Friends with social benefits: Host-microbe interactions as a driver of brain evolution and development?

Frontiers in Cellular and Infection Microbiology

Volumn 4, Issue OCT, 2014, Pages

  Stilling, Roman M ^a,b   Bordenstein, Seth R ^c   Dinan, Timothy G ^a,b   Cryan, John F ^a,b  

^a UNIVERSITY COLLEGE CORK   (Ireland)

^b UNIVERSITY COLLEGE CORK   (Ireland)

^c VANDERBILT UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

Brain evolution; Commensal; Epigenetics; Evo devo; Gene environment interactions; Hologenome; Host microbe; Host parasite; Host pathogen; Microbiome; Microbiota; Neurodevelopment; Neuroparasite; Non coding RNA; Sociality; Symbiosis; Transgenerational

Indexed keywords

4 AMINOBUTYRIC ACID; DOPAMINE; HISTAMINE; MICRORNA; OXYTOCIN; RNA; SEROTONIN; SHORT CHAIN FATTY ACID; SMALL INTERFERING RNA; TRYPTOPHAN; UNTRANSLATED RNA; VASOPRESSIN;

ADAPTATION; ARTICLE; BRAIN DEVELOPMENT; BRAIN FUNCTION; COGNITION; EPIGENETICS; EVOLUTION; GENE; GENE EXPRESSION; GENOME; HOST PATHOGEN INTERACTION; HUMAN; MICROBIOLOGY; MICROBIOME; MICROFLORA; NEUROSCIENCE; NONHUMAN; PLASTICITY; RNA EDITING; SOCIAL BEHAVIOR; SYMBIOSIS; TRANSLATION REGULATION; ANIMAL; BEHAVIOR; BRAIN; GENETIC EPIGENESIS; GENOTYPE ENVIRONMENT INTERACTION; PHYSIOLOGY;

ADAPTATION, BIOLOGICAL; ANIMALS; BEHAVIOR; BIOLOGICAL EVOLUTION; BRAIN; EPIGENESIS, GENETIC; GENE-ENVIRONMENT INTERACTION; HOST-PATHOGEN INTERACTIONS; HUMANS; MICROBIOTA; SYMBIOSIS;

EID: 84908210053     PISSN: None     EISSN: 22352988     Source Type: Journal    
DOI: 10.3389/fcimb.2014.00147     Document Type: Article

References (209)

1. Aagaard, K., Ma, J., Antony, K. M., Ganu, R., Petrosino, J., and Versalovic, J. (2014). The Placenta Harbors a Unique Microbiome. Sci. Transl. Med. 6, 237ra65-237ra65. doi:10.1126/scitranslmed.3008599
2. Aiello, L. C., and Wheeler, P. (1995). The Expensive-Tissue Hypothesis: The Brain and the Digestive System in Human and Primate Evolution. Curr. Anthropol. 36, 199-221
3. Al Akeel, R. (2013). Role of epigenetic reprogramming of host genes in bacterial pathogenesis. Saudi J. Biol. Sci. 20, 305-309. doi:10.1016/j.sjbs.2013.05.003
4. Alcock, J., Maley, C. C., and Aktipis, C. A. (2014). Is eating behavior manipulated by the gastrointestinal microbiota? Evolutionary pressures and potential mechanisms. BioEssays News Rev. Mol. Cell. Dev. Biol. doi:10.1002/bies.201400071
5. Alenghat, T., Osborne, L. C., Saenz, S. A., Kobuley, D., Ziegler, C. G. K., Mullican, S. E., Choi, I., Grunberg, S., Sinha, R., Wynosky-Dolfi, M., et al. (2013). Histone deacetylase 3 coordinates commensal-bacteria-dependent intestinal homeostasis. Nature 504, 153-157. doi:10.1038/nature12687
6. Arai, J. A., Li, S., Hartley, D. M., and Feig, L. A. (2009). Transgenerational rescue of a genetic defect in long-term potentiation and memory formation by juvenile enrichment. J. Neurosci. Off. J. Soc. Neurosci. 29, 1496-1502. doi:10.1523/JNEUROSCI.5057-08.2009
7. Arpaia, N., Campbell, C., Fan, X., Dikiy, S., van der Veeken, J., deRoos, P., Liu, H., Cross, J. R., Pfeffer, K., Coffer, P. J., et al. (2013). Metabolites produced by commensal bacteria promote peripheral regulatory T-cell generation. Nature 504, 451-455. doi:10.1038/nature12726
8. Arumugam, M., Raes, J., Pelletier, E., Le Paslier, D., Yamada, T., Mende, D. R., Fernandes, G. R., Tap, J., Bruls, T., Batto, J.-M., et al. (2011). Enterotypes of the human gut microbiome. Nature 473, 174-180. doi:10.1038/nature09944
9. Ausubel, F. M. (2005). Are innate immune signaling pathways in plants and animals conserved? Nat. Immunol. 6, 973-979. doi:10.1038/ni1253
10. Badyaev, A. V., and Uller, T. (2009). Parental effects in ecology and evolution: mechanisms, processes and implications. Philos. Trans. R. Soc. B Biol. Sci. 364, 1169-1177. doi:10.1098/rstb.2008.0302
11. Bailey, M. T., and Coe, C. L. (1999). Maternal separation disrupts the integrity of the intestinal microflora in infant rhesus monkeys. Dev. Psychobiol. 35, 146-155
12. Bailey, M. T., Dowd, S. E., Galley, J. D., Hufnagle, A. R., Allen, R. G., and Lyte, M. (2011). Exposure to a social stressor alters the structure of the intestinal microbiota: implications for stressor induced immunomodulation. Brain. Behav. Immun. 25, 397-407. doi:10.1016/j.bbi.2010.10.023
13. Baron-Cohen, S. (2009). Autism: the empathizing-systemizing (E-S) theory. Ann. N. Y. Acad. Sci. 1156, 68-80. doi:10.1111/j.1749-6632.2009.04467.x
14. Barry, G. (2014). Integrating the roles of long and small non-coding RNA in brain function and disease. Mol. Psychiatry 19, 410-416. doi:10.1038/mp.2013.196
15. Barry, G., and Mattick, J. S. (2012). The role of regulatory RNA in cognitive evolution. Trends Cogn. Sci. 16, 497-503. doi:10.1016/j.tics.2012.08.007
16. 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. U. S. A. 107, 18933-18938. doi:10.1073/pnas.1007028107
17. Berdoy, M., Webster, J. P., and Macdonald, D. W. (2000). Fatal attraction in rats infected with Toxoplasma gondii. Proc. Biol. Sci. 267, 1591-1594. doi:10.1098/rspb.2000.1182
18. Bhavsar, A. P., Guttman, J. A., and Finlay, B. B. (2007). Manipulation of host-cell pathways by bacterial pathogens. Nature 449, 827-834. doi:10.1038/nature06247
19. Bierne, H. (2013). Nuclear microbiology-bacterial assault on the nucleolus. EMBO Rep. 14, 663-664. doi:10.1038/embor.2013.105
20. Bierne, H., and Cossart, P. (2012). When bacteria target the nucleus: the emerging family of nucleomodulins. Cell. Microbiol. 14, 622-633. doi:10.1111/j.1462-5822.2012.01758.x
21. Bierne, H., Hamon, M., and Cossart, P. (2012). Epigenetics and bacterial infections. Cold Spring Harb. Perspect. Med. 2, a010272. doi:10.1101/cshperspect.a010272
22. Blow, M., Futreal, P. A., Wooster, R., and Stratton, M. R. (2004). A survey of RNA editing in human brain. Genome Res. 14, 2379-2387. doi:10.1101/gr.2951204
23. Bohacek, J., Gapp, K., Saab, B. J., and Mansuy, I. M. (2013). Transgenerational Epigenetic Effects on Brain Functions. Biol. Psychiatry 73, 313-320. doi:10.1016/j.biopsych.2012.08.019
24. Booth, A. (2014). Symbiosis, selection, and individuality. Biol. Philos., 1-17. doi:10.1007/s10539- 014-9449-8
25. Borody, T. J., and Khoruts, A. (2012). Fecal microbiota transplantation and emerging applications. Nat. Rev. Gastroenterol. Hepatol. 9, 88-96. doi:10.1038/nrgastro.2011.244
26. Borre, Y. E., O'Keeffe, G. W., Clarke, G., Stanton, C., Dinan, T. G., and Cryan, J. F. (2014). Microbiota and neurodevelopmental windows: implications for brain disorders. Trends Mol. Med. 0. doi:10.1016/j.molmed.2014.05.002
27. Brucker, R. M., and Bordenstein, S. R. (2012a). Speciation by symbiosis. Trends Ecol. Evol. 27, 443-451. doi:10.1016/j.tree.2012.03.011
28. Brucker, R. M., and Bordenstein, S. R. (2013a). The capacious hologenome. Zool. Jena Ger. 116, 260-261. doi:10.1016/j.zool.2013.08.003
29. Brucker, R. M., and Bordenstein, S. R. (2013b). The Hologenomic Basis of Speciation: Gut Bacteria Cause Hybrid Lethality in the Genus Nasonia. Science 341, 667-669. doi:10.1126/science.1240659
30. Brucker, R. M., and Bordenstein, S. R. (2012b). The roles of host evolutionary relationships (genus: Nasonia) and development in structuring microbial communities. Evol. Int. J. Org. Evol. 66, 349- 362. doi:10.1111/j.1558-5646.2011.01454.x
31. Burns, C. M., Chu, H., Rueter, S. M., Hutchinson, L. K., Canton, H., Sanders-Bush, E., and Emeson, R. B. (1997). Regulation of serotonin-2C receptor G-protein coupling by RNA editing. Nature 387, 303-308. doi:10.1038/387303a0
32. Cameron, N. M., Shahrokh, D., Del Corpo, A., Dhir, S. K., Szyf, M., Champagne, F. A., and Meaney, M. J. (2008). Epigenetic Programming of Phenotypic Variations in Reproductive Strategies in the Rat Through Maternal Care. J. Neuroendocrinol. 20, 795-801. doi:10.1111/j.1365-2826.2008.01725.x
33. Candido, E. P., Reeves, R., and Davie, J. R. (1978). Sodium butyrate inhibits histone deacetylation in cultured cells. Cell 14, 105-113
34. CAO, X., LIN, P., JIANG, P., and LI, C. (2013). Characteristics of the gastrointestinal microbiome in children with autism spectrum disorder: a systematic review. Shanghai Arch. Psychiatry 25, 342-353
35. Cézilly, F., Thomas, F., Médoc, V., and Perrot-Minnot, M.-J. (2010). Host-manipulation by parasites with complex life cycles: adaptive or not? Trends Parasitol. 26, 311-317. doi:10.1016/j.pt.2010.03.009
36. Chang, P. V., Hao, L., Offermanns, S., and Medzhitov, R. (2014). The microbial metabolite butyrate regulates intestinal macrophage function via histone deacetylase inhibition. Proc. Natl. Acad. Sci. U. S. A. doi:10.1073/pnas.1322269111
37. 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. doi:10.1016/j.cell.2012.04.037
38. Claesson, M. J., Jeffery, I. B., Conde, S., Power, S. E., O'Connor, E. M., Cusack, S., Harris, H. M. B., Coakley, M., Lakshminarayanan, B., O'Sullivan, O., et al. (2012). Gut microbiota composition correlates with diet and health in the elderly. Nature 488, 178-184. doi:10.1038/nature11319
39. Clarke, G., Grenham, S., Scully, P., Fitzgerald, P., Moloney, R. D., Shanahan, F., Dinan, T. G., and Cryan, J. F. (2013). The microbiome-gut-brain axis during early life regulates the hippocampal serotonergic system in a sex-dependent manner. Mol. Psychiatry 18, 666-673. doi:10.1038/mp.2012.77
40. Crow, T. J. (1995). Aetiology of schizophrenia: an evolutionary theory. Int. Clin. Psychopharmacol. 10 Suppl 3, 49-56
41. Crow, T. J. (1997). Is schizophrenia the price that Homo sapiens pays for language? Schizophr. Res. 28, 127-141
42. Crumeyrolle-Arias, M., Jaglin, M., Bruneau, A., Vancassel, S., Cardona, A., Daugé, V., Naudon, L., and Rabot, S. (2014). Absence of the gut microbiota enhances anxiety-like behavior and neuroendocrine response to acute stress in rats. Psychoneuroendocrinology 42, 207-217. doi:10.1016/j.psyneuen.2014.01.014
43. 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. doi:10.1038/nrn3346
44. Cryan, J. F., and O'Mahony, S. M. (2011). The microbiome-gut-brain axis: from bowel to behavior. Neurogastroenterol. Motil. Off. J. Eur. Gastrointest. Motil. Soc. 23, 187-192. doi:10.1111/j.1365- 2982.2010.01664.x
45. Dale, C., and Moran, N. A. (2006). Molecular interactions between bacterial symbionts and their hosts. Cell 126, 453-465. doi:10.1016/j.cell.2006.07.014
46. Dave, M., Higgins, P. D., Middha, S., and Rioux, K. P. (2012). The human gut microbiome: current knowledge, challenges, and future directions. Transl. Res. J. Lab. Clin. Med. 160, 246-257. doi:10.1016/j.trsl.2012.05.003
47. Davie, J. R. (2003). Inhibition of Histone Deacetylase Activity by Butyrate. J. Nutr. 133, 2485S- 2493S
48. Dawkins, R. (1983). The extended phenotype: the long reach of the gene. Oxford; New York: Oxford University Press
49. Day, J. J., and Sweatt, J. D. (2011). Epigenetic Mechanisms in Cognition. Neuron 70, 813-829. doi:10.1016/j.neuron.2011.05.019
50. Derrien, T., Johnson, R., Bussotti, G., Tanzer, A., Djebali, S., Tilgner, H., Guernec, G., Martin, D., Merkel, A., Knowles, D. G., et al. (2012). The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. Genome Res. 22, 1775-1789. doi:10.1101/gr.132159.111
51. Desbonnet, L., Clarke, G., Shanahan, F., Dinan, T. G., and Cryan, J. F. (2014). Microbiota is essential for social development in the mouse. Mol. Psychiatry 19, 146-148. doi:10.1038/mp.2013.65
52. 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. doi:10.1038/nature06245
53. Van De Vondervoort, I. I. G. M., Gordebeke, P. M., Khoshab, N., Tiesinga, P. H. E., Buitelaar, J. K., Kozicz, T., Glennon, J. C., and Aschrafi, A. (2013). Long non-coding RNAs in neurodevelopmental disorders. Front. Mol. Neurosci. 6, 53. doi:10.3389/fnmol.2013.00053
54. Dias, B. G., and Ressler, K. J. (2014). Parental olfactory experience influences behavior and neural structure in subsequent generations. Nat. Neurosci. 17, 89-96. doi:10.1038/nn.3594
55. Dinan, T. G., Stanton, C., and Cryan, J. F. (2013). Psychobiotics: a novel class of psychotropic. Biol. Psychiatry 74, 720-726. doi:10.1016/j.biopsych.2013.05.001
56. Dobzhansky, T. (1973). Nothing in Biology Makes Sense Except in Light of Evolution. Am. Biol. Teach. 35, 125-129
57. Douglas, A. E. (2014). Symbiosis as a general principle in eukaryotic evolution. Cold Spring Harb. Perspect. Biol. 6. doi:10.1101/cshperspect.a016113
58. Dracheva, S., Elhakem, S. L., Marcus, S. M., Siever, L. J., McGurk, S. R., and Haroutunian, V. (2003). RNA editing and alternative splicing of human serotonin 2C receptor in schizophrenia. J. Neurochem. 87, 1402-1412
59. Dubrovsky, B. (2002). Evolutionary psychiatry. Adaptationist and nonadaptationist conceptualizations. Prog. Neuropsychopharmacol. Biol. Psychiatry 26, 1-19
60. Dulac, C. (2010). Brain function and chromatin plasticity. Nature 465, 728-735. doi:10.1038/nature09231
61. Dunbar, R. I. M. (1998). The social brain hypothesis. Evol. Anthropol. 6, 178-190. doi:10.1002/(SICI)1520-6505(1998)6:5<178::AID-EVAN5>3.0.CO;2-8
62. Eskandarian, H. A., Impens, F., Nahori, M.-A., Soubigou, G., Coppée, J.-Y., Cossart, P., and Hamon, M. A. (2013). A role for SIRT2-dependent histone H3K18 deacetylation in bacterial infection. Science 341, 1238858. doi:10.1126/science.1238858
63. Ezenwa, V. O., Gerardo, N. M., Inouye, D. W., Medina, M., and Xavier, J. B. (2012). Animal Behavior and the Microbiome. Science 338, 198-199. doi:10.1126/science.1227412
64. Fischer, A. (2014a). Epigenetic memory: the Lamarckian brain. EMBO J. doi:10.1002/embj.201387637
65. Fischer, A. (2014b). Targeting histone-modifications in Alzheimer's disease. What is the evidence that this is a promising therapeutic avenue? Neuropharmacology 80C, 95-102. doi:10.1016/j.neuropharm.2014.01.038
66. Fischer, A., Sananbenesi, F., Mungenast, A., and Tsai, L.-H. (2010). Targeting the correct HDAC(s) to treat cognitive disorders. Trends Pharmacol. Sci. 31, 605-617. doi:10.1016/j.tips.2010.09.003
67. Fischer, A., Sananbenesi, F., Wang, X., Dobbin, M., and Tsai, L.-H. (2007). Recovery of learning and memory is associated with chromatin remodelling. Nature 447, 178-182. doi:10.1038/nature05772
68. Fitzpatrick, B. M. (2014). Symbiote transmission and maintenance of extra-genomic associations. Front. Microbiol. 5, 46. doi:10.3389/fmicb.2014.00046
69. Forsythe, P., and Kunze, W. A. (2013). Voices from within: gut microbes and the CNS. Cell. Mol. Life Sci. 70, 55-69. doi:10.1007/s00018-012-1028-z
70. Frank, D. N., and Pace, N. R. (2008). Gastrointestinal microbiology enters the metagenomics era. Curr. Opin. Gastroenterol. 24, 4-10. doi:10.1097/MOG.0b013e3282f2b0e8
71. Franklin, T. B., Russig, H., Weiss, I. C., Gräff, J., Linder, N., Michalon, A., Vizi, S., and Mansuy, I. M. (2010). Epigenetic Transmission of the Impact of Early Stress Across Generations. Biol. Psychiatry 68, 408-415. doi:10.1016/j.biopsych.2010.05.036
72. Franzenburg, S., Walter, J., Künzel, S., Wang, J., Baines, J. F., Bosch, T. C. G., and Fraune, S. (2013). Distinct antimicrobial peptide expression determines host species-specific bacterial associations. Proc. Natl. Acad. Sci. U. S. A. 110, E3730-3738. doi:10.1073/pnas.1304960110
73. Fraune, S., and Bosch, T. C. G. (2007). Long-term maintenance of species-specific bacterial microbiota in the basal metazoan Hydra. Proc. Natl. Acad. Sci. 104, 13146-13151. doi:10.1073/pnas.0703375104
74. Funkhouser, L. J., and Bordenstein, S. R. (2013). Mom Knows Best: The Universality of Maternal Microbial Transmission. PLoS Biol 11, e1001631. doi:10.1371/journal.pbio.1001631
75. 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. doi:10.1038/nature12721
76. Gapp, K., Jawaid, A., Sarkies, P., Bohacek, J., Pelczar, P., Prados, J., Farinelli, L., Miska, E., and Mansuy, I. M. (2014). Implication of sperm RNAs in transgenerational inheritance of the effects of early trauma in mice. Nat. Neurosci. 17, 667-669. doi:10.1038/nn.3695
77. Gilbert, S. F., McDonald, E., Boyle, N., Buttino, N., Gyi, L., Mai, M., Prakash, N., and Robinson, J. (2010). Symbiosis as a source of selectable epigenetic variation: taking the heat for the big guy. Philos. Trans. R. Soc. B Biol. Sci. 365, 671-678. doi:10.1098/rstb.2009.0245
78. Govindarajan, N., Agis-Balboa, R. C., Walter, J., Sananbenesi, F., and Fischer, A. (2011). Sodium butyrate improves memory function in an Alzheimer's disease mouse model when administered at an advanced stage of disease progression. J. Alzheimers Dis. JAD 26, 187-197. doi:10.3233/JAD-2011-110080
79. Gräff, J., and Tsai, L.-H. (2013). The potential of HDAC inhibitors as cognitive enhancers. Annu. Rev. Pharmacol. Toxicol. 53, 311-330. doi:10.1146/annurev-pharmtox-011112-140216
80. Hamilton, W. D. (1964). The genetical evolution of social behaviour. II. J. Theor. Biol. 7, 17-52.
81. Hamon, M. A., and Cossart, P. (2008). Histone modifications and chromatin remodeling during bacterial infections. Cell Host Microbe 4, 100-109. doi:10.1016/j.chom.2008.07.009
82. Hansen, T. F. (2006). The Evolution of Genetic Architecture. Annu. Rev. Ecol. Evol. Syst. 37, 123-157. doi:10.1146/annurev.ecolsys.37.091305.110224
83. Hari Dass, S. A., and Vyas, A. (2014). Toxoplasma gondii infection reduces predator aversion in rats through epigenetic modulation in the host medial amygdala. Mol. Ecol., n/a-n/a. doi:10.1111/mec.12888
84. Heijtz, R. D., Wang, S., Anuar, F., Qian, Y., Björkholm, B., Samuelsson, A., Hibberd, M. L., Forssberg, H., and Pettersson, S. (2011). Normal gut microbiota modulates brain development and behavior. Proc. Natl. Acad. Sci. U. S. A. 108, 3047-3052. doi:10.1073/pnas.1010529108
85. Holliday, R. (1987). The inheritance of epigenetic defects. Science 238, 163-170.
86. Hrvoj-Mihic, B., Bienvenu, T., Stefanacci, L., Muotri, A. R., and Semendeferi, K. (2013). Evolution, development, and plasticity of the human brain: from molecules to bones. Front. Hum. Neurosci. 7. doi:10.3389/fnhum.2013.00707
87. 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. doi:10.1016/j.cell.2013.11.024
88. Human Microbiome Project Consortium (2012). Structure, function and diversity of the healthy human microbiome. Nature 486, 207-214. doi:10.1038/nature11234
89. Igaz, L. M., Bekinschtein, P., Vianna, M. M. R., Izquierdo, I., and Medina, J. H. (2004). Gene expression during memory formation. Neurotox. Res. 6, 189-204
90. Igaz, L. M., Vianna, M. R. M., Medina, J. H., and Izquierdo, I. (2002). Two time periods of hippocampal mRNA synthesis are required for memory consolidation of fear-motivated learning. J. Neurosci. Off. J. Soc. Neurosci. 22, 6781-6789. doi:20026642
91. Insel, T. R. (2010). The challenge of translation in social neuroscience: a review of oxytocin, vasopressin, and affiliative behavior. Neuron 65, 768-779. doi:10.1016/j.neuron.2010.03.005
92. Khatri, N., and Man, H.-Y. (2013). Synaptic Activity and Bioenergy Homeostasis: Implications in Brain Trauma and Neurodegenerative Diseases. Front. Neurol. 4. doi:10.3389/fneur.2013.00199
93. Kilgore, M., Miller, C. A., Fass, D. M., Hennig, K. M., Haggarty, S. J., Sweatt, J. D., and Rumbaugh, G. (2010). Inhibitors of class 1 histone deacetylases reverse contextual memory deficits in a mouse model of Alzheimer's disease. Neuropsychopharmacol. Off. Publ. Am. Coll. Neuropsychopharmacol. 35, 870-880. doi:10.1038/npp.2009.197
94. Kodaman, N., Pazos, A., Schneider, B. G., Piazuelo, M. B., Mera, R., Sobota, R. S., Sicinschi, L. A., Shaffer, C. L., Romero-Gallo, J., de Sablet, T., et al. (2014). Human and Helicobacter pylori coevolution shapes the risk of gastric disease. Proc. Natl. Acad. Sci. U. S. A. 111, 1455-1460. doi:10.1073/pnas.1318093111
95. Koenig, J. E., Spor, A., Scalfone, N., Fricker, A. D., Stombaugh, J., Knight, R., Angenent, L. T., and Ley, R. E. (2011). Succession of microbial consortia in the developing infant gut microbiome. Proc. Natl. Acad. Sci. U. S. A. 108 Suppl 1, 4578-4585. doi:10.1073/pnas.1000081107
96. Koren, O., Goodrich, J. K., Cullender, T. C., Spor, A., Laitinen, K., Bäckhed, H. K., 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. doi:10.1016/j.cell.2012.07.008
97. Kornblihtt, A. R., Schor, I. E., Alló, M., Dujardin, G., Petrillo, E., and Muñoz, M. J. (2013). Alternative splicing: a pivotal step between eukaryotic transcription and translation. Nat. Rev. Mol. Cell Biol. 14, 153-165. doi:10.1038/nrm3525
98. Kosik, K. S., Rapp, P. R., Raz, N., Small, S. A., Sweatt, J. D., and Tsai, L.-H. (2012). Mechanisms of Age-Related Cognitive Change and Targets for Intervention: Epigenetics. J. Gerontol. A. Biol. Sci. Med. Sci. doi:10.1093/gerona/gls110
99. Kovacs, A., Ben-Jacob, N., Tayem, H., Halperin, E., Iraqi, F. A., and Gophna, U. (2011). Genotype is a stronger determinant than sex of the mouse gut microbiota. Microb. Ecol. 61, 423-428. doi:10.1007/s00248-010-9787-2
100. Landry, C. D., Kandel, E. R., and Rajasethupathy, P. (2013). New mechanisms in memory storage: piRNAs and epigenetics. Trends Neurosci. 36, 535-542. doi:10.1016/j.tins.2013.05.004
101. Lederbogen, F., Kirsch, P., Haddad, L., Streit, F., Tost, H., Schuch, P., Wüst, S., Pruessner, J. C., Rietschel, M., Deuschle, M., et al. (2011). City living and urban upbringing affect neural social stress processing in humans. Nature 474, 498-501. doi:10.1038/nature10190
102. Ledford, H. (2008). Language: Disputed definitions. Nature 455, 1023-1028. doi:10.1038/4551023a
103. Lee, Y. K., and Mazmanian, S. K. (2014). Microbial Learning Lessons: SFB Educate the Immune System. Immunity 40, 457-459. doi:10.1016/j.immuni.2014.04.002
104. Libersat, F., Delago, A., and Gal, R. (2009). Manipulation of Host Behavior by Parasitic Insects and Insect Parasites. Annu. Rev. Entomol. 54, 189-207. doi:10.1146/annurev.ento.54.110807.090556
105. 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. doi:10.1038/nbt.2942
106. Lin, L., Shen, S., Jiang, P., Sato, S., Davidson, B. L., and Xing, Y. (2010). Evolution of alternative splicing in primate brain transcriptomes. Hum. Mol. Genet. 19, 2958-2973. doi:10.1093/hmg/ddq201
107. Liu, H., Wang, X., Wang, H.-D., Wu, J., Ren, J., Meng, L., Wu, Q., Dong, H., Wu, J., Kao, T.-Y., et al. (2012). Escherichia coli noncoding RNAs can affect gene expression and physiology of Caenorhabditis elegans. Nat. Commun. 3, 1073. doi:10.1038/ncomms2071
108. Li, Z., Bammann, H., Li, M., Liang, H., Yan, Z., Phoebe Chen, Y.-P., Zhao, M., and Khaitovich, P. (2013). Evolutionary and ontogenetic changes in RNA editing in human, chimpanzee, and macaque brains. RNA 19, 1693-1702. doi:10.1261/rna.039206.113
109. Lombardo, M. P. (2008). Access to mutualistic endosymbiotic microbes: an underappreciated benefit of group living. Behav. Ecol. Sociobiol. 62, 479-497. doi:10.1007/s00265-007-0428-9
110. Luckey, T. D. (1972). Introduction to intestinal microecology. Am. J. Clin. Nutr. 25, 1292-1294
111. Luco, R. F., Allo, M., Schor, I. E., Kornblihtt, A. R., and Misteli, T. (2011). Epigenetics in alternative pre-mRNA splicing. Cell 144, 16-26. doi:10.1016/j.cell.2010.11.056
112. Lukas, M., Toth, I., Veenema, A. H., and Neumann, I. D. (2013). Oxytocin mediates rodent social memory within the lateral septum and the medial amygdala depending on the relevance of the social stimulus: male juvenile versus female adult conspecifics. Psychoneuroendocrinology 38, 916-926. doi:10.1016/j.psyneuen.2012.09.018
113. Lyte, M. (2011). Probiotics function mechanistically as delivery vehicles for neuroactive compounds: Microbial endocrinology in the design and use of probiotics. BioEssays News Rev. Mol. Cell. Dev. Biol. 33, 574-581. doi:10.1002/bies.201100024
114. Lyte, M., and Freestone, P. P. E. (2010). Microbial endocrinology interkingdom signaling in infectious disease and health. New York: Springer Available at: http://public.eblib.com/EBLPublic/PublicView.do?ptiID=571526 [Accessed October 20, 2013]
115. MacFabe, D. F., Cain, N. E., Boon, F., Ossenkopp, K.-P., and Cain, D. P. (2011). Effects of the enteric bacterial metabolic product propionic acid on object-directed behavior, social behavior, cognition, and neuroinflammation in adolescent rats: Relevance to autism spectrum disorder. Behav. Brain Res. 217, 47-54. doi:10.1016/j.bbr.2010.10.005
116. Marazzi, I., Ho, J. S. Y., Kim, J., Manicassamy, B., Dewell, S., Albrecht, R. A., Seibert, C. W., Schaefer, U., Jeffrey, K. L., Prinjha, R. K., et al. (2012). Suppression of the antiviral response by an influenza histone mimic. Nature 483, 428-433. doi:10.1038/nature10892
117. Marques, T. M., Wall, R., Ross, R. P., Fitzgerald, G. F., Ryan, C. A., and Stanton, C. (2010). Programming infant gut microbiota: influence of dietary and environmental factors. Curr. Opin. Biotechnol. 21, 149-156. doi:10.1016/j.copbio.2010.03.020
118. Mason, M. R., Nagaraja, H. N., Camerlengo, T., Joshi, V., and Kumar, P. S. (2013). Deep Sequencing Identifies Ethnicity-Specific Bacterial Signatures in the Oral Microbiome. PLoS ONE 8, e77287. doi:10.1371/journal.pone.0077287
119. Mattick, J. S. (2009). Has evolution learnt how to learn? EMBO Rep. 10, 665. doi:10.1038/embor.2009.135
120. McFall-Ngai, M., Hadfield, M. G., Bosch, T. C. G., Carey, H. V., Domazet-Lošo, T., Douglas, A. E., Dubilier, N., Eberl, G., Fukami, T., Gilbert, S. F., et al. (2013). Animals in a bacterial world, a new imperative for the life sciences. Proc. Natl. Acad. Sci. 110, 3229-3236. doi:10.1073/pnas.1218525110
121. McLoughlin, G. (2002). Is depression normal in human beings? A critique of the evolutionary perspective. Int. J. Ment. Health Nurs. 11, 170-173
122. McQuown, S. C., and Wood, M. A. (2011). HDAC3 and the Molecular Brake Pad Hypothesis. Neurobiol. Learn. Mem. 96, 27-34. doi:10.1016/j.nlm.2011.04.005
123. Meaney, M. J., and Szyf, M. (2005). Environmental programming of stress responses through DNA methylation: life at the interface between a dynamic environment and a fixed genome. Dialogues Clin. Neurosci. 7, 103-123
124. Mellios, N., and Sur, M. (2012). The Emerging Role of microRNAs in Schizophrenia and Autism Spectrum Disorders. Front. Psychiatry 3, 39. doi:10.3389/fpsyt.2012.00039
125. Meyer, K. D., Saletore, Y., Zumbo, P., Elemento, O., Mason, C. E., and Jaffrey, S. R. (2012). Comprehensive analysis of mRNA methylation reveals enrichment in 3' UTRs and near stop codons. Cell 149, 1635-1646. doi:10.1016/j.cell.2012.05.003
126. Meyer-Lindenberg, A., and Tost, H. (2012). Neural mechanisms of social risk for psychiatric disorders. Nat. Neurosci. 15, 663-668. doi:10.1038/nn.3083
127. Mika, F., and Hengge, R. (2013). Small Regulatory RNAs in the Control of Motility and Biofilm Formation in E. coli and Salmonella. Int. J. Mol. Sci. 14, 4560-4579. doi:10.3390/ijms14034560
128. Minárovits, J. (2009). Microbe-induced epigenetic alterations in host cells: the coming era of pathoepigenetics of microbial infections. A review. Acta Microbiol. Immunol. Hung. 56, 1-19. doi:10.1556/AMicr.56.2009.1.1
129. Ming, X., Stein, T. P., Barnes, V., Rhodes, N., and Guo, L. (2012). Metabolic perturbance in autism spectrum disorders: a metabolomics study. J. Proteome Res. 11, 5856-5862. doi:10.1021/pr300910n
130. Moeller, A. H., Degnan, P. H., Pusey, A. E., Wilson, M. L., Hahn, B. H., and Ochman, H. (2012). Chimpanzees and humans harbour compositionally similar gut enterotypes. Nat. Commun. 3, 1179. doi:10.1038/ncomms2159
131. Montiel-Castro, A. J., González-Cervantes, R. M., Bravo-Ruiseco, G., and Pacheco-López, G. (2013). The microbiota-gut-brain axis: neurobehavioral correlates, health and sociality. Front. Integr. Neurosci. 7, 70. doi:10.3389/fnint.2013.00070
132. Montiel-Castro, null, Augusto, J., Baez-Yanez, null, Mario, G., and Pacheco-Lopez, G. (2014). Social neuroeconomics: the influence of microbiota in partner-choice and sociality. Curr. Pharm. Des. 20, 4774-4783
133. Moran, N. A. (2006). Symbiosis. Curr. Biol. 16, R866-R871. doi:10.1016/j.cub.2006.09.019
134. Müller, C., and Leutz, A. (2001). Chromatin remodeling in development and differentiation. Curr. Opin. Genet. Dev. 11, 167-174. doi:10.1016/S0959-437X(00)00175-1
135. Munck, A., Guyre, P. M., and Holbrook, N. J. (1984). Physiological functions of glucocorticoids in stress and their relation to pharmacological actions. Endocr. Rev. 5, 25-44. doi:10.1210/edrv-5-1-25
136. Murata, K., Fox-Talbot, K., Qian, Z., Takahashi, K., Stahl, G. L., Baldwin, W. M., and Wasowska, B. A. (2007). Synergistic Deposition of C4d by Complement-Activating and Non-activating Antibodies in Cardiac Transplants. Am. J. Transplant. 7, 2605-2614. doi:10.1111/j.1600- 6143.2007.01971.x
137. Navarrete, A., van Schaik, C. P., and Isler, K. (2011). Energetics and the evolution of human brain size. Nature 480, 91-93. doi:10.1038/nature10629
138. Nesse, R. M. (2000). Is depression an adaptation? Arch. Gen. Psychiatry 57, 14-20.
139. Neufeld, K. M., Kang, N., Bienenstock, J., and Foster, J. A. (2011). Reduced anxiety-like behavior and central neurochemical change in germ-free mice. Neurogastroenterol. Motil. 23, 255-e119. doi:10.1111/j.1365-2982.2010.01620.x
140. Ng, S.-Y., Lin, L., Soh, B. S., and Stanton, L. W. (2013). Long noncoding RNAs in development and disease of the central nervous system. Trends Genet. 29, 461-468. doi:10.1016/j.tig.2013.03.002
141. Niu, Y., Zhao, X., Wu, Y.-S., Li, M.-M., Wang, X.-J., and Yang, Y.-G. (2013). N6-methyl-adenosine (m6A) in RNA: an old modification with a novel epigenetic function. Genomics Proteomics Bioinformatics 11, 8-17. doi:10.1016/j.gpb.2012.12.002
142. O'Connor, R. M., Dinan, T. G., and Cryan, J. F. (2012). Little things on which happiness depends: microRNAs as novel therapeutic targets for the treatment of anxiety and depression. Mol. Psychiatry 17, 359-376. doi:10.1038/mp.2011.162
143. O'Mahony, S. M., Marchesi, J. R., Scully, P., Codling, C., Ceolho, A.-M., Quigley, E. M. M., Cryan, J. F., and Dinan, T. G. (2009). Early Life Stress Alters Behavior, Immunity, and Microbiota in Rats: Implications for Irritable Bowel Syndrome and Psychiatric Illnesses. Biol. Psychiatry 65, 263-267. doi:10.1016/j.biopsych.2008.06.026
144. Pantoja-Feliciano, I. G., Clemente, J. C., Costello, E. K., Perez, M. E., Blaser, M. J., Knight, R., and Dominguez-Bello, M. G. (2013). Biphasic assembly of the murine intestinal microbiota during early development. ISME J. 7, 1112-1115. doi:10.1038/ismej.2013.15
145. Parent, A., and Carpenter, M. B. (1996). Carpenter's human neuroanatomy. Baltimore: Williams & Wilkins.
146. Paschos, K., and Allday, M. J. (2010). Epigenetic reprogramming of host genes in viral and microbial pathogenesis. Trends Microbiol. 18, 439-447. doi:10.1016/j.tim.2010.07.003
147. Paul, M. S., and Bass, B. L. (1998). Inosine exists in mRNA at tissue-specific levels and is most abundant in brain mRNA. EMBO J. 17, 1120-1127. doi:10.1093/emboj/17.4.1120
148. Peleg, S., Sananbenesi, F., Zovoilis, A., Burkhardt, S., Bahari-Javan, S., Agis-Balboa, R. C., Cota, P., Wittnam, J. L., Gogol-Doering, A., Opitz, L., et al. (2010). Altered Histone Acetylation Is Associated with Age-Dependent Memory Impairment in Mice. Science 328, 753-756. doi:10.1126/science.1186088
149. Pennini, M. E., Perrinet, S., Dautry-Varsat, A., and Subtil, A. (2010). Histone Methylation by NUE, a Novel Nuclear Effector of the Intracellular Pathogen Chlamydia trachomatis. PLoS Pathog 6, e1000995. doi:10.1371/journal.ppat.1000995
150. Pigliucci, M. (2008). Is evolvability evolvable? Nat. Rev. Genet. 9, 75-82. doi:10.1038/nrg2278
151. Ptashne, M. (2013a). Epigenetics: Core misconcept. Proc. Natl. Acad. Sci. U. S. A. 110, 7101-7103. doi:10.1073/pnas.1305399110
152. Ptashne, M. (2013b). Faddish stuff: epigenetics and the inheritance of acquired characteristics. FASEB J. Off. Publ. Fed. Am. Soc. Exp. Biol. 27, 1-2. doi:10.1096/fj.13-0101ufm
153. Ptashne, M. (2007). On the use of the word "epigenetic." Curr. Biol. CB 17, R233-236. doi:10.1016/j.cub.2007.02.030
154. Qin, J., Li, R., Raes, J., Arumugam, M., Burgdorf, K. S., Manichanh, C., Nielsen, T., Pons, N., Levenez, F., Yamada, T., et al. (2010). A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464, 59-65. doi:10.1038/nature08821
155. Qureshi, I. A., and Mehler, M. F. (2012). Emerging roles of non-coding RNAs in brain evolution, development, plasticity and disease. Nat. Rev. Neurosci. 13, 528-541. doi:10.1038/nrn3234
156. Rausch, P., Rehman, A., Künzel, S., Häsler, R., Ott, S. J., Schreiber, S., Rosenstiel, P., Franke, A., and Baines, J. F. (2011). Colonic mucosa-associated microbiota is influenced by an interaction of Crohn disease and FUT2 (Secretor) genotype. Proc. Natl. Acad. Sci. U. S. A. 108, 19030-19035. doi:10.1073/pnas.1106408108
157. Ravel, J., Gajer, P., Abdo, Z., Schneider, G. M., Koenig, S . S. K., McCulle, S. L., Karlebach, S., Gorle, R., Russell, J., Tacket, C. O., et al. (2011). Vaginal microbiome of reproductive-age women. Proc. Natl. Acad. Sci. U. S. A. 108 Suppl 1, 4680-4687. doi:10.1073/pnas.1002611107
158. Rennoll-Bankert, K. E., and Dumler, J. S. (2012). Lessons from Anaplasma phagocytophilum: chromatin remodeling by bacterial effectors. Infect. Disord. Drug Targets 12, 380-387
159. Rinn, J. L., Kertesz, M., Wang, J. K., Squazzo, S. L., Xu, X., Brugmann, S. A., Goodnough, L. H., Helms, J. A., Farnham, P. J., Segal, E., et al. (2007). Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs. Cell 129, 1311-1323. doi:10.1016/j.cell.2007.05.022
160. Rolando, M., Sanulli, S., Rusniok, C., Gomez-Valero, L., Bertholet, C., Sahr, T., Margueron, R., and Buchrieser, C. (2013). Legionella pneumophila Effector RomA Uniquely Modifies Host Chromatin to Repress Gene Expression and Promote Intracellular Bacterial Replication. Cell Host Microbe 13, 395-405. doi:10.1016/j.chom.2013.03.004
161. Rosenberg, E., Koren, O., Reshef, L., Efrony, R., and Zilber-Rosenberg, I. (2007). The role of microorganisms in coral health, disease and evolution. Nat. Rev. Microbiol. 5, 355-362. doi:10.1038/nrmicro1635
162. Rosenberg, E., and Zilber-Rosenberg, I. (2014). The Hologenome Concept: Human, Animal and Plant Microbiota. Springer International Publishing
163. Saab, B. J., and Mansuy, I. M. (2014). Neuroepigenetics of memory formation and impairment: The role of microRNAs. Neuropharmacology 80C, 61-69. doi:10.1016/j.neuropharm.2014.01.026
164. Sanchez-Elsner, T., Gou, D., Kremmer, E., and Sauer, F. (2006). Noncoding RNAs of Trithorax Response Elements Recruit Drosophila Ash1 to Ultrabithorax. Science 311, 1118-1123. doi:10.1126/science.1117705
165. Schaukowitch, K., and Kim, T.-K. (2014). Emerging epigenetic mechanisms of long non-coding RNAs. Neuroscience 264, 25-38. doi:10.1016/j.neuroscience.2013.12.009
166. Schellekens, H., Clarke, G., Jeffery, I. B., Dinan, T. G., and Cryan, J. F. (2012). Dynamic 5-HT2C receptor editing in a mouse model of obesity. PloS One 7, e32266. doi:10.1371/journal.pone.0032266
167. Schloissnig, S., Arumugam, M., Sunagawa, S., Mitreva, M., Tap, J., Zhu, A., Waller, A., Mende, D. R., Kultima, J. R., Martin, J., et al. (2013). Genomic variation landscape of the human gut microbiome. Nature 493, 45-50. doi:10.1038/nature11711
168. Schor, I. E., Fiszbein, A., Petrillo, E., and Kornblihtt, A. R. (2013). Intragenic epigenetic changes modulate NCAM alternative splicing in neuronal differentiation. EMBO J. doi:10.1038/emboj.2013.167
169. Schor, I. E., Rascovan, N., Pelisch, F., Alló, M., and Kornblihtt, A. R. (2009). Neuronal cell depolarization induces intragenic chromatin modifications affecting NCAM alternative splicing. Proc. Natl. Acad. Sci. 106, 4325-4330. doi:10.1073/pnas.0810666106
170. Selkrig, J., Wong, P., Zhang, X., and Pettersson, S. (2014). Metabolic tinkering by the gut microbiome: Implications for brain development and function. Gut Microbes 5, 0-1
171. Selye, H. (1978). The Stress of Life. 2 edition. New York: McGraw-Hill
172. Shenderov, B. A. (2012). Gut indigenous microbiota and epigenetics. Microb. Ecol. Health Dis. 23. doi:10.3402/mehd.v23i0.17195
173. Shenderov, B. A., and Midtvedt, T. (2014). Epigenomic programing: a future way to health? Microb. Ecol. Health Dis. 25. doi:10.3402/mehd.v25.24145
174. Silmon de Monerri, N. C., and Kim, K. (2014). Pathogens hijack the epigenome: a new twist on host1213 pathogen interactions. Am. J. Pathol. 184, 897-911. doi:10.1016/j.ajpath.2013.12.022
175. Da Silva, W. C., Bonini, J. S., Bevilaqua, L. R. M., Medina, J. H., Izquierdo, I., and Cammarota, M. (2008). Inhibition of mRNA synthesis in the hippocampus impairs consolidation and reconsolidation of spatial memory. Hippocampus 18, 29-39. doi:10.1002/hipo.20362
176. Skuse, D. H., Lori, A., Cubells, J. F., Lee, I., Conneely, K. N., Puura, K., Lehtimäki, T., Binder, E. B., and Young, L. J. (2014). Common polymorphism in the oxytocin receptor gene (OXTR) is associated with human social recognition skills. Proc. Natl. Acad. Sci. U. S. A. 111, 1987-1992. doi:10.1073/pnas.1302985111
177. Smith, P. M., Howitt, M. R., Panikov, N., Michaud, M., Gallini, C. A., Bohlooly-Y, M., Glickman, J. N., and Garrett, W. S. (2013). The Microbial Metabolites, Short-Chain Fatty Acids, Regulate Colonic Treg Cell Homeostasis. Science 341, 569-573. doi:10.1126/science.1241165
178. Smythies, J., Edelstein, L., and Ramachandran, V. (2014). Molecular mechanisms for the inheritance of acquired characteristics-exosomes, microRNA shuttling, fear and stress: Lamarck resurrected? Epigenomics Epigenetics 5, 133. doi:10.3389/fgene.2014.00133
179. Speakman, J. R. (2013). Functional analysis of seven genes linked to body mass index and adiposity by genome-wide association studies: a review. Hum. Hered. 75, 57-79. doi:10.1159/000353585
180. 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. doi:10.1038/nrmicro2540
181. Stazi, M. A., and Toccaceli, V. (2014). [Genome and microbiome: hologenome. Is epigenetics their link?]. Epidemiol. Prev. 38, 67-68
182. Steffen, P. A., and Ringrose, L. (2014). What are memories made of? How Polycomb and Trithorax proteins mediate epigenetic memory. Nat. Rev. Mol. Cell Biol. 15, 340-356. doi:10.1038/nrm3789
183. Stevens, A., and Price, J. (2000). Evolutionary Psychiatry, s econd edition: A New Beginning. 2 edition. London ; Philadelphia: Routledge
184. Stilling, R. M., Dinan, T. G., and Cryan, J. F. (2014). Microbial genes, brain & behaviour - epigenetic regulation of the gut-brain axis. Genes Brain Behav. 13, 69-86. doi:10.1111/gbb.12109
185. Stilling, R. M., and Fischer, A. (2011). The role of histone acetylation in age-associated memory impairment and Alzheimer's disease. Neurobiol. Learn. Mem. 96, 19-26. doi:10.1016/j.nlm.2011.04.002
186. 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. doi:10.1113/jphysiol.2004.063388
187. Sweatt, J. D. (2013). The Emerging Field of Neuroepigenetics. Neuron 80, 624-632. doi:10.1016/j.neuron.2013.10.023
188. Szyf, M. (2014). Lamarck revisited: epigenetic inheritance of ancestral odor fear conditioning. Nat. Neurosci. 17, 2-4. doi:10.1038/nn.3603
189. Thomas, C. M., Hong, T., van Pijkeren, J. P., Hemarajata, P., Trinh, D. V., Hu, W., Britton, R. A., Kalkum, M., and Versalovic, J. (2012a). Histamine derived from probiotic Lactobacillus reuteri suppresses TNF via modulation of PKA and ERK signaling. PloS One 7, e31951. doi:10.1371/journal.pone.0031951
190. Thomas, F., Poulin, R., and Brodeur, J. (2010). Host manipulation by parasites: a multidimensional phenomenon. Oikos 119, 1217-1223. doi:10.1111/j.1600-0706.2009.18077.x
191. Thomas, R. H., Meeking, M. M., Mepham, J. R., Tichenoff, L., Possmayer, F., Liu, S., and MacFabe, D. F. (2012b). The enteric bacterial metabolite propionic acid alters brain and plasma phospholipid molecular species: further development of a rodent model of autism spectrum disorders. J. Neuroinflammation 9, 153. doi:10.1186/1742-2094-9-153
192. Tong, M., McHardy, I., Ruegger, P., Goudarzi, M., Kashyap, P. C., Haritunians, T., Li, X., Graeber, T. G., Schwager, E., Huttenhower, C., et al. (2014). Reprograming of gut microbiome energy metabolism by the FUT2 Crohn's disease risk polymorphism. ISME J. doi:10.1038/ismej.2014.64
193. Troyer, K. (1984). Microbes, herbivory and the evolution of social behavior. J. Theor. Biol. 106, 157-169
194. Turnbaugh, P. J., Ley, R. E., Hamady, M., Fraser-Liggett, C. M., Knight, R., and Gordon, J. I. (2007). The Human Microbiome Project. Nature 449, 804-810. doi:10.1038/nature06244
195. 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, 1027-1031. doi:10.1038/nature05414
196. Virgin, H. W. (2014). The Virome in Mammalian Physiology and Disease. Cell 157, 142-150. doi:10.1016/j.cell.2014.02.032
197. Wacklin, P., Tuimala, J., Nikkilä, J., Sebastian Tims, Mäkivuokko, H., Alakulppi, N., Laine, P., Rajilic-Stojanovic, M., Paulin, L., de Vos, W. M., et al. (2014). Faecal microbiota composition in adults is associated with the FUT2 gene determining the secretor status. PloS One 9, e94863. doi:10.1371/journal.pone.0094863
198. Waddington, C. H. (1953). Epigenetics and Evolution. Symp. Soc. Exp. Biol. 7, 186-199.
199. Wall, R., Cryan, J. F., Ross, R. P., Fitzger, G. F., Dinan, T. G., and Stanton, C. (2014). "Bacterial Neuroactive Compounds Produced by Psychobiotics," in Microbial Endocrinology: The Microbiota- Gut-Brain Axis in Health and Disease (Heidelberg: Springer)
200. Warren, D. L., and Iglesias, T. L. (2012). No evidence for the "expensive-tissue hypothesis" from intraspecific study in a highly variable species. J. Evol. Biol. 25, 1226-1231. doi:10.1111/j.1420- 9101.2012.02503.x
201. Weaver, I. C. G., Cervoni, N., Champagne, F. A., D'Alessio, A. C., Sharma, S., Seckl, J. R., Dymov, S., Szyf, M., and Meaney, M. J. (2004). Epigenetic programming by maternal behavior. Nat. Neurosci. 7, 847-854. doi:10.1038/nn1276
202. Williams, A. C., and Dunbar, R. I. M. (2014). Big brains, meat, tuberculosis and the nicotinamide switches: Co-evolutionary relationships with modern repercussions on longevity and disease? Med. Hypotheses. doi:10.1016/j.mehy.2014.04.003
203. Woldemichael, B. T., Bohacek, J., Gapp, K., and Mansuy, I. M. (2014). Epigenetics of memory and plasticity. Prog. Mol. Biol. Transl. Sci. 122, 305-340. doi:10.1016/B978-0-12-420170-5.00011-8
204. Xing, Y., and Lee, C. (2006). Alternative splicing and RNA selection pressure--evolutionary consequences for eukaryotic genomes. Nat. Rev. Genet. 7, 499-509. doi:10.1038/nrg1896
205. Youngster, I., Sauk, J., Pindar, C., Wilson, R. G., Kaplan, J. L., Smith, M. B., Alm, E. J., Gevers, D., Russell, G. H., and Hohmann, E. L. (2014). Fecal Microbiota Transplant for Relapsing Clostridium difficile Infection Using a Frozen Inoculum From Unrelated Donors: A Randomized, Open-Label, Controlled Pilot Study. Clin. Infect. Dis., ciu135. doi:10.1093/cid/ciu135
206. Zaneveld, J., Turnbaugh, P. J., Lozupone, C., Ley, R. E., Hamady, M., Gordon, J. I., and Knight, R. (2008). Host-bacterial coevolution and the search for new drug targets. Curr. Opin. Chem. Biol. 12, 109-114. doi:10.1016/j.cbpa.2008.01.015
207. Zheng, G., Dahl, J. A., Niu, Y., Fu, Y., Klungland, A., Yang, Y.-G., and He, C. (2013). Sprouts of RNA epigenetics: the discovery of mammalian RNA demethylases. RNA Biol. 10, 915-918. doi:10.4161/rna.24711
208. Ziats, M. N., and Rennert, O. M. (2013). Aberrant expression of long noncoding RNAs in autistic brain. J. Mol. Neurosci. MN 49, 589-593. doi:10.1007/s12031-012-9880-8
209. Zoetendal, E. G., Akkermans, A. D., Akkermans-van Vliet, W. M., de Visser, J. A. G., and de Vos, W. M. (2001). The host genotype affects the bacterial community in the human gastronintestinal tract. Microb. Ecol. Health Dis. 13, 129-134.