Relevance of organ(s)-on-a-chip systems to the investigation of food-gut microbiota-host interactions

References

• Abadpour S, Aizenshtadt A, Olsen PA, Shoji K, Wilson SR, Krauss S, Scholz H. 2020. Pancreas-on-a-Chip Technology for Transplantation Applications. Curr Diab Rep. 820(12):72–72.
   PubMed Web of Science ®Google Scholar
• Albillos A, de Gottardi A, Rescigno M. 2020. The gut-liver axis in liver disease: pathophysiological basis for therapy. J Hepatol. 72(3):558–577.
   PubMed Web of Science ®Google Scholar
• Almeida AS, Tran TTT, Ghosh TS, Ribiere C, Foley C, Alves LA, et al. 2021. Fiber-associated Lachnospiraceae reduce colon tumorigenesis by modulation of the tumor-immune microenvironment. bioRxiv.
   Google Scholar
• And HC, Hoover DG. 2003. Bacteriocins and their Food Applications. Compr Rev Food Sci Food Saf. 2(3):82–100.
   PubMedGoogle Scholar
• Angeloni C, Businaro R, Vauzour D. 2020. The role of diet in preventing and reducing cognitive decline. Curr Opin Psychiatry. 33(4):432–438.
   PubMed Web of Science ®Google Scholar
• Annunziata G, Arnone A, Ciampaglia R, Tenore GC, Novellino E. 2020. Fermentation of foods and beverages as a tool for increasing availability of bioactive compounds. focus on short-chain fatty acids. foods. Basel Switz. 9(8):999.
   Google Scholar
• Arneth BM. 2018. Gut-brain axis biochemical signalling from the gastrointestinal tract to the central nervous system: gut dysbiosis and altered brain function. Postgrad Med J. 94(1114):446–452.
   PubMed Web of Science ®Google Scholar
• Ashammakhi N, Nasiri R, Barros N. R d, Tebon P, Thakor J, Goudie M, Shamloo A, Martin MG, Khademhosseini A. 2020. Gut-on-a-chip: Current progress and future opportunities. Biomaterials. 255:120196.
   PubMed Web of Science ®Google Scholar
• Azzini E, Maiani G. 2015. Chapter 23 - mediterranean diet: antioxidant nutritional status. In: Preedy VR, Watson RR, editors. The mediterranean diet [Internet]. San Diego: Academic Press. p. 249–257. Available from: https://www.sciencedirect.com/science/article/pii/B9780124078499000233.
   Google Scholar
• Bajaj JS, Hylemon PB, Ridlon JM, Heuman DM, Daita K, White MB, Monteith P, Noble NA, Sikaroodi M, Gillevet PM. 2012. Colonic mucosal microbiome differs from stool microbiome in cirrhosis and hepatic encephalopathy and is linked to cognition and inflammation. Am J Physiol Gastrointest Liver Physiol. 303(6):G675–85.
   PubMed Web of Science ®Google Scholar
• Balaguer F, Enrique M, Llopis S, Barrena M, Navarro V, Álvarez B, Chenoll E, Ramón D, Tortajada M, Martorell P, et al. 2021. Lipoteichoic acid from Bifidobacterium animalis subsp. lactis BPL1: a novel postbiotic that reduces fat deposition via IGF-1 pathway. Microb Biotechnol. 1–12.
   Web of Science ®Google Scholar
• Barash NR, Maloney JG, Singer SM, Dawson SC. 2017. Giardia Alters Commensal Microbial Diversity throughout the Murine Gut. Appleton JA, editor. Infect Immun. 85(6):e00948–16.
   PubMed Web of Science ®Google Scholar
• Barbieri F, Montanari C, Gardini F, Tabanelli G. 2019. Biogenic Amine Production by Lactic Acid Bacteria: A Review. Foods Basel Switz. 8(1):17.
   Web of Science ®Google Scholar
• Bartfeld S. 2016. Modeling infectious diseases and host-microbe interactions in gastrointestinal organoids. Dev Biol. 420(2):262–270.
   PubMed Web of Science ®Google Scholar
• Bastiaanssen TFS, Cowan CSM, Claesson MJ, Dinan TG, Cryan JF. 2019. Making sense of … the microbiome in psychiatry. Int J Neuropsychopharmacol. 22(1):37–52.
   PubMed Web of Science ®Google Scholar
• Bauer S, Wennberg Huldt C, Kanebratt KP, Durieux I, Gunne D, Andersson S, Ewart L, Haynes WG, Maschmeyer I, Winter A, et al. 2017. Functional coupling of human pancreatic islets and liver spheroids on-a-chip: Towards a novel human ex vivo type 2 diabetes model. Sci Rep. 7(1):14620.
   PubMedGoogle Scholar
• Beaurivage C, Kanapeckaite A, Loomans C, Erdmann KS, Stallen J, Janssen RAJ. 2020. Development of a human primary gut-on-a-chip to model inflammatory processes. Sci Rep. 10(1):21475.
   PubMed Web of Science ®Google Scholar
• Beaurivage C, Naumovska E, Chang YX, Elstak ED, Nicolas A, Wouters H, et al. 2019. Development of a gut-on-a-chip model for high throughput disease modeling and drug discovery. Int J Mol Sci. 20(22):5661.
   Web of Science ®Google Scholar
• Bein A, Shin W, Jalili-Firoozinezhad S, Park MH, Sontheimer-Phelps A, Tovaglieri A, Chalkiadaki A, Kim HJ, Ingber DE. 2018. Microfluidic organ-on-a-chip models of human intestine. Cell Mol Gastroenterol Hepatol. 5(4):659–668.
   PubMed Web of Science ®Google Scholar
• Belkaid Y, Hand TW. 2014. Role of the microbiota in immunity and inflammation. Cell. 157(1):121–141.
   PubMed Web of Science ®Google Scholar
• Bell V, Ferrão J, Pimentel L, Pintado M, Fernandes T. 2018. One health, fermented foods, and gut microbiota. Foods Basel Switz. 7(12):195.
   Web of Science ®Google Scholar
• Beulens JWJ, Booth SL, van den Heuvel EGHM, Stoecklin E, Baka A, Vermeer C. 2013. The role of menaquinones (vitamin K2) in human health. Br J Nutr. 110(8):1357–1368.
   PubMed Web of Science ®Google Scholar
• Bricks T, Paullier P, Legendre A, Fleury M-J, Zeller P, Merlier F, Anton PM, Leclerc E. 2014. Development of a new microfluidic platform integrating co-cultures of intestinal and liver cell lines. Toxicol in Vitro. 28(5):885–895.
   PubMed Web of Science ®Google Scholar
• Broussard JL, Devkota S. 2016. The changing microbial landscape of Western society: diet, dwellings and discordance. Mol Metab. 5(9):737–742.
   PubMed Web of Science ®Google Scholar
• Bulutoglu B, Rey-Bedón C, Kang YB, Mert S, Yarmush ML, Usta OB. 2019. A microfluidic patterned model of non-alcoholic fatty liver disease: applications to disease progression and zonation. Lab Chip. 19(18):3022–3031.
   PubMed Web of Science ®Google Scholar
• Cabrera-Rubio R, Patterson AM, Cotter PD, Beraza N. 2019. Cholestasis induced by bile duct ligation promotes changes in the intestinal microbiome in mice. Sci Rep. 9(1):12324.
   PubMedGoogle Scholar
• Camarillo-Guerrero LF, Almeida A, Rangel-Pineros G, Finn RD, Lawley TD. 2021. Massive expansion of human gut bacteriophage diversity. Cell. 184(4):1098–1109.e9.
   PubMed Web of Science ®Google Scholar
• Castaner O, Goday A, Park Y-M, Lee S-H, Magkos F, Shiow S-ATE, Schröder H. 2018. The Gut Microbiome Profile in Obesity: A Systematic Review. Int J Endocrinol.2018:4095789–4095789.
   PubMed Web of Science ®Google Scholar
• Celebioglu HU. 2021. Effects of potential synbiotic interaction between Lactobacillus rhamnosus GG and salicylic acid on human colon and prostate cancer cells. Arch Microbiol. 203(3):1221–1229. Available from:.
   PubMed Web of Science ®Google Scholar
• Ceppa F, Mancini A, Tuohy K. 2019. Current evidence linking diet to gut microbiota and brain development and function. Int J Food Sci Nutr. 70(1):1–19.
   PubMed Web of Science ®Google Scholar
• Chen HJ, Miller P, Shuler ML. 2018. A pumpless body-on-a-chip model using a primary culture of human intestinal cells and a 3D culture of liver cells. Lab Chip. 18(14):2036–2046.
   PubMed Web of Science ®Google Scholar
• Chen M, Sun Q, Giovannucci E, Mozaffarian D, Manson JE, Willett WC, Hu FB. 2014. Dairy consumption and risk of type 2 diabetes: 3 cohorts of US adults and an updated meta-analysis. BMC Med. 12(1):215–215.
   PubMedGoogle Scholar
• Chi M, Yi B, Oh S, Park D-J, Sung JH, Park S. 2015. A microfluidic cell culture device (μFCCD) to culture epithelial cells with physiological and morphological properties that mimic those of the human intestine. Biomed Microdevices. 17(3):9966.
   PubMed Web of Science ®Google Scholar
• Cho H‐J, Kim H‐J, Lee KJu, Lasli S, Ung A, Hoffman T, Nasiri R, Bandaru P, Ahadian S, Dokmeci MR, et al. 2021. Liver-on-a-chip: bioengineered multicellular liver microtissues for modeling advanced hepatic fibrosis driven through non-alcoholic fatty liver disease (Small 14/2021). Small. 17(14):2170061.
   Web of Science ®Google Scholar
• Choe A, Ha SK, Choi I, Choi N, Sung JH. 2017. Microfluidic Gut-liver chip for reproducing the first pass metabolism. Biomed Microdev. 19(1):4.
   PubMed Web of Science ®Google Scholar
• Chong PP, Chin VK, Looi CY, Wong WF, Madhavan P, Yong VC. 2019. The microbiome and irritable bowel syndrome - a review on the pathophysiology, current research and future therapy. Front Microbiol.10:1136–1136.
   PubMed Web of Science ®Google Scholar
• Claesson MJ, Jeffery IB, Conde S, Power SE, O'Connor EM, Cusack S, Harris HMB, Coakley M, Lakshminarayanan B, O'Sullivan O, et al. 2012. Gut microbiota composition correlates with diet and health in the elderly. Nature. 488(7410):178–184.
   PubMed Web of Science ®Google Scholar
• Codoñer FM, Ramírez-Bosca A, Climent E, Carrión-Gutierrez M, Guerrero M, Pérez-Orquín JM, Horga de la Parte J, Genovés S, Ramón D, Navarro-López V, et al. 2018. Gut microbial composition in patients with psoriasis. Sci Rep. 8(1):3812.
   PubMedGoogle Scholar
• Collado MC, Vinderola G, Salminen S. 2019. Postbiotics: facts and open questions. A position paper on the need for a consensus definition. Benef Microbes. 10(7):711–719.
   PubMed Web of Science ®Google Scholar
• Cotter PD, Hill C, Ross RP. 2005. Bacteriocins: developing innate immunity for food. Nat Rev Microbiol. (10):777–3:788.
   PubMed Web of Science ®Google Scholar
• Crespo-Piazuelo D, Migura-Garcia L, Estellé J, Criado-Mesas L, Revilla M, Castelló A, Muñoz M, García-Casco JM, Fernández AI, Ballester M, et al. 2019. Association between the pig genome and its gut microbiota composition. Sci Rep. 9(1):8791.
   PubMedGoogle Scholar
• Cryan JF, O'Riordan KJ, Cowan CSM, Sandhu KV, Bastiaanssen TFS, Boehme M, Codagnone MG, Cussotto S, Fulling C, Golubeva AV, et al. 2019. The microbiota-gut-brain axis. Physiol Rev. 99(4):1877–2013.
   PubMed Web of Science ®Google Scholar
• Dahlberg T, Stangner T, Zhang H, Wiklund K, Lundberg P, Edman L, Andersson M. 2018. 3D printed water-soluble scaffolds for rapid production of PDMS micro-fluidic flow chambers. Sci Rep. 8(1):3372.
   PubMedGoogle Scholar
• De Filippis F, Pasolli E, Ercolini D. 2020. The food-gut axis: lactic acid bacteria and their link to food, the gut microbiome and human health. FEMS Microbiol Rev. 44(4):454–489.
   PubMed Web of Science ®Google Scholar
• de Goffau MC, Lager S, Salter SJ, Wagner J, Kronbichler A, Charnock-Jones DS, Peacock SJ, Smith GCS, Parkhill J. 2018. Recognizing the reagent microbiome. Nat Microbiol. 3(8):851–853.
   PubMed Web of Science ®Google Scholar
• de Haan P, Ianovska MA, Mathwig K, van Lieshout GAA, Triantis V, Bouwmeester H, Verpoorte E. 2019. Digestion-on-a-chip: a continuous-flow modular microsystem recreating enzymatic digestion in the gastrointestinal tract. Lab Chip. 19(9):1599–1609.
   PubMed Web of Science ®Google Scholar
• de Haan P, Santbergen MJC, van der Zande M, Bouwmeester H, Nielen MWF, Verpoorte E. 2021. A versatile, compartmentalised gut-on-a-chip system for pharmacological and toxicological analyses. Sci Rep. 11(1):4920.
   PubMed Web of Science ®Google Scholar
• De Simone C. 2018. Letter: what gastroenterologists should know about VSL#3. Aliment Pharmacol Ther. 47(5):698–699.
   PubMed Web of Science ®Google Scholar
• Degen LP, Phillips SF. 1996. Variability of gastrointestinal transit in healthy women and men. Gut. 39(2):299–305.
   PubMed Web of Science ®Google Scholar
• Deng J, Wei W, Chen Z, Lin B, Zhao W, Luo Y. 2019. Engineered liver-on-a-chip platform to mimic liver functions and its biomedical applications: a review. Micromachines. 10(10):676.
   Web of Science ®Google Scholar
• Devkota S, Chang EB. 2015. Interactions between diet, bile acid metabolism, gut microbiota, and inflammatory bowel diseases. Dig Dis. 33(3):351–356.
   PubMed Web of Science ®Google Scholar
• Diaz M, Kellingray L, Akinyemi N, Adefiranye OO, Olaonipekun AB, Bayili GR, Ibezim J, Du Plessis AS, Houngbédji M, Kamya D, et al. Comparison of the microbial composition of African fermented foods using amplicon sequencing. Sci Rep. 2019. 9(1):13863.
   PubMedGoogle Scholar
• Diaz M, Ladero V, Redruello B, Sanchez-Llana E, del Rio B, Fernandez M, Martin MC, Alvarez MA. 2016. A PCR-DGGE method for the identification of histamine-producing bacteria in cheese. Food Control. 63:216–223.
   Web of Science ®Google Scholar
• Distrutti E, Monaldi L, Ricci P, Fiorucci S. 2016. Gut microbiota role in irritable bowel syndrome: New therapeutic strategies. World J Gastroenterol. 22(7):2219–2241.
   PubMed Web of Science ®Google Scholar
• Donaldson GP, Lee SM, Mazmanian SK. 2016. Gut biogeography of the bacterial microbiota. Nat Rev Microbiol. 14(1):20–32.
   PubMed Web of Science ®Google Scholar
• Donia MS, Fischbach MA. 2015. Human Microbiota. Small molecules from the human microbiota. Science. 349(6246):1254766.
   PubMed Web of Science ®Google Scholar
• Donkers JM, Eslami Amirabadi H, van de Steeg E. 2021. Intestine-on-a-chip: next level in vitro research model of the human intestine. Curr Opin Toxicol.25:6–14.
   Web of Science ®Google Scholar
• Eain MMG, Baginska J, Greenhalgh K, Fritz JV, Zenhausern F, Wilmes P. 2017. Engineering solutions for representative models of the gastrointestinal human-microbe interface. Engineering. 3(1):60–65.
   Web of Science ®Google Scholar
• Esch EW, Bahinski A, Huh D. 2015. Organs-on-chips at the frontiers of drug discovery. Nat Rev Drug Discov. 14(4):248–260.
   PubMed Web of Science ®Google Scholar
• Filosa S, Di Meo F, Crispi S. 2018. Polyphenols-gut microbiota interplay and brain neuromodulation. Neural Regen Res. 13(12):2055–2059.
   PubMed Web of Science ®Google Scholar
• Firth J, Gangwisch JE, Borisini A, Wootton RE, Mayer EA. 2020. Food and mood: how do diet and nutrition affect mental wellbeing? BMJ.369:m2382.
   PubMedGoogle Scholar
• Freag MS, Namgung B, Reyna Fernandez ME, Gherardi E, Sengupta S, Jang HL. 2021. Human nonalcoholic steatohepatitis on a chip. Hepatol Commun. 5(2):217–233.
   PubMed Web of Science ®Google Scholar
• Fritz JV, Desai MS, Shah P, Schneider JG, Wilmes P. 2013. From meta-omics to causality: experimental models for human microbiome research. Microbiome. 1(1):14.
   PubMedGoogle Scholar
• Garcia-Gutierrez E, Mayer MJ, Cotter PD, Narbad A. 2019. Gut microbiota as a source of novel antimicrobials. Gut Microbes. 10(1):1–21.
   PubMed Web of Science ®Google Scholar
• Garcia-Gutierrez E, Narbad A, Rodríguez JM. 2020. Autism spectrum disorder associated with gut microbiota at immune, metabolomic, and neuroactive level. Front Neurosci.14:578666.
   PubMed Web of Science ®Google Scholar
• Garcia-Gutierrez E. 2019. New antimicrobials to target gut and food pathogens. [Thesis]. University of East Anglia
   Google Scholar
• Ghosh TS, Rampelli S, Jeffery IB, Santoro A, Neto M, Capri M, Giampieri E, Jennings A, Candela M, Turroni S, et al. 2020. Mediterranean diet intervention alters the gut microbiome in older people reducing frailty and improving health status: the NU-AGE 1-year dietary intervention across five European countries. Gut. 69(7):1218–1228.
   PubMed Web of Science ®Google Scholar
• Gibson GR, Hutkins R, Sanders ME, Prescott SL, Reimer RA, Salminen SJ, Scott K, Stanton C, Swanson KS, Cani PD, et al. 2017. Expert consensus document: the international scientific association for probiotics and prebiotics (ISAPP) consensus statement on the definition and scope of prebiotics. Nat Rev Gastroenterol Hepatol. 14(8):491–502.
   PubMed Web of Science ®Google Scholar
• Gibson PR, Halmos EP, Muir JG. 2020. Review article: FODMAPS, prebiotics and gut health-the FODMAP hypothesis revisited. Aliment Pharmacol Ther. 52(2):233–246.
   PubMed Web of Science ®Google Scholar
• Gokaltun A, Yarmush ML, Asatekin A, Usta OB. 2017. Recent advances in nonbiofouling PDMS surface modification strategies applicable to microfluidic technology. Technology. 5(1):1–12.
   PubMed Web of Science ®Google Scholar
• Gori M, Simonelli MC, Giannitelli SM, Businaro L, Trombetta M, Rainer A. 2016. Investigating nonalcoholic fatty liver disease in a liver-on-a-chip microfluidic device. PLOS One. 11(7):e0159729.
   PubMed Web of Science ®Google Scholar
• Grangette C, Nutten S, Palumbo E, Morath S, Hermann C, Dewulf J, Pot B, Hartung T, Hols P, Mercenier A, et al. 2005. Enhanced antiinflammatory capacity of a Lactobacillus plantarum mutant synthesizing modified teichoic acids. Proc Natl Acad Sci U S A. 102(29):10321–10326.
   PubMed Web of Science ®Google Scholar
• Grassart A, Malardé V, Gobaa S, Sartori-Rupp A, Kerns J, Karalis K, Marteyn B, Sansonetti P, Sauvonnet N. 2019. Bioengineered human organ-on-chip reveals intestinal microenvironment and mechanical forces impacting shigella infection. Cell Host Microbe. 26(3):435–444.e4.
   PubMed Web of Science ®Google Scholar
• Guenat OT, Berthiaume F. 2018. Incorporating mechanical strain in organs-on-a-chip: lung and skin. Biomicrofluidics. 12(4):042207–042207.
   PubMed Web of Science ®Google Scholar
• 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(4):295–308.
   PubMed Web of Science ®Google Scholar
• Hassan S, Sebastian S, Maharjan S, Lesha A, Carpenter A-M, Liu X, Xie X, Livermore C, Zhang YS, Zarrinpar A, et al. 2020. Liver-on-a-chip models of fatty liver disease. Hepatology. 71(2):733–740.
   PubMed Web of Science ®Google Scholar
• Hermann E, Foligne B. 2017. Healthy gut microbiota can resolve undernutrition. Hepatobiliary Surg Nutr. 6(2):141–143.
   PubMed Web of Science ®Google Scholar
• Hill C, Guarner F, Reid G, Gibson GR, Merenstein DJ, Pot B, Morelli L, Canani RB, Flint HJ, Salminen S, et al. 2014. Expert consensus document. The International Scientific Association for Probiotics and Prebiotics consensus statement on the scope and appropriate use of the term probiotic. Nat Rev Gastroenterol Hepatol. 11(8):506–514.
   PubMed Web of Science ®Google Scholar
• Hills RD, Jr, Pontefract BA, Mishcon HR, Black CA, Sutton SC, Theberge CR. 2019. Gut microbiome: profound implications for diet and disease. Nutrients. 11(7):1613.
   PubMed Web of Science ®Google Scholar
• Holscher HD. 2017. Dietary fiber and prebiotics and the gastrointestinal microbiota. Gut Microbes. 8(2):172–184.
   PubMed Web of Science ®Google Scholar
• Huh D, Hamilton GA, Ingber DE. 2011. From 3D cell culture to organs-on-chips. Trends Cell Biol. 21(12):745–754.
   PubMed Web of Science ®Google Scholar
• Ingber DE. 2018. Developmentally inspired human ‘organs on chips. Dev Camb Engl. 145(16):dev156125.
   PubMed Web of Science ®Google Scholar
• Isaacs-Ten A, Echeandia M, Moreno-Gonzalez M, Brion A, Goldson A, Philo M, et al. 2020. Intestinal microbiome-macrophage crosstalk contributes to cholestatic liver disease by promoting intestinal permeability. Hepatology. 72:2090–2108. Available from:.
   PubMed Web of Science ®Google Scholar
• Jalili-Firoozinezhad S, Gazzaniga FS, Calamari EL, Camacho DM, Fadel CW, Bein A, Swenor B, Nestor B, Cronce MJ, Tovaglieri A, et al. 2019. A complex human gut microbiome cultured in an anaerobic intestine-on-a-chip. Nat Biomed Eng. 3(7):520–531.
   PubMed Web of Science ®Google Scholar
• Jandhyala SM, Talukdar R, Subramanyam C, Vuyyuru H, Sasikala M, Nageshwar Reddy D. 2015. Role of the normal gut microbiota. World J Gastroenterol. 21(29):8787–8803.
   PubMed Web of Science ®Google Scholar
• Jang K-J, Otieno MA, Ronxhi J, Lim H-K, Ewart L, Kodella KR, Petropolis DB, Kulkarni G, Rubins JE, Conegliano D, et al. 2019. Reproducing human and cross-species drug toxicities using a Liver-Chip. Sci Transl Med. 11(517):eaax5516.
   PubMed Web of Science ®Google Scholar
• Johnson KVA. 2020. Gut microbiome composition and diversity are related to human personality traits. Hum Microb J. 15. DOI:https://doi.org/10.1016/j.humic.2019.100069
   Google Scholar
• Junaid A, Mashaghi A, Hankemeier T, Vulto P. 2017. An end-user perspective on Organ-on-a-Chip: assays and usability aspects. Curr Opin Biomed Eng. 1:15–22.
   Google Scholar
• Kaarj K, Yoon J-Y. 2019. Methods of delivering mechanical stimuli to organ-on-a-chip. Micromachines. 10(10):700.
   PubMed Web of Science ®Google Scholar
• Kasendra M, Luc R, Yin J, Manatakis DV, Kulkarni G, Lucchesi C, et al. 2020. Duodenum Intestine-Chip for preclinical drug assessment in a human relevant model. eLife.9:e50135.
   PubMed Web of Science ®Google Scholar
• Kilic T, Navaee F, Stradolini F, Renaud P, Carrara S. 2018. Organs-on-chip monitoring: sensors and other strategies. Microphysiol Syst. 1:1–1. [cited 2018 Jan 1]; Available from: http://mps.amegroups.com/article/view/4689.
   Google Scholar
• Kim HJ, Huh D, Hamilton G, Ingber DE. 2012. Human gut-on-a-chip inhabited by microbial flora that experiences intestinal peristalsis-like motions and flow. Lab Chip. 12(12):2165–2174.
   PubMed Web of Science ®Google Scholar
• Kim HJ, Ingber DE. 2013. Gut-on-a-Chip microenvironment induces human intestinal cells to undergo villus differentiation. Integr Biol. 5(9):1130–1140.
   Google Scholar
• Kim HJ, Li H, Collins JJ, Ingber DE. 2016. Contributions of microbiome and mechanical deformation to intestinal bacterial overgrowth and inflammation in a human gut-on-a-chip. Proc Natl Acad Sci USA. 113(1):E7–15.
   PubMed Web of Science ®Google Scholar
• Kim J, Koo B-K, Knoblich JA. 2020. Human organoids: model systems for human biology and medicine. Nat Rev Mol Cell Biol. 21(10):571–584.
   PubMed Web of Science ®Google Scholar
• Konstantinov SR, Smidt H, de Vos WM, Bruijns SCM, Singh SK, Valence F, et al. 2008. S layer protein A of Lactobacillus acidophilus NCFM regulates immature dendritic cell and T cell functions. Proc Natl Acad Sci. 105(49):19474.
   PubMed Web of Science ®Google Scholar
• Kostic AD, Howitt MR, Garrett WS. 2013. Exploring host-microbiota interactions in animal models and humans. Genes Dev. 27(7):701–718.
   PubMed Web of Science ®Google Scholar
• Koudoufio M, Desjardins Y, Feldman F, Spahis S, Delvin E, Levy E. 2020. Insight into polyphenol and gut microbiota crosstalk: are their metabolites the key to understand protective effects against metabolic disorders? Antioxid Basel Switz. 9(10):982.
   Web of Science ®Google Scholar
• Kowalski K, Mulak A. 2019. Brain-gut-microbiota axis in alzheimer's disease. J Neurogastroenterol Motil. 25(1):48–60.
   PubMed Web of Science ®Google Scholar
• Kulthong K, Duivenvoorde L, Mizera BZ, Rijkers D, Dam G. Oegema G, Puzyn T, Bouwmeester H, van der Zande M. 2018.Implementation of a dynamic intestinal gut-on-a-chip barrier model for transport studies of lipophilic dioxin congeners. RSC Adv. 8(57):32440–32453.
   PubMed Web of Science ®Google Scholar
• Kulthong K, Duivenvoorde L, Sun H, Confederat S, Wu J, Spenkelink B, de Haan L, Marin V, van der Zande M, Bouwmeester H, et al. 2020. Microfluidic chip for culturing intestinal epithelial cell layers: Characterization and comparison of drug transport between dynamic and static models. Toxicol in Vitro. 65:104815.
   PubMed Web of Science ®Google Scholar
• Laforest-Lapointe I, Arrieta M-C. 2018. Microbial eukaryotes: a missing link in gut microbiome studies. mSystems. 3(2):e00201–17.
   PubMed Web of Science ®Google Scholar
• Lawrence GW, Begley M, Cotter PD, Guinane CM. 2020. The more we learn, the less we know: deciphering the link between human gut fusobacteria and colorectal cancer. Dig Med Res. 3:21–21. [Internet].[cited 2020 Jan 1].
   Google Scholar
• Lea T. 2015. Caco-2 cell line. In: Verhoeckx K, Cotter P, López-Expósito I, Kleiveland C, Lea T, Mackie A, et al. editors. The impact of food bioactives on health: in vitro and ex vivo models [Internet]. Cham: Springer International Publishing. p. 103–111. Available from:.
   Google Scholar
• Lebeer S, Claes I, Tytgat HLP, Verhoeven TLA, Marien E, von Ossowski I, Reunanen J, Palva A, Vos W. M d, Keersmaecker SCJD, et al. 2012. Functional analysis of lactobacillus rhamnosus gg pili in relation to adhesion and immunomodulatory interactions with intestinal epithelial cells. Appl Environ Microbiol. 78(1):185–193.
   PubMed Web of Science ®Google Scholar
• Lee B, Moon KM, Kim CY. 2018. Tight junction in the intestinal epithelium: its association with diseases and regulation by phytochemicals. J Immunol Res.2018:2645465–2645465.
   PubMed Web of Science ®Google Scholar
• Leng B, Sørensen MB, Kot W, Thymann T, Krych L, Nielsen DS. 2019. Severe gut microbiota dysbiosis caused by malnourishment can be partly restored during 3 weeks of refeeding with fortified corn-soy-blend in a piglet model of childhood malnutrition. BMC Microbiol. 19(1):277.
   PubMed Web of Science ®Google Scholar
• Li C, Kwok L-Y, Mi Z, Bala J, Xue J, Yang J, Ma Y, Zhang H, ChenY 2017Characterization of the angiotensin-converting enzyme inhibitory activity of fermented milks produced with Lactobacillus casei. J Dairy Sci. . 100(12):9495–9507.
   PubMed Web of Science ®Google Scholar
• Li X, Tian T. 2018. Recent advances in an organ-on-a-chip: biomarker analysis and applications. Anal Methods. 10(26):3122–3130.
   Web of Science ®Google Scholar
• Lin A, Sved Skottvoll F, Rayner S, Pedersen-Bjergaard S, Sullivan G, Krauss S, Ray Wilson S, Harrison S. 2020. 3D cell culture models and organ-on-a-chip: Meet separation science and mass spectrometry. Electrophoresis.41(1-2):56–64.
   PubMed Web of Science ®Google Scholar
• Linares DM, Gómez C, Renes E, Fresno JM, Tornadijo ME, Ross RP, Stanton C. 2017. Lactic acid bacteria and bifidobacteria with potential to design natural biofunctional health-promoting dairy foods. Front Microbiol. 8:846–846.
   PubMed Web of Science ®Google Scholar
• Linares DM, O'Callaghan TF, O'Connor PM, Ross RP, Stanton C. 2016. Streptococcus thermophilus APC151 Strain Is Suitable for the Manufacture of Naturally GABA-Enriched Bioactive Yogurt. Front Microbiol.7:1876–1876.
   PubMed Web of Science ®Google Scholar
• Liwinski T, Zenouzi R, John C, Ehlken H, Rühlemann MC, Bang C, Groth S, Lieb W, Kantowski M, Andersen N, et al. 2020. Alterations of the bile microbiome in primary sclerosing cholangitis. Gut. 69(4):665–672.
   PubMed Web of Science ®Google Scholar
• Low LA, Mummery C, Berridge BR, Austin CP, Tagle DA. 2021. Organs-on-chips: into the next decade. Nat Rev Drug Discov. 20(5):345–361.
   PubMed Web of Science ®Google Scholar
• Lozupone CA, Stombaugh JI, Gordon JI, Jansson JK, Knight R. 2012. Diversity, stability and resilience of the human gut microbiota. Nature. 489(7415):220–230.
   PubMed Web of Science ®Google Scholar
• Lynch KE, Parke EC, O’Malley MA. 2019. How causal are microbiomes? A comparison with the Helicobacter pylori explanation of ulcers. Biol Philos. 34(6):62.
   Web of Science ®Google Scholar
• Ma C, Peng Y, Li H, Chen W. 2021. Organ-on-a-chip: a new paradigm for drug development. Trends Pharmacol Sci. 42(2):119–133.
   PubMed Web of Science ®Google Scholar
• Ma L, Kim J, Hatzenpichler R, Karymov MA, Hubert N, Hanan IM, Chang EB, Ismagilov RF. 2014. Gene-targeted microfluidic cultivation validated by isolation of a gut bacterium listed in Human Microbiome Project's Most Wanted taxa. Proc Natl Acad Sci USA. 111(27):9768–9773.
   PubMed Web of Science ®Google Scholar
• Mackie A, Mulet-Cabero A-I, Torcello-Gómez A. 2020. Simulating human digestion: developing our knowledge to create healthier and more sustainable foods. Food Funct. 11:9397–9431. DOI:https://doi.org/10.1039/D0FO01981J
   PubMed Web of Science ®Google Scholar
• Macori G, Cotter PD. 2018. Novel insights into the microbiology of fermented dairy foods. Curr Opin Biotechnol.49:172–178.
   PubMed Web of Science ®Google Scholar
• Maeda Y, Takeda K. 2017. Role of gut microbiota in rheumatoid arthritis. J Clin Med. 6(6):60.
   Web of Science ®Google Scholar
• Mah J-H, Park YK, Jin YH, Lee J-H, Hwang H-J. 2019. Bacterial production and control of biogenic amines in Asian fermented soybean foods. Foods Basel Switz. 8(2):85.
   Web of Science ®Google Scholar
• Makki K, Deehan EC, Walter J, Bäckhed F. 2018. The impact of dietary fiber on gut microbiota in host health and disease. Cell Host Microbe. 23(6):705–715.
   PubMed Web of Science ®Google Scholar
• Marco ML, Heeney D, Binda S, Cifelli CJ, Cotter PD, Foligné B, Gänzle M, Kort R, Pasin G, Pihlanto A, et al. 2017. Health benefits of fermented foods: microbiota and beyond. Curr Opin Biotechnol.44:94–102.
   PubMed Web of Science ®Google Scholar
• Marco ML, Sanders ME, Gänzle M, Arrieta MC, Cotter PD, De Vuyst L, Hill C, Holzapfel W, Lebeer S, Merenstein D, et al. 2021.The international scientific association for probiotics and prebiotics (isapp) consensus statement on fermented foods. Nat Rev Gastroenterol Hepatol. 18(3):196–208. Available from:.
   PubMed Web of Science ®Google Scholar
• Maschmeyer I, Lorenz AK, Schimek K, Hasenberg T, Ramme AP, Hübner J, Lindner M, Drewell C, Bauer S, Thomas A, et al. 2015. A four-organ-chip for interconnected long-term co-culture of human intestine, liver, skin and kidney equivalents. Lab Chip. 15(12):2688–2699.
   PubMed Web of Science ®Google Scholar
• Mata A, Fleischman AJ, Roy S. 2005. Characterization of Polydimethylsiloxane (PDMS) Properties for Biomedical Micro/Nanosystems. Biomed Microdevices. 7(4):281–293.
   PubMed Web of Science ®Google Scholar
• Maurer M, Gresnigt MS, Last A, Wollny T, Berlinghof F, Pospich R, Cseresnyes Z, Medyukhina A, Graf K, Gröger M, et al. 2019. A three-dimensional immunocompetent intestine-on-chip model as in vitro platform for functional and microbial interaction studies. Biomaterials.220:119396.
   PubMed Web of Science ®Google Scholar
• McDonald JC, Whitesides GM. 2002. Poly(dimethylsiloxane) as a material for fabricating microfluidic devices. Acc Chem Res. 35(7):491–499.
   PubMed Web of Science ®Google Scholar
• McGrane MM, Essery E, Obbagy J, Lyon J, Macneil P, Spahn J, Van Horn L. 2011. Dairy consumption, blood pressure, and risk of hypertension: an evidence-based review of recent literature. Curr Cardiovasc Risk Rep. 5(4):287–298.
   PubMedGoogle Scholar
• Merra G, Noce A, Marrone G, Cintoni M, Tarsitano MG, Capacci A, et al. 2021. Influence of mediterranean diet on human gut microbiota. Nutrients. 13(1):7.
   Web of Science ®Google Scholar
• Meslier V, Laiola M, Roager HM, De Filippis F, Roume H, Quinquis B, Giacco R, Mennella I, Ferracane R, Pons N, et al. 2020. Mediterranean diet intervention in overweight and obese subjects lowers plasma cholesterol and causes changes in the gut microbiome and metabolome independently of energy intake. Gut. 69(7):1258–1268.
   PubMed Web of Science ®Google Scholar
• Mikkonen R, Puistola P, Jönkkäri I, Mäntysalo M. 2020. Inkjet printable polydimethylsiloxane for all-inkjet-printed multilayered soft electrical applications. ACS Appl Mater Interfaces. 12(10):11990–11997.
   PubMed Web of Science ®Google Scholar
• Milani C, Duranti S, Bottacini F, Casey E, Turroni F, Mahony J, et al. 2017. The first microbial colonizers of the human gut: composition, activities, and health implications of the infant gut microbiota. Microbiol Mol Biol Rev. 81(4):e00036–e00017.
   PubMed Web of Science ®Google Scholar
• Million M, Angelakis E, Maraninchi M, Henry M, Giorgi R, Valero R, Vialettes B, Raoult D. 2013. Correlation between body mass index and gut concentrations of Lactobacillus reuteri, Bifidobacterium animalis, Methanobrevibacter smithii and Escherichia coli. Int J Obes. 37(11):1460–1466.
   PubMed Web of Science ®Google Scholar
• Miraglia F, Colla E. 2019. Microbiome, parkinson’s disease and molecular mimicry. Cells. 8(3):222.
   Web of Science ®Google Scholar
• Molinero N, Ruiz L, Milani C, Gutiérrez-Díaz I, Sánchez B, Mangifesta M, Segura J, Cambero I, Campelo AB, García-Bernardo CM, et al. 2019. The human gallbladder microbiome is related to the physiological state and the biliary metabolic profile. Microbiome. 7(1):100.
   PubMedGoogle Scholar
• Molinero N, Ruiz L, Sánchez B, Margolles A, Delgado S. 2019. Intestinal bacteria interplay with bile and cholesterol metabolism: implications on host physiology. Front Physiol.10:185–185.
   PubMed Web of Science ®Google Scholar
• Moreno-Gonzalez M, Beraza N. 2021. The role of the microbiome in liver cancer. Cancers. 13(10). DOI:https://doi.org/10.3390/cancers13102330
   Google Scholar
• Morton JT, Aksenov AA, Nothias LF, Foulds JR, Quinn RA, Badri MH, Swenson TL, Van Goethem MW, Northen TR, Vazquez-Baeza Y, et al. 2019. Learning representations of microbe-metabolite interactions. Nat Methods. 16(12):1306–1314.
   PubMed Web of Science ®Google Scholar
• Mousa WK, Athar B, Merwin NJ, Magarvey NA. 2017. Antibiotics and specialized metabolites from the human microbiota. Nat Prod Rep. 34(11):1302–1331.
   PubMed Web of Science ®Google Scholar
• Mozaffarian D, Hao T, Rimm EB, Willett WC, Hu FB. 2011. Changes in diet and lifestyle and long-term weight gain in women and men. N Engl J Med. 364(25):2392–2404.
   PubMed Web of Science ®Google Scholar
• Myhrstad MCW, Tunsjø H, Charnock C, Telle-Hansen VH. 2020. Dietary Fiber, gut microbiota, and metabolic regulation-current status in human randomized trials. Nutrients. 12(3):859.
   Web of Science ®Google Scholar
• Nampoothiri KM, Beena DJ, Vasanthakumari DS, Ismail B. 2017. Chapter 3 - Health Benefits of Exopolysaccharides in Fermented Foods. In: Frias J, Martinez-Villaluenga C, Peñas E, editors. Fermented Foods in Health and Disease Prevention [Internet]. Boston: Academic Press; p. 49–62. Available from: http://www.sciencedirect.com/science/article/pii/B9780128023099000030.
   Google Scholar
• Nash AK, Auchtung TA, Wong MC, Smith DP, Gesell JR, Ross MC, Stewart CJ, Metcalf GA, Muzny DM, Gibbs RA, et al. 2017. The gut mycobiome of the Human Microbiome Project healthy cohort. Microbiome. 5(1):153.
   PubMedGoogle Scholar
• Nawroth JC, Petropolis DB, Manatakis DV, Maulana TI, Burchett G, Schlünder K, et al. 2020. Modeling alcoholic liver disease in a human Liver-Chip. bioRxiv.
   Google Scholar
• Nguyen TLA, Vieira-Silva S, Liston A, Raes J. 2015. How informative is the mouse for human gut microbiota research? Dis Model Mech. 8(1):1–16.
   PubMed Web of Science ®Google Scholar
• Nishida A, Inoue R, Inatomi O, Bamba S, Naito Y, Andoh A. 2018. Gut microbiota in the pathogenesis of inflammatory bowel disease. Clin J Gastroenterol. 11(1):1–10.
   PubMed Web of Science ®Google Scholar
• Nkamga VD, Henrissat B, Drancourt M. 2017. Archaea: essential inhabitants of the human digestive microbiota. Hum Microbiome J.3:1–8.
   Google Scholar
• Nogacka AM, Ruas-Madiedo P, Gómez E, Solís G, Fernández N, Suárez M, Suárez A, Salazar N, de Los Reyes-Gavilán CG, Gueimonde M, et al. 2018. Real-time monitoring of HT29 epithelial cells as an in vitro model for assessing functional differences among intestinal microbiotas from different human population groups. J Microbiol Methods.152:210–216.
   PubMed Web of Science ®Google Scholar
• Nogacka AM. 2020. Modelos de interacción microbiota-hospedador en el entorno intestinal y su aplicación en el desarrollo de productos probióticos y prebióticos [Tesis Doctoral]. Oviedo: Universidad de Oviedo.
   Google Scholar
• Novak R, Didier M, Calamari E, Ng CF, Choe Y, Clauson SL, et al. 2018. Scalable fabrication of stretchable, dual channel, microfluidic organ chips. J Vis Exp JoVE.140:58151.
   Google Scholar
• Nueno-Palop C, Narbad A. 2011. Probiotic assessment of Enterococcus faecalis CP58 isolated from human gut. Int J Food Microbiol. 145(2-3):390–394.
   PubMed Web of Science ®Google Scholar
• Ochs CJ, Kasuya J, Pavesi A, Kamm RD. 2014. Oxygen levels in thermoplastic microfluidic devices during cell culture. Lab Chip. 14(3):459–462.
   PubMed Web of Science ®Google Scholar
• Odijk M, van der Meer AD, Levner D, Kim HJ, van der Helm MW, Segerink LI, Frimat J-P, Hamilton GA, Ingber DE, van den Berg A, et al. 2015. Measuring direct current trans-epithelial electrical resistance in organ-on-a-chip microsystems. Lab Chip. 15(3):745–752.
   PubMed Web of Science ®Google Scholar
• O'Donnell MM, Rea MC, Shanahan F, Ross RP. 2018. The use of a mini-bioreactor fermentation system as a reproducible, high-throughput ex vivo batch model of the distal colon. Front Microbiol.9:1844.
   PubMed Web of Science ®Google Scholar
• Oedit A, Vulto P, Ramautar R, Lindenburg PW, Hankemeier T. 2015. Lab-on-a-Chip hyphenation with mass spectrometry: strategies for bioanalytical applications. Curr Opin Biotechnol.31:79–85.
   PubMed Web of Science ®Google Scholar
• Onyszkiewicz M, Gawrys-Kopczynska M, Konopelski P, Aleksandrowicz M, Sawicka A, Koźniewska E, Samborowska E, Ufnal M. 2019. Butyric acid, a gut bacteria metabolite, lowers arterial blood pressure via colon-vagus nerve signaling and GPR41/43 receptors. Pflugers Arch.471(11-12):1441–1453.
   PubMed Web of Science ®Google Scholar
• Parian AM, Mullin GE, Langhorst J, Brown AC. 2018. Chapter 50 - inflammatory bowel disease. In: Rakel D, editor. Integrative medicine 4th ed. [Internet]. Philadelphia (PA): Elsevier; p. 501–516.e8. Available from: https://www.sciencedirect.com/science/article/pii/B9780323358682000505.
   Google Scholar
• Pasolli E, De Filippis F, Mauriello IE, Cumbo F, Walsh AM, Leech J, Cotter PD, Segata N, Ercolini D. 2020. Large-scale genome-wide analysis links lactic acid bacteria from food with the gut microbiome. Nat Commun. 11(1):2610.
   PubMed Web of Science ®Google Scholar
• Pasolli E, Schiffer L, Manghi P, Renson A, Obenchain V, Truong DT, Beghini F, Malik F, Ramos M, Dowd JB, et al. 2017. Accessible, curated metagenomic data through Experiment Hub. Nat Methods. 14(11):1023–1024.
   PubMed Web of Science ®Google Scholar
• Patil Y, Gooneratne R, Ju X-H. 2020. Interactions between host and gut microbiota in domestic pigs: a review. Gut Microbes. 11(3):310–334.
   PubMed Web of Science ®Google Scholar
• Pessione E, Cirrincione S. 2016. Bioactive molecules released in food by lactic acid bacteria: encrypted peptides and biogenic amines. Front Microbiol.7:876.
   PubMed Web of Science ®Google Scholar
• Pontifex MG, Malik MMAH, Connell E, Müller M, Vauzour D. 2021. Citrus polyphenols in brain health and disease: current perspectives. Front Neurosci.15:115.
   Web of Science ®Google Scholar
• Ramadan Q, Jafarpoorchekab H, Huang C, Silacci P, Carrara S, Koklü G, Ghaye J, Ramsden J, Ruffert C, Vergeres G, et al. 2013. NutriChip: nutrition analysis meets microfluidics. Lab Chip. 13(2):196–203.
   PubMed Web of Science ®Google Scholar
• Redfern WS, Bialecki R, Ewart L, Hammond TG, Kinter L, Lindgren S, Pollard CE, Rolf M, Valentin J-P. 2010. Impact and prevalence of safety pharmacology-related toxicities throughout the pharmaceutical life cycle. Seventh Annu Focus Issue Methods Saf Pharmacol Part II. 62(2):e29.
   Google Scholar
• Reid G, Younes JA, Van der Mei HC, Gloor GB, Knight R, Busscher HJ. 2011. Microbiota restoration: natural and supplemented recovery of human microbial communities. Nat Rev Microbiol. 9(1):27–38.
   PubMed Web of Science ®Google Scholar
• Riquelme E, Zhang Y, Zhang L, Montiel M, Zoltan M, Dong W, Quesada P, Sahin I, Chandra V, San Lucas A, et al. 2019. Tumor microbiome diversity and composition influence pancreatic cancer outcomes. Cell. 178(4):795–806.e12.
   PubMed Web of Science ®Google Scholar
• Rodríguez JM, Murphy K, Stanton C, Ross RP, Kober OI, Juge N, Avershina E, Rudi K, Narbad A, Jenmalm MC, et al. 2015. The composition of the gut microbiota throughout life, with an emphasis on early life. Microb Ecol Health Dis. 26:26050–26050.
   PubMed Web of Science ®Google Scholar
• Rogal J, Zbinden A, Schenke-Layland K, Loskill P. 2019. Stem-cell based organ-on-a-chip models for diabetes research. Adv Drug Deliv Rev.140:101–128.
   PubMed Web of Science ®Google Scholar
• Ronaldson-Bouchard K, Vunjak-Novakovic G. 2018. Organs-on-a-chip: a fast track for engineered human tissues in drug development. Cell Stem Cell. 22(3):310–324.
   PubMed Web of Science ®Google Scholar
• Rowan S, Jiang S, Korem T, Szymanski J, Chang M-L, Szelog J, Cassalman C, Dasuri K, McGuire C, Nagai R, et al. 2017. Involvement of a gut-retina axis in protection against dietary glycemia-induced age-related macular degeneration. Proc Natl Acad Sci USA. 114(22):E4472–E4481.
   PubMed Web of Science ®Google Scholar
• Salazar N, Valdés-Varela L, González S, Gueimonde M, de Los Reyes-Gavilán CG. 2017. Nutrition and the gut microbiome in the elderly. Gut Microbes. 8(2):82–97.
   PubMed Web of Science ®Google Scholar
• Sambuy Y, De Angelis I, Ranaldi G, Scarino M, Stammati A, Zucco F. 2005. The Caco-2 cell line as a model of the intestinal barrier: influence of cell and culture-related factors on Caco-2 cell functional characteristics. Cell Biol Toxicol. 21(1):1–26.
   PubMed Web of Science ®Google Scholar
• Sangwan V, Tomar SK, Ali B, Singh RRB, Singh AK. 2015. Production of β-galactosidase from streptococcus thermophilus for galactooligosaccharides synthesis. J Food Sci Technol. 52(7):4206–4215.
   PubMed Web of Science ®Google Scholar
• Şanlier N, Gökcen BB, Sezgin AC. 2019. Health benefits of fermented foods. Crit Rev Food Sci Nutr. 59(3):506–527.
   PubMed Web of Science ®Google Scholar
• Saqib S, Akram A, Halim SA, Tassaduq R. 2017. Sources of β-galactosidase and its applications in food industry. 3 Biotech. 7(1):79–79.
   PubMedGoogle Scholar
• Saubade F, Hemery YM, Guyot J-P, Humblot C. 2017. Lactic acid fermentation as a tool for increasing the folate content of foods. Crit Rev Food Sci Nutr. 257(18):3894–3910.
   PubMed Web of Science ®Google Scholar
• Sender R, Fuchs S, Milo R. 2016. Are we really vastly outnumbered? revisiting the ratio of bacterial to host cells in humans. Cell. 164(3):337–340.
   PubMed Web of Science ®Google Scholar
• Seok J, Warren HS, Cuenca AG, Mindrinos MN, Baker HV, Xu W, Richards DR, McDonald-Smith GP, Gao H, Hennessy L, et al. 2013. Genomic responses in mouse models poorly mimic human inflammatory diseases. Proc Natl Acad Sci USA. 110(9):3507–3512.
   PubMed Web of Science ®Google Scholar
• Shah P, Fritz JV, Glaab E, Desai MS, Greenhalgh K, Frachet A, Niegowska M, Estes M, Jäger C, Seguin-Devaux C, et al. 2016. A microfluidics-based in vitro model of the gastrointestinal human-microbe interface. Nat Commun. 7(1):11535.
   PubMedGoogle Scholar
• Shakerian M, Razavi SH, Ziai SA, Khodaiyan F, Yarmand MS, Moayedi A. 2015. Proteolytic and ACE-inhibitory activities of probiotic yogurt containing non-viable bacteria as affected by different levels of fat, inulin and starter culture. J Food Sci Technol. 52(4):2428–2433.
   PubMed Web of Science ®Google Scholar
• Shanahan F, Ghosh TS, O'Toole PW. 2021. The Healthy microbiome-what is the definition of a healthy gut microbiome?. Gastroenterology. 160(2):483–494.
   PubMed Web of Science ®Google Scholar
• Sharma N, Angural S, Rana M, Puri N, Kondepudi KK, Gupta N. 2020. Phytase producing lactic acid bacteria: Cell factories for enhancing micronutrient bioavailability of phytate rich foods. Trends Food Sci Technol. 96:1–12.
   Web of Science ®Google Scholar
• Shi Z. 2019. Gut microbiota: an important link between Western Diet and chronic diseases. Nutrients. 11(10):2287.
   PubMed Web of Science ®Google Scholar
• Shik Mun K, Arora K, Huang Y, Yang F, Yarlagadda S, Ramananda Y, Abu-El-Haija M, Palermo JJ, Appakalai BN, Nathan JD, et al. 2019. Patient-derived pancreas-on-a-chip to model cystic fibrosis-related disorders. Nat Commun. 10(1):3124.
   PubMedGoogle Scholar
• Shimizu H, Masujima Y, Ushiroda C, Mizushima R, Taira S, Ohue-Kitano R, Kimura I. 2019. Dietary short-chain fatty acid intake improves the hepatic metabolic condition via FFAR3. Sci Rep. 9(1):16574.
   PubMedGoogle Scholar
• Shin W, Kim HJ. 2018. Intestinal barrier dysfunction orchestrates the onset of inflammatory host-microbiome cross-talk in a human gut inflammation-on-a-chip. Proc Natl Acad Sci USA. 115(45):E10539–E10547.
   PubMed Web of Science ®Google Scholar
• Shkoporov AN, Clooney AG, Sutton TDS, Ryan FJ, Daly KM, Nolan JA, McDonnell SA, Khokhlova EV, Draper LA, Forde A, et al. 2019. The human gut virome is highly diverse, stable, and individual specific. Cell Host Microbe. 26(4):527–541.e5.
   PubMed Web of Science ®Google Scholar
• Silva CCG, Silva SPM, Ribeiro SC. 2018. Application of Bacteriocins and Protective Cultures in Dairy Food Preservation. Front Microbiol. 9:594–594.
   PubMed Web of Science ®Google Scholar
• Simon Sarkadi L. 2017. Chapter 27 - Biogenic Amines in Fermented Foods and Health Implications. In: Frias J, Martinez-Villaluenga C, Peñas E, editors. Fermented foods in health and disease prevention. Boston: Academic Press. p. 625–651. Available from: https://www.sciencedirect.com/science/article/pii/B9780128023099000273.
   Google Scholar
• So D, Whelan K, Rossi M, Morrison M, Holtmann G, Kelly JT, Shanahan ER, Staudacher HM, Campbell KL. 2018. Dietary fiber intervention on gut microbiota composition in healthy adults: a systematic review and meta-analysis. Am J Clin Nutr. 107(6):965–983.
   PubMed Web of Science ®Google Scholar
• Sokolowska P, Janikiewicz J, Jastrzebska E, Brzozka Z, Dobrzyn A. 2020. Combinations of regenerative medicine and Lab-on-a-chip systems: New hope to restoring the proper function of pancreatic islets in diabetes. Biosens Bioelectron.167:112451.
   PubMed Web of Science ®Google Scholar
• Sokovic Bajic S, Djokic J, Dinic M, Veljovic K, Golic N, Mihajlovic S, Tolinacki M. 2019. GABA-producing natural dairy isolate from artisanal zlatar cheese attenuates gut inflammation and strengthens gut epithelial barrier in vitro. Front Microbiol.10:527.
   PubMed Web of Science ®Google Scholar
• Spano G, Russo P, Lonvaud-Funel A, Lucas P, Alexandre H, Grandvalet C, Coton E, Coton M, Barnavon L, Bach B, et al. 2010. Biogenic amines in fermented foods. Eur J Clin Nutr.64(Suppl 3):S95–S100.
   PubMedGoogle Scholar
• Spence JR, Mayhew CN, Rankin SA, Kuhar MF, Vallance JE, Tolle K, Hoskins EE, Kalinichenko VV, Wells SI, Zorn AM, et al. 2011. Directed differentiation of human pluripotent stem cells into intestinal tissue in vitro. Nature. 470(7332):105–109.
   PubMed Web of Science ®Google Scholar
• Srinivasan B, Kolli AR, Esch MB, Abaci HE, Shuler ML, Hickman JJ. 2015. TEER measurement techniques for in vitro barrier model systems. J Lab Autom. 20(2):107–126.
   PubMedGoogle Scholar
• Sriram G, Alberti M, Dancik Y, Wu B, Wu R, Feng Z, Ramasamy S, Bigliardi PL, Bigliardi-Qi M, Wang Z, et al. 2018. Full-thickness human skin-on-chip with enhanced epidermal morphogenesis and barrier function. Mater Today. 21(4):326–340.
   Web of Science ®Google Scholar
• Steinway SN, Saleh J, Koo B-K, Delacour D, Kim D-H. 2020. Human microphysiological models of intestinal tissue and gut microbiome. Front Bioeng Biotechnol. 8:725–725.
   PubMed Web of Science ®Google Scholar
• Storck LJ, Imoberdorf R, Ballmer PE. 2019. Nutrition in gastrointestinal disease: liver, pancreatic, and inflammatory bowel disease. J Clin Med. 8(8):1098.
   Web of Science ®Google Scholar
• Strati F, Cavalieri D, Albanese D, De Felice C, Donati C, Hayek J, Jousson O, Leoncini S, Renzi D, Calabrò A, et al. 2017. New evidences on the altered gut microbiota in autism spectrum disorders. Microbiome. 5(1):24–24.
   PubMedGoogle Scholar
• Sun J, Furio L, Mecheri R, van der Does AM, Lundeberg E, Saveanu L, Chen Y, van Endert P, Agerberth B, Diana J, et al. 2015. Pancreatic β-cells limit autoimmune diabetes via an immunoregulatory antimicrobial peptide expressed under the influence of the gut microbiota. Immunity. 43(2):304–317.
   PubMed Web of Science ®Google Scholar
• Sutton TDS, Hill C. 2019. Gut bacteriophage: current understanding and challenges. Front Endocrinol.10:784.
   PubMed Web of Science ®Google Scholar
• Swanson KS, Gibson GR, Hutkins R, Reimer RA, Reid G, Verbeke K, Scott KP, Holscher HD, Azad MB, Delzenne NM, et al. 2020. The international scientific association for probiotics and prebiotics (isapp) consensus statement on the definition and scope of synbiotics. Nat Rev Gastroenterol Hepatol. 17(11):687–701.
   PubMed Web of Science ®Google Scholar
• Takahashi T. 2011. Flow Behavior of Digesta and the Absorption of Nutrients in the Gastrointestine. J Nutr Sci Vitaminol. 57(4):265–273.
   PubMed Web of Science ®Google Scholar
• Thomas RM, Jobin C. 2020. Microbiota in pancreatic health and disease: the next frontier in microbiome research. Nat Rev Gastroenterol Hepatol. 17(1):53–64.
   PubMed Web of Science ®Google Scholar
• Tiew PY, Mac Aogain M, Ali NABM, Thng KX, Goh K, Lau KJX, Chotirmall SH. 2020. The mycobiome in health and disease: emerging concepts, methodologies and challenges. Mycopathologia. 185(2):207–231.
   PubMed Web of Science ®Google Scholar
• Tilg H, Moschen AR. 2014. Microbiota and diabetes: an evolving relationship. Gut. 63(9):1513–1521.
   PubMed Web of Science ®Google Scholar
• Trietsch SJ, Naumovska E, Kurek D, Setyawati MC, Vormann MK, Wilschut KJ, Lanz HL, Nicolas A, Ng CP, Joore J, et al. 2017. Membrane-free culture and real-time barrier integrity assessment of perfused intestinal epithelium tubes. Nat Commun. 8(1):262.
   PubMedGoogle Scholar
• Tsamandouras N, Chen WLK, Edington CD, Stokes CL, Griffith LG, Cirit M. 2017. Integrated gut and liver microphysiological systems for quantitative in vitro pharmacokinetic studies . 9(5):1499–1512.
   Google Scholar
• van den Berg A, Mummery CL, Passier R, van der Meer AD. 2019. Personalised organs-on-chips: functional testing for precision medicine. Lab Chip. 19(2):198–205.
   PubMed Web of Science ®Google Scholar
• van der Helm MW, van der Meer AD, Eijkel JCT, van den Berg A, Segerink LI. 2016. Microfluidic organ-on-chip technology for blood-brain barrier research. Tissue Barriers. 4(1):e1142493.
   PubMed Web of Science ®Google Scholar
• van Poll ML, Zhou F, Ramstedt M, Hu L, Huck WTS. A self-assembly approach to chemical micropatterning of Poly(dimethylsiloxane). Angew Chem Int Ed Engl. 2007. 46(35):6634–6637.
   PubMed Web of Science ®Google Scholar
• Vergères G, Bogicevic B, Buri C, Carrara S, Chollet M, Corbino-Giunta L, Egger L, Gille D, Kopf-Bolanz K, Laederach K, et al. 2012. The NutriChip project-translating technology into nutritional knowledge. Br J Nutr. 108(5):762–768.
   PubMed Web of Science ®Google Scholar
• Vernetti L, Gough A, Baetz N, Blutt S, Broughman JR, Brown JA, Foulke-Abel J, Hasan N, In J, Kelly E, et al. 2017. Corrigendum: functional coupling of human microphysiology systems: intestine, liver, kidney proximal tubule, blood-brain barrier and skeletal Muscle. Sci Rep. 7(1):44517.
   PubMedGoogle Scholar
• Villarreal-Soto SA, Bouajila J, Pace M, Leech J, Cotter PD, Souchard J-P, Taillandier P, Beaufort S. 2020. Metabolome-microbiome signatures in the fermented beverage, Kombucha. Int J Food Microbiol. 333:108778.
   PubMed Web of Science ®Google Scholar
• Villenave R, Wales SQ, Hamkins-Indik T, Papafragkou E, Weaver JC, Ferrante TC, Bahinski A, Elkins CA, Kulka M, Ingber DE, et al. 2017. Human gut-on-a-chip supports polarized infection of coxsackie B1 virus in vitro. PLoS One.12(2):e0169412.
   PubMed Web of Science ®Google Scholar
• Vinderola G, Reinheimer J, Salminen S. 2019. The enumeration of probiotic issues: from unavailable standardised culture media to a recommended procedure? Int Dairy J.96:58–65.
   Web of Science ®Google Scholar
• Virumbrales-Muñoz M, Ayuso JM, Gong MM, Humayun M, Livingston MK, Lugo-Cintrón KM, McMinn P, Álvarez-García YR, Beebe DJ. 2020. Microfluidic lumen-based systems for advancing tubular organ modeling. Chem Soc Rev. 49(17):6402–6442.
   PubMed Web of Science ®Google Scholar
• Walter J, Armet AM, Finlay BB, Shanahan F. 2020. Establishing or exaggerating causality for the gut microbiome: lessons from human microbiota-associated rodents. Cell. 180(2):221–232.
   PubMed Web of Science ®Google Scholar
• Walther B, Karl JP, Booth SL, Boyaval P. 2013. Menaquinones, bacteria, and the food supply: the relevance of dairy and fermented food products to vitamin K requirements. Adv Nutr. 4(4):463–473.
   PubMed Web of Science ®Google Scholar
• Wang H, Yan Y, Yi X, Duan Y, Wang J, Li S, Luo L, Huang T, Inglis B, Li X, et al. 2019. Histopathological features and composition of gut microbiota in rhesus monkey of alcoholic liver disease. Front Microbiol.10:165.
   PubMed Web of Science ®Google Scholar
• Wang YI, Carmona C, Hickman JJ, Shuler ML. 2018. Multiorgan microphysiological systems for drug development: strategies, advances, and challenges. Adv Healthc Mater. 7(2):10.
   Web of Science ®Google Scholar
• Warburton R. 2017. A microbiological assessment of the human biliary tract in health and disease. [Thesis]. University of East Anglia.
   Google Scholar
• Wekerle H, Hohlfeld R. 2016. Chapter 9 - gut microbiota in multiple sclerosis: a bioreactor driving brain autoimmunity. In: Arnon R, Miller A, editors. Translational neuroimmunology in multiple sclerosis. San Diego: Academic Press; p. 113–125. Available from: http://www.sciencedirect.com/science/article/pii/B978012801914600009X.
   Google Scholar
• Wilkinson M. 2019. The potential of organ on chip technology for replacing animal testing. Leiden: Brill. p. 639–653. Available from: https://brill.com/view/book/edcoll/9789004391192/BP000033.xml.
   Google Scholar
• Williams CF, Walton GE, Jiang L, Plummer S, Garaiova I, Gibson GR. 2015. Comparative analysis of intestinal tract models. Annu Rev Food Sci Technol. 6(1):329–350.
   PubMedGoogle Scholar
• Wolf MP, Salieb-Beugelaar GB, Hunziker P. 2018. PDMS with designer functionalities—Properties, modifications strategies, and applications. Prog Polym Sci.83:97–134.
   Web of Science ®Google Scholar
• Wu J, He Z, Chen Q, Lin J-M. 2016. Biochemical analysis on microfluidic chips. TrAC Trends Anal Chem. 80:213–231.
   Web of Science ®Google Scholar
• Xiang Y, Wen H, Yu Y, Li M, Fu X, Huang S. 2020. Gut-on-chip: recreating human intestine in vitro. J Tissue Eng. 11:2041731420965318.
   Web of Science ®Google Scholar
• Xu C, Zhu H, Qiu P. 2019. Aging progression of human gut microbiota. BMC Microbiol. 19(1):236.
   PubMed Web of Science ®Google Scholar
• Yeste J, Illa X, Alvarez M, Villa R. 2018. Engineering and monitoring cellular barrier models. J Biol Eng.12:18–18.
   PubMed Web of Science ®Google Scholar
• Zhang B, Korolj A, Lai BFL, Radisic M. 2018. Advances in organ-on-a-chip engineering. Nat Rev Mater. 3(8):257–278.
   Web of Science ®Google Scholar
• Zhang K, Dai H, Liang W, Zhang L, Deng Z. 2019. Fermented dairy foods intake and risk of cancer. Int J Cancer. 144(9):2099–2108.
   PubMed Web of Science ®Google Scholar
• Zhang YS, Aleman J, Shin SR, Kilic T, Kim D, Mousavi Shaegh SA, Massa S, Riahi R, Chae S, Hu N, et al. 2017. Multisensor-integrated organs-on-chips platform for automated and continual in situ monitoring of organoid behaviors. Proc Natl Acad Sci USA. 114(12):E2293–E2302.
   PubMed Web of Science ®Google Scholar
• Zinöcker MK, Lindseth IA. 2018. The Western Diet–microbiome-host interaction and its role in metabolic disease. Nutrients. 10(3):365.
   PubMed Web of Science ®Google Scholar
• Zmora N, Zilberman-Schapira G, Suez J, Mor U, Dori-Bachash M, Bashiardes S, Kotler E, Zur M, Regev-Lehavi D, Brik RB-Z, et al. 2018. Personalized gut mucosal colonization resistance to empiric probiotics is associated with unique host and microbiome features. Cell. 174(6):1388–1405.e21.
   PubMed Web of Science ®Google Scholar