human gut virome is highly diverse, stable, and individual specific. Cell Host Microbe 26
(4):527–541 e525. https://doi.org/10.1016/j.chom.2019.09.009
Sing D, Sing CF (2010) Impact of direct soil exposures from airborne dust and geophagy on human
health. Int J Environ Res Public Health 7(3):1205–1223. https://doi.org/10.3390/ijerph7031205
Smillie CS, Smith MB, Friedman J, Cordero OX, David LA, Alm EJ (2011) Ecology drives a global
network of gene exchange connecting the human microbiome. Nature 480(7376):241–244.
https://doi.org/10.1038/nature10571
Sonnenburg ED, Smits SA, Tikhonov M, Higginbottom SK, Wingreen NS, Sonnenburg JL (2016)
Diet-induced extinctions in the gut microbiota compound over generations. Nature 529
(7585):212–215. https://doi.org/10.1038/nature16504
Sousa A, Frazão N, Ramiro RS, Gordo I (2017) Evolution of commensal bacteria in the intestinal
tract of mice. Curr Opin Microbiol 38:114–121. https://doi.org/10.1016/j.mib.2017.05.007
Sozanska B, Blaszczyk M, Pearce N, Cullinan P (2014) Atopy and allergic respiratory disease in
rural Poland before and after accession to the European Union. J Allergy Clin Immunol 133
(5):1347–1353. https://doi.org/10.1016/j.jaci.2013.10.035
Stein MM, Hrusch CL, Gozdz J, Igartua C, Pivniouk V, Murray SE, Ledford JG, Marques dos
Santos M, Anderson RL, Metwali N, Neilson JW, Maier RM, Gilbert JA, Holbreich M, Thorne
PS, Martinez FD, von Mutius E, Vercelli D, Ober C, Sperling AI (2016) Innate immunity and
asthma risk in amish and hutterite farm children. N Engl J Med 375(5):411–421. https://doi.org/
10.1056/NEJMoa1508749
Stilling RM, van de Wouw M, Clarke G, Stanton C, Dinan TG, Cryan JF (2016) The neuropharmacology of butyrate: The bread and butter of the microbiota-gut-brain axis? Neurochem Int
99:110–132. https://doi.org/10.1016/j.neuint.2016.06.011
Strachan DP (1989) Hay fever, hygiene, and household size. Brit Med J 299(6710):1259–1260
Strzępa A, Lobo FM, Majewska-Szczepanik M, Szczepanik M (2018) Antibiotics and autoimmune
and allergy diseases: Causative factor or treatment? Int Immunopharmacol 65:328–341. https://
doi.org/10.1016/j.intimp.2018.10.021
Su LF, Kidd BA, Han A, Kotzin JJ, Davis MM (2013) Virus-specific CD4(+) memory-phenotype T
cells are abundant in unexposed adults. Immunity 38(2):373–383. https://doi.org/10.1016/j.
immuni.2012.10.021
Sudo N, Chida Y, Aiba Y, Sonoda J, Oyama N, Yu XN, Kubo C, Koga Y (2004) Postnatal
microbial colonization programs the hypothalamic-pituitary-adrenal system for stress response
in mice. J Physiol 558 (Pt 1):263-275. doi:https://doi.org/10.1113/jphysiol.2004.063388
Swain MR, Anandharaj M, Ray RC, Parveen Rani R (2014) Fermented fruits and vegetables of
Asia: a potential source of probiotics. Biotechnol Res Int 2014:250424. https://doi.org/10.1155/
2014/250424
Tam NK, Uyen NQ, Hong HA, Duc le H, Hoa TT, Serra CR, Henriques AO, Cutting SM (2006)
The intestinal life cycle of Bacillus subtilis and close relatives. J Bacteriol 188(7):2692–2700.
https://doi.org/10.1128/JB.188.7.2692-2700.2006
Tillisch K, Labus J, Kilpatrick L, Jiang Z, Stains J, Ebrat B, Guyonnet D, Legrain-Raspaud S,
Trotin B, Naliboff B, Mayer EA (2013) Consumption of fermented milk product with probiotic
modulates brain activity. Gastroenterology 144 (7):1394–1401, 1401 e1391–1394. https://doi.
org/10.1053/j.gastro.2013.02.043
Tran HQ, Ley RE, Gewirtz AT, Chassaing B (2019) Flagellin-elicited adaptive immunity suppresses flagellated microbiota and vaccinates against chronic inflammatory diseases. Nat
Commun 10(1):5650. https://doi.org/10.1038/s41467-019-13538-y
Troyer K (1984) Behavioral acquisition of the hindgut fermentation system by hatchling Iguana
iguana. Behav Ecol Sociobiol 14 (3):189–193. https://doi.org/10.1007/BF00299618
Tsui C, Kong EF, Jabra-Rizk MA (2016) Pathogenesis of Candida albicans biofilm. Pathog Dis 74
(4). https://doi.org/10.1093/femspd/ftw018
Van Belleghem JD, Dabrowska K, Vaneechoutte M, Barr JJ, Bollyky PL (2018) Interactions
between bacteriophage, bacteria, and the mammalian immune system. Viruses 11(1). https://
doi.org/10.3390/v11010010
18 Darwinian Medicine: We Evolved to Require Continuing Contact with the. . .
363
(4):527–541 e525. https://doi.org/10.1016/j.chom.2019.09.009
Sing D, Sing CF (2010) Impact of direct soil exposures from airborne dust and geophagy on human
health. Int J Environ Res Public Health 7(3):1205–1223. https://doi.org/10.3390/ijerph7031205
Smillie CS, Smith MB, Friedman J, Cordero OX, David LA, Alm EJ (2011) Ecology drives a global
network of gene exchange connecting the human microbiome. Nature 480(7376):241–244.
https://doi.org/10.1038/nature10571
Sonnenburg ED, Smits SA, Tikhonov M, Higginbottom SK, Wingreen NS, Sonnenburg JL (2016)
Diet-induced extinctions in the gut microbiota compound over generations. Nature 529
(7585):212–215. https://doi.org/10.1038/nature16504
Sousa A, Frazão N, Ramiro RS, Gordo I (2017) Evolution of commensal bacteria in the intestinal
tract of mice. Curr Opin Microbiol 38:114–121. https://doi.org/10.1016/j.mib.2017.05.007
Sozanska B, Blaszczyk M, Pearce N, Cullinan P (2014) Atopy and allergic respiratory disease in
rural Poland before and after accession to the European Union. J Allergy Clin Immunol 133
(5):1347–1353. https://doi.org/10.1016/j.jaci.2013.10.035
Stein MM, Hrusch CL, Gozdz J, Igartua C, Pivniouk V, Murray SE, Ledford JG, Marques dos
Santos M, Anderson RL, Metwali N, Neilson JW, Maier RM, Gilbert JA, Holbreich M, Thorne
PS, Martinez FD, von Mutius E, Vercelli D, Ober C, Sperling AI (2016) Innate immunity and
asthma risk in amish and hutterite farm children. N Engl J Med 375(5):411–421. https://doi.org/
10.1056/NEJMoa1508749
Stilling RM, van de Wouw M, Clarke G, Stanton C, Dinan TG, Cryan JF (2016) The neuropharmacology of butyrate: The bread and butter of the microbiota-gut-brain axis? Neurochem Int
99:110–132. https://doi.org/10.1016/j.neuint.2016.06.011
Strachan DP (1989) Hay fever, hygiene, and household size. Brit Med J 299(6710):1259–1260
Strzępa A, Lobo FM, Majewska-Szczepanik M, Szczepanik M (2018) Antibiotics and autoimmune
and allergy diseases: Causative factor or treatment? Int Immunopharmacol 65:328–341. https://
doi.org/10.1016/j.intimp.2018.10.021
Su LF, Kidd BA, Han A, Kotzin JJ, Davis MM (2013) Virus-specific CD4(+) memory-phenotype T
cells are abundant in unexposed adults. Immunity 38(2):373–383. https://doi.org/10.1016/j.
immuni.2012.10.021
Sudo N, Chida Y, Aiba Y, Sonoda J, Oyama N, Yu XN, Kubo C, Koga Y (2004) Postnatal
microbial colonization programs the hypothalamic-pituitary-adrenal system for stress response
in mice. J Physiol 558 (Pt 1):263-275. doi:https://doi.org/10.1113/jphysiol.2004.063388
Swain MR, Anandharaj M, Ray RC, Parveen Rani R (2014) Fermented fruits and vegetables of
Asia: a potential source of probiotics. Biotechnol Res Int 2014:250424. https://doi.org/10.1155/
2014/250424
Tam NK, Uyen NQ, Hong HA, Duc le H, Hoa TT, Serra CR, Henriques AO, Cutting SM (2006)
The intestinal life cycle of Bacillus subtilis and close relatives. J Bacteriol 188(7):2692–2700.
https://doi.org/10.1128/JB.188.7.2692-2700.2006
Tillisch K, Labus J, Kilpatrick L, Jiang Z, Stains J, Ebrat B, Guyonnet D, Legrain-Raspaud S,
Trotin B, Naliboff B, Mayer EA (2013) Consumption of fermented milk product with probiotic
modulates brain activity. Gastroenterology 144 (7):1394–1401, 1401 e1391–1394. https://doi.
org/10.1053/j.gastro.2013.02.043
Tran HQ, Ley RE, Gewirtz AT, Chassaing B (2019) Flagellin-elicited adaptive immunity suppresses flagellated microbiota and vaccinates against chronic inflammatory diseases. Nat
Commun 10(1):5650. https://doi.org/10.1038/s41467-019-13538-y
Troyer K (1984) Behavioral acquisition of the hindgut fermentation system by hatchling Iguana
iguana. Behav Ecol Sociobiol 14 (3):189–193. https://doi.org/10.1007/BF00299618
Tsui C, Kong EF, Jabra-Rizk MA (2016) Pathogenesis of Candida albicans biofilm. Pathog Dis 74
(4). https://doi.org/10.1093/femspd/ftw018
Van Belleghem JD, Dabrowska K, Vaneechoutte M, Barr JJ, Bollyky PL (2018) Interactions
between bacteriophage, bacteria, and the mammalian immune system. Viruses 11(1). https://
doi.org/10.3390/v11010010
18 Darwinian Medicine: We Evolved to Require Continuing Contact with the. . .
363