References

• Akers, K. G., Martinez-Canabal, A., Restivo, L., Yiu, A. P., De Cristofaro, A., Hsiang, H. L.... Frankland P. W. google scholar
• (2014). Hippocampal neurogenesis regulates forgetting during adulthood and infancy. Science, 344(6184), 598-602. google scholar
• Bauer, P. J. (2015). A complementary processes account of the development of childhood amnesia and a personal Past. Psychological Review, 122(2), 204-231. google scholar
• Abt, M. C., McKenney, P. T., & Pamer, E. G. (2016). Clostridium difficile colitis: pathogenesis and host defence. Nat Rev Microbiol, 14(10), 609-620. doi:10.1038/nrmicro.2016.108 google scholar
• Alavi, S., Mitchell, J. D., Cho, J. Y., Liu, R., Macbeth, J. C., & Hsiao, A. (2020). Interpersonal Gut Microbi-ome Variation Drives Susceptibility and Resistance to Cholera Infection. Cell, 181(7), 1533-1546.e1513. doi:10.1016/j.cell.2020.05.036 google scholar
• Âlvarez Â, H., Martmez Velazquez, M., & Prado Montes de Oca, E. (2018). Human p-defensin 1 update: Po-tential clinical applications of the restless warrior. Int J Biochem Cell Biol, 104, 133-137. doi:10.1016/j. biocel.2018.09.007 google scholar
• Andoh, A., Benno, Y., Kanauchi, O., & Fujiyama, Y. (2009). Recent advances in molecular appro-aches to gut microbiota in inflammatory bowel disease. Curr Pharm Des, 15(18), 2066-2073. doi:10.2174/138161209788489186 google scholar
• Andres, E., Loukili, N. H., Noel, E., Kaltenbach, G., Abdelgheni, M. B., Perrin, A. E., . . . Blickle, J. F. (2004). Vitamin B12 (cobalamin) deficiency in elderly patients. Cmaj, 171(3), 251-259. doi:10.1503/cmaj.1031155 google scholar
• Anthony, W. E., Wang, B., Sukhum, K. V., D’Souza, A. W., Hink, T., Cass, C., . . . Kwon, J. H. (2022). Acute and persistent effects of commonly used antibiotics on the gut microbiome and resistome in healthy adults. Cell Rep, 39(2), 110649. doi:https://doi.org/10.1016/j.celrep.2022.110649 google scholar
• Arumugam, M., Raes, J., Pelletier, E., Le Paslier, D., Yamada, T., Mende, D. R., . . . Bork, P. (2011). Enterotypes of the human gut microbiome. Nature, 473(7346), 174-180. doi:10.1038/nature09944 google scholar
• Avuthu, N., & Guda, C. (2022). Meta-Analysis of Altered Gut Microbiota Reveals Microbial and Metabolic Biomarkers for Colorectal Cancer. Microbiol Spectr, 10(4), e0001322. doi:10.1128/spectrum.00013-22 google scholar
• Bachmann, V., Kostiuk, B., Unterweger, D., Diaz-Satizabal, L., Ogg, S., & Pukatzki, S. (2015). Bile Salts Mo-dulate the Mucin-Activated Type VI Secretion System of Pandemic Vibrio cholerae. PLoS Negl Trop Dis, 9(8), e0004031. doi:10.1371/journal.pntd.0004031 google scholar
• Bajaj, J. S., Ridlon, J. M., Hylemon, P. B., Thacker, L. R., Heuman, D. M., Smith, S., . . . Gillevet, P. M. (2012). Linkage of gut microbiome with cognition in hepatic encephalopathy. Am J Physiol Gastrointest Liver Physiol, 302(1), G168-175. doi:10.1152/ajpgi.00190.2011 google scholar
• Basler, M., Pilhofer, M., Henderson, G. P., Jensen, G. J., & Mekalanos, J. J. (2012). Type VI secretion requires a dynamic contractile phage tail-like structure. Nature, 483(7388), 182-186. doi:10.1038/nature10846 google scholar
• Beyhan, S., Bilecen, K., Salama, S. R., Casper-Lindley, C., & Yildiz, F. H. (2007). Regulation of rugosity and biofilm formation in Vibrio cholerae: comparison of VpsT and VpsR regulons and epistasis analysis of vpsT, vpsR, and hapR. J Bacteriol, 189(2), 388-402. doi:10.1128/jb.00981-06 google scholar
• Bhattarai, Y., Muniz Pedrogo, D. A., & Kashyap, P. C. (2017). Irritable bowel syndrome: a gut microbiota-related disorder? Am J Physiol Gastrointest Liver Physiol, 312(1), G52-g62. doi:10.1152/ajpgi.00338.2016 google scholar
• Bina, X. R., Provenzano, D., Nguyen, N., & Bina, J. E. (2008). Vibrio cholerae RND family efflux systems are required for antimicrobial resistance, optimal virulence factor production, and colonization of the infant mouse small intestine. Infect Immun, 76(8), 3595-3605. doi:10.1128/iai.01620-07 google scholar
• Buffie, C. G., & Pamer, E. G. (2013). Microbiota-mediated colonization resistance against intestinal pathogens. Nat Rev Immunol, 13(11), 790-801. doi:10.1038/nri3535 google scholar
• Byrd, A. L., Belkaid, Y., & Segre, J. A. (2018). The human skin microbiome. Nat Rev Microbiol, 16(3), 143-155. doi:10.1038/nrmicro.2017.157 google scholar
• Caio, G., Lungaro, L., Segata, N., Guarino, M., Zoli, G., Volta, U., & De Giorgio, R. (2020). Effect of Glu-ten-Free Diet on Gut Microbiota Composition in Patients with Celiac Disease and Non-Celiac Gluten/Wheat Sensitivity. Nutrients, 12(6). doi:10.3390/nu12061832 google scholar
• Campion, D., Giovo, I., Ponzo, P., Saracco, G. M., Balzola, F., & Alessandria, C. (2019). Dietary approach and gut microbiota modulation for chronic hepatic encephalopathy in cirrhosis. World J Hepatol, 11(6), 489-512. doi:10.4254/wjh.v11.i6.489 google scholar
• Cani, P. D. (2013). Gut microbiota and obesity: lessons from the microbiome. Brief Funct Genomics, 12(4), 381-387. doi:10.1093/bfgp/elt014 google scholar
• Carmona-Cruz, S., Orozco-Covarrubias, L., & Saez-de-Ocariz, M. (2022). The Human Skin Microbiome in Selected Cutaneous Diseases. Front Cell Infect Microbiol, 12, 834135. doi:10.3389/fcimb.2022.834135 google scholar
• Catlett, J. L., Carr, S., Cashman, M., Smith, M. D., Walter, M., Sakkaff, Z., . . . Buan, N. R. (2022). Metabolic Sy-nergy between Human Symbionts Bacteroides and Methanobrevibacter. Microbiol Spectr, 10(3), e0106722. doi:10.1128/spectrum.01067-22 google scholar
• Cattaneo, A., Cattane, N., Galluzzi, S., Provasi, S., Lopizzo, N., Festari, C., . . . Frisoni, G. B. (2017). Associa-tion of brain amyloidosis with pro-inflammatory gut bacterial taxa and peripheral inflammation markers in cognitively impaired elderly. Neurobiol Aging, 49, 60-68. doi:10.1016/j.neurobiolaging.2016.08.019 google scholar
• Chairatana, P., & Nolan, E. M. (2017). Human a-Defensin 6: A Small Peptide That Self-Assembles and Protects the Host by Entangling Microbes. Acc Chem Res, 50(4), 960-967. doi:10.1021/acs.accounts.6b00653 google scholar
• Chander, A. M., Yadav, H., Jain, S., Bhadada, S. K., & Dhawan, D. K. (2018). Cross-Talk Between Gluten, In-testinal Microbiota and Intestinal Mucosa in Celiac Disease: Recent Advances and Basis of Autoimmunity. Front Microbiol, 9, 2597. doi:10.3389/fmicb.2018.02597 google scholar
• Chatterjee, A., Chaudhuri, S., Saha, G., Gupta, S., & Chowdhury, R. (2004). Effect of bile on the cell surface permeability barrier and efflux system of Vibrio cholerae. J Bacteriol, 186(20), 6809-6814. doi:10.1128/ jb.186.20.6809-6814.2004 google scholar
• Chen, D., Wu, J., Jin, D., Wang, B., & Cao, H. (2019). Fecal microbiota transplantation in cancer management: Current status and perspectives. Int J Cancer, 145(8), 2021-2031. doi:10.1002/ijc.32003 google scholar
• Chen, H., Li, H., & Liu, Z. (2020). Interplay of intestinal microbiota and mucosal immunity in inflamma-tory bowel disease: a relationship of frenemies. Therap Adv Gastroenterol, 13, 1756284820935188. doi:10.1177/1756284820935188 google scholar
• Chung, H., Pamp, S. J., Hill, J. A., Surana, N. K., Edelman, S. M., Troy, E. B., . . . Kasper, D. L. (2012). Gut immune maturation depends on colonization with a host-specific microbiota. Cell, 149(7), 1578-1593. doi:10.1016/j.cell.2012.04.037 google scholar
• Chung, L. K., & Raffatellu, M. (2019). G.I. pros: Antimicrobial defense in the gastrointestinal tract. Semin Cell Dev Biol, 88, 129-137. doi:10.1016/j.semcdb.2018.02.001 google scholar
• Cianfanelli, F. R., Alcoforado Diniz, J., Guo, M., De Cesare, V., Trost, M., & Coulthurst, S. J. (2016). VgrG and PAAR Proteins Define Distinct Versions of a Functional Type VI Secretion System. PLoS Pathog, 12(6), e1005735. doi:10.1371/journal.ppat.1005735 google scholar
• Collado, M. C., Donat, E., Ribes-Koninckx, C., Calabuig, M., & Sanz, Y. (2008). Imbalances in faecal and duodenal Bifidobacterium species composition in active and non-active coeliac disease. BMC Microbiol, 8, 232. doi:10.1186/1471-2180-8-232 google scholar
• Collins, M. D., Lawson, P. A., Willems, A., Cordoba, J. J., Fernandez-Garayzabal, J., Garcia, P., . . . Farrow, J. A. (1994). The phylogeny of the genus Clostridium: proposal of five new genera and eleven new species combinations. Int J Syst Bacteriol, 44(4), 812-826. doi:10.1099/00207713-44-4-812 google scholar
• Collins, S. L., Stine, J. G., Bisanz, J. E., Okafor, C. D., & Patterson, A. D. (2022). Bile acids and the gut micro-biota: metabolic interactions and impacts on disease. Nat Rev Microbiol. doi:10.1038/s41579-022-00805-x google scholar
• Cunningham, A. L., Stephens, J. W., & Harris, D. A. (2021). Gut microbiota influence in type 2 diabetes mellitus (T2DM). Gut Pathog, 13(1), 50. doi:10.1186/s13099-021-00446-0 google scholar
• Dalile, B., Van Oudenhove, L., Vervliet, B., & Verbeke, K. (2019). The role of short-chain fatty acids in mic-robiota-gut-brain communication. Nat Rev Gastroenterol Hepatol, 16(8), 461-478. doi:10.1038/s41575-019-0157-3 google scholar
• De Palma, G., Nadal, I., Medina, M., Donat, E., Ribes-Koninckx, C., Calabuig, M., & Sanz, Y. (2010). Intestinal dysbiosis and reduced immunoglobulin-coated bacteria associated with coeliac disease in children. BMC Microbiol, 10, 63. doi:10.1186/1471-2180-10-63 google scholar
• Degnan, P. H., Taga, M. E., & Goodman, A. L. (2014). Vitamin B12 as a modulator of gut microbial ecology. Cell Metab, 20(5), 769-778. doi:10.1016/j.cmet.2014.10.002 google scholar
• Del Fiol, F. S., Balcao, V. M., Barberato-Fillho, S., Lopes, L. C., & Bergamaschi, C. C. (2018). Obesity: A New Adverse Effect of Antibiotics? Front Pharmacol, 9, 1408. doi:10.3389/fphar.2018.01408 google scholar
• Dempsey, E., & Corr, S. C. (2022). Lactobacillus spp. for Gastrointestinal Health: Current and Future Perspec-tives. Front Immunol, 13, 840245. doi:10.3389/fimmu.2022.840245 google scholar
• Derrien, M., Vaughan, E. E., Plugge, C. M., & de Vos, W. M. (2004). Akkermansia muciniphila gen. nov., sp. nov., a human intestinal mucin-degrading bacterium. Int J Syst Evol Microbiol, 54(Pt 5), 1469-1476. doi:10.1099/ijs.0.02873-0 google scholar
• Deshpande, N. P., Riordan, S. M., Castano-Rodriguez, N., Wilkins, M. R., & Kaakoush, N. O. (2018). Signatures within the esophageal microbiome are associated with host genetics, age, and disease. Microbiome, 6(1), 227. doi:10.1186/s40168-018-0611-4 google scholar
• Dethlefsen, L., Huse, S., Sogin, M. L., & Relman, D. A. (2008). The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing. PLoS Biol, 6(11), e280. doi:10.1371/ journal.pbio.0060280 google scholar
• Dethlefsen, L., & Relman, D. A. (2011). Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation. Proc Natl Acad Sci U S A, 108 Suppl 1(Suppl 1), 45544561. doi:10.1073/pnas.1000087107 google scholar
• Di Biase, A. R., Marasco, G., Ravaioli, F., Dajti, E., Colecchia, L., Righi, B., . . . Colecchia, A. (2021). Gut micro-biota signatures and clinical manifestations in celiac disease children at onset: a pilot study. J Gastroenterol Hepatol, 36(2), 446-454. doi:10.1111/jgh.15183 google scholar
• Diamond, G., & Bevins, C. L. (1998). beta-Defensins: endogenous antibiotics of the innate host defense respon-se. Clin Immunol Immunopathol, 88(3), 221-225. doi:10.1006/clin.1998.4587 google scholar
• Dong, T. G., Ho, B. T., Yoder-Himes, D. R., & Mekalanos, J. J. (2013). Identification of T6SS-dependent ef-fector and immunity proteins by Tn-seq in Vibrio cholerae. Proc Natl Acad Sci U S A, 110(7), 2623-2628. doi:10.1073/pnas.1222783110 google scholar
• Duan, F., & March, J. C. (2008). Interrupting Vibrio cholerae infection of human epithelial cells with engineered commensal bacterial signaling. Biotechnol Bioeng, 101(1), 128-134. doi:10.1002/bit.21897 google scholar
• Duan, F., & March, J. C. (2010). Engineered bacterial communication prevents Vibrio cholerae virulence in an infant mouse model. Proc Natl Acad Sci U S A, 107(25), 11260-11264. doi:10.1073/pnas.1001294107 google scholar
• Duncan, S. H., Lobley, G. E., Holtrop, G., Ince, J., Johnstone, A. M., Louis, P., & Flint, H. J. (2008). Human colonic microbiota associated with diet, obesity and weight loss. Int J Obes (Lond), 32(11), 1720-1724. doi:10.1038/ijo.2008.155 google scholar
• Fachi, J. L., Felipe, J. S., Pral, L. P., da Silva, B. K., Correa, R. O., de Andrade, M. C. P., . . . Vinolo, M. A. R. (2019). Butyrate Protects Mice from Clostridium difficile-Induced Colitis through an HIF-1-Dependent Mechanism. Cell Rep, 27(3), 750-761.e757. doi:10.1016/j.celrep.2019.03.054 google scholar
• Fan, Y., & Pedersen, O. (2021). Gut microbiota in human metabolic health and disease. Nat Rev Microbiol, 19(1), 55-71. doi:10.1038/s41579-020-0433-9 google scholar
• Fast, D., Kostiuk, B., Foley, E., & Pukatzki, S. (2018). Commensal pathogen competition impacts host viability. Proc Natl Acad Sci U S A, 115(27), 7099-7104. doi:10.1073/pnas.1802165115 google scholar
• Fast, D., Petkau, K., Ferguson, M., Shin, M., Galenza, A., Kostiuk, B., . . . Foley, E. (2020). Vibrio cholerae-Sy-mbiont Interactions Inhibit Intestinal Repair in Drosophila. Cell Rep, 30(4), 1088-1100.e1085. doi:10.1016/j. celrep.2019.12.094 google scholar
• Finegold, S. M. (2011). Desulfovibrio species are potentially important in regressive autism. Med Hypotheses, 77(2), 270-274. doi:10.1016/j.mehy.2011.04.032 google scholar
• Finegold, S. M., Downes, J., & Summanen, P. H. (2012). Microbiology of regressive autism. Anaerobe, 18(2), 260-262. doi:10.1016/j.anaerobe.2011.12.018 google scholar
• Finegold, S. M., Molitoris, D., Song, Y., Liu, C., Vaisanen, M. L., Bolte, E., . . . Kaul, A. (2002). Gastrointestinal microflora studies in late-onset autism. Clin Infect Dis, 35(Suppl 1), S6-s16. doi:10.1086/341914 google scholar
• Frank, D. N., St Amand, A. L., Feldman, R. A., Boedeker, E. C., Harpaz, N., & Pace, N. R. (2007). Molecu-lar-phylogenetic characterization of microbial community imbalances in human inflammatory bowel dise-ases. Proc Natl Acad Sci U S A, 104(34), 13780-13785. doi:10.1073/pnas.0706625104 google scholar
• Fu, Y., Ho, B. T., & Mekalanos, J. J. (2018). Tracking Vibrio cholerae Cell-Cell Interactions during Infection Reveals Bacterial Population Dynamics within Intestinal Microenvironments. Cell Host Microbe, 23(2), 274-281.e272. doi:10.1016/j.chom.2017.12.006 google scholar
• Fu, Y., Waldor, M. K., & Mekalanos, J. J. (2013). Tn-Seq analysis of Vibrio cholerae intestinal colonization reveals a role for T6SS-mediated antibacterial activity in the host. Cell Host Microbe, 14(6), 652-663. doi:10.1016/j.chom.2013.11.001 google scholar
• Gabay, J. E., Scott, R. W., Campanelli, D., Griffith, J., Wilde, C., Marra, M. N., . . . Nathan, C. F. (1989). An-tibiotic proteins of human polymorphonuclear leukocytes. Proc Natl Acad Sci U S A, 86(14), 5610-5614. doi:10.1073/pnas.86.14.5610 google scholar
• Gallo, R. L. (2017). Human Skin Is the Largest Epithelial Surface for Interaction with Microbes. J Invest Der-matol, 137(6), 1213-1214. doi:10.1016/j.jid.2016.11.045 google scholar
• Geurts, L., Lazarevic, V., Derrien, M., Everard, A., Van Roye, M., Knauf, C., . . . Cani, P. D. (2011). Altered gut microbiota and endocannabinoid system tone in obese and diabetic leptin-resistant mice: impact on apelin regulation in adipose tissue. Front Microbiol, 2, 149. doi:10.3389/fmicb.2011.00149 google scholar
• Gill, S. R., Pop, M., Deboy, R. T., Eckburg, P. B., Turnbaugh, P. J., Samuel, B. S., . . . Nelson, K. E. (2006). Metagenomic analysis of the human distal gut microbiome. Science, 312(5778), 1355-1359. doi:10.1126/ science.1124234 google scholar
• Gomaa, E. Z. (2020). Human gut microbiota/microbiome in health and diseases: a review. Antonie Van Leeuwen-hoek, 113(12), 2019-2040. doi:10.1007/s10482-020-01474-7 google scholar
• Gorelik, O., Levy, N., Shaulov, L., Yegodayev, K., Meijler, M. M., & Sal-Man, N. (2019). Vibrio cholerae au-toinducer-1 enhances the virulence of enteropathogenic Escherichia coli. Sci Rep, 9(1), 4122. doi:10.1038/ s41598-019-40859-1 google scholar
• Grizotte-Lake, M., Zhong, G., Duncan, K., Kirkwood, J., Iyer, N., Smolenski, I., . . . Vaishnava, S. (2018). Commensals Suppress Intestinal Epithelial Cell Retinoic Acid Synthesis to Regulate Interleukin-22 Activity and Prevent Microbial Dysbiosis. Immunity, 49(6), 1103-1115.e1106. doi:10.1016/j.immuni.2018.11.018 google scholar
• Guh, A. Y., & Kutty, P. K. (2018). Clostridioides difficile Infection. Ann Intern Med, 169(7), Itc49-itc64. doi:10.7326/aitc201810020 google scholar
• Hang, S., Purdy, A. E., Robins, W. P., Wang, Z., Mandal, M., Chang, S., . . . Watnick, P. I. (2014). The acetate switch of an intestinal pathogen disrupts host insulin signaling and lipid metabolism. Cell Host Microbe, 16(5), 592-604. doi:10.1016/j.chom.2014.10.006 google scholar
• Hansen, R., Russell, R. K., Reiff, C., Louis, P., McIntosh, F., Berry, S. H., . . . Hold, G. L. (2012). Microbiota of de-novo pediatric IBD: increased Faecalibacterium prausnitzii and reduced bacterial diversity in Crohn’s but not in ulcerative colitis. Am J Gastroenterol, 107(12), 1913-1922. doi:10.1038/ajg.2012.335 google scholar
• Harwig, S. S., Park, A. S., & Lehrer, R. I. (1992). Characterization of defensin precursors in mature human neutrophils. Blood, 79(6), 1532-1537. google scholar
• Hill-Burns, E. M., Debelius, J. W., Morton, J. T., Wissemann, W. T., Lewis, M. R., Wallen, Z. D., . . . Payami, H. (2017). Parkinson’s disease and Parkinson’s disease medications have distinct signatures of the gut microbiome. Mov Disord, 32(5), 739-749. doi:10.1002/mds.26942 google scholar
• Hirota, S. A., Fines, K., Ng, J., Traboulsi, D., Lee, J., Ihara, E., . . . Beck, P. L. (2010). Hypoxia-inducible factor signaling provides protection in Clostridium difficile-induced intestinal injury. Gastroenterology, 139(1), 259-269.e253. doi:10.1053/j.gastro.2010.03.045 google scholar
• Hopfner, F., Künstner, A., Müller, S. H., Künzel, S., Zeuner, K. E., Margraf, N. G., . . . Kuhlenbaumer, G. (2017). Gut microbiota in Parkinson disease in a northern German cohort. Brain Res, 1667, 41-45. doi:10.1016/j. brainres.2017.04.019 google scholar
• Hu, Z., Zhang, C., Sifuentes-Dominguez, L., Zarek, C. M., Propheter, D. C., Kuang, Z., . . . Hooper, L. V. (2021). Small proline-rich protein 2A is a gut bactericidal protein deployed during helminth infection. Science, 374(6568), eabe6723. doi:10.1126/science.abe6723 google scholar
• Iatsenko, I., Boquete, J. P., & Lemaitre, B. (2018). Microbiota-Derived Lactate Activates Production of Reactive Oxygen Species by the Intestinal NADPH Oxidase Nox and Shortens Drosophila Lifespan. Immunity, 49(5), 929-942.e925. doi:10.1016/j.immuni.2018.09.017 google scholar
• Iizumi, T., Battaglia, T., Ruiz, V., & Perez Perez, G. I. (2017). Gut Microbiome and Antibiotics. Arch Med Res, 48(8), 727-734. doi:10.1016/j.arcmed.2017.11.004 google scholar
• Jakobsson, H. E., Jernberg, C., Andersson, A. F., Sjölund-Karlsson, M., Jansson, J. K., & Engstrand, L. (2010). Short-term antibiotic treatment has differing long-term impacts on the human throat and gut microbiome. PLoS One, 5(3), e9836. doi:10.1371/journal.pone.0009836 google scholar
• Jemal, A., Bray, F., Center, M. M., Ferlay, J., Ward, E., & Forman, D. (2011). Global cancer statistics. CA Cancer J Clin, 61(2), 69-90. doi:10.3322/caac.20107 google scholar
• Jemielita, M., Wingreen, N. S., & Bassler, B. L. (2018). Quorum sensing controls Vibrio cholerae multicellular aggregate formation. Elife, 7. doi:10.7554/eLife.42057 google scholar
• Jones, D. E., & Bevins, C. L. (1993). Defensin-6 mRNA in human Paneth cells: implications for antimic-robial peptides in host defense of the human bowel. FEBS Lett, 315(2), 187-192. doi:10.1016/0014-5793(93)81160-2 google scholar
• Joossens, M., Huys, G., Cnockaert, M., De Preter, V., Verbeke, K., Rutgeerts, P., . . . Vermeire, S. (2011). Dys-biosis of the faecal microbiota in patients with Crohn’s disease and their unaffected relatives. Gut, 60(5), 631-637. doi:10.1136/gut.2010.223263 google scholar
• Kasai, C., Sugimoto, K., Moritani, I., Tanaka, J., Oya, Y., Inoue, H., . . . Takase, K. (2015). Comparison of the gut microbiota composition between obese and non-obese individuals in a Japanese population, as analyzed by terminal restriction fragment length polymorphism and next-generation sequencing. BMC Gastroenterol, 15, 100. doi:10.1186/s12876-015-0330-2 google scholar
• Kelly, R. C., Bolitho, M. E., Higgins, D. A., Lu, W., Ng, W. L., Jeffrey, P. D., . . . Bassler, B. L. (2009). The Vibrio cholerae quorum-sensing autoinducer CAI-1: analysis of the biosynthetic enzyme CqsA. Nat Chem Biol, 5(12), 891-895. doi:10.1038/nchembio.237 google scholar
• Keshavarzian, A., Green, S. J., Engen, P. A., Voigt, R. M., Naqib, A., Forsyth, C. B., . . . Shannon, K. M. (2015). Colonic bacterial composition in Parkinson’s disease. Mov Disord, 30(10), 1351-1360. doi:10.1002/ mds.26307 google scholar
• Kim, E. K., Lee, K. A., Hyeon, D. Y., Kyung, M., Jun, K. Y., Seo, S. H., . . . Lee, W. J. (2020). Bacterial Nucleo-side Catabolism Controls Quorum Sensing and Commensal-to-Pathogen Transition in the Drosophila Gut. Cell Host Microbe, 27(3), 345-357.e346. doi:10.1016/j.chom.2020.01.025 google scholar
• Kim, K. A., Gu, W., Lee, I. A., Joh, E. H., & Kim, D. H. (2012). High fat diet-induced gut microbiota exacerbates inflammation and obesity in mice via the TLR4 signaling pathway. PLoS One, 7(10), e47713. doi:10.1371/ journal.pone.0047713 google scholar
• Kim, S., Covington, A., & Pamer, E. G. (2017). The intestinal microbiota: Antibiotics, colonization resistance, and enteric pathogens. Immunol Rev, 279(1), 90-105. doi:10.1111/imr.12563 google scholar
• Kostic, A. D., Gevers, D., Pedamallu, C. S., Michaud, M., Duke, F., Earl, A. M., . . . Meyerson, M. (2012). Genomic analysis identifies association of Fusobacterium with colorectal carcinoma. Genome Res, 22(2), 292-298. doi:10.1101/gr.126573.111 google scholar
• Krogius-Kurikka, L., Lyra, A., Malinen, E., Aarnikunnas, J., Tuimala, J., Paulin, L., . . . Palva, A. (2009). Microbial community analysis reveals high level phylogenetic alterations in the overall gastrointestinal microbiota of diarrhoea-predominant irritable bowel syndrome sufferers. BMC Gastroenterol, 9, 95. do-i:10.1186/1471-230x-9-95 google scholar
• Kunkle, D. E., Bina, X. R., & Bina, J. E. (2020). Vibrio cholerae OmpR Contributes to Virulence Repression and Fitness at Alkaline pH. Infect Immun, 88(6). doi:10.1128/iai.00141-20 google scholar
• Kurokawa, K., Itoh, T., Kuwahara, T., Oshima, K., Toh, H., Toyoda, A., . . . Hattori, M. (2007). Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes. DNA Res, 14(4), 169-181. doi:10.1093/dnares/dsm018 google scholar
• Larsen, N., Vogensen, F. K., van den Berg, F. W., Nielsen, D. S., Andreasen, A. S., Pedersen, B. K., . . . Jakobsen, M. (2010). Gut microbiota in human adults with type 2 diabetes differs from non-diabetic adults. PLoS One, 5(2), e9085. doi:10.1371/journal.pone.0009085 google scholar
• Lee, D., Kim, E. J., Baek, Y., Lee, J., Yoon, Y., Nair, G. B., . . . Kim, D. W. (2020). Alterations in glucose metabolism in Vibrio cholerae serogroup O1 El Tor biotype strains. Sci Rep, 10(1), 308. doi:10.1038/ s41598-019-57093-4 google scholar
• Levison, M. E., & Levison, J. H. (2009). Pharmacokinetics and pharmacodynamics of antibacterial agents. Infect Dis Clin North Am, 23(4), 791-815, vii. doi:10.1016/j.idc.2009.06.008 google scholar
• Lewis, B. B., Buffie, C. G., Carter, R. A., Leiner, I., Toussaint, N. C., Miller, L. C., . . . Pamer, E. G. (2015). Loss of Microbiota-Mediated Colonization Resistance to Clostridium difficile Infection With Oral Vancomycin Compared With Metronidazole. J Infect Dis, 212(10), 1656-1665. doi:10.1093/infdis/jiv256 google scholar
• Ley, R. E., Backhed, F., Turnbaugh, P., Lozupone, C. A., Knight, R. D., & Gordon, J. I. (2005). Obesity alters gut microbial ecology. Proc Natl Acad Sci U S A, 102(31), 11070-11075. doi:10.1073/pnas.0504978102 google scholar
• Li, Q., Han, Y., Dy, A. B. C., & Hagerman, R. J. (2017). The Gut Microbiota and Autism Spectrum Disorders. Front Cell Neurosci, 11, 120. doi:10.3389/fncel.2017.00120 google scholar
• Li, X., Watanabe, K., & Kimura, I. (2017). Gut Microbiota Dysbiosis Drives and Implies Novel Therapeutic Strategies for Diabetes Mellitus and Related Metabolic Diseases. Front Immunol, 8, 1882. doi:10.3389/ fimmu.2017.01882 google scholar
• Louis, P., & Flint, H. J. (2017). Formation of propionate and butyrate by the human colonic microbiota. Environ Microbiol, 19(1), 29-41. doi:10.1111/1462-2920.13589 google scholar
• Lozupone, C. A., Stombaugh, J. I., Gordon, J. I., Jansson, J. K., & Knight, R. (2012). Diversity, stability and resilience of the human gut microbiota. Nature, 489(7415), 220-230. doi:10.1038/nature11550 google scholar
• Luo, M., Xin, R. J., Hu, F. R., Yao, L., Hu, S. J., & Bai, F. H. (2023). Role of gut microbiota in the pathogenesis and therapeutics of minimal hepatic encephalopathy via the gut-liver-brain axis. World J Gastroenterol, 29(1), 144-156. doi:10.3748/wjg.v29.i1.144 google scholar
• Lynch, S. V., & Pedersen, O. (2016). The Human Intestinal Microbiome in Health and Disease. N Engl J Med, 375(24), 2369-2379. doi:10.1056/NEJMra1600266 google scholar
• Machiels, K., Joossens, M., Sabino, J., De Preter, V., Arijs, I., Eeckhaut, V., . . . Vermeire, S. (2014). A decrease of the butyrate-producing species Roseburia hominis and Faecalibacterium prausnitzii defines dysbiosis in patients with ulcerative colitis. Gut, 63(8), 1275-1283. doi:10.1136/gutjnl-2013-304833 google scholar
• Marasco, G., Di Biase, A. R., Schiumerini, R., Eusebi, L. H., Iughetti, L., Ravaioli, F., . . . Festi, D. (2016). Gut Microbiota and Celiac Disease. Dig Dis Sci, 61(6), 1461-1472. doi:10.1007/s10620-015-4020-2 google scholar
• Mayer, E. A., Nance, K., & Chen, S. (2022). The Gut-Brain Axis. Annu Rev Med, 73, 439-453. doi:10.1146/ annurev-med-042320-014032 google scholar
• McDonald, D., Ackermann, G., Khailova, L., Baird, C., Heyland, D., Kozar, R., . . . Wischmeyer, P. E. (2016). Extreme Dysbiosis of the Microbiome in Critical Illness. mSphere, 1(4). doi:10.1128/mSphere.00199-16 google scholar
• McLoughlin, I. J., Wright, E. M., Tagg, J. R., Jain, R., & Hale, J. D. F. (2022). Skin Microbiome-The Next Frontier for Probiotic Intervention. Probiotics Antimicrob Proteins, 14(4), 630-647. doi:10.1007/s12602-021-09824-1 google scholar
• Meng, M., Klingensmith, N. J., & Coopersmith, C. M. (2017). New insights into the gut as the driver of critical illness and organ failure. Curr Opin Crit Care, 23(2), 143-148. doi:10.1097/mcc.0000000000000386 google scholar
• Milani, C., Duranti, S., Bottacini, F., Casey, E., Turroni, F., Mahony, J., . . . Ventura, M. (2017). The First Mic-robial Colonizers of the Human Gut: Composition, Activities, and Health Implications of the Infant Gut Microbiota. Microbiol Mol Biol Rev, 81(4). doi:10.1128/mmbr.00036-17 google scholar
• Monira, S., Hoq, M. M., Chowdhury, A. K., Suau, A., Magne, F., Endtz, H. P., . . . Alam, N. H. (2010). Short-cha-in fatty acids and commensal microbiota in the faeces of severely malnourished children with cholera rehyd-rated with three different carbohydrates. Eur J Clin Nutr, 64(10), 1116-1124. doi:10.1038/ejcn.2010.123 google scholar
• Nadal, I., Donant, E., Ribes-Koninckx, C., Calabuig, M., & Sanz, Y. (2007). Imbalance in the composition of the duodenal microbiota of children with coeliac disease. J Med Microbiol, 56(Pt 12), 1669-1674. doi:10.1099/ jmm.0.47410-0 google scholar
• Nakamoto, N., Sasaki, N., Aoki, R., Miyamoto, K., Suda, W., Teratani, T., . . . Kanai, T. (2019). Gut pathobionts underlie intestinal barrier dysfunction and liver T helper 17 cell immune response in primary sclerosing cholangitis. Nat Microbiol, 4(3), 492-503. doi:10.1038/s41564-018-0333-1 google scholar
• Nava, G. M., Friedrichsen, H. J., & Stappenbeck, T. S. (2011). Spatial organization of intestinal microbiota in the mouse ascending colon. Isme j, 5(4), 627-638. doi:10.1038/ismej.2010.161 google scholar
• Ojima, M., Motooka, D., Shimizu, K., Gotoh, K., Shintani, A., Yoshiya, K., . . . Shimazu, T. (2016). Metagenomic Analysis Reveals Dynamic Changes of Whole Gut Microbiota in the Acute Phase of Intensive Care Unit Patients. Dig Dis Sci, 61(6), 1628-1634. doi:10.1007/s10620-015-4011-3 google scholar
• Patel, V. C., Lee, S., McPhail, M. J. W., Da Silva, K., Guilly, S., Zamalloa, A., . . . Shawcross, D. L. (2022). Rifaximin-a reduces gut-derived inflammation and mucin degradation in cirrhosis and encephalopathy: RIFSYS randomised controlled trial. J Hepatol, 76(2), 332-342. doi:10.1016/j.jhep.2021.09.010 google scholar
• Perez-Cobas, A. E., Artacho, A., Knecht, H., Ferrus, M. L., Friedrichs, A., Ott, S. J., . . . Gosalbes, M. J. (2013). Differential effects of antibiotic therapy on the structure and function of human gut microbiota. PLoS One, 8(11), e80201. doi:10.1371/journal.pone.0080201 google scholar
• Picard, C., Fioramonti, J., Francois, A., Robinson, T., Neant, F., & Matuchansky, C. (2005). Review article: bifidobacteria as probiotic agents -- physiological effects and clinical benefits. Aliment Pharmacol Ther, 22(6), 495-512. doi:10.1111/j.1365-2036.2005.02615.x google scholar
• Porter, E. M., Liu, L., Oren, A., Anton, P. A., & Ganz, T. (1997). Localization of human intestinal defensin 5 in Paneth cell granules. Infect Immun, 65(6), 2389-2395. doi:10.1128/iai.65.6.2389-2395.1997 google scholar
• Porter, E. M., Poles, M. A., Lee, J. S., Naitoh, J., Bevins, C. L., & Ganz, T. (1998). Isolation of human intestinal defensins from ileal neobladder urine. FEBS Lett, 434(3), 272-276. doi:10.1016/s0014-5793(98)00994-6 google scholar
• Pral, L. P., Fachi, J. L., Correa, R. O., Colonna, M., & Vinolo, M. A. R. (2021). Hypoxia and HIF-1 as key regu-lators of gut microbiota and host interactions. Trends Immunol, 42(7), 604-621. doi:10.1016/j.it.2021.05.004 google scholar
• Pukatzki, S., Ma, A. T., Revel, A. T., Sturtevant, D., & Mekalanos, J. J. (2007). Type VI secretion system trans-locates a phage tail spike-like protein into target cells where it cross-links actin. Proc Natl Acad Sci U S A, 104(39), 15508-15513. doi:10.1073/pnas.0706532104 google scholar
• Pukatzki, S., Ma, A. T., Sturtevant, D., Krastins, B., Sarracino, D., Nelson, W. C., . . . Mekalanos, J. J. (2006). Identification of a conserved bacterial protein secretion system in Vibrio cholerae using the Dictyostelium host model system. Proc Natl Acad Sci U S A, 103(5), 1528-1533. doi:10.1073/pnas.0510322103 google scholar
• Qin, J., Li, R., Raes, J., Arumugam, M., Burgdorf, K. S., Manichanh, C., . . . Wang, J. (2010). A human gut microbial gene catalogue established by metagenomic sequencing. Nature, 464(7285), 59-65. doi:10.1038/ nature08821 google scholar
• Qin, J., Li, Y., Cai, Z., Li, S., Zhu, J., Zhang, F., . . . Wang, J. (2012). A metagenome-wide association study of gut microbiota in type 2 diabetes. Nature, 490(7418), 55-60. doi:10.1038/nature11450 google scholar
• Quraishi, M. N., Sergeant, M., Kay, G., Iqbal, T., Chan, J., Constantinidou, C., . . . Hirschfield, G. M. (2017). The gut-adherent microbiota of PSC-IBD is distinct to that of IBD. Gut, 66(2), 386-388. doi:10.1136/ gutjnl-2016-311915 google scholar
• Raethong, N., Nakphaichit, M., Suratannon, N., Sathitkowitchai, W., Weerapakorn, W., Keawsompong, S., & Vongsangnak, W. (2021). Analysis of Human Gut Microbiome: Taxonomy and Metabolic Functions in Thai Adults. Genes (Basel), 12(3). doi:10.3390/genes12030331 google scholar
• Ramirez, J., Guarner, F., Bustos Fernandez, L., Maruy, A., Sdepanian, V. L., & Cohen, H. (2020). Antibio-tics as Major Disruptors of Gut Microbiota. Front Cell Infect Microbiol, 10, 572912. doi:10.3389/ fcimb.2020.572912 google scholar
• Reichardt, N., Duncan, S. H., Young, P., Belenguer, A., McWilliam Leitch, C., Scott, K. P., . . . Louis, P. (2014). Phylogenetic distribution of three pathways for propionate production within the human gut microbiota. Isme j, 8(6), 1323-1335. doi:10.1038/ismej.2014.14 google scholar
• Rice, W. G., Ganz, T., Kinkade, J. M., Jr., Selsted, M. E., Lehrer, R. I., & Parmley, R. T. (1987). Defensin-rich dense granules of human neutrophils. Blood, 70(3), 757-765. google scholar
• Ridlon, J. M., Harris, S. C., Bhowmik, S., Kang, D. J., & Hylemon, P. B. (2016). Consequences of bile salt biotransformations by intestinal bacteria. Gut Microbes, 7(1), 22-39. doi:10.1080/19490976.2015.1127483 google scholar
• Ridlon, J. M., Kang, D. J., Hylemon, P. B., & Bajaj, J. S. (2014). Bile acids and the gut microbiome. Curr Opin Gastroenterol, 30(3), 332-338. doi:10.1097/mog.0000000000000057 google scholar
• Rinninella, E., Mele, M. C., Merendino, N., Cintoni, M., Anselmi, G., Caporossi, A., . . . Minnella, A. M. (2018). The Role of Diet, Micronutrients and the Gut Microbiota in Age-Related Macular Degeneration: New Pers-pectives from the Gut“Retina Axis. Nutrients, 10 (11). doi:10.3390/nu10111677 google scholar
• Rinninella, E., Raoul, P., Cintoni, M., Franceschi, F., Miggiano, G. A. D., Gasbarrini, A., & Mele, M. C. (2019). What is the Healthy Gut Microbiota Composition? A Changing Ecosystem across Age, Environment, Diet, and Diseases. Microorganisms, 7(1). doi:10.3390/microorganisms7010014 google scholar
• Rivera-Chavez, F., & Mekalanos, J. J. (2019). Cholera toxin promotes pathogen acquisition of host-derived nutrients. Nature, 572(7768), 244-248. doi:10.1038/s41586-019-1453-3 google scholar
• Rodriguez, J. M., Murphy, K., Stanton, C., Ross, R. P., Kober, O. I., Juge, N., . . . Collado, M. C. (2015). The composition of the gut microbiota throughout life, with an emphasis on early life. Microb Ecol Health Dis, 26, 26050. doi:10.3402/mehd.v26.26050 google scholar
• Roy, C. C., Kien, C. L., Bouthillier, L., & Levy, E. (2006). Short-chain fatty acids: ready for prime time? Nutr Clin Pract, 21(4), 351-366. doi:10.1177/0115426506021004351 google scholar
• Russell, A. B., Hood, R. D., Bui, N. K., LeRoux, M., Vollmer, W., & Mougous, J. D. (2011). Type VI secretion delivers bacteriolytic effectors to target cells. Nature, 475(7356), 343-347. doi:10.1038/nature10244 google scholar
• Russell, A. B., LeRoux, M., Hathazi, K., Agnello, D. M., Ishikawa, T., Wiggins, P. A., . . . Mougous, J. D. (2013). Diverse type VI secretion phospholipases are functionally plastic antibacterial effectors. Nature, 496(7446), 508-512. doi:10.1038/nature12074 google scholar
• Sah, D. K., Arjunan, A., Park, S. Y., & Jung, Y. D. (2022). Bile acids and microbes in metabolic disease. World J Gastroenterol, 28(48), 6846-6866. doi:10.3748/wjg.v28.i48.6846 google scholar
• Salonen, A., de Vos, W. M., & Palva, A. (2010). Gastrointestinal microbiota in irritable bowel syndrome: present state and perspectives. Microbiology (Reading), 156(Pt 11), 3205-3215. doi:10.1099/mic.0.043257-0 google scholar
• Sankar, S. A., Lagier, J. C., Pontarotti, P., Raoult, D., & Fournier, P. E. (2015). The human gut microbiome, a taxonomic conundrum. Syst Appl Microbiol, 38(4), 276-286. doi:10.1016/j.syapm.2015.03.004 google scholar
• Sasso, J. M., Ammar, R. M., Tenchov, R., Lemmel, S., Kelber, O., Grieswelle, M., & Zhou, Q. A. (2023). Gut Microbiome-Brain Alliance: A Landscape View into Mental and Gastrointestinal Health and Disorders. ACS Chem Neurosci, 14(10), 1717-1763. doi:10.1021/acschemneuro.3c00127 google scholar
• Sayin, S. I., Wahlström, A., Felin, J., Jantti, S., Marschall, H. U., Bamberg, K., . . . Backhed, F. (2013). Gut microbiota regulates bile acid metabolism by reducing the levels of tauro-beta-muricholic acid, a naturally occurring FXR antagonist. Cell Metab, 17(2), 225-235. doi:10.1016/j.cmet.2013.01.003 google scholar
• Schauder, S., Shokat, K., Surette, M. G., & Bassler, B. L. (2001). The LuxS family of bacterial autoinducers: bi-osynthesis of a novel quorum-sensing signal molecule. Mol Microbiol, 41(2), 463-476. doi:10.1046/j.1365-2958.2001.02532.x google scholar
• Scheperjans, F., Aho, V., Pereira, P. A., Koskinen, K., Paulin, L., Pekkonen, E., . . . Auvinen, P. (2015). Gut mic-robiota are related to Parkinson’s disease and clinical phenotype. Mov Disord, 30(3), 350-358. doi:10.1002/ mds.26069 google scholar
• Schwarz, S., West, T. E., Boyer, F., Chiang, W. C., Carl, M. A., Hood, R. D., . . . Mougous, J. D. (2010). Burkhol-deria type VI secretion systems have distinct roles in eukaryotic and bacterial cell interactions. PLoS Pathog, 6(8), e1001068. doi:10.1371/journal.ppat.1001068 google scholar
• Schwiertz, A., Taras, D., Schafer, K., Beijer, S., Bos, N. A., Donus, C., & Hardt, P. D. (2010). Microbiota and SCFA in lean and overweight healthy subjects. Obesity (Silver Spring), 18(1), 190-195. doi:10.1038/ oby.2009.167 google scholar
• Scott, K. P., Martin, J. C., Campbell, G., Mayer, C. D., & Flint, H. J. (2006). Whole-genome transcription profi-ling reveals genes up-regulated by growth on fucose in the human gut bacterium “Roseburia inulinivorans”. J Bacteriol, 188(12), 4340-4349. doi:10.1128/jb.00137-06 google scholar
• Selsted, M. E., Miller, S. I., Henschen, A. H., & Ouellette, A. J. (1992). Enteric defensins: antibiotic peptide components of intestinal host defense. J Cell Biol, 118(4), 929-936. doi:10.1083/jcb.118.4.929 google scholar
• Shen, X. J., Rawls, J. F., Randall, T., Burcal, L., Mpande, C. N., Jenkins, N., . . . Keku, T. O. (2010). Molecular characterization of mucosal adherent bacteria and associations with colorectal adenomas. Gut Microbes, 1(3), 138-147. doi:10.4161/gmic.1.3.12360 google scholar
• Shin, N. R., Whon, T. W., & Bae, J. W. (2015). Proteobacteria: microbial signature of dysbiosis in gut microbiota. Trends Biotechnol, 33(9), 496-503. doi:10.1016/j.tibtech.2015.06.011 google scholar
• Shirin, T., Rahman, A., Danielsson, Â., Uddin, T., Bhuyian, T. R., Sheikh, A., . . . Hammarström, M. L. (2011). Antimicrobial peptides in the duodenum at the acute and convalescent stages in patients with diarrhea due to Vibrio cholerae O1 or enterotoxigenic Escherichia coli infection. Microbes Infect, 13(12-13), 1111-1120. doi:10.1016/j.micinf.2011.06.014 google scholar
• Shneider, M. M., Buth, S. A., Ho, B. T., Basler, M., Mekalanos, J. J., & Leiman, P. G. (2013). PAAR-repeat proteins sharpen and diversify the type VI secretion system spike. Nature, 500(7462), 350-353. doi:10.1038/ nature12453 google scholar
• Sokol, H., Pigneur, B., Watterlot, L., Lakhdari, O., Bermudez-Humaran, L. G., Gratadoux, J. J., . . . Langella, P. (2008). Faecalibacterium prausnitzii is an anti-inflammatory commensal bacterium identified by gut mic-robiota analysis of Crohn disease patients. Proc Natl Acad Sci U S A, 105(43), 16731-16736. doi:10.1073/ pnas.0804812105 google scholar
• Stacy, A., Andrade-Oliveira, V., McCulloch, J. A., Hild, B., Oh, J. H., Perez-Chaparro, P. J., . . . Belkaid, Y. (2021). Infection trains the host for microbiota-enhanced resistance to pathogens. Cell, 184(3), 615-627. e617. doi:10.1016/j.cell.2020.12.011 google scholar
• Taur, Y., & Pamer, E. G. (2013). The intestinal microbiota and susceptibility to infection in immunocompromised patients. Curr Opin Infect Dis, 26(4), 332-337. doi:10.1097/QCO.0b013e3283630dd3 google scholar
• Taur, Y., & Pamer, E. G. (2016). Microbiome mediation of infections in the cancer setting. Genome Med, 8(1), 40. doi:10.1186/s13073-016-0306-z google scholar
• Taur, Y., Xavier, J. B., Lipuma, L., Ubeda, C., Goldberg, J., Gobourne, A., . . . Pamer, E. G. (2012). Intestinal domination and the risk of bacteremia in patients undergoing allogeneic hematopoietic stem cell transplan-tation. Clin Infect Dis, 55(7), 905-914. doi:10.1093/cid/cis580 google scholar
• Thuny, F., Richet, H., Casalta, J. P., Angelakis, E., Habib, G., & Raoult, D. (2010). Vancomycin treatment of infective endocarditis is linked with recently acquired obesity. PLoS One, 5(2), e9074. doi:10.1371/journal. pone.0009074 google scholar
• Tosh, P. K., & McDonald, L. C. (2012). Infection control in the multidrug-resistant era: tending the human microbiome. Clin Infect Dis, 54(5), 707-713. doi:10.1093/cid/cir899 google scholar
• Toska, J., Ho, B. T., & Mekalanos, J. J. (2018). Exopolysaccharide protects Vibrio cholerae from exogenous attacks by the type 6 secretion system. Proc Natl Acad Sci U S A, 115(31), 7997-8002. doi:10.1073/ pnas.1808469115 google scholar
• Turnbaugh, P. J., Ley, R. E., Mahowald, M. A., Magrini, V., Mardis, E. R., & Gordon, J. I. (2006). An obesit-y-associated gut microbiome with increased capacity for energy harvest. Nature, 444(7122), 1027-1031. doi:10.1038/nature05414 google scholar
• Velasco, E., Byington, R., Martins, C. A., Schirmer, M., Dias, L. M., & Gonçalves, V. M. (2006). Comparative study of clinical characteristics of neutropenic and non-neutropenic adult cancer patients with bloodstream infections. Eur J Clin Microbiol Infect Dis, 25(1), 1-7. doi:10.1007/s10096-005-0077-8 google scholar
• Vogt, N. M., Kerby, R. L., Dill-McFarland, K. A., Harding, S. J., Merluzzi, A. P., Johnson, S. C., . . . Rey, F. E. (2017). Gut microbiome alterations in Alzheimer’s disease. Sci Rep, 7(1), 13537. doi:10.1038/s41598-017-13601-y google scholar
• Wahlström, A., Sayin, S. I., Marschall, H. U., & Backhed, F. (2016). Intestinal Crosstalk between Bile Acids and Microbiota and Its Impact on Host Metabolism. Cell Metab, 24(1), 41-50. doi:10.1016/j.cmet.2016.05.005 google scholar
• Walsh, C. J., Guinane, C. M., O’Toole, P. W., & Cotter, P. D. (2014). Beneficial modulation of the gut microbiota. FEBS Lett, 588(22), 4120-4130. doi:10.1016/j.febslet.2014.03.035 google scholar
• Wang, L., Christophersen, C. T., Sorich, M. J., Gerber, J. P., Angley, M. T., & Conlon, M. A. (2011). Low rela-tive abundances of the mucolytic bacterium Akkermansia muciniphila and Bifidobacterium spp. in feces of children with autism. Appl Environ Microbiol, 77(18), 6718-6721. doi:10.1128/aem.05212-11 google scholar
• Wang, T., Cai, G., Qiu, Y., Fei, N., Zhang, M., Pang, X., . . . Zhao, L. (2012). Structural segregation of gut microbiota between colorectal cancer patients and healthy volunteers. Isme j, 6(2), 320-329. doi:10.1038/ ismej.2011.109 google scholar
• Wexler, H. M. (2007). Bacteroides: the good, the bad, and the nitty-gritty. Clin Microbiol Rev, 20(4), 593-621. doi:10.1128/cmr.00008-07 google scholar
• Williams, B. L., Hornig, M., Parekh, T., & Lipkin, W. I. (2012). Application of novel PCR-based methods for detection, quantitation, and phylogenetic characterization of Sutterella species in intestinal biopsy samples from children with autism and gastrointestinal disturbances. mBio, 3(1). doi:10.1128/mBio.00261-11 google scholar
• Y ang, M., Liu, Z., Hughes, C., Stern, A. M., Wang, H., Zhong, Z., . . . Zhu, J. (2013). Bile salt-induced inter-molecular disulfide bond formation activates Vibrio cholerae virulence. Proc Natl Acad Sci U S A, 110(6), 2348-2353. doi:10.1073/pnas.1218039110 google scholar
• Y ardeni, T., Tanes, C. E., Bittinger, K., Mattei, L. M., Schaefer, P. M., Singh, L. N., . . . Wallace, D. C. (2019). Host mitochondria influence gut microbiome diversity: A role for ROS. Sci Signal, 12(588). doi:10.1126/ scisignal.aaw3159 google scholar
• Y in, J., Zhou, C., Yang, K., Ren, Y., Qiu, Y., Xu, P., . . . Yang, H. (2020). Mutual regulation between butyrate and hypoxia-inducible factor-1a in epithelial cell promotes expression of tight junction proteins. Cell Biol Int, 44(6), 1405-1414. doi:10.1002/cbin.11336 google scholar
• Y oon, M. Y., Min, K. B., Lee, K. M., Yoon, Y., Kim, Y., Oh, Y. T., . . . Yoon, S. S. (2016). A single gene of a commensal microbe affects host susceptibility to enteric infection. Nat Commun, 7, 11606. doi:10.1038/ ncomms11606 google scholar
• Y oon, S. H., & Waters, C. M. (2019). Vibrio cholerae. Trends Microbiol, 27(9), 806-807. doi:10.1016/j. tim.2019.03.005 google scholar
• Y ou, J. S., Yong, J. H., Kim, G. H., Moon, S., Nam, K. T., Ryu, J. H., . . . Yoon, S. S. (2019). Commensal-deri-ved metabolites govern Vibrio cholerae pathogenesis in host intestine. Microbiome, 7(1), 132. doi:10.1186/ s40168-019-0746-y google scholar
• Z hang, C., Zhang, M., Wang, S., Han, R., Cao, Y., Hua, W., . . . Zhao, L. (2010). Interactions between gut microbiota, host genetics and diet relevant to development of metabolic syndromes in mice. Isme j, 4(2), 232-241. doi:10.1038/ismej.2009.112 google scholar
• Z hao, W., Caro, F., Robins, W., & Mekalanos, J. J. (2018). Antagonism toward the intestinal microbiota and its effect on Vibrio cholerae virulence. Science, 359(6372), 210-213. doi:10.1126/science.aap8775 google scholar
• Z hou, A., Yuan, Y., Yang, M., Huang, Y., Li, X., Li, S., . . . Tang, B. (2022). Crosstalk Between the Gut Micro-biota and Epithelial Cells Under Physiological and Infectious Conditions. Front Cell Infect Microbiol, 12, 832672. doi:10.3389/fcimb.2022.832672 google scholar