Bordenstein SR, Theis KR. 12.  2015. Host biology in light of the microbiome: ten principles of holobionts and hologenomes. PLOS Biol. 13:e1002226 [Google Scholar]
13. Braschler TR, Merino S, Tomas JM, Graf J. 13.  2003. Complement resistance is essential for colonization of the digestive tract of Hirudo medicinalis by Aeromonas strains. Appl. Environ. Microbiol. 69:4268–71 [Google Scholar]
14. Broderick NA, Lemaitre B. 14.  2012. Gut-associated microbes of Drosophila melanogaster. Gut Microbes 3:307–21 [Google Scholar]
15. Broderick NA, Raffa KF, Goodman RM, Handelsman J. 15.  2004. Census of the bacterial community of the gypsy moth larval midgut by using culturing and culture-independent methods. Appl. Environ. Microbiol. 70:293–300 [Google Scholar]
16. Brune A. 16.  2014. Symbiotic digestion of lignocellulose in termite guts. Nat. Rev. Microbiol. 12:168–80 [Google Scholar]
17. Brune A, Ohkuma M. 17.  2010. Role of the termite gut microbiota in symbiotic digestion. Biology of Termites: A Modern Synthesis ED Bignell, Y Roisin, N Lo 439–75 Dordrecht, Neth: Springer [Google Scholar]
18. Buchner P. 18.  1955. Endosymbiose der Tiere mit pflanzlichen Mikroorganismen Basel: Springer
19. Casadevall A, Pirofski LA. 19.  2000. Host-pathogen interactions: basic concepts of microbial commensalism, colonization, infection, and disease. Infect. Immun. 68:6511–18 [Google Scholar]
20. Chaston J, Goodrich-Blair H. 20.  2010. Common trends in mutualism revealed by model associations between invertebrates and bacteria. FEMS Microbiol. Rev. 34:41–58 [Google Scholar]
21. Chaston JM, Murfin KE, Heath-Heckman EA, Goodrich-Blair H. 21.  2013. Previously unrecognized stages of species-specific colonization in the mutualism between Xenorhabdus bacteria and Steinernema nematodes. Cell Microbiol. 15:1545–59 [Google Scholar]
22. Chun CK, Troll JV, Koroleva I, Brown B, Manzella L. 22.  et al. 2008. Effects of colonization, luminescence, and autoinducer on host transcription during development of the squid-vibrio association. PNAS 105:11323–28 [Google Scholar]
23. Ciche TA, Kim KS, Kaufmann-Daszczuk B, Nguyen KC, Hall DH. 23.  2008. Cell invasion and matricide during Photorhabdus luminescens transmission by Heterorhabditis bacteriophora nematodes. Appl. Environ. Microbiol. 74:2275–87 [Google Scholar]
24. Cragg SM, Beckham GT, Bruce NC, Bugg TD, Distel DL. 24.  et al. 2015. Lignocellulose degradation mechanisms across the Tree of Life. Curr. Opin. Chem. Biol. 29:108–19 [Google Scholar]
25. Dale C, Young SA, Haydon DT, Welburn SC. 25.  2001. The insect endosymbiont Sodalis glossinidius utilizes a type III secretion system for cell invasion. PNAS 98:1883–88 [Google Scholar]
26. Dalevi D, Ivanova NN, Mavromatis K, Hooper SD, Szeto E. 26.  et al. 2008. Annotation of metagenome short reads using proxygenes. Bioinformatics 24:i7–13 [Google Scholar]
27. Darby CH, Scott J. 27.  2007. Innate defense evicts bacterial squatters. Nat. Immunol. 3:602–4 [Google Scholar]
28. de Hoon MJ, Imoto S, Nolan J, Miyano S. 28.  2004. Open source clustering software. Bioinformatics 20:1453–54 [Google Scholar]
29. Dethlefsen L, McFall-Ngai M, Relman DA. 29.  2007. An ecological and evolutionary perspective on human-microbe mutualism and disease. Nature 449:811–18 [Google Scholar]
30. Dick GJ, Andersson AF, Baker BJ, Simmons SL, Thomas BC. 30.  et al. 2009. Community-wide analysis of microbial genome sequence signatures. Genome Biol. 10:R85 [Google Scholar]
31. Dillon RJ, Dillon VM. 31.  2004. The gut bacteria of insects: nonpathogenic interactions. Annu. Rev. Entomol. 49:71–92 [Google Scholar]
32. Dobson AJ, Chaston JM, Newell PD, Donahue L, Hermann SL. 32.  et al. 2015. Host genetic determinants of microbiota-dependent nutrition revealed by genome-wide analysis of Drosophila melanogaster. Nat. Commun. 6:6312 [Google Scholar]
33. Douglas AE. 33.  2010. The Symbiotic Habit Princeton, NJ: Princeton Univ. Press
34. Duguma D, Hall MW, Rugman-Jones P, Stouthamer R, Terenius O. 34.  et al. 2015. Developmental succession of the microbiome of Culex mosquitoes. BMC Microbiol. 15:140 [Google Scholar]
35. Dunn AK, Stabb EV. 35.  2005. Culture-independent characterization of the microbiota of the ant lion Myrmeleon mobilis (Neuroptera: Myrmeleontidae). Appl. Environ. Microbiol. 71:8784–94 [Google Scholar]
36. Engel P, Martinson VG, Moran NA. 36.  2012. Functional diversity within the simple gut microbiota of the honey bee. PNAS 109:11002–7 [Google Scholar]
37. Engel P, Moran NA. 37.  2013. Functional and evolutionary insights into the simple yet specific gut microbiota of the honey bee from metagenomic analysis. Gut. Microbes 4:60–65 [Google Scholar]
38. Engel P, Moran NA. 38.  2013. The gut microbiota of insects—diversity in structure and function. FEMS Microbiol. Rev. 37:699–735 [Google Scholar]
39. Engel P, Stepanauskas R, Moran NA. 39.  2014. Hidden diversity in honey bee gut symbionts detected by single-cell genomics. PLOS Genet. 10:e1004596 [Google Scholar]
40. Engelbrektson A, Kunin V, Wrighton KC, Zvenigorodsky N, Chen F. 40.  et al. 2010. Experimental factors affecting PCR-based estimates of microbial species richness and evenness. ISME J. 4:642–47 [Google Scholar]
41. Fraune S, Bosch TC. 41.  2010. Why bacteria matter in animal development and evolution. Bioessays 32:571–80 [Google Scholar]
42. Friar JL, Goldman T, Perez-Mercader J. 42.  2012. Genome sizes and the Benford distribution. PLOS ONE 7:e36624 [Google Scholar]
43. Frias-Lopez J, Shi Y, Tyson GW, Coleman ML, Schuster SC. 43.  et al. 2008. Microbial community gene expression in ocean surface waters. PNAS 105:3805–10 [Google Scholar]
44. Giannoukos G, Ciulla DM, Huang K, Haas BJ, Izard J. 44.  et al. 2012. Efficient and robust RNA-seq process for cultured bacteria and complex community transcriptomes. Genome Biol. 13:R23 [Google Scholar]
45. Goodman AL, McNulty NP, Zhao Y, Leip D, Mitra RD. 45.  et al. 2009. Identifying genetic determinants needed to establish a human gut symbiont in its habitat. Cell Host Microbe 6:279–89 [Google Scholar]
46. Goodman AL, Wu M, Gordon JI. 46.  2011. Identifying microbial fitness determinants by insertion sequencing using genome-wide transposon mutant libraries. Nat. Protoc. 6:1969–80 [Google Scholar]
47. Goodrich-Blair H, Clarke DJ. 47.  2007. Mutualism and pathogenesis in Xenorhabdus and Photorhabdus: two roads to the same destination. Mol. Microbiol. 64:260–68 [Google Scholar]
48. Graf J. 48.  1999. Symbiosis of Aeromonas veronii biovar sobria and Hirudo medicinalis, the medicinal leech: a novel model for digestive tract associations. Infect. Immun. 67:1–7 [Google Scholar]
49. Graf J. 49.  2006. Molecular requirements for the colonization of Hirudo medicinalis by Aeromonas veronii. Prog. Mol. Subcell. Biol 41:291–303 [Google Scholar]
50. Gupta VK, Chaudhari NM, Iskepalli S, Dutta C. 50.  2015. Divergences in gene repertoire among the reference Prevotella genomes derived from distinct body sites of human. BMC Genomics 16:153 [Google Scholar]
51. He S, Ivanova N, Kirton E, Allgaier M, Bergin C. 51.  et al. 2013. Comparative metagenomic and metatranscriptomic analysis of hindgut paunch microbiota in wood- and dung-feeding higher termites. PLOS ONE 8:e61126 [Google Scholar]
52. Henderson G, Cox F, Kittelmann S, Miri VH, Zethof M. 52.  et al. 2013. Effect of DNA extraction methods and sampling techniques on the apparent structure of cow and sheep rumen microbial communities. PLOS ONE 8:e74787 [Google Scholar]
53. Hensel M, Shea JE, Gleeson C, Jones MD, Dalton E, Holden DW. 53.  1995. Simultaneous identification of bacterial virulence genes by negative selection. Science 269:400–3 [Google Scholar]
54. Hentschel U, Steinert M, Hacker J. 54.  2000. Common molecular mechanisms of symbiosis and pathogenesis. Trends Microbiol. 8:226–31 [Google Scholar]
55. Heungens K, Cowles CE, Goodrich-Blair H. 55.  2002. Identification of Xenorhabdus nematophila genes required for mutualistic colonization of Steinernema carpocapsae nematodes. Mol. Microbiol. 45:1337–53 [Google Scholar]
56. Hooper LV, Xu J, Falk PG, Midtvedt T, Gordon JI. 56.  1999. A molecular sensor that allows a gut commensal to control its nutrient foundation in a competitive ecosystem. PNAS 96:9833–38 [Google Scholar]
57. Hrusa G, Farmer W, Weiss BL, Applebaum T, Roma JS. 57.  et al. 2015. TonB-dependent heme iron acquisition in the tsetse fly symbiont Sodalis glossinidius. Appl. Environ. Microbiol. 81:2900–9 [Google Scholar]
58. Huang X-F, Bakker MG, Judd TM, Reardon KF, Vivanco JM. 58.  2013. Variations in diversity and richness of gut bacterial communities of termites (Reticulitermes flavipes) fed with grassy and woody plant substrates. Microb. Ecol. 65:531–36 [Google Scholar]
59. 59. Hum. Microbiome Proj. Consort 2012. A framework for human microbiome research. Nature 486:215–21 [Google Scholar]
60. 60. Hum. Microbiome Proj. Consort 2012. Structure, function and diversity of the healthy human microbiome. Nature 486:207–14 [Google Scholar]
61. Hussa EA, Goodrich-Blair H. 61.  2013. It takes a village: ecological and fitness impacts of multipartite mutualism. Annu. Rev. Microbiol. 67:161–78 [Google Scholar]
62. Indergand S, Graf J. 62.  2000. Ingested blood contributes to the specificity of the symbiosis of Aeromonas veronii biovar sobria and Hirudo medicinalis, the medicinal leech. Appl. Environ. Microbiol. 66:4735–41 [Google Scholar]
63. Johnson KH, Vogt KA, Clark HJ, Schmitz OJ, Vogt DJ. 63.  1996. Biodiversity and the productivity and stability of ecosystems. Trends Ecol. Evol. 11:372–77 [Google Scholar]
64. Jones RT, Sanchez LG, Fierer N. 64.  2013. A cross-taxon analysis of insect-associated bacterial diversity. PLOS ONE 8:e61218 [Google Scholar]
65. Kikuchi Y, Bomar L, Graf J. 65.  2009. Stratified bacterial community in the bladder of the medicinal leech, Hirudo verbana. Environ. Microbiol. 11:2758–70 [Google Scholar]
66. Kikuchi Y, Graf J. 66.  2007. Spatial and temporal population dynamics of a naturally occurring two-species microbial community inside the digestive tract of the medicinal leech. Appl. Environ. Microbiol 73:1984–91 [Google Scholar]
67. Kikuchi Y, Hosokawa T, Fukatsu T. 67.  2007. Insect-microbe mutualism without vertical transmission: A stinkbug acquires a beneficial gut symbiont from the environment every generation. Appl. Environ. Microbiol. 73:4308–16 [Google Scholar]
68. Kikuchi Y, Hosokawa T, Nikoh N, Meng XY, Kamagata Y, Fukatsu T. 68.  2009. Host-symbiont co-speciation and reductive genome evolution in gut symbiotic bacteria of acanthosomatid stinkbugs. BMC Biol. 7:2 [Google Scholar]
69. Knight R, Jansson J, Field D, Fierer N, Desai N. 69.  et al. 2012. Unlocking the potential of metagenomics through replicated experimental design. Nat. Biotechnol. 30:513–20 [Google Scholar]
70. Koenig JE, Spor A, Scalfone N, Fricker AD, Stombaugh J. 70.  et al. 2011. Succession of microbial consortia in the developing infant gut microbiome. PNAS 108:Suppl. 14578–85 [Google Scholar]
71. Konig H, Li L, Frohlich J. 71.  2013. The cellulolytic system of the termite gut. Appl. Microbiol. Biotechnol. 97:7943–62 [Google Scholar]
72. Kremer N, Philipp EE, Carpentier MC, Brennan CA, Kraemer L. 72.  et al. 2013. Initial symbiont contact orchestrates host-organ-wide transcriptional changes that prime tissue colonization. Cell Host Microbe 14:183–94 [Google Scholar]
73. Kunin V, Copeland A, Lapidus A, Mavromatis K, Hugenholtz P. 73.  2008. A bioinformatician's guide to metagenomics. Microbiol. Mol. Biol. Rev. 72:557–78 [Google Scholar]
74. Kwong WK, Engel P, Koch H, Moran NA. 74.  2014. Genomics and host specialization of honey bee and bumble bee gut symbionts. PNAS 111:11509–14 [Google Scholar]
75. Kwong WK, Moran NA. 75.  2013. Cultivation and characterization of the gut symbionts of honey bees and bumble bees: description of Snodgrassella alvi gen. nov., sp. nov., a member of the family Neisseriaceae of the Betaproteobacteria, and Gilliamella apicola gen. nov., sp. nov., a member of Orbaceae fam. nov., Orbales ord. nov., a sister taxon to the order ‘Enterobacteriales’ of the Gammaproteobacteria. Int. J. Syst. Evol. Microbiol. 63:2008–18 [Google Scholar]
76. Langille MG, Zaneveld J, Caporaso JG, McDonald D, Knights D. 76.  et al. 2013. Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nat. Biotechnol. 31:814–21 [Google Scholar]
77. Lechene CP, Luyten Y, McMahon G, Distel DL. 77.  2007. Quantitative imaging of nitrogen fixation by individual bacteria within animal cells. Science 317:1563–66 [Google Scholar]
78. Lee MM, Stock SP. 78.  2010. A multilocus approach to assessing co-evolutionary relationships between Steinernema spp. (Nematoda: Steinernematidae) and their bacterial symbionts Xenorhabdus spp. (γ-Proteobacteria: Enterobacteriaceae). Syst. Parasitol. 77:1–12 [Google Scholar]
79. Lemaitre B, Miguel-Aliaga I. 79.  2013. The digestive tract of Drosophila melanogaster. Annu. Rev. Genet. 47:377–404 [Google Scholar]
80. Ley RE, Hamady M, Lozupone C, Turnbaugh PJ, Ramey RR. 80.  et al. 2008. Evolution of mammals and their gut microbes. Science 320:1647–51 [Google Scholar]
81. Long JE, DeJesus M, Ward D, Baker RE, Ioerger T, Sassetti CM. 81.  2015. Identifying essential genes in Mycobacterium tuberculosis by global phenotypic profiling. Methods Mol. Biol. 1279:79–95 [Google Scholar]
82. Maltz M, Graf J. 82.  2011. The type II secretion system is essential for erythrocyte lysis and gut colonization by the leech digestive tract symbiont Aeromonas veronii. Appl. Environ. Microbiol. 77:597–603 [Google Scholar]
83. Maltz M, LeVarge B, Graf J. 83.  2015. Identification of iron and heme utilization genes in Aeromonas and their role in the colonization of the leech digestive tract. Front. Microbiol. 6:763 [Google Scholar]
84. Maltz MA, Bomar L, Lapierre P, Morrison HG, McClure EA. 84.  et al. 2014. Metagenomic analysis of the medicinal leech gut microbiota. Front. Microbiol. 5:151 [Google Scholar]
85. McArthur RH. 85.  1955. Fluctuations of animal populations and a measure of community stability. Ecology 36:533–36 [Google Scholar]
86. McCann KS. 86.  2000. The diversity-stability debate. Nature 405:228–33 [Google Scholar]
87. McFall-Ngai MJ. 87.  1998. The development of cooperative associations between animals and bacteria: establishing detente among domains. Amer. Zool. 38:593–608 [Google Scholar]
88. McFall-Ngai MJ. 88.  2007. Adaptive immunity: care for the community. Nature 445:153 [Google Scholar]
89. McFall-Ngai MJ, Hadfield MG, Bosch TC, Carey HV, Domazet-Loso T. 89.  et al. 2013. Animals in a bacterial world, a new imperative for the life sciences. PNAS 110:3229–36 [Google Scholar]
90. Mitra S, Rupek P, Richter DC, Urich T, Gilbert JA. 90.  et al. 2011. Functional analysis of metagenomes and metatranscriptomes using SEED and KEGG. BMC Bioinform. 12:Suppl. 1S21 [Google Scholar]
91. Moran NA, Hansen AK, Powell JE, Sabree ZL. 91.  2012. Distinctive gut microbiota of honey bees assessed using deep sampling from individual worker bees. PLOS ONE 7:e36393 [Google Scholar]
92. Moran NA, Wernegreen JJ. 92.  2000. Lifestyle evolution in symbiotic bacteria: insights from genomics. Trends Ecol. Evol. 15:321–26 [Google Scholar]
93. Murfin KE, Dillman AR, Foster JM, Bulgheresi S, Slatko BE. 93.  et al. 2012. Nematode-bacterium symbioses—cooperation and conflict revealed in the “omics” age. Biol. Bull. 223:85–102 [Google Scholar]
94. Nelson M, Bomar L, Maltz M, Graf J. 94.  2015. Mucinivorans hirudinis gen. nov., sp. nov., an anaerobic, mucin-degrading bacterium isolated from the digestive tract of the medicinal leech, Hirudo verbana. Int. J. Syst. Evol. Microbiol. 65:990–95 [Google Scholar]
95. Nelson MC, Bomar L, Graf J. 95.  2015. Complete genome sequence of the novel leech symbiont Mucinivorans hirudinis M3T. Genome Announc. 3:e01530–14 [Google Scholar]
96. Nelson MC, Graf J. 96.  2012. Bacterial symbioses of the medicinal leech Hirudo verbana. Gut. Microbes 3:322–31 [Google Scholar]
97. Nelson MC, Morrison HG, Benjamino J, Grim SL, Graf J. 97.  2014. Analysis, optimization and verification of Illumina-generated 16S rRNA gene amplicon surveys. PLOS ONE 9:e94249 [Google Scholar]
98. Newell PD, Chaston JM, Wang Y, Winans NJ, Sannino DR. 98.  et al. 2014. In vivo function and comparative genomic analyses of the Drosophila gut microbiota identify candidate symbiosis factors. Front. Microbiol. 5:576 [Google Scholar]
99. Nikolakakis K, Lehnert E, McFall-Ngai MJ, Ruby EG. 99.  2015. Use of hybridization chain reaction-fluorescent in situ hybridization to track gene expression by both partners during initiation of symbiosis. Appl. Environ. Microbiol. 81:4728–35 [Google Scholar]
100. Nyholm SV, Graf J. 100.  2012. Knowing your friends: Invertebrate innate immunity fosters beneficial bacterial symbioses. Nat. Rev. Microbiol. 10:815–27 [Google Scholar]
101. Ohbayashi T, Takeshita K, Kitagawa W, Nikoh N, Koga R. 101.  et al. 2015. Insect's intestinal organ for symbiont sorting. PNAS 112:E5179–88 [Google Scholar]
102. Pascault N, Loux V, Derozier S, Martin V, Debroas D. 102.  et al. 2015. Technical challenges in metatranscriptomic studies applied to the bacterial communities of freshwater ecosystems. Genetica 143:157–67 [Google Scholar]
103. Pernice M, Simpson SJ, Ponton F. 103.  2014. Towards an integrated understanding of gut microbiota using insects as model systems. J. Insect. Physiol. 69:12–18 [Google Scholar]
104. Podell S, Ugalde JA, Narasingarao P, Banfield JF, Heidelberg KB, Allen EE. 104.  2013. Assembly-driven community genomics of a hypersaline microbial ecosystem. PLOS ONE 8:e61692 [Google Scholar]
105. Poulsen M, Hu H, Li C, Chen Z, Xu L. 105.  et al. 2014. Complementary symbiont contributions to plant decomposition in a fungus-farming termite. PNAS 111:14500–5 [Google Scholar]
106. Roossinck MJ. 106.  2015. Move over, bacteria! Viruses make their mark as mutualistic microbial symbionts. J. Virol. 89:6532–35 [Google Scholar]
107. Ruby EG. 107.  2008. Symbiotic conversations are revealed under genetic interrogation. Rev. Microbiol. 6:752–62 [Google Scholar]
108. Ruby EG, Lee KH. 108.  1998. The Vibrio fischeri-Euprymna scolopes light organ association: current ecological paradigms. Appl. Environ. Microbiol 64:805–12 [Google Scholar]
109. Runyen-Janecky LJ, Brown AN, Ott B, Tujuba HG, Rio RV. 109.  2010. Regulation of high-affinity iron acquisition homologues in the tsetse fly symbiont Sodalis glossinidius. J. Bacteriol. 192:3780–87 [Google Scholar]
110. Salonen A, Nikkila J, Jalanka-Tuovinen J, Immonen O, Rajilic-Stojanovic M. 110.  et al. 2010. Comparative analysis of fecal DNA extraction methods with phylogenetic microarray: Effective recovery of bacterial and archaeal DNA using mechanical cell lysis. J. Microbiol. Methods 81:127–34 [Google Scholar]
111. Savage DC. 111.  1977. Microbial ecology of the gastrointestinal tract. Annu. Rev. Microbiol. 31:107–33 [Google Scholar]
112. Scharf ME. 112.  2015. Omic research in termites: an overview and a roadmap. Front. Genet. 6:76 [Google Scholar]
113. Scully ED, Geib SM, Hoover K, Tien M, Tringe SG. 113.  et al. 2013. Metagenomic profiling reveals lignocellulose degrading system in a microbial community associated with a wood-feeding beetle. PLOS ONE 8:e73827 [Google Scholar]
114. Shade A, Peter H, Allison SD, Baho DL, Berga M. 114.  et al. 2012. Fundamentals of microbial community resistance and resilience. Front. Microbiol. 3:417 [Google Scholar]
115. Shi W, Xie S, Chen X, Sun S, Zhou X. 115.  et al. 2013. Correction: Comparative genomic analysis of the microbiome of herbivorous insects reveals eco-environmental adaptations: biotechnology applications. PLOS Genet. 9:e1003131 [Google Scholar]
116. Silver AC, Kikuchi Y, Fadl AA, Sha J, Chopra AK, Graf J. 116.  2007. Interaction between innate immune cells and a bacterial type III secretion system in mutualistic and pathogenic associations. PNAS 104:9481–86 [Google Scholar]
117. Silver AC, Rabinowitz NM, Kuffer S, Graf J. 117.  2007. Identification of Aeromonas veronii genes required for colonization of the medicinal leech, Hirudo verbana. J. Bacteriol. 189:6763–72 [Google Scholar]
118. Smith CL, Weiss BL, Aksoy S, Runyen-Janecky LJ. 118.  2013. Characterization of the achromobactin iron acquisition operon in Sodalis glossinidius. Appl. Environ. Microbiol. 79:2872–81 [Google Scholar]
119. Steinert M, Hentschel U, Hacker J. 119.  2000. Symbiosis and pathogenesis: Evolution of the microbe-host interaction. Naturwissenschaften 87:1–11 [Google Scholar]
120. Tarpy DR, Mattila HR, Newton IL. 120.  2015. Development of the honey bee gut microbiome throughout the queen-rearing process. Appl. Environ. Microbiol. 81:3182–91 [Google Scholar]
121. Tartar A, Wheeler MM, Zhou X, Coy MR, Boucias DG, Scharf ME. 121.  2009. Parallel metatranscriptome analyses of host and symbiont gene expression in the gut of the termite Reticulitermes flavipes. Biotechnol. Biofuels 2:25 [Google Scholar]
122. Turnbaugh PJ, Ley RE, Hamady M, Fraser-Liggett CM, Knight R, Gordon JI. 122.  2007. The human microbiome project. Nature 449:804–10 [Google Scholar]
123. Ultsch A, Moörchen F. 123.  2005. ESOM-Maps: tools for clustering, visualization, and classification with Emergent SOM. Tech. Rep., Dep. Math. Comput. Sci., Univ. Marburg, Ger.
124. Ursell LK, Metcalf JL, Parfrey LW, Knight R. 124.  2012. Defining the human microbiome. Nutr. Rev. 70:Suppl. 1S38–44 [Google Scholar]
125. Valm AM, Mark Welch JL, Rieken CW, Hasegawa Y, Sogin ML. 125.  et al. 2011. Systems-level analysis of microbial community organization through combinatorial labeling and spectral imaging. PNAS 108:4152–57 [Google Scholar]
126. Wang Y, Gilbreath TM 3rd, Kukutla P, Yan G, Xu J. 126.  2011. Dynamic gut microbiome across life history of the malaria mosquito Anopheles gambiae in Kenya. PLOS ONE 6:e24767 [Google Scholar]
127. Warnecke F, Hugenholtz P. 127.  2007. Building on basic metagenomics with complementary technologies. Genome Biol. 8:231 [Google Scholar]
128. Warnecke F, Luginbühl P, Ivanova N, Ghassemian M, Richardson TH. 128.  et al. 2007. Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite. Nature 450:560–65 [Google Scholar]
129. Watanabe H, Tokuda G. 129.  2010. Cellulolytic systems in insects. Annu. Rev. Entomol. 55:609–32 [Google Scholar]
130. Weaver N. 130.  1966. Physiology of caste determination. Annu. Rev. Entomol. 11:79–102 [Google Scholar]
131. Wegley L, Edwards R, Rodriguez-Brito B, Liu H, Rohwer F. 131.  2007. Metagenomic analysis of the microbial community associated with the coral Porites astreoides. Environ. Microbiol. 9:2707–19 [Google Scholar]
132. Weiss BL, Wu Y, Schwank JJ, Tolwinski NS, Aksoy S. 132.  2008. An insect symbiosis is influenced by bacterium-specific polymorphisms in outer-membrane protein A. PNAS 105:15088–93 [Google Scholar]
133. Welch LM, Rossetti BJ, Rieken CW, Dewhirst FE, Borisy GG. 133.  2016. Biogeography of a human oral microbiome at the micron scale. PNAS 113:E791–800 [Google Scholar]
134. Wetmore KM, Price MN, Waters RJ, Lamson JS, He J. 134.  et al. 2015. Rapid quantification of mutant fitness in diverse bacteria by sequencing randomly bar-coded transposons. mBio 6:e00306–15 [Google Scholar]
135. Wong AC, Chaston JM, Douglas AE. 135.  2013. The inconstant gut microbiota of Drosophila species revealed by 16S rRNA gene analysis. ISME J. 7:1922–32 [Google Scholar]
136. Wong CN, Ng P, Douglas AE. 136.  2011. Low-diversity bacterial community in the gut of the fruitfly Drosophila melanogaster. Environ. Microbiol. 13:1889–900 [Google Scholar]
137. Wong LJ, H'Ng PS, Wong SY, Lee SH, Lum WC. 137.  et al. 2014. Termite digestomes as a potential source of symbiotic microbiota for lignocelluloses degradation: a review. Pak. J. Biol. Sci. 17:956–63 [Google Scholar]
138. Worthen PL, Gode CJ, Graf J. 138.  2006. Culture-independent characterization of the digestive-tract microbiota of the medicinal leech reveals a tripartite symbiosis. Appl. Environ. Microbiol. 72:4775–81 [Google Scholar]
139. Yang H, Schmitt-Wagner D, Stingl U, Brune A. 139.  2005. Niche heterogeneity determines bacterial community structure in the termite gut (Reticulitermes santonensis). Environ. Microbiol. 7:916–32 [Google Scholar]
140. Yun JH, Roh SW, Whon TW, Jung MJ, Kim MS. 140.  et al. 2014. Insect gut bacterial diversity determined by environmental habitat, diet, developmental stage, and phylogeny of host. Appl. Environ. Microbiol. 80:5254–64 [Google Scholar]
141. Zhang Y, Lin K. 141.  2012. A phylogenomic analysis of Escherichia coli / Shigella group: implications of genomic features associated with pathogenicity and ecological adaptation. BMC Evol. Biol. 12:174 [Google Scholar]
142. Zhou J, He Z, Yang Y, Deng Y, Tringe SG, Alvarez-Cohen L. 142.  2015. High-throughput metagenomic technologies for complex microbial community analysis: open and closed formats. mBio 6:e02288–14 [Google Scholar]
143. Zilber-Rosenberg I, Rosenberg E. 143.  2008. Role of microorganisms in the evolution of animals and plants: the hologenome theory of evolution. FEMS Microbiol. Rev. 32:723–35 [Google Scholar]