Principles in Microbiome Engineering

87 87 Craig, W.J. (2009). Health effects of vegan diets. Am. J. Clin. Nutr. 89 (5): 1627s–1633s.

88 88 Tomova, A., Bukovsky, I., Rembert, E., et al. (2019). The effects of vegetarian and vegan diets on gut microbiota. Front. Nutr. 6: 47.

89 89 Parada Venegas, D., Fuente, M.K.D., Landskron, G., et al. (2019). Short chain fatty acids (SCFAs)‐mediated gut epithelial and immune regulation and its relevance for inflammatory bowel diseases. Front. Immunol. 10: 277.

90 90 Glick‐Bauer, M. and Yeh, M.‐C. (2014). The health advantage of a vegan diet: exploring the gut microbiota connection. Nutrients 6 (11): 4822–4838.

91 91 Liu, Z., Lin, X.C., Huang, G.W., et al. (2014). Prebiotic effects of almonds and almond skins on intestinal microbiota in healthy adult humans. Anaerobe 26: 1–6.

92 92 Walker, A.W., Ince, J., Duncan, S.H., Webster, L.M., et al. (2011). Dominant and diet‐responsive groups of bacteria within the human colonic microbiota. ISME J. 5 (2): 220–230.

93 93 Hildebrandt, M.A., Hoffmann, C., Sherrill‐Mix, S.A., et al. (2009). High‐fat diet determines the composition of the murine gut microbiome independently of obesity. Gastroenterology 137 (5): 1716–24.e1‐2.

94 94 Zhang, M. and Yang, X.‐J. (2016). Effects of a high fat diet on intestinal microbiota and gastrointestinal diseases. World J. Gastroenterol. 22 (40): 8905–8909.

95 95 Fava, F., Gitau, R., Griffin, B.A., et al. (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 (2): 216–223.

96 96 Wu, G.D., Chen, J., Hoffmann, C., et al. (2011). Linking long‐term dietary patterns with gut microbial enterotypes. Science (New York, NY) 334 (6052): 105–108.

97 97 Cani, P.D., Bibiloni, R., Knauf, C., et al. (2008). Changes in gut microbiota control metabolic endotoxemia‐induced inflammation in high‐fat diet–induced obesity and diabetes in mice. Diabetes 57 (6): 1470–1481.

98 98 Lecomte, V., Kaakoush, N.O., Maloney, C.A., et al. (2015). Changes in gut microbiota in rats fed a high fat diet correlate with obesity‐associated metabolic parameters. PLoS One 10 (5): e0126931.

99 99 Urwin, H.J., Miles, E.A., Noakes, P.S., et al. (2014). Effect of salmon consumption during pregnancy on maternal and infant faecal microbiota, secretory IgA and calprotectin. Br. J. Nutr. 111 (5): 773–784.

100 100 Chen, J., He, X., and Huang, J. (2014). Diet effects in gut microbiome and obesity. J. Food Sci. 79 (4): R442–R451.

101 101 LaMagna, M. (2018). This map shows where the wealthy — and not so wealthy — of the world live. See how much citizens of the wealthiest countries have, compared with the least November 13, 2018. https://www.marketwatch.com/story/this-map-shows-where-the-wealthy-and-not-so-wealthy-of-the-world-live-2018-11-13(accessed 14 December 2021).

102 102 McLeod, S. (2020). Maslow's hierarchy of needs. Simply Psychology. https://www.simplypsychology.org/maslow.html(accessed 14 December 2021).

103 103 Saravia, L., González‐Zapata, L.I., Rendo‐Urteaga, T., et al. (2018). Development of a food frequency questionnaire for assessing dietary intake in children and adolescents in South America. Obesity (Silver Spring) 26 (Suppl. 1): S31–s40.

104 104 Kolady, D.E., Kattelmann, K., and Scaria, J. (2019). Effects of health‐related claims on millennials' willingness to pay for probiotics in the U.S.: implications for regulation. J. Funct. Foods 60: 103434.

105 105 Engstrand, L. and Lindberg, M. (2013). Helicobacter pylori and the gastric microbiota. Best Pract. Res. Clin. Gastroenterol. 27 (1): 39–45.

106 106 Swidsinski, A., Sydora, B.C., Doerffel, Y., et al. (2007). Viscosity gradient within the mucus layer determines the mucosal barrier function and the spatial organization of the intestinal microbiota. Inflamm. Bowel Dis. 13 (8): 963–970.

107 107 Lim, M.Y., Yoon, H.S., Rho, M., et al. (2016). Analysis of the association between host genetics, smoking, and sputum microbiota in healthy humans. Sci. Rep. 6: 23745.

108 108 Vallès, Y., Inman, C.K., Peters, B.A., et al. (2018). Types of tobacco consumption and the oral microbiome in the United Arab Emirates Healthy Future (UAEHFS) pilot study. Sci. Rep. 8 (1): 11327.

109 109 Capurso, G. and Lahner, E. (2017). The interaction between smoking, alcohol and the gut microbiome. Best Pract. Res. Clin. Gastroenterol. 31 (5): 579–588.

110 110 Koenig, J.E., Spor, A., Scalfone, N., et al. (2011). Succession of microbial consortia in the developing infant gut microbiome. Proc. Natl. Acad. Sci. U.S.A. 108 (Suppl. 1): 4578–4585.

111 111 Biagi, E., Nylund, L., Candela, M., et al. (2010). Through ageing, and beyond: gut microbiota and inflammatory status in seniors and centenarians. PLoS One 5 (5): e10667.

112 112 Biasucci, G., Benenati, B., Morelli, L., et al. (2008). Cesarean delivery may affect the early biodiversity of intestinal bacteria. J. Nutr. 138 (9): 1796s–1800s.

113 113 Biasucci, G., Rubini, M., Riboni, S., et al. (2010). Mode of delivery affects the bacterial community in the newborn gut. Early Hum. Dev. 86 (Suppl. 1): 13–15.

114 114 Dominguez‐Bello, M.G., Costello, E.K., Contreras, M., et al. (2010). Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns. PNAS. 107(26): 11971‐5.

115 115 Schwartz, S., Friedberg, I., Ivanov, I.V., et al. (2012). A metagenomic study of diet‐dependent interaction between gut microbiota and host in infants reveals differences in immune response. Genome Biol. 13 (4): r32.

116 116 Tanaka, M. and Nakayama, J. (2017). Development of the gut microbiota in infancy and its impact on health in later life. Allergol. Int. 66 (4): 515–522.

117 117 Cabrera‐Rubio, R., Collado, M.C., Laitinen, K., et al. (2012). The human milk microbiome changes over lactation and is shaped by maternal weight and mode of delivery. Am. J. Clin. Nutr. 96 (3): 544–551.

118 118 Hunt, K.M., Foster, J.A., Forney, L.J., et al. (2011). Characterization of the diversity and temporal stability of bacterial communities in human milk. PLoS One 6 (6): e21313.

119 119 Zivkovic, A.M., Germana, J.B., Lebrillaa, C.B., and Mills, D.A. (2010). Human milk glycobiome and its impact on the infant gastrointestinal microbiota. PNAS 108 (Suppl. 1): 4653–4658.

120 120 Hopkins, M.J., Macfarlane, G.T., Furrie, E., et al. (2005). Characterisation of intestinal bacteria in infant stools using real‐time PCR and northern hybridisation analyses. FEMS Microbiol. Ecol. 54 (1): 77–85.

121 121 Penders, J., Vink, C., Driessen, C., et al. (2005). Quantification of Bifidobacterium spp., Escherichia coli and Clostridium difficile in faecal samples of breast‐fed and formula‐fed infants by real‐time PCR. FEMS Microbiol. Lett. 243 (1): 141–147.

122 122 Derrien, M., Alvarez, A.S., and de Vos, W.M. (2019). The gut microbiota in the first decade of life. Trends Microbiol. 27 (12): 997–1010.

123 123 Fallani, M., Young, D., Scott, J., et al. (2010). Intestinal microbiota of 6‐week‐old infants across Europe: geographic influence beyond delivery mode, breast‐feeding, and antibiotics. J. Pediatr. Gastroenterol. Nutr. 51 (1): 77–84.

124 124 Matsuyama, M., Morrison, M., Cao, K.‐A.L., et al. (2019). Dietary intake influences gut microbiota development of healthy Australian children from the age of one to two years. Sci. Rep. 9 (1): 12476.

125 125 Rinninella, E., Raoul, P., Cintoni, M., et al. (2019). What is the healthy gut microbiota composition? A changing ecosystem across age, environment, diet, and diseases. Microorganisms Jan 10; 7 (1): 14.

126 126 Hollister, E.B., Riehle, K., Luna, R.A., et al. (2015). Structure and function of the healthy pre‐adolescent pediatric gut microbiome. Microbiome Aug 26; 3: 36.