BÖLÜM


DOI :10.26650/B/LS34CH11CH22/2024.011.001   IUP :10.26650/B/LS34CH11CH22/2024.011.001    Tam Metin (PDF)

Bağırsak Mi̇krobiyotasının Beslenme ve Sağlıktaki̇ Rolü

Mustafa Oral ÖncülZerrin Aktaş

Mikrobiyota bakterileri, arkeleri, virüsleri, fajları ve mantarları içerir. Bugünkü bilgilerimize göre, bakteriler, özellikle türler açısından en belirgin mikrobiyota olma özelliğindedir. Mikrobiyomlar, insanın incelenen her ekolojik nişinde, yani ağız boşluğunda, cilt yüzeyinde, bağırsak yolunda, yemek borusunda, akciğerlerde ve diğer bölgelerinde mevcuttur. Tahminler değişiklik göstermekle birlikte insan mikrobiyotasını oluşturan 1000’den fazla farklı mikroorganizma türü olabilir. Bağırsak mikrobiyomunun bakteri türleri, vücudun diğer bölgelerindeki mikrobiyomlardan daha fazla çeşitlilik gösterir. Bağırsak mikrobiyotası, konakçı sindirimi ve beslenmesinin ayrılmaz bir parçasıdır ve substratlardan besin üretebilirler. Bağırsak mikrobiyotası, bağışıklık sisteminin gelişimini şekillendirerek, diyetteki besinleri (yağ asitleri, glikoz ve safra asitleri gibi) ve ilaçları metabolize ederek, karmaşık sindirilmeyen polisakkaritleri sindirerek ve vitaminleri ve biyoaktif molekülleri sentezleyerek konak sağlığında önemli bir rol oynar. Bu simbiyotik ilişki, vücut sağlıklı olduğu sürece mikroorganizmalara ve konakçılarına yarar sağlar. Bağırsak mikrobiyomunun bileşimi ve işlevindeki değişkenlik, bağırsak mikrobiyotasının çeşitliliği veya belirli taksonların varlığı, yokluğu veya miktarı gibi özellikleri ile konakçı sağlığı arasındaki ilişkiyi araştıran çok sayıda çalışma vardır. Bağırsak mikroorganizmalarının bağırsak ve ekstraistestinal bozukluklar da dahil olmak üzere çok çeşitli insan hastalıklarında rol oynadığı çeşitli çalışmalarda gösterilmiştir.


DOI :10.26650/B/LS34CH11CH22/2024.011.001   IUP :10.26650/B/LS34CH11CH22/2024.011.001    Tam Metin (PDF)

Gut Microbiota in Human Metabolic Health and Disease

Mustafa Oral ÖncülZerrin Aktaş

The human microbiome comprises of collective genomes of microbiota inhabiting us, namely protozoa, archaea, eukaryotes, viruses and predominantly bacteria that live symbiotically on and within various sites of the human body. According to our current knowledge, bacteria tend to be the most prominent microbiota, particularly in terms of species. Microbiomes exist in every human ecological niche that has been examined, the oral cavity, skin surface, intestinal tract, oesophagus, lungs and other. Estimates vary, but there could be over 1,000 different species of microorganisms making up the human microbiota. The bacterial species of the gut microbiome present a greater degree of diversity than microbiomes at other body sites. The gut microbiota are integral to host digestion and nutrition, and they can generate nutrients from substrates. The gut microbiota plays a major role in host health by shaping the development of the immune system, metabolizing dietary nutrients (such as fatty acids, glucose and bile acids) and drugs, digesting complex indigestible polysaccharides and synthesizing vitamins and bioactive molecules. This symbiotic relationship benefits microbes and their hosts as long as the body is in a healthy state. There are numerous studies investigating the relationship between the variability in the composition and function of the gut microbiome, the diversity of the gut microbiota, or the presence, absence or quantity of certain taxa, and host health. Various studies have shown that intestinal microorganisms play a role in a wide variety of human diseases, including intestinal and extra-intestinal disorders.



Referanslar

  • 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


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