Int J Stem Cells.  2022 Feb;15(1):70-84. 10.15283/ijsc21243.

From the Dish to the Real World: Modeling Interactions between the Gut and Microorganisms in Gut Organoids by Tailoring the Gut Milieu

• Park NY
• Koh A

• KMID: 2526739
• DOI: http://doi.org/10.15283/ijsc21243

Abstract

The advent of human intestinal organoid systems has revolutionized the way we understand the interactions between the human gut and microorganisms given the host tropism of human microorganisms. The gut microorganisms have regionality (i.e., small versus large intestine) and the expression of various virulence factors in pathogens is influenced by the gut milieu. However, the culture conditions, optimized for human intestinal organoids, often do not fully support the proliferation and functionality of gut microorganisms. In addition, the regional identity of human intestinal organoids has not been considered to study specific microorganisms with regional preference. In this review we provide an overview of current efforts to understand the role of microorganisms in human intestinal organoids. Specifically, we will emphasize the importance of matching the regional preference of microorganisms in the gut and tailoring the appropriate luminal environmental conditions (i.e., oxygen, pH, and biochemical levels) for modeling real interactions between the gut and the microorganisms with human intestinal organoids.

Keyword

Human intestinal organoids; Gut microbiota; Gut milieu; Enteric pathogens; Regionality

Figure

• 

  Fig. 1 A schematic depiction of the gut milieu in which the interaction between hosts and microorganisms occurs. Enteric microorganisms have different regional preferences along the length of the intestine with different biochemical environments such as oxygen and pH. Interactions between the intestinal epithelium and microorganisms affect these biochemical environments. For example, microbial fermentation of dietary fibers produces SCFAs, reducing pH, while butyrate utilization in the colonocytes consumes oxygen, lowering oxygen concentrations and thus allowing for the growth of strict anaerobes. Microbial growth, viability, and virulence expressions are affected by the surrounding environment. Moreover, intestinal homeostasis is maintained by the interaction between intestinal microbiota and immune cells. Given that iPSCs-derived organoids retain small intestinal properties, caution is needed when studying commensals with preference to the large intestine in iPSCs-derived organoids. For better modeling interactions between the gut and microorganisms using intestinal organoids, it would be necessary to consider various gut environments (i.e., pH, oxygen, microbial metabolites, glucose, immune cells) as well as the regional preference of the microorganisms. AdSCs: Adult stem cells, iPSCs: inducible pluripotent stem cells.

Reference

References

1. Guinane CM, Cotter PD. 2013; Role of the gut microbiota in health and chronic gastrointestinal disease: understanding a hidden metabolic organ. Therap Adv Gastroenterol. 6:295–308. DOI: 10.1177/1756283X13482996. PMID: 23814609. PMCID: PMC3667473.

2. Rothschild D, Weissbrod O, Barkan E, Kurilshikov A, Korem T, Zeevi D, Costea PI, Godneva A, Kalka IN, Bar N, Shilo S, Lador D, Vila AV, Zmora N, Pevsner-Fischer M, Israeli D, Kosower N, Malka G, Wolf BC, Avnit-Sagi T, Lotan-Pompan M, Weinberger A, Halpern Z, Carmi S, Fu J, Wijmenga C, Zhernakova A, Elinav E, Segal E. 2018; Environment dominates over host genetics in shaping human gut microbiota. Nature. 555:210–215. DOI: 10.1038/nature25973. PMID: 29489753.

3. Schroeder BO, Bäckhed F. 2016; Signals from the gut microbiota to distant organs in physiology and disease. Nat Med. 22:1079–1089. DOI: 10.1038/nm.4185. PMID: 27711063.

4. Turnbaugh PJ, Ridaura VK, Faith JJ, Rey FE, Knight R, Gordon JI. 2009; The effect of diet on the human gut microbiome: a metagenomic analysis in humanized gnotobiotic mice. Sci Transl Med. 1:6ra14. DOI: 10.1126/scitranslmed.3000322. PMID: 20368178. PMCID: PMC2894525.

5. Ridaura VK, Faith JJ, Rey FE, Cheng J, Duncan AE, Kau AL, Griffin NW, Lombard V, Henrissat B, Bain JR, Muehlbauer MJ, Ilkayeva O, Semenkovich CF, Funai K, Hayashi DK, Lyle BJ, Martini MC, Ursell LK, Clemente JC, Van Treuren W, Walters WA, Knight R, Newgard CB, Heath AC, Gordon JI. 2013; Gut microbiota from twins discordant for obesity modulate metabolism in mice. Science. 341:1241214. DOI: 10.1126/science.1241214. PMID: 24009397. PMCID: PMC3829625.

6. Arrieta MC, Walter J, Finlay BB. 2016; Human microbiota-associated mice: a model with challenges. Cell Host Microbe. 19:575–578. DOI: 10.1016/j.chom.2016.04.014. PMID: 27173924.

7. Britton GJ, Contijoch EJ, Mogno I, Vennaro OH, Llewellyn SR, Ng R, Li Z, Mortha A, Merad M, Das A, Gevers D, McGovern DPB, Singh N, Braun J, Jacobs JP, Clemente JC, Grinspan A, Sands BE, Colombel JF, Dubinsky MC, Faith JJ. 2019; Microbiotas from humans with inflammatory bowel disease alter the balance of gut Th17 and RORγt＋ regulatory T cells and exacerbate colitis in mice. Immunity. 50:212–224.e4. DOI: 10.1016/j.immuni.2018.12.015. PMID: 30650377. PMCID: PMC6512335.

8. Sampson TR, Debelius JW, Thron T, Janssen S, Shastri GG, Ilhan ZE, Challis C, Schretter CE, Rocha S, Gradinaru V, Chesselet MF, Keshavarzian A, Shannon KM, Krajmalnik-Brown R, Wittung-Stafshede P, Knight R, Mazmanian SK. 2016; Gut microbiota regulate motor deficits and neuroinflammation in a model of Parkinson's disease. Cell. 167:1469–1480.e12. DOI: 10.1016/j.cell.2016.11.018. PMID: 27912057. PMCID: PMC5718049.

9. Sharon G, Cruz NJ, Kang DW, Gandal MJ, Wang B, Kim YM, Zink EM, Casey CP, Taylor BC, Lane CJ, Bramer LM, Isern NG, Hoyt DW, Noecker C, Sweredoski MJ, Moradian A, Borenstein E, Jansson JK, Knight R, Metz TO, Lois C, Geschwind DH, Krajmalnik-Brown R, Mazmanian SK. 2019; Human gut microbiota from autism spectrum disorder promote behavioral symptoms in mice. Cell. 177:1600–1618.e17. DOI: 10.1016/j.cell.2019.05.004. PMID: 31150625. PMCID: PMC6993574.

10. Staley C, Kaiser T, Beura LK, Hamilton MJ, Weingarden AR, Bobr A, Kang J, Masopust D, Sadowsky MJ, Khoruts A. 2017; Stable engraftment of human microbiota into mice with a single oral gavage following antibiotic conditioning. Microbiome. 5:87. DOI: 10.1186/s40168-017-0306-2. PMID: 28760163. PMCID: PMC5537947.

11. Hintze KJ, Cox JE, Rompato G, Benninghoff AD, Ward RE, Broadbent J, Lefevre M. 2014; Broad scope method for creating humanized animal models for animal health and disease research through antibiotic treatment and human fecal transfer. Gut Microbes. 5:183–191. DOI: 10.4161/gmic.28403. PMID: 24637796. PMCID: PMC4063843.

12. Cox LM, Yamanishi S, Sohn J, Alekseyenko AV, Leung JM, Cho I, Kim SG, Li H, Gao Z, Mahana D, Zárate Rodriguez JG, Rogers AB, Robine N, Loke P, Blaser MJ. 2014; Altering the intestinal microbiota during a critical developmental window has lasting metabolic consequences. Cell. 158:705–721. DOI: 10.1016/j.cell.2014.05.052. PMID: 25126780. PMCID: PMC4134513.

13. Nguyen TL, Vieira-Silva S, Liston A, Raes J. 2015; How informative is the mouse for human gut microbiota research? Dis Model Mech. 8:1–16. DOI: 10.1242/dmm.017400. PMID: 25561744. PMCID: PMC4283646.

14. Chung H, Pamp SJ, Hill JA, Surana NK, Edelman SM, Troy EB, Reading NC, Villablanca EJ, Wang S, Mora JR, Umesaki Y, Mathis D, Benoist C, Relman DA, Kasper DL. 2012; Gut immune maturation depends on colonization with a host-specific microbiota. Cell. 149:1578–1593. DOI: 10.1016/j.cell.2012.04.037. PMID: 22726443. PMCID: PMC3442780.

15. Winston JA, Theriot CM. 2020; Diversification of host bile acids by members of the gut microbiota. Gut Microbes. 11:158–171. DOI: 10.1080/19490976.2019.1674124. PMID: 31595814. PMCID: PMC7053883. PMID: 2d1d8891264645709fb6e93bb37d99c1.

16. Spor A, Koren O, Ley R. 2011; Unravelling the effects of the environment and host genotype on the gut microbiome. Nat Rev Microbiol. 9:279–290. DOI: 10.1038/nrmicro2540. PMID: 21407244.

17. Casadevall A, Pirofski LA. 2009; Virulence factors and their mechanisms of action: the view from a damage-response framework. J Water Health. 7 Suppl 1:S2–S18. DOI: 10.2166/wh.2009.036. PMID: 19717929.

18. Sarkar S, Heise MT. 2019; Mouse models as resources for studying infectious diseases. Clin Ther. 41:1912–1922. DOI: 10.1016/j.clinthera.2019.08.010. PMID: 31540729. PMCID: PMC7112552.

19. Swearengen JR. 2018; Choosing the right animal model for infectious disease research. Animal Model Exp Med. 1:100–108. DOI: 10.1002/ame2.12020. PMID: 30891554. PMCID: PMC6388060.

20. Kolawole AO, Wobus CE. 2020; Gastrointestinal organoid technology advances studies of enteric virus biology. PLoS Pathog. 16:e1008212. DOI: 10.1371/journal.ppat.1008212. PMID: 31999791. PMCID: PMC6991956. PMID: a7c35bb50e8c418e90dc62abc9c630e8.

21. Baker BM, Chen CS. 2012; Deconstructing the third dimension: how 3D culture microenvironments alter cellular cues. J Cell Sci. 125(Pt 13):3015–3024. DOI: 10.1242/jcs.079509. PMID: 22797912. PMCID: PMC3434846.

22. Kapałczyńska M, Kolenda T, Przybyła W, Zajączkowska M, Teresiak A, Filas V, Ibbs M, Bliźniak R, Łuczewski Ł, Lamperska K. 2018; 2D and 3D cell cultures - a comparison of different types of cancer cell cultures. Arch Med Sci. 14:910–919. DOI: 10.5114/aoms.2016.63743. PMID: 30002710. PMCID: PMC6040128.

23. Pampaloni F, Reynaud EG, Stelzer EH. 2007; The third dimension bridges the gap between cell culture and live tissue. Nat Rev Mol Cell Biol. 8:839–845. DOI: 10.1038/nrm2236. PMID: 17684528.

24. Kim J, Koo BK, Knoblich JA. 2020; Human organoids: model systems for human biology and medicine. Nat Rev Mol Cell Biol. 21:571–584. DOI: 10.1038/s41580-020-0259-3. PMID: 32636524. PMCID: PMC7339799.

25. Angus HC, Butt AG, Schultz M, Kemp RA. 2020; Intestinal organoids as a tool for inflammatory bowel disease research. Front Med (Lausanne). 6:334. DOI: 10.3389/fmed.2019.00334. PMID: 32010704. PMCID: PMC6978713. PMID: fbe13b4e28064edb9a11b5e5f9534012.

26. Hentschel V, Arnold F, Seufferlein T, Azoitei N, Kleger A, Müller M. 2021; Enteropathogenic infections: organoids go bacterial. Stem Cells Int. 2021:8847804. DOI: 10.1155/2021/8847804. PMID: 33505475. PMCID: PMC7810537.

27. Min S, Kim S, Cho SW. 2020; Gastrointestinal tract modeling using organoids engineered with cellular and microbiota niches. Exp Mol Med. 52:227–237. DOI: 10.1038/s12276-020-0386-0. PMID: 32103122. PMCID: PMC7062772. PMID: 2bb77a6b61684d79a3525dbeddc5abb9.

28. Allam-Ndoul B, Castonguay-Paradis S, Veilleux A. 2020; Gut microbiota and intestinal trans-epithelial permeability. Int J Mol Sci. 21:6402. DOI: 10.3390/ijms21176402. PMID: 32899147. PMCID: PMC7503654. PMID: 79676aa3a9344219b2be8bbbb2766a65.

29. Bartfeld S. 2016; Modeling infectious diseases and host-microbe interactions in gastrointestinal organoids. Dev Biol. 420:262–270. DOI: 10.1016/j.ydbio.2016.09.014. PMID: 27640087.

30. Barker N, van Es JH, Kuipers J, Kujala P, van den Born M, Cozijnsen M, Haegebarth A, Korving J, Begthel H, Peters PJ, Clevers H. 2007; Identification of stem cells in small intestine and colon by marker gene Lgr5. Nature. 449:1003–1007. DOI: 10.1038/nature06196. PMID: 17934449.

31. Sato T, Vries RG, Snippert HJ, van de Wetering M, Barker N, Stange DE, van Es JH, Abo A, Kujala P, Peters PJ, Clevers H. 2009; Single Lgr5 stem cells build crypt-villus structures in vitro without a mesenchymal niche. Nature. 459:262–265. DOI: 10.1038/nature07935. PMID: 19329995.

32. Sato T, Stange DE, Ferrante M, Vries RG, Van Es JH, Van den Brink S, Van Houdt WJ, Pronk A, Van Gorp J, Siersema PD, Clevers H. 2011; Long-term expansion of epithelial organoids from human colon, adenoma, adenocarcinoma, and Barrett's epithelium. Gastroenterology. 141:1762–1772. DOI: 10.1053/j.gastro.2011.07.050. PMID: 21889923.

33. Trillhaase A, Maertens M, Aherrahrou Z, Erdmann J. 2021; Induced pluripotent stem cells (iPSCs) in vascular research: from two-to three-dimensional organoids. Stem Cell Rev Rep. 17:1741–1753. DOI: 10.1007/s12015-021-10149-3. PMID: 33738695. PMCID: PMC7972819.

34. Tsuruta S, Uchida H, Akutsu H. 2020; Intestinal organoids generated from human pluripotent stem cells. JMA J. 3:9–19. DOI: 10.31662/jmaj.2019-0027. PMID: 33324771. PMCID: PMC7733741.

35. Kim K, Doi A, Wen B, Ng K, Zhao R, Cahan P, Kim J, Aryee MJ, Ji H, Ehrlich LI, Yabuuchi A, Takeuchi A, Cunniff KC, Hongguang H, McKinney-Freeman S, Naveiras O, Yoon TJ, Irizarry RA, Jung N, Seita J, Hanna J, Murakami P, Jaenisch R, Weissleder R, Orkin SH, Weissman IL, Feinberg AP, Daley GQ. 2010; Epigenetic memory in induced pluripotent stem cells. Nature. 467:285–290. DOI: 10.1038/nature09342. PMID: 20644535. PMCID: PMC3150836.

36. Watanabe N, Santostefano KE, Yachnis AT, Terada N. 2017; A pathologist's perspective on induced pluripotent stem cells. Lab Invest. 97:1126–1132. DOI: 10.1038/labinvest.2017.81. PMID: 28759008. PMCID: PMC5918271.

37. Spence JR, Mayhew CN, Rankin SA, Kuhar MF, Vallance JE, Tolle K, Hoskins EE, Kalinichenko VV, Wells SI, Zorn AM, Shroyer NF, Wells JM. 2011; Directed differentiation of human pluripotent stem cells into intestinal tissue in vitro. Nature. 470:105–109. DOI: 10.1038/nature09691. PMID: 21151107. PMCID: PMC3033971.

38. Sommer CA, Capilla A, Molina-Estevez FJ, Gianotti-Sommer A, Skvir N, Caballero I, Chowdhury S, Mostoslavsky G. 2018; Modeling APC mutagenesis and familial adenomatous polyposis using human iPS cells. PLoS One. 13:e0200657. DOI: 10.1371/journal.pone.0200657. PMID: 30024920. PMCID: PMC6053155.

39. Takahashi Y, Sato S, Kurashima Y, Yamamoto T, Kurokawa S, Yuki Y, Takemura N, Uematsu S, Lai CY, Otsu M, Matsuno H, Osawa H, Mizushima T, Nishimura J, Hayashi M, Yamaguchi T, Kiyono H. 2018; A refined culture system for human induced pluripotent stem cell-derived intestinal epithelial organoids. Stem Cell Reports. 10:314–328. DOI: 10.1016/j.stemcr.2017.11.004. PMID: 29233552. PMCID: PMC5768885. PMID: c4006f10f2d34228a3837a3832bd0c9b.

40. Crespo M, Vilar E, Tsai SY, Chang K, Amin S, Srinivasan T, Zhang T, Pipalia NH, Chen HJ, Witherspoon M, Gordillo M, Xiang JZ, Maxfield FR, Lipkin S, Evans T, Chen S. 2017; Colonic organoids derived from human induced pluripotent stem cells for modeling colorectal cancer and drug testing. Nat Med. 23:878–884. Erratum in: Nat Med 2018;24:526. DOI: 10.1038/nm0418-526a. PMID: 29634683.

41. Kraiczy J, Nayak KM, Howell KJ, Ross A, Forbester J, Salvestrini C, Mustata R, Perkins S, Andersson-Rolf A, Leenen E, Liebert A, Vallier L, Rosenstiel PC, Stegle O, Dougan G, Heuschkel R, Koo BK, Zilbauer M. 2019; DNA methylation defines regional identity of human intestinal epithelial organoids and undergoes dynamic changes during development. Gut. 68:49–61. DOI: 10.1136/gutjnl-2017-314817. PMID: 29141958. PMCID: PMC6839835.

42. Han X, Mslati MA, Davies E, Chen Y, Allaire JM, Vallance BA. 2021; Creating a more perfect union: modeling intestinal bacteria-epithelial interactions using organoids. Cell Mol Gastroenterol Hepatol. 12:769–782. DOI: 10.1016/j.jcmgh.2021.04.010. PMID: 33895425. PMCID: PMC8273413.

43. Poletti M, Arnauts K, Ferrante M, Korcsmaros T. 2021; Organoid-based models to study the role of host-microbiota interactions in IBD. J Crohns Colitis. 15:1222–1235. DOI: 10.1093/ecco-jcc/jjaa257. PMID: 33341879. PMCID: PMC8256633.

44. Williamson IA, Arnold JW, Samsa LA, Gaynor L, DiSalvo M, Cocchiaro JL, Carroll I, Azcarate-Peril MA, Rawls JF, Allbritton NL, Magness ST. 2018; A high-throughput organoid microinjection platform to study gastrointestinal microbiota and luminal physiology. Cell Mol Gastroenterol Hepatol. 6:301–319. DOI: 10.1016/j.jcmgh.2018.05.004. PMID: 30123820. PMCID: PMC6092482.

45. Leslie JL, Huang S, Opp JS, Nagy MS, Kobayashi M, Young VB, Spence JR. 2015; Persistence and toxin production by Clostridium difficile within human intestinal organoids result in disruption of epithelial paracellular barrier function. Infect Immun. 83:138–145. DOI: 10.1128/IAI.02561-14. PMID: 25312952. PMCID: PMC4288864.

46. Blount ZD. 2015; The unexhausted potential of E. coli. Elife. 4:e05826. DOI: 10.7554/eLife.05826. PMID: 25807083. PMCID: PMC4373459. PMID: 0dec92df648d4db59dd563d07a49a524.

47. Hill DR, Huang S, Nagy MS, Yadagiri VK, Fields C, Mukherjee D, Bons B, Dedhia PH, Chin AM, Tsai YH, Thodla S, Schmidt TM, Walk S, Young VB, Spence JR. 2017; Bacterial colonization stimulates a complex physiological response in the immature human intestinal epithelium. Elife. 6:e29132. DOI: 10.7554/eLife.29132. PMID: 29110754. PMCID: PMC5711377. PMID: 4f3e225ce6c5433682f7583fb2e61dd3.

48. Jump RL, Pultz MJ, Donskey CJ. 2007; Vegetative Clostridium difficile survives in room air on moist surfaces and in gastric contents with reduced acidity: a potential mechanism to explain the association between proton pump inhibitors and C. difficile-associated diarrhea? Antimicrob Agents Chemother. 51:2883–2887. DOI: 10.1128/AAC.01443-06. PMID: 17562803. PMCID: PMC1932506.

49. Engevik MA, Yacyshyn MB, Engevik KA, Wang J, Darien B, Hassett DJ, Yacyshyn BR, Worrell RT. 2015; Human Clostridium difficile infection: altered mucus production and composition. Am J Physiol Gastrointest Liver Physiol. 308:G510–G524. DOI: 10.1152/ajpgi.00091.2014. PMID: 25552581. PMCID: PMC4422372.

50. Puschhof J, Pleguezuelos-Manzano C, Martinez-Silgado A, Akkerman N, Saftien A, Boot C, de Waal A, Beumer J, Dutta D, Heo I, Clevers H. 2021; Intestinal organoid cocultures with microbes. Nat Protoc. 16:4633–4649. DOI: 10.1038/s41596-021-00589-z. PMID: 34381208.

51. Co JY, Margalef-Català M, Li X, Mah AT, Kuo CJ, Monack DM, Amieva MR. 2019; Controlling epithelial polarity: a human enteroid model for host-pathogen interactions. Cell Rep. 26:2509–2520.e4. DOI: 10.1016/j.celrep.2019.01.108. PMID: 30811997. PMCID: PMC6391775.

52. Li Y, Yang N, Chen J, Huang X, Zhang N, Yang S, Liu G, Liu G. 2020; Next-generation porcine intestinal organoids: an apical-out organoid model for swine enteric virus infection and immune response investigations. J Virol. 94:e01006–20. DOI: 10.1128/JVI.01006-20. PMID: 32796075. PMCID: PMC7565635.

53. Thorne CA, Chen IW, Sanman LE, Cobb MH, Wu LF, Altschuler SJ. 2018; Enteroid monolayers reveal an autonomous WNT and BMP circuit controlling intestinal epithelial growth and organization. Dev Cell. 44:624–633.e4. DOI: 10.1016/j.devcel.2018.01.024. PMID: 29503158. PMCID: PMC5849535.

54. In J, Foulke-Abel J, Zachos NC, Hansen AM, Kaper JB, Bernstein HD, Halushka M, Blutt S, Estes MK, Donowitz M, Kovbasnjuk O. 2016; Enterohemorrhagic Escherichia coli reduce mucus and intermicrovillar bridges in human stem cell-derived colonoids. Cell Mol Gastroenterol Hepatol. 2:48–62.e3. DOI: 10.1016/j.jcmgh.2015.10.001. PMID: 26855967. PMCID: PMC4740923.

55. Sasaki N, Miyamoto K, Maslowski KM, Ohno H, Kanai T, Sato T. 2020; Development of a scalable coculture system for gut anaerobes and human colon epithelium. Gastroenterology. 159:388–390.e5. DOI: 10.1053/j.gastro.2020.03.021. PMID: 32199883.

56. Wang Y, Chiang IL, Ohara TE, Fujii S, Cheng J, Muegge BD, Ver Heul A, Han ND, Lu Q, Xiong S, Chen F, Lai CW, Janova H, Wu R, Whitehurst CE, VanDussen KL, Liu TC, Gordon JI, Sibley LD, Stappenbeck TS. 2019; Long-term culture captures injury-repair cycles of colonic stem cells. Cell. 179:1144–1159.e15. DOI: 10.1016/j.cell.2019.10.015. PMID: 31708126. PMCID: PMC6904908.

57. Nossol C, Diesing AK, Walk N, Faber-Zuschratter H, Hartig R, Post A, Kluess J, Rothkötter HJ, Kahlert S. 2011; Air-liquid interface cultures enhance the oxygen supply and trigger the structural and functional differentiation of intestinal porcine epithelial cells (IPEC). Histochem Cell Biol. 136:103–115. DOI: 10.1007/s00418-011-0826-y. PMID: 21681518. PMCID: PMC3132278.

58. Ootani A, Li X, Sangiorgi E, Ho QT, Ueno H, Toda S, Sugihara H, Fujimoto K, Weissman IL, Capecchi MR, Kuo CJ. 2009; Sustained in vitro intestinal epithelial culture within a Wnt-dependent stem cell niche. Nat Med. 15:701–706. DOI: 10.1038/nm.1951. PMID: 19398967. PMCID: PMC2919216.

59. Wilke G, Funkhouser-Jones LJ, Wang Y, Ravindran S, Wang Q, Beatty WL, Baldridge MT, VanDussen KL, Shen B, Kuhlenschmidt MS, Kuhlenschmidt TB, Witola WH, Stappenbeck TS, Sibley LD. 2019; A stem-cell-derived platform enables complete Cryptosporidium development in vitro and genetic tractability. Cell Host Microbe. 26:123–134.e8. DOI: 10.1016/j.chom.2019.05.007. PMID: 31231046. PMCID: PMC6617391.

60. Choi KG, Wu BC, Lee AH, Baquir B, Hancock REW. 2020; Utilizing organoid and air-liquid interface models as a screening method in the development of new host defense peptides. Front Cell Infect Microbiol. 10:228. DOI: 10.3389/fcimb.2020.00228. PMID: 32509598. PMCID: PMC7251080. PMID: 8f772fa5525f461285d39a5ba67b128d.

61. Karve SS, Pradhan S, Ward DV, Weiss AA. 2017; Intestinal organoids model human responses to infection by commensal and Shiga toxin producing Escherichia coli. PLoS One. 12:e0178966. DOI: 10.1371/journal.pone.0178966. PMID: 28614372. PMCID: PMC5470682.

62. Park SH, Seung HJ, Jeong HW, Park SY, Jung JH, Jin YH, Han SH, Kim HS, Kim JS, Park JH, Gong YJ, Hong CK, Lee JH, Kim IY, Jung K. 2018; Molecular characterization of enterotoxigenic escherichia coli in foodborne outbreak. J Bacteriol Virol. 48:113–120. DOI: 10.4167/jbv.2018.48.4.113.

63. Pacheco AR, Sperandio V. 2012; Shiga toxin in enterohemorrhagic E.coli: regulation and novel anti-virulence strategies. Front Cell Infect Microbiol. 2:81. DOI: 10.3389/fcimb.2012.00081. PMID: 22919672. PMCID: PMC3417539.

64. Vermeire B, Gonzalez LM, Jansens RJJ, Cox E, Devriendt B. 2021; Porcine small intestinal organoids as a model to explore ETEC-host interactions in the gut. Vet Res. 52:94. Erratum in: Vet Res 2021;52:107. DOI: 10.1186/s13567-021-00961-7. PMID: 34174960. PMCID: PMC8235647. PMID: 8d83712726cf4c89819507d8bd9e82b1.

65. Noel G, Baetz NW, Staab JF, Donowitz M, Kovbasnjuk O, Pasetti MF, Zachos NC. 2017; A primary human macrophage-enteroid co-culture model to investigate mucosal gut physiology and host-pathogen interactions. Sci Rep. 7:45270. Erratum in: Sci Rep 2017;7:46790. DOI: 10.1038/srep46790. PMID: 28467395. PMCID: PMC5414479.

66. Zaidi MB, Estrada-García T. 2014; Shigella: a highly virulent and elusive pathogen. Curr Trop Med Rep. 1:81–87. DOI: 10.1007/s40475-014-0019-6. PMID: 25110633. PMCID: PMC4126259.

67. Ranganathan S, Doucet M, Grassel CL, Delaine-Elias B, Zachos NC, Barry EM. 2019; Evaluating shigella flexneri pathogenesis in the human enteroid model. Infect Immun. 87:e00740–18. DOI: 10.1128/IAI.00740-18. PMID: 30642900. PMCID: PMC6434113.

68. Koestler BJ, Ward CM, Fisher CR, Rajan A, Maresso AW, Payne SM. 2019; Human intestinal enteroids as a model system of Shigella pathogenesis. Infect Immun. 87:e00733–18. DOI: 10.1128/IAI.00733-18. PMID: 30642906. PMCID: PMC6434139.

69. Verma S, Senger S, Cherayil BJ, Faherty CS. 2020; Spheres of influence: insights into Salmonella pathogenesis from intestinal organoids. Microorganisms. 8:504. DOI: 10.3390/microorganisms8040504. PMID: 32244707. PMCID: PMC7232497. PMID: f11e35ed31c244bb86ef4b3a7eb2e513.

70. Forbester JL, Goulding D, Vallier L, Hannan N, Hale C, Pickard D, Mukhopadhyay S, Dougan G. 2015; Interaction of salmonella enterica serovar typhimurium with intestinal organoids derived from human induced pluripotent stem cells. Infect Immun. 83:2926–2934. DOI: 10.1128/IAI.00161-15. PMID: 25964470. PMCID: PMC4468523.

71. Rouch JD, Scott A, Lei NY, Solorzano-Vargas RS, Wang J, Hanson EM, Kobayashi M, Lewis M, Stelzner MG, Dunn JC, Eckmann L, Martín MG. 2016; Development of functional microfold (M) cells from intestinal stem cells in primary human enteroids. PLoS One. 11:e0148216. DOI: 10.1371/journal.pone.0148216. PMID: 26820624. PMCID: PMC4731053.

72. Zhang YG, Wu S, Xia Y, Sun J. 2014; Salmonella-infected crypt-derived intestinal organoid culture system for host-bacterial interactions. Physiol Rep. 2:e12147. DOI: 10.14814/phy2.12147. PMID: 25214524. PMCID: PMC4270227.

73. Nickerson KP, Senger S, Zhang Y, Lima R, Patel S, Ingano L, Flavahan WA, Kumar DKV, Fraser CM, Faherty CS, Sztein MB, Fiorentino M, Fasano A. 2018; Salmonella typhi colonization provokes extensive transcriptional changes aimed at evading host mucosal immune defense during early infection of human intestinal tissue. EBioMedicine. 31:92–109. DOI: 10.1016/j.ebiom.2018.04.005. PMID: 29735417. PMCID: PMC6013756.

74. Silva AJ, Benitez JA. 2016; Vibrio cholerae biofilms and cholera pathogenesis. PLoS Negl Trop Dis. 10:e0004330. DOI: 10.1371/journal.pntd.0004330. PMID: 26845681. PMCID: PMC4741415.

75. Bharati K, Ganguly NK. 2011; Cholera toxin: a paradigm of a multifunctional protein. Indian J Med Res. 133:179–187. PMID: 21415492. PMCID: PMC3089049.

76. Subramanya SB, Rajendran VM, Srinivasan P, Nanda Kumar NS, Ramakrishna BS, Binder HJ. 2007; Differential regulation of cholera toxin-inhibited Na-H exchange isoforms by butyrate in rat ileum. Am J Physiol Gastrointest Liver Physiol. 293:G857–G863. DOI: 10.1152/ajpgi.00462.2006. PMID: 17690171.

77. Cervin J, Wands AM, Casselbrant A, Wu H, Krishnamurthy S, Cvjetkovic A, Estelius J, Dedic B, Sethi A, Wallom KL, Riise R, Bäckström M, Wallenius V, Platt FM, Lebens M, Teneberg S, Fändriks L, Kohler JJ, Yrlid U. 2018; GM1 ganglioside-independent intoxication by Cholera toxin. PLoS Pathog. 14:e1006862. DOI: 10.1371/journal.ppat.1006862. PMID: 29432456. PMCID: PMC5825173. PMID: f798db5d3c714c6f9abd3318d6d329e7.

78. Cervin J, Boucher A, Youn G, Björklund P, Wallenius V, Mottram L, Sampson NS, Yrlid U. 2020; Fucose-galactose polymers inhibit cholera toxin binding to fucosylated structures and galactose-dependent intoxication of human enteroids. ACS Infect Dis. 6:1192–1203. DOI: 10.1021/acsinfecdis.0c00009. PMID: 32134631. PMCID: PMC7227030.

79. Zomer-van Ommen DD, Pukin AV, Fu O, Quarles van Ufford LH, Janssens HM, Beekman JM, Pieters RJ. 2016; Functional characterization of cholera toxin inhibitors using human intestinal organoids. J Med Chem. 59:6968–6972. DOI: 10.1021/acs.jmedchem.6b00770. PMID: 27347611.

80. Foulke-Abel J, In J, Kovbasnjuk O, Zachos NC, Ettayebi K, Blutt SE, Hyser JM, Zeng XL, Crawford SE, Broughman JR, Estes MK, Donowitz M. 2014; Human enteroids as an ex-vivo model of host-pathogen interactions in the gastrointestinal tract. Exp Biol Med (Maywood). 239:1124–1134. DOI: 10.1177/1535370214529398. PMID: 24719375. PMCID: PMC4380516.

81. Kuhlmann FM, Santhanam S, Kumar P, Luo Q, Ciorba MA, Fleckenstein JM. 2016; Blood group O-dependent cellular responses to cholera toxin: parallel clinical and epidemiological links to severe cholera. Am J Trop Med Hyg. 95:440–443. DOI: 10.4269/ajtmh.16-0161. PMID: 27162272. PMCID: PMC4973196.

82. Fekety R. 1997; Guidelines for the diagnosis and management of Clostridium difficile-associated diarrhea and colitis. American College of Gastroenterology, Practice Parameters Committee. Am J Gastroenterol. 92:739–750. PMID: 9149180.

83. Di Bella S, Ascenzi P, Siarakas S, Petrosillo N, di Masi A. 2016; Clostridium difficile toxins A and B: insights into pathogenic properties and extraintestinal effects. Toxins (Basel). 8:134. DOI: 10.3390/toxins8050134. PMID: 27153087. PMCID: PMC4885049.

84. Engevik MA, Danhof HA, Chang-Graham AL, Spinler JK, Engevik KA, Herrmann B, Endres BT, Garey KW, Hyser JM, Britton RA, Versalovic J. 2020; Human intestinal enteroids as a model of Clostridioides difficile-induced enteritis. Am J Physiol Gastrointest Liver Physiol. 318:G870–G888. DOI: 10.1152/ajpgi.00045.2020. PMID: 32223302. PMCID: PMC7272722.

85. Zhu Z, Schnell L, Müller B, Müller M, Papatheodorou P, Barth H. 2019; The antibiotic bacitracin protects human intestinal epithelial cells and stem cell-derived intestinal organoids from Clostridium difficile toxin TcdB. Stem Cells Int. 2019:4149762. DOI: 10.1155/2019/4149762. PMID: 31467562. PMCID: PMC6701344.

86. Ramani S, Atmar RL, Estes MK. 2014; Epidemiology of human noroviruses and updates on vaccine development. Curr Opin Gastroenterol. 30:25–33. DOI: 10.1097/MOG.0000000000000022. PMID: 24232370. PMCID: PMC3955997.

87. Duizer E, Schwab KJ, Neill FH, Atmar RL, Koopmans MPG, Estes MK. 2004; Laboratory efforts to cultivate noroviruses. J Gen Virol. 85(Pt 1):79–87. DOI: 10.1099/vir.0.19478-0. PMID: 14718622.

88. Takanashi S, Saif LJ, Hughes JH, Meulia T, Jung K, Scheuer KA, Wang Q. 2014; Failure of propagation of human norovirus in intestinal epithelial cells with microvilli grown in three-dimensional cultures. Arch Virol. 159:257–266. DOI: 10.1007/s00705-013-1806-4. PMID: 23974469. PMCID: PMC3946686.

89. Ettayebi K, Crawford SE, Murakami K, Broughman JR, Karandikar U, Tenge VR, Neill FH, Blutt SE, Zeng XL, Qu L, Kou B, Opekun AR, Burrin D, Graham DY, Ramani S, Atmar RL, Estes MK. 2016; Replication of human noroviruses in stem cell-derived human enteroids. Science. 353:1387–1393. DOI: 10.1126/science.aaf5211. PMID: 27562956. PMCID: PMC5305121.

90. Costantini V, Morantz EK, Browne H, Ettayebi K, Zeng XL, Atmar RL, Estes MK, Vinjé J. 2018; Human norovirus replication in human intestinal enteroids as model to evaluate virus inactivation. Emerg Infect Dis. 24:1453–1464. DOI: 10.3201/eid2408.180126. PMID: 30014841. PMCID: PMC6056096.

91. Arnold MM, Sen A, Greenberg HB, Patton JT. 2013; The battle between rotavirus and its host for control of the interferon signaling pathway. PLoS Pathog. 9:e1003064. DOI: 10.1371/journal.ppat.1003064. PMID: 23359266. PMCID: PMC3554623. PMID: 6ad866c212a5451092ec18ad334c112d.

92. Yin Y, Bijvelds M, Dang W, Xu L, van der Eijk AA, Knipping K, Tuysuz N, Dekkers JF, Wang Y, de Jonge J, Sprengers D, van der Laan LJ, Beekman JM, Ten Berge D, Metselaar HJ, de Jonge H, Koopmans MP, Peppelenbosch MP, Pan Q. 2015; Modeling rotavirus infection and antiviral therapy using primary intestinal organoids. Antiviral Res. 123:120–131. DOI: 10.1016/j.antiviral.2015.09.010. PMID: 26408355.

93. Saxena K, Blutt SE, Ettayebi K, Zeng XL, Broughman JR, Crawford SE, Karandikar UC, Sastri NP, Conner ME, Opekun AR, Graham DY, Qureshi W, Sherman V, Foulke-Abel J, In J, Kovbasnjuk O, Zachos NC, Donowitz M, Estes MK. 2015; Human intestinal enteroids: a new model to study human rotavirus infection, host restriction, and pathophysiology. J Virol. 90:43–56. DOI: 10.1128/JVI.01930-15. PMID: 26446608. PMCID: PMC4702582.

94. Khan R, Petersen FC, Shekhar S. 2019; Commensal bacteria: an emerging player in defense against respiratory pathogens. Front Immunol. 10:1203. DOI: 10.3389/fimmu.2019.01203. PMID: 31214175. PMCID: PMC6554327.

95. Martín R, Miquel S, Ulmer J, Kechaou N, Langella P, Bermúdez-Humarán LG. 2013; Role of commensal and probiotic bacteria in human health: a focus on inflammatory bowel disease. Microb Cell Fact. 12:71. DOI: 10.1186/1475-2859-12-71. PMID: 23876056. PMCID: PMC3726476.

96. Heeney DD, Gareau MG, Marco ML. 2018; Intestinal Lactobacillus in health and disease, a driver or just along for the ride? Curr Opin Biotechnol. 49:140–147. DOI: 10.1016/j.copbio.2017.08.004. PMID: 28866243. PMCID: PMC5808898.

97. Rinninella E, Raoul P, Cintoni M, Franceschi F, Miggiano GAD, Gasbarrini A, Mele MC. 2019; What is the healthy gut microbiota composition? A changing ecosystem across age, environment, diet, and diseases. Microorganisms. 7:14. DOI: 10.3390/microorganisms7010014. PMID: 30634578. PMCID: PMC6351938.

98. Lordan C, Thapa D, Ross RP, Cotter PD. 2020; Potential for enriching next-generation health-promoting gut bacteria through prebiotics and other dietary components. Gut Microbes. 11:1–20. DOI: 10.1080/19490976.2019.1613124. PMID: 31116628. PMCID: PMC6973326. PMID: 86c9abd4fe1e41118035d35a7711d4cc.

99. Han X, Lee A, Huang S, Gao J, Spence JR, Owyang C. 2019; Lactobacillus rhamnosus GG prevents epithelial barrier dysfunction induced by interferon-gamma and fecal supernatants from irritable bowel syndrome patients in human intestinal enteroids and colonoids. Gut Microbes. 10:59–76. DOI: 10.1080/19490976.2018.1479625. PMID: 30040527. PMCID: PMC6363076.

100. Wu H, Xie S, Miao J, Li Y, Wang Z, Wang M, Yu Q. 2020; Lactobacillus reuteri maintains intestinal epithelial regeneration and repairs damaged intestinal mucosa. Gut Microbes. 11:997–1014. DOI: 10.1080/19490976.2020.1734423. PMID: 32138622. PMCID: PMC7524370.

101. Son YS, Ki SJ, Thanavel R, Kim JJ, Lee MO, Kim J, Jung CR, Han TS, Cho HS, Ryu CM, Kim SH, Park DS, Son MY. 2020; Maturation of human intestinal organoids in vitro facilitates colonization by commensal lactobacilli by reinforcing the mucus layer. FASEB J. 34:9899–9910. DOI: 10.1096/fj.202000063R. PMID: 32602623.

102. Shin W, Wu A, Massidda MW, Foster C, Thomas N, Lee DW, Koh H, Ju Y, Kim J, Kim HJ. 2019; A robust longitudinal co-culture of obligate anaerobic gut microbiome with human intestinal epithelium in an anoxic-oxic interface-on-a-chip. Front Bioeng Biotechnol. 7:13. DOI: 10.3389/fbioe.2019.00013. PMID: 30792981. PMCID: PMC6374617.

103. Nickerson KP, Llanos-Chea A, Ingano L, Serena G, Miranda-Ribera A, Perlman M, Lima R, Sztein MB, Fasano A, Senger S, Faherty CS. 2021; A versatile human intestinal organoid-derived epithelial monolayer model for the study of enteric pathogens. Microbiol Spectr. 9:e0000321. DOI: 10.1128/Spectrum.00003-21. PMID: 34106568. PMCID: PMC8552518. PMID: 72c9a39e47f844738b9c99362443b4b3.

104. Kelly CP, LaMont JT. 1998; Clostridium difficile infection. Annu Rev Med. 49:375–390. DOI: 10.1146/annurev.med.49.1.375. PMID: 9509270.

105. Roxas JL, Koutsouris A, Bellmeyer A, Tesfay S, Royan S, Falzari K, Harris A, Cheng H, Rhee KJ, Hecht G. 2010; Enterohemorrhagic E. coli alters murine intestinal epithelial tight junction protein expression and barrier function in a Shiga toxin independent manner. Lab Invest. 90:1152–1168. DOI: 10.1038/labinvest.2010.91. PMID: 20479715. PMCID: PMC2912457.

106. Koh A, De Vadder F, Kovatcheva-Datchary P, Bäckhed F. 2016; From dietary fiber to host physiology: short-chain fatty acids as key bacterial metabolites. Cell. 165:1332–1345. DOI: 10.1016/j.cell.2016.05.041. PMID: 27259147.

107. Byndloss MX, Olsan EE, Rivera-Chávez F, Tiffany CR, Cevallos SA, Lokken KL, Torres TP, Byndloss AJ, Faber F, Gao Y, Litvak Y, Lopez CA, Xu G, Napoli E, Giulivi C, Tsolis RM, Revzin A, Lebrilla CB, Bäumler AJ. 2017; Microbiota-activated PPAR-γ signaling inhibits dysbiotic Enterobacteriaceae expansion. Science. 357:570–575. DOI: 10.1126/science.aam9949. PMID: 28798125. PMCID: PMC5642957.

108. Kelly CJ, Zheng L, Campbell EL, Saeedi B, Scholz CC, Bayless AJ, Wilson KE, Glover LE, Kominsky DJ, Magnuson A, Weir TL, Ehrentraut SF, Pickel C, Kuhn KA, Lanis JM, Nguyen V, Taylor CT, Colgan SP. 2015; Crosstalk between microbiota-derived short-chain fatty acids and intestinal epithelial HIF augments tissue barrier function. Cell Host Microbe. 17:662–671. DOI: 10.1016/j.chom.2015.03.005. PMID: 25865369. PMCID: PMC4433427.

109. Konjar Š, Pavšič M, Veldhoen M. 2021; Regulation of oxygen homeostasis at the intestinal epithelial barrier site. Int J Mol Sci. 22:9170. DOI: 10.3390/ijms22179170. PMID: 34502078. PMCID: PMC8431628. PMID: 74fd954f471649d896c2fbf200a92149.

110. Friedman ES, Bittinger K, Esipova TV, Hou L, Chau L, Jiang J, Mesaros C, Lund PJ, Liang X, FitzGerald GA, Goulian M, Lee D, Garcia BA, Blair IA, Vinogradov SA, Wu GD. 2018; Microbes vs. chemistry in the origin of the anaerobic gut lumen. Proc Natl Acad Sci U S A. 115:4170–4175. DOI: 10.1073/pnas.1718635115. PMID: 29610310. PMCID: PMC5910840.

111. Singhal R, Shah YM. 2020; Oxygen battle in the gut: hypoxia and hypoxia-inducible factors in metabolic and inflammatory responses in the intestine. J Biol Chem. 295:10493–10505. DOI: 10.1074/jbc.REV120.011188. PMID: 32503843. PMCID: PMC7383395.

112. Lind Due V, Bonde J, Kann T, Perner A. 2003; Extremely low oxygen tension in the rectal lumen of human subjects. Acta Anaesthesiol Scand. 47:372. DOI: 10.1034/j.1399-6576.2003.00542.x. PMID: 12648210.

113. Walker AW, Duncan SH, McWilliam Leitch EC, Child MW, Flint HJ. 2005; pH and peptide supply can radically alter bacterial populations and short-chain fatty acid ratios within microbial communities from the human colon. Appl Environ Microbiol. 71:3692–3700. DOI: 10.1128/AEM.71.7.3692-3700.2005. PMID: 16000778. PMCID: PMC1169066.

114. Evans DF, Pye G, Bramley R, Clark AG, Dyson TJ, Hardcastle JD. 1988; Measurement of gastrointestinal pH profiles in normal ambulant human subjects. Gut. 29:1035–1041. DOI: 10.1136/gut.29.8.1035. PMID: 3410329. PMCID: PMC1433896.

115. Jubelin G, Desvaux M, Schüller S, Etienne-Mesmin L, Muniesa M, Blanquet-Diot S. 2018; Modulation of enterohaemorrhagic Escherichia coli survival and virulence in the human gastrointestinal tract. Microorganisms. 6:115. DOI: 10.3390/microorganisms6040115. PMID: 30463258. PMCID: PMC6313751.

116. Fallingborg J, Pedersen P, Jacobsen BA. 1998; Small intestinal transit time and intraluminal pH in ileocecal resected patients with Crohn's disease. Dig Dis Sci. 43:702–705. DOI: 10.1023/A:1018893409596. PMID: 9558022.

117. Takeshima T, Adler M, Nacchiero M, Rudick J, Dreiling DA. 1977; Effects of duodenal alkalinization on pancreatic secretion. Am J Gastroenterol. 67:54–62. PMID: 851106.

118. Duncan SH, Louis P, Thomson JM, Flint HJ. 2009; The role of pH in determining the species composition of the human colonic microbiota. Environ Microbiol. 11:2112–2122. DOI: 10.1111/j.1462-2920.2009.01931.x. PMID: 19397676.

119. Koh A, Bäckhed F. 2020; From association to causality: the role of the gut microbiota and its functional products on host metabolism. Mol Cell. 78:584–596. DOI: 10.1016/j.molcel.2020.03.005. PMID: 32234490.

120. Williams AN, Sherman MB, Smith HQ, Taube S, Pettitt BM, Wobus CE, Smith TJ. 2021; A norovirus uses bile salts to escape antibody recognition while enhancing receptor binding. J Virol. 95:e0017621. DOI: 10.1128/JVI.00176-21. PMID: 33827952. PMCID: PMC8315966.

121. Liu JR, Miao H, Deng DQ, Vaziri ND, Li P, Zhao YY. 2021; Gut microbiota-derived tryptophan metabolism mediates renal fibrosis by aryl hydrocarbon receptor signaling activation. Cell Mol Life Sci. 78:909–922. DOI: 10.1007/s00018-020-03645-1. PMID: 32965514.

122. Alexeev EE, Lanis JM, Kao DJ, Campbell EL, Kelly CJ, Battista KD, Gerich ME, Jenkins BR, Walk ST, Kominsky DJ, Colgan SP. 2018; Microbiota-derived indole metabolites promote human and murine intestinal homeostasis through regulation of interleukin-10 receptor. Am J Pathol. 188:1183–1194. DOI: 10.1016/j.ajpath.2018.01.011. PMID: 29454749. PMCID: PMC5906738.

123. Viggiano D, Ianiro G, Vanella G, Bibbò S, Bruno G, Simeone G, Mele G. 2015; Gut barrier in health and disease: focus on childhood. Eur Rev Med Pharmacol Sci. 19:1077–1085. PMID: 25855935.

124. Hou Q, Huang J, Ayansola H, Masatoshi H, Zhang B. 2021; Intestinal stem cells and immune cell relationships: potential therapeutic targets for inflammatory bowel diseases. Front Immunol. 11:623691. DOI: 10.3389/fimmu.2020.623691. PMID: 33584726. PMCID: PMC7874163. PMID: f735b04a2411496d816b623782d98dbb.

125. Fulde M, Sommer F, Chassaing B, van Vorst K, Dupont A, Hensel M, Basic M, Klopfleisch R, Rosenstiel P, Bleich A, Bäckhed F, Gewirtz AT, Hornef MW. 2018; Neonatal selection by Toll-like receptor 5 influences long-term gut microbiota composition. Nature. 560:489–493. Erratum in: Nature 2018;563:E25. DOI: 10.1038/s41586-018-0395-5. PMID: 30089902.

126. Zheng D, Liwinski T, Elinav E. 2020; Interaction between microbiota and immunity in health and disease. Cell Res. 30:492–506. DOI: 10.1038/s41422-020-0332-7. PMID: 32433595. PMCID: PMC7264227.

127. Belkaid Y, Hand TW. 2014; Role of the microbiota in immunity and inflammation. Cell. 157:121–141. DOI: 10.1016/j.cell.2014.03.011. PMID: 24679531. PMCID: PMC4056765.

128. Okkelman IA, Foley T, Papkovsky DB, Dmitriev RI. 2017; Live cell imaging of mouse intestinal organoids reveals heterogeneity in their oxygenation. Biomaterials. 146:86–96. DOI: 10.1016/j.biomaterials.2017.08.043. PMID: 28898760.

129. Bezirtzoglou E. 1997; The intestinal microflora during the first weeks of life. Anaerobe. 3:173–177. DOI: 10.1006/anae.1997.0102. PMID: 16887585.

130. Adlerberth I. Hanson LA, Yolken RH, editors. 1999. Establishment of a normal intestinal microflora in the newborn infant. Probiotics, other nutritional factors, and intestinal microflora. Lippincott-Raven;Philadelphia: p. 63–78.

131. Moore TA, Hanson CK, Anderson-Berry A. 2011; Colonization of the gastrointestinal tract in neonates: a review. Infant Child Adolesc Nutr. 3:291–295. DOI: 10.1177/1941406411421629.

132. Schaffer K, Taylor CT. 2015; The impact of hypoxia on bacterial infection. FEBS J. 282:2260–2266. DOI: 10.1111/febs.13270. PMID: 25786849.

133. Salvi PS, Cowles RA. 2021; Butyrate and the intestinal epithelium: modulation of proliferation and inflammation in homeostasis and disease. Cells. 10:1775. DOI: 10.3390/cells10071775. PMID: 34359944. PMCID: PMC8304699. PMID: 473f2cbe475a4a28a4005e46d618255d.

134. Bultman SJ. 2016; Butyrate consumption of differentiated colonocytes in the upper crypt promotes homeostatic proliferation of stem and progenitor cells near the crypt base. Transl Cancer Res. 5(Suppl 3):S526–S528. DOI: 10.21037/tcr.2016.08.36. PMID: 30568890. PMCID: PMC6296489.

135. Singh B, Halestrap AP, Paraskeva C. 1997; Butyrate can act as a stimulator of growth or inducer of apoptosis in human colonic epithelial cell lines depending on the presence of alternative energy sources. Carcinogenesis. 18:1265–1270. DOI: 10.1093/carcin/18.6.1265. PMID: 9214612.

136. Yin X, Farin HF, van Es JH, Clevers H, Langer R, Karp JM. 2014; Niche-independent high-purity cultures of Lgr5＋ intestinal stem cells and their progeny. Nat Methods. 11:106–112. DOI: 10.1038/nmeth.2737. PMID: 24292484. PMCID: PMC3951815.

137. Gurvich N, Tsygankova OM, Meinkoth JL, Klein PS. 2004; Histone deacetylase is a target of valproic acid-mediated cellular differentiation. Cancer Res. 64:1079–1086. DOI: 10.1158/0008-5472.CAN-03-0799. PMID: 14871841.

138. Amaretti A, Gozzoli C, Simone M, Raimondi S, Righini L, Pérez-Brocal V, García-López R, Moya A, Rossi M. 2019; Profiling of protein degraders in cultures of human gut microbiota. Front Microbiol. 10:2614. DOI: 10.3389/fmicb.2019.02614. PMID: 31803157. PMCID: PMC6874058.

139. den Besten G, van Eunen K, Groen AK, Venema K, Reijngoud DJ, Bakker BM. 2013; The role of short-chain fatty acids in the interplay between diet, gut microbiota, and host energy metabolism. J Lipid Res. 54:2325–2340. DOI: 10.1194/jlr.R036012. PMID: 23821742. PMCID: PMC3735932.

140. Fang FC, Frawley ER, Tapscott T, Vázquez-Torres A. 2016; Bacterial stress responses during host infection. Cell Host Microbe. 20:133–143. DOI: 10.1016/j.chom.2016.07.009. PMID: 27512901. PMCID: PMC4985009.

141. Marteyn B, West NP, Browning DF, Cole JA, Shaw JG, Palm F, Mounier J, Prévost MC, Sansonetti P, Tang CM. 2010; Modulation of Shigella virulence in response to available oxygen in vivo. Nature. 465:355–358. DOI: 10.1038/nature08970. PMID: 20436458. PMCID: PMC3750455.

142. Nickerson KP, Faherty CS. 2018; Bile salt-induced biofilm formation in enteric pathogens: techniques for identification and quantification. J Vis Exp. (135):57322. DOI: 10.3791/57322. PMID: 29781989. PMCID: PMC6101122.

143. Nickerson KP, Chanin RB, Sistrunk JR, Rasko DA, Fink PJ, Barry EM, Nataro JP, Faherty CS. 2017; Analysis of Shigella flexneri resistance, biofilm formation, and transcriptional profile in response to bile salts. Infect Immun. 85:e01067–16. DOI: 10.1128/IAI.01067-16. PMID: 28348056. PMCID: PMC5442615.