References
1. Fan, Y. & Pedersen, O. Gut microbiota in human metabolic health and
disease. Nature Reviews Microbiology 19 , 55-71 (2021).
2. Ursell, L.K., Metcalf, J.L., Parfrey, L.W. & Knight, R. Defining the
human microbiome. Nutr. Rev. 70 Suppl 1 , S38-44 (2012).
3. Wrede, C., Dreier, A., Kokoschka, S. & Hoppert, M. Archaea in
symbioses. Archaea 2012 , 596846 (2012).
4. Mafra, D., et al. Archaea from the gut microbiota of humans:
Could be linked to chronic diseases? Anaerobe 77 , 102629
(2022).
5. Erturk-Hasdemir, D. & Kasper, D.L. Resident commensals shaping
immunity. Curr. Opin. Immunol. 25 , 450-455 (2013).
6. Candela, M., et al. Interaction of probiotic Lactobacillus and
Bifidobacterium strains with human intestinal epithelial cells: adhesion
properties, competition against enteropathogens and modulation of IL-8
production. Int. J. Food Microbiol. 125 , 286-292 (2008).
7. Fukuda, S., et al. Bifidobacteria can protect from
enteropathogenic infection through production of acetate. Nature469 , 543-547 (2011).
8. Sonnenburg, J.L., et al. Glycan foraging in vivo by an
intestine-adapted bacterial symbiont. Science 307 ,
1955-1959 (2005).
9. Round, J.L. & Mazmanian, S.K. The gut microbiota shapes intestinal
immune responses during health and disease. Nat. Rev. Immunol.9 , 313-323 (2009).
10. Khoruts, A., Dicksved, J., Jansson, J.K. & Sadowsky, M.J. Changes
in the composition of the human fecal microbiome after bacteriotherapy
for recurrent Clostridium difficile-associated diarrhea. J. Clin.
Gastroenterol. 44 , 354-360 (2010).
11. Garrett, W.S. The gut microbiota and colon cancer. Science364 , 1133-1135 (2019).
12. Duan, J. & Kasper, D.L. Regulation of T cells by gut commensal
microbiota. Curr. Opin. Rheumatol. 23 , 372-376 (2011).
13. Chung, H. & Kasper, D.L. Microbiota-stimulated immune mechanisms to
maintain gut homeostasis. Curr. Opin. Immunol. 22 ,
455-460 (2010).
14. Kudelka, M.R., Ju, T., Heimburg-Molinaro, J. & Cummings, R.D.
Simple sugars to complex disease–mucin-type O-glycans in cancer.Adv. Cancer Res. 126 , 53-135 (2015).
15. Varki, A. Biological roles of glycans. Glycobiology27 , 3-49 (2017).
16. Slavin, J. Fiber and prebiotics: mechanisms and health benefits.Nutrients 5 , 1417-1435 (2013).
17. Koropatkin, N.M., Cameron, E.A. & Martens, E.C. How glycan
metabolism shapes the human gut microbiota. Nat. Rev. Microbiol.10 , 323-335 (2012).
18. O’Hara, A.M. & Shanahan, F. The gut flora as a forgotten organ.EMBO Rep 7 , 688-693 (2006).
19. Sekirov, I., Russell, S.L., Antunes, L.C. & Finlay, B.B. Gut
microbiota in health and disease. Physiol. Rev. 90 ,
859-904 (2010).
20. Thursby, E. & Juge, N. Introduction to the human gut microbiota.Biochem. J. 474 , 1823-1836 (2017).
21. Zhang, L., et al. Bacterial Species Associated With Human
Inflammatory Bowel Disease and Their Pathogenic Mechanisms. Front.
Microbiol. 13 , 801892 (2022).
22. Wagner, C.L., Taylor, S.N. & Johnson, D. Host factors in amniotic
fluid and breast milk that contribute to gut maturation. Clin.
Rev. Allergy Immunol. 34 , 191-204 (2008).
23. Collado, M.C., Cernada, M., Baüerl, C., Vento, M. & Pérez-Martínez,
G. Microbial ecology and host-microbiota interactions during early life
stages. Gut Microbes 3 , 352-365 (2012).
24. Dominguez-Bello, M.G., Blaser, M.J., Ley, R.E. & Knight, R.
Development of the human gastrointestinal microbiota and insights from
high-throughput sequencing. Gastroenterology 140 ,
1713-1719 (2011).
25. Ajslev, T.A., Andersen, C.S., Gamborg, M., Sørensen, T.I. & Jess,
T. Childhood overweight after establishment of the gut microbiota: the
role of delivery mode, pre-pregnancy weight and early administration of
antibiotics. Int. J. Obes. (Lond.) 35 , 522-529 (2011).
26. Palmer, C., Bik, E.M., DiGiulio, D.B., Relman, D.A. & Brown, P.O.
Development of the human infant intestinal microbiota. PLoS Biol.5 , e177 (2007).
27. Eckburg, P.B., et al. Diversity of the human intestinal
microbial flora. Science 308 , 1635-1638 (2005).
28. Rinninella, E., et al. What is the Healthy Gut Microbiota
Composition? A Changing Ecosystem across Age, Environment, Diet, and
Diseases. Microorganisms 7 (2019).
29. Arumugam, M., et al. Enterotypes of the human gut microbiome.Nature 473 , 174-180 (2011).
30. Sommer, F. & Bäckhed, F. The gut microbiota — masters of host
development and physiology. Nature Reviews Microbiology11 , 227-238 (2013).
31. Smith, K., McCoy, K.D. & Macpherson, A.J. Use of axenic animals in
studying the adaptation of mammals to their commensal intestinal
microbiota. Semin. Immunol. 19 , 59-69 (2007).
32. Willing, B.P., Vacharaksa, A., Croxen, M., Thanachayanont, T. &
Finlay, B.B. Altering Host Resistance to Infections through Microbial
Transplantation. PLoS One 6 , e26988 (2011).
33. Biagi, E., et al. Through ageing, and beyond: gut microbiota
and inflammatory status in seniors and centenarians. PLoS One5 , e10667 (2010).
34. Yatsunenko, T., et al. Human gut microbiome viewed across age
and geography. Nature 486 , 222-227 (2012).
35. Dethlefsen, L. & Relman, D.A. Incomplete recovery and
individualized responses of the human distal gut microbiota to repeated
antibiotic perturbation. Proc. Natl. Acad. Sci. U. S. A.108 Suppl 1 , 4554-4561 (2011).
36. Jernberg, C., Löfmark, S., Edlund, C. & Jansson, J.K. Long-term
impacts of antibiotic exposure on the human intestinal microbiota.Microbiology (Reading) 156 , 3216-3223 (2010).
37. Dethlefsen, L., Huse, S., Sogin, M.L. & Relman, D.A. The pervasive
effects of an antibiotic on the human gut microbiota, as revealed by
deep 16S rRNA sequencing. PLoS Biol. 6 , e280 (2008).
38. Belkaid, Y. & Hand, T.W. Role of the microbiota in immunity and
inflammation. Cell 157 , 121-141 (2014).
39. Wong, C.C. & Yu, J. Gut microbiota in colorectal cancer development
and therapy. Nat. Rev. Clin. Oncol. 20 , 429-452 (2023).
40. Le Chatelier, E., et al. Richness of human gut microbiome
correlates with metabolic markers. Nature 500 , 541-546
(2013).
41. Ley, R.E., Turnbaugh, P.J., Klein, S. & Gordon, J.I. Microbial
ecology: human gut microbes associated with obesity. Nature444 , 1022-1023 (2006).
42. Turnbaugh, P.J., et al. An obesity-associated gut microbiome
with increased capacity for energy harvest. Nature 444 ,
1027-1031 (2006).
43. Wiström, J., et al. Frequency of antibiotic-associated
diarrhoea in 2462 antibiotic-treated hospitalized patients: a
prospective study. J. Antimicrob. Chemother. 47 , 43-50
(2001).
44. Palleja, A., et al. Recovery of gut microbiota of healthy
adults following antibiotic exposure. Nat Microbiol 3 ,
1255-1265 (2018).
45. Kostic, A.D., Xavier, R.J. & Gevers, D. The microbiome in
inflammatory bowel disease: current status and the future ahead.Gastroenterology 146 , 1489-1499 (2014).
46. Carroll, I.M., et al. Molecular analysis of the luminal- and
mucosal-associated intestinal microbiota in diarrhea-predominant
irritable bowel syndrome. Am. J. Physiol. Gastrointest. Liver
Physiol. 301 , G799-807 (2011).
47. Chang, J.Y., et al. Decreased diversity of the fecal
Microbiome in recurrent Clostridium difficile-associated diarrhea.J. Infect. Dis. 197 , 435-438 (2008).
48. Young, V.B. & Schmidt, T.M. Antibiotic-associated diarrhea
accompanied by large-scale alterations in the composition of the fecal
microbiota. J. Clin. Microbiol. 42 , 1203-1206 (2004).
49. Feng, Q., et al. Gut microbiome development along the
colorectal adenoma-carcinoma sequence. Nat Commun 6 ,
6528 (2015).
50. Siegel, R.L., Miller, K.D., Fuchs, H.E. & Jemal, A. Cancer
statistics, 2022. CA Cancer J. Clin. 72 , 7-33 (2022).
51. Wu, S., et al. A human colonic commensal promotes colon
tumorigenesis via activation of T helper type 17 T cell responses.Nat. Med. 15 , 1016-1022 (2009).
52. Arthur, J.C., et al. Intestinal inflammation targets
cancer-inducing activity of the microbiota. Science 338 ,
120-123 (2012).
53. Andres-Franch, M., et al. Streptococcus gallolyticus
infection in colorectal cancer and association with biological and
clinical factors. PLoS One 12 , e0174305 (2017).
54. Yachida, S., et al. Metagenomic and metabolomic analyses
reveal distinct stage-specific phenotypes of the gut microbiota in
colorectal cancer. Nat. Med. 25 , 968-976 (2019).
55. Goto, Y. & Ivanov, I.I. Intestinal epithelial cells as mediators of
the commensal–host immune crosstalk. Immunol. Cell Biol.91 , 204-214 (2013).
56. Bergstrom, K.S. & Xia, L. Mucin-type O-glycans and their roles in
intestinal homeostasis. Glycobiology 23 , 1026-1037
(2013).
57. Wang, B.X., Wu, C.M. & Ribbeck, K. Home, sweet home: how mucus
accommodates our microbiota. Febs j 288 , 1789-1799
(2021).
58. Peterson, D.A., McNulty, N.P., Guruge, J.L. & Gordon, J.I. IgA
response to symbiotic bacteria as a mediator of gut homeostasis.Cell Host Microbe 2 , 328-339 (2007).
59. Vaishnava, S., et al. The Antibacterial Lectin RegIIIγ
Promotes the Spatial Segregation of Microbiota and Host in the
Intestine. Science 334 , 255-258 (2011).
60. Salzman, N.H., et al. Enteric defensins are essential
regulators of intestinal microbial ecology. Nat. Immunol.11 , 76-83 (2010).
61. Schluter, J. & Foster, K.R. The Evolution of Mutualism in Gut
Microbiota Via Host Epithelial Selection. PLoS Biol. 10 ,
e1001424 (2012).
62. Hooper, L.V., Xu, J., Falk, P.G., Midtvedt, T. & Gordon, J.I. A
molecular sensor that allows a gut commensal to control its nutrient
foundation in a competitive ecosystem. Proc. Natl. Acad. Sci. U.
S. A. 96 , 9833-9838 (1999).
63. McLoughlin, K., Schluter, J., Rakoff-Nahoum, S., Smith, A.L. &
Foster, K.R. Host Selection of Microbiota via Differential Adhesion.Cell Host Microbe 19 , 550-559 (2016).
64. Eberl, G. & Lochner, M. The development of intestinal lymphoid
tissues at the interface of self and microbiota. Mucosal Immunol.2 , 478-485 (2009).
65. Mörbe, U.M., et al. Human gut-associated lymphoid tissues
(GALT); diversity, structure, and function. Mucosal Immunol.14 , 793-802 (2021).
66. Olszak, T., et al. Microbial exposure during early life has
persistent effects on natural killer T cell function. Science336 , 489-493 (2012).
67. Garrett, W.S., Gordon, J.I. & Glimcher, L.H. Homeostasis and
inflammation in the intestine. Cell 140 , 859-870 (2010).
68. Hooper, L.V., et al. Molecular analysis of commensal
host-microbial relationships in the intestine. Science291 , 881-884 (2001).
69. Hapfelmeier, S., et al. Reversible Microbial Colonization of
Germ-Free Mice Reveals the Dynamics of IgA Immune Responses.Science 328 , 1705-1709 (2010).
70. Ivanov, II, et al. Induction of intestinal Th17 cells by
segmented filamentous bacteria. Cell 139 , 485-498
(2009).
71. Hooper, L.V., Littman, D.R. & Macpherson, A.J. Interactions between
the microbiota and the immune system. Science 336 ,
1268-1273 (2012).
72. Shanahan, F. The Colonic Microbiota and Colonic Disease. Curr.
Gastroenterol. Rep. 14 , 446-452 (2012).
73. McFall-Ngai, M. Adaptive immunity: care for the community.Nature 445 , 153 (2007).
74. Kawai, T. & Akira, S. Toll-like receptors and their crosstalk with
other innate receptors in infection and immunity. Immunity34 , 637-650 (2011).
75. Smythies, L.E., et al. Human intestinal macrophages display
profound inflammatory anergy despite avid phagocytic and bacteriocidal
activity. J. Clin. Invest. 115 , 66-75 (2005).
76. Franchi, L., et al. NLRC4-driven production of IL-1β
discriminates between pathogenic and commensal bacteria and promotes
host intestinal defense. Nat. Immunol. 13 , 449-456
(2012).
77. Diehl, G.E., et al. Microbiota restricts trafficking of
bacteria to mesenteric lymph nodes by CX(3)CR1(hi) cells. Nature494 , 116-120 (2013).
78. Mazzini, E., Massimiliano, L., Penna, G. & Rescigno, M. Oral
tolerance can be established via gap junction transfer of fed antigens
from CX3CR1⁺ macrophages to CD103⁺ dendritic cells. Immunity40 , 248-261 (2014).
79. Gurram, R.K. & Zhu, J. Orchestration between ILC2s and Th2 cells in
shaping type 2 immune responses. Cell. Mol. Immunol. 16 ,
225-235 (2019).
80. Mazmanian, S.K., Liu, C.H., Tzianabos, A.O. & Kasper, D.L. An
immunomodulatory molecule of symbiotic bacteria directs maturation of
the host immune system. Cell 122 , 107-118 (2005).
81. Johansson, M.E., et al. The inner of the two Muc2
mucin-dependent mucus layers in colon is devoid of bacteria. Proc.
Natl. Acad. Sci. U. S. A. 105 , 15064-15069 (2008).
82. Vaishnava, S., Behrendt, C.L., Ismail, A.S., Eckmann, L. & Hooper,
L.V. Paneth cells directly sense gut commensals and maintain homeostasis
at the intestinal host-microbial interface. Proc. Natl. Acad. Sci.
U. S. A. 105 , 20858-20863 (2008).
83. Kyd, J.M. & Cripps, A.W. Functional differences between M cells and
enterocytes in sampling luminal antigens. Vaccine 26 ,
6221-6224 (2008).
84. Stappenbeck, T.S. & Miyoshi, H. The role of stromal stem cells in
tissue regeneration and wound repair. Science 324 ,
1666-1669 (2009).
85. Deguine, J. & Barton, G.M. MyD88: a central player in innate immune
signaling. F1000Prime Rep 6 , 97 (2014).
86. Burgueño, J.F. & Abreu, M.T. Epithelial Toll-like receptors and
their role in gut homeostasis and disease. Nature Reviews
Gastroenterology & Hepatology 17 , 263-278 (2020).
87. Beau, I., Cotte-Laffitte, J., Amsellem, R. & Servin, A.L. A protein
kinase A-dependent mechanism by which rotavirus affects the distribution
and mRNA level of the functional tight junction-associated protein,
occludin, in human differentiated intestinal Caco-2 cells. J.
Virol. 81 , 8579-8586 (2007).
88. Amieva, M. Shigella navigates tight corners. Cell Host
Microbe 11 , 319-320 (2012).
89. Nusrat, A., et al. Clostridium difficile toxins disrupt
epithelial barrier function by altering membrane microdomain
localization of tight junction proteins. Infect. Immun.69 , 1329-1336 (2001).
90. Jepson, M.A., Schlecht, H.B. & Collares-Buzato, C.B. Localization
of dysfunctional tight junctions in Salmonella enterica serovar
typhimurium-infected epithelial layers. Infect. Immun.68 , 7202-7208 (2000).
91. Li, Y., Jin, L. & Chen, T. The Effects of Secretory IgA in the
Mucosal Immune System. Biomed Res Int 2020 , 2032057
(2020).
92. Pabst, O. New concepts in the generation and functions of IgA.Nat. Rev. Immunol. 12 , 821-832 (2012).
93. Woof, J.M. & Russell, M.W. Structure and function relationships in
IgA. Mucosal Immunol. 4 , 590-597 (2011).
94. Pabst, O. & Izcue, A. Secretory IgA: controlling the gut
microbiota. Nat. Rev. Gastroenterol. Hepatol. 19 ,
149-150 (2022).
95. Ding, L., Chen, X., Cheng, H., Zhang, T. & Li, Z. Advances in IgA
glycosylation and its correlation with diseases. Frontiers in
Chemistry 10 (2022).
96. Corthésy, B. Multi-faceted functions of secretory IgA at mucosal
surfaces. Front. Immunol. 4 , 185 (2013).
97. Mantis, N.J., Rol, N. & Corthésy, B. Secretory IgA’s complex roles
in immunity and mucosal homeostasis in the gut. Mucosal Immunol.4 , 603-611 (2011).
98. Jin, K.T., et al. Recent advances in carbohydrate-based
cancer vaccines. Biotechnol. Lett. 41 , 641-650 (2019).
99. Verathamjamras, C., et al. Aberrant RL2 O-GlcNAc antibody
reactivity against serum-IgA1 of patients with colorectal cancer.Glycoconj. J. 38 , 55-65 (2021).
100. Cash, H.L., Whitham, C.V., Behrendt, C.L. & Hooper, L.V. Symbiotic
Bacteria Direct Expression of an Intestinal Bactericidal Lectin.Science 313 , 1126-1130 (2006).
101. Zhao, D., et al. Survival signal REG3α prevents crypt
apoptosis to control acute gastrointestinal graft-versus-host disease.J. Clin. Invest. 128 , 4970-4979 (2018).
102. Everard, A., et al. Microbiome of prebiotic-treated mice
reveals novel targets involved in host response during obesity.Isme j 8 , 2116-2130 (2014).
103. Paschall, A.V., Middleton, D.R. & Avci, F.Y. Complex Glycans and
Immune Regulation. in Encyclopedia of Cell Biology (Second
Edition) (eds. Bradshaw, R.A., Hart, G.W. & Stahl, P.D.) 404-414
(Academic Press, Oxford, 2023).
104. Prado Acosta, M. & Lepenies, B. Bacterial glycans and their
interactions with lectins in the innate immune system. Biochem.
Soc. Trans. 47 , 1569-1579 (2019).
105. Mayer, S., Raulf, M.-K. & Lepenies, B. C-type lectins: their
network and roles in pathogen recognition and immunity. Histochem.
Cell Biol. 147 , 223-237 (2017).
106. Martínez-López, M., et al. Microbiota Sensing by Mincle-Syk
Axis in Dendritic Cells Regulates Interleukin-17 and -22 Production and
Promotes Intestinal Barrier Integrity. Immunity 50 ,
446-461.e449 (2019).
107. Devi, S., Rajakumara, E. & Ahmed, N. Induction of Mincle by
Helicobacter pylori and consequent anti-inflammatory signaling denote a
bacterial survival strategy. Sci. Rep. 5 , 15049 (2015).
108. Gringhuis, S.I., den Dunnen, J., Litjens, M., van der Vlist, M. &
Geijtenbeek, T.B. Carbohydrate-specific signaling through the DC-SIGN
signalosome tailors immunity to Mycobacterium tuberculosis, HIV-1 and
Helicobacter pylori. Nat. Immunol. 10 , 1081-1088 (2009).
109. Kang, E.A., et al. Soluble Siglec-9 alleviates intestinal
inflammation through inhibition of the NF-κB pathway. Int.
Immunopharmacol. 86 , 106695 (2020).
110. Stephenson, H.N., et al. Pseudaminic Acid on Campylobacter
jejuni Flagella Modulates Dendritic Cell IL-10 Expression via Siglec-10
Receptor: A Novel Flagellin-Host Interaction. The Journal of
Infectious Diseases 210 , 1487-1498 (2014).
111. Vasta, G.R. Roles of galectins in infection. Nature Reviews
Microbiology 7 , 424-438 (2009).
112. Rabinovich, G.A., Toscano, M.A., Jackson, S.S. & Vasta, G.R.
Functions of cell surface galectin-glycoprotein lattices. Curr.
Opin. Struct. Biol. 17 , 513-520 (2007).
113. Rabinovich, G.A. & Toscano, M.A. Turning ’sweet’ on immunity:
galectin-glycan interactions in immune tolerance and inflammation.Nat. Rev. Immunol. 9 , 338-352 (2009).
114. Lo, T.-H., et al. Galectin-3 promotes noncanonical
inflammasome activation through intracellular binding to
lipopolysaccharide glycans. Proceedings of the National Academy of
Sciences 118 , e2026246118 (2021).
115. Ferreira, R.G., et al. Galectin-3 aggravates experimental
polymicrobial sepsis by impairing neutrophil recruitment to the
infectious focus. J. Infect. 77 , 391-397 (2018).
116. Stillman, B.N., et al. Galectin-3 and galectin-1 bind
distinct cell surface glycoprotein receptors to induce T cell death.J. Immunol. 176 , 778-789 (2006).
117. Toscano, M.A., et al. Differential glycosylation of TH1, TH2
and TH-17 effector cells selectively regulates susceptibility to cell
death. Nat. Immunol. 8 , 825-834 (2007).
118. Sundblad, V., et al. Galectins in Intestinal Inflammation:
Galectin-1 Expression Delineates Response to Treatment in Celiac Disease
Patients. Front. Immunol. 9 , 379 (2018).
119. Tsai, H.F., et al. Galectin-3 suppresses mucosal
inflammation and reduces disease severity in experimental colitis.J. Mol. Med. (Berl.) 94 , 545-556 (2016).
120. Santucci, L., et al. Galectin-1 suppresses experimental
colitis in mice. Gastroenterology 124 , 1381-1394 (2003).
121. Fowler, M., Thomas, R.J., Atherton, J., Roberts, I.S. & High, N.J.
Galectin-3 binds to Helicobacter pylori O-antigen: it is upregulated and
rapidly secreted by gastric epithelial cells in response to H. pylori
adhesion. Cell. Microbiol. 8 , 44-54 (2006).
122. Li, F.-Y., Wang, S.-F., Bernardes, E.S. & Liu, F.-T. Galectins in
Host Defense Against Microbial Infections. in Lectin in Host
Defense Against Microbial Infections (ed. Hsieh, S.-L.) 141-167
(Springer Singapore, Singapore, 2020).
123. Li, C.-S., et al. Cytosolic galectin-4 enchains bacteria,
restricts their motility, and promotes inflammasome activation in
intestinal epithelial cells. Proceedings of the National Academy
of Sciences 120 , e2207091120 (2023).
124. Jansen, S.A., et al. Chemotherapy-induced intestinal injury
promotes Galectin-9-driven modulation of T cell function. bioRxiv(2023).
125. Sharba, S., et al. Interleukin 4 induces rapid mucin
transport, increases mucus thickness and quality and decreases colitis
and Citrobacter rodentium in contact with epithelial cells.Virulence 10 , 97-117 (2019).
126. Turner, J.-E., Stockinger, B. & Helmby, H. IL-22 Mediates Goblet
Cell Hyperplasia and Worm Expulsion in Intestinal Helminth Infection.PLoS Pathog. 9 , e1003698 (2013).
127. Mussarat, A., et al. Intestinal overexpression of
interleukin (IL)-15 promotes tissue eosinophilia and goblet cell
hyperplasia. Immunol. Cell Biol. 96 , 273-283 (2018).
128. Hasnain, S.Z., et al. IL-10 promotes production of
intestinal mucus by suppressing protein misfolding and endoplasmic
reticulum stress in goblet cells. Gastroenterology 144 ,
357-368.e359 (2013).
129. Giron, L.B., et al. Sialylation and fucosylation modulate
inflammasome-activating eIF2 Signaling and microbial translocation
during HIV infection. Mucosal Immunol. 13 , 753-766
(2020).
130. Sun, X., Ju, T. & Cummings, R.D. Differential expression of Cosmc,
T-synthase and mucins in Tn-positive colorectal cancers. BMC
Cancer 18 , 827 (2018).
131. Hart, G.W. & Copeland, R.J. Glycomics hits the big time.Cell 143 , 672-676 (2010).
132. van Kooyk, Y. & Rabinovich, G.A. Protein-glycan interactions in
the control of innate and adaptive immune responses. Nat.
Immunol. 9 , 593-601 (2008).
133. Ouwerkerk, J.P., de Vos, W.M. & Belzer, C. Glycobiome: Bacteria
and mucus at the epithelial interface. Best Practice & Research
Clinical Gastroenterology 27 , 25-38 (2013).
134. Arike, L., Holmén-Larsson, J. & Hansson, G.C. Intestinal Muc2
mucin O-glycosylation is affected by microbiota and regulated by
differential expression of glycosyltranferases. Glycobiology27 , 318-328 (2017).
135. Bansil, R. & Turner, B.S. The biology of mucus: Composition,
synthesis and organization. Advanced Drug Delivery Reviews124 , 3-15 (2018).
136. Dekker, J., Rossen, J.W.A., Büller, H.A. & Einerhand, A.W.C. The
MUC family: an obituary. Trends Biochem. Sci. 27 ,
126-131 (2002).
137. Linden, S.K., Sutton, P., Karlsson, N.G., Korolik, V. & McGuckin,
M.A. Mucins in the mucosal barrier to infection. Mucosal Immunol.1 , 183-197 (2008).
138. Larsson, J.M.H., et al. Altered O-glycosylation profile of
MUC2 mucin occurs in active ulcerative colitis and is associated with
increased inflammation. Inflamm. Bowel Dis. 17 ,
2299-2307 (2011).
139. Bergstrom, K., et al. Proximal colon-derived O-glycosylated
mucus encapsulates and modulates the microbiota. Science370 , 467-472 (2020).
140. Cummings, R.D., et al. Principles of Glycan Recognition. inEssentials of Glycobiology (eds. Varki, A., et al. )
387-402 (Cold Spring Harbor Laboratory Press
Copyright © 2022 The Consortium of Glycobiology Editors, La Jolla,
California; published by Cold Spring Harbor Laboratory Press;
doi:10.1101/glycobiology.4e.29. All rights reserved., Cold Spring Harbor
(NY), 2022).
141. Grondin, J.A., Kwon, Y.H., Far, P.M., Haq, S. & Khan, W.I. Mucins
in Intestinal Mucosal Defense and Inflammation: Learning From Clinical
and Experimental Studies. Front. Immunol. 11 , 2054
(2020).
142. Tran, D.T. & Ten Hagen, K.G. Mucin-type O-glycosylation during
development. J. Biol. Chem. 288 , 6921-6929 (2013).
143. Tailford, L.E., Crost, E.H., Kavanaugh, D. & Juge, N. Mucin glycan
foraging in the human gut microbiome. Front Genet 6 , 81
(2015).
144. Moran, A.P., Gupta, A. & Joshi, L. Sweet-talk: role of host
glycosylation in bacterial pathogenesis of the gastrointestinal tract.Gut 60 , 1412-1425 (2011).
145. Eloe-Fadrosh, E.A. & Rasko, D.A. The Human Microbiome: From
Symbiosis to Pathogenesis. Annu. Rev. Med. 64 , 145-163
(2013).
146. Bell, A. & Juge, N. Mucosal glycan degradation of the host by the
gut microbiota. Glycobiology 31 , 691-696 (2021).
147. Juge, N. Microbial adhesins to gastrointestinal mucus. Trends
Microbiol. 20 , 30-39 (2012).
148. Weingarden, A.R. & Vaughn, B.P. Intestinal microbiota, fecal
microbiota transplantation, and inflammatory bowel disease. Gut
Microbes 8 , 238-252 (2017).
149. Johansson, M.E., et al. Bacteria penetrate the normally
impenetrable inner colon mucus layer in both murine colitis models and
patients with ulcerative colitis. Gut 63 , 281-291
(2014).
150. Naughton, J.A., et al. Divergent mechanisms of interaction
of Helicobacter pylori and Campylobacter jejuni with mucus and mucins.Infect. Immun. 81 , 2838-2850 (2013).
151. Derrien, M., et al. Mucin-bacterial interactions in the
human oral cavity and digestive tract. Gut Microbes 1 ,
254-268 (2010).
152. Kudelka, M.R., Stowell, S.R., Cummings, R.D. & Neish, A.S.
Intestinal epithelial glycosylation in homeostasis and gut microbiota
interactions in IBD. Nat. Rev. Gastroenterol. Hepatol.17 , 597-617 (2020).
153. McGovern, D.P.B., et al. Fucosyltransferase 2 (FUT2)
non-secretor status is associated with Crohn’s disease. Hum. Mol.
Genet. 19 , 3468-3476 (2010).
154. Wang, Y., et al. Fucosylation Deficiency in Mice Leads to
Colitis and Adenocarcinoma. Gastroenterology 152 ,
193-205.e110 (2017).
155. Rausch, P., et al. Colonic mucosa-associated microbiota is
influenced by an interaction of Crohn disease and FUT2 (Secretor)
genotype. Proc. Natl. Acad. Sci. U. S. A. 108 ,
19030-19035 (2011).
156. Brazil, J.C. & Parkos, C.A. Finding the sweet spot: glycosylation
mediated regulation of intestinal inflammation. Mucosal Immunol.15 , 211-222 (2022).
157. Pacheco, A.R., et al. Fucose sensing regulates bacterial
intestinal colonization. Nature 492 , 113-117 (2012).
158. Goto, Y., et al. IL-10-producing CD4+ T cells negatively
regulate fucosylation of epithelial cells in the gut. Sci. Rep.5 , 15918 (2015).
159. Dias, A.M., et al. Glycans as critical regulators of gut
immunity in homeostasis and disease. Cell. Immunol. 333 ,
9-18 (2018).
160. Miyoshi, J., et al. Ectopic expression of blood type
antigens in inflamed mucosa with higher incidence of FUT2 secretor
status in colonic Crohn’s disease. J. Gastroenterol. 46 ,
1056-1063 (2011).
161. Fang, J., et al. Slimy partners: the mucus barrier and gut
microbiome in ulcerative colitis. Exp. Mol. Med. 53 ,
772-787 (2021).
162. Werlang, C., Cárcarmo-Oyarce, G. & Ribbeck, K. Engineering mucus
to study and influence the microbiome. Nature Reviews Materials4 , 134-145 (2019).
163. Huang, J.Y., Lee, S.M. & Mazmanian, S.K. The human commensal
Bacteroides fragilis binds intestinal mucin. Anaerobe17 , 137-141 (2011).
164. Glowacki, R.W.P. & Martens, E.C. If You Eat It or Secrete It, They
Will Grow: the Expanding List of Nutrients Utilized by Human Gut
Bacteria. J. Bacteriol. 203 , e00481-00420 (2021).
165. Lee, S., et al. Glycan-mediated molecular interactions in
bacterial pathogenesis. Trends Microbiol. 30 , 254-267
(2022).
166. Tiralongo, J., et al. YesU from Bacillus subtilis
preferentially binds fucosylated glycans. Sci. Rep. 8 ,
13139 (2018).
167. Suwandi, A., et al. Std fimbriae-fucose interaction
increases Salmonella-induced intestinal inflammation and prolongs
colonization. PLoS Pathog. 15 , e1007915 (2019).
168. Sicard, J.F., Le Bihan, G., Vogeleer, P., Jacques, M. & Harel, J.
Interactions of Intestinal Bacteria with Components of the Intestinal
Mucus. Front Cell Infect Microbiol 7 , 387 (2017).
169. Antoni, L., Nuding, S., Wehkamp, J. & Stange, E.F. Intestinal
barrier in inflammatory bowel disease. World J. Gastroenterol.20 , 1165-1179 (2014).
170. Pullan, R.D., et al. Thickness of adherent mucus gel on
colonic mucosa in humans and its relevance to colitis. Gut35 , 353-359 (1994).
171. Dorofeyev, A.E., Vasilenko, I.V., Rassokhina, O.A. & Kondratiuk,
R.B. Mucosal barrier in ulcerative colitis and Crohn’s disease.Gastroenterol. Res. Pract. 2013 , 431231 (2013).
172. Fu, J., et al. Loss of intestinal core 1-derived O-glycans
causes spontaneous colitis in mice. J. Clin. Invest.121 , 1657-1666 (2011).
173. An , G., et al. Increased susceptibility to colitis and
colorectal tumors in mice lacking core 3–derived O-glycans. J.
Exp. Med. 204 , 1417-1429 (2007).
174. Wlodarska, M., et al. Antibiotic treatment alters the
colonic mucus layer and predisposes the host to exacerbated Citrobacter
rodentium-induced colitis. Infect. Immun. 79 , 1536-1545
(2011).
175. Godl, K., et al. The N terminus of the MUC2 mucin forms
trimers that are held together within a trypsin-resistant core fragment.J. Biol. Chem. 277 , 47248-47256 (2002).
176. Johansson, M.E.V. & Hansson, G.C. Immunological aspects of
intestinal mucus and mucins. Nature Reviews Immunology16 , 639-649 (2016).
177. Consortium, T.U. UniProt: the Universal Protein Knowledgebase in
2023. Nucleic Acids Res. 51 , D523-D531 (2022).
178. Kudelka, M.R., et al. Cosmc is an X-linked inflammatory
bowel disease risk gene that spatially regulates gut microbiota and
contributes to sex-specific risk. Proc. Natl. Acad. Sci. U. S. A.113 , 14787-14792 (2016).
179. Van der Sluis, M., et al. Muc2-Deficient Mice Spontaneously
Develop Colitis, Indicating That MUC2 Is Critical for Colonic
Protection. Gastroenterology 131 , 117-129 (2006).
180. Swidsinski, A., Loening-Baucke, V. & Herber, A. Mucosal flora in
Crohn’s disease and ulcerative colitis - an overview. J. Physiol.
Pharmacol. 60 Suppl 6 , 61-71 (2009).
181. Heazlewood, C.K., et al. Aberrant mucin assembly in mice
causes endoplasmic reticulum stress and spontaneous inflammation
resembling ulcerative colitis. PLoS Med. 5 , e54 (2008).
182. Dharmani, P., Srivastava, V., Kissoon-Singh, V. & Chadee, K. Role
of intestinal mucins in innate host defense mechanisms against
pathogens. J. Innate Immun. 1 , 123-135 (2009).
183. Hayashi, F., et al. The innate immune response to bacterial
flagellin is mediated by Toll-like receptor 5. Nature410 , 1099-1103 (2001).
184. Birchenough, G.M., Nyström, E.E., Johansson, M.E. & Hansson, G.C.
A sentinel goblet cell guards the colonic crypt by triggering
Nlrp6-dependent Muc2 secretion. Science 352 , 1535-1542
(2016).
185. Johansson, Malin E.V., et al. Normalization of Host
Intestinal Mucus Layers Requires Long-Term Microbial Colonization.Cell Host Microbe 18 , 582-592 (2015).
186. Deplancke, B. & Gaskins, H.R. Microbial modulation of innate
defense: goblet cells and the intestinal mucus layer. Am. J. Clin.
Nutr. 73 , 1131s-1141s (2001).
187. Smirnova, M.G., Guo, L., Birchall, J.P. & Pearson, J.P. LPS
up-regulates mucin and cytokine mRNA expression and stimulates mucin and
cytokine secretion in goblet cells. Cell. Immunol. 221 ,
42-49 (2003).
188. Mack, D.R., Ahrne, S., Hyde, L., Wei, S. & Hollingsworth, M.A.
Extracellular MUC3 mucin secretion follows adherence of Lactobacillus
strains to intestinal epithelial cells in vitro. Gut 52 ,
827-833 (2003).
189. Mack, D.R., Michail, S., Wei, S., McDougall, L. & Hollingsworth,
M.A. Probiotics inhibit enteropathogenic E. coli adherence in vitro by
inducing intestinal mucin gene expression. Am. J. Physiol.276 , G941-950 (1999).
190. Alemka, A., et al. Probiotic colonization of the adherent
mucus layer of HT29MTXE12 cells attenuates Campylobacter jejuni
virulence properties. Infect. Immun. 78 , 2812-2822
(2010).
191. Lau, S.K., Weiss, L.M. & Chu, P.G. Differential expression of
MUC1, MUC2, and MUC5AC in carcinomas of various sites: an
immunohistochemical study. Am. J. Clin. Pathol. 122 ,
61-69 (2004).
192. Limburg, P.J., et al. Immunodiscrimination of colorectal
neoplasia using MUC1 antibodies: discrepant findings in tissue versus
stool. Dig. Dis. Sci. 45 , 494-499 (2000).
193. Xu, F., Liu, F., Zhao, H., An, G. & Feng, G. Prognostic
Significance of Mucin Antigen MUC1 in Various Human Epithelial Cancers:
A Meta-Analysis. Medicine 94 , e2286 (2015).
194. Wang, H., et al. Expression of survivin, MUC2 and MUC5 in
colorectal cancer and their association with clinicopathological
characteristics. Oncol. Lett. 14 , 1011-1016 (2017).
195. Rico, S.D., et al. Elevated MUC5AC expression is associated
with mismatch repair deficiency and proximal tumor location but not with
cancer progression in colon cancer. Med. Mol. Morphol.54 , 156-165 (2021).
196. Robbe, C., et al. Evidence of Regio-specific Glycosylation
in Human Intestinal Mucins: PRESENCE OF AN ACIDIC GRADIENT ALONG THE
INTESTINAL TRACT*. J. Biol. Chem. 278 , 46337-46348
(2003).
197. Bell, A., Severi, E., Owen, C.D., Latousakis, D. & Juge, N.
Biochemical and structural basis of sialic acid utilization by gut
microbes. J. Biol. Chem. 299 , 102989 (2023).
198. Yao, Y., et al. Mucus sialylation determines intestinal
host-commensal homeostasis. Cell 185 , 1172-1188.e1128
(2022).
199. Juge, N., Tailford, L. & Owen, C.D. Sialidases from gut bacteria:
a mini-review. Biochem. Soc. Trans. 44 , 166-175 (2016).
200. Šimurina, M., et al. Glycosylation of Immunoglobulin G
Associates With Clinical Features of Inflammatory Bowel Diseases.Gastroenterology 154 , 1320-1333.e1310 (2018).
201. Martens, E.C., Chiang, H.C. & Gordon, J.I. Mucosal glycan foraging
enhances fitness and transmission of a saccharolytic human gut bacterial
symbiont. Cell Host Microbe 4 , 447-457 (2008).
202. Lozupone, C.A., et al. The convergence of carbohydrate
active gene repertoires in human gut microbes. Proc. Natl. Acad.
Sci. U. S. A. 105 , 15076-15081 (2008).
203. Pereira, F.C. & Berry, D. Microbial nutrient niches in the gut.Environ. Microbiol. 19 , 1366-1378 (2017).
204. Bhattacharya, T., Ghosh, T.S. & Mande, S.S. Global Profiling of
Carbohydrate Active Enzymes in Human Gut Microbiome. PLoS One10 , e0142038 (2015).
205. Martens, E.C., Koropatkin, N.M., Smith, T.J. & Gordon, J.I.
Complex glycan catabolism by the human gut microbiota: the Bacteroidetes
Sus-like paradigm. J. Biol. Chem. 284 , 24673-24677
(2009).
206. Png, C.W., et al. Mucolytic bacteria with increased
prevalence in IBD mucosa augment in vitro utilization of mucin by other
bacteria. Am. J. Gastroenterol. 105 , 2420-2428 (2010).
207. Bry, L., Falk, P.G., Midtvedt, T. & Gordon, J.I. A model of
host-microbial interactions in an open mammalian ecosystem.Science 273 , 1380-1383 (1996).
208. Wrzosek, L., et al. Bacteroides thetaiotaomicron and
Faecalibacterium prausnitzii influence the production of mucus glycans
and the development of goblet cells in the colonic epithelium of a
gnotobiotic model rodent. BMC Biol. 11 , 61 (2013).
209. Kang, Y., Park, H., Choe, B.H. & Kang, B. The Role and Function of
Mucins and Its Relationship to Inflammatory Bowel Disease. Front
Med (Lausanne) 9 , 848344 (2022).
210. Özcan, E. & Sela, D.A. Inefficient Metabolism of the Human Milk
Oligosaccharides Lacto-N-tetraose and Lacto-N-neotetraose Shifts
Bifidobacterium longum subsp. infantis Physiology. Front Nutr5 , 46 (2018).
211. Bondue, P., et al. Cell-Free Spent Media Obtained from
Bifidobacterium bifidum and Bifidobacterium crudilactis Grown in Media
Supplemented with 3’-Sialyllactose Modulate Virulence Gene Expression in
Escherichia coli O157:H7 and Salmonella Typhimurium. Front.
Microbiol. 7 , 1460 (2016).
212. Lawson, M.A.E., et al. Breast milk-derived human milk
oligosaccharides promote Bifidobacterium interactions within a single
ecosystem. Isme j 14 , 635-648 (2020).
213. Kulinich, A. & Liu, L. Human milk oligosaccharides: The role in
the fine-tuning of innate immune responses. Carbohydr. Res.432 , 62-70 (2016).
214. Chleilat, F., et al. Human Milk Oligosaccharide
Supplementation Affects Intestinal Barrier Function and Microbial
Composition in the Gastrointestinal Tract of Young Sprague Dawley Rats.Nutrients 12 , 1532 (2020).
215. Eiwegger, T., et al. Prebiotic oligosaccharides: In vitro
evidence for gastrointestinal epithelial transfer and immunomodulatory
properties. Pediatr. Allergy Immunol. 21 , 1179-1188
(2010).
216. den Besten, G., et al. The role of short-chain fatty acids
in the interplay between diet, gut microbiota, and host energy
metabolism. J. Lipid Res. 54 , 2325-2340 (2013).
217. Morrison, D.J. & Preston, T. Formation of short chain fatty acids
by the gut microbiota and their impact on human metabolism. Gut
Microbes 7 , 189-200 (2016).
218. Litvak, Y., Byndloss, M.X. & Bäumler, A.J. Colonocyte metabolism
shapes the gut microbiota. Science 362 (2018).
219. Beaumont, M., et al. Gut microbiota derived metabolites
contribute to intestinal barrier maturation at the suckling-to-weaning
transition. Gut Microbes 11 , 1268-1286 (2020).
220. Lupton, J.R. Microbial degradation products influence colon cancer
risk: the butyrate controversy. J. Nutr. 134 , 479-482
(2004).
221. Roediger, W.E. The colonic epithelium in ulcerative colitis: an
energy-deficiency disease? Lancet 2 , 712-715 (1980).
222. De Filippis, F., et al. High-level adherence to a
Mediterranean diet beneficially impacts the gut microbiota and
associated metabolome. Gut 65 , 1812-1821 (2016).
223. Fehlbaum, S., et al. In Vitro Fermentation of Selected
Prebiotics and Their Effects on the Composition and Activity of the
Adult Gut Microbiota. Int. J. Mol. Sci. 19 (2018).
224. Sonnenburg, E.D., et al. Diet-induced extinctions in the gut
microbiota compound over generations. Nature 529 ,
212-215 (2016).
225. Wu, G.D., et al. Linking long-term dietary patterns with gut
microbial enterotypes. Science 334 , 105-108 (2011).
226. Marcobal, A., Southwick, A.M., Earle, K.A. & Sonnenburg, J.L. A
refined palate: bacterial consumption of host glycans in the gut.Glycobiology 23 , 1038-1046 (2013).
227. Ndeh, D. & Gilbert, H.J. Biochemistry of complex glycan
depolymerisation by the human gut microbiota. FEMS Microbiol.
Rev. 42 , 146-164 (2018).
228. Shin, J., et al. Elucidation of Akkermansia muciniphila
Probiotic Traits Driven by Mucin Depletion. Front. Microbiol.10 , 1137 (2019).
229. Paone, P. & Cani, P.D. Mucus barrier, mucins and gut microbiota:
the expected slimy partners? Gut 69 , 2232-2243 (2020).
230. Yoshihara, T., et al. The protective effect of
Bifidobacterium bifidum G9-1 against mucus degradation by Akkermansia
muciniphila following small intestine injury caused by a proton pump
inhibitor and aspirin. Gut Microbes 11 , 1385-1404
(2020).
231. Breugelmans, T., et al. The role of mucins in
gastrointestinal barrier function during health and disease.Lancet Gastroenterol Hepatol 7 , 455-471 (2022).
232. Burger-van Paassen, N., et al. The regulation of intestinal
mucin MUC2 expression by short-chain fatty acids: implications for
epithelial protection. Biochem. J. 420 , 211-219 (2009).
233. Tan, F.Y.Y., Tang, C.M. & Exley, R.M. Sugar coating: bacterial
protein glycosylation and host–microbe interactions.Trends Biochem. Sci. 40 , 342-350 (2015).
234. Castric, P. pilO, a gene required for glycosylation of Pseudomonas
aeruginosa 1244 pilin. Microbiology 141 , 1247-1254
(1995).
235. Ku, S.C., Schulz, B.L., Power, P.M. & Jennings, M.P. The pilin
O-glycosylation pathway of pathogenic Neisseria is a general system that
glycosylates AniA, an outer membrane nitrite reductase. Biochem.
Biophys. Res. Commun. 378 , 84-89 (2009).
236. Latousakis, D. & Juge, N. How Sweet Are Our Gut Beneficial
Bacteria? A Focus on Protein Glycosylation in Lactobacillus. Int.
J. Mol. Sci. 19 , 136 (2018).
237. Linton, D., et al. Functional analysis of the Campylobacter
jejuni N-linked protein glycosylation pathway. Mol. Microbiol.55 , 1695-1703 (2005).
238. Abouelhadid, S., et al. Quantitative Analyses Reveal Novel
Roles for
<i>N-</i>Glycosylation in
a Major Enteric Bacterial Pathogen. mBio 10 ,
10.1128/mbio.00297-00219 (2019).
239. Adibekian, A., et al. Comparative bioinformatics analysis of
the mammalian and bacterial glycomes. Chemical Science2 , 337-344 (2011).
240. Kerrigan, A.M. & Brown, G.D. C-type lectins and phagocytosis.Immunobiology 214 , 562-575 (2009).
241. Rabinovich, Gabriel A. & Croci, Diego O. Regulatory Circuits
Mediated by Lectin-Glycan Interactions in Autoimmunity and Cancer.Immunity 36 , 322-335 (2012).
242. Avci, F.Y. & Kasper, D.L. How Bacterial Carbohydrates Influence
the Adaptive Immune System. Annu. Rev. Immunol. 28 ,
107-130 (2010).
243. Round, J.L. & Mazmanian, S.K. Inducible Foxp3+ regulatory T-cell
development by a commensal bacterium of the intestinal microbiota.Proc. Natl. Acad. Sci. U. S. A. 107 , 12204-12209 (2010).
244. Geijtenbeek, T.B.H. & Gringhuis, S.I. Signalling through C-type
lectin receptors: shaping immune responses. Nature Reviews
Immunology 9 , 465-479 (2009).
245. Coyne, M.J., Reinap, B., Lee, M.M. & Comstock, L.E. Human
symbionts use a host-like pathway for surface fucosylation.Science 307 , 1778-1781 (2005).
246. Naegeli, A., et al. Streptococcus pyogenes evades adaptive
immunity through specific IgG glycan hydrolysis. J. Exp. Med.216 , 1615-1629 (2019).
247. Walker, M.J., et al. Disease Manifestations and Pathogenic
Mechanisms of Group A Streptococcus. Clin. Microbiol. Rev.27 , 264-301 (2014).
248. Wong, S.H., et al. Gavage of Fecal Samples From Patients
With Colorectal Cancer Promotes Intestinal Carcinogenesis in Germ-Free
and Conventional Mice. Gastroenterology 153 ,
1621-1633.e1626 (2017).
249. Cheng, Y., Ling, Z. & Li, L. The Intestinal Microbiota and
Colorectal Cancer. Front. Immunol. 11 , 615056 (2020).
250. Tjalsma, H., Boleij, A., Marchesi, J.R. & Dutilh, B.E. A bacterial
driver-passenger model for colorectal cancer: beyond the usual suspects.Nat. Rev. Microbiol. 10 , 575-582 (2012).
251. Campbell, B.J., Finnie, I.A., Hounsell, E.F. & Rhodes, J.M. Direct
demonstration of increased expression of Thomsen-Friedenreich (TF)
antigen in colonic adenocarcinoma and ulcerative colitis mucin and its
concealment in normal mucin. J. Clin. Invest. 95 ,
571-576 (1995).
252. Abed, J., et al. Fap2 Mediates Fusobacterium nucleatum
Colorectal Adenocarcinoma Enrichment by Binding to Tumor-Expressed
Gal-GalNAc. Cell Host Microbe 20 , 215-225 (2016).
253. Khalili, H., et al. The role of diet in the
aetiopathogenesis of inflammatory bowel disease. Nat. Rev.
Gastroenterol. Hepatol. 15 , 525-535 (2018).
254. Wolters, M., et al. Dietary fat, the gut microbiota, and
metabolic health - A systematic review conducted within the MyNewGut
project. Clin. Nutr. 38 , 2504-2520 (2019).
255. Coker, J.K., Moyne, O., Rodionov, D.A. & Zengler, K. Carbohydrates
great and small, from dietary fiber to sialic acids: How glycans
influence the gut microbiome and affect human health. Gut
Microbes 13 , 1-18 (2021).
256. Chloe, A.A., et al. Human milk oligosaccharide composition
predicts risk of necrotising enterocolitis in preterm infants.Gut 67 , 1064 (2018).
257. Caballero-Franco, C., Keller, K., De Simone, C. & Chadee, K. The
VSL#3 probiotic formula induces mucin gene expression and secretion in
colonic epithelial cells. Am. J. Physiol. Gastrointest. Liver
Physiol. 292 , G315-322 (2007).
258. Finnie, I.A., Dwarakanath, A.D., Taylor, B.A. & Rhodes, J.M.
Colonic mucin synthesis is increased by sodium butyrate. Gut36 , 93-99 (1995).
259. Bron, P.A., van Baarlen, P. & Kleerebezem, M. Emerging molecular
insights into the interaction between probiotics and the host intestinal
mucosa. Nature Reviews Microbiology 10 , 66-78 (2012).
260. Kristensen, N.B., et al. Alterations in fecal microbiota
composition by probiotic supplementation in healthy adults: a systematic
review of randomized controlled trials. Genome Med. 8 ,
52 (2016).
261. Borody, T.J. & Khoruts, A. Fecal microbiota transplantation and
emerging applications. Nature Reviews Gastroenterology &
Hepatology 9 , 88-96 (2012).
262. Basson, A.R., Zhou, Y., Seo, B., Rodriguez-Palacios, A. &
Cominelli, F. Autologous fecal microbiota transplantation for the
treatment of inflammatory bowel disease. Transl. Res.226 , 1-11 (2020).
263. Brandt, L.J. & Reddy, S.S. Fecal microbiota transplantation for
recurrent clostridium difficile infection. J. Clin.
Gastroenterol. 45 Suppl , S159-167 (2011).
264. Mellow, M.H. & Kanatzar, A. Colonoscopic fecal bacteriotherapy in
the treatment of recurrent Clostridium difficile infection–results
and follow-up. J. Okla. State Med. Assoc. 104 , 89-91
(2011).
265. Silverman, M.S., Davis, I. & Pillai, D.R. Success of
self-administered home fecal transplantation for chronic Clostridium
difficile infection. Clin. Gastroenterol. Hepatol. 8 ,
471-473 (2010).
266. Matsuoka, K. Fecal microbiota transplantation for ulcerative
colitis. Immunol Med 44 , 30-34 (2021).
267. Colman, R.J. & Rubin, D.T. Fecal microbiota transplantation as
therapy for inflammatory bowel disease: A systematic review and
meta-analysis. Journal of Crohn’s and Colitis 8 ,
1569-1581 (2014).
268. Dailey, F.E., Turse, E.P., Daglilar, E. & Tahan, V. The dirty
aspects of fecal microbiota transplantation: a review of its adverse
effects and complications. Curr. Opin. Pharmacol. 49 ,
29-33 (2019).
269. Merrick, B., et al. Regulation, risk and safety of Faecal
Microbiota Transplant. Infect Prev Pract 2 , 100069
(2020).
270. Vich Vila, A., et al. Gut microbiota composition and
functional changes in inflammatory bowel disease and irritable bowel
syndrome. Sci. Transl. Med. 10 (2018).
271. Lloyd-Price, J., et al. Multi-omics of the gut microbial
ecosystem in inflammatory bowel diseases. Nature 569 ,
655-662 (2019).
272. Pittayanon, R., et al. Differences in Gut Microbiota in
Patients With vs Without Inflammatory Bowel Diseases: A Systematic
Review. Gastroenterology 158 , 930-946.e931 (2020).
273. Bankole, E., Read, E., Curtis, M.A., Neves, J.F. & Garnett, J.A.
The Relationship between Mucins and Ulcerative Colitis: A Systematic
Review. J Clin Med 10 (2021).
274. Yamamoto-Furusho, J.K., Mendivil, E.J. & Fonseca-Camarillo, G.
Reduced expression of mucin 9 (MUC9) in patients with ulcerative
colitis. Inflamm. Bowel Dis. 18 , E601 (2012).
275. Yamamoto-Furusho, J.K., Ascaño-Gutiérrez, I., Furuzawa-Carballeda,
J. & Fonseca-Camarillo, G. Differential Expression of MUC12, MUC16, and
MUC20 in Patients with Active and Remission Ulcerative Colitis.Mediators Inflamm. 2015 , 659018 (2015).
276. Gersemann, M., et al. Differences in goblet cell
differentiation between Crohn’s disease and ulcerative colitis.Differentiation 77 , 84-94 (2009).
277. Hashash, J.G., et al. Altered Expression of the Epithelial
Mucin MUC1 Accompanies Endoscopic Recurrence of Postoperative Crohn’s
Disease. J. Clin. Gastroenterol. 55 , 127-133 (2021).
278. Battat, R., et al. Fucosyltransferase 2 Mutations Are
Associated With a Favorable Clinical Course in Crohn’s Disease. J.
Clin. Gastroenterol. 56 , e166-e170 (2022).
279. Wang, T., et al. Structural segregation of gut microbiota
between colorectal cancer patients and healthy volunteers. Isme j6 , 320-329 (2012).
280. Veziant, J., et al. Association of colorectal cancer with
pathogenic Escherichia coli: Focus on mechanisms using optical imaging.World J. Clin. Oncol. 7 , 293-301 (2016).
281. Mima, K., et al. Fusobacterium nucleatum in colorectal
carcinoma tissue and patient prognosis. Gut 65 ,
1973-1980 (2016).
282. Gupta, A., Madani, R. & Mukhtar, H. Streptococcus bovis
endocarditis, a silent sign for colonic tumour. Colorectal Dis.12 , 164-171 (2010).
283. Kumar, R., et al. Streptococcus gallolyticus subsp.
gallolyticus promotes colorectal tumor development. PLoS Pathog.13 , e1006440 (2017).
284. Zhao, L., et al. Parvimonas micra promotes colorectal
tumorigenesis and is associated with prognosis of colorectal cancer
patients. Oncogene 41 , 4200-4210 (2022).
285. Li, C., et al. Prognostic and clinicopathological value of
MUC1 expression in colorectal cancer: A meta-analysis. Medicine
(Baltimore) 98 , e14659 (2019).
286. Cecchini, M.J., et al. CDX2 and Muc2 immunohistochemistry as
prognostic markers in stage II colon cancer. Hum. Pathol.90 , 70-79 (2019).
287. Pothuraju, R., et al. Mechanistic and Functional Shades of
Mucins and Associated Glycans in Colon Cancer. Cancers (Basel)12 (2020).
288. Jumper, J., et al. Highly accurate protein structure
prediction with AlphaFold. Nature 596 , 583-589 (2021).
289. Tunyasuvunakool, K., et al. Highly accurate protein
structure prediction for the human proteome. Nature 596 ,
590-596 (2021).