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参考文献

Abbott, A.C. (1894) The Principles of Bacteriology (Philadelphia: Lea Bros & Co.).

Acuna, R., Padilla, B.E., Florez-Ramos, C.P., Rubio, J.D., Herrera, J.C., Benavides,

P., Lee, S-J., Yeats, T.H., Egan, A.N., Doyle, J.J., et al. (2012) ‘Adaptive horizontal transfer of a bacterial gene to an invasive insect pest of coffee’, Proc. Natl. Acad. Sci . 109, 4197–4202.

Adams, A.S., Aylward, F.O., Adams, S.M., Erbilgin, N., Aukema, B.H., Currie, C.R.,

Suen, G., and Raffa, K.F. (2013) ‘Mountain pine beetles colonizing historical and naive host trees are associated with a bacterial community highly enriched in genes contributing to terpene metabolism’, Appl. Environ. Microbiol. 79, 3468–3475.

Adams, R.I., Bateman, A.C., Bik, H.M., and Meadow, J.F. (2015) ‘Microbiota of the indoor environment: a meta-analysis’, Microbiome 3. doi: 10.1186/s40168-015-0108-3.

Alang, N. and Kelly, C.R. (2015) ‘Weight gain after fecal microbiota transplantation’, Open Forum Infect. Dis. 2, ofv004–ofv004.

Alcaide, M., Messina, E., Richter, M., Bargiela, R., Peplies, J., Huws, S.A., Newbold, C.J., Golyshin, P.N., Simón, M.A., López, G., et al. (2012) ‘Gene sets for utilization of primary and secondary nutrition supplies in the distal gut of endangered Iberian lynx’, PLoS ONE 7, e51521.

Alcock, J., Maley, C.C., and Aktipis, C.A. (2014) ‘Is eating behavior manipulated by the gastrointestinal microbiota? Evolutionary pressures and potential mechanisms’, BioEssays 36, 940–949.

Alegado, R.A. and King, N. (2014) ‘Bacterial influences on animal origins’, Cold Spring Harb. Perspect. Biol. 6, a016162–a016162.

Alegado, R.A., Brown, L.W., Cao, S., Dermenjian, R.K., Zuzow, R., Fairclough, S.R., Clardy, J., and King, N. (2012) ‘A bacterial sulfonolipid triggers multicellular development in the closest living relatives of animals’, Elife 1, e00013.

AlFaleh, K. and Anabrees, J. (2014) ‘Probiotics for prevention of necrotizing enterocolitis in preterm infants’, in Cochrane Database of Systematic Reviews , The Cochrane Collaboration (Chichester, UK: John Wiley & Sons).

Alivisatos, A.P., Blaser, M.J., Brodie, E.L., Chun, M., Dangl, J.L., Donohue, T.J., Dorrestein, P.C., Gilbert, J.A., Green, J.L., Jansson, J.K., et al. (2015) ‘A unified initiative to harness Earth’s microbiomes’, Science 350, 507–508.

Allen, S.J., Martinez, E.G., Gregorio, G.V., and Dans, L.F. (2010) ‘Probiotics for treating acute infectious diarrhoea’, in Cochrane Database of Systematic Reviews , The Cochrane Collaboration (Chichester, UK: John Wiley & Sons).

Allison, M.J., Mayberry, W.R., Mcsweeney, C.S., and Stahl, D.A. (1992) ‘Synergistes jonesii, gen. nov., sp.nov.: a rumen bacterium that degrades toxic pyridinediols’, Syst. Appl. Microbiol. 15, 522–529.

The Allium (2014) ‘New Salmonella diet achieves ‘amazing’ weight-loss for microbiologist’.

Altman, L.K. (April 1993) ‘Dr. Denis Burkitt is dead at 82; thesis changed diets of millions’, New York Times.

Amato, K.R., Leigh, S.R., Kent, A., Mackie, R.I., Yeoman, C.J., Stumpf, R.M., Wilson, B.A., Nelson, K.E., White, B.A., and Garber, P.A. (2015) ‘The gut microbiota appears to compensate for seasonal diet variation in the wild black howler monkey ( Alouatta pigra )’, Microb. Ecol. 69, 434–443.

American Chemical Society (1999) Alexander Fleming Discovery and Development of Penicillin. http://www.acs.org/content/acs/en/education/whatischemistry/landmarks/flemingpenicillin.xhtml#alexander-fleming-penicillin.

Amphibian Ark (2012) Chytrid fungus – causing global amphibian mass extinction. http:\\www.amphibianark.org/the-crisis/chytrid-fungus/.

Anderson, D. (2014) ‘Still going strong: Leeuwenhoek at eighty’, Antonie Van Leeuwenhoek 106, 3–26.

Anderson, J.L., Edney, R.J., and Whelan, K. (2012) ‘Systematic review: faecal microbiota transplantation in the management of inflammatory bowel disease’, Aliment. Pharmacol. Ther. 36, 503–516.

Anukam, K.C. and Reid, G. (2007) ‘Probiotics: 100 years (1907–2007) after Elie Metchnikoff’s observation’, in Communicating Current Research and Educational Topics and Trends in Applied Microbiology (FORMATEX).

Archibald. J. (2014) One Plus One Equals One: Symbiosis and the Evolution of Complex Life (Oxford: Oxford University Press).

Archie, E.A. and Theis, K.R. (2011) ‘Animal behaviour meets microbial ecology’, Anim. Behav. 82, 425–436.

Aroniadis, O.C. and Brandt, L.J. (2014) ‘Intestinal microbiota and the efficacy of fecal microbiota transplantation in gastrointestinal disease’, Gastroenterol. Hepatol. 10, 230–237.

Arrieta, M-C., Stiemsma, L.T., Dimitriu, P.A., Thorson, L., Russell, S., YuristDoutsch, S., Kuzeljevic, B., Gold, M.J., Britton, H.M., Lefebvre, D.L., et al. (2015) ‘Early infancy microbial and metabolic alterations affect risk of childhood asthma’, Sci. Transl. Med. 7, 307ra152.

Asano, Y., Hiramoto, T., Nishino, R., Aiba, Y., Kimura, T., Yoshihara, K., Koga, Y., and Sudo, N. (2012) ‘Critical role of gut microbiota in the production of biologically active, free catecholamines in the gut lumen of mice’, AJP Gastrointest. Liver Physiol. 303, G1288–G1295.

Atarashi, K., Tanoue, T., Shima, T., Imaoka, A., Kuwahara, T., Momose, Y., Cheng, G., Yamasaki, S., Saito, T., Ohba, Y., et al. (2011) ‘Induction of colonic regulatory T cells by indigenous Clostridium species ’, Science 331, 337–341.

Atarashi, K., Tanoue, T., Oshima, K., Suda, W., Nagano, Y., Nishikawa, H., Fukuda, S., Saito, T., Narushima, S., Hase, K., et al. (2013) ‘Treg induction by a rationally selected mixture of Clostridia strains from the human microbiota’, Nature 500, 232–236.

Aung, A. (2007) Feeding of Leucaena Mimosine on Small Ruminants: Investigation on the Control of its Toxicity in Small Ruminants (Göttingen: Cuvillier Verlag).

Bäckhed, F., Ding, H., Wang, T., Hooper, L.V., Koh, G.Y., Nagy, A., Semenkovich, C.F., and Gordon, J.I. (2004) ‘The gut microbiota as an environmental factor that regulates fat storage’, Proc. Natl. Acad. Sci. U. S. A. 101, 15718–15723.

Bäckhed, F., Fraser, C.M., Ringel, Y., Sanders, M.E., Sartor, R.B., Sherman, P.M., Versalovic, J., Young, V., and Finlay, B.B. (2012) ‘Defining a healthy human gut microbiome: current concepts, future directions, and clinical applications’, Cell Host Microbe 12, 611–622.

Bäckhed, F., Roswall, J., Peng, Y., Feng, Q., Jia, H., Kovatcheva-Datchary, P., Li, Y., Xia, Y., Xie, H., Zhong, H., et al. (2015) ‘Dynamics and stabilization of the human gut microbiome during the first year of life’, Cell Host Microbe 17, 690–703.

Ballal, S.A., Veiga, P., Fenn, K., Michaud, M., Kim, J.H., Gallini, C.A., Glickman, J.N., Quéré, G., Garault, P., Béal, C., et al. (2015) ‘Host lysozyme-mediated lysis of Lactococcus lactis facilitates delivery of colitis-attenuating superoxide dismutase to inflamed colons’, Proc. Natl. Acad. Sci. 112, 7803–7808.

Barott, K.L., and Rohwer, F.L. (2012) ‘Unseen players shape benthic competition on coral reefs’, Trends Microbiol. 20, 621–628.

Barr, J.J., Auro, R., Furlan, M., Whiteson, K.L., Erb, M.L., Pogliano, J., Stotland, A., Wolkowicz, R., Cutting, A.S., and Doran, K.S. (2013) ‘Bacteriophage adhering to mucus provide a non–host-derived immunity’, Proc. Natl. Acad. Sci. 110, 10771–10776.

Bates, J.M., Mittge, E., Kuhlman, J., Baden, K.N., Cheesman, S.E., and Guillemin, K. (2006) ‘Distinct signals from the microbiota promote different aspects of zebrafish gut differentiation’, Dev. Biol. 297, 374–386.

Baumann, P., Lai, C., Baumann, L., Rouhbakhsh, D., Moran, N.A., and Clark, M.A. (1995) ‘Mutualistic associations of aphids and prokaryotes: biology of the genus Buchnera’, Appl. Environ. Microbiol. 61, 1–7.

BBC (23 January 2015) The 25 biggest turning points in Earth’s history.

Beasley, D.E., Koltz, A.M., Lambert, J.E., Fierer, N., and Dunn, R.R. (2015) ‘The evolution of stomach acidity and its relevance to the human microbiome’, PloS One 10, e0134116.

Beaumont, W. (1838) Experiments and Observations on the Gastric Juice, and the Physiology of Digestion (Edinburgh: Maclachlan & Stewart).

Becerra, J.X., Venable, G.X., and Saeidi, V. (2015) ‘ Wolbachia -free heteropterans do not produce defensive chemicals or alarm pheromones’, J. Chem. Ecol. 41, 593–601.

Becker, M.H., Walke, J.B., Cikanek, S., Savage, A.E., Mattheus, N., Santiago, C.N., Minbiole, K.P.C., Harris, R.N., Belden, L.K. and Gratwicke, B. (2015) ‘Composition of symbiotic bacteria predicts survival in Panamanian golden frogs infected with a lethal fungus’, Proc. R. Soc. B Biol. Sci. 282, doi: 10.1098/rspb.2014.2881.

Belkaid, Y. and Hand, T.W. (2014) ‘Role of the microbiota in immunity and inflammation; Cell 157, 121–141.

Bennett, G.M. and Moran, N.A. (2013) ‘Small, smaller, smallest: the origins and evolution of ancient dual symbioses in a phloem-feeding insect’, Genome Biol. Evol. 5, 1675–1688.

Bennett, G.M. and Moran, N.A. (2015) ‘Heritable symbiosis: the advantages and perils of an evolutionary rabbit hole’, Proc. Natl. Acad. Sci. 112, 10169–10176.

Benson, A.K., Kelly, S.A., Legge, R., Ma, F., Low, S.J., Kim, J., Zhang, M., Oh, P.L., Nehrenberg, D., Hua, K., et al. (2010) ‘Individuality in gut microbiota composition is a complex polygenic trait shaped by multiple environmental and host genetic factors’, Proc. Natl. Acad. Sci. 107, 18933–18938.

Bercik, P., Denou, E., Collins, J., Jackson, W., Lu, J., Jury, J., Deng, Y., Blennerhassett, P., Macri, J., McCoy, K.D., et al. (2011) ‘The intestinal microbiota affect central levels of brain-derived neurotropic factor and behavior in mice’, Gastroenterology 141, 599–609.e3.

Berer, K., Mues, M., Koutrolos, M., Rasbi, Z.A., Boziki, M., Johner, C., Wekerle, H., and Krishnamoorthy, G. (2011) ‘Commensal microbiota and myelin autoantigen cooperate to trigger autoimmune demyelination’, Nature 479, 538–541.

Bergman, E.N. (1990) ‘Energy contributions of volatile fatty acids from the gastrointestinal tract in various species’, Physiol. Rev. 70, 567–590.

Bevins, C.L. and Salzman, N.H. (2011) ‘The potter’s wheel: the host’s role in sculpting its microbiota’, Cell. Mol. Life Sci. 68, 3675–3685.

Bezier, A., Annaheim, M., Herbiniere, J., Wetterwald, C., Gyapay, G., BernardSamain, S., Wincker, P., Roditi, I., Heller, M., Belghazi, M., et al. (2009) ‘Polydnaviruses of braconid wasps derive from an ancestral nudivirus’, Science 323, 926–930.

Bian, G., Joshi, D., Dong, Y., Lu, P., Zhou, G., Pan, X., Xu, Y., Dimopoulos, G., and Xi, Z. (2013). ‘ Wolbachia invades Anopheles stephensi populations and induces refractoriness to Plasmodium infection’, Science 340, 748–751.

Bindels, L.B., Delzenne, N.M., Cani, P.D., and Walter, J. (2015) ‘Towards a more comprehensive concept for prebiotics’, Nat. Rev. Gastroenterol. Hepatol. 12, 303–310.

Blakeslee, S. (15 October 1996) ‘Microbial life’s steadfast champion’, New York Times .

Blaser, M. (1 February 2005) ‘An endangered species in the stomach; Sci. Am .

Blaser, M. (2010) ‘Helicobacter pylori and esophageal disease: wake-up call?’, Gastroenterology 139, 1819–1822.

Blaser, M. (2014) Missing Microbes: How the Overuse of Antibiotics Is Fueling Our Modern Plagues (New York: Henry Holt & Co.).

Blaser, M. and Falkow, S. (2009) ‘What are the consequences of the disappearing human microbiota?’ Nat. Rev. Microbiol. 7, 887–894.

Blazejak, A., Erseus, C., Amann, R., and Dubilier, N. (2005) ‘Coexistence of bacterial sulfide oxidizers, sulfate reducers, and spirochetes in a gutless worm (Oligochaeta) from the Peru Margin’, Appl. Environ. Microbiol. 71, 1553–1561.

Bletz, M.C., Loudon, A.H., Becker, M.H., Bell, S.C., Woodhams, D.C., Minbiole, K.P.C., and Harris, R.N. (2013) ‘Mitigating amphibian chytridiomycosis with bioaugmentation: characteristics of effective probiotics and strategies for their selection and use’, Ecol. Lett. 16, 807–820.

Blumberg, R. and Powrie, F. (2012) ‘Microbiota, disease, and back to health: a metastable journey’, Sci. Transl. Med. 4, 137rv7–rv137rv7.

Bode, L. (2012) ‘Human milk oligosaccharides: every baby needs a sugar mama’, Glycobiology 22, 1147–1162.

Bode, L., Kuhn, L., Kim, H-Y., Hsiao, L., Nissan, C., Sinkala, M., Kankasa, C., Mwiya, M., Thea, D.M., and Aldrovandi, G.M. (2012) ‘Human milk oligosaccharide concentration and risk of postnatal transmission of HIV through breastfeeding’, Am. J. Clin. Nutr. 96, 831–839.

Bohnhoff, M., Miller, C.P., and Martin, W.R. (1964) ‘Resistance of the mouse’s intestinal tract to experimental Salmonella infection’, J. Exp. Med. 120, 817–828.

Boone, C.K., Keefover-Ring, K., Mapes, A.C., Adams, A.S., Bohlmann, J., and Raffa, K.F. (2013) ‘Bacteria associated with a tree-killing insect reduce concentrations of plant defense compounds’, J. Chem. Ecol. 39, 1003–1006.

Bordenstein, S.R. and Theis, K.R. (2015) ‘Host biology in light of the microbiome: ten principles of holobionts and hologenomes’, PLoS Biol. 13, e1002226.

Bordenstein, S.R., O’Hara, F.P., and Werren, J.H. (2001) ‘ Wolbachia -induced incompatibility precedes other hybrid incompatibilities in Nasonia’, Nature 409, 707–710.

Bosch, T.C. (2012) ‘What Hydra has to say about the role and origin of symbiotic interactions’, Biol. Bull. 223, 78–84.

Boto, L. (2014) ‘Horizontal gene transfer in the acquisition of novel traits by metazoans’, Proc. R. Soc. B Biol. Sci. 281, doi: 10.1098/rspb.2013.2450.

Bouskra, D., Brézillon, C., Bérard, M., Werts, C., Varona, R., Boneca, I.G., and Eberl, G. (2008) ‘Lymphoid tissue genesis induced by commensals through NOD1 regulates intestinal homeostasis’, Nature 456, 507–510.

Bouslimani, A., Porto, C., Rath, C.M., Wang, M., Guo, Y., Gonzalez, A., Berg-Lyon, D., Ackermann, G., Moeller Christensen, G.J., Nakatsuji, T. et al. (2015) ‘Molecular cartography of the human skin surface in 3D’, Proc. Natl. Acad. Sci. U. S. A. 112, E2120–E2129.

Braniste, V., Al-Asmakh, M., Kowal, C., Anuar, F., Abbaspour, A., Tóth, M., Korecka, A., Bakocevic, N., Ng, L.G., Kundu, P. et al. (2014) ‘The gut microbiota influences blood-brain barrier permeability in mice’, Sci. Transl. Med. 6, 263ra158.

Bravo, J.A., Forsythe, P., Chew, M.V., Escaravage, E., Savignac, H.M., Dinan, T.G., Bienenstock, J., and Cryan, J.F. (2011) ‘Ingestion of Lactobacillus strain regulates emotional behavior and central GABA receptor expression in a mouse via the vagus nerve’, Proc. Natl. Acad. Sci. 108, 16050–16055.

Broderick, N.A., Raffa, K.F., and Handelsman, J. (2006) ‘Midgut bacteria required for Bacillus thuringiensis insecticidal activity’, Proc. Natl. Acad. Sci. 103, 15196–15199.

Brown, C.T., Hug, L.A., Thomas, B.C., Sharon, I., Castelle, C.J., Singh, A., Wilkins, M.J., Wrighton, K.C., Williams, K.H., and Banfield, J.F. (2015) ‘Unusual biology across a group comprising more than 15% of domain bacteria’, Nature 523, 208–211.

Brown, E.M., Arrieta, M-C., and Finlay, B.B. (2013) ‘A fresh look at the hygiene hypothesis: how intestinal microbial exposure drives immune effector responses in atopic disease’, Semin. Immunol. 25, 378–387.

Bruce-Keller, A.J., Salbaum, J.M., Luo, M., Blanchard, E., Taylor, C.M., Welsh, D.A., and Berthoud, H-R. (2015) ‘Obese-type gut microbiota induce neurobehavioral changes in the absence of obesity’, Biol. Psychiatry 77, 607–615.

Brucker, R.M. and Bordenstein, S.R. (2013) ‘The hologenomic basis of speciation: gut bacteria cause hybrid lethality in the genus Nasonia’, Science 341, 667–669.

Brucker, R.M., and Bordenstein, S.R. (2014) Response to Comment on ‘The hologenomic basis of speciation: gut bacteria cause hybrid lethality in the genus Nasonia’, Science 345, 1011–1011.

Bshary, R. (2002) ‘Biting cleaner fish use altruism to deceive image-scoring client reef fish’, Proc. Biol. Sci. 269, 2087–2093.

Buchner, P. (1965) Endosymbiosis of Animals with Plant Microorganisms (New York: Interscience Publishers / John Wiley).

Buffie, C.G., Bucci, V., Stein, R.R., McKenney, P.T., Ling, L., Gobourne, A., No, D., Liu, H., Kinnebrew, M., Viale, A., et al. (2014) ‘Precision microbiome reconstitution restores bile acid mediated resistance to Clostridium difficile ’, Nature 517, 205–208.

Bull, J.J. and Turelli, M. (2013) ‘ Wolbachia versus dengue: evolutionary forecasts’, Evol. Med. Public Health 2013, 197–201.

Bulloch, W. (1938) The History of Bacteriology (Oxford: Oxford University Press).

Cadwell, K., Patel, K.K., Maloney, N.S., Liu, T-C., Ng, A.C.Y., Storer, C.E., Head, R.D., Xavier, R., Stappenbeck, T.S., and Virgin, H.W. (2010) ‘Virus-plussusceptibility gene interaction determines Crohn’s Disease gene Atg16L1 phenotypes in intestine’, Cell 141, 1135–1145.

Cafaro, M.J., Poulsen, M., Little, A.E.F., Price, S.L., Gerardo, N.M., Wong, B., Stuart, A.E., Larget, B., Abbot, P., and Currie, C.R. (2011) ‘Specificity in the symbiotic association between fungus-growing ants and protective Pseudonocardia bacteria’, Proc. R. Soc. B Biol. Sci. 278, 1814–1822.

Campbell, M.A., Leuven, J.T.V., Meister, R.C., Carey, K.M., Simon, C., and McCutcheon, J.P. (2015), ‘Genome expansion via lineage splitting and genome reduction in the cicada endosymbiont Hodgkinia’, Proc. Natl. Acad. Sci. 112, 10192–10199.

Caporaso, J.G., Lauber, C.L., Costello, E.K., Berg-Lyons, D., Gonzalez, A., Stombaugh, J., Knights, D., Gajer, P., Ravel, J., and Fierer, N. (2011) ‘Moving pictures of the human microbiome’, Genome Biol. 12, R50.

Carmody, R.N. and Turnbaugh, P.J. (2014) ‘Host–microbial interactions in the metabolism of therapeutic and diet-derived xenobiotics’, J. Clin. Invest. 124, 4173–4181.

Caspi-Fluger, A., Inbar, M., Mozes-Daube, N., Katzir, N., Portnoy, V., Belausov, E., Hunter, M.S., and Zchori-Fein, E. (2012) ‘Horizontal transmission of the insect symbiont Rickettsia is plant-mediated’, Proc. R. Soc. B Biol. Sci. 279, 1791–1796.

Cavanaugh, C.M., Gardiner, S.L., Jones, M.L., Jannasch, H.W., and Waterbury, J.B. (1981) ‘Prokaryotic cells in the hydrothermal vent tube worm Riftia pachyptila Jones: possible chemoautotrophic symbionts’, Science 213, 340–342.

Ceja-Navarro, J.A., Vega, F.E., Karaoz, U., Hao, Z., Jenkins, S., Lim, H.C., Kosina, P., Infante, F., Northen, T.R., and Brodie, E.L. (2015) ‘Gut microbiota mediate caffeine detoxification in the primary insect pest of coffee’, Nat. Commun. 6, 7618.

Chandler, J.A. and Turelli, M. (2014) Comment on ‘The hologenomic basis of speciation: gut bacteria cause hybrid lethality in the genus Nasonia’, Science 345, 1011–1011.

Chassaing, B., Koren, O., Goodrich, J.K., Poole, A.C., Srinivasan, S., Ley, R.E., and Gewirtz, A.T. (2015) ‘Dietary emulsifiers impact the mouse gut microbiota promoting colitis and metabolic syndrome’, Nature 519, 92–96.

Chau, R., Kalaitzis, J.A., and Neilan, B.A. (2011) ‘On the origins and biosynthesis of tetrodotoxin’, Aquat. Toxicol. Amst. Neth. 104, 61–72.

Cheesman, S.E. and Guillemin, K. (2007) ‘We know you are in there: conversing with the indigenous gut microbiota’, Res. Microbiol. 158, 2–9.

Chen, Y., Segers, S., and Blaser, M.J. (2013) ‘Association between Helicobacter pylori and mortality in the NHANES III study’, Gut 62, 1262–1269.

Chichlowski, M., German, J.B., Lebrilla, C.B., and Mills, D.A. (2011) ‘The influence of milk oligosaccharides on microbiota of infants: opportunities for formulas’, Annu. Rev. Food Sci. Technol. 2, 331–351.

Cho, I. and Blaser, M.J. (2012) ‘The human microbiome: at the interface of health and disease’, Nat. Rev. Genet. 13, 260–270.

Cho, I., Yamanishi, S., Cox, L., Methé, B.A., Zavadil, J., Li, K., Gao, Z., Mahana, D., Raju, K., Teitler, I., et al. (2012) ‘Antibiotics in early life alter the murine colonic microbiome and adiposity’, Nature 488, 621–626.

Chou, S., Daugherty, M.D., Peterson, S.B., Biboy, J., Yang, Y., Jutras, B.L., FritzLaylin, L.K., Ferrin, M.A., Harding, B.N., Jacobs-Wagner, C., et al. (2014) ‘Transferred interbacterial antagonism genes augment eukaryotic innate immune function’, Nature 518, 98–101.

Chrostek, E., Marialva, M.S.P., Esteves, S.S., Weinert, L.A., Martinez, J., Jiggins, F.M., and Teixeira, L. (2013) ‘ Wolbachia variants induce differential protection to viruses in Drosophila melanogaster: a phenotypic and phylogenomic analysis’, PLoS Genet. 9, e1003896.

Chu, C-C., Spencer, J.L., Curzi, M.J., Zavala, J.A., and Seufferheld, M.J. (2013) ‘Gut bacteria facilitate adaptation to crop rotation in the western corn rootworm’, Proc. Natl. Acad. Sci. 110, 11917–11922.

Chung, K-T. and Bryant, M.P. (1997) ‘Robert E. Hungate: pioneer of anaerobic microbial ecology’, Anaerobe 3, 213–217.

Chung, K-T. and Ferris, D.H. (1996) ‘Martinus Willem Beijerinck’, ASM News 62, 539–543.

Chung, H., Pamp, S.J., Hill, J.A., Surana, N.K., Edelman, S.M., Troy, E.B., Reading , N.C., Villablanca, E.J., Wang, S., Mora, J.R., et al. (2012) ‘Gut immune maturation depends on colonization with a host-specific microbiota’, Cell 149, 1578–1593.

Chung, S.H., Rosa, C., Scully, E.D., Peiffer, M., Tooker, J.F., Hoover, K., Luthe, D.S., and Felton, G.W. (2013) ‘Herbivore exploits orally secreted bacteria to suppress plant defenses’, Proc. Natl. Acad. Sci . U. S. A. 110, 15728–15733.

Ciorba, M.A. (2012) ‘A gastroenterologist’s guide to probiotics’, Clin. Gastroenterol. Hepatol. 10, 960–968.

Claesen, J. and Fischbach, M.A. (2015) ‘Synthetic microbes as drug delivery systems’, ACS Synth. Biol. 4, 358–364.

Clayton, A.L., Oakeson, K.F., Gutin, M., Pontes, A., Dunn, D.M., von Niederhausern, A.C., Weiss, R.B., Fisher, M., and Dale, C. (2012) ‘A novel human-infectionderived bacterium provides insights into the evolutionary origins of mutualistic insect–bacterial symbioses’, PLoS Genet. 8, e1002990.

Clayton, T.A., Baker, D., Lindon, J.C., Everett, J.R., and Nicholson, J.K. (2009) ‘Pharmacometabonomic identification of a significant host–microbiome metabolic interaction affecting human drug metabolism’, Proc. Natl. Acad. Sci. U. S. A. 106, 14728–14733.

Clemente, J.C., Pehrsson, E.C., Blaser, M.J., Sandhu, K., Gao, Z., Wang, B., Magris, M., Hidalgo, G., Contreras, M., Noya-Alarcon, O., et al. (2015) ‘The microbiome of uncontacted Amerindians’, Sci. Adv. 1, e1500183.

Cobb, M. (3 June 2013) ‘Oswald T. Avery, the unsung hero of genetic science’, The Guardian .

Cockburn, S.N., Haselkorn, T.S., Hamilton, P.T., Landzberg, E., Jaenike, J., and Perlman, S.J. (2013) ‘Dynamics of the continent-wide spread of a Drosophila defensive symbiont’, Ecol. Lett. 16, 609–616.

Collins, S.M., Surette, M., and Bercik, P. (2012) ‘The interplay between the intestinal microbiota and the brain’, Nat. Rev. Microbiol. 10, 735–742.

Coon, K.L., Vogel, K.J., Brown, M.R., and Strand, M.R. (2014) ‘Mosquitoes rely on their gut microbiota for development’, Mol. Ecol. 23, 2727–2739.

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.

Cox, L.M. and Blaser, M.J. (2014) ‘Antibiotics in early life and obesity’, Nat. Rev. Endocrinol. 11, 182–190.

Cox, L.M., Yamanishi, S., Sohn, J., Alekseyenko, A.V., Leung, J.M., Cho, I., Kim, S.G., Li, H., Gao, Z., Mahana, D., et al. (2014) ‘Altering the intestinal microbiota during a critical developmental window has lasting metabolic consequences’, Cell 158, 705–721.

Cryan, J.F. and Dinan, T.G. (2012) ‘Mind-altering microorganisms: the impact of the gut microbiota on brain and behaviour’, Nat. Rev. Neurosci. 13, 701–712.

CSIROpedia Leucaena toxicity solution.

Dalal, S.R., and Chang, E.B. (2014) ‘The microbial basis of inflammatory bowel diseases’, J. Clin. Invest. 124, 4190–4196.

Dale, C. and Moran, N.A. (2006) ‘Molecular interactions between bacterial symbionts and their hosts’, Cell 126, 453–465.

Danchin, E.G.J. and Rosso, M-N. (2012) ‘Lateral gene transfers have polished animal genomes: lessons from nematodes’, Front. Cell. Infect. Microbiol. 2. doi: 10.3389/fcimb.2012.00027.

Danchin, E.G.J., Rosso, M-N., Vieira, P., de Almeida-Engler, J., Coutinho, P.M., Henrissat, B., and Abad, P. (2010) ‘Multiple lateral gene transfers and duplications have promoted plant parasitism ability in nematodes’, Proc. Natl. Acad. Sci. 107, 17651–17656.

Darmasseelane, K., Hyde, M.J., Santhakumaran, S., Gale, C., and Modi, N. (2014) ‘Mode of delivery and offspring body mass index, overweight and obesity in adult life: a systematic review and meta-analysis’, PloS One 9, e87896.

David, L.A., Maurice, C.F., Carmody, R.N., Gootenberg, D.B., Button, J.E., Wolfe, B.E., Ling, A.V., Devlin, A.S., Varma, Y., Fischbach, M.A., et al. (2013) ‘Diet rapidly and reproducibly alters the human gut microbiome’, Nature 505, 559–563.

David, L.A., Materna, A.C., Friedman, J., Campos-Baptista, M.I., Blackburn, M.C., Perrotta, A., Erdman, S.E., and Alm, E.J. (2014) ‘Host lifestyle affects human microbiota on daily timescales’, Genome Biol . 15, R89.

Dawkins, Richard (1982) The Extended Phenotype (Oxford: Oxford University Press).

De Filippo, C., Cavalieri, D., Di Paola, M., Ramazzotti, M., Poullet, J.B., Massart, S., Collini, S., Pieraccini, G., and Lionetti, P. (2010) ‘Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa’, Proc. Natl. Acad. Sci. 107, 14691–14696.

Delsuc, F., Metcalf, J.L., Wegener Parfrey, L., Song, S.J., González, A., and Knight, R. (2014) ‘Convergence of gut microbiomes in myrmecophagous mammals’, Mol. Ecol. 23, 1301–1317.

Delzenne, N.M., Neyrinck, A.M., and Cani, P.D. (2013) ‘Gut microbiota and metabolic disorders: how prebiotic can work?’ Br. J. Nutr. 109, S81–S85.

Derrien, M., and van Hylckama Vlieg, J.E.T. (2015) ‘Fate, activity, and impact of ingested bacteria within the human gut microbiota’, Trends Microbiol. 23, 354–366.

Dethlefsen, L. and Relman, D.A. (2011) ‘Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation’, Proc. Natl. Acad. Sci. 108, 4554–4561.

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.

Dethlefsen, L., Huse, S., Sogin, M.L., and Relman, D.A. (2008) ‘The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing’, PLoS Biol. 6, e280.

Devkota, S., Wang, Y., Musch, M.W., Leone, V., Fehlner-Peach, H., Nadimpalli, A., Antonopoulos, D.A., Jabri, B., and Chang, E.B. (2012) ‘Dietary-fat-induced taurocholic acid promotes pathobiont expansion and colitis in ll10−/− mice’, Nature 487, 104–108.

Dill-McFarland, K.A., Weimer, P.J., Pauli, J.N., Peery, M.Z., and Suen, G. (2015) ‘Diet specialization selects for an unusual and simplified gut microbiota in two- and three-toed sloths’, Environ. Microbiol. 509, 357–360.

Dillon, R.J., Vennard, C.T., and Charnley, A.K. (2000) ‘Pheromones: exploitation of gut bacteria in the locust’, Nature 403, 851.

Ding, T. and Schloss, P.D. (2014) ‘Dynamics and associations of microbial community types across the human body’, Nature 509, 357–360.

Dinsdale, E.A., Pantos, O., Smriga, S., Edwards, R.A., Angly, F., Wegley, L., Hatay, M., Hall, D., Brown, E., Haynes, M., et al. (2008) ‘Microbial ecology of four coral atolls in the Northern Line Islands’, PLoS ONE 3, e1584.

Dobell, C. (1932) Antony Van Leeuwenhoek and His ‘Little Animals’ (New York: Dover Publications).

Dobson, A.J., Chaston, J.M., Newell, P.D., Donahue, L., Hermann, S.L., Sannino, D.R., Westmiller, S., Wong, A.C-N., Clark, A.G., Lazzaro, B.P., et al. (2015) ‘Host genetic determinants of microbiota-dependent nutrition revealed by genome-wide analysis of Drosophila melanogaster’, Nat. Commun. 6, 6312.

Dodd, D.M.B. (1989) ‘Reproductive isolation as a consequence of adaptive divergence in Drosophila pseudoobscura’, Evolution 43, 1308–1311.

Dominguez-Bello, M.G., Costello, E.K., Contreras, M., Magris, M., Hidalgo, G., Fierer, N., and Knight, R. (2010) ‘Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns’, Proc. Natl. Acad. Sci. 107, 11971–11975.

Dorrestein, P.C., Mazmanian, S.K., and Knight, R. (2014) ‘Finding the missing links among metabolites, microbes, and the host’, Immunity 40, 824–832.

Doudoumis, V., Alam, U., Aksoy, E., Abd-Alla, A.M.M., Tsiamis, G., Brelsfoard, C., Aksoy, S., and Bourtzis, K. (2013) ‘Tsetse– Wolbachia symbiosis: comes of age and has great potential for pest and disease control’, J. Invertebr. Pathol. 112, S94–S103.

Douglas, A.E. (2006) ‘Phloem-sap feeding by animals: problems and solutions’, J. Exp. Bot. 57, 747–754.

Douglas, A.E. (2008) ‘Conflict, cheats and the persistence of symbioses’, New Phytol. 177, 849–858.

Dubilier, N., Mülders, C., Ferdelman, T., de Beer, D., Pernthaler, A., Klein, M., Wagner, M., Erséus, C., Thiermann, F., Krieger, J., et al. (2001) ‘Endosymbiotic sulphate-reducing and sulphide-oxidizing bacteria in an oligochaete worm’, Nature 411, 298–302.

Dubilier, N., Bergin, C., and Lott, C. (2008) ‘Symbiotic diversity in marine animals: the art of harnessing chemosynthesis’, Nat. Rev. Microbiol. 6, 725–740.

Dubos, R.J. (1965) Man Adapting (New Haven and London: Yale University Press).

Dubos, R.J. (1987) Mirage of Health: Utopias, Progress, and Biological Change (New Brunswick, NJ: Rutgers University Press).

Dunlap, P.V. and Nakamura, M. (2011) ‘Functional morphology of the luminescence system of Siphamia versicolor (Perciformes: Apogonidae), a bacterially luminous coral reef fish’, J. Morphol. 272, 897–909.

Dunning-Hotopp, J.C. (2011) ‘Horizontal gene transfer between bacteria and animals’, Trends Genet. 27, 157–163.

Eakin, E. (1 December 2014) ‘The excrement experiment’, New Yorker .

Eckburg, P.B. (2005) ‘Diversity of the human intestinal microbial flora’, Science 308, 1635–1638.

Eisen, J. (2014) Overselling the microbiome award: Time Magazine & Martin Blaser for ‘antibiotics are extinguishing our microbiome’. http://phylogenomics.blogspot.co.uk/2014/05/overselling-microbiome-awardtime.html.

Elahi, S., Ertelt, J.M., Kinder, J.M., Jiang, T.T., Zhang, X., Xin, L., Chaturvedi, V., Strong, B.S., Qualls, J.E., Steinbrecher, K.A., et al. (2013) ‘Immunosuppressive CD71+ erythroid cells compromise neonatal host defence against infection’, Nature 504, 158–162.

Ellis, M.L., Shaw, K.J., Jackson, S.B., Daniel, S.L., and Knight, J. (2015) ‘Analysis of commercial kidney stone probiotic supplements’, Urology 85, 517–521.

Eskew, E.A. and Todd, B.D. (2013) ‘Parallels in amphibian and bat declines from pathogenic fungi’, Emerg. Infect. Dis. 19, 379–385.

Everard, A., Belzer, C., Geurts, L., Ouwerkerk, J.P., Druart, C., Bindels, L.B., Guiot, Y., Derrien, M., Muccioli, G.G., Delzenne, N.M., et al. (2013) ‘Cross-talk between Akkermansia muciniphila and intestinal epithelium controls dietinduced obesity’, Proc. Natl. Acad. Sci, 110, 9066–9071.

Ezenwa, V.O. and Williams, A.E. (2014) ‘Microbes and animal olfactory communication: where do we go from here?’, BioEssays 36, 847–854.

Faith, J.J., Guruge, J.L., Charbonneau, M., Subramanian, S., Seedorf, H., Goodman, A.L., Clemente, J.C., Knight, R., Heath, A.C., and Leibel, R.L. (2013) ‘The long-term stability of the human gut microbiota’, Science 341. doi: 10.1126/ science.1237439.

Falkow, S. (2013) Fecal Transplants in the ‘Good Old Days’. http://schaechter. asmblog.org/schaechter/2013/05/fecal-transplants-in-the-good-old-days.html.

Feldhaar, H. (2011) ‘Bacterial symbionts as mediators of ecologically important traits of insect hosts’, Ecol. Entomol. 36, 533–543.

Fierer, N., Hamady, M., Lauber, C.L., and Knight, R. (2008) ‘The influence of sex, handedness, and washing on the diversity of hand surface bacteria’, Proc. Natl. Acad. Sci. U. S. A. 105, 17994–17999.

Finucane, M.M., Sharpton, T.J., Laurent, T.J., and Pollard, K.S. (2014) ‘A taxonomic signature of obesity in the microbiome? Getting to the guts of the matter’, PLoS ONE 9, e84689.

Fischbach, M.A. and Sonnenburg, J.L. (2011) ‘Eating for two: how metabolism establishes interspecies interactions in the gut’, Cell Host Microbe 10, 336–347.

Folsome, C. (1985) Microbes, in The Biosphere Catalogue (Fort Worth, Texas: Synergistic Press).

Franzenburg, S., Walter, J., Kunzel, S., Wang, J., Baines, J.F., Bosch, T.C.G., and Fraune, S. (2013) ‘Distinct antimicrobial peptide expression determines host speciesspecific bacterial associations’, Proc. Natl. Acad. Sci. 110, E3730–E3738.

Fraune, S. and Bosch, T.C. (2007) ‘Long-term maintenance of species-specific bacterial microbiota in the basal metazoan Hydra’, Proc. Natl. Acad. Sci. 104, 13146–13151.

Fraune, S. and Bosch, T.C.G. (2010) ‘Why bacteria matter in animal development and evolution’, BioEssays 32, 571–580.

Fraune, S., Abe, Y., and Bosch, T.C.G. (2009) ‘Disturbing epithelial homeostasis in the metazoan Hydra leads to drastic changes in associated microbiota’, Environ. Microbiol. 11, 2361–2369.

Fraune, S., Augustin, R., Anton-Erxleben, F., Wittlieb, J., Gelhaus, C., Klimovich, V.B., Samoilovich, M.P., and Bosch, T.C.G. (2010) ‘In an early branching metazoan, bacterial colonization of the embryo is controlled by maternal antimicrobial peptides’, Proc. Natl. Acad. Sci. 107, 18067–18072.

Freeland, W.J. and Janzen, D.H. (1974) ‘Strategies in herbivory by mammals: the role of plant secondary compounds’, Am. Nat. 108, 269–289.

Frese, S.A., Benson, A.K., Tannock, G.W., Loach, D.M., Kim, J., Zhang, M., Oh, P.L., Heng, N.C.K., Patil, P.B., Juge, N., et al. (2011) ‘The evolution of host specialization in the vertebrate gut symbiont Lactobacillus reuteri’, PLoS Genet. 7, e1001314.

Fujimura, K.E. and Lynch, S.V. (2015) ‘Microbiota in allergy and asthma and the emerging relationship with the gut microbiome’, Cell Host Microbe 17, 592–602.

Fujimura, K.E., Demoor, T., Rauch, M., Faruqi, A.A., Jang, S., Johnson, C.C., Boushey, H.A., Zoratti, E., Ownby, D., Lukacs, N.W., et al. (2014) ‘House dust exposure mediates gut microbiome Lactobacillus enrichment and airway immune defense against allergens and virus infection’, Proc. Natl. Acad. Sci. 111, 805–810.

Funkhouser, L.J. and Bordenstein, S.R. (2013) ‘Mom knows best: the universality of maternal microbial transmission’, PLoS Biol. 11, e1001631.

Furusawa, Y., Obata, Y., Fukuda, S., Endo, T.A., Nakato, G., Takahashi, D., Nakanishi, Y., Uetake, C., Kato, K., Kato, T., et al. (2013) ‘Commensal microbe-derived butyrate induces the differentiation of colonic regulatory T cells’, Nature 504, 446–450.

Gajer, P., Brotman, R.M., Bai, G., Sakamoto, J., Schutte, U.M.E., Zhong, X., Koenig, S.S.K., Fu, L., Ma, Z., Zhou, X., et al. (2012) ‘Temporal dynamics of the human vaginal microbiota’, Sci. Transl. Med. 4, 132ra52–ra132ra52.

Garcia, J.R. and Gerardo, N.M. (2014) ‘The symbiont side of symbiosis: do microbes really benefit?’ Front. Microbiol. 5. doi: 10.3389/fmicb.2014.00510.

Gareau, M.G., Sherman, P.M., and Walker, W.A. (2010) ‘Probiotics and the gut microbiota in intestinal health and disease’, Nat. Rev. Gastroenterol. Hepatol. 7, 503–514.

Garrett, W.S., Lord, G.M., Punit, S., Lugo-Villarino, G., Mazmanian, S.K., Ito, S., Glickman, J.N., and Glimcher, L.H. (2007) ‘Communicable ulcerative colitis induced by T-bet deficiency in the innate immune system’, Cell 131, 33–45.

Garrett, W.S., Gallini, C.A., Yatsunenko, T., Michaud, M., DuBois, A., Delaney, M.L., Punit, S., Karlsson, M., Bry, L., Glickman, J.N., et al. (2010) ‘Enterobacteriaceae act in concert with the gut microbiota to induce spontaneous and maternally transmitted colitis’, Cell Host Microbe 8, 292–300.

Gehrer, L. and Vorburger, C. (2012) ‘Parasitoids as vectors of facultative bacterial endosymbionts in aphids’, Biol. Lett. 8, 613–615.

Gerrard, J.W., Geddes, C.A., Reggin, P.L., Gerrard, C.D., and Horne, S. (1976) ‘Serum IgE levels in white and Metis communities in Saskatchewan’, Ann. Allergy 37, 91–100.

Gerritsen, J., Smidt, H., Rijkers, G.T., and Vos, W.M. (2011) ‘Intestinal microbiota in human health and disease: the impact of probiotics’, Genes Nutr. 6, 209–240.

Gevers, D., Kugathasan, S., Denson, L.A., Vázquez-Baeza, Y., Van Treuren, W., Ren, B., Schwager, E., Knights, D., Song, S.J., Yassour, M., et al. (2014) ‘The treatment-naive microbiome in new-onset Crohn’s Disease’, Cell Host Microbe 15, 382–392.

Gibbons, S.M., Schwartz, T., Fouquier, J., Mitchell, M., Sangwan, N., Gilbert, J.A., and Kelley, S.T. (2015) ‘Ecological succession and viability of humanassociated microbiota on restroom surfaces’, Appl. Environ. Microbiol. 81, 765–773.

Gilbert, J.A. and Neufeld, J.D. (2014) ‘Life in a world without microbes’, PLoS Biol. 12, e1002020.

Gilbert, J.A., Meyer, F., Antonopoulos, D., Balaji, P., Brown, C.T., Desai, N., Eisen, J.A., Evers, D., Field, D., et al. (2010) ‘Meeting Report: The Terabase Metagenomics Workshop and the Vision of an Earth Microbiome Project’, Stand. Genomic Sci. 3, 243–248.

Gilbert, S.F., Sapp, J., and Tauber, A.I. (2012) ‘A symbiotic view of life: we have never been individuals’, Q. Rev. Biol. 87, 325–341.

Godoy-Vitorino, F., Goldfarb, K.C., Karaoz, U., Leal, S., Garcia-Amado, M.A., Hugenholtz, P., Tringe, S.G., Brodie, E.L., and Dominguez-Bello, M.G. (2012) ‘Comparative analyses of foregut and hindgut bacterial communities in hoatzins and cows’, ISME J. 6, 531–541.

Goldenberg, J.Z., Ma, S.S., Saxton, J.D., Martzen, M.R., Vandvik, P.O., Thorlund, K., Guyatt, G.H., and Johnston, B.C. (2013) ‘Probiotics for the prevention of Clostridium difficile -associated diarrhea in adults and children’, in Cochrane Database of Systematic Reviews, The Cochrane Collaboration , ed. (Chichester, UK: John Wiley & Sons).

Gomez, A., Petrzelkova, K., Yeoman, C.J., Burns, M.B., Amato, K.R., Vlckova, K., Modry, D., Todd, A., Robbinson, C.A.J., Remis, M., et al. (2015) ‘Ecological and evolutionary adaptations shape the gut microbiome of BaAka African rainforest hunter-gatherers’, bioRxiv 019232.

Goodrich, J.K., Waters, J.L., Poole, A.C., Sutter, J.L., Koren, O., Blekhman, R., Beaumont, M., Van Treuren, W., Knight, R., Bell, J.T., et al. (2014) ‘Human genetics shape the gut microbiome’, Cell 159, 789–799.

Graham, D.Y. (1997) ‘The only good Helicobacter pylori is a dead Helicobacter pylori ’, Lancet 350, 70–71; author reply 72.

Green, J. (2011). Are we filtering the wrong microbes? TED https://www.ted.com/talks/jessica_green_are_we_filtering_the_wrong_microbes.

Green, J.L. (2014) ‘Can bioinformed design promote healthy indoor ecosystems?’ Indoor Air 24, 113–115.

Gruber-Vodicka, H.R., Dirks, U., Leisch, N., Baranyi, C., Stoecker, K., Bulgheresi, S., Heindl, N.R., Horn, M., Lott, C., Loy, A., et al. (2011) ‘Paracatenula, an ancient symbiosis between thiotrophic Alphaproteobacteria and catenulid flatworms’, Proc. Natl. Acad. Sci. 108, 12078–12083.

Hadfield, M.G. (2011) ‘Biofilms and marine invertebrate larvae: what bacteria produce that larvae use to choose settlement sites’, Annu. Rev. Mar. Sci. 3, 453–470.

Haiser, H.J. and Turnbaugh, P.J. (2012) ‘Is it time for a metagenomic basis of therapeutics?’ Science 336, 1253–1255.

Haiser, H.J., Gootenberg, D.B., Chatman, K., Sirasani, G., Balskus, E.P., and Turnbaugh, P.J. (2013) ‘Predicting and manipulating cardiac drug inactivation by the human gut bacterium Eggerthella lenta’, Science 341, 295–298.

Hamilton, M.J., Weingarden, A.R., Unno, T., Khoruts, A., and Sadowsky, M.J. (2013) ‘High-throughput DNA sequence analysis reveals stable engraftment of gut microbiota following transplantation of previously frozen fecal bacteria’, Gut Microbes 4, 125–135.

Handelsman, J. (2007) ‘Metagenomics and microbial communities’, in Encyclopedia of Life Sciences (Chichester, UK: John Wiley & Sons).

Harley, I.T.W. and Karp, C.L. (2012) ‘Obesity and the gut microbiome: striving for causality’, Mol. Metab. 1, 21–31.

Harris, R.N., James, T.Y., Lauer, A., Simon, M.A., and Patel, A. (2006) ‘Amphibian pathogen Batrachochytrium dendrobatidis is inhibited by the cutaneous bacteria of amphibian species’, EcoHealth 3, 53–56.

Harris, R.N., Brucker, R.M., Walke, J.B., Becker, M.H., Schwantes, C.R., Flaherty, D.C., Lam, B.A., Woodhams, D.C., Briggs, C.J., Vredenburg, V.T., et al. (2009) ‘Skin microbes on frogs prevent morbidity and mortality caused by a lethal skin fungus’, ISME J. 3, 818–824.

Haselkorn, T.S., Cockburn, S.N., Hamilton, P.T., Perlman, S.J., and Jaenike, J. (2013) ‘Infectious adaptation: potential host range of a defensive endosymbiont in Drosophila: host range of Spiroplasma in Drosophila’, Evolution 67, 934–945.

Hecht, G.A., Blaser, M.J., Gordon, J., Kaplan, L.M., Knight, R., Laine, L., Peek, R., Sanders, M.E., Sartor, B., Wu, G.D., et al. (2014) ‘What is the value of a food and drug administration investigational new drug application for fecal microbiota transplantation to treat Clostridium difficile infection?’ Clin. Gastroenterol. Hepatol. Off. Clin. Pract. J. Am . Gastroenterol. Assoc. 12, 289–291.

Hedges, L.M., Brownlie, J.C., O’Neill, S.L., and Johnson, K.N. (2008) ‘ Wolbachia and virus protection in insects’, Science 322, 702.

Hehemann, J-H., Correc, G., Barbeyron, T., Helbert, W., Czjzek, M., and Michel, G. (2010) ‘Transfer of carbohydrate-active enzymes from marine bacteria to Japanese gut microbiota’, Nature 464, 908–912.

Heijtz, R.D., Wang, S., Anuar, F., Qian, Y., Bjorkholm, B., Samuelsson, A., Hibberd, M.L., Forssberg, H., and Pettersson, S. (2011) ‘Normal gut microbiota modulates brain development and behavior’, Proc. Natl. Acad. Sci. 108, 3047–3052.

Heil, M., Barajas-Barron, A., Orona-Tamayo, D., Wielsch, N., and Svatos, A. (2014) ‘Partner manipulation stabilises a horizontally transmitted mutualism’, Ecol. Lett. 17, 185–192.

Henry, L.M., Peccoud, J., Simon, J-C., Hadfield, J.D., Maiden, M.J.C., Ferrari, J., and Godfray, H.C.J. (2013) ‘Horizontally transmitted symbionts and host colonization of ecological niches’, Curr. Biol. 23, 1713–1717.

Herbert, E.E. and Goodrich-Blair, H. (2007) ‘Friend and foe: the two faces of Xenorhabdus nematophila’, Nat. Rev. Microbiol. 5, 634–646.

Herniou, E.A., Huguet, E., Thézé, J., Bézier, A., Periquet, G., and Drezen, J-M. (2013) ‘When parasitic wasps hijacked viruses: genomic and functional evolution of polydnaviruses’, Philos. Trans. R. Soc. Lond. B Biol. Sci. 368, 20130051.

Hilgenboecker, K., Hammerstein, P., Schlattmann, P., Telschow, A., and Werren, J.H. (2008) ‘How many species are infected with Wolbachia ? – a statistical analysis of current data: Wolbachia infection rates’, FEMS Microbiol. Lett. 281, 215–220.

Hill, C., Guarner, F., Reid, G., Gibson, G.R., Merenstein, D.J., Pot, B., Morelli, L., Canani, R.B., Flint, H.J., Salminen, S., et al. (2014) ‘Expert consensus document: The International Scientific Association for Probiotics and Prebiotics consensus statement on the scope and appropriate use of the term probiotic’, Nat. Rev. Gastroenterol. Hepatol. 11, 506–514.

Himler, A.G., Adachi-Hagimori, T., Bergen, J.E., Kozuch, A., Kelly, S.E., Tabashnik, B.E., Chiel, E., Duckworth, V.E., Dennehy, T.J., Zchori-Fein, E., et al. (2011) ‘Rapid spread of a bacterial symbiont in an invasive whitefly is driven by fitness benefits and female bias’, Science 332, 254–256.

Hird, S.M., Carstens, B.C., Cardiff, S.W., Dittmann, D.L., and Brumfield, R.T. (2014) ‘Sampling locality is more detectable than taxonomy or ecology in the gut microbiota of the brood-parasitic Brown-headed Cowbird (Molothrus ater)’, PeerJ 2 , e321.

Hiss, P.H. and Zinsser, H. (1910) A Text-book of Bacteriology: a Practical Treatise for Students and Practitioners of Medicine (New York and London: D. Appleton & Co.).

Hoerauf, A., Volkmann, L., Hamelmann, C., Adjei, O., Autenrieth, I.B., Fleischer, B., and Büttner, D.W. (2000) ‘Endosymbiotic bacteria in worms as targets for a novel chemotherapy in filariasis’, Lancet 355, 1242–1243.

Hoerauf, A., Mand, S., Adjei, O., Fleischer, B., and Büttner, D.W. (2001) ‘Depletion of Wolbachia endobacteria in Onchocerca volvulus by doxycycline and microfilaridermia after ivermectin treatment’, Lancet 357, 1415–1416.

Hof, C., Araújo, M.B., Jetz, W., and Rahbek, C. (2011) ‘Additive threats from pathogens, climate and land-use change for global amphibian diversity’, Nature 480, 516–519.

Hoffmann, A.A., Montgomery, B.L., Popovici, J., Iturbe-Ormaetxe, I., Johnson, P.H., Muzzi, F., Greenfield, M., Durkan, M., Leong, Y.S., Dong, Y., et al. (2011) ‘Successful establishment of Wolbachia in Aedes populations to suppress dengue transmission’, Nature 476, 454–457.

Holmes, E., Kinross, J., Gibson, G., Burcelin, R., Jia, W., Pettersson, S., and Nicholson, J. (2012) ‘Therapeutic modulation of microbiota–host metabolic interactions’, Sci. Transl. Med. 4, 137rv6.

Honda, K., and Littman, D.R. (2012). ‘The Microbiome in Infectious Disease and Inflammation’, Annu. Rev. Immunol. 30, 759–795.

Hongoh, Y. (2011) ‘Toward the functional analysis of uncultivable, symbiotic microorganisms in the termite gut’, Cell. Mol. Life Sci. 68, 1311–1325.

Hooper, L.V. (2001) ‘Molecular analysis of commensal host-microbial relationships in the intestine’, Science 291, 881–884.

Hooper, L.V., Stappenbeck, T.S., Hong, C.V., and Gordon, J.I. (2003) ‘Angiogenins: a new class of microbicidal proteins involved in innate immunity’, Nat. Immunol. 4, 269–273.

Hooper, L.V., Littman, D.R., and Macpherson, A.J. (2012) ‘Interactions between the microbiota and the immune system’, Science 336, 1268–1273.

Hornett, E.A., Charlat, S., Wedell, N., Jiggins, C.D., and Hurst, G.D.D. (2009) ‘Rapidly shifting sex ratio across a species range’, Curr. Biol. 19, 1628–1631.

Hosokawa, T., Kikuchi, Y., Shimada, M., and Fukatsu, T. (2008) ‘Symbiont acquisition alters behaviour of stinkbug nymphs’, Biol. Lett. 4, 45–48.

Hosokawa, T., Koga, R., Kikuchi, Y., Meng, X.-Y., and Fukatsu, T. (2010). ‘ Wolbachia as a bacteriocyte-associated nutritional mutualist’, Proc. Natl. Acad. Sci. 107, 769–774.

Hosokawa, T., Hironaka, M., Mukai, H., Inadomi, K., Suzuki, N., and Fukatsu, T. (2012) ‘Mothers never miss the moment: a fine-tuned mechanism for vertical symbiont transmission in a subsocial insect’, Anim. Behav. 83, 293–300.

Hotopp, J.C.D., Clark, M.E., Oliveira, D.C.S.G., Foster, J.M., Fischer, P., Torres, M.C.M., Giebel, J.D., Kumar, N., Ishmael, N., Wang, S., et al. (2007) ‘Widespread lateral gene transfer from intracellular bacteria to multicellular eukaryotes’, Science 317, 1753–1756.

Hsiao, E.Y., McBride, S.W., Hsien, S., Sharon, G., Hyde, E.R., McCue, T., Codelli, J.A., Chow, J., Reisman, S.E., Petrosino, J.F., et al. (2013) ‘Microbiota modulate behavioral and physiological abnormalities associated with neurodevelopmental disorders’, Cell 155, 1451–1463.

Huang, L., Chen, Q., Zhao, Y., Wang, W., Fang, F., and Bao, Y. (2015) ‘Is elective Cesarean section associated with a higher risk of asthma? A meta-analysis’, J. Asthma Off. J. Assoc. Care Asthma 52, 16–25.

Hughes, G.L., Dodson, B.L., Johnson, R.M., Murdock, C.C., Tsujimoto, H., Suzuki, Y., Patt, A.A., Cui, L., Nossa, C.W., Barry, R.M., et al. (2014) ‘Native microbiome impedes vertical transmission of Wolbachia in Anopheles mosquitoes’, Proc. Natl. Acad. Sci. 111, 12498–12503.

Husnik, F., Nikoh, N., Koga, R., Ross, L., Duncan, R.P., Fujie, M., Tanaka, M., Satoh, N., Bachtrog, D., Wilson, A.C.C., et al. (2013) ‘Horizontal gene transfer from diverse bacteria to an insect genome enables a tripartite nested mealybug symbiosis’, Cell 153, 1567–1578.

Huttenhower, C., Gevers, D., Knight, R., Abubucker, S., Badger, J.H., Chinwalla, A.T., Creasy, H.H., Earl, A.M., FitzGerald, M.G., Fulton, R.S., et al. (2012) ‘Structure, function and diversity of the healthy human microbiome’, Nature 486, 207–214.

Huttenhower, C., Kostic, A.D., and Xavier, R.J. (2014) ‘Inflammatory bowel disease as a model for translating the microbiome’, Immunity 40, 843–854.

Iturbe-Ormaetxe, I., Walker, T., and O’ Neill, S.L. (2011) ‘ Wolbachia and the biological control of mosquito-borne disease’, EMBO Rep . 12, 508–518.

Ivanov, I.I., Atarashi, K., Manel, N., Brodie, E.L., Shima, T., Karaoz, U., Wei, D., Goldfarb, K.C., Santee, C.A., Lynch, S.V., et al. (2009) ‘Induction of intestinal Th17 cells by segmented filamentous bacteria’, Cell 139, 485–498.

Jaenike, J., Polak, M., Fiskin, A., Helou, M., and Minhas, M. (2007) ‘Interspecific transmission of endosymbiotic Spiroplasma by mites’, Biol. Lett. 3, 23–25.

Jaenike, J., Unckless, R., Cockburn, S.N., Boelio, L.M., and Perlman, S.J. (2010) ‘Adaptation via symbiosis: recent spread of a Drosophila defensive symbiont’, Science 329, 212–215.

Jakobsson, H.E., Jernberg, C., Andersson, A.F., Sjölund-Karlsson, M., Jansson, J.K., and Engstrand, L. (2010) ‘Short-term antibiotic treatment has differing long-term impacts on the human throat and gut microbiome’, PLoS ONE 5, e9836.

Jansson, J.K. and Prosser, J.I. (2013) ‘Microbiology: the life beneath our feet’, Nature 494, 40–41.

Jefferson, R. (2010). The hologenome theory of evolution – Science as Social Enterprise. http://blogs.cambia.org/ raj/ 2010/11/16/the-hologenome-theoryof-evolution/.

Jernberg, C., Lofmark, S., Edlund, C., and Jansson, J.K. (2010) ‘Long-term impacts of antibiotic exposure on the human intestinal microbiota’, Microbiology 156, 3216–3223.

Jiggins, F.M. and Hurst, G.D.D. (2011) ‘Rapid insect evolution by symbiont transfer’, Science 332, 185–186.

Johnston, K.L., Ford, L., and Taylor, M.J. (2014) ‘Overcoming the challenges of drug discovery for neglected tropical diseases: the A·WoL experience’, J. Biomol. Screen. 19, 335–343.

Jones, R.J. and Megarrity, R.G. (1986) ‘Successful transfer of DHP-degrading bacteria from Hawaiian goats to Australian ruminants to overcome the toxicity of Leucaena’, Aust. Vet. J. 63, 259–262.

Kaiser, W., Huguet, E., Casas, J., Commin, C., and Giron, D. (2010) ‘Plant greenisland phenotype induced by leaf-miners is mediated by bacterial symbionts’, Proc. R. Soc. B Biol. Sci. 277, 2311–2319.

Kaiwa, N., Hosokawa, T., Nikoh, N., Tanahashi, M., Moriyama, M., Meng, X-Y., Maeda, T., Yamaguchi, K., Shigenobu, S., Ito, M., et al. (2014) ‘Symbiontsupplemented maternal investment underpinning host’s ecological adaptation’, Curr. Biol. 24, 2465–2470.

Kaltenpoth, M., Göttler, W., Herzner, G., and Strohm, E. (2005) ‘Symbiotic bacteria protect wasp larvae from fungal infestation’, Curr. Biol. 15, 475–479.

Kaltenpoth, M., Roeser-Mueller, K., Koehler, S., Peterson, A., Nechitaylo, T.Y., Stubblefield, J.W., Herzner, G., Seger, J., and Strohm, E. (2014) ‘Partner choice and fidelity stabilize coevolution in a Cretaceous-age defensive symbiosis’, Proc. Natl. Acad. Sci. 111, 6359–6364.

Kane, M., Case, L.K., Kopaskie, K., Kozlova, A., MacDearmid, C., Chervonsky, A.V., and Golovkina, T.V. (2011) ‘Successful transmission of a retrovirus depends on the commensal microbiota’, Science 334, 245–249.

Karasov, W.H., Martínez del Rio, C., and Caviedes-Vidal, E. (2011) ‘Ecological physiology of diet and digestive systems’, Annu. Rev. Physiol. 73, 69–93.

Katan, M.B. (2012) ‘Why the European Food Safety Authority was right to reject health claims for probiotics’, Benef. Microbes 3, 85–89.

Kau, A.L., Planer, J.D., Liu, J., Rao, S., Yatsunenko, T., Trehan, I., Manary, M.J., Liu, T-C., Stappenbeck, T.S., Maleta, K.M., et al. (2015) ‘Functional characterization of IgA-targeted bacterial taxa from undernourished Malawian children that produce diet-dependent enteropathy’, Sci. Transl. Med. 7, 276ra24–ra276ra24.

Keeling, P.J. and Palmer, J.D. (2008) ‘Horizontal gene transfer in eukaryotic evolution’, Nat. Rev. Genet. 9, 605–618.

Kelly, L.W., Barott, K.L., Dinsdale, E., Friedlander, A.M., Nosrat, B., Obura, D., Sala, E., Sandin, S.A., Smith, J.E., and Vermeij, M.J. (2012) ‘Black reefs: iron-induced phase shifts on coral reefs’, ISME J . 6, 638–649.

Kembel, S.W., Jones, E., Kline, J., Northcutt, D., Stenson, J., Womack, A.M., Bohannan, B.J., Brown, G.Z., and Green, J.L. (2012) ‘Architectural design influences the diversity and structure of the built environment microbiome’, ISME J . 6, 1469–1479.

Kembel, S.W., Meadow, J.F., O’Connor, T.K., Mhuireach, G., Northcutt, D., Kline, J., Moriyama, M., Brown, G.Z., Bohannan, B.J.M., and Green, J.L. (2014) ‘Architectural design drives the biogeography of indoor bacterial communities’, PLoS ONE 9, e87093.

Kendall, A.I. (1909) ‘Some observations on the study of the intestinal bacteria’, J. Biol. Chem. 6, 499–507.

Kendall, A.I. (1921) Bacteriology, General, Pathological and Intestinal (Philadelphia and New York: Lea & Febiger).

Kendall, A.I. (1923) Civilization and the Microbe (Boston: Houghton Mifflin).

Kernbauer, E., Ding, Y., and Cadwell, K. (2014) ‘An enteric virus can replace the beneficial function of commensal bacteria’, Nature 516, 94–98.

Khoruts, A. (2013) ‘Faecal microbiota transplantation in 2013: developing human gut microbiota as a class of therapeutics’, Nat. Rev. Gastroenterol. Hepatol. 11, 79–80.

Kiers, E.T. and West, S.A. (2015) ‘Evolving new organisms via symbiosis’, Science 348, 392–394.

Kikuchi, Y., Hayatsu, M., Hosokawa, T., Nagayama, A., Tago, K., and Fukatsu, T. (2012) ‘Symbiont-mediated insecticide resistance’, Proc. Natl. Acad. Sci. 109, 8618–8622.

Kilpatrick, A.M., Briggs, C.J., and Daszak, P. (2010) ‘The ecology and impact of chytridiomycosis: an emerging disease of amphibians’, Trends Ecol. Evol. 25, 109–118.

Kirk, R.G. (2012) ‘“Life in a germ-free world” : isolating life from the laboratory animal to the bubble boy’, Bull. Hist. Med. 86, 237–275.

Koch, H. and Schmid-Hempel, P. (2011) ‘Socially transmitted gut microbiota protect bumble bees against an intestinal parasite’, Proc. Natl. Acad. Sci. 108, 19288–19292.

Kohl, K.D., Weiss, R.B., Cox, J., Dale, C., and Denise Dearing, M. (2014) ‘Gut microbes of mammalian herbivores facilitate intake of plant toxins’, Ecol. Lett. 17, 1238–1246.

Koren, O., Goodrich, J.K., Cullender, T.C., Spor, A., Laitinen, K., Kling Bäckhed, H., Gonzalez, A., Werner, J.J., Angenent, L.T., Knight, R., et al. (2012) ‘Host remodeling of the gut microbiome and metabolic changes during pregnancy’, Cell 150, 470–480.

Koropatkin, N.M., Cameron, E.A., and Martens, E.C. (2012) ‘How glycan metabolism shapes the human gut microbiota’, Nat. Rev. Microbiol. 10, 323–335.

Koropatnick, T.A., Engle, J.T., Apicella, M.A., Stabb, E.V., Goldman, W.E., and McFall-Ngai, M.J. (2004) ‘Microbial factor-mediated development in a host– bacterial mutualism’, Science 306, 1186–1188.

Kostic, A.D., Gevers, D., Siljander, H., Vatanen, T., Hyötyläinen, T., Hämäläinen, A-M., Peet, A., Tillmann, V., Pöhö, P., Mattila, I., et al. (2015) ‘The dynamics of the human infant gut microbiome in development and in progression toward Type 1 Diabetes’, Cell Host Microbe 17, 260–273.

Kotula, J.W., Kerns, S.J., Shaket, L.A., Siraj, L., Collins, J.J., Way, J.C., and Silver, P.A. (2014) ‘Programmable bacteria detect and record an environmental signal in the mammalian gut’, Proc. Natl. Acad. Sci. 111, 4838–4843.

Kozek, W.J. (1977) ‘Transovarially-transmitted intracellular microorganisms in adult and larval stages of Brugia malayi’, J. Parasitol. 63, 992–1000.

Kozek, W.J., and Rao, R.U. (2007) ‘The Discovery of Wolbachia in arthropods and nematodes – a historical perspective’, in Wolbachia: A Bug’s Life in another Bug , A. Hoerauf and R.U. Rao, eds., pp. 1–14 (Basel: Karger).

Kremer, N., Philipp, E.E.R., Carpentier, M-C., Brennan, C.A., Kraemer, L., Altura, M.A., Augustin, R., Häsler, R., Heath-Heckman, E.A.C., Peyer, S.M., et al. (2013) ‘Initial symbiont contact orchestrates host–organ-wide transcriptional changes that prime tissue colonization’, Cell Host Microbe 14, 183–194.

Kroes, I., Lepp, P.W., and Relman, D.A. (1999) ‘Bacterial diversity within the human subgingival crevice’, Proc. Natl. Acad. Sci. 96, 14547–14552.

Kruif, P.D. (2002) Microbe Hunters (Boston: Houghton Mifflin Harcourt).

Kueneman, J.G., Parfrey, L.W., Woodhams, D.C., Archer, H.M., Knight, R., and McKenzie, V.J. (2014) ‘The amphibian skin-associated microbiome across species, space and life history stages’, Mol. Ecol. 23, 1238–1250.

Kunz, C. (2012) ‘Historical aspects of human milk oligosaccharides’, Adv. Nutr. Int. Rev. J. 3, 430S – 439S.

Kunzig, R. (2000) Mapping the Deep: The Extraordinary Story of Ocean Science (New York: W. W. Norton & Co.).

Kuss, S.K., Best, G.T., Etheredge, C.A., Pruijssers, A.J., Frierson, J.M., Hooper, L.V., Dermody, T.S., and Pfeiffer, J.K. (2011) ‘Intestinal microbiota promote enteric virus replication and systemic pathogenesis’, Science 334, 249–252.

Kwong, W.K. and Moran, N.A. (2015) ‘Evolution of host specialization in gut microbes: the bee gut as a model’, Gut Microbes 6, 214–220.

Lander, E.S., Linton, L.M., Birren, B., Nusbaum, C., Zody, M.C., Baldwin, J., Devon, K., Dewar, K., Doyle, M., FitzHugh, W., et al. (2001) ‘Initial sequencing and analysis of the human genome’, Nature 409, 860–921.

Lane, N. (2015a) The Vital Question: Why Is Life the Way It Is? (London: Profile Books).

Lane, N. (2015b) ‘The unseen world: reflections on Leeuwenhoek (1677) “Concerning little animals”’ Philos. Trans. R. Soc. B Biol. Sci. 370, doi: 10.1098/rstb. 2014. 0344.

Lang, J.M., Eisen, J.A., and Zivkovic, A.M. (2014) ‘The microbes we eat: abundance and taxonomy of microbes consumed in a day’s worth of meals for three diet types’, PeerJ 2 , e659.

Lawley, T.D., Clare, S., Walker, A.W., Stares, M.D., Connor, T.R., Raisen, C., Goulding, D., Rad, R., Schreiber, F., Brandt, C., et al. (2012) ‘Targeted restoration of the intestinal microbiota with a simple, defined bacteriotherapy resolves relapsing Clostridium difficile disease in mice’, PLoS Pathog. 8, e1002995.

Lax, S. and Gilbert, J.A. (2015) ‘Hospital-associated microbiota and implications for nosocomial infections’, Trends Mol. Med. 21, 427–432.

Lax, S., Smith, D.P., Hampton-Marcell, J., Owens, S.M., Handley, K.M., Scott, N.M., Gibbons, S.M., Larsen, P., Shogan, B.D., Weiss, S., et al. (2014) ‘Longitudinal analysis of microbial interaction between humans and the indoor environment’, Science 345, 1048–1052.

Le Chatelier, E., Nielsen, T., Qin, J., Prifti, E., Hildebrand, F., Falony, G., Almeida, M., Arumugam, M., Batto, J-M., Kennedy, S., et al. (2013) ‘Richness of human gut microbiome correlates with metabolic markers’, Nature 500, 541–546.

Le Clec’h, W., Chevalier, F.D., Genty, L., Bertaux, J., Bouchon, D., and Sicard, M. (2013) ‘Cannibalism and predation as paths for horizontal passage of Wolbachia between terrestrial isopods’, PLoS ONE 8, e60232.

Lee, Y.K. and Mazmanian, S.K. (2010) ‘Has the microbiota played a critical role in the evolution of the adaptive immune system?’, Science 330, 1768–1773.

Lee, B.K., Magnusson, C., Gardner, R.M., Blomström, Å., Newschaffer, C.J., Burstyn, I., Karlsson, H., and Dalman, C. (2015) ‘Maternal hospitalization with infection during pregnancy and risk of autism spectrum disorders’, Brain. Behav. Immun. 44, 100–105.

Leewenhoeck, A. van (1677) ‘Observation, communicated to the publisher by Mr. Antony van Leewenhoeck, in a Dutch letter of the 9 Octob. 1676 here English’d: concerning little animals by him observed in rain-well-sea and snow water; as also in water wherein pepper had lain infused’, Phil. Trans. 12, 821–831.

Leewenhook, A. van (1674), More Observations from Mr. Leewenhook, in a Letter of Sept. 7, 1674. sent to the Publisher’, Phil Trans 12, 178–182.

Lemon, K.P., Armitage, G.C., Relman, D.A., and Fischbach, M.A. (2012) ‘Microbiotatargeted therapies: an ecological perspective’, Sci. Transl. Med. 4, 137rv5–rv137rv5.

LePage, D., and Bordenstein, S.R. (2013) ‘ Wolbachia : can we save lives with a great pandemic?’, Trends Parasitol. 29, 385–393.

Leroi, A.M. (2014) The Lagoon: How Aristotle Invented Science (New York: Viking Books).

Leroy, P.D., Sabri, A., Heuskin, S., Thonart, P., Lognay, G., Verheggen, F.J., Francis, F., Brostaux, Y., Felton, G.W., and Haubruge, E. (2011) ‘Microorganisms from aphid honeydew attract and enhance the efficacy of natural enemies’, Nat. Commun. 2, 348.

Ley, R.E., Bäckhed, F., Turnbaugh, P., Lozupone, C.A., Knight, R.D., and Gordon, J.I. (2005) ‘Obesity alters gut microbial ecology’, Proc. Natl. Acad. Sci. U. S. A. 102, 11070–11075.

Ley, R.E., Peterson, D.A., and Gordon, J.I. (2006) ‘Ecological and evolutionary forces shaping microbial diversity in the human intestine’, Cell 124, 837–848.

Ley, R.E., Hamady, M., Lozupone, C., Turnbaugh, P.J., Ramey, R.R., Bircher, J.S., Schlegel, M.L., Tucker, T.A., Schrenzel, M.D., Knight, R., et al. (2008a) ‘Evolution of mammals and their gut microbes’, Science 320, 1647–1651.

Ley, R.E., Lozupone, C.A., Hamady, M., Knight, R., and Gordon, J.I. (2008b) ‘Worlds within worlds: evolution of the vertebrate gut microbiota’, Nat. Rev. Microbiol. 6, 776–788.

Li, J., Jia, H., Cai, X., Zhong, H., Feng, Q., Sunagawa, S., Arumugam, M., Kultima, J.R., Prifti, E., Nielsen, T., et al. (2014) ‘An integrated catalog of reference genes in the human gut microbiome’, Nat. Biotechnol. 32, 834–841.

Linz, B., Balloux, F., Moodley, Y., Manica, A., Liu, H., Roumagnac, P., Falush, D., Stamer, C., Prugnolle, F., van der Merwe, S.W., et al. (2007) ‘An African origin for the intimate association between humans and Helicobacter pylori’, Nature 445, 915–918.

Liou, A.P., Paziuk, M., Luevano, J.-M., Machineni, S., Turnbaugh, P.J., and Kaplan, L.M. (2013) ‘Conserved shifts in the gut microbiota due to gastric bypass reduce host weight and adiposity’, Sci. Transl. Med. 5, 178ra41.

Login, F.H. and Heddi, A. (2013) ‘Insect immune system maintains long-term resident bacteria through a local response’, J. Insect Physiol. 59, 232–239.

Lombardo, M.P. (2008) ‘Access to mutualistic endosymbiotic microbes: an underappreciated benefit of group living’, Behav. Ecol. Sociobiol. 62, 479–497.

Lyte, M., Varcoe, J.J., and Bailey, M.T. (1998) ‘Anxiogenic effect of subclinical bacterial infection in mice in the absence of overt immune activation’, Physiol. Behav. 65, 63–68.

Ma, B., Forney, L.J., and Ravel, J. (2012) ‘Vaginal microbiome: rethinking health and disease,’ Annu. Rev. Microbiol. 66, 371–389.

Malkova, N.V., Yu, C.Z., Hsiao, E.Y., Moore, M.J., and Patterson, P.H. (2012) ‘Maternal immune activation yields offspring displaying mouse versions of the three core symptoms of autism’, Brain. Behav. Immun. 26, 607–616.

Manichanh, C., Borruel, N., Casellas, F., and Guarner, F. (2012) ‘The gut microbiota in IBD’, Nat. Rev. Gastroenterol. Hepatol. 9, 599–608.

Marcobal, A., Barboza, M., Sonnenburg, E.D., Pudlo, N., Martens, E.C., Desai, P., Lebrilla, C.B., Weimer, B.C., Mills, D.A., German, J.B., et al. (2011) ‘Bacteroides in the infant gut consume milk oligosaccharides via mucusutilization pathways’, Cell Host Microbe 10, 507–514.

Margulis, L., and Fester, R. (1991) Symbiosis as a Source of Evolutionary Innovation: Speciation and Morphogenesis (Cambridge, Mass: The MIT Press).

Margulis, L. and Sagan, D. (2002) Acquiring Genomes: A Theory of the Origin of Species (New York: Perseus Books Group).

Martel, A., Sluijs, A.S. der, Blooi, M., Bert, W., Ducatelle, R., Fisher, M.C., Woeltjes, A., Bosman, W., Chiers, K., Bossuyt, F., et al. (2013) ‘Batrachochytrium salamandrivorans sp. nov. causes lethal chytridiomycosis in amphibians’, Proc. Natl. Acad. Sci. 110, 15325–15329.

Martens, E.C., Kelly, A.G., Tauzin, A.S., and Brumer, H. (2014) ‘The devil lies in the details: how variations in polysaccharide fine-structure impact the physiology and evolution of gut microbes’, J. Mol. Biol. 426, 3851–3865.

Martínez, I., Stegen, J.C., Maldonado-Gómez, M.X., Eren, A.M., Siba, P.M., Greenhill, A.R., and Walter, J. (2015) ‘The gut microbiota of rural Papua New Guineans: composition, diversity patterns, and ecological processes’, Cell Rep. 11, 527–538.

Mayer, E.A., Tillisch, K., and Gupta, A. (2015) ‘Gut/brain axis and the microbiota’, J. Clin. Invest. 125, 926–938.

Maynard, C.L., Elson, C.O., Hatton, R.D., and Weaver, C.T. (2012) ‘Reciprocal interactions of the intestinal microbiota and immune system’, Nature 489, 231–241.

Mazmanian, S.K., Liu, C.H., Tzianabos, A.O., and Kasper, D.L. (2005) ‘An immunomodulatory molecule of symbiotic bacteria directs maturation of the host immune system’, Cell 122, 107–118.

Mazmanian, S.K., Round, J.L., and Kasper, D.L. (2008) ‘A microbial symbiosis factor prevents intestinal inflammatory disease’, Nature 453, 620–625.

McCutcheon, J.P. (2013) ‘Genome evolution: a bacterium with a Napoleon Complex’, Curr. Biol. 23, R657–R659.

McCutcheon, J.P. and Moran, N.A. (2011) ‘Extreme genome reduction in symbiotic bacteria’, Nat. Rev. Microbiol. 10, 13–26.

McDole, T., Nulton, J., Barott, K.L., Felts, B., Hand, C., Hatay, M., Lee, H., Nadon, M.O., Nosrat, B., Salamon, P., et al. (2012) ‘Assessing coral reefs on a Pacificwide scale using the microbialization score’, PLoS ONE 7, e43233.

McFall-Ngai, M.J. (1998) ‘The development of cooperative associations between animals and bacteria: establishing detente among domains’, Integr. Comp. Biol. 38, 593–608.

McFall-Ngai, M. (2007) ‘Adaptive immunity: care for the community’, Nature 445, 153.

McFall-Ngai, M. (2014) ‘Divining the essence of symbiosis: insights from the Squid-Vibrio Model’, PLoS Biol. 12, e1001783.

McFall-Ngai, M.J. and Ruby, E.G. (1991) ‘Symbiont recognition and subsequent morphogenesis as early events in an animal–bacterial mutualism’, Science 254, 1491–1494.

McFall-Ngai, M., Hadfield, M.G., Bosch, T.C., Carey, H.V., Domazet-Lošo, T., Douglas, A.E., Dubilier, N., Eberl, G., Fukami, T., and Gilbert, S.F. (2013) ‘Animals in a bacterial world, a new imperative for the life sciences’, Proc. Natl. Acad. Sci. 110, 3229–3236.

McFarland, L.V. (2014) ‘Use of probiotics to correct dysbiosis of normal microbiota following disease or disruptive events: a systematic review’, BMJ Open 4, e005047.

McGraw, E.A. and O’Neill, S.L. (2013) ‘Beyond insecticides: new thinking on an ancient problem’, Nat. Rev. Microbiol. 11, 181–193.

McKenna, M. (2010) Superbug: The Fatal Menace of MRSA (New York: Free Press).

McKenna, M. (2013) Imagining the Post-Antibiotics Future. https://medium.com/@fernnews/imagining-the-post-antibiotics-future-892b57499e77.

Mclaren, D.J., Worms, M.J., Laurence, B.R., and Simpson, M.G. (1975) ‘Micro-organisms in filarial larvae (Nematoda)’, Trans. R. Soc. Trop. Med. Hyg. 69, 509–514.

McMaster, J. (2004). How Did Life Begin? http:www.pbs.org/wgbn/nova/evolution/how-did-life-begin.html.

McMeniman, C.J., Lane, R.V., Cass, B.N., Fong, A.W.C., Sidhu, M., Wang, Y-F., and O’Neill, S.L. (2009) ‘Stable introduction of a life-shortening Wolbachia infection into the mosquito Aedes aegypti’, Science 323, 141–144.

McNulty, N.P., Yatsunenko, T., Hsiao, A., Faith, J.J., Muegge, B.D., Goodman, A.L., Henrissat, B., Oozeer, R., Cools-Portier, S., Gobert, G., et al. (2011) ‘The impact of a consortium of fermented milk strains on the gut microbiome of gnotobiotic mice and monozygotic twins’, Sci. Transl. Med. 3, 106ra106.

Meadow, J.F., Bateman, A.C., Herkert, K.M., O’Connor, T.K., and Green, J.L. (2013) ‘Significant changes in the skin microbiome mediated by the sport of roller derby’, PeerJ 1, e53.

Meadow, J.F., Altrichter, A.E., Bateman, A.C., Stenson, J., Brown, G.Z., Green, J.L., and Bohannan, B.J.M. (2015) ‘Humans differ in their personal microbial cloud’, PeerJ 3, e1258.

Metcalf, J.A., Funkhouser-Jones, L.J., Brileya, K., Reysenbach, A-L., and Bordenstein, S.R. (2014) ‘Antibacterial gene transfer across the tree of life’, eLife 3.

Miller, A.W., Kohl, K.D., and Dearing, M.D. (2014) ‘The gastrointestinal tract of the white-throated woodrat (Neotoma albigula) harbors distinct consortia of oxalate-degrading bacteria’, Appl. Environ. Microbiol. 80, 1595–1601.

Mimee, M., Tucker, A.C., Voigt, C.A., and Lu, T.K. (2015) ‘Programming a human commensal bacterium, Bacteroides thetaiotaomicron, to sense and respond to stimuli in the murine gut microbiota’, Cell Syst. 1, 62–71.

Min, K.-T., and Benzer, S. (1997) ‘ Wolbachia , normally a symbiont of Drosophila, can be virulent, causing degeneration and early death’, Proc. Natl. Acad. Sci. U. S. A. 94, 10792–10796.

Moberg, S. (2005) René Dubos, Friend of the Good Earth: Microbiologist, Medical Scientist, Environmentalist (Washington, DC: ASM Press).

Moeller, A.H., Li, Y., Mpoudi Ngole, E., Ahuka-Mundeke, S., Lonsdorf, E.V., Pusey, A.E., Peeters, M., Hahn, B.H., and Ochman, H. (2014) ‘Rapid changes in the gut microbiome during human evolution’, Proc. Natl. Acad. Sci. U. S. A. 111, 16431–16435.

Montgomery, M.K. and McFall-Ngai, M. (1994) ‘Bacterial symbionts induce host organ morphogenesis during early postembryonic development of the squid Euprymna scolopes’, Dev. Camb. Engl. 120, 1719–1729.

Moran, N.A. and Dunbar, H.E. (2006) ‘Sexual acquisition of beneficial symbionts in aphids’, Proc. Natl. Acad. Sci. 103, 12803–12806.

Moran, N.A. and Sloan, D.B. (2015) ‘The Hologenome Concept: helpful or hollow?’ PLoS Biol. 13, e1002311.

Moran, N.A., Degnan, P.H., Santos, S.R., Dunbar, H.E., and Ochman, H. (2005) ‘The players in a mutualistic symbiosis: insects, bacteria, viruses, and virulence genes’, Proc. Natl. Acad. Sci. U. S. A. 102, 16919–16926.

Moreira, L.A., Iturbe-Ormaetxe, I., Jeffery, J.A., Lu, G., Pyke, A.T., Hedges, L.M., Rocha, B.C., Hall-Mendelin, S., Day, A., Riegler, M., et al. (2009) ‘A Wolbachia symbiont in Aedes aegypti limits infection with dengue, chikungunya, and plasmodium’, Cell 139, 1268–1278.

Morell, V. (1997) ‘Microbial biology: microbiology’s scarred revolutionary’, Science 276, 699–702.

Morgan, X.C., Tickle, T.L., Sokol, H., Gevers, D., Devaney, K.L., Ward, D.V., Reyes, J.A., Shah, S.A., LeLeiko, N., Snapper, S.B., et al. (2012) ‘Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment’, Genome Biol. 13, R79.

Mukherjee, S. (2011) The Emperor of All Maladies (London:Fourth Estate).

Mullard, A. (2008) ‘Microbiology: the inside story’, Nature 453, 578–580.

National Research Council (US) Committee on Metagenomics (2007) The New Science of Metagenomics: Revealing the Secrets of Our Microbial Planet (Washington, DC: National Academies Press (US)).

Nature (1975) ‘Oh, New Delhi; oh, Geneva’, Nature 256, 355–357.

Nature (2013) ‘Culture shock’, Nature 493, 133–134.

Nelson, B. (2014). Medicine’s dirty secret. http://mosaicscience.com/story/medicine%E2%80%99s-dirty-secret.

Neufeld, K.M., Kang, N., Bienenstock, J., and Foster, J.A. (2011) ‘Reduced anxietylike behavior and central neurochemical change in germ-free mice: behavior in germ-free mice’, Neurogastroenterol. Motil. 23, 255–e119.

Newburg, D.S., Ruiz-Palacios, G.M., and Morrow, A.L. (2005) ‘Human milk glycans protect infants against enteric pathogens’, Annu. Rev. Nutr. 25, 37–58.

New York Times (12 February 1985) ‘Science watch: miracle plant tested as cattle fodder’.

Nicholson, J.K., Holmes, E., Kinross, J., Burcelin, R., Gibson, G., Jia, W., and Pettersson, S. (2012) ‘Host–Gut Microbiota Metabolic Interactions’, Science 336, 1262–1267.

Nightingale, F. (1859) Notes on Nursing: What It Is, and What It Is Not (New York: D. Appleton & Co.).

Nougué, O., Gallet, R., Chevin, L-M., and Lenormand, T. (2015) ‘Niche limits of symbiotic gut microbiota constrain the salinity tolerance of brine shrimp’, Am. Nat. 186, 390–403.

Nováková, E., Hypša, V., Klein, J., Foottit, R.G., von Dohlen, C.D., and Moran, N.A. (2013) ‘Reconstructing the phylogeny of aphids (Hemiptera: Aphididae) using DNA of the obligate symbiont Buchnera aphidicola’, Mol. Phylogenet. Evol. 68, 42–54.

Obregon-Tito, A.J., Tito, R.Y., Metcalf, J., Sankaranarayanan, K., Clemente, J.C., Ursell, L.K., Zech Xu, Z., Van Treuren, W., Knight, R., Gaffney, P.M., et al. (2015) ‘Subsistence strategies in traditional societies distinguish gut microbiomes’, Nat. Commun. 6, 6505.

Ochman, H., Lawrence, J.G., and Groisman, E.A. (2000) ‘Lateral gene transfer and the nature of bacterial innovation’, Nature 405, 299–304.

Ohbayashi, T., Takeshita, K., Kitagawa, W., Nikoh, N., Koga, R., Meng, X-Y., Tago, K., Hori, T., Hayatsu, M., Asano, K., et al. (2015) ‘Insect’s intestinal organ for symbiont sorting’, Proc. Natl. Acad. Sci. 112, E5179–E5188.

Oliver, K.M., Moran, N.A., and Hunter, M.S. (2005) ‘Variation in resistance to parasitism in aphids is due to symbionts not host genotype’, Proc. Natl. Acad. Sci. U. S. A. 102, 12795–12800.

Oliver, K.M., Campos, J., Moran, N.A., and Hunter, M.S. (2008) ‘Population dynamics of defensive symbionts in aphids’, Proc. R. Soc. B Biol. Sci. 275, 293–299.

Olle, B. (2013) ‘Medicines from microbiota’, Nat. Biotechnol. 31, 309–315.

Olszak, T., An, D., Zeissig, S., Vera, M.P., Richter, J., Franke, A., Glickman, J.N., Siebert, R., Baron, R.M., Kasper, D.L., et al. (2012) ‘Microbial exposure during early life has persistent effects on natural killer T cell function’, Science 336, 489–493.

O’Malley, M.A. (2009) ‘What did Darwin say about microbes, and how did microbiology respond?’, Trends Microbiol. 17, 341–347.

Osawa, R., Blanshard, W., and Ocallaghan, P. (1993) ‘Microbiological studies of the intestinal microflora of the Koala, Phascolarctos-Cinereus .2. Pap, a special maternal feces consumed by juvenile koalas’, Aust. J. Zool. 41, 611–620.

Ott, S.J., Musfeldt, M., Wenderoth, D.F., Hampe, J., Brant, O., Fölsch, U.R., Timmis, K.N., and Schreiber, S. (2004) ‘Reduction in diversity of the colonic mucosa associated bacterial microflora in patients with active inflammatory bowel disease’, Gut 53, 685–693.

Ott, B.M., Rickards, A., Gehrke, L., and Rio, R.V.M. (2015) ‘Characterization of shed medicinal leech mucus reveals a diverse microbiota’, Front. Microbiol. 5. doi: 10.3389/fmicb.2014.00757.

Pace, N.R., Stahl, D.A., Lane, D.J., and Olsen, G.J. (1986) ‘The analysis of natural microbial populations by ribosomal RNA Sequences’, in Advances in Microbial Ecology , K.C. Marshall, ed. (New York: Springer US), pp. 1–55.

Paine, R.T., Tegner, M.J., and Johnson, E.A. (1998) ‘Compounded perturbations yield ecological surprises’, Ecosystems 1, 535–545.

Pais, R., Lohs, C., Wu, Y., Wang, J., and Aksoy, S. (2008) ‘The obligate mutualist Wigglesworthia glossinidia influences reproduction, digestion, and immunity processes of its host, the tsetse fly’, Appl. Environ. Microbiol. 74, 5965–5974.

Pannebakker, B.A., Loppin, B., Elemans, C.P., Humblot, L., and Vavre, F. (2007) ‘Parasitic inhibition of cell death facilitates symbiosis’, Proc. Natl. Acad. Sci. 104, 213–215.

Payne, A.S. (1970) The Cleere Observer. A Biography of Antoni Van Leeuwenhoek (London: Macmillan).

Petrof, E.O. and Khoruts, A. (2014) ‘From stool transplants to next-generation microbiota therapeutics’, Gastroenterology 146, 1573–1582.

Petrof, E., Gloor, G., Vanner, S., Weese, S., Carter, D., Daigneault, M., Brown, E., Schroeter, K., and Allen-Vercoe, E. (2013) ‘Stool substitute transplant therapy for the eradication of Clostridium difficile infection: ‘RePOOPulating’ the gut’, Microbiome 2013, 3.

Petschow, B., Doré, J., Hibberd, P., Dinan, T., Reid, G., Blaser, M., Cani, P.D., Degnan, F.H., Foster, J., Gibson, G., et al. (2013) ‘Probiotics, prebiotics, and the host microbiome: the science of translation’, Ann. N. Y. Acad. Sci. 1306, 1–17.

Pickard, J.M., Maurice, C.F., Kinnebrew, M.A., Abt, M.C., Schenten, D., Golovkina, T.V., Bogatyrev, S.R., Ismagilov, R.F., Pamer, E.G., Turnbaugh, P.J., et al. (2014) ‘Rapid fucosylation of intestinal epithelium sustains host–commensal symbiosis in sickness’, Nature 514, 638–641.

Poulsen, M., Hu, H., Li, C., Chen, Z., Xu, L., Otani, S., Nygaard, S., Nobre, T., Klaubauf, S., Schindler, P.M., et al. (2014) ‘Complementary symbiont contributions to plant decomposition in a fungus-farming termite’, Proc. Natl. Acad. Sci. 111, 14500–14505.

Qian, J., Hospodsky, D., Yamamoto, N., Nazaroff, W.W., and Peccia, J. (2012). ‘Sizeresolved emission rates of airborne bacteria and fungi in an occupied classroom: size-resolved bioaerosol emission rates’, Indoor Air 22, 339–351.

Quammen, D. (1997) The Song of the Dodo: Island Biogeography in an Age of Extinction (New York: Scribner).

Rawls, J.F., Samuel, B.S., and Gordon, J.I. (2004) ‘Gnotobiotic zebrafish reveal evolutionarily conserved responses to the gut microbiota’, Proc. Natl. Acad. Sci. U. S. A. 101, 4596–4601.

Rawls, J.F., Mahowald, M.A., Ley, R.E., and Gordon, J.I. (2006) ‘Reciprocal gut microbiota transplants from zebrafish and mice to germ-free recipients reveal host habitat selection’, Cell 127, 423–433.

Redford, K.H., Segre, J.A., Salafsky, N., del Rio, C.M., and McAloose, D. (2012) ‘Conservation and the Microbiome: Editorial. Conserv. Biol. 26, 195–197.

Reid, G. (2011) ‘Opinion paper: Quo vadis – EFSA?’, Benef. Microbes 2, 177–181.

Relman, D.A. (2008), ‘“Til death do us part”: coming to terms with symbiotic relationships’, Foreword. Nat. Rev. Microbiol. 6, 721–724.

Relman, D.A. (2012) ‘The human microbiome: ecosystem resilience and health’, Nutr. Rev. 70, S2–S9.

Ridaura, V.K., Faith, J.J., Rey, F.E., Cheng, J., Duncan, A.E., Kau, A.L., Griffin, N.W., Lombard, V., Henrissat, B., Bain, J.R., et al. (2013). ‘Gut microbiota from twins discordant for obesity modulate metabolism in mice’, Science 341, 1241214.

Rigaud, T., and Juchault, P. (1992). Heredity – Abstract of article: ‘Genetic control of the vertical transmission of a cytoplasmic sex factor in Armadillidium vulgare Latr. (Crustacea, Oniscidea)’, Heredity 68, 47–52.

Riley, D.R., Sieber, K.B., Robinson, K.M., White, J.R., Ganesan, A., Nourbakhsh, S., and Dunning Hotopp, J.C. (2013) ‘Bacteria–human somatic cell lateral gene transfer is enriched in cancer samples’, PLoS Comput. Biol. 9, e1003107.

Roberts, C.S. (1990) ‘William Beaumont, the man and the opportunity’, in Clinical Methods: The History, Physical, and Laboratory Examinations, H.K. Walker, W.D. Hall, and J.W. Hurst, eds (Boston: Butterworths).

Roberts, S.C., Gosling, L.M., Spector, T.D., Miller, P., Penn, D.J., and Petrie, M. (2005) ‘Body Odor Similarity in Noncohabiting Twins’, Chem. Senses 30, 651–656.

Rogier, E.W., Frantz, A.L., Bruno, M.E., Wedlund, L., Cohen, D.A., Stromberg, A.J., and Kaetzel, C.S. (2014) ‘Secretory antibodies in breast milk promote longterm intestinal homeostasis by regulating the gut microbiota and host gene expression’, Proc. Natl. Acad. Sci. 111, 3074–3079.

Rohwer, F. and Youle, M. (2010) Coral Reefs in the Microbial Seas (United States: Plaid Press).

Rook, G.A.W., Lowry, C.A., and Raison, C.L. (2013) ‘Microbial ‘Old Friends’, immunoregulation and stress resilience’, Evol. Med. Public Health 2013, 46–64.

Rosebury, T. (1962) Microorganisms Indigenous to Man (New York: McGraw-Hill).

Rosebury, T. (1969) Life on Man (New York: Viking Press).

Rosenberg, E., Sharon, G., and Zilber-Rosenberg, I. (2009) ‘The hologenome theory of evolution contains Lamarckian aspects within a Darwinian framework’, Environ. Microbiol. 11, 2959–2962.

Rosner, J. (2014) ‘Ten times more microbial cells than body cells in humans?’, Microbe 9, 47.

Round, J.L., and Mazmanian, S.K. (2009) ‘The gut microbiota shapes intestinal immune responses during health and disease’, Nat. Rev. Immunol. 9, 313–323.

Round, J.L. and Mazmanian, S.K. (2010) ‘Inducible Foxp3+ regulatory T-cell development by a commensal bacterium of the intestinal microbiota’, Proc. Natl. Acad. Sci. U. S. A. 107, 12204–12209.

Russell, C.W., Bouvaine, S., Newell, P.D., and Douglas, A.E. (2013a) ‘Shared metabolic pathways in a coevolved insect–bacterial symbiosis’, Appl. Environ. Microbiol. 79, 6117–6123.

Russell, J.A., Funaro, C.F., Giraldo, Y.M., Goldman-Huertas, B., Suh, D., Kronauer, D.J.C., Moreau, C.S., and Pierce, N.E. (2012) ‘A veritable menagerie of heritable bacteria from ants, butterflies, and beyond: broad molecular surveys and a systematic review’, PLoS ONE 7, e51027.

Russell, J.A., Weldon, S., Smith, A.H., Kim, K.L., Hu, Y., Łukasik, P., Doll, S., Anastopoulos, I., Novin, M., and Oliver, K.M. (2013b) ‘Uncovering symbiontdriven genetic diversity across North American pea aphids’, Mol. Ecol. 22, 2045–2059.

Rutherford, A. (2013). Creation: The Origin of Life / The Future of Life (London: Penguin).

Sachs, J.L., Skophammer, R.G., and Regus, J.U. (2011) ‘Evolutionary transitions in bacterial symbiosis’, Proc. Natl. Acad. Sci. 108, 10800–10807. Sacks, O. (23 April 2015) ‘A General Feeling of Disorder.’ N. Y. Rev. Books.

Saeidi, N., Wong, C.K., Lo, T-M., Nguyen, H.X., Ling, H., Leong, S.S.J., Poh, C.L., and Chang, M.W. (2011) ‘Engineering microbes to sense and eradicate

Pseudomonas aeruginosa, a human pathogen’, Mol. Syst. Biol. 7, 521.

Sagan, L. (1967) ‘On the origin of mitosing cells’, J. Theor. Biol. 14, 255–274.

Salter, S.J., Cox, M.J., Turek, E.M., Calus, S.T., Cookson, W.O., Moffatt, M.F., Turner, P., Parkhill, J., Loman, N.J., and Walker, A.W. (2014) ‘Reagent and laboratory contamination can critically impact sequence-based microbiome analyses’, BMC Biol. 12, 87.

Salzberg, S.L. (2001) ‘Microbial genes in the human genome: lateral transfer or gene loss?’, Science 292, 1903–1906.

Salzberg, S.L., Hotopp, J.C., Delcher, A.L., Pop, M., Smith, D.R., Eisen, M.B., and Nelson, W.C. (2005) ‘Serendipitous discovery of Wolbachia genomes in multiple Drosophila species’, Genome Biol. 6, R23.

Sanders, J.G., Beichman, A.C., Roman, J., Scott, J.J., Emerson, D., McCarthy, J.J., and Girguis, P.R. (2015) ‘Baleen whales host a unique gut microbiome with similarities to both carnivores and herbivores’, Nat. Commun. 6, 8285.

Sangodeyi, F.I. (2014) ‘The Making of the Microbial Body, 1900s–2012.’ Harvard University.

Sapp, J. (1994) Evolution by Association: A History of Symbiosis (New York: Oxford University Press).

Sapp, J. (2002) ‘Paul Buchner (1886–1978) and hereditary symbiosis in insects’, Int. Microbiol. 5, 145–150.

Sapp, J. (2009) The New Foundations of Evolution: On the Tree of Life (Oxford and New York: Oxford University Press).

Savage, D.C. (2001) ‘Microbial biota of the human intestine: a tribute to some pioneering scientists’, Curr. Issues Intest. Microbiol. 2, 1–15.

Schilthuizen, M.O. and Stouthamer, R. (1997) Horizontal transmission of parthenogenesis-inducing microbes in Trichogramma wasps’, Proc. R. Soc. Lond. B Biol. Sci. 264, 361–366.

Schluter, J. and Foster, K.R. (2012) ‘The evolution of mutualism in gut microbiota via host epithelial selection’, PLoS Biol. 10, e1001424.

Schmidt, C. (2013) ‘The startup bugs’, Nat. Biotechnol. 31, 279–281.

Schmidt, T.M., DeLong, E.F., and Pace, N.R. (1991) ‘Analysis of a marine picoplankton community by 16S rRNA gene cloning and sequencing’, J. Bacteriol . 173, 4371–4378.

Schnorr, S.L., Candela, M., Rampelli, S., Centanni, M., Consolandi, C., Basaglia, G., Turroni, S., Biagi, E., Peano, C., Severgnini, M., et al. (2014) ‘Gut microbiome of the Hadza hunter-gatherers’, Nat. Commun. 5, 3654.

Schubert, A.M., Sinani, H., and Schloss, P.D. (2015) ‘Antibiotic-induced alterations of the murine gut microbiota and subsequent effects on colonization resistance against Clostridium difficile’, mBio 6, e00974–15.

Sela, D.A. and Mills, D.A. (2014) ‘The marriage of nutrigenomics with the microbiome: the case of infant-associated bifidobacteria and milk’, Am. J. Clin. Nutr. 99, 697S–703S.

Sela, D.A., Chapman, J., Adeuya, A., Kim, J.H., Chen, F., Whitehead, T.R., Lapidus, A., Rokhsar, D.S., Lebrilla, C.B., and German, J.B. (2008) ‘The genome sequence of Bifidobacterium longum subsp. infantis reveals adaptations for milk utilization within the infant microbiome’, Proc. Natl. Acad. Sci. 105, 18964–18969.

Selosse, M-A., Bessis, A., and Pozo, M.J. (2014) ‘Microbial priming of plant and animal immunity: symbionts as developmental signals’, Trends Microbiol. 22, 607–613.

Shanahan, F. (2010) ‘Probiotics in perspective’, Gastroenterology 139, 1808–1812.

Shanahan, F. (2012) ‘The microbiota in inflammatory bowel disease: friend, bystander, and sometime-villain’, Nutr. Rev. 70, S31–S37.

Shanahan, F. and Quigley, E.M.M. (2014) ‘Manipulation of the microbiota for treatment of IBS and IBD – challenges and controversies’, Gastroenterology 146, 1554–1563.

Sharon, G., Segal, D., Ringo, 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. 107, 20051–20056.

Sharon, G., Garg, N., Debelius, J., Knight, R., Dorrestein, P.C., and Mazmanian, S.K. (2014) ‘Specialized metabolites from the microbiome in health and disease. Cell Metab. 20, 719–730.

Shikuma, N.J., Pilhofer, M., Weiss, G.L., Hadfield, M.G., Jensen, G.J., and Newman, D.K. (2014) ‘Marine tubeworm metamorphosis induced by arrays of bacterial phage tail-Like structures’, Science 343, 529–533.

Six, D.L. (2013) ‘The Bark Beetle holobiont: why microbes matter’, J. Chem. Ecol. 39, 989–1002.

Sjögren, K., Engdahl, C., Henning, P., Lerner, U.H., Tremaroli, V., Lagerquist, M.K., Bäckhed, F., and Ohlsson, C. (2012) ‘The gut microbiota regulates bone mass in mice’, J. Bone Miner. Res. Off. J. Am. Soc. Bone Miner. Res. 27, 1357–1367.

Slashinski, M.J., McCurdy, S.A., Achenbaum, L.S., Whitney, S.N., and McGuire, A.L. (2012) ‘‘Snake-oil,’‘quack medicine,’ and ‘industrially cultured organisms:’ biovalue and the commercialization of human microbiome research’, BMC Med. Ethics 13, 28.

Slatko, B.E., Taylor, M.J., and Foster, J.M. (2010) ‘The Wolbachia endosymbiont as an anti-filarial nematode target’, Symbiosis 51, 55–65.

Smillie, C.S., Smith, M.B., Friedman, J., Cordero, O.X., David, L.A., and Alm, E.J. (2011) ‘Ecology drives a global network of gene exchange connecting the human microbiome’, Nature 480, 241–244.

Smith, C.C., Snowberg, L.K., Gregory Caporaso, J., Knight, R., and Bolnick, D.I. (2015) ‘Dietary input of microbes and host genetic variation shape amongpopulation differences in stickleback gut microbiota’, ISME J. 9 , 2515–2526.

Smith, J.E., Shaw, M., Edwards, R.A., Obura, D., Pantos, O., Sala, E., Sandin, S.A., Smriga, S., Hatay, M., and Rohwer, F.L. (2006) ‘Indirect effects of algae on coral: algae-mediated, microbe-induced coral mortality’, Ecol. Lett. 9, 835–845.

Smith, M., Kelly, C., and Alm, E. (2014) ‘How to regulate faecal transplants’, Nature 506, 290–291.

Smith, M.I., Yatsunenko, T., Manary, M.J., Trehan, I., Mkakosya, R., Cheng, J., Kau, A.L., Rich, S.S., Concannon, P., Mychaleckyj, J.C., et al. (2013a) ‘Gut microbiomes of Malawian twin pairs discordant for kwashiorkor’, Science 339, 548–554.

Smith, P.M., Howitt, M.R., Panikov, N., Michaud, M., Gallini, C.A., Bohlooly-Y, M., Glickman, J.N., and Garrett, W.S. (2013b) ‘The microbial metabolites, short-chain fatty acids, regulate colonic Treg cell homeostasis’, Science 341, 569–573.

Smithsonian National Museum of Natural History (2010) Giant Tube Worm: Riftia pachyptila. http://www.mnh.si.edu/onehundredyears/featured-objects/Riftia.html.

Sneed, J.M., Sharp, K.H., Ritchie, K.B., and Paul, V.J. (2014) ‘The chemical cue tetrabromopyrrole from a biofilm bacterium induces settlement of multiple Caribbean corals’, Proc. R. Soc. B Biol. Sci. 281, 20133086.

Sokol, H., Pigneur, B., Watterlot, L., Lakhdari, O., Bermúdez-Humarán, L.G., Gratadoux, J-J., Blugeon, S., Bridonneau, C., Furet, J-P., Corthier, G., et al. (2008) ‘Faecalibacterium prausnitzii is an anti-inflammatory commensal bacterium identified by gut microbiota analysis of Crohn disease patients’, Proc. Natl. Acad. Sci.

Soler, J.J., Martín-Vivaldi, M., Ruiz-Rodríguez, M., Valdivia, E., Martín-Platero, A.M., Martínez-Bueno, M., Peralta-Sánchez, J.M., and Méndez, M. (2008) ‘Symbiotic association between hoopoes and antibiotic-producing bacteria that live in their uropygial gland’, Funct. Ecol. 22, 864–871.

Sommer, F. and Bäckhed, F. (2013) ‘The gut microbiota —masters of host development and physiology’, Nat. Rev. Microbiol. 11, 227–238.

Sonnenburg, E.D. and Sonnenburg, J.L. (2014) ‘Starving our microbial self: the deleterious consequences of a diet deficient in microbiota-accessible carbohydrates’, Cell Metab. 20, 779–786.

Sonnenburg, E.D., Smits, S.A., Tikhonov, M., Higginbottom, S.K., Wingreen, N.S., and Sonnenburg, J.L. (2016) ‘Diet-induced extinctions in the gut microbiota compound over generations’, Nature 529, 212–215.

Sonnenburg, J.L., and Fischbach, M.A. (2011) ‘Community health care: therapeutic opportunities in the human microbiome’, Sci. Transl. Med. 3, 78ps12.

Sonnenburg, J. and Sonnenburg, E. (2015) The Good Gut: Taking Control of Your Weight, Your Mood, and Your Long-Term Health (New York: The Penguin Press).

Spor, A., Koren, O., and Ley, R. (2011) ‘Unravelling the effects of the environment and host genotype on the gut microbiome’, Nat. Rev. Microbiol. 9, 279–290.

Stahl, D.A., Lane, D.J., Olsen, G.J., and Pace, N.R. (1985) ‘Characterization of a Yellowstone hot spring microbial community by 5S rRNA sequences’, Appl. Environ. Microbiol. 49, 1379–1384.

Stappenbeck, T.S., Hooper, L.V., and Gordon, J.I. (2002) ‘Developmental regulation of intestinal angiogenesis by indigenous microbes via Paneth cells’, Proc. Natl. Acad. Sci. U. S. A. 99, 15451–15455.

Stefka, A.T., Feehley, T., Tripathi, P., Qiu, J., McCoy, K., Mazmanian, S.K., Tjota, M.Y., Seo, G-Y., Cao, S., Theriault, B.R., et al. (2014) ‘Commensal bacteria protect against food allergen sensitization’, Proc. Natl. Acad. Sci. 111, 13145–13150.

Stevens, C.E. and Hume, I.D. (1998) ‘Contributions of microbes in vertebrate gastrointestinal tract to production and conservation of nutrients’, Physiol. Rev. 78, 393–427.

Stewart, F.J. and Cavanaugh, C.M. (2006) ‘Symbiosis of thioautotrophic bacteria with Riftia pachyptila’, Prog. Mol. Subcell. Biol. 41, 197–225.

Stilling, R.M., Dinan, T.G., and Cryan, J.F. (2015) ‘The brain’s Geppetto – microbes as puppeteers of neural function and behaviour?’, J. Neurovirol. doi: 10.3389/fcimb.2014.00147.

Stoll, S., Feldhaar, H., Fraunholz, M.J., and Gross, R. (2010) ‘Bacteriocyte dynamics during development of a holometabolous insect, the carpenter ant Camponotus floridanus’, BMC Microbiol. 10, 308.

Strachan, D.P. (1989) ‘Hay fever, hygiene, and household size’, BMJ 299, 1259–1260.

Strachan, D.P. (2015). Re: ‘The ‘hygiene hypothesis’ for allergic disease is a misnomer.’ BMJ 349, g5267.

Strand, M.R. and Burke, G.R. (2012) ‘Polydnaviruses as symbionts and gene delivery systems’, PLoS Pathog . 8, e1002757.

Subramanian, S., Huq, S., Yatsunenko, T., Haque, R., Mahfuz, M., Alam, M.A., Benezra, A., DeStefano, J., Meier, M.F., Muegge, B.D., et al. (2014) ‘Persistent gut microbiota immaturity in malnourished Bangladeshi children’, Nature 510, 417–421.

Sudo, N., Chida, Y., Aiba, Y., Sonoda, J., Oyama, N., Yu, X-N., Kubo, C., and Koga, Y. (2004) ‘Postnatal microbial colonization programs the hypothalamic-pituitary–adrenal system for stress response in mice’, J. Physiol. 558, 263–275.

Sundset, M.A., Barboza, P.S., Green, T.K., Folkow, L.P., Blix, A.S., and Mathiesen, S.D. (2010) ‘Microbial degradation of usnic acid in the reindeer rumen’, Naturwissenschaften 97, 273–278.

Svoboda, E. (2015) How Soil Microbes Affect the Environment. http://www.quantamagazine.org/20150616-soil-microbes-bacteria-climate-change/.

Tang, W.H.W. and Hazen, S.L. (2014) ‘The contributory role of gut microbiota in cardiovascular disease’, J. Clin. Invest. 124, 4204–4211.

Taylor, M.J. and Hoerauf, A. (1999) ‘ Wolbachia bacteria of filarial nematodes’, Parasitol. Today 15, 437–442.

Taylor, M.J., Makunde, W.H., McGarry, H.F., Turner, J.D., Mand, S., and Hoerauf, A. (2005) ‘Macrofilaricidal activity after doxycycline treatment of Wuchereria bancrofti: a double-blind, randomised placebo-controlled trial’, Lancet 365, 2116–2121.

Taylor, M.J., Hoerauf, A., and Bockarie, M. (2010) ‘Lymphatic filariasis and onchocerciasis’, Lancet 376, 1175–1185.

Taylor, M.J., Voronin, D., Johnston, K.L., and Ford, L. (2013) ‘ Wolbachia filarial interactions: Wolbachia filarial cellular and molecular interactions’, Cell. Microbiol. 15, 520–526.

Taylor, M.J., Hoerauf, A., Townson, S., Slatko, B.E., and Ward, S.A. (2014) ‘Anti- Wolbachia drug discovery and development: safe macrofilaricides for onchocerciasis and lymphatic filariasis’, Parasitology 141, 119–127.

Teixeira, L., Ferreira, Á., and Ashburner, M. (2008) ‘The bacterial symbiont Wolbachia induces resistance to RNA viral infections in Drosophila melanogaster ’, PLoS Biol . 6, e1000002.

Thacker, R.W. and Freeman, C.J. (2012) ‘Sponge–microbe symbioses’, in Advances in Marine Biology (Philadelphia: Elsevier), pp. 57–111.

Thaiss, C.A., Zeevi, D., Levy, M., Zilberman-Schapira, G., Suez, J., Tengeler, A.C., Abramson, L., Katz, M.N., Korem, T., Zmora, N., et al. (2014) ‘Transkingdom control of microbiota diurnal oscillations promotes metabolic homeostasis’, Cell 159, 514–529.

Theis, K.R., Venkataraman, A., Dycus, J.A., Koonter, K.D., Schmitt-Matzen, E.N., Wagner, A.P., Holekamp, K.E., and Schmidt, T.M. (2013) ‘Symbiotic bacteria appear to mediate hyena social odors’, Proc. Natl. Acad. Sci. 110, 19832–19837.

Thurber, R.L.V., Barott, K.L., Hall, D., Liu, H., Rodriguez-Mueller, B., Desnues, C., Edwards, R.A., Haynes, M., Angly, F.E., Wegley, L., et al. (2008) ‘Metagenomic analysis indicates that stressors induce production of herpeslike viruses in the coral Porites compressa’, Proc. Natl. Acad. Sci. 105, 18413–18418.

Thurber, R.V., Willner-Hall, D., Rodriguez-Mueller, B., Desnues, C., Edwards, R.A., Angly, F., Dinsdale, E., Kelly, L., and Rohwer, F. (2009) ‘Metagenomic analysis of stressed coral holobionts’, Environ. Microbiol. 11, 2148–2163.

Tillisch, K., Labus, J., Kilpatrick, L., Jiang, Z., Stains, J., Ebrat, B., Guyonnet, D., Legrain-Raspaud, S., Trotin, B., Naliboff, B., et al. (2013) ‘Consumption of fermented milk product with probiotic modulates brain activity’, Gastroenterology 144, 1394–1401.e4.

Tito, R.Y., Knights, D., Metcalf, J., Obregon-Tito, A.J., Cleeland, L., Najar, F., Roe, B., Reinhard, K., Sobolik, K., Belknap, S., et al. (2012) ‘Insights from “Characterizing Extinct Human Gut Microbiomes”’, PLoS ONE 7, e51146.

Trasande, L., Blustein, J., Liu, M., Corwin, E., Cox, L.M., and Blaser, M.J. (2013) ‘Infant antibiotic exposures and early-life body mass’, Int. J. Obes. 2005 37, 16–23.

Tung, J., Barreiro, L.B., Burns, M.B., Grenier, J-C., Lynch, J., Grieneisen, L.E., Altmann, J., Alberts, S.C., Blekhman, R., and Archie, E.A. (2015) ‘Social networks predict gut microbiome composition in wild baboons’, eLife 4.

Turnbaugh, P.J., Ley, R.E., Mahowald, M.A., Magrini, V., Mardis, E.R., and Gordon, J.I. (2006) ‘An obesity-associated gut microbiome with increased capacity for energy harvest’, Nature 444, 1027–1131.

Underwood, M.A., Salzman, N.H., Bennett, S.H., Barman, M., Mills, D.A., Marcobal, A., Tancredi, D.J., Bevins, C.L., and Sherman, M.P. (2009) ‘A randomized placebo-controlled comparison of 2 prebiotic/probiotic combinations in preterm infants: impact on weight gain, intestinal microbiota, and fecal short-chain fatty acids’, J. Pediatr. Gastroenterol. Nutr. 48, 216–225.

University of Utah (2012). How Insects Domesticate Bacteria. http://archive.unews.utah.edu/news-releases/how-insects-domesticate-bacteria/.

Vaishnava, S., Behrendt, C.L., Ismail, A.S., Eckmann, L., and Hooper, L.V. (2008) ‘Paneth cells directly sense gut commensals and maintain homeostasis at the intestinal host–microbial interface’, Proc. Natl. Acad. Sci. 105, 20858–20863.

Van Bonn, W., LaPointe, A., Gibbons, S.M., Frazier, A., Hampton-Marcell, J., and Gilbert, J. (2015) ‘Aquarium microbiome response to ninety-percent system water change: clues to microbiome management’, Zoo Biol. 34, 360–367.

Van Leuven, J.T., Meister, R.C., Simon, C., and McCutcheon, J.P. (2014) ‘Sympatric speciation in a bacterial endosymbiont results in two genomes with the functionality of one’, Cell 158, 1270–1280.

Van Nood, E., Vrieze, A., Nieuwdorp, M., Fuentes, S., Zoetendal, E.G., de Vos, W.M., Visser, C.E., Kuijper, E.J., Bartelsman, J.F.W.M., Tijssen, J.G.P., et al. (2013) ‘Duodenal infusion of donor feces for recurrent Clostridium difficile’, N. Engl. J. Med. 368, 407–415.

Verhulst, N.O., Qiu, Y.T., Beijleveld, H., Maliepaard, C., Knights, D., Schulz, S., Berg-Lyons, D., Lauber, C.L., Verduijn, W., Haasnoot, G.W., et al. (2011) ‘Composition of human skin microbiota affects attractiveness to malaria mosquitoes’, PLoS ONE 6, e28991.

Vétizou, M., Pitt, J.M., Daillère, R., Lepage, P., Waldschmitt, N., Flament, C., Rusakiewicz, S., Routy, B., Roberti, M.P., Duong, C.P.M., et al. (2015) ‘Anticancer immunotherapy by CTLA–4 blockade relies on the gut microbiota’, Science 350, 1079–1084.

Vigneron, A., Masson, F., Vallier, A., Balmand, S., Rey, M., Vincent-Monégat, C., Aksoy, E., Aubailly-Giraud, E., Zaidman-Rémy, A., and Heddi, A. (2014) ‘Insects recycle endosymbionts when the benefit is over’, Curr. Biol. 24, 2267–2273.

Voronin, D., Cook, D.A.N., Steven, A., and Taylor, M.J. (2012) ‘Autophagy regulates Wolbachia populations across diverse symbiotic associations’, Proc. Natl. Acad. Sci. 109, E1638–E1646.

Vrieze, A., Van Nood, E., Holleman, F., Salojärvi, J., Kootte, R.S., Bartelsman, J.F.W.M., Dallinga-Thie, G.M., Ackermans, M.T., Serlie, M.J., Oozeer, R., et al.
(2012) ‘Transfer of intestinal microbiota from lean donors increases insulin sensitivity in individuals with metabolic syndrome’, Gastroenterology 143, 913–916.e7.

Wada-Katsumata, A., Zurek, L., Nalyanya, G., Roelofs, W.L., Zhang, A., and Schal, C. (2015) ‘Gut bacteria mediate aggregation in the German cockroach’, Proc. Natl. Acad. Sci doi : 10.1073/pnas.1504031112.

Wahl, M., Goecke, F., Labes, A., Dobretsov, S., and Weinberger, F. (2012) ‘The second skin: ecological role of epibiotic biofilms on marine organisms’, Front. Microbiol . 3 doi: 10.3389/fmicb.2012.00292.

Walke, J.B., Becker, M.H., Loftus, S.C., House, L.L., Cormier, G., Jensen, R.V., and Belden, L.K. (2014) ‘Amphibian skin may select for rare environmental microbes’, ISME J. 8, 2207–2217.

Walker, T., Johnson, P.H., Moreira, L.A., Iturbe-Ormaetxe, I., Frentiu, F.D., McMeniman, C.J., Leong, Y.S., Dong, Y., Axford, J., Kriesner, P., et al. (2011) ‘The wMel Wolbachia strain blocks dengue and invades caged Aedes aegypti populations’, Nature 476, 450–453.

Wallace, A.R. (1855) ‘On the law which has regulated the introduction of new species’, Ann. Mag. Nat. Hist. 16, 184–196.

Wallin, I.E. (1927) Symbionticism and the Origin of Species (Baltimore: Williams & Wilkins Co.).

Walter, J. and Ley, R. (2011) ‘The human gut microbiome: ecology and recent evolutionary changes’, Annu. Rev. Microbiol. 65, 411–429.

Walters, W.A., Xu, Z., and Knight, R. (2014) ‘Meta-analyses of human gut microbes associated with obesity and IBD’, FEBS Lett. 588, 4223–4233.

Wang, Z., Roberts, A.B., Buffa, J.A., Levison, B.S., Zhu, W., Org, E., Gu, X., Huang, Y., Zamanian-Daryoush, M., Culley, M.K., et al. (2015) ‘Non-lethal inhibition of gut microbial trimethylamine production for the treatment of atherosclerosis. Cell 163, 1585–1595.

Ward, R.E., Ninonuevo, M., Mills, D.A., Lebrilla, C.B., and German, J.B. (2006) ‘In vitro fermentation of breast milk oligosaccharides by Bifidobacterium infantis and Lactobacillus gasseri’, Appl. Environ. Microbiol. 72, 4497–4499.

Weeks, P. (2000) ‘Red-billed oxpeckers: vampires or tickbirds?’, Behav. Ecol. 11, 154–160.

Wells, H.G., Huxley, J., and Wells, G.P. (1930) The Science of Life (London: Cassell).

Wernegreen, J.J. (2004) ‘Endosymbiosis: lessons in conflict resolution’, PLoS Biol. 2, e68.

Wernegreen, J.J. (2012) ‘Mutualism meltdown in insects: bacteria constrain thermal adaptation’, Curr. Opin. Microbiol. 15, 255–262.

Wernegreen, J.J., Kauppinen, S.N., Brady, S.G., and Ward, P.S. (2009) ‘One nutritional symbiosis begat another: phylogenetic evidence that the ant tribe Camponotini acquired Blochmannia by tending sap-feeding insects’, BMC Evol. Biol. 9, 292.

Werren, J.H., Baldo, L., and Clark, M.E. (2008) ‘ Wolbachia : master manipulators of invertebrate biology’, Nat. Rev. Microbiol. 6, 741–751.

West, S.A., Fisher, R.M., Gardner, A., and Kiers, E.T. (2015) ‘Major evolutionary transitions in individuality’, Proc. Natl. Acad. Sci. U. S. A. 112, 10112–10119.

Westwood, J., Burnett, M., Spratt, D., Ball, M., Wilson, D.J., Wellsteed, S., Cleary, D., Green, A., Hutley, E., Cichowska, A., et al. (2014). The Hospital Microbiome Project: meeting report for the UK science and innovation network UK–USA workshop ‘Beating the superbugs: hospital microbiome studies for tackling antimicrobial resistance’, 14 October 2013. Stand. Genomic Sci. 9, 12.

The Wilde Lecture (1901) ‘The Wilde Medal and Lecture of the Manchester Literary and Philosophical Society.’ Br. Med. J. 1, 1027–1028.

Willingham, E. (2012). Autism, immunity, inflammation, and the New York Times . http://www.emilywillinghamphd.com/2012/08/autism-immunity-inflammation-and-new.html.

Wilson, A.C.C., Ashton, P.D., Calevro, F., Charles, H., Colella, S., Febvay, G., Jander, G., Kushlan, P.F., Macdonald, S.J., Schwartz, J.F., et al. (2010) ‘Genomic insight into the amino acid relations of the pea aphid, Acyrthosiphon pisum, with its symbiotic bacterium Buchnera aphidicola’, Insect Mol. Biol. 19 Suppl. 2, 249–258.

Wlodarska, M., Kostic, A.D., and Xavier, R.J. (2015) ‘An integrative view of microbiome-host interactions in inflammatory bowel diseases’, Cell Host Microbe 17, 577–591.

Woese, C.R. and Fox, G.E. (1977) ‘Phylogenetic structure of the prokaryotic domain: the primary kingdoms’, Proc. Natl. Acad. Sci. U. S. A. 74, 5088–5090.

Woodhams, D.C., Vredenburg, V.T., Simon, M-A., Billheimer, D., Shakhtour, B., Shyr, Y., Briggs, C.J., Rollins-Smith, L.A., and Harris, R.N. (2007) ‘Symbiotic bacteria contribute to innate immune defenses of the threatened mountain yellow-legged frog, Rana muscosa’, Biol. Conserv. 138, 390–398.

Woodhams, D.C., Brandt, H., Baumgartner, S., Kielgast, J., Küpfer, E., Tobler, U., Davis, L.R., Schmidt, B.R., Bel, C., Hodel, S., et al. (2014) ‘Interacting symbionts and immunity in the amphibian skin mucosome predict disease risk and probiotic effectiveness’, PLoS ONE 9, e96375.

Wu, H., Tremaroli, V., and Bäckhed, F. (2015) ‘Linking microbiota to human diseases: a systems biology perspective’, Trends Endocrinol. Metab . 26, 758–770.

Wybouw, N., Dermauw, W., Tirry, L., Stevens, C., Grbić, M., Feyereisen, R., and Van Leeuwen, T. (2014) ‘A gene horizontally transferred from bacteria protects arthropods from host plant cyanide poisoning’, eLife 3.

Yatsunenko, T., Rey, F.E., Manary, M.J., Trehan, I., Dominguez-Bello, M.G., Contreras, M., Magris, M., Hidalgo, G., Baldassano, R.N., Anokhin, A.P., et al. (2012) ‘Human gut microbiome viewed across age and geography’, Nature 486 (7402), 222–227.

Yong, E. (2014a) The Unique Merger That Made You (and Ewe, and Yew). http://nautil.us/issue/10/mergers-acquisitions/the-unique-merger-that-made-youand-ewe-and-yew.

Yong, E. (2014b) Zombie roaches and other parasite tales. https://www.ted.com/talks/ed_yong_suicidal_wasps_zombie_roaches_and_other_tales_of_parasites?language=en.

Yong, E. (2014c) ‘There is no ‘healthy’ microbiome’, N. Y. Times .

Yong, E. (2015a) ‘A visit to Amsterdam’s Microbe Museum’, New Yorker .

Yong, E. (2015b) ‘Microbiology: here’s looking at you, squid’, Nature 517, 262–264.

Yong, E. (2015c) ‘Bugs on patrol’, New Sci. 226, 40–43.

Yoshida, N., Oeda, K., Watanabe, E., Mikami, T., Fukita, Y., Nishimura, K., Komai, K., and Matsuda, K. (2001) ‘Protein function: chaperonin turned insect toxin’, Nature 411, 44–44.

Youngster, I., Russell, G.H., Pindar, C., Ziv-Baran, T., Sauk, J., and Hohmann, E.L. (2014) ‘Oral, capsulized, frozen fecal microbiota transplantation for relapsing Clostridium difficile infection’, JAMA 312, 1772.

Zhang, F., Luo, W., Shi, Y., Fan, Z., and Ji, G. (2012) ‘Should we standardize the 1,700-year-old fecal microbiota transplantation?’, Am. J. Gastroenterol. 107, 1755–1755.

Zhang, Q., Raoof, M., Chen, Y., Sumi, Y., Sursal, T., Junger, W., Brohi, K., Itagaki, K., and Hauser, C.J. (2010) ‘Circulating mitochondrial DAMPs cause inflammatory responses to injury’, Nature 464, 104–107.

Zhao, L. (2013) ‘The gut microbiota and obesity: from correlation to causality’, Nat. Rev. Microbiol. 11, 639–647.

Zilber-Rosenberg, I. and Rosenberg, E. (2008) ‘Role of microorganisms in the evolution of animals and plants: the hologenome theory of evolution’, FEMS Microbiol. Rev. 32, 723–735.

Zimmer, C. (2008) Microcosm: E-coli and The New Science of Life (London: William Heinemann).

Zug, R. and Hammerstein, P. (2012) ‘Still a host of hosts for Wolbachia : analysis of recent data suggests that 40% of terrestrial arthropod species are infected’, PLoS ONE 7, e38544. 3mfY7GBc+uZvyIDpkKxSaTXKtncgMfCDcsnZzuv/m2wSJ28vI5Bfn0k5RmL/IY/Q

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