123. Han, D.Y.; Fraser, A.G.; Dryland, P.; Ferguson, L.R. Environmental factors in the development of chronic inflammation: A case-control study on risk factors for Crohn's disease within New Zealand. *Mutat. Res.* **2010**, *690*, 116-122. [CrossRef]

124. Vahedi, H.; Chaharmahali, M.; Momtahen, S.; Kolahdoozan, S.; Khademi, H.; Olfati, G.; Tabrizian, T.; Rashtak, S.; Khaleghnejad, R.; Naserimoghadam, S.; et al. A Case-Control study on the risk factors of IBD in 258 Iranian patients. *Govaresh* **2011**, *16*, 61-67.

125. Ng, S.C.; Tang, W.; Leong, R.W.; Chen, M.; Ko, Y.; Studd, C.; Niewiadomski, O.; Bell, S.; Kamm, M.A.; de Silva, H.J.; et al. Environmental risk factors in inflammatory bowel disease: A population-based case-control study in Asia-Pacific. *Gut* **2015**, *64*, 1063-1071. [CrossRef] [PubMed]

126. Wang, Y.F.; Ou-Yang, Q.; Xia, B.; Liu, L.N.; Gu, F.; Zhou, K.F.; Mei, Q.; Shi, R.H.; Ran, Z.H.; Wang, X.D.; et al. Multicenter case-control study of the risk factors for ulcerative colitis in China. *World J. Gastroenterol.* **2013**, *19*, 1827-1833. [CrossRef]

127. Ko, Y.; Kariyawasam, V.; Karnib, M.; Butcher, R.; Samuel, D.; Alrubaie, A.; Rahme, N.; McDonald, C.; Cowlishaw, J.; Katelaris, P.; et al. Inflammatory Bowel Disease Environmental Risk Factors: A Population-Based Case-Control Study of Middle Eastern Migration to Australia. *Clin. Gastroenterol. Hepatol.* **2015**, *13*, 1453-1463.e1451. [CrossRef] [PubMed]

128. Koletzko, S.; Griffiths, A.; Corey, M.; Smith, C.; Sherman, P. Infant feeding practices and ulcerative colitis in childhood. *BMJ* **1991**, *302*, 1580-1581. [CrossRef] [PubMed]

129. Koletzko, S.; Sherman, P.; Corey, M.; Griffiths, A.; Smith, C. Role of infant feeding practices in development of Crohn's disease in childhood. *BMJ* **1989**, *298*, 1617-1618. [CrossRef]

130. Rigas, A.; Rigas, B.; Glassman, M.; Yen, Y.Y.; Lan, S.J.; Petridou, E.; Hsieh, C.C.; Trichopoulos, D. Breast-feeding and maternal smoking in the etiology of Crohn's disease and ulcerative colitis in childhood. *Ann. Epidemiol.* **1993**, *3*, 387-392. [CrossRef]

131. Gruber, M.; Marshall, J.R.; Zielezny, M.; Lance, P. A case-control study to examine the influence of maternal perinatal behaviors on the incidence of Crohn's disease. *Gastroenterol. Nurs.* **1996**, *19*, 53-59. [CrossRef]

132. Amre, D.K.; Lambrette, P.; Law, L.; Krupoves, A.; Chotard, V.; Costea, F.; Grimard, G.; Israel, D.; Mack, D.; Seidman, E.G. Investigating the hygiene hypothesis as a risk factor in pediatric onset Crohn's disease: A case-control study. *Am. J. Gastroenterol.* **2006**, *101*, 1005-1011. [CrossRef] [PubMed]

133. Bernstein, C.N.; Banerjee, A.; Targownik, L.E.; Singh, H.; Ghia, J.E.; Burchill, C.; Chateau, D.; Roos, L.L. Cesarean Section Delivery Is Not a Risk Factor for Development of Inflammatory Bowel Disease: A Population-based Analysis. *Clin. Gastroenterol. Hepatol.* **2016**, *14*, 50-57. [CrossRef] [PubMed]

134. Hutfless, S.; Li, D.K.; Heyman, M.B.; Bayless, T.M.; Abramson, O.; Herrinton, L.J. Prenatal and perinatal characteristics associated with pediatric-onset inflammatory bowel disease. *Dig. Dis. Sci.* **2012**, *57*, 2149-2156. [CrossRef] [PubMed]

135. Salgado, V.C.L.; Luiz, R.R.; Boechat, N.; Schorr, B.C.; Leao, I.S.; Nunes, T.; Zaltman, C. Crohn's disease environmental factors in the developing world: A case-control study in a statewide catchment area in Brazil. *World J. Gastroenterol.* **2017**, *23*, 5549-5556. [CrossRef] [PubMed]

136. Lautenschlager, S.A.; Fournier, N.; Biedermann, L.; Pittet, V.; Schreiner, P.; Misselwitz, B.; Scharl, M.; Rogler, G.; Siebenhuner, A.R. The Influence of Breastfeeding, Cesarean Section, Pet Animals, and Urbanization on the Development of Inflammatory Bowel Disease: Data from the Swiss IBD Cohort Study. *Inflamm. Intest. Dis.* **2020**, *5*, 170-179. [CrossRef]

137. Van der Sloot, K.W.J.; Weersma, R.K.; Alizadeh, B.Z.; Dijkstra, G. Identification of Environmental Risk Factors Associated with the Development of Inflammatory Bowel Disease. *J. Crohns Colitis* **2020**, *14*, 1662-1671. [CrossRef]

138. Ekbom, A.; Adami, H.O.; Helmick, C.G.; Jonzon, A.; Zack, M.M. Perinatal risk factors for inflammatory bowel disease: A case-control study. *Am. J. Epidemiol.* **1990**, *132*, 1111-1119. [CrossRef]

139. Strisciuglio, C.; Giugliano, F.; Martinelli, M.; Cenni, S.; Greco, L.; Staiano, A.; Miele, E. Impact of Environmental and Familial Factors in a Cohort of Pediatric Patients with Inflammatory Bowel Disease. *J. Pediatr. Gastroenterol. Nutr.* **2017**, *64*, 569-574. [CrossRef]

140. Bergstrand, O.; Hellers, G. Breast-feeding during infancy in patients who later develop Crohn's disease. *Scand. J. Gastroenterol.* **1983**, *18*, 903-906. [CrossRef]

141. Samuelsson, S.M.; Ekbom, A.; Zack, M.; Helmick, C.G.; Adami, H.O. Risk factors for extensive ulcerative colitis and ulcerative proctitis: A population based case-control study. *Gut* **1991**, *32*, 1526-1530. [CrossRef]

142. Persson, P.G.; Leijonmarck, C.E.; Bernell, O.; Hellers, G.; Ahlbom, A. Risk indicators for inflammatory bowel disease. *Int. J. Epidemiol.* **1993**, *22*, 268-272. [CrossRef] [PubMed]

143. Corrao, G.; Tragnone, A.; Caprilli, R.; Trallori, G.; Papi, C.; Andreoli, A.; Di Paolo, M.; Riegler, G.; Rigo, G.P.; Ferrau, O.; et al. Risk of inflammatory bowel disease attributable to smoking, oral contraception and breastfeeding in Italy: A nationwide case-control study. Cooperative Investigators of the Italian Group for the Study of the Colon and the Rectum (GISC). *Int. J. Epidemiol.* **1998**, *27*, 397-404. [CrossRef] [PubMed]

144. Thompson, N.P.; Montgomery, S.M.; Wadsworth, M.E.; Pounder, R.E.; Wakefield, A.J. Early determinants of inflammatory bowel disease: Use of two national longitudinal birth cohorts. *Eur. J. Gastroenterol. Hepatol.* **2000**, *12*, 25-30. [CrossRef] [PubMed]

145. Lopez-Serrano, P.; Perez-Calle, J.L.; Perez-Fernandez, M.T.; Fernandez-Font, J.M.; Boixeda de Miguel, D.; Fernandez-Rodriguez, C.M. Environmental risk factors in inflammatory bowel diseases. Investigating the hygiene hypothesis: A Spanish case-control study. *Scand. J. Gastroenterol.* **2010**, *45*, 1464-1471. [CrossRef] [PubMed]

146. Russel, M.G.; Engels, L.G.; Muris, J.W.; Limonard, C.B.; Volovics, A.; Brummer, R.J.; Stockbrugger, R.W. Modern life' in the epidemiology of inflammatory bowel disease: A case-control study with special emphasis on nutritional factors. *Eur. J. Gastroenterol. Hepatol.* **1998**, *10*, 243-249. [CrossRef] [PubMed]
147. Baron, S.; Turck, D.; Leplat, C.; Merle, V.; Gower-Rousseau, C.; Marti, R.; Yzet, T.; Lerebours, E.; Dupas, J.L.; Debeugny, S.; et al. Environmental risk factors in paediatric inflammatory bowel diseases: A population based case control study. *Gut* **2005**, *54*, 357–363. [CrossRef] [PubMed]

148. Decker, E.; Engelmann, G.; Findeisen, A.; Gerner, P.; Laass, M.; Ney, D.; Posovszky, C.; Hoy, L.; Hornef, M.W. Cesarean delivery is associated with celiac disease but not inflammatory bowel disease in children. *Pediatrics* **2010**, *125*, e1433–e1440. [CrossRef] [PubMed]

149. Hansen, T.S.; Jess, T.; Vind, I.; Elkjaer, M.; Nielsen, M.F.; Gamborg, M.; Munkholm, P. Environmental factors in inflammatory bowel disease: A case-control study based on a Danish inception cohort. *J. Crohns Colitis* **2011**, *5*, 577–584. [CrossRef]

150. Sonntag, B.; Stolze, B.; Heinecke, A.; Luegering, A.; Heidemann, J.; Lebiedz, P.; Rijcken, E.; Kiesel, L.; Domschke, W.; Kucharzik, T.; et al. Preterm birth but not mode of delivery is associated with an increased risk of developing inflammatory bowel disease later in life. *Inflamm. Bowel Dis.* **2007**, *13*, 1385–1390. [CrossRef]

151. Radon, K.; Windstetter, D.; Poluda, A.L.; Mueller, B.; von Mutius, E.; Koletzko, S.; Chronische Autoimmunerkrankungen und Kontakt zu Tieren Study, G. Contact with farm animals in early life and juvenile inflammatory bowel disease: A case-control study. *Pediatrics* **2007**, *120*, 354–361. [CrossRef]

152. Jakobsen, C.; Paerregaard, A.; Munkholm, P.; Wewer, V. Environmental factors and risk of developing paediatric inflammatory bowel disease—A population based study 2007–2009. *J. Crohns Colitis* **2013**, *7*, 79–88. [CrossRef] [PubMed]

153. Castiglione, F.; Diaferia, M.; Morace, F.; Labianca, O.; Meucci, C.; Cuomo, A.; Panarese, A.; Romano, M.; Sorrentini, I.; D’Onofrio, C.; et al. Risk factors for inflammatory bowel diseases according to the “hygiene hypothesis”: A case-control, multi-centre, prospective study in Southern Italy. *J. Crohns Colitis* **2012**, *6*, 324–329. [CrossRef] [PubMed]

154. Whorwell, P.J.; Holdstock, G.; Whorwell, G.M.; Wright, R. Bottle feeding, early gastroenteritis, and inflammatory bowel disease. *Br. Med. J.* **1979**, *1*, 382. [CrossRef] [PubMed]

155. Hlavaty, T.; Toth, J.; Koller, T.; Krajcovicova, A.; Oravcova, S.; Zelinkova, Z.; Huorka, M. Smoking, breastfeeding, physical inactivity, contact with animals, and size of the family influence the risk of inflammatory bowel disease: A Slovak case-control study. *United Eur. Gastroenterol. J.* **2013**, *1*, 109–119. [CrossRef] [PubMed]

156. Klein, I.; Reif, S.; Farbstein, H.; Halak, A.; Gilat, T. Preillness non dietary factors and habits in inflammatory bowel disease. *Ital. J. Gastroenterol. Hepatol.* **1998**, *30*, 247–251.

157. Velosa, M.; Hochner, H.; Yerushalmi, B.; Harel, S.; Friss, C.; Calderon-Margalit, R.; Paltiel, O.; Manor, O.; Balicer, R.D.; Greenfeld, S.; et al. Pre- and Perinatal Factors Predicting Inflammatory Bowel Disease: A Population-Based Study with Fifty Years of Follow-Up. *J. Crohns Colitis* **2022**, *16*, 1397–1404. [CrossRef] [PubMed]

158. Gilat, T.; Hacohen, D.; Lilos, P.; Langman, M.J. Childhood factors in ulcerative colitis and Crohn’s disease. An international cooperative study. *Scand. J. Gastroenterol.* **1987**, *22*, 1009–1024. [CrossRef]

159. Piovani, D.; Danese, S.; Peyrin-Biroulet, L.; Nikolopoulos, G.K.; Lytras, T.; Bonovas, S. Environmental Risk Factors for Inflammatory Bowel Diseases: An Umbrella Review of Meta-analyses. *Gastroenterology* **2019**, *157*, 647–659.e644. [CrossRef]

160. Ananthakrishnan, A.N. Epidemiology and risk factors for IBD. *Nat. Rev. Gastroenterol. Hepatol.* **2015**, *12*, 205–217. [CrossRef]

161. Adolph, T.E.; Zhang, J. Diet fuelling inflammatory bowel diseases: Preclinical and clinical concepts. *Gut* **2022**, *71*, 2574–2586. [CrossRef]

162. Van der Sloot, K.W.J.; Amini, M.; Peters, V.; Dijkstra, G.; Alizadeh, B.Z. Inflammatory Bowel Diseases: Review of Known Environmental Protective and Risk Factors Involved. *Inflamm. Bowel Dis.* **2017**, *23*, 1499–1509. [CrossRef]

163. Raygoza Garay, J.A.; Turpin, W.; Lee, S.H.; Smith, M.I.; Goethel, A.; Griffiths, A.M.; Moayyedi, P.; Espin-Garcia, O.; Abreu, M.; Aumais, G.L.; et al. Gut Microbiome Composition Is Associated with Future Onset of Crohn’s Disease in Healthy First-Degree Relatives. *Gastroenterology* **2023**, *165*, 670–681. [CrossRef] [PubMed]

164. Gilliland, A.; Chan, J.; De Wolfe, T.J.; Yang, H.; Vallance, B.A. Pathobionts in Inflammatory Bowel Disease: Origins, Underlying Mechanisms, and Implications for Clinical Care. *Gastroenterology* **2023**, in press. [CrossRef] [PubMed]

165. Barone, M.; Ramayo-Caldas, Y.; Estelle, J.; Tambosco, K.; Chadi, S.; Maillard, F.; Gallopin, M.; Planchais, J.; Chain, F.; Kropp, C.; et al. Gut barrier-microbiota imbalances in early life lead to higher sensitivity to inflammation in a murine model of C-section delivery. *Microbiome* **2023**, *11*, 140. [CrossRef]

166. Torres, J.; Hu, J.; Seki, A.; Eisele, C.; Nair, N.; Huang, R.; Tarassishin, L.; Jharap, B.; Cote-Daigneault, J.; Mao, Q.; et al. Infants born to mothers with IBD present with altered gut microbiome that transfers abnormalities of the adaptive immune system to germ-free mice. *Gut* **2020**, *69*, 42–51. [CrossRef] [PubMed]

167. Kim, E.S.; Tarassishin, L.; Eisele, C.; Barre, A.; Nair, N.; Rendon, A.; Hawkins, K.; Debebe, A.; White, S.; Thjomoe, A.; et al. Longitudinal Changes in Fecal Calprotectin Levels among Pregnant Women with and without Inflammatory Bowel Disease and Their Babies. *Gastroenterology* **2021**, *160*, 1118–1130.e1113. [CrossRef]

168. Quin, C.; Gibson, D.L. Human behavior, not race or geography, is the strongest predictor of microbial succession in the gut bacteriome of infants. *Gut Microbes* **2020**, *11*, 1143–1171. [CrossRef]

169. Voreades, N.; Kozil, A.; Weir, T.L. Diet and the development of the human intestinal microbiome. *Front. Microbiol.* **2014**, *5*, 494. [CrossRef]

170. Roswall, J.; Olsson, L.M.; Kovatcheva-Datchary, P.; Nilsson, S.; Tremaroli, V.; Simon, M.C.; Kiilerich, P.; Akrami, R.; Kramer, M.; Uhlen, M.; et al. Developmental trajectory of the healthy human gut microbiota during the first 5 years of life. *Cell Host Microbe* **2021**, *29*, 765–776.e763. [CrossRef]
147. Baron, S.; Turck, D.; Leplat, C.; Merle, V.; Gower-Rousseau, C.; Marti, R.; Yzet, T.; Lerebours, E.; Dupas, J.L.; Debeugny, S.; et al. Environmental risk factors in paediatric inflammatory bowel diseases: A population based case control study. *Gut* **2005**, *54*, 357–363. [CrossRef] [PubMed]

148. Decker, E.; Engelmann, G.; Findeisen, A.; Gerner, P.; Laass, M.; Ney, D.; Posovszky, C.; Hoy, L.; Hornef, M.W. Cesarean delivery is associated with celiac disease but not inflammatory bowel disease in children. *Pediatrics* **2010**, *125*, e1433–e1440. [CrossRef] [PubMed]

149. Hansen, T.S.; Jess, T.; Vind, I.; Elkjaer, M.; Nielsen, M.F.; Gamborg, M.; Munkholm, P. Environmental factors in inflammatory bowel disease: A case-control study based on a Danish inception cohort. *J. Crohns Colitis* **2011**, *5*, 577–584. [CrossRef]

150. Sonntag, B.; Stolze, B.; Heinecke, A.; Luegering, A.; Heidemann, J.; Lebiedz, P.; Rijcken, E.; Kiesel, L.; Domschke, W.; Kucharzik, T.; et al. Preterm birth but not mode of delivery is associated with an increased risk of developing inflammatory bowel disease later in life. *Inflamm. Bowel Dis.* **2007**, *13*, 1385–1390. [CrossRef]

151. Radon, K.; Windstetter, D.; Poluda, A.L.; Mueller, B.; von Mutius, E.; Koletzko, S.; Chronische Autoimmunerkrankungen und Kontakt zu Tieren Study, G. Contact with farm animals in early life and juvenile inflammatory bowel disease: A case-control study. *Pediatrics* **2007**, *120*, 354–361. [CrossRef]

152. Jakobsen, C.; Paerregaard, A.; Munkholm, P.; Wewer, V. Environmental factors and risk of developing paediatric inflammatory bowel disease—A population based study 2007–2009. *J. Crohns Colitis* **2013**, *7*, 79–88. [CrossRef] [PubMed]

153. Castiglione, F.; Diaferia, M.; Morace, F.; Labianca, O.; Meucci, C.; Cuomo, A.; Panarese, A.; Romano, M.; Sorrentini, I.; D’Onofrio, C.; et al. Risk factors for inflammatory bowel diseases according to the “hygiene hypothesis”: A case-control, multi-centre, prospective study in Southern Italy. *J. Crohns Colitis* **2012**, *6*, 324–329. [CrossRef] [PubMed]

154. Whorwell, P.J.; Holdstock, G.; Whorwell, G.M.; Wright, R. Bottle feeding, early gastroenteritis, and inflammatory bowel disease. *Br. Med. J.* **1979**, *1*, 382. [CrossRef] [PubMed]

155. Hlavaty, T.; Toth, J.; Koller, T.; Krajcovicova, A.; Oravcova, S.; Zelinkova, Z.; Huorka, M. Smoking, breastfeeding, physical inactivity, contact with animals, and size of the family influence the risk of inflammatory bowel disease: A Slovak case-control study. *United Eur. Gastroenterol. J.* **2013**, *1*, 109–119. [CrossRef] [PubMed]

156. Klein, I.; Reif, S.; Farbstein, H.; Halak, A.; Gilat, T. Preillness non dietary factors and habits in inflammatory bowel disease. *Ital. J. Gastroenterol. Hepatol.* **1998**, *30*, 247–251.

157. Velosa, M.; Hochner, H.; Yerushalmi, B.; Harel, S.; Friss, C.; Calderon-Margalit, R.; Paltiel, O.; Manor, O.; Balicer, R.D.; Greenfeld, S.; et al. Pre- and Perinatal Factors Predicting Inflammatory Bowel Disease: A Population-Based Study with Fifty Years of Follow-Up. *J. Crohns Colitis* **2022**, *16*, 1397–1404. [CrossRef] [PubMed]

158. Gilat, T.; Hacohen, D.; Lilos, P.; Langman, M.J. Childhood factors in ulcerative colitis and Crohn’s disease. An international cooperative study. *Scand. J. Gastroenterol.* **1987**, *22*, 1009–1024. [CrossRef]

159. Piovani, D.; Danese, S.; Peyrin-Biroulet, L.; Nikolopoulos, G.K.; Lytras, T.; Bonovas, S. Environmental Risk Factors for Inflammatory Bowel Diseases: An Umbrella Review of Meta-analyses. *Gastroenterology* **2019**, *157*, 647–659.e644. [CrossRef]

160. Ananthakrishnan, A.N. Epidemiology and risk factors for IBD. *Nat. Rev. Gastroenterol. Hepatol.* **2015**, *12*, 205–217. [CrossRef]

161. Adolph, T.E.; Zhang, J. Diet fuelling inflammatory bowel diseases: Preclinical and clinical concepts. *Gut* **2022**, *71*, 2574–2586. [CrossRef]

162. Van der Sloot, K.W.J.; Amini, M.; Peters, V.; Dijkstra, G.; Alizadeh, B.Z. Inflammatory Bowel Diseases: Review of Known Environmental Protective and Risk Factors Involved. *Inflamm. Bowel Dis.* **2017**, *23*, 1499–1509. [CrossRef]

163. Raygoza Garay, J.A.; Turpin, W.; Lee, S.H.; Smith, M.I.; Goethel, A.; Griffiths, A.M.; Moayyedi, P.; Espin-Garcia, O.; Abreu, M.; Aumais, G.L.; et al. Gut Microbiome Composition Is Associated with Future Onset of Crohn’s Disease in Healthy First-Degree Relatives. *Gastroenterology* **2023**, *165*, 670–681. [CrossRef] [PubMed]

164. Gilliland, A.; Chan, J.; De Wolfe, T.J.; Yang, H.; Vallance, B.A. Pathobionts in Inflammatory Bowel Disease: Origins, Underlying Mechanisms, and Implications for Clinical Care. *Gastroenterology* **2023**, in press. [CrossRef] [PubMed]

165. Barone, M.; Ramayo-Caldas, Y.; Estelle, J.; Tambosco, K.; Chadi, S.; Maillard, F.; Gallopin, M.; Planchais, J.; Chain, F.; Kropp, C.; et al. Gut barrier-microbiota imbalances in early life lead to higher sensitivity to inflammation in a murine model of C-section delivery. *Microbiome* **2023**, *11*, 140. [CrossRef]

166. Torres, J.; Hu, J.; Seki, A.; Eisele, C.; Nair, N.; Huang, R.; Tarassishin, L.; Jharap, B.; Cote-Daigneault, J.; Mao, Q.; et al. Infants born to mothers with IBD present with altered gut microbiome that transfers abnormalities of the adaptive immune system to germ-free mice. *Gut* **2020**, *69*, 42–51. [CrossRef] [PubMed]

167. Kim, E.S.; Tarassishin, L.; Eisele, C.; Barre, A.; Nair, N.; Rendon, A.; Hawkins, K.; Debebe, A.; White, S.; Thjomoe, A.; et al. Longitudinal Changes in Fecal Calprotectin Levels among Pregnant Women with and without Inflammatory Bowel Disease and Their Babies. *Gastroenterology* **2021**, *160*, 1118–1130.e1113. [CrossRef]

168. Quin, C.; Gibson, D.L. Human behavior, not race or geography, is the strongest predictor of microbial succession in the gut bacteriome of infants. *Gut Microbes* **2020**, *11*, 1143–1171. [CrossRef]

169. Voreades, N.; Kozil, A.; Weir, T.L. Diet and the development of the human intestinal microbiome. *Front. Microbiol.* **2014**, *5*, 494. [CrossRef]

170. Roswall, J.; Olsson, L.M.; Kovatcheva-Datchary, P.; Nilsson, S.; Tremaroli, V.; Simon, M.C.; Kiilerich, P.; Akrami, R.; Kramer, M.; Uhlen, M.; et al. Developmental trajectory of the healthy human gut microbiota during the first 5 years of life. *Cell Host Microbe* **2021**, *29*, 765–776.e763. [CrossRef]
171. Palmela, C.; Chevarin, C.; Xu, Z.; Torres, J.; Sevrin, G.; Hirten, R.; Barnich, N.; Ng, S.C.; Colombel, J.F. Adherent-invasive *Escherichia coli* in inflammatory bowel disease. *Gut* **2018**, *67*, 574–587. [CrossRef]

172. Conte, M.P.; Longhi, C.; Marazzato, M.; Conte, A.L.; Aleandri, M.; Lepanto, M.S.; Zagaglia, C.; Nicoletti, M.; Aloi, M.; Totino, V.; et al. Adherent-invasive *Escherichia coli* (AIEC) in pediatric Crohn's disease patients: Phenotypic and genetic pathogenic features. *BMC Res. Notes* **2014**, *7*, 748. [CrossRef] [PubMed]

173. Wymore Brand, M.; Proctor, A.L.; Hostetter, J.M.; Zhou, N.; Friedberg, I.; Jergens, A.E.; Phillips, G.J.; Wannemuehler, M.J. Vertical transmission of attaching and invasive *E. coli* from the dam to neonatal mice predisposes to more severe colitis following exposure to a colitic insult later in life. *PLoS ONE* **2022**, *17*, e0266005. [CrossRef] [PubMed]

174. Jost, T.; Lacroix, C.; Braegger, C.P.; Rochat, F.; Chassard, C. Vertical mother-neonate transfer of maternal gut bacteria via breastfeeding. *Environ. Microbiol.* **2014**, *16*, 2891–2904. [CrossRef] [PubMed]

175. Makino, H.; Martin, R.; Ishikawa, E.; Gawad, A.; Kubota, H.; Sakai, T.; Oishi, K.; Tanaka, R.; Ben-Amor, K.; Knol, J.; et al. Multilocus sequence typing of bifidobacterial strains from infant's faeces and human milk: Are bifidobacteria being sustainably shared during breastfeeding? *Benef. Microbes* **2015**, *6*, 563–572. [CrossRef]

176. Li, H.; Ma, L.; Zhang, L.; Liu, N.; Li, Z.; Zhang, F.; Liu, X.; Ma, X. Dietary Inulin Regulated Gut Microbiota and Improved Neonatal Health in a Pregnant Sow Model. *Front. Nutr.* **2021**, *8*, 716723. [CrossRef]

177. Chatelais, L.; Jamin, A.; Gras-Le Guen, C.; Lalles, J.P.; Le Huerou-Luron, I.; Boudry, G. The level of protein in milk formula modifies ileal sensitivity to LPS later in life in a piglet model. *PLoS ONE* **2011**, *6*, e19594. [CrossRef] [PubMed]

178. Boudry, G.; Jamin, A.; Chatelais, L.; Gras-Le Guen, C.; Michel, C.; Le Huerou-Luron, I. Dietary protein excess during neonatal life alters colonic microbiota and mucosal response to inflammatory mediators later in life in female pigs. *J. Nutr.* **2013**, *143*, 1225–1232. [CrossRef]

179. Reddy, K.V.; Naidu, K.A. Maternal and neonatal dietary intake of balanced n-6/n-3 fatty acids modulates experimental colitis in young adult rats. *Eur. J. Nutr.* **2016**, *55*, 1875–1890. [CrossRef]

180. Le, A.; Mantel, M.; Marchix, J.; Bodinier, M.; Jan, G.; Rolli-Derkinderen, M. Inflammatory bowel disease therapeutic strategies by modulation of the microbiota: How and when to introduce pre-, pro-, syn-, or postbiotics? *Am. J. Physiol. Gastrointest. Liver Physiol.* **2022**, *323*, G523–G553. [CrossRef]

181. Haskey, N.; Dahl, W.J. Synbiotic therapy: A promising new adjunctive therapy for ulcerative colitis. *Nutr. Rev.* **2006**, *64*, 132–138. [CrossRef]

182. Savino, F.; Cordisco, L.; Tarasco, V.; Palumeri, E.; Calabrese, R.; Oggero, R.; Roos, S.; Matteuzzi, D. Lactobacillus reuteri DSM 17938 in infantile colic: A randomized, double-blind, placebo-controlled trial. *Pediatrics* **2010**, *126*, e526–e533. [CrossRef]

183. Guo, F.; Cai, D.; Li, Y.; Gu, H.; Qu, H.; Zong, Q.; Bao, W.; Chen, A.; Liu, H.Y. How Early-Life Gut Microbiota Alteration Sets Trajectories for Health and Inflammatory Bowel Disease? *Front. Nutr.* **2021**, *8*, 690073. [CrossRef]

184. Al Nabhani, Z.; Dulauroy, S.; Marques, R.; Cousu, C.; Al Bounny, S.; Dejardin, F.; Sparwasser, T.; Berard, M.; Cerf-Bensussan, N.; Eberl, G. A Weaning Reaction to Microbiota Is Required for Resistance to Immunopathologies in the Adult. *Immunity* **2019**, *50*, 1276–1288.e1275. [CrossRef] [PubMed]

185. Stiemsma, L.T.; Michels, K.B. The Role of the Microbiome in the Developmental Origins of Health and Disease. *Pediatrics* **2018**, *141*, e20172437. [CrossRef] [PubMed]

186. Kronman, M.P.; Zaoutis, T.E.; Haynes, K.; Feng, R.; Coffin, S.E. Antibiotic exposure and IBD development among children: A population-based cohort study. *Pediatrics* **2012**, *130*, e794–e803. [CrossRef] [PubMed]

187. Theochari, N.A.; Stefanopoulos, A.; Mylonas, K.S.; Economopoulos, K.P. Antibiotics exposure and risk of inflammatory bowel disease: A systematic review. *Scand. J. Gastroenterol.* **2018**, *53*, 1–7. [CrossRef] [PubMed]

188. Benchimol, E.I.; Kaplan, G.G.; Otley, A.R.; Nguyen, G.C.; Underwood, F.E.; Guttmann, A.; Jones, J.L.; Potter, B.K.; Catley, C.A.; Nugent, Z.J.; et al. Rural and Urban Residence During Early Life is Associated with Risk of Inflammatory Bowel Disease: A Population-Based Inception and Birth Cohort Study. *Am. J. Gastroenterol.* **2017**, *112*, 1412–1422. [CrossRef]

189. Meng, X.; Dunsmore, G.; Koleva, P.; Elloumi, Y.; Wu, R.Y.; Sutton, R.T.; Ambrosio, L.; Hotte, N.; Nguyen, V.; Madsen, K.L.; et al. The Profile of Human Milk Metabolome, Cytokines, and Antibodies in Inflammatory Bowel Diseases Versus Healthy Mothers, and Potential Impact on the Newborn. *J. Crohns Colitis* **2019**, *13*, 431–441. [CrossRef]

**Disclaimer/Publisher's Note:** The statements, opinions and data contained in all publications are solely those of the individual author(s) and contributor(s) and not of MDPI and/or the editor(s). MDPI and/or the editor(s) disclaim responsibility for any injury to people or property resulting from any ideas, methods, instructions or products referred to in the content.
171. Palmela, C.; Chevarin, C.; Xu, Z.; Torres, J.; Sevrin, G.; Hirten, R.; Barnich, N.; Ng, S.C.; Colombel, J.F. Adherent-invasive *Escherichia coli* in inflammatory bowel disease. *Gut* **2018**, *67*, 574–587. [CrossRef]

172. Conte, M.P.; Longhi, C.; Marazzato, M.; Conte, A.L.; Aleandri, M.; Lepanto, M.S.; Zagaglia, C.; Nicoletti, M.; Aloi, M.; Totino, V.; et al. Adherent-invasive *Escherichia coli* (AIEC) in pediatric Crohn's disease patients: Phenotypic and genetic pathogenic features. *BMC Res. Notes* **2014**, *7*, 748. [CrossRef] [PubMed]

173. Wymore Brand, M.; Proctor, A.L.; Hostetter, J.M.; Zhou, N.; Friedberg, I.; Jergens, A.E.; Phillips, G.J.; Wannemuehler, M.J. Vertical transmission of attaching and invasive *E. coli* from the dam to neonatal mice predisposes to more severe colitis following exposure to a colitic insult later in life. *PLoS ONE* **2022**, *17*, e0266005. [CrossRef] [PubMed]

174. Jost, T.; Lacroix, C.; Braegger, C.P.; Rochat, F.; Chassard, C. Vertical mother-neonate transfer of maternal gut bacteria via breastfeeding. *Environ. Microbiol.* **2014**, *16*, 2891–2904. [CrossRef] [PubMed]

175. Makino, H.; Martin, R.; Ishikawa, E.; Gawad, A.; Kubota, H.; Sakai, T.; Oishi, K.; Tanaka, R.; Ben-Amor, K.; Knol, J.; et al. Multilocus sequence typing of bifidobacterial strains from infant's faeces and human milk: Are bifidobacteria being sustainably shared during breastfeeding? *Benef. Microbes* **2015**, *6*, 563–572. [CrossRef]

176. Li, H.; Ma, L.; Zhang, L.; Liu, N.; Li, Z.; Zhang, F.; Liu, X.; Ma, X. Dietary Inulin Regulated Gut Microbiota and Improved Neonatal Health in a Pregnant Sow Model. *Front. Nutr.* **2021**, *8*, 716723. [CrossRef]

177. Chatelais, L.; Jamin, A.; Gras-Le Guen, C.; Lalles, J.P.; Le Huerou-Luron, I.; Boudry, G. The level of protein in milk formula modifies ileal sensitivity to LPS later in life in a piglet model. *PLoS ONE* **2011**, *6*, e19594. [CrossRef] [PubMed]

178. Boudry, G.; Jamin, A.; Chatelais, L.; Gras-Le Guen, C.; Michel, C.; Le Huerou-Luron, I. Dietary protein excess during neonatal life alters colonic microbiota and mucosal response to inflammatory mediators later in life in female pigs. *J. Nutr.* **2013**, *143*, 1225–1232. [CrossRef]

179. Reddy, K.V.; Naidu, K.A. Maternal and neonatal dietary intake of balanced n-6/n-3 fatty acids modulates experimental colitis in young adult rats. *Eur. J. Nutr.* **2016**, *55*, 1875–1890. [CrossRef]

180. Le, A.; Mantel, M.; Marchix, J.; Bodinier, M.; Jan, G.; Rolli-Derkinderen, M. Inflammatory bowel disease therapeutic strategies by modulation of the microbiota: How and when to introduce pre-, pro-, syn-, or postbiotics? *Am. J. Physiol. Gastrointest. Liver Physiol.* **2022**, *323*, G523–G553. [CrossRef]

181. Haskey, N.; Dahl, W.J. Synbiotic therapy: A promising new adjunctive therapy for ulcerative colitis. *Nutr. Rev.* **2006**, *64*, 132–138. [CrossRef]

182. Savino, F.; Cordisco, L.; Tarasco, V.; Palumeri, E.; Calabrese, R.; Oggero, R.; Roos, S.; Matteuzzi, D. Lactobacillus reuteri DSM 17938 in infantile colic: A randomized, double-blind, placebo-controlled trial. *Pediatrics* **2010**, *126*, e526–e533. [CrossRef]

183. Guo, F.; Cai, D.; Li, Y.; Gu, H.; Qu, H.; Zong, Q.; Bao, W.; Chen, A.; Liu, H.Y. How Early-Life Gut Microbiota Alteration Sets Trajectories for Health and Inflammatory Bowel Disease? *Front. Nutr.* **2021**, *8*, 690073. [CrossRef]

184. Al Nabhani, Z.; Dulauroy, S.; Marques, R.; Cousu, C.; Al Bounny, S.; Dejardin, F.; Sparwasser, T.; Berard, M.; Cerf-Bensussan, N.; Eberl, G. A Weaning Reaction to Microbiota Is Required for Resistance to Immunopathologies in the Adult. *Immunity* **2019**, *50*, 1276–1288.e1275. [CrossRef] [PubMed]

185. Stiemsma, L.T.; Michels, K.B. The Role of the Microbiome in the Developmental Origins of Health and Disease. *Pediatrics* **2018**, *141*, e20172437. [CrossRef] [PubMed]

186. Kronman, M.P.; Zaoutis, T.E.; Haynes, K.; Feng, R.; Coffin, S.E. Antibiotic exposure and IBD development among children: A population-based cohort study. *Pediatrics* **2012**, *130*, e794–e803. [CrossRef] [PubMed]

187. Theochari, N.A.; Stefanopoulos, A.; Mylonas, K.S.; Economopoulos, K.P. Antibiotics exposure and risk of inflammatory bowel disease: A systematic review. *Scand. J. Gastroenterol.* **2018**, *53*, 1–7. [CrossRef] [PubMed]

188. Benchimol, E.I.; Kaplan, G.G.; Otley, A.R.; Nguyen, G.C.; Underwood, F.E.; Guttmann, A.; Jones, J.L.; Potter, B.K.; Catley, C.A.; Nugent, Z.J.; et al. Rural and Urban Residence During Early Life is Associated with Risk of Inflammatory Bowel Disease: A Population-Based Inception and Birth Cohort Study. *Am. J. Gastroenterol.* **2017**, *112*, 1412–1422. [CrossRef]

189. Meng, X.; Dunsmore, G.; Koleva, P.; Elloumi, Y.; Wu, R.Y.; Sutton, R.T.; Ambrosio, L.; Hotte, N.; Nguyen, V.; Madsen, K.L.; et al. The Profile of Human Milk Metabolome, Cytokines, and Antibodies in Inflammatory Bowel Diseases Versus Healthy Mothers, and Potential Impact on the Newborn. *J. Crohns Colitis* **2019**, *13*, 431–441. [CrossRef]

**Disclaimer/Publisher's Note:** The statements, opinions and data contained in all publications are solely those of the individual author(s) and contributor(s) and not of MDPI and/or the editor(s). MDPI and/or the editor(s) disclaim responsibility for any injury to people or property resulting from any ideas, methods, instructions or products referred to in the content.