Effects of psychological, environmental and physical stressors on the gut microbiota

Frontiers in Microbiology

Volumn 9, Issue SEP, 2018, Pages

  Karl, Philip J ^a   Hatch, Adrienne M ^a   Arcidiacono, Steven M ^b   Pearce, Sarah C ^b   Pantoja Feliciano, Ida G ^b   Doherty, Laurel A ^b   Soares, Jason W ^b  

^a U S ARMY RESEARCH INSTITUTE OF ENVIRONMENTAL MEDICINE   (United States)

^b DEVELOPMENT AND ENGINEERING CENTER   (United States)

Author keywords

Environment; Microbiome; Military; Nutrition; Physiology; Psychology; Stress

Indexed keywords

TOXIN;

ALTITUDE; CIRCADIAN RHYTHM; COLD EXPOSURE; COMMUNITY STRUCTURE; DIET; ENTEROPATHOGEN; ENVIRONMENTAL STRESS; HEAT STRESS; HUMAN; INTESTINE FLORA; MENTAL STRESS; METABOLISM; NOISE; NONHUMAN; PHYSICAL ACTIVITY; PHYSICAL STRESS; POLLUTANT; REVIEW; SLEEP DISORDER;

EID: 85053155573     PISSN: None     EISSN: 1664302X     Source Type: Journal    
DOI: 10.3389/fmicb.2018.02013     Document Type: Review

References (368)

1. Abeles, S. R., Jones, M. B., Santiago-Rodriguez, T. M., Ly, M., Klitgord, N., Yooseph, S., et al. (2016). Microbial diversity in individuals and their household contacts following typical antibiotic courses. Microbiome 4:39. doi: 10.1186/s40168-016-0187-9
2. Abell, G. C., Cooke, C. M., Bennett, C. N., Conlon, M. A., and McOrist, A. L. (2008). Phylotypes related to Ruminococcus bromii are abundant in the large bowel of humans and increase in response to a diet high in resistant starch. FEMS Microbiol. Ecol. 66, 505-515. doi: 10.1111/j.1574-6941.2008.00527.x
3. Adak, A., Maity, C., Ghosh, K., and Mondal, K. C. (2014). Alteration of predominant gastrointestinal flora and oxidative damage of large intestine under simulated hypobaric hypoxia. Z. Gastroenterol. 52, 180-186. doi: 10.1055/s-0033-1336007
4. Adak, A., Maity, C., Ghosh, K., Pati, B. R., and Mondal, K. C. (2013). Dynamics of predominant microbiota in the human gastrointestinal tract and change in luminal enzymes and immunoglobulin profile during high-altitude adaptation. Folia Microbiol. (Praha) 58, 523-528. doi: 10.1007/s12223-013-0241-y
5. Albenberg, L., Esipova, T. V., Judge, C. P., Bittinger, K., Chen, J., Laughlin, A., et al. (2014). Correlation between intraluminal oxygen gradient and radial partitioning of intestinal microbiota. Gastroenterology 147, 1055.e8-1063.e8. doi: 10.1053/j.gastro.2014.07.020
6. Alexander, D. A., and Klein, S. (2009). First responders after disasters: a review of stress reactions, at-risk, vulnerability, and resilience factors. Prehosp. Disaster Med. 24, 87-94. doi: 10.1017/S1049023X00006610
7. Allen, J. M., Berg Miller, M. E., Pence, B. D., Whitlock, K., Nehra, V., Gaskins, H. R., et al. (2015). Voluntary and forced exercise differentially alters the gut microbiome in C57BL/6J mice. J. Appl. Physiol. 118, 1059-1066. doi: 10.1152/japplphysiol.01077.2014
8. Allen, J. M., Mailing, L. J., Cohrs, J., Salmonson, C., Fryer, J. D., Nehra, V., et al. (2018). Exercise training-induced modification of the gut microbiota persists after microbiota colonization and attenuates the response to chemically-induced colitis in gnotobiotic mice. Gut Microbes 9, 115-130. doi: 10.1080/19490976.2017.1372077
9. Allen, J. M., Mailing, L. J., Niemiro, G. M., Moore, R., Cook, M. D., White, B. A., et al. (2018). Exercise alters gut microbiota composition and function in lean and obese humans. Med. Sci. Sports Exerc. 50, 747-757. doi: 10.1249/MSS.0000000000001495
10. Anand, A. C., Sashindran, V. K., and Mohan, L. (2006). Gastrointestinal problems at high altitude. Trop. Gastroenterol. 27, 147-153
11. Aoki-Yoshida, A., Aoki, R., Moriya, N., Goto, T., Kubota, Y., Toyoda, A., et al. (2016). Omics studies of the murine intestinal ecosystem exposed to subchronic and mild social defeat stress. J. Proteome Res. 15, 3126-3138. doi: 10.1021/acs.jproteome.6b00262
12. Arcidiacono, S., Soares, J. W., Karl, J. P., Chrisey, L., Dancy, B. C. R., Goodson, M., et al. (2018). The current state and future direction of DoD gut microbiome research: a summary of the first DoD gut microbiome informational meeting. Std Genomic Sci. 13:5. doi: 10.1186/s40793-018-0308-0
13. Asher, G., and Sassone-Corsi, P. (2015). Time for food: the intimate interplay between nutrition, metabolism, and the circadian clock. Cell 161, 84-92. doi: 10.1016/j.cell.2015.03.015
14. 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. doi: 10.1002/(SICI)1098-2302(199909)35:2<146::AID-DEV7>3.0.CO;2-G
15. 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
16. Bailey, M. T., Dowd, S. E., Parry, N. M., Galley, J. D., Schauer, D. B., and Lyte, M. (2010). Stressor exposure disrupts commensal microbial populations in the intestines and leads to increased colonization by Citrobacter rodentium. Infect. Immun. 78, 1509-1519. doi: 10.1128/IAI.00862-09
17. Bailey, M. T., Lubach, G. R., and Coe, C. L. (2004). Prenatal stress alters bacterial colonization of the gut in infant monkeys. J. Pediatr. Gastroenterol. Nutr. 38, 414-421. doi: 10.1097/00005176-200404000-00009
18. Bansal, T., Alaniz, R. C., Wood, T. K., and Jayaraman, A. (2010). The bacterial signal indole increases epithelial-cell tight-junction resistance and attenuates indicators of inflammation. Proc. Natl. Acad. Sci. U.S.A. 107, 228-233. doi: 10.1073/pnas.0906112107
19. Batacan, R. B., Fenning, A. S., Dalbo, V. J., Scanlan, A. T., Duncan, M. J., Moore, R. J., et al. (2017). A gut reaction: the combined influence of exercise and diet on gastrointestinal microbiota in rats. J. Appl. Microbiol. 122, 1627-1638. doi: 10.1111/jam.13442
20. Beaumont, M., Portune, K. J., Steuer, N., Lan, A., Cerrudo, V., Audebert, M., et al. (2017). Quantity and source of dietary protein influence metabolite production by gut microbiota and rectal mucosa gene expression: a randomized, parallel, double-blind trial in overweight humans. Am. J. Clin. Nutr. 106, 1005-1019. doi: 10.3945/ajcn.117.158816
21. Benedict, C., Vogel, H., Jonas, W., Woting, A., Blaut, M., Schurmann, A., et al. (2016). Gut microbiota and glucometabolic alterations in response to recurrent partial sleep deprivation in normal-weight young individuals. Mol. Metab. 5, 1175-1186. doi: 10.1016/j.molmet.2016.10.003
22. Bharwani, A., Mian, M. F., Foster, J. A., Surette, M. G., Bienenstock, J., and Forsythe, P. (2016). Structural & functional consequences of chronic psychosocial stress on the microbiome & host. Psychoneuroendocrinology 63, 217-227. doi: 10.1016/j.psyneuen.2015.10.001
23. Biesalski, H. K. (2016). Nutrition meets the microbiome: micronutrients and the microbiota. Ann. N. Y. Acad. Sci. 1372, 53-64. doi: 10.1111/nyas.13145
24. Bijlsma, P. B., van Raaij, M. T., Dobbe, C. J., Timmerman, A., Kiliaan, A. J., Taminiau, J. A., et al. (2001). Subchronic mild noise stress increases HRP permeability in rat small intestine in vitro. Physiol. Behav. 73, 43-49. doi: 10.1016/S0031-9384(01)00424-3
25. Bird, A. R., Conlon, M. A., Christophersen, C. T., and Topping, D. L. (2010). Resistant starch, large bowel fermentation and a broader perspective of prebiotics and probiotics. Benef. Microbes 1, 423-431. doi: 10.3920/BM2010.0041
26. Blanton, L. V., Charbonneau, M. R., Salih, T., Barratt, M. J., Venkatesh, S., Ilkaveya, O., et al. (2016). Gut bacteria that prevent growth impairments transmitted by microbiota from malnourished children. Science 351:aad3311. doi: 10.1126/science.aad3311
27. Blaser, M. J., and Falkow, S. (2009). What are the consequences of the disappearing human microbiota? Nat. Rev. Microbiol. 7, 887-894. doi: 10.1038/nrmicro2245
28. Breland, J. Y., Phibbs, C. S., Hoggatt, K. J., Washington, D. L., Lee, J., Haskell, S., et al. (2017). The obesity epidemic in the veterans health administration: prevalence among key populations of women and men veterans. J. Gen. Intern. Med. 32(Suppl. 1), 11-17. doi: 10.1007/s11606-016-3962-1
29. Breton, J., Massart, S., Vandamme, P., De Brandt, E., Pot, B., and Foligne, B. (2013). Ecotoxicology inside the gut: impact of heavy metals on the mouse microbiome. BMC Pharmacol. Toxicol. 14:62. doi: 10.1186/2050-6511-14-62
30. Bridgewater, L. C., Zhang, C., Wu, Y., Hu, W., Zhang, Q., Wang, J., et al. (2017). Gender-based differences in host behavior and gut microbiota composition in response to high fat diet and stress in a mouse model. Sci. Rep. 7:10776. doi: 10.1038/s41598-017-11069-4
31. Brinkworth, G. D., Noakes, M., Clifton, P. M., and Bird, A. R. (2009). Comparative effects of very low-carbohydrate, high-fat and high-carbohydrate, low-fat weight-loss diets on bowel habit and faecal short-chain fatty acids and bacterial populations. Br. J. Nutr. 101, 1493-1502. doi: 10.1017/S0007114508094658
32. Caesar, R., Tremaroli, V., Kovatcheva-Datchary, P., Cani, P. D., and Backhed, F. (2015). Crosstalk between gut microbiota and dietary lipids aggravates WAT inflammation through TLR signaling. Cell Metab. 22, 658-668. doi: 10.1016/j.cmet.2015.07.026
33. Campbell, S. C., Wisniewski, P. J., Noji, M., McGuinness, L. R., Haggblom, M. M., Lightfoot, S. A., et al. (2016). The effect of diet and exercise on intestinal integrity and microbial diversity in mice. PLoS One 11:e0150502. doi: 10.1371/journal.pone.0150502
34. Canani, R. B., Costanzo, M. D., Leone, L., Pedata, M., Meli, R., and Calignano, A. (2011). Potential beneficial effects of butyrate in intestinal and extraintestinal diseases. World J. Gastroenterol. 17, 1519-1528. doi: 10.3748/wjg.v17.i12.1519
35. Cani, P. D. (2012). Crosstalk between the gut microbiota and the endocannabinoid system: impact on the gut barrier function and the adipose tissue. Clin. Microbiol. Infect 18(Suppl. 4), 50-53. doi: 10.1111/j.1469-0691.2012.03866.x
36. Cani, P. D., Bibiloni, R., Knauf, C., Waget, A., Neyrinck, A. M., Delzenne, N. M., et al. (2008). Changes in gut microbiota control metabolic endotoxemia-induced inflammation in high-fat diet-induced obesity and diabetes in mice. Diabetes Metab. Res. Rev. 57, 1470-1481. doi: 10.2337/db07-1403
37. Cani, P. D., Osto, M., Geurts, L., and Everard, A. (2012). Involvement of gut microbiota in the development of low-grade inflammation and type 2 diabetes associated with obesity. Gut Microbes 3, 279-288. doi: 10.4161/gmic.19625
38. Carey, H. V., Walters, W. A., and Knight, R. (2013). Seasonal restructuring of the ground squirrel gut microbiota over the annual hibernation cycle. Am. J. Physiol. Regul. Integr. Comp. Physiol. 304, R33-R42. doi: 10.1152/ajpregu.00387.2012
39. Castellani, J. W., and Young, A. J. (2016). Human physiological responses to cold exposure: acute responses and acclimatization to prolonged exposure. Auton. Neurosci. 196, 63-74. doi: 10.1016/j.autneu.2016.02.009
40. Cerda, B., Perez, M., Perez-Santiago, J. D., Tornero-Aguilera, J. F., Gonzalez-Soltero, R., and Larrosa, M. (2016). Gut microbiota modification: another piece in the puzzle of the benefits of physical exercise in health? Front. Physiol. 7:51. doi: 10.3389/fphys.2016.00051
41. Chassaing, B., Koren, O., Goodrich, J. K., Poole, A. C., Srinivasan, S., Ley, R. E., et al. (2015). Dietary emulsifiers impact the mouse gut microbiota promoting colitis and metabolic syndrome. Nature 519, 92-96. doi: 10.1038/nature14232
42. Chassaing, B., Van de Wiele, T., De Bodt, J., Marzorati, M., and Gewirtz, A. T. (2017). Dietary emulsifiers directly alter human microbiota composition and gene expression ex vivo potentiating intestinal inflammation. Gut 66, 1414-1427. doi: 10.1136/gutjnl-2016-313099
43. Chevalier, C., Stojanovic, O., Colin, D. J., Suarez-Zamorano, N., Tarallo, V., Veyrat-Durebex, C., et al. (2015). Gut microbiota orchestrates energy homeostasis during cold. Cell 163, 1360-1374. doi: 10.1016/j.cell.2015.11.004
44. Chi, L., Bian, X., Gao, B., Ru, H., Tu, P., and Lu, K. (2016). Sex-specific effects of arsenic exposure on the trajectory and function of the gut microbiome. Chem. Res. Toxicol. 29, 949-951. doi: 10.1021/acs.chemrestox.6b00066
45. Choi, J. J., Eum, S. Y., Rampersaud, E., Daunert, S., Abreu, M. T., and Toborek, M. (2013). Exercise attenuates PCB-induced changes in the mouse gut microbiome. Environ. Health Perspect. 121, 725-730. doi: 10.1289/ehp.1306534
46. Clark, A., and Mach, N. (2016). Exercise-induced stress behavior, gut-microbiota-brain axis and diet: a systematic review for athletes. J. Int. Soc. Sports Nutr. 13:43. doi: 10.1186/s12970-016-0155-6
47. Colgan, S. P., and Taylor, C. T. (2010). Hypoxia: an alarm signal during intestinal inflammation. Nat. Rev. Gastroenterol. Hepatol. 7, 281-287. doi: 10.1038/nrgastro.2010.39
48. Connor, P., Porter, C. K., Swierczewski, B., and Riddle, M. S. (2012). Diarrhoea during military deployment: current concepts and future directions. Curr. Opin. Infect. Dis. 25, 546-554. doi: 10.1097/QCO.0b013e3283582ebc
49. Coskun, T., Yegen, B. C., Alican, I., Peker, O., and Kurtel, H. (1996). Cold restraint stress-induced gastric mucosal dysfunction, role of nitric oxide. Dig. Dis. Sci. 41, 956-963. doi: 10.1007/BF02091537
50. Costabile, A., Klinder, A., Fava, F., Napolitano, A., Fogliano, V., Leonard, C., et al. (2008). Whole-grain wheat breakfast cereal has a prebiotic effect on the human gut microbiota: a double-blind, placebo-controlled, crossover study. Br. J. Nutr. 99, 110-120. doi: 10.1017/S0007114507793923
51. Costello, E. K., Gordon, J. I., Secor, S. M., and Knight, R. (2010). Postprandial remodeling of the gut microbiota in Burmese pythons. ISME J. 4, 1375-1385. doi: 10.1038/ismej.2010.71
52. 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. doi: 10.1126/science.1177486
53. Crane, J. K., Byrd, I. W., and Boedeker, E. C. (2011). Virulence inhibition by zinc in shiga-toxigenic Escherichia coli. Infect. Immun. 79, 1696-1705. doi: 10.1128/IAI.01099-10
54. Crawford, P. A., Crowley, J. R., Sambandam, N., Muegge, B. D., Costello, E. K., Hamady, M., et al. (2009). Regulation of myocardial ketone body metabolism by the gut microbiota during nutrient deprivation. Proc. Natl. Acad. Sci. U.S.A. 106, 11276-11281. doi: 10.1073/pnas.0902366106
55. 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
56. Cui, B., Su, D., Li, W., She, X., Zhang, M., Wang, R., et al. (2018). Effects of chronic noise exposure on the microbiome-gut-brain axis in senescence-accelerated prone mice: implications for Alzheimer's disease. J. Neuroinflamm. 15:190. doi: 10.1186/s12974-018-1223-4
57. Curtis, A. M., Bellet, M. M., Sassone-Corsi, P., and O'Neill, L. A. (2014). Circadian clock proteins and immunity. Immunity 40, 178-186. doi: 10.1016/j.immuni.2014.02.002
58. David, L. A., Maurice, C. F., Carmody, R. N., Gootenberg, D. B., Button, J. E., Wolfe, B. E., et al. (2014). Diet rapidly and reproducibly alters the human gut microbiome. Nature 505, 559-563. doi: 10.1038/nature12820
59. David, L. A., Weil, A., Ryan, E. T., Calderwood, S. B., Harris, J. B., Chowdhury, F., et al. (2015). Gut microbial succession follows acute secretory diarrhea in humans. mBio 6:e381-15. doi: 10.1128/mBio.00381-15
60. de La Serre, C. B., Ellis, C. L., Lee, J., Hartman, A. L., Rutledge, J. C., and Raybould, H. E. (2010). Propensity to high-fat diet-induced obesity in rats is associated with changes in the gut microbiota and gut inflammation. Am. J. Physiol. Gastrointest. Liver Physiol. 299, G440-G448. doi: 10.1152/ajpgi.00098.2010
61. Defois, C., Ratel, J., Denis, S., Batut, B., Beugnot, R., Peyretaillade, E., et al. (2017). Environmental pollutant benzo[a]pyrene impacts the volatile metabolome and transcriptome of the human gut microbiota. Front. Microbiol. 8:1562. doi: 10.3389/fmicb.2017.01562
62. Degnan, P. H., Taga, M. E., and Goodman, A. L. (2014). Vitamin B12 as a modulator of gut microbial ecology. Cell Metab. 20, 769-778. doi: 10.1016/j.cmet.2014.10.002
63. Deitch, E. A., Winterton, J., and Berg, R. (1987). Effect of starvation, malnutrition, and trauma on the gastrointestinal tract flora and bacterial translocation. Arch. Surg. 122, 1019-1024. doi: 10.1001/archsurg.1987.01400210057008
64. Demehri, F. R., Barrett, M., and Teitelbaum, D. H. (2015). Changes to the intestinal microbiome with parenteral nutrition: review of a murine model and potential clinical implications. Nutr. Clin. Pract. 30, 798-806. doi: 10.1177/0884533615609904
65. Denou, E., Marcinko, K., Surette, M. G., Steinberg, G. R., and Schertzer, J. D. (2016). High-intensity exercise training increases the diversity and metabolic capacity of the mouse distal gut microbiota during diet-induced obesity. Am. J. Physiol. Endocrinol. Metab. 310, E982-E993. doi: 10.1152/ajpendo.00537.2015
66. Deplancke, B., Vidal, O., Ganessunker, D., Donovan, S. M., Mackie, R. I., and Gaskins, H. R. (2002). Selective growth of mucolytic bacteria including Clostridium perfringens in a neonatal piglet model of total parenteral nutrition. Am. J. Clin. Nutr. 76, 1117-1125. doi: 10.1093/ajcn/76.5.1117
67. Desai, M. S., Seekatz, A. M., Koropatkin, N. M., Kamada, N., Hickey, C. A., Wolter, M., et al. (2016). A dietary fiber-deprived gut microbiota degrades the colonic mucus barrier and enhances pathogen susceptibility. Cell 167, 1339.e21-1353.e21. doi: 10.1016/j.cell.2016.10.043
68. 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. U.S.A. 108(Suppl. 1), 4554-4561. doi: 10.1073/pnas.1000087107
69. Devkota, S., and Chang, E. B. (2013). Diet-induced expansion of pathobionts in experimental colitis: implications for tailored therapies. Gut Microbes 4, 172-174. doi: 10.4161/gmic.23589
70. Devkota, S., and Chang, E. B. (2015). Interactions between Diet, bile acid metabolism, gut microbiota, and inflammatory bowel diseases. Dig. Dis. 33, 351-356. doi: 10.1159/000371687
71. Devkota, S., Wang, Y., Musch, M. W., Leone, V., Fehlner-Peach, H., Nadimpalli, A., et al. (2012). Dietary-fat-induced taurocholic acid promotes pathobiont expansion and colitis in Il10-/-mice. Nature 487, 104-108. doi: 10.1038/nature11225
72. Dewar, M. L., Arnould, J. P., Krause, L., Trathan, P., Dann, P., and Smith, S. C. (2014). Influence of fasting during moult on the faecal microbiota of penguins. PLoS One 9:e99996. doi: 10.1371/journal.pone.0099996
73. Diaz Tartera, H. O., Webb, D. L., Al-Saffar, A. K., Halim, M. A., Lindberg, G., Sangfelt, P., et al. (2017). Validation of SmartPill((R)) wireless motility capsule for gastrointestinal transit time: Intra-subject variability, software accuracy and comparison with video capsule endoscopy. Neurogastroenterol. Motil. 29, 1-9. doi: 10.1111/nmo.13107
74. Dienstbier, R. A. (1989). Arousal and physiological toughness: implications for mental and physical health. Psychol. Rev. 96, 84-100. doi: 10.1037/0033-295X.96.1.84
75. Dietert, R. R., and Silbergeld, E. K. (2015). Biomarkers for the 21st century: listening to the microbiome. Toxicol. Sci. 144, 208-216. doi: 10.1093/toxsci/kfv013
76. Ding, T., and Schloss, P. D. (2014). Dynamics and associations of microbial community types across the human body. Nature 509, 357-360. doi: 10.1038/nature13178
77. Dokladny, K., Zuhl, M. N., and Moseley, P. L. (2016). Intestinal epithelial barrier function and tight junction proteins with heat and exercise. J. Appl. Physiol. 120, 692-701. doi: 10.1152/japplphysiol.00536.2015
78. Dosek, A., Ohno, H., Acs, Z., Taylor, A. W., and Radak, Z. (2007). High altitude and oxidative stress. Respir. Physiol. Neurobiol. 158, 128-131. doi: 10.1016/j.resp.2007.03.013
79. Dostal, A., Chassard, C., Hilty, F. M., Zimmermann, M. B., Jaeggi, T., Rossi, S., et al. (2012). Iron depletion and repletion with ferrous sulfate or electrolytic iron modifies the composition and metabolic activity of the gut microbiota in rats. J. Nutr. 142, 271-277. doi: 10.3945/jn.111.148643
80. Dostal, A., Fehlbaum, S., Chassard, C., Zimmermann, M. B., and Lacroix, C. (2013). Low iron availability in continuous in vitro colonic fermentations induces strong dysbiosis of the child gut microbial consortium and a decrease in main metabolites. FEMS Microbiol. Ecol. 83, 161-175. doi: 10.1111/j.1574-6941.2012.01461.x
81. Dostal, A., Lacroix, C., Bircher, L., Pham, V. T., Follador, R., Zimmermann, M. B., et al. (2015). Iron modulates butyrate production by a child gut microbiota in vitro. mBio 6:e1453-15. doi: 10.1128/mBio.01453-15
82. Dostal, A., Lacroix, C., Pham, V. T., Zimmermann, M. B., Del'homme, C., Bernalier-Donadille, A., et al. (2014). Iron supplementation promotes gut microbiota metabolic activity but not colitis markers in human gut microbiota-associated rats. Br. J. Nutr. 111, 2135-2145. doi: 10.1017/S000711451400021X
83. Douben, P. E. T. (2003). PAHs: An Ecotoxicological Perspective. Hoboken, NJ: John Wiley & Sons, Inc. doi: 10.1002/0470867132
84. Duenas, M., Munoz-Gonzalez, I., Cueva, C., Jimenez-Giron, A., Sanchez-Patan, F., Santos-Buelga, C., et al. (2015). A survey of modulation of gut microbiota by dietary polyphenols. Biomed. Res. Int. 2015:850902. doi: 10.1155/2015/850902
85. Duncan, S. H., Belenguer, A., Holtrop, G., Johnstone, A. M., Flint, H. J., and Lobley, G. E. (2007). Reduced dietary intake of carbohydrates by obese subjects results in decreased concentrations of butyrate and butyrate-producing bacteria in feces. Appl. Environ. Microbiol. 73, 1073-1078. doi: 10.1128/AEM.02340-06
86. Duncan, S. H., Lobley, G. E., Holtrop, G., Ince, J., Johnstone, A. M., Louis, P., et al. (2008). Human colonic microbiota associated with diet, obesity and weight loss. Int. J. Obes. (Lond.) 32, 1720-1724. doi: 10.1038/ijo.2008.155
87. DuPont, H. L. (2016). Review article: the antimicrobial effects of rifaximin on the gut microbiota. Aliment. Pharmacol. Ther. 43(Suppl. 1), 3-10. doi: 10.1111/apt.13434
88. Engelbrecht, J. P., McDonald, E. V., Gillies, J. A., Jayanty, R. K., Casuccio, G., and Gertler, A. W. (2009). Characterizing mineral dusts and other aerosols from the Middle East-Part 1: ambient sampling. Inhal. Toxicol. 21, 297-326. doi: 10.1080/08958370802464273
89. Espin, J. C., Gonzalez-Sarrias, A., and Tomas-Barberan, F. A. (2017). The gut microbiota: a key factor in the therapeutic effects of (poly)phenols. Biochem. Pharmacol. 139, 82-93. doi: 10.1016/j.bcp.2017.04.033
90. Evans, C. C., LePard, K. J., Kwak, J. W., Stancukas, M. C., Laskowski, S., Dougherty, J., et al. (2014). Exercise prevents weight gain and alters the gut microbiota in a mouse model of high fat diet-induced obesity. PLoS One 9:e92193. doi: 10.1371/journal.pone.0092193
91. Everson, C. A., Henchen, C. J., Szabo, A., and Hogg, N. (2014). Cell injury and repair resulting from sleep loss and sleep recovery in laboratory rats. Sleep 37, 1929-1940. doi: 10.5665/sleep.4244
92. Everson, C. A., and Toth, L. A. (2000). Systemic bacterial invasion induced by sleep deprivation. Am. J. Physiol. Regul. Integr. Comp. Physiol. 278, R905-R916. doi: 10.1152/ajpregu.2000.278.4.R905
93. Faith, J. J., Guruge, J. L., Charbonneau, M., Subramanian, S., Seedorf, H., Goodman, A. L., et al. (2013). The long-term stability of the human gut microbiota. Science 341:1237439. doi: 10.1126/science.1237439
94. Faith, J. J., McNulty, N. P., Rey, F. E., and Gordon, J. I. (2011). Predicting a human gut microbiota's response to diet in gnotobiotic mice. Science 333, 101-104. doi: 10.1126/science.1206025
95. Falony, G., Joossens, M., Vieira-Silva, S., Wang, J., Darzi, Y., Faust, K., et al. (2016). Population-level analysis of gut microbiome variation. Science 352, 560-564. doi: 10.1126/science.aad3503
96. Falvo, M. J., Osinubi, O. Y., Sotolongo, A. M., and Helmer, D. A. (2015). Airborne hazards exposure and respiratory health of Iraq and Afghanistan veterans. Epidemiol. Rev. 37, 116-130. doi: 10.1093/epirev/mxu009
97. Fava, F., Gitau, R., Griffin, B. A., Gibson, G. R., Tuohy, K. M., and Lovegrove, J. A. (2013). The type and quantity of dietary fat and carbohydrate alter faecal microbiome and short-chain fatty acid excretion in a metabolic syndrome 'at-risk' population. Int. J. Obes (Lond.) 37, 216-223. doi: 10.1038/ijo.2012.33
98. Ferrer, M., Mendez-Garcia, C., Rojo, D., Barbas, C., and Moya, A. (2017). Antibiotic use and microbiome function. Biochem. Pharmacol. 134, 114-126. doi: 10.1016/j.bcp.2016.09.007
99. Flint, H. J. (2012). The impact of nutrition on the human microbiome. Nutr. Rev. 70(Suppl. 1), S10-S13. doi: 10.1111/j.1753-4887.2012.00499.x
100. Forsythe, P., Kunze, W., and Bienenstock, J. (2016). Moody microbes or fecal phrenology: what do we know about the microbiota-gut-brain axis? BMC Med 14:58. doi: 10.1186/s12916-016-0604-8
101. Foster, J. A., and McVey Neufeld, K. A. (2013). Gut-brain axis: how the microbiome influences anxiety and depression. Trends Neurosci. 36, 305-312. doi: 10.1016/j.tins.2013.01.005
102. Gaffney-Stomberg, E., and McClung, J. P. (2012). Inflammation and diminished iron status: mechanisms and functional outcomes. Curr. Opin. Clin. Nutr. Metab. Care 15, 605-613. doi: 10.1097/MCO.0b013e328357f63b
103. Galley, J. D., and Bailey, M. T. (2014). Impact of stressor exposure on the interplay between commensal microbiota and host inflammation. Gut Microbes 5, 390-396. doi: 10.4161/gmic.28683
104. Galley, J. D., Mackos, A. R., Varaljay, V. A., and Bailey, M. T. (2017). Stressor exposure has prolonged effects on colonic microbial community structure in Citrobacter rodentium-challenged mice. Sci. Rep. 7:45012. doi: 10.1038/srep45012
105. Galley, J. D., Parry, N. M., Ahmer, B. M. M., Fox, J. G., and Bailey, M. T. (2017). The commensal microbiota exacerbate infectious colitis in stressor-exposed mice. Brain Behav. Immun. 60, 44-50. doi: 10.1016/j.bbi.2016.09.010
106. Galley, J. D., Nelson, M. C., Yu, Z., Dowd, S. E., Walter, J., Kumar, P. S., et al. (2014). Exposure to a social stressor disrupts the community structure of the colonic mucosa-associated microbiota. BMC Microbiol. 14:189. doi: 10.1186/1471-2180-14-189
107. Galley, J. D., Yu, Z., Kumar, P., Dowd, S. E., Lyte, M., and Bailey, M. T. (2014). The structures of the colonic mucosa-associated and luminal microbial communities are distinct and differentially affected by a prolonged murine stressor. Gut Microbes 5, 748-760. doi: 10.4161/19490976.2014.972241
108. Gao, X., Cao, Q., Cheng, Y., Zhao, D., Wang, Z., Yang, H., et al. (2018). Chronic stress promotes colitis by disturbing the gut microbiota and triggering immune system response. Proc. Natl. Acad. Sci. U.S.A. 115, E2960-E2969. doi: 10.1073/pnas.1720696115
109. Gareau, M. G., Silva, M. A., and Perdue, M. H. (2008). Pathophysiological mechanisms of stress-induced intestinal damage. Curr. Mol. Med. 8, 274-281. doi: 10.2174/156652408784533760
110. Gautam, A., D'Arpa, P., Donohue, D. E., Muhie, S., Chakraborty, N., Luke, B. T., et al. (2015). Acute and chronic plasma metabolomic and liver transcriptomic stress effects in a mouse model with features of post-traumatic stress disorder. PLoS One 10:e0117092. doi: 10.1371/journal.pone.0117092
111. Gautam, A., Kumar, R., Chakraborty, N., Muhie, S., Hoke, A., Hammamieh, R., et al. (2018). Altered fecal microbiota composition in all male aggressor-exposed rodent model simulating features of post-traumatic stress disorder. J. Neurosci. Res. 96, 1311-1323. doi: 10.1002/jnr.24229
112. Genton, L., Cani, P. D., and Schrenzel, J. (2015). Alterations of gut barrier and gut microbiota in food restriction, food deprivation and protein-energy wasting. Clin. Nutr. 34, 341-349. doi: 10.1016/j.clnu.2014.10.003
113. Ghosh, S., DeCoffe, D., Brown, K., Rajendiran, E., Estaki, M., Dai, C., et al. (2013). Fish oil attenuates omega-6 polyunsaturated fatty acid-induced dysbiosis and infectious colitis but impairs LPS dephosphorylation activity causing sepsis. PLoS One 8:e55468. doi: 10.1371/journal.pone.0055468
114. Gibson, G. R., Hutkins, R., Sanders, M. E., Prescott, S. L., Reimer, R. A., Salminen, S. J., et al. (2017). Expert consensus document: the international scientific association for probiotics and prebiotics (ISAPP) consensus statement on the definition and scope of prebiotics. Nat. Rev. Gastroenterol. Hepatol. 14, 491-502. doi: 10.1038/nrgastro.2017.75
115. Gibson, G. R., Macfarlane, G. T., and Cummings, J. H. (1993). Sulphate reducing bacteria and hydrogen metabolism in the human large intestine. Gut 34, 437-439. doi: 10.1136/gut.34.4.437
116. Gilbert, J. A., Quinn, R. A., Debelius, J., Xu, Z. Z., Morton, J., Garg, N., et al. (2016). Microbiome-wide association studies link dynamic microbial consortia to disease. Nature 535, 94-103. doi: 10.1038/nature18850
117. 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. doi: 10.1086/668166
118. Glaser, R., and Kiecolt-Glaser, J. K. (2005). Stress-induced immune dysfunction: implications for health. Nat. Rev. Immunol. 5, 243-251. doi: 10.1038/nri1571
119. Glaven, S., Racicot, K., Leary, D.H., Karl, J.P., Arcidiacono, S., Dancy, B.C.R., et al. (2018). The current and future state of department of defense (DoD) microbiome research: a summary of the inaugural DoD tri-service microbiome consortium informational meeting. mSystems 3:e00086-18. doi: 10.1128/mSystems.00086-18
120. Golubeva, A. V., Crampton, S., Desbonnet, L., Edge, D., O'Sullivan, O., Lomasney, K. W., et al. (2015). Prenatal stress-induced alterations in major physiological systems correlate with gut microbiota composition in adulthood. Psychoneuroendocrinology 60, 58-74. doi: 10.1016/j.psyneuen.2015.06.002
121. Gorvitovskaia, A., Holmes, S. P., and Huse, S. M. (2016). Interpreting prevotella and Bacteroides as biomarkers of diet and lifestyle. Microbiome 4:15. doi: 10.1186/s40168-016-0160-7
122. Gue, M., Peeters, T., Depoortere, I., Vantrappen, G., and Bueno, L. (1989). Stress-induced changes in gastric emptying, postprandial motility, and plasma gut hormone levels in dogs. Gastroenterology 97, 1101-1107. doi: 10.1016/0016-5085(89)91678-8
123. Ha, C. W., Lam, Y. Y., and Holmes, A. J. (2014). Mechanistic links between gut microbial community dynamics, microbial functions and metabolic health. World J. Gastroenterol. 20, 16498-16517. doi: 10.3748/wjg.v20.i44.16498
124. 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. doi: 10.1126/science.1235872
125. Halmos, E. P., Christophersen, C. T., Bird, A. R., Shepherd, S. J., Gibson, P. R., and Muir, J. G. (2015). Diets that differ in their FODMAP content alter the colonic luminal microenvironment. Gut 64, 93-100. doi: 10.1136/gutjnl-2014-307264
126. Halvorson, H. A., Schlett, C. D., and Riddle, M. S. (2006). Postinfectious irritable bowel syndrome-a meta-analysis. Am. J. Gastroenterol. 101, 1894-1899; quiz 1942. doi: 10.1111/j.1572-0241.2006.00654.x
127. Hamer, H. M., Jonkers, D., Venema, K., Vanhoutvin, S., Troost, F. J., and Brummer, R. J. (2008). Review article: the role of butyrate on colonic function. Aliment. Pharmacol. Ther. 27, 104-119. doi: 10.1111/j.1365-2036.2007.03562.x
128. Hammamieh, R., Chakraborty, N., De Lima, T. C., Meyerhoff, J., Gautam, A., Muhie, S., et al. (2012). Murine model of repeated exposures to conspecific trained aggressors simulates features of post-traumatic stress disorder. Behav. Brain Res. 235, 55-66. doi: 10.1016/j.bbr.2012.07.022
129. Harvey, R. B., Andrews, K., Droleskey, R. E., Kansagra, K. V., Stoll, B., Burrin, D. G., et al. (2006). Qualitative and quantitative comparison of gut bacterial colonization in enterally and parenterally fed neonatal pigs. Curr. Issues Intest. Microbiol. 7, 61-64
130. Hennigar, S. R., and McClung, J. P. (2016). Hepcidin attenuates zinc efflux in caco-2 cells. J. Nutr. 146, 2167-2173. doi: 10.3945/jn.116.237081
131. Henning, P. C., Park, B. S., and Kim, J. S. (2011). Physiological decrements during sustained military operational stress. Mil. Med. 176, 991-997. doi: 10.7205/MILMED-D-11-00053
132. Hibberd, M.C., Wu, M., Rodionov, D.A., Li, X., Cheng, J., Griffin, N.W., et al. (2017). The effects of micronutrient deficiencies on bacterial species from the human gut microbiota. Sci. Transl. Med. 9:eaal4069. doi: 10.1126/scitranslmed.aal4069
133. Hildebrandt, M. A., Hoffmann, C., Sherrill-Mix, S. A., Keilbaugh, S. A., Hamady, M., Chen, Y. Y., et al. (2009). High-fat diet determines the composition of the murine gut microbiome independently of obesity. Gastroenterology 137, 1716.e1-2-1724.e1-2. doi: 10.1053/j.gastro.2009.08.042
134. Hill, C., Guarner, F., Reid, G., Gibson, G. R., Merenstein, D. J., Pot, B., 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. doi: 10.1038/nrgastro.2014.66
135. Hodin, C. M., Visschers, R. G., Rensen, S. S., Boonen, B., Olde Damink, S. W., Lenaerts, K., et al. (2012). Total parenteral nutrition induces a shift in the Firmicutes to Bacteroidetes ratio in association with Paneth cell activation in rats. J. Nutr. 142, 2141-2147. doi: 10.3945/jn.112.162388
136. Hoerster, K. D., Lehavot, K., Simpson, T., McFall, M., Reiber, G., and Nelson, K. M. (2012). Health and health behavior differences: U.S. Military, veteran, and civilian men. Am. J. Prev. Med. 43, 483-489. doi: 10.1016/j.amepre.2012.07.029
137. Hoge, C. W., Castro, C. A., Messer, S. C., McGurk, D., Cotting, D. I., and Koffman, R. L. (2004). Combat duty in Iraq and Afghanistan, mental health problems, and barriers to care. N. Engl. J. Med. 351, 13-22. doi: 10.1056/NEJMoa040603
138. Holmes, A. J., Chew, Y. V., Colakoglu, F., Cliff, J. B., Klaassens, E., Read, M. N., et al. (2017). Diet-microbiome interactions in health are controlled by intestinal nitrogen source constraints. Cell Metab. 25, 140-151. doi: 10.1016/j.cmet.2016.10.021
139. Holmes, E., Li, J. V., Marchesi, J. R., and Nicholson, J. K. (2012). Gut microbiota composition and activity in relation to host metabolic phenotype and disease risk. Cell Metab. 16, 559-564. doi: 10.1016/j.cmet.2012.10.007
140. Hoogerwerf, W. A. (2009). Role of biological rhythms in gastrointestinal health and disease. Rev. Endocr. Metab. Disord. 10, 293-300. doi: 10.1007/s11154-009-9119-3
141. Hooper, L. V., Littman, D. R., and Macpherson, A. J. (2012). Interactions between the microbiota and the immune system. Science 336, 1268-1273. doi: 10.1126/science.1223490
142. Huang, E. Y., Leone, V. A., Devkota, S., Wang, Y., Brady, M. J., and Chang, E. B. (2013). Composition of dietary fat source shapes gut microbiota architecture and alters host inflammatory mediators in mouse adipose tissue. JPEN J. Parenter. Enteral. Nutr. 37, 746-754. doi: 10.1177/0148607113486931
143. Huderson, A. C., Myers, J. N., Niaz, M. S., Washington, M. K., and Ramesh, A. (2013). Chemoprevention of benzo(a)pyrene-induced colon polyps in ApcMin mice by resveratrol. J. Nutr. Biochem. 24, 713-724. doi: 10.1016/j.jnutbio.2012.04.005
144. Hurley, J. C. (1995). Endotoxemia: methods of detection and clinical correlates. Clin. Microbiol. Rev. 8, 268-292
145. Huttenhower, C., Gevers, D., and Knight, R. (2012). Structure, function and diversity of the healthy human microbiome. Nature 486, 207-214. doi: 10.1038/nature11234
146. Huttenhower, C., Kostic, A. D., and Xavier, R. J. (2014). Inflammatory bowel disease as a model for translating the microbiome. Immunity 40, 843-854. doi: 10.1016/j.immuni.2014.05.013
147. Institute of Medicine (1999). Military Strategies for Sustainment of Nutrition and Immune Function in the Field. Washington, DC: National Academies Press
148. Ising, H., and Kruppa, B. (2004). Health effects caused by noise: evidence in the literature from the past 25 years. Noise Health 6, 5-13
149. Jacobs, J. M., Cameron, K. L., and Bojescul, J. A. (2014). Lower extremity stress fractures in the military. Clin. Sports Med. 33, 591-613. doi: 10.1016/j.csm.2014.06.002
150. Jaeggi, T., Kortman, G. A., Moretti, D., Chassard, C., Holding, P., Dostal, A., et al. (2015). Iron fortification adversely affects the gut microbiome, increases pathogen abundance and induces intestinal inflammation in Kenyan infants. Gut 64, 731-742. doi: 10.1136/gutjnl-2014-307720
151. Jakobsson, H. E., Jernberg, C., Andersson, A. F., Sjolund-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. doi: 10.1371/journal.pone.0009836
152. James, S. M., Honn, K. A., Gaddameedhi, S., and Van Dongen, H. P. A. (2017). Shift work: disrupted circadian rhythms and sleep-implications for health and well-being. Curr. Sleep Med. Rep. 3, 104-112. doi: 10.1007/s40675-017-0071-6
153. Jansson, J., Willing, B., Lucio, M., Fekete, A., Dicksved, J., Halfvarson, J., et al. (2009). Metabolomics reveals metabolic biomarkers of Crohn's disease. PLoS One 4:e6386. doi: 10.1371/journal.pone.0006386
154. Jernberg, C., Lofmark, S., Edlund, C., and Jansson, J. K. (2007). Long-term ecological impacts of antibiotic administration on the human intestinal microbiota. ISME J. 1, 56-66. doi: 10.1038/ismej.2007.3
155. Joly, C., Gay-Queheillard, J., Leke, A., Chardon, K., Delanaud, S., Bach, V., et al. (2013). Impact of chronic exposure to low doses of chlorpyrifos on the intestinal microbiota in the Simulator of the Human Intestinal Microbial Ecosystem (SHIME) and in the rat. Environ. Sci. Pollut. Res. Int. 20, 2726-2734. doi: 10.1007/s11356-012-1283-4
156. Jovel, J., Patterson, J., Wang, W., Hotte, N., O'Keefe, S., Mitchel, T., et al. (2016). Characterization of the gut microbiome using 16S or shotgun metagenomics. Front. Microbiol. 7:459. doi: 10.3389/fmicb.2016.00459
157. Jumpertz, R., Le, D. S., Turnbaugh, P. J., Trinidad, C., Bogardus, C., Gordon, J. I., et al. (2011). Energy-balance studies reveal associations between gut microbes, caloric load, and nutrient absorption in humans. Am. J. Clin. Nutr. 94, 58-65. doi: 10.3945/ajcn.110.010132
158. Kaczmarek, J. L., Musaad, S. M., and Holscher, H. D. (2017). Time of day and eating behaviors are associated with the composition and function of the human gastrointestinal microbiota. Am. J. Clin. Nutr. 106, 1220-1231. doi: 10.3945/ajcn.117.156380
159. Kaiko, G. E., Ryu, S. H., Koues, O. I., Collins, P. L., Solnica-Krezel, L., Pearce, E. J., et al. (2016). The colonic crypt protects stem cells from microbiota-derived metabolites. Cell 165, 1708-1720. doi: 10.1016/j.cell.2016.05.018
160. Kalantar-Zadeh, K., Berean, K. J., Na, H., Chrimes, A. F., Xu, K., Grando, D., et al. (2018). A human pilot trial of ingestible electronic capsules capable of sensing different gases in the gut. Nat. Electron. 1, 79-87. doi: 10.1038/s41928-017-0004-x
161. Kaliannan, K., Wang, B., Li, X. Y., Kim, K. J., and Kang, J. X. (2015). A host-microbiome interaction mediates the opposing effects of omega-6 and omega-3 fatty acids on metabolic endotoxemia. Sci. Rep. 5:11276. doi: 10.1038/srep11276
162. Kampmann, C., Dicksved, J., Engstrand, L., and Rautelin, H. (2016). Composition of human faecal microbiota in resistance to Campylobacter infection. Clin. Microbiol. Infect 22, 61.e1-61.e8 doi: 10.1016/j.cmi.2015.09.004
163. Kang, S. S., Jeraldo, P. R., Kurti, A., Miller, M. E., Cook, M. D., Whitlock, K., et al. (2014). Diet and exercise orthogonally alter the gut microbiome and reveal independent associations with anxiety and cognition. Mol. Neurodegener. 9:36. doi: 10.1186/1750-1326-9-36
164. Karl, J. P., Lieberman, H. R., Cable, S. J., Williams, K. W., Young, A. J., and McClung, J. P. (2010). Randomized, double-blind, placebo-controlled trial of an iron-fortified food product in female soldiers during military training: relations between iron status, serum hepcidin, and inflammation. Am. J. Clin. Nutr. 92, 93-100. doi: 10.3945/ajcn.2010.29185
165. Karl, J. P., Margolis, L. M., Madslien, E. H., Murphy, N. E., Castellani, J. W., Gundersen, Y., et al. (2017). Changes in intestinal microbiota composition and metabolism coincide with increased intestinal permeability in young adults under prolonged physiological stress. Am. J. Physiol. Gastrointest. Liver Physiol. 312, G559-G571. doi: 10.1152/ajpgi.00066.2017
166. Karl, J. P., Margolis, L. M., Murphy, N. E., Carrigan, C. T., Castellani, J. W., Madslien, E. H., et al. (2017). Military training elicits marked increases in plasma metabolomic signatures of energy metabolism, lipolysis, fatty acid oxidation, and ketogenesis. Physiol. Rep. 5:e13407. doi: 10.14814/phy2.13407
167. Kato-Kataoka, A., Nishida, K., Takada, M., Kawai, M., Kikuchi-Hayakawa, H., Suda, K., et al. (2016). Fermented milk containing lactobacillus casei strain shirota preserves the diversity of the gut microbiota and relieves abdominal dysfunction in healthy medical students exposed to academic stress. Appl. Environ. Microbiol. 82, 3649-3658. doi: 10.1128/AEM.04134-15
168. Kelly, J. R., Kennedy, P. J., Cryan, J. F., Dinan, T. G., Clarke, G., and Hyland, N. P. (2015). Breaking down the barriers: the gut microbiome, intestinal permeability and stress-related psychiatric disorders. Front. Cell Neurosci. 9:392. doi: 10.3389/fncel.2015.00392
169. Kight, C. R., and Swaddle, J. P. (2011). How and why environmental noise impacts animals: an integrative, mechanistic review. Ecol. Lett. 14, 1052-1061. doi: 10.1111/j.1461-0248.2011.01664.x
170. Kish, L., Hotte, N., Kaplan, G. G., Vincent, R., Tso, R., Ganzle, M., et al. (2013). Environmental particulate matter induces murine intestinal inflammatory responses and alters the gut microbiome. PLoS One 8:e62220. doi: 10.1371/journal.pone.0062220
171. Kleessen, B., Schroedl, W., Stueck, M., Richter, A., Rieck, O., and Krueger, M. (2005). Microbial and immunological responses relative to high-altitude exposure in mountaineers. Med. Sci. Sports Exerc. 37, 1313-1318. doi: 10.1249/01.mss.0000174888.22930.e0
172. Knowles, S. R., Nelson, E. A., and Palombo, E. A. (2008). Investigating the role of perceived stress on bacterial flora activity and salivary cortisol secretion: a possible mechanism underlying susceptibility to illness. Biol. Psychol. 77, 132-137. doi: 10.1016/j.biopsycho.2007.09.010
173. Knutson, K. L., Spiegel, K., Penev, P., and Van Cauter, E. (2007). The metabolic consequences of sleep deprivation. Sleep Med. Rev. 11, 163-178. doi: 10.1016/j.smrv.2007.01.002
174. Koeth, R. A., Wang, Z., Levison, B. S., Buffa, J. A., Org, E., Sheehy, B. T., et al. (2013). Intestinal microbiota metabolism of L-carnitine, a nutrient in red meat, promotes atherosclerosis. Nat. Med. 19, 576-585. doi: 10.1038/nm.3145
175. Kohl, K. D., Amaya, J., Passement, C. A., Dearing, M. D., and McCue, M. D. (2014). Unique and shared responses of the gut microbiota to prolonged fasting: a comparative study across five classes of vertebrate hosts. FEMS Microbiol. Ecol. 90, 883-894. doi: 10.1111/1574-6941.12442
176. Konturek, P. C., Brzozowski, T., and Konturek, S. J. (2011). Stress and the gut: pathophysiology, clinical consequences, diagnostic approach and treatment options. J. Physiol. Pharmacol. 62, 591-599
177. 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. doi: 10.1038/nrmicro2746
178. Korpela, K., Salonen, A., Virta, L. J., Kekkonen, R. A., Forslund, K., Bork, P., et al. (2016). Intestinal microbiome is related to lifetime antibiotic use in Finnish pre-school children. Nat. Commun. 7:10410. doi: 10.1038/ncomms10410
179. Kortman, G. A., Raffatellu, M., Swinkels, D. W., and Tjalsma, H. (2014). Nutritional iron turned inside out: intestinal stress from a gut microbial perspective. FEMS Microbiol. Rev. 38, 1202-1234. doi: 10.1111/1574-6976.12086
180. Kostic, A. D., Gevers, D., Pedamallu, C. S., Michaud, M., Duke, F., Earl, A. M., et al. (2012). Genomic analysis identifies association of Fusobacterium with colorectal carcinoma. Genome Res. 22, 292-298. doi: 10.1101/gr.126573.111
181. Kovatcheva-Datchary, P., Nilsson, A., Akrami, R., Lee, Y. S., De Vadder, F., Arora, T., et al. (2015). Dietary fiber-induced improvement in glucose metabolism is associated with increased abundance of prevotella. Cell Metab. 22, 971-982. doi: 10.1016/j.cmet.2015.10.001
182. Ladirat, S. E., Schoterman, M. H., Rahaoui, H., Mars, M., Schuren, F. H., Gruppen, H., et al. (2014). Exploring the effects of galacto-oligosaccharides on the gut microbiota of healthy adults receiving amoxicillin treatment. Br. J. Nutr. 112, 536-546. doi: 10.1017/S0007114514001135
183. Lafuse, W. P., Gearinger, R., Fisher, S., Nealer, C., Mackos, A. R., and Bailey, M. T. (2017). Exposure to a social stressor induces translocation of commensal Lactobacilli to the spleen and priming of the innate immune system. J. Immunol. 198, 2383-2393. doi: 10.4049/jimmunol.1601269
184. Lam, Y. Y., Ha, C. W., Hoffmann, J. M., Oscarsson, J., Dinudom, A., Mather, T. J., et al. (2015). Effects of dietary fat profile on gut permeability and microbiota and their relationships with metabolic changes in mice. Obesity (Silver Spring) 23, 1429-1439. doi: 10.1002/oby.21122
185. Lambert, G. P. (2008). Intestinal barrier dysfunction, endotoxemia, and gastrointestinal symptoms: the 'canary in the coal mine' during exercise-heat stress? Med. Sport Sci. 53, 61-73. doi: 10.1159/000151550
186. Lambert, J. E., Myslicki, J. P., Bomhof, M. R., Belke, D. D., Shearer, J., and Reimer, R. A. (2015). Exercise training modifies gut microbiota in normal and diabetic mice. Appl. Physiol. Nutr. Metab. 40, 749-752. doi: 10.1139/apnm-2014-0452
187. Lamoureux, E. V., Grandy, S. A., and Langille, M. G. I. (2017). Moderate exercise has limited but distinguishable effects on the mouse microbiome. mSystems 2:e00006-17. doi: 10.1128/mSystems.00006-17
188. Lamprecht, M., and Frauwallner, A. (2012). Exercise, intestinal barrier dysfunction and probiotic supplementation. Med. Sport Sci. 59, 47-56. doi: 10.1159/000342169
189. Leclercq, S., Forsythe, P., and Bienenstock, J. (2016). Posttraumatic stress disorder: does the gut microbiome hold the key? Can. J. Psychiatry 61, 204-213. doi: 10.1177/0706743716635535
190. Lehavot, K., Hoerster, K. D., Nelson, K. M., Jakupcak, M., and Simpson, T. L. (2012). Health indicators for military, veteran, and civilian women. Am. J. Prev. Med. 42, 473-480. doi: 10.1016/j.amepre.2012.01.006
191. Leone, V., Gibbons, S. M., Martinez, K., Hutchison, A. L., Huang, E. Y., Cham, C. M., et al. (2015). Effects of diurnal variation of gut microbes and high-fat feeding on host circadian clock function and metabolism. Cell Host Microbe 17, 681-689. doi: 10.1016/j.chom.2015.03.006
192. Leslie, J. L., and Young, V. B. (2015). The rest of the story: the microbiome and gastrointestinal infections. Curr. Opin. Microbiol. 23, 121-125. doi: 10.1016/j.mib.2014.11.010
193. Ley, R. E., Turnbaugh, P. J., Klein, S., and Gordon, J. I. (2006). Microbial ecology: human gut microbes associated with obesity. Nature 444, 1022-1023. doi: 10.1038/4441022a
194. Li, X., Kan, E. M., Lu, J., Cao, Y., Wong, R. K., Keshavarzian, A., et al. (2013). Combat-training increases intestinal permeability, immune activation and gastrointestinal symptoms in soldiers. Aliment. Pharmacol. Ther. 37, 799-809. doi: 10.1111/apt.12269
195. Li, X., Wilder-Smith, C. H., Kan, M. E., Lu, J., Cao, Y., and Wong, R. K. (2014). Combat-training stress in soldiers increases S100B, a marker of increased blood-brain-barrier permeability, and induces immune activation. Neuro Endocrinol. Lett. 35, 58-63
196. Liang, X., Bushman, F. D., and FitzGerald, G. A. (2015). Rhythmicity of the intestinal microbiota is regulated by gender and the host circadian clock. Proc. Natl. Acad. Sci. U.S.A. 112, 10479-10484. doi: 10.1073/pnas.1501305112
197. Lieberman, H. R., Bathalon, G. P., Falco, C. M., Morgan, C. A. III, Niro, P. J., and Tharion, W. J. (2005). The fog of war: decrements in cognitive performance and mood associated with combat-like stress. Aviat. Space Environ. Med. 76(7 Suppl.), C7-C14
198. Lin, R., Liu, W., Piao, M., and Zhu, H. (2017). A review of the relationship between the gut microbiota and amino acid metabolism. Amino Acids 49, 2083-2090. doi: 10.1007/s00726-017-2493-3
199. Liu, G. S., Huang, Y. X., Li, S. W., Pan, B. R., Wang, X., Sun, D. Y., et al. (1998). Experimental study on mechanism and protection of stress ulcer produced by explosive noise. World J. Gastroenterol. 4, 519-523. doi: 10.3748/wjg.v4.i6.519
200. Lloyd-Price, J., Abu-Ali, G., and Huttenhower, C. (2016). The healthy human microbiome. Genome Med. 8:51. doi: 10.1186/s13073-016-0307-y
201. Lorenzo-Zuniga, V., Bartoli, R., Planas, R., Hofmann, A. F., Vinado, B., Hagey, L. R., et al. (2003). Oral bile acids reduce bacterial overgrowth, bacterial translocation, and endotoxemia in cirrhotic rats. Hepatology 37, 551-557. doi: 10.1053/jhep.2003.50116
202. Louis, P., Flint, H. J., and Michel, C. (2016). How to manipulate the microbiota: prebiotics. Adv. Exp. Med. Biol. 902, 119-142. doi: 10.1007/978-3-319-31248-4_9
203. Lozupone, C. A., Stombaugh, J. I., Gordon, J. I., Jansson, J. K., and Knight, R. (2012). Diversity, stability and resilience of the human gut microbiota. Nature 489, 220-230. doi: 10.1038/nature11550
204. Lu, K., Abo, R. P., Schlieper, K. A., Graffam, M. E., Levine, S., Wishnok, J. S., et al. (2014). Arsenic exposure perturbs the gut microbiome and its metabolic profile in mice: an integrated metagenomics and metabolomics analysis. Environ. Health Perspect. 122, 284-291. doi: 10.1289/ehp.1307429
205. Luna, R. A., and Foster, J. A. (2015). Gut brain axis: diet microbiota interactions and implications for modulation of anxiety and depression. Curr. Opin. Biotechnol. 32, 35-41. doi: 10.1016/j.copbio.2014.10.007
206. Luo, B., Xiang, D., Nieman, D. C., and Chen, P. (2014). The effects of moderate exercise on chronic stress-induced intestinal barrier dysfunction and antimicrobial defense. Brain Behav. Immun. 39, 99-106. doi: 10.1016/j.bbi.2013.11.013
207. Lyte, M. (2014). Microbial endocrinology: host-microbiota neuroendocrine interactions influencing brain and behavior. Gut Microbes 5, 381-389. doi: 10.4161/gmic.28682
208. Lyte, M., and Ernst, S. (1992). Catecholamine induced growth of gram negative bacteria. Life Sci. 50, 203-212. doi: 10.1016/0024-3205(92)90273-R
209. Macfarlane, G. T., and Macfarlane, S. (2012). Bacteria, colonic fermentation, and gastrointestinal health. J. AOAC Int. 95, 50-60. doi: 10.5740/jaoacint.SGE_Macfarlane
210. Mach, N., and Clark, A. (2017). Micronutrient deficiencies and the human gut microbiota. Trends Microbiol. 25, 607-610. doi: 10.1016/j.tim.2017.06.004
211. Mach, N., and Fuster-Botella, D. (2017). Micronutrient deficiencies and the human gut microbiota. J. Sport Health Sci. 6, 179-197. doi: 10.1016/j.jshs.2016.05.001
212. Mackos, A. R., Maltz, R., and Bailey, M. T. (2017). The role of the commensal microbiota in adaptive and maladaptive stressor-induced immunomodulation. Horm. Behav. 88, 70-78. doi: 10.1016/j.yhbeh.2016.10.006
213. Margolis, L. M., Murphy, N. E., Martini, S., Gundersen, Y., Castellani, J. W., Karl, J. P., et al. (2016). Effects of supplemental energy on protein balance during 4-d arctic military training. Med. Sci. Sports Exerc. 48, 1604-1612. doi: 10.1249/MSS.0000000000000944
214. Marin, I. A., Goertz, J. E., Ren, T., Rich, S. S., Onengut-Gumuscu, S., Farber, E., et al. (2017). Microbiota alteration is associated with the development of stress-induced despair behavior. Sci. Rep. 7:43859. doi: 10.1038/srep43859
215. 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. doi: 10.1016/j.jmb.2014.06.022
216. Martinez, I., Kim, J., Duffy, P. R., Schlegel, V. L., and Walter, J. (2010). Resistant starches types 2 and 4 have differential effects on the composition of the fecal microbiota in human subjects. PLoS One 5:e15046. doi: 10.1371/journal.pone.0015046
217. Martinez, I., Lattimer, J. M., Hubach, K. L., Case, J. A., Yang, J., Weber, C. G., et al. (2013). Gut microbiome composition is linked to whole grain-induced immunological improvements. ISME J. 7, 269-280. doi: 10.1038/ismej.2012.104
218. Masiol, M., Mallon, C. T., Haines, K. M. Jr., Utell, M. J., and Hopke, P. K. (2016). Airborne Dioxins, furans, and polycyclic aromatic hydrocarbons exposure to military personnel in Iraq. J. Occup. Environ. Med. 58(8 Suppl. 1), S22-S30. doi: 10.1097/JOM.0000000000000771
219. Matsumoto, M., Inoue, R., Tsukahara, T., Ushida, K., Chiji, H., Matsubara, N., et al. (2008). Voluntary running exercise alters microbiota composition and increases n-butyrate concentration in the rat cecum. Biosci. Biotechnol. Biochem. 72, 572-576. doi: 10.1271/bbb.70474
220. Maurice, C. F., Haiser, H. J., and Turnbaugh, P. J. (2013). Xenobiotics shape the physiology and gene expression of the active human gut microbiome. Cell 152, 39-50. doi: 10.1016/j.cell.2012.10.052
221. Mawdsley, J. E., and Rampton, D. S. (2005). Psychological stress in IBD: new insights into pathogenic and therapeutic implications. Gut 54, 1481-1491. doi: 10.1136/gut.2005.064261
222. Mayneris-Perxachs, J., Bolick, D. T., Leng, J., Medlock, G. L., Kolling, G. L., Papin, J. A., et al. (2016). Protein-and zinc-deficient diets modulate the murine microbiome and metabolic phenotype. Am. J. Clin. Nutr. 104, 1253-1262. doi: 10.3945/ajcn.116.131797
223. McClung, J. P., and Gaffney-Stomberg, E. (2016). Optimizing performance, health, and well-being: nutritional factors. Mil. Med. 181(1 Suppl.), 86-91. doi: 10.7205/MILMED-D-15-00202
224. McClung, J. P., Karl, J. P., Cable, S. J., Williams, K. W., Nindl, B. C., Young, A. J., et al. (2009). Randomized, double-blind, placebo-controlled trial of iron supplementation in female soldiers during military training: effects on iron status, physical performance, and mood. Am. J. Clin. Nutr. 90, 124-131. doi: 10.3945/ajcn.2009.27774
225. McClung, J. P., Karl, J. P., Cable, S. J., Williams, K. W., Young, A. J., and Lieberman, H. R. (2009). Longitudinal decrements in iron status during military training in female soldiers. Br. J. Nutr. 102, 605-609. doi: 10.1017/S0007114509220873
226. McClung, J. P., Martini, S., Murphy, N. E., Montain, S. J., Margolis, L. M., Thrane, I., et al. (2013). Effects of a 7-day military training exercise on inflammatory biomarkers, serum hepcidin, and iron status. Nutr. J. 12:141. doi: 10.1186/1475-2891-12-141
227. Mellies, J. L., Thomas, K., Turvey, M., Evans, N. R., Crane, J., Boedeker, E., et al. (2012). Zinc-induced envelope stress diminishes type III secretion in enteropathogenic Escherichia coli. BMC Microbiol. 12:123. doi: 10.1186/1471-2180-12-123
228. Mika, A., Van Treuren, W., Gonzalez, A., Herrera, J. J., Knight, R., and Fleshner, M. (2015). Exercise is more effective at altering gut microbial composition and producing stable changes in lean mass in juvenile versus adult male F344 Rats. PLoS One 10:e0125889. doi: 10.1371/journal.pone.0125889
229. Millet, G. P., Faiss, R., and Pialoux, V. (2012). Point: hypobaric hypoxia induces different physiological responses from normobaric hypoxia. J. Appl. Physiol. 112, 1783-1784. doi: 10.1152/japplphysiol.00067.2012
230. Mineur, Y. S., Belzung, C., and Crusio, W. E. (2006). Effects of unpredictable chronic mild stress on anxiety and depression-like behavior in mice. Behav. Brain Res. 175, 43-50. doi: 10.1016/j.bbr.2006.07.029
231. Miranda, S., and Roux, M. E. (2017). Acoustic stress induces long term severe intestinal inflammation in the mouse. Toxicol. Lett. 280, 1-9. doi: 10.1016/j.toxlet.2017.07.898
232. Miyasaka, E. A., Feng, Y., Poroyko, V., Falkowski, N. R., Erb-Downward, J., Gillilland, M. G., et al. (2013). Total parenteral nutrition-associated lamina propria inflammation in mice is mediated by a MyD88-dependent mechanism. J. Immunol. 190, 6607-6615. doi: 10.4049/jimmunol.1201746
233. Modi, S. R., Collins, J. J., and Relman, D. A. (2014). Antibiotics and the gut microbiota. J. Clin. Invest. 124, 4212-4218. doi: 10.1172/JCI72333
234. Monda, V., Villano, I., Messina, A., Valenzano, A., Esposito, T., Moscatelli, F., et al. (2017). Exercise modifies the gut microbiota with positive health effects. Oxid. Med. Cell. Longev. 2017:3831972. doi: 10.1155/2017/3831972
235. Mu, Z. B., Huang, Y. X., Zhao, B. M., Liu, Z. X., Zhang, B. H., and Wang, Q. L. (2006). Effect of explosive noise on gastrointestinal transit and plasma levels of polypeptide hormones. World J. Gastroenterol. 12, 2284-2287
236. Murakami, M., Tognini, P., Liu, Y., Eckel-Mahan, K. L., Baldi, P., and Sassone-Corsi, P. (2016). Gut microbiota directs PPARgamma-driven reprogramming of the liver circadian clock by nutritional challenge. EMBO Rep. 17, 1292-1303. doi: 10.15252/embr.201642463
237. Mutlu, E. A., Engen, P. A., Soberanes, S., Urich, D., Forsyth, C. B., Nigdelioglu, R., et al. (2011). Particulate matter air pollution causes oxidant-mediated increase in gut permeability in mice. Part Fibre. Toxicol. 8:19. doi: 10.1186/1743-8977-8-19
238. Navaneethan, U., and Giannella, R. A. (2008). Mechanisms of infectious diarrhea. Nat. Clin. Pract. Gastroenterol. Hepatol. 5, 637-647. doi: 10.1038/ncpgasthep1264
239. Nguyen, T. L., Vieira-Silva, S., Liston, A., and Raes, J. (2015). How informative is the mouse for human gut microbiota research? Dis. Model Mech. 8, 1-16. doi: 10.1242/dmm.017400
240. Nicholson, J. K., Holmes, E., Kinross, J., Burcelin, R., Gibson, G., Jia, W., et al. (2012). Host-gut microbiota metabolic interactions. Science 336, 1262-1267. doi: 10.1126/science.1223813
241. Nindl, B. C., Barnes, B. R., Alemany, J. A., Frykman, P. N., Shippee, R. L., and Friedl, K. E. (2007). Physiological consequences of U.S. Army ranger training. Med. Sci. Sports Exerc. 39, 1380-1387. doi: 10.1249/MSS.0b013e318067e2f7
242. Oettle, G. J. (1991). Effect of moderate exercise on bowel habit. Gut 32, 941-944. doi: 10.1136/gut.32.8.941
243. O'Keefe, S. J. (2016). Diet, microorganisms and their metabolites, and colon cancer. Nat. Rev. Gastroenterol. Hepatol. 13, 691-706. doi: 10.1038/nrgastro.2016.165
244. O'Keefe, S. J., Li, J. V., Lahti, L., Ou, J., Carbonero, F., Mohammed, K., et al. (2015). Fat, fibre and cancer risk in African Americans and rural Africans. Nat. Commun. 6:6342. doi: 10.1038/ncomms7342
245. Ou, J., Carbonero, F., Zoetendal, E. G., DeLany, J. P., Wang, M., Newton, K., et al. (2013). Diet, microbiota, and microbial metabolites in colon cancer risk in rural Africans and African Americans. Am. J. Clin. Nutr. 98, 111-120. doi: 10.3945/ajcn.112.056689
246. Paganini, D., Uyoga, M. A., Kortman, G. A. M., Cercamondi, C. I., Moretti, D., Barth-Jaeggi, T., et al. (2017). Prebiotic galacto-oligosaccharides mitigate the adverse effects of iron fortification on the gut microbiome: a randomised controlled study in Kenyan infants. Gut 66, 1956-1967. doi: 10.1136/gutjnl-2017-314418
247. Paganini, D., and Zimmermann, M. B. (2017). The effects of iron fortification and supplementation on the gut microbiome and diarrhea in infants and children: a review. Am. J. Clin. Nutr. 106(Suppl. 6), 1688S-1693S. doi: 10.3945/ajcn.117.156067
248. Pagel, R., Bar, F., Schroder, T., Sunderhauf, A., Kunstner, A., Ibrahim, S. M., et al. (2017). Circadian rhythm disruption impairs tissue homeostasis and exacerbates chronic inflammation in the intestine. FASEB J. 31, 4707-4719. doi: 10.1096/fj.201700141RR
249. Pasiakos, S. M., Margolis, L. M., Murphy, N. E., McClung, H. L., Martini, S., Gundersen, Y., et al. (2016). Effects of exercise mode, energy, and macronutrient interventions on inflammation during military training. Physiol. Rep. 4:e12820. doi: 10.14814/phy2.12820
250. Pearce, S. C., Sanz-Fernandez, M. V., Hollis, J. H., Baumgard, L. H., and Gabler, N. K. (2014). Short-term exposure to heat stress attenuates appetite and intestinal integrity in growing pigs. J. Anim. Sci. 92, 5444-5454. doi: 10.2527/jas.2014-8407
251. Petersen, C., and Round, J. L. (2014). Defining dysbiosis and its influence on host immunity and disease. Cell Microbiol. 16, 1024-1033. doi: 10.1111/cmi.12308
252. Petriz, B. A., Castro, A. P., Almeida, J. A., Gomes, C. P., Fernandes, G. R., Kruger, R. H., et al. (2014). Exercise induction of gut microbiota modifications in obese, non-obese and hypertensive rats. BMC Genomics 15:511. doi: 10.1186/1471-2164-15-511
253. Phua, L. C., Wilder-Smith, C. H., Tan, Y. M., Gopalakrishnan, T., Wong, R. K., Li, X., et al. (2015). Gastrointestinal symptoms and altered intestinal permeability induced by combat training are associated with distinct metabotypic changes. J. Proteome Res. 14, 4734-4742. doi: 10.1021/acs.jproteome.5b00603
254. Ponziani, F. R., Scaldaferri, F., Petito, V., Paroni Sterbini, F., Pecere, S., Lopetuso, L. R., et al. (2016). The role of antibiotics in gut microbiota modulation: the eubiotic effects of rifaximin. Dig. Dis. 34, 269-278. doi: 10.1159/000443361
255. Pop, M., Paulson, J. N., Chakraborty, S., Astrovskaya, I., Lindsay, B. R., Li, S., et al. (2016). Individual-specific changes in the human gut microbiota after challenge with enterotoxigenic Escherichia coli and subsequent ciprofloxacin treatment. BMC Genomics 17:440. doi: 10.1186/s12864-016-2777-0
256. Poroyko, V. A., Carreras, A., Khalyfa, A., Khalyfa, A. A., Leone, V., Peris, E., et al. (2016). Chronic sleep disruption alters gut microbiota, induces systemic and adipose tissue inflammation and insulin resistance in mice. Sci. Rep. 6:35405. doi: 10.1038/srep35405
257. Porter, C. K., Gloor, K., Cash, B. D., and Riddle, M. S. (2011). Risk of functional gastrointestinal disorders in U.S. military following self-reported diarrhea and vomiting during deployment. Dig Dis. Sci. 56, 3262-3269. doi: 10.1007/s10620-011-1762-3
258. Porter, C. K., Olson, S., Hall, A., and Riddle, M. S. (2017). Travelers' diarrhea: an update on the incidence, etiology, and risk in military deployments and similar travel populations. Mil. Med. 182, 4-10. doi: 10.7205/MILMED-D-17-00064
259. Porter, C. K., Thura, N., and Riddle, M. S. (2013). Quantifying the incidence and burden of postinfectious enteric sequelae. Mil. Med. 178, 452-469. doi: 10.7205/MILMED-D-12-00510
260. Qamar, M. I., and Read, A. E. (1987). Effects of exercise on mesenteric blood flow in man. Gut 28, 583-587. doi: 10.1136/gut.28.5.583
261. Qin, J., Li, R., Raes, J., Arumugam, M., Burgdorf, K. S., Manichanh, C., et al. (2010). A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464, 59-65. doi: 10.1038/nature08821
262. Queipo-Ortuno, M. I., Seoane, L. M., Murri, M., Pardo, M., Gomez-Zumaquero, J. M., Cardona, F., et al. (2013). Gut microbiota composition in male rat models under different nutritional status and physical activity and its association with serum leptin and ghrelin levels. PLoS One 8:e65465. doi: 10.1371/journal.pone.0065465
263. Rashid, M. U., Zaura, E., Buijs, M. J., Keijser, B. J., Crielaard, W., Nord, C. E., et al. (2015). Determining the long-term effect of antibiotic administration on the human normal intestinal microbiota using culture and pyrosequencing methods. Clin. Infect. Dis. 60(Suppl. 2), S77-S84. doi: 10.1093/cid/civ137
264. Rastall, R. A. (2010). Functional oligosaccharides: application and manufacture. Annu. Rev. Food. Sci. Technol. 1, 305-339. doi: 10.1146/annurev.food.080708.100746
265. Read, M. N., and Holmes, A. J. (2017). Towards an integrative understanding of diet-host-gut microbiome interactions. Front. Immunol. 8:538. doi: 10.3389/fimmu.2017.00538
266. Reed, S., Neuman, H., Moscovich, S., Glahn, R. P., Koren, O., and Tako, E. (2015). Chronic zinc deficiency alters chick gut microbiota composition and function. Nutrients 7, 9768-9784. doi: 10.3390/nu7125497
267. Reynolds, A. C., Paterson, J. L., Ferguson, S. A., Stanley, D., Wright, K. P. Jr., et al. (2017). The shift work and health research agenda: considering changes in gut microbiota as a pathway linking shift work, sleep loss and circadian misalignment, and metabolic disease. Sleep Med. Rev. 34, 3-9. doi: 10.1016/j.smrv.2016.06.009
268. Ribiere, C., Peyret, P., Parisot, N., Darcha, C., Dechelotte, P. J., Barnich, N., et al. (2016). Oral exposure to environmental pollutant benzo[a]pyrene impacts the intestinal epithelium and induces gut microbial shifts in murine model. Sci. Rep. 6:31027. doi: 10.1038/srep31027
269. Riddle, M. S., and Connor, B. A. (2016). The traveling microbiome. Curr. Infect. Dis. Rep. 18:29. doi: 10.1007/s11908-016-0536-7
270. Riddle, M. S., DuPont, H. L., and Connor, B. A. (2016). ACG Clinical Guideline: diagnosis, treatment, and prevention of acute diarrheal infections in adults. Am. J. Gastroenterol. 111, 602-622. doi: 10.1038/ajg.2016.126
271. Riddle, M. S., Martin, G. J., Murray, C. K., Burgess, T. H., Connor, P., Mancuso, J. D., et al. (2017). Management of acute diarrheal illness during deployment: a deployment health guideline and expert panel report. Mil. Med. 182, 34-52. doi: 10.7205/MILMED-D-17-00077
272. Riddle, M. S., Tribble, D. R., Putnam, S. D., Mostafa, M., Brown, T. R., Letizia, A., et al. (2008). Past trends and current status of self-reported incidence and impact of disease and nonbattle injury in military operations in Southwest Asia and the Middle East. Am. J. Public Health 98, 2199-2206. doi: 10.2105/AJPH.2007.131680
273. Roager, H. M., Hansen, L. B., Bahl, M. I., Frandsen, H. L., Carvalho, V., Gobel, R. J., et al. (2016). Colonic transit time is related to bacterial metabolism and mucosal turnover in the gut. Nat. Microbiol. 1:16093. doi: 10.1038/nmicrobiol.2016.93
274. Roberfroid, M., Gibson, G. R., Hoyles, L., McCartney, A. L., Rastall, R., Rowland, I., et al. (2010). Prebiotic effects: metabolic and health benefits. Br. J. Nutr. 104(Suppl. 2), S1-S63. doi: 10.1017/S0007114510003363
275. Russell, A., and Deuster, P. A. (2017). Human performance optimization and precision performance: the future of special operations human performance efforts. J. Spec. Oper. Med. 17, 80-89
276. Russell, S. L., Gold, M. J., Hartmann, M., Willing, B. P., Thorson, L., Wlodarska, M., et al. (2012). Early life antibiotic-driven changes in microbiota enhance susceptibility to allergic asthma. EMBO Rep. 13, 440-447. doi: 10.1038/embor.2012.32
277. Russell, W. R., Gratz, S. W., Duncan, S. H., Holtrop, G., Ince, J., Scobbie, L., et al. (2011). High-protein, reduced-carbohydrate weight-loss diets promote metabolite profiles likely to be detrimental to colonic health. Am. J. Clin. Nutr. 93, 1062-1072. doi: 10.3945/ajcn.110.002188
278. Salim, S. Y., Kaplan, G. G., and Madsen, K. L. (2014). Air pollution effects on the gut microbiota: a link between exposure and inflammatory disease. Gut Microbes 5, 215-219. doi: 10.4161/gmic.27251
279. Salonen, A., and de Vos, W. M. (2014). Impact of diet on human intestinal microbiota and health. Annu. Rev. Food Sci. Technol. 5, 239-262. doi: 10.1146/annurev-food-030212-182554
280. Sanchez, J. L., Cooper, M. J., Myers, C. A., Cummings, J. F., Vest, K. G., Russell, K. L., et al. (2015). Respiratory infections in the U.S. military: recent experience and control. Clin. Microbiol. Rev. 28, 743-800. doi: 10.1128/CMR.00039-14
281. Sanders, J. W., Putnam, S. D., Riddle, M. S., Tribble, D. R., Jobanputra, N. K., Jones, J. J., et al. (2004). The epidemiology of self-reported diarrhea in operations Iraqi freedom and enduring freedom. Diagn. Microbiol. Infect. Dis. 50, 89-93. doi: 10.1016/j.diagmicrobio.2004.06.008
282. Sartor, R. B. (2008). Microbial influences in inflammatory bowel diseases. Gastroenterology 134, 577-594. doi: 10.1053/j.gastro.2007.11.059
283. Saunders, P. R., Kosecka, U., McKay, D. M., and Perdue, M. H. (1994). Acute stressors stimulate ion secretion and increase epithelial permeability in rat intestine. Am. J. Physiol. 267(5 Pt 1), G794-G799. doi: 10.1152/ajpgi.1994.267.5.G794
284. Scalbert, A., and Williamson, G. (2000). Dietary intake and bioavailability of polyphenols. J. Nutr. 130(8S Suppl), 2073S-2085S. doi: 10.1093/jn/130.8.2073S
285. Scher, J. U., Sczesnak, A., Longman, R. S., Segata, N., Ubeda, C., Bielski, C., et al. (2013). Expansion of intestinal Prevotella copri correlates with enhanced susceptibility to arthritis. Elife 2:e01202. doi: 10.7554/eLife.01202
286. Schmid, S. M., Hallschmid, M., and Schultes, B. (2015). The metabolic burden of sleep loss. Lancet Diabetes Endocrinol. 3, 52-62. doi: 10.1016/S2213-8587(14)70012-9
287. Schroeder, B. O., Birchenough, G. M. H., Stahlman, M., Arike, L., Johansson, M. E. V., Hansson, G. C., et al. (2018). Bifidobacteria or fiber protects against diet-induced microbiota-mediated colonic mucus deterioration. Cell Host Microbe 23, 27.e7-40.e7. doi: 10.1016/j.chom.2017.11.004
288. Schwarcz, R., Bruno, J. P., Muchowski, P. J., and Wu, H. Q. (2012). Kynurenines in the mammalian brain: when physiology meets pathology. Nat. Rev. Neurosci. 13, 465-477. doi: 10.1038/nrn3257
289. Schwellnus, M., Soligard, T., Alonso, J. M., Bahr, R., Clarsen, B., Dijkstra, H. P., et al. (2016). How much is too much? (Part 2) International Olympic Committee consensus statement on load in sport and risk of illness. Br. J. Sports Med. 50, 1043-1052. doi: 10.1136/bjsports-2016-096572
290. Schwille-Kiuntke, J., Mazurak, N., and Enck, P. (2015). Systematic review with meta-analysis: post-infectious irritable bowel syndrome after travellers' diarrhoea. Aliment. Pharmacol. Ther. 41, 1029-1037. doi: 10.1111/apt.13199
291. Scott, K. P., Duncan, S. H., and Flint, H. J. (2008). Dietary fibre and the gut microbiota. Nutr. Bull. 33, 201-211. doi: 10.1111/j.1467-3010.2008.00706.x
292. Seganfredo, F. B., Blume, C. A., Moehlecke, M., Giongo, A., Casagrande, D. S., Spolidoro, J. V. N., et al. (2017). Weight-loss interventions and gut microbiota changes in overweight and obese patients: a systematic review. Obes. Rev. 18, 832-851. doi: 10.1111/obr.12541
293. Segerstrom, S. C., and Miller, G. E. (2004). Psychological stress and the human immune system: a meta-analytic study of 30 years of inquiry. Psychol. Bull. 130, 601-630. doi: 10.1037/0033-2909.130.4.601
294. Senay, E. C., and Levine, R. J. (1967). Synergism between cold and restraint for rapid production of stress ulcers in rats. Proc. Soc. Exp. Biol. Med. 124, 1221-1223. doi: 10.3181/00379727-124-31970
295. Sender, R., Fuchs, S., and Milo, R. (2016). Revised estimates for the number of human and bacteria cells in the body. PLoS Biol. 14:e1002533. doi: 10.1371/journal.pbio.1002533
296. Shen, W., Gaskins, H. R., and McIntosh, M. K. (2014). Influence of dietary fat on intestinal microbes, inflammation, barrier function and metabolic outcomes. J. Nutr. Biochem. 25, 270-280. doi: 10.1016/j.jnutbio.2013.09.009
297. Shimada, Y., Kinoshita, M., Harada, K., Mizutani, M., Masahata, K., Kayama, H., et al. (2013). Commensal bacteria-dependent indole production enhances epithelial barrier function in the colon. PLoS One 8:e80604. doi: 10.1371/journal.pone.0080604
298. Silbergeld, E. K. (2017). The microbiome. Toxicol. Pathol. 45, 190-194. doi: 10.1177/0192623316672073
299. Singh, R. K., Chang, H. W., Yan, D., Lee, K. M., Ucmak, D., Wong, K., et al. (2017). Influence of diet on the gut microbiome and implications for human health. J. Transl. Med. 15:73. doi: 10.1186/s12967-017-1175-y
300. Sket, R., Debevec, T., Kublik, S., Schloter, M., Schoeller, A., Murovec, B., et al. (2018). Intestinal metagenomes and metabolomes in healthy young males: inactivity and hypoxia generated negative physiological symptoms precede microbial dysbiosis. Front. Physiol. 9:198. doi: 10.3389/fphys.2018.00198
301. Sket, R., Treichel, N., Debevec, T., Eiken, O., Mekjavic, I., Schloter, M., et al. (2017). Hypoxia and inactivity related physiological changes (constipation, inflammation) are not reflected at the level of gut metabolites and butyrate producing microbial community: the PlanHab study. Front. Physiol. 8:250. doi: 10.3389/fphys.2017.00250
302. Sket, R., Treichel, N., Kublik, S., Debevec, T., Eiken, O., Mekjavic, I., et al. (2017). Hypoxia and inactivity related physiological changes precede or take place in absence of significant rearrangements in bacterial community structure: The PlanHab randomized trial pilot study. PLoS One 12:e0188556. doi: 10.1371/journal.pone.0188556
303. Smith, M. I., Yatsunenko, T., Manary, M. J., Trehan, I., Mkakosya, R., Cheng, J., et al. (2013). Gut microbiomes of malawian twin pairs discordant for kwashiorkor. Science 339, 548-554. doi: 10.1126/science.1229000
304. Sohail, M. U., Hume, M. E., Byrd, J. A., Nisbet, D. J., Shabbir, M. Z., Ijaz, A., et al. (2015). Molecular analysis of the caecal and tracheal microbiome of heat-stressed broilers supplemented with prebiotic and probiotic. Avian. Pathol. 44, 67-74. doi: 10.1080/03079457.2015.1004622
305. Song, J., Xiao, K., Ke, Y. L., Jiao, L. F., Hu, C. H., Diao, Q. Y., et al. (2014). Effect of a probiotic mixture on intestinal microflora, morphology, and barrier integrity of broilers subjected to heat stress. Poult. Sci. 93, 581-588. doi: 10.3382/ps.2013-03455
306. 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. doi: 10.1038/nature16504
307. 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. doi: 10.1016/j.cmet.2014.07.003
308. Sonnenburg, J. L., and Backhed, F. (2016). Diet-microbiota interactions as moderators of human metabolism. Nature 535, 56-64. doi: 10.1038/nature18846
309. Sonoyama, K., Fujiwara, R., Takemura, N., Ogasawara, T., Watanabe, J., Ito, H., et al. (2009). Response of gut microbiota to fasting and hibernation in Syrian hamsters. Appl. Environ. Microbiol. 75, 6451-6456. doi: 10.1128/AEM.00692-09
310. Stallings, J. D., Ippolito, D. L., Wallqvist, A., and Reifman, J. (2015). Host response to environmental hazards: using literature, bioinformatics, and computation to derive candidate biomarkers of toxic industrial chemical exposure. STO-MP-HFM-254 7, 1-14. doi: 10.21236/AD1003903
311. Stevenson, T. J., Duddleston, K. N., and Buck, C. L. (2014). Effects of season and host physiological state on the diversity, density, and activity of the arctic ground squirrel cecal microbiota. Appl. Environ. Microbiol. 80, 5611-5622. doi: 10.1128/AEM.01537-14
312. Suez, J., Korem, T., Zeevi, D., Zilberman-Schapira, G., Thaiss, C. A., Maza, O., et al. (2014). Artificial sweeteners induce glucose intolerance by altering the gut microbiota. Nature 514, 181-186. doi: 10.1038/nature13793
313. Sullivan, K., Krengel, M., Bradford, W., Stone, C., Thompson, T. A., Heeren, T., et al. (2018). Neuropsychological functioning in military pesticide applicators from the Gulf War: effects on information processing speed, attention and visual memory. Neurotoxicol. Teratol. 65, 1-13. doi: 10.1016/j.ntt.2017.11.002
314. Summa, K. C., Voigt, R. M., Forsyth, C. B., Shaikh, M., Cavanaugh, K., Tang, Y., et al. (2013). Disruption of the circadian clock in mice increases intestinal permeability and promotes alcohol-induced hepatic pathology and inflammation. PLoS One 8:e67102. doi: 10.1371/journal.pone.0067102
315. Tahara, Y., Yamazaki, M., Sukigara, H., Motohashi, H., Sasaki, H., Miyakawa, H., et al. (2018). Gut microbiota-derived short chain fatty acids induce circadian clock entrainment in mouse peripheral tissue. Sci. Rep. 8:1395. doi: 10.1038/s41598-018-19836-7
316. Tannock, G. W., and Savage, D. C. (1974). Influences of dietary and environmental stress on microbial populations in the murine gastrointestinal tract. Infect. Immun. 9, 591-598
317. Thaiss, C. A., Levy, M., Korem, T., Dohnalova, L., Shapiro, H., Jaitin, D. A., et al. (2016). Microbiota diurnal rhythmicity programs host transcriptome oscillations. Cell 167, 1495.e12-1510.e12. doi: 10.1016/j.cell.2016.11.003
318. Thaiss, C. A., Nobs, S. P., and Elinav, E. (2017). NFIL-trating the Host circadian rhythm-microbes fine-tune the epithelial clock. Cell Metab. 26, 699-700. doi: 10.1016/j.cmet.2017.10.014
319. Thaiss, C. A., Zeevi, D., Levy, M., Zilberman-Schapira, G., Suez, J., Tengeler, A. C., et al. (2014). Transkingdom control of microbiota diurnal oscillations promotes metabolic homeostasis. Cell 159, 514-529. doi: 10.1016/j.cell.2014.09.048
320. Theodoroff, S. M., Lewis, M. S., Folmer, R. L., Henry, J. A., and Carlson, K. F. (2015). Hearing impairment and tinnitus: prevalence, risk factors, and outcomes in US service members and veterans deployed to the Iraq and Afghanistan wars. Epidemiol. Rev. 37, 71-85. doi: 10.1093/epirev/mxu005
321. Toloza, E. M., Lam, M., and Diamond, J. (1991). Nutrient extraction by cold-exposed mice: a test of digestive safety margins. Am. J. Physiol. 261(4 Pt 1), G608-G620. doi: 10.1152/ajpgi.1991.261.4.G608
322. Tompkins, G. R., O'Dell, N. L., Bryson, I. T., and Pennington, C. B. (2001). The effects of dietary ferric iron and iron deprivation on the bacterial composition of the mouse intestine. Curr. Microbiol. 43, 38-42. doi: 10.1007/s002840010257
323. Topping, D. L., Fukushima, M., and Bird, A. R. (2003). Resistant starch as a prebiotic and synbiotic: state of the art. Proc. Nutr. Soc. 62, 171-176. doi: 10.1079/PNS2002224
324. Tran, C. D., Grice, D. M., Wade, B., Kerr, C. A., Bauer, D. C., Li, D., et al. (2015). Gut permeability, its interaction with gut microflora and effects on metabolic health are mediated by the lymphatics system, liver and bile acid. Future Microbiol. 10, 1339-1353. doi: 10.2217/FMB.15.54
325. Tremaroli, V., and Backhed, F. (2012). Functional interactions between the gut microbiota and host metabolism. Nature 489, 242-249. doi: 10.1038/nature11552
326. Tribble, D. R. (2017). Antibiotic Therapy for Acute Watery Diarrhea and Dysentery. Mil. Med. 182, 17-25. doi: 10.7205/MILMED-D-17-00068
327. Tuohy, K. M., Conterno, L., Gasperotti, M., and Viola, R. (2012). Up-regulating the human intestinal microbiome using whole plant foods, polyphenols, and/or fiber. J. Agric. Food Chem. 60, 8776-8782. doi: 10.1021/jf2053959
328. Turnbaugh, P. J., Backhed, F., Fulton, L., and Gordon, J. I. (2008). Diet-induced obesity is linked to marked but reversible alterations in the mouse distal gut microbiome. Cell Host Microbe 3, 213-223. doi: 10.1016/j.chom.2008.02.015
329. Turnbaugh, P. J., Hamady, M., Yatsunenko, T., Cantarel, B. L., Duncan, A., Ley, R. E., et al. (2009). A core gut microbiome in obese and lean twins. Nature 457, 480-484. doi: 10.1038/nature07540
330. Ulrich-Lai, Y. M., and Herman, J. P. (2009). Neural regulation of endocrine and autonomic stress responses. Nat. Rev. Neurosci. 10, 397-409. doi: 10.1038/nrn2647
331. Vaahtovuo, J., Munukka, E., Korkeamaki, M., Luukkainen, R., and Toivanen, P. (2008). Fecal microbiota in early rheumatoid arthritis. J. Rheumatol. 35, 1500-1505
332. van Wijck, K., Lenaerts, K., Grootjans, J., Wijnands, K. A., Poeze, M., van Loon, L. J., et al. (2012). Physiology and pathophysiology of splanchnic hypoperfusion and intestinal injury during exercise: strategies for evaluation and prevention. Am. J. Physiol. Gastrointest. Liver Physiol. 303, G155-G168. doi: 10.1152/ajpgi.00066.2012
333. Vanegas, S. M., Meydani, M., Barnett, J. B., Goldin, B., Kane, A., Rasmussen, H., et al. (2017). Substituting whole grains for refined grains in a 6-wk randomized trial has a modest effect on gut microbiota and immune and inflammatory markers of healthy adults. Am. J. Clin. Nutr. 105, 635-650. doi: 10.3945/ajcn.116.146928
334. Verbeke, K. A., Boobis, A. R., Chiodini, A., Edwards, C. A., Franck, A., Kleerebezem, M., et al. (2015). Towards microbial fermentation metabolites as markers for health benefits of prebiotics. Nutr. Res. Rev. 28, 42-66. doi: 10.1017/S0954422415000037
335. Voigt, R. M., Forsyth, C. B., Green, S. J., Engen, P. A., and Keshavarzian, A. (2016). Circadian rhythm and the gut microbiome. Int. Rev. Neurobiol. 131, 193-205. doi: 10.1016/bs.irn.2016.07.002
336. Voigt, R. M., Summa, K. C., Forsyth, C. B., Green, S. J., Engen, P., Naqib, A., et al. (2016). The circadian clock mutation promotes intestinal dysbiosis. Alcohol. Clin. Exp. Res. 40, 335-347. doi: 10.1111/acer.12943
337. Voigt, R. M., Forsyth, C. B., Green, S. J., Mutlu, E., Engen, P., Vitaterna, M. H., et al. (2014). Circadian disorganization alters intestinal microbiota. PLoS One 9:e97500. doi: 10.1371/journal.pone.0097500
338. Wahlstrom, A., Sayin, S. I., Marschall, H. U., and Backhed, F. (2016). Intestinal crosstalk between bile acids and microbiota and its impact on host metabolism. Cell Metab. 24, 41-50. doi: 10.1016/j.cmet.2016.05.005
339. Walker, A. W., Ince, J., Duncan, S. H., Webster, L. M., Holtrop, G., Ze, X., et al. (2011). Dominant and diet-responsive groups of bacteria within the human colonic microbiota. ISME J. 5, 220-230. doi: 10.1038/ismej.2010.118
340. Walsh, N. P., Gleeson, M., Shephard, R. J., Gleeson, M., Woods, J. A., Bishop, N. C., et al. (2011). Position statement, part one: immune function and exercise. Exerc. Immunol. Rev. 17, 6-63
341. Wang, Y., Kuang, Z., Yu, X., Ruhn, K. A., Kubo, M., and Hooper, L. V. (2017). The intestinal microbiota regulates body composition through NFIL3 and the circadian clock. Science 357, 912-916. doi: 10.1126/science.aan0677
342. Wang, Z., Tang, W. H., Buffa, J. A., Fu, X., Britt, E. B., Koeth, R. A., et al. (2014). Prognostic value of choline and betaine depends on intestinal microbiota-generated metabolite trimethylamine-N-oxide. Eur. Heart J. 35, 904-910. doi: 10.1093/eurheartj/ehu002
343. Weaver, C. M. (2015). Diet, gut microbiome, and bone health. Curr. Osteoporos Rep. 13, 125-130. doi: 10.1007/s11914-015-0257-0
344. Weeks, S. R., McAuliffe, C. L., Durussel, D., and Pasquina, P. F. (2010). Physiological and psychological fatigue in extreme conditions: the military example. PMR 2, 438-441. doi: 10.1016/j.pmrj.2010.03.023
345. Wells, J. M., Brummer, R. J., Derrien, M., MacDonald, T. T., Troost, F., Cani, P. D., et al. (2017). Homeostasis of the gut barrier and potential biomarkers. Am. J. Physiol. Gastrointest. Liver Physiol. 312, G171-G193. doi: 10.1152/ajpgi.00048.2015
346. Welly, R. J., Liu, T. W., Zidon, T. M., Rowles, J. L. III, Park, Y. M., Smith, T. N., et al. (2016). Comparison of diet versus exercise on metabolic function and gut microbiota in obese rats. Med. Sci. Sports Exerc. 48, 1688-1698. doi: 10.1249/MSS.0000000000000964
347. Werner, T., Wagner, S. J., Martinez, I., Walter, J., Chang, J. S., Clavel, T., et al. (2011). Depletion of luminal iron alters the gut microbiota and prevents Crohn's disease-like ileitis. Gut 60, 325-333. doi: 10.1136/gut.2010.216929
348. White, B. A., Lamed, R., Bayer, E. A., and Flint, H. J. (2014). Biomass utilization by gut microbiomes. Annu. Rev. Microbiol. 68, 279-296. doi: 10.1146/annurev-micro-092412-155618
349. Wilson, T. E., Sauder, C. L., Kearney, M. L., Kuipers, N. T., Leuenberger, U. A., Monahan, K. D., et al. (2007). Skin-surface cooling elicits peripheral and visceral vasoconstriction in humans. J. Appl. Physiol. 103, 1257-1262. doi: 10.1152/japplphysiol.00401.2007
350. Windey, K., De Preter, V., Louat, T., Schuit, F., Herman, J., Vansant, G., et al. (2012). Modulation of protein fermentation does not affect fecal water toxicity: a randomized cross-over study in healthy subjects. PLoS One 7:e52387. doi: 10.1371/journal.pone.0052387
351. Wu, G. D., Chen, J., Hoffmann, C., Bittinger, K., Chen, Y. Y., Keilbaugh, S. A., et al. (2011). Linking long-term dietary patterns with gut microbial enterotypes. Science 334, 105-108. doi: 10.1126/science.1208344
352. Xu, C. L., Sun, R., Qiao, X. J., Xu, C. C., Shang, X. Y., and Niu, W. N. (2014). Protective effect of glutamine on intestinal injury and bacterial community in rats exposed to hypobaric hypoxia environment. World J. Gastroenterol. 20, 4662-4674. doi: 10.3748/wjg.v20.i16.4662
353. Xu, D., Gao, J., Gillilland, M. III, Wu, X., Song, I., Kao, J. Y., et al. (2014). Rifaximin alters intestinal bacteria and prevents stress-induced gut inflammation and visceral hyperalgesia in rats. Gastroenterology 146, 484.e4-496.e4. doi: 10.1053/j.gastro.2013.10.026
354. Yao, C. K., Muir, J. G., and Gibson, P. R. (2016). Review article: insights into colonic protein fermentation, its modulation and potential health implications. Aliment. Pharmacol. Ther. 43, 181-196. doi: 10.1111/apt.13456
355. Youmans, B. P., Ajami, N. J., Jiang, Z. D., Campbell, F., Wadsworth, W. D., Petrosino, J. F., et al. (2015). Characterization of the human gut microbiome during travelers' diarrhea. Gut Microbes 6, 110-119. doi: 10.1080/19490976.2015.1019693
356. Zackular, J. P., Moore, J. L., Jordan, A. T., Juttukonda, L. J., Noto, M. J., Nicholson, M. R., et al. (2016). Dietary zinc alters the microbiota and decreases resistance to Clostridium difficile infection. Nat. Med. 22, 1330-1334. doi: 10.1038/nm.4174
357. Zanella Terrier, M. C., Simonet, M. L., Bichard, P., and Frossard, J. L. (2014). Recurrent Clostridium difficile infections: the importance of the intestinal microbiota. World J. Gastroenterol. 20, 7416-7423. doi: 10.3748/wjg.v20.i23.7416
358. Zarrinpar, A., Chaix, A., Yooseph, S., and Panda, S. (2014). Diet and feeding pattern affect the diurnal dynamics of the gut microbiome. Cell Metab. 20, 1006-1017. doi: 10.1016/j.cmet.2014.11.008
359. Zaura, E., Brandt, B. W., Teixeira, de Mattos, M. J., Buijs, M. J., Caspers, M. P., et al. (2015). Same exposure but two radically different responses to antibiotics: resilience of the salivary microbiome versus long-term microbial shifts in feces. mBio 6:e1693-15. doi: 10.1128/mBio.01693-15
360. Zeevi, D., Korem, T., Zmora, N., Israeli, D., Rothschild, D., Weinberger, A., et al. (2015). Personalized nutrition by prediction of glycemic responses. Cell 163, 1079-1094. doi: 10.1016/j.cell.2015.11.001
361. Zhang, F., Wu, W., Deng, Z., Zheng, X., Zhang, J., Deng, S., et al. (2015). High altitude increases the expression of hypoxia-inducible factor 1alpha and inducible nitric oxide synthase with intest-inal mucosal barrier failure in rats. Int. J. Clin. Exp. Pathol. 8, 5189-5195
362. Zhang, S., Jin, Y., Zeng, Z., Liu, Z., and Fu, Z. (2015). Subchronic exposure of mice to cadmium perturbs their hepatic energy metabolism and gut microbiome. Chem. Res. Toxicol. 28, 2000-2009. doi: 10.1021/acs.chemrestox.5b00237
363. Zhang, S. L., Bai, L., Goel, N., Bailey, A., Jang, C. J., Bushman, F. D., et al. (2017). Human and rat gut microbiome composition is maintained following sleep restriction. Proc. Natl. Acad. Sci. U.S.A. 114, E1564-E1571. doi: 10.1073/pnas.1620673114
364. Zhou, Q. Q., Yang, D. Z., Luo, Y. J., Li, S. Z., Liu, F. Y., and Wang, G. S. (2011). Over-starvation aggravates intestinal injury and promotes bacterial and endotoxin translocation under high-altitude hypoxic environment. World J. Gastroenterol. 17, 1584-1593. doi: 10.3748/wjg.v17.i12.1584
365. Zietak, M., Kovatcheva-Datchary, P., Markiewicz, L. H., Stahlman, M., Kozak, L. P., and Backhed, F. (2016). Altered microbiota contributes to reduced diet-induced obesity upon cold exposure. Cell Metab. 23, 1216-1223. doi: 10.1016/j.cmet.2016.05.001
366. Zimmermann, M. B., Chassard, C., Rohner, F., N'Goran E. K., Nindjin, C., Dostal, A., et al. (2010). The effects of iron fortification on the gut microbiota in African children: a randomized controlled trial in Cote d'Ivoire. Am. J. Clin. Nutr. 92, 1406-1415. doi: 10.3945/ajcn.110.004564
367. Zmora, N., Zeevi, D., Korem, T., Segal, E., and Elinav, E. (2016). Taking it personally: personalized utilization of the human microbiome in health and disease. Cell Host Microbe 19, 12-20. doi: 10.1016/j.chom.2015.12.016
368. Zuhl, M., Schneider, S., Lanphere, K., Conn, C., Dokladny, K., and Moseley, P. (2014). Exercise regulation of intestinal tight junction proteins. Br. J. Sports Med. 48, 980-986. doi: 10.1136/bjsports-2012-091585