159 (4): 789–799.11 11 Grice, E.A., Kong, H.H., Conlan, S., et al. (2009). Topographical and temporal diversity of the human skin microbiome. Science 324 (5931): 1190–1192.
12 12 Hilt, E.E., McKinley, K., Pearce, M.M., et al. (2014). Urine is not sterile: use of enhanced urine culture techniques to detect resident bacterial flora in the adult female bladder. J. Clin. Microbiol. 52 (3): 871–876.
13 13 Mameli, C., Cattaneo, C., Panelli, S., et al. (2019). Taste perception and oral microbiota are associated with obesity in children and adolescents. PLoS One 14 (9): e0221656.
14 14 Stewart, C.J., Ajami, N.J., O'Brien, J.L., et al. (2018). Temporal development of the gut microbiome in early childhood from the TEDDY study. Nature 562 (7728): 583–588.
15 15 Vatanen, T., Franzosa, E.A., Schwager, R., et al. (2018). The human gut microbiome in early‐onset type 1 diabetes from the TEDDY study. Nature 562 (7728): 589–594.
16 16 Ferretti, P., Pasolli, E., Tett, A., et al. (2018). Mother‐to‐infant microbial transmission from different body sites shapes the developing infant gut microbiome. Cell Host Microbe 24 (1): 133.e5–145.e5.
17 17 Fox, C. and Eichelberger, K.Y. (2015). Maternal microbiome and pregnancy outcomes. Fertil. Steril. 104 (6): 1358–1363.
18 18 Bik, E.M., Eckburg, P.B., Gill, S.R., et al. (2006). Molecular analysis of the bacterial microbiota in the human stomach. Proc. Natl. Acad. Sci. U.S.A. 103 (3): 732–737.
19 19 Andersson, A.F., Lindberg, M., Jakobsson, H., et al. (2008). Comparative analysis of human gut microbiota by barcoded pyrosequencing. PLoS One 3 (7): e2836.
20 20 Dorer, M.S., Talarico, S., and Salama, N.R. (2009). Helicobacter pylori's unconventional role in health and disease. PLoS Pathog. 5 (10): e1000544.
21 21 Booijink, C.C., El‐Aidy, S., Rajilić‐Stojanović, M., et al. (2010). High temporal and inter‐individual variation detected in the human ileal microbiota. Environ. Microbiol. 12 (12): 3213–3227.
22 22 Zoetendal, E.G., Raes, J., van den Bogert, B., et al. (2012). The human small intestinal microbiota is driven by rapid uptake and conversion of simple carbohydrates. ISME J. 6 (7): 1415–1426.
23 23 Collado, M.C., Donat, E., Ribes‐Koninckx, C., et al. (2009). Specific duodenal and faecal bacterial groups associated with paediatric coeliac disease. J. Clin. Pathol. 62 (3): 264–269.
24 24 Willing, B., Halfvarson, J., Dicksved, J., et al. (2009). Twin studies reveal specific imbalances in the mucosa‐associated microbiota of patients with ileal Crohn's disease. Inflamm. Bowel Dis. 15 (5): 653–660.
25 25 Nam, Y.D., Jung, M.J., Roh, S.W., et al. (2011). Comparative analysis of Korean human gut microbiota by barcoded pyrosequencing. PLoS One 6 (7): e22109.
26 26 Flint, H.J., Duncan, S.H., Scott, K.P., and Louis, P. (2007). Interactions and competition within the microbial community of the human colon: links between diet and health. Environ. Microbiol. 9 (5): 1101–1111.
27 27 Arumugam, M., Raes, J., Pelletier, E., et al. (2011). Enterotypes of the human gut microbiome. Nature 473 (7346): 174–180.
28 28 Grice, E.A. and Segre, J.A. (2011). The skin microbiome. Nat. Rev. Microbiol. 9 (4): 244–253.
29 29 Nakatsuji, T., Chiang, H., Jiang, S.B., et al. (2013). The microbiome extends to subepidermal compartments of normal skin. Nat. Commun. 4: 1431.
30 30 Selhub, E.M., Logan, A.C., and Bested, A.C. (2014). Fermented foods, microbiota, and mental health: ancient practice meets nutritional psychiatry. J. Physiol. Anthropol. 33 (1): 2.
31 31 Bassis, C.M., Tang, A.L., Young, V.B., and Pynnonen, M.A., et al. (2014). The nasal cavity microbiota of healthy adults. Microbiome 2: 27.
32 32 Ditz, B., Christenson, S., Rossen, J., et al. (2020). Sputum microbiome profiling in COPD: beyond singular pathogen detection. Thorax 75 (4): 338–344.
33 33 Segal, L.N., Alekseyenko, A.V., Clemente, J.C., et al. (2013). Enrichment of lung microbiome with supraglottic taxa is associated with increased pulmonary inflammation. Microbiome 1 (1): 19.
34 34 Charlson, E.S., Bittinger, K., Haas, A.R., et al. (2011). Topographical continuity of bacterial populations in the healthy human respiratory tract. Am. J. Respir. Crit. Care Med. 184 (8): 957–963.
35 35 Siddiqui, H., Lagersen, K., Nederbragt, A.J., et al. (2012). Alterations of microbiota in urine from women with interstitial cystitis. BMC Microbiol. 12: 205–205.
36 36 Thomas‐White, K., Brady, M., Wolfe, A.J., and Mueller, E.R. (2016). The bladder is not sterile: history and current discoveries on the urinary microbiome. Curr. Bladder Dysfunct. Rep. 11 (1): 18–24.
37 37 Aagaard, K., Ma, J., Antony, K.M., et al. (2014). The placenta harbors a unique microbiome. Sci. Transl. Med. 6 (237): 237ra65.
38 38 Ronald, A. (2002). The etiology of urinary tract infection: traditional and emerging pathogens. Am. J. Med. 113 (Suppl. 1A): 14s–19s.
39 39 Soriano, F. and Tauch, A. (2008). Microbiological and clinical features of Corynebacterium urealyticum: urinary tract stones and genomics as the Rosetta Stone. Clin. Microbiol. Infect. 14 (7): 632–643.
40 40 Lee, J.W., Shim, Y.H., and Lee, S.J. (2009). Lactobacillus colonization status in infants with urinary tract infection. Pediatr. Nephrol. 24 (1): 135–139.
41 41 Latthe, P.M., Toozs‐Hobson, P., and Gray, J. (2008). Mycoplasma and ureaplasma colonisation in women with lower urinary tract symptoms. J. Obstet. Gynaecol. 28 (5): 519–521.
42 42 Gajer, P., Brotman, R.M., Bai, G., et al. (2012). Temporal dynamics of the human vaginal microbiota. Sci. Transl. Med. 4 (132): 132ra52.
43 43 Ott, S.J., Musfeldt, M., Wenderoth, D.F., et al. (2004). Reduction in diversity of the colonic mucosa associated bacterial microflora in patients with active inflammatory bowel disease. Gut 53 (5): 685–693.
44 44 Freire, M., Moustafa, A., Harkins, D.M., et al. (2020). Longitudinal study of oral microbiome variation in twins. Sci. Rep. 10 (1): 7954.
45 45 Turnbaugh, P.J., Hamady, M., Yatsunenko, T., et al. (2009). A core gut microbiome in obese and lean twins. Nature 457 (7228): 480–484.
46 46 Preidis, G.A. and Versalovic, J. (2009). Targeting the human microbiome with antibiotics, probiotics, and prebiotics: gastroenterology enters the metagenomics era. Gastroenterology 136 (6): 2015–2031.
47 47 Dewulf, E.M., Cani, P.D., Claus, S.P., et al. (2013). Insight into the prebiotic concept: lessons from an exploratory, double blind intervention study with inulin‐type fructans in obese women. Gut 62 (8): 1112–1121.
48 48 Petschow, B., Doré, J., Hibberd, P., et al. (2013). Probiotics, prebiotics, and the host microbiome: the science of translation. Ann. N. Y. Acad. Sci. 1306 (1): 1–17.
49 49 Wieërs, G., Belkhir, L., Enaud, R., et al. (2020). How probiotics affect the microbiota. Front. Cell. Infect. Microbiol. 9: 454–454.
50 50 Mandel, D.R., Eichas, K., and Holmes, J. (2010). Bacillus coagulans: a viable adjunct therapy for relieving symptoms of rheumatoid arthritis according to a randomized, controlled trial. BMC Complement. Altern. Med. 10: 1.
51 51 Hempel, S., Newberry, S.,
