Vatanen T, Kostic AD, d’Hennezel E, Siljander H, Franzosa EA, Yassour M, Kolde R, Vlamakis H,
Arthur TD, Hamalainen AM, Peet A, Tillmann V, Uibo R, Mokurov S, Dorshakova N, Ilonen J,
Virtanen SM, Szabo SJ, Porter JA, Lahdesmaki H, Huttenhower C, Gevers D, Cullen TW,
Knip M, Group DS, Xavier RJ (2016) Variation in microbiome LPS immunogenicity contributes to autoimmunity in humans. Cell 165(4):842–853. https://doi.org/10.1016/j.cell.2016.04.
007
Vierbuchen T, Bang C, Rosigkeit H, Schmitz RA, Heine H (2017) The human-associated archaeon
methanosphaera stadtmanae is recognized through its RNA and induces TLR8-dependent
NLRP3 inflammasome activation. Front Immunol 8(1535). https://doi.org/10.3389/fimmu.
2017.01535
von Hertzen L, Hanski I, Haahtela T (2011) Natural immunity. Biodiversity loss and inflammatory
diseases are two global megatrends that might be related. EMBO Rep 12(11):1089–1093.
https://doi.org/10.1038/embor.2011.195
Waltner-Toews D (2013) The origin of feces : what excrement tells us about evolution, ecology, and
a sustainable society. ECW, Toronto, ON
Wang S, Ahmadi S, Nagpal R, Jain S, Mishra SP, Kavanagh K, Zhu X, Wang Z, McClain DA,
Kritchevsky SB, Kitzman DW, Yadav H (2019) Lipoteichoic acid from the cell wall of a heat
killed Lactobacillus paracasei D3-5 ameliorates aging-related leaky gut, inflammation and
improves physical and cognitive functions: from C. elegans to mice. GeroScience. https://doi.
org/10.1007/s11357-019-00137-4
Wassermann B, Müller H, Berg G (2019) An apple a day: which bacteria do we eat with organic and
conventional apples? Front Microbiol 10(1629). https://doi.org/10.3389/fmicb.2019.01629
Weber J, Illi S, Nowak D, Schierl R, Holst O, von Mutius E, Ege MJ (2015) Asthma and the
hygiene hypothesis. Does cleanliness matter? Am J Respir Crit Care Med 191(5):522–529.
https://doi.org/10.1164/rccm.201410-1899OC
Whitlock DR, Feelisch M (2009) Soil bacteria, nitrite, and the skin. In: Rook GAW (ed) The
hygiene hypothesis and darwinian medicine. Progress in inflammation research. Birkhäuser,
Basel, pp 103–116
Wikoff WR, Anfora AT, Liu J, Schultz PG, Lesley SA, Peters EC, Siuzdak G (2009) Metabolomics
analysis reveals large effects of gut microflora on mammalian blood metabolites. Proc Natl Acad
Sci U S A 106(10):3698–3703. https://doi.org/10.1073/pnas.0812874106. 0812874106 [pii]
Yaffe E, Relman DA (2019) Tracking microbial evolution in the human gut using Hi-C reveals
extensive horizontal gene transfer, persistence and adaptation. Nat Microbiol. https://doi.org/10.
1038/s41564-019-0625-0
Zelante T, Iannitti RG, Fallarino F, Gargaro M, De Luca A, Moretti S, Bartoli A, Romani L (2014)
Tryptophan feeding of the IDO1-AhR axis in host-microbial symbiosis. Front Immunol 5:640.
https://doi.org/10.3389/fimmu.2014.00640
Zhao G, Vatanen T, Droit L, Park A, Kostic AD, Poon TW, Vlamakis H, Siljander H, Härkönen T,
Hämäläinen A-M, Peet A, Tillmann V, Ilonen J, Wang D, Knip M, Xavier RJ, Virgin HW
(2017) Intestinal virome changes precede autoimmunity in type I diabetes-susceptible children.
Proc Natl Acad Sci U S A 114(30):E6166–E6175. https://doi.org/10.1073/pnas.1706359114
Zheng P, Zeng B, Zhou C, Liu M, Fang Z, Xu X, Zeng L, Chen J, Fan S, Du X, Zhang X, Yang D,
Yang Y, Meng H, Li W, Melgiri ND, Licinio J, Wei H, Xie P (2016) Gut microbiome
remodeling induces depressive-like behaviors through a pathway mediated by the host’s
metabolism. Mol Psychiatry 21(6):786–796. https://doi.org/10.1038/mp.2016.44
Zhou Q, Wang H, Schwartz DM, Stoffels M, Park YH, Zhang Y, Yang D, Demirkaya E,
Takeuchi M, Tsai WL, Lyons JJ, Yu X, Ouyang C, Chen C, Chin DT, Zaal K,
Chandrasekharappa SC, Hanson EP, Yu Z, Mullikin JC, Hasni SA, Wertz IE, Ombrello AK,
Stone DL, Hoffmann P, Jones A, Barham BK, Leavis HL, van Royen-Kerkof A, Sibley C, Batu
ED, Gul A, Siegel RM, Boehm M, Milner JD, Ozen S, Gadina M, Chae J, Laxer RM, Kastner
DL, Aksentijevich I (2016) Loss-of-function mutations in TNFAIP3 leading to A20
haploinsufficiency cause an early-onset autoinflammatory disease. Nat Genet 48(1):67–73.
https://doi.org/10.1038/ng.3459
364
G. A. W. Rook
Arthur TD, Hamalainen AM, Peet A, Tillmann V, Uibo R, Mokurov S, Dorshakova N, Ilonen J,
Virtanen SM, Szabo SJ, Porter JA, Lahdesmaki H, Huttenhower C, Gevers D, Cullen TW,
Knip M, Group DS, Xavier RJ (2016) Variation in microbiome LPS immunogenicity contributes to autoimmunity in humans. Cell 165(4):842–853. https://doi.org/10.1016/j.cell.2016.04.
007
Vierbuchen T, Bang C, Rosigkeit H, Schmitz RA, Heine H (2017) The human-associated archaeon
methanosphaera stadtmanae is recognized through its RNA and induces TLR8-dependent
NLRP3 inflammasome activation. Front Immunol 8(1535). https://doi.org/10.3389/fimmu.
2017.01535
von Hertzen L, Hanski I, Haahtela T (2011) Natural immunity. Biodiversity loss and inflammatory
diseases are two global megatrends that might be related. EMBO Rep 12(11):1089–1093.
https://doi.org/10.1038/embor.2011.195
Waltner-Toews D (2013) The origin of feces : what excrement tells us about evolution, ecology, and
a sustainable society. ECW, Toronto, ON
Wang S, Ahmadi S, Nagpal R, Jain S, Mishra SP, Kavanagh K, Zhu X, Wang Z, McClain DA,
Kritchevsky SB, Kitzman DW, Yadav H (2019) Lipoteichoic acid from the cell wall of a heat
killed Lactobacillus paracasei D3-5 ameliorates aging-related leaky gut, inflammation and
improves physical and cognitive functions: from C. elegans to mice. GeroScience. https://doi.
org/10.1007/s11357-019-00137-4
Wassermann B, Müller H, Berg G (2019) An apple a day: which bacteria do we eat with organic and
conventional apples? Front Microbiol 10(1629). https://doi.org/10.3389/fmicb.2019.01629
Weber J, Illi S, Nowak D, Schierl R, Holst O, von Mutius E, Ege MJ (2015) Asthma and the
hygiene hypothesis. Does cleanliness matter? Am J Respir Crit Care Med 191(5):522–529.
https://doi.org/10.1164/rccm.201410-1899OC
Whitlock DR, Feelisch M (2009) Soil bacteria, nitrite, and the skin. In: Rook GAW (ed) The
hygiene hypothesis and darwinian medicine. Progress in inflammation research. Birkhäuser,
Basel, pp 103–116
Wikoff WR, Anfora AT, Liu J, Schultz PG, Lesley SA, Peters EC, Siuzdak G (2009) Metabolomics
analysis reveals large effects of gut microflora on mammalian blood metabolites. Proc Natl Acad
Sci U S A 106(10):3698–3703. https://doi.org/10.1073/pnas.0812874106. 0812874106 [pii]
Yaffe E, Relman DA (2019) Tracking microbial evolution in the human gut using Hi-C reveals
extensive horizontal gene transfer, persistence and adaptation. Nat Microbiol. https://doi.org/10.
1038/s41564-019-0625-0
Zelante T, Iannitti RG, Fallarino F, Gargaro M, De Luca A, Moretti S, Bartoli A, Romani L (2014)
Tryptophan feeding of the IDO1-AhR axis in host-microbial symbiosis. Front Immunol 5:640.
https://doi.org/10.3389/fimmu.2014.00640
Zhao G, Vatanen T, Droit L, Park A, Kostic AD, Poon TW, Vlamakis H, Siljander H, Härkönen T,
Hämäläinen A-M, Peet A, Tillmann V, Ilonen J, Wang D, Knip M, Xavier RJ, Virgin HW
(2017) Intestinal virome changes precede autoimmunity in type I diabetes-susceptible children.
Proc Natl Acad Sci U S A 114(30):E6166–E6175. https://doi.org/10.1073/pnas.1706359114
Zheng P, Zeng B, Zhou C, Liu M, Fang Z, Xu X, Zeng L, Chen J, Fan S, Du X, Zhang X, Yang D,
Yang Y, Meng H, Li W, Melgiri ND, Licinio J, Wei H, Xie P (2016) Gut microbiome
remodeling induces depressive-like behaviors through a pathway mediated by the host’s
metabolism. Mol Psychiatry 21(6):786–796. https://doi.org/10.1038/mp.2016.44
Zhou Q, Wang H, Schwartz DM, Stoffels M, Park YH, Zhang Y, Yang D, Demirkaya E,
Takeuchi M, Tsai WL, Lyons JJ, Yu X, Ouyang C, Chen C, Chin DT, Zaal K,
Chandrasekharappa SC, Hanson EP, Yu Z, Mullikin JC, Hasni SA, Wertz IE, Ombrello AK,
Stone DL, Hoffmann P, Jones A, Barham BK, Leavis HL, van Royen-Kerkof A, Sibley C, Batu
ED, Gul A, Siegel RM, Boehm M, Milner JD, Ozen S, Gadina M, Chae J, Laxer RM, Kastner
DL, Aksentijevich I (2016) Loss-of-function mutations in TNFAIP3 leading to A20
haploinsufficiency cause an early-onset autoinflammatory disease. Nat Genet 48(1):67–73.
https://doi.org/10.1038/ng.3459
364
G. A. W. Rook