Regulation of Gut Microbiota by Herbal Medicines

Yogita      Shinde; Gitanjali      Deokar
doi:10.2174/0113892002287336240328083220
Abstract

Preserving host health and homeostasis is largely dependent on the human gut microbiome, a varied and ever-changing population of bacteria living in the gastrointestinal tract. This article aims to explore the multifaceted functions of the gut microbiome and shed light on the evolving field of research investigating the impact of herbal medicines on both the composition and functionality of the gut microbiome. Through a comprehensive overview, we aim to provide insights into the intricate relationship between herbal remedies and the gut microbiome, fostering a better understanding of their potential implications for human health.The gut microbiota is composed of trillions of microorganisms, predominantly bacteria, but also viruses, fungi, and archaea. It functions as a complex ecosystem that interacts with the host in various ways. It aids in nutrient metabolism, modulates the immune system, provides protection against pathogens, and influences host physiology. Moreover, it has been linked to a range of health outcomes, including digestion, metabolic health, and even mental well-being. Recent research has shed light on the potential of herbal medicines to modulate the gut microbiome. Herbal medicines, derived from plants and often used in traditional medicine systems, contain a diverse array of phytochemicals, which can directly or indirectly impact gut microbial composition. These phytochemicals can either act as prebiotics, promoting the growth of beneficial bacteria, or possess antimicrobial properties, targeting harmful pathogens. Several studies have demonstrated the effects of specific herbal medicines on the gut microbiome. For example, extracts from herbs have been shown to enhance the abundance of beneficial bacteria, such as Bifidobacterium and Lactobacillus, while reducing potentially harmful microbes. Moreover, herbal medicines have exhibited promising antimicrobial effects against certain pathogenic bacteria. The modulation of the gut microbiome by herbal medicines has potential therapeutic implications. Research suggests herbal interventions could be harnessed to alleviate gastrointestinal disorders, support immune function, and even impact metabolic health. However, it is important to note that individual responses to herbal treatments can vary due to genetics, diet, and baseline microbiome composition.
In conclusion, the gut microbiome is a critical player in maintaining human health, and its modulation by herbal medicines is a burgeoning area of research. Understanding the complex interactions between herbal compounds and gut microbiota will pave the way for innovative approaches to personalized healthcare and the development of herbal-based therapeutics aimed at promoting gut health and overall well-being.
[1]
Bengmark, S. Ecological control of the gastrointestinal tract. The role of probiotic flora. Gut,  1998, 42(1), 2-7.
 [http://dx.doi.org/10.1136/gut.42.1.2] [PMID: 9505873]

[2]
Backhed, F; Ley, RE; Sonnenburg, JL; Peterson, DA; Gordon, JI Host-bacterial mutualism in the human intestine. Science,  2005, 307(5717), 1915-20.

[3]
Neish, A.S. Microbes in gastrointestinal health and disease. Gastroenterology,  2009, 136(1), 65-80.
 [http://dx.doi.org/10.1053/j.gastro.2008.10.080] [PMID: 19026645]

[4]
Gill, SR; Pop, M; DeBoy, RT; Eckburg, PB; Turnbaugh, PJ; Samuel, BS Metagenomic analysis of the human distal gut microbiome. Science,  2006, 312(5778), 1355-1359.

[5]
Thursby, E.; Juge, N. Introduction to the human gut microbiota. Biochem. J.,  2017, 474(11), 1823-1836.
 [http://dx.doi.org/10.1042/BCJ20160510] [PMID: 28512250]

[6]
Sender, R.; Fuchs, S.; Milo, R. Revised estimates for the number of human and bacteria cells in the body. PLoS Biol.,  2016, 14(8), e1002533.
 [http://dx.doi.org/10.1371/journal.pbio.1002533] [PMID: 27541692]

[7]
Luckey, T.D. Introduction to intestinal microecology; Oxford University Press, 1972, pp. 1292-1294.

[8]
Bäumler, A.J.; Sperandio, V. Interactions between the microbiota and pathogenic bacteria in the gut. Nature,  2016, 535(7610), 85-93.
 [http://dx.doi.org/10.1038/nature18849] [PMID: 27383983]

[9]
Gensollen, T.; Iyer, S.S.; Kasper, D.L.; Blumberg, R.S. How colonization by microbiota in early life shapes the immune system. Science,  2016, 352(6285), 539-544.
 [http://dx.doi.org/10.1126/science.aad9378] [PMID: 27126036]

[10]
Chang, C.; Lin, H. Dysbiosis in gastrointestinal disorders. Best Pract. Res. Clin. Gastroenterol.,  2016, 30(1), 3-15.
 [http://dx.doi.org/10.1016/j.bpg.2016.02.001] [PMID: 27048892]

[11]
Schroeder, B.O.; Bäckhed, F. Signals from the gut microbiota to distant organs in physiology and disease. Nat. Med.,  2016, 22(10), 1079-1089.
 [http://dx.doi.org/10.1038/nm.4185] [PMID: 27711063]

[12]
Moore, W.E.C.; Holdeman, L.V. Human fecal flora: The normal flora of 20 Japanese-Hawaiians. Appl. Microbiol.,  1974, 27(5), 961-979.
 [http://dx.doi.org/10.1128/am.27.5.961-979.1974] [PMID: 4598229]

[13]
Poretsky, R.; R, R.L.M.; Luo, C.; Tsementzi, D.; Konstantinidis, K.T. Strengths and limitations of 16S rRNA gene amplicon sequencing in revealing temporal microbial community dynamics. PLoS One,  2014, 9(4), e93827.
 [http://dx.doi.org/10.1371/journal.pone.0093827] [PMID: 24714158]

[14]
Suau, A.; Bonnet, R.; Sutren, M.; Godon, J.J.; Gibson, G.R.; Collins, M.D.; Doré, J. Direct analysis of genes encoding 16S rRNA from complex communities reveals many novel molecular species within the human gut. Appl. Environ. Microbiol.,  1999, 65(11), 4799-4807.
 [http://dx.doi.org/10.1128/AEM.65.11.4799-4807.1999] [PMID: 10543789]

[15]
Man, M.O.; Davenport, E.R.; Gilad, Y. Taxonomic classification of bacterial 16S rRNA genes using short sequencing reads: Evaluation of effective study designs. PLoS One,  2013, 8(1), e53608.
 [http://dx.doi.org/10.1371/journal.pone.0053608] [PMID: 23308262]

[16]
Hugon, P.; Dufour, J.C.; Colson, P.; Fournier, P.E.; Sallah, K.; Raoult, D. A comprehensive repertoire of prokaryotic species identified in human beings. Lancet Infect. Dis.,  2015, 15(10), 1211-1219.
 [http://dx.doi.org/10.1016/S1473-3099(15)00293-5] [PMID: 26311042]

[17]
Li, J.; Jia, H.; Cai, X.; Zhong, H.; Feng, Q.; Sunagawa, S.; Arumugam, M.; Kultima, J.R.; Prifti, E.; Nielsen, T.; Juncker, A.S.; Manichanh, C.; Chen, B.; Zhang, W.; Levenez, F.; Wang, J.; Xu, X.; Xiao, L.; Liang, S.; Zhang, D.; Zhang, Z.; Chen, W.; Zhao, H.; Aama, A.J.Y.; Edris, S.; Yang, H.; Wang, J.; Hansen, T.; Nielsen, H.B.; Brunak, S.; Kristiansen, K.; Guarner, F.; Pedersen, O.; Doré, J.; Ehrlich, S.D.; Bork, P.; Wang, J. An integrated catalog of reference genes in the human gut microbiome. Nat. Biotechnol.,  2014, 32(8), 834-841.
 [http://dx.doi.org/10.1038/nbt.2942] [PMID: 24997786]

[18]
Schluter, J.; Foster, K.R. The evolution of mutualism in gut microbiota via host epithelial selection. PLoS Biol.,  2012, 10(11), e1001424.
 [http://dx.doi.org/10.1371/journal.pbio.1001424] [PMID: 23185130]

[19]
Costello, EK; Lauber, CL; Hamady, M; Fierer, N; Gordon, JI; Knight, R Bacterial community variation in human body habitats across space and time. Science.,  2009, 326(5960), 1694-7.

[20]
Cobas, P.A.E.; Gosalbes, M.J.; Friedrichs, A.; Knecht, H.; Artacho, A.; Eismann, K.; Otto, W.; Rojo, D.; Bargiela, R.; von Bergen, M.; Neulinger, S.C.; Däumer, C.; Heinsen, F.A.; Latorre, A.; Barbas, C.; Seifert, J.; dos Santos, V.M.; Ott, S.J.; Ferrer, M.; Moya, A. Gut microbiota disturbance during antibiotic therapy: A multi-omic approach. Gut,  2013, 62(11), 1591-1601.
 [http://dx.doi.org/10.1136/gutjnl-2012-303184] [PMID: 23236009]

[21]
Moya, A.; Ferrer, M. Functional redundancy-induced stability of gut microbiota subjected to disturbance. Trends Microbiol.,  2016, 24(5), 402-413.
 [http://dx.doi.org/10.1016/j.tim.2016.02.002] [PMID: 26996765]

[22]
Aagaard, K; Ma, J; Antony, KM; Ganu, R; Petrosino, J.; Versalovic, J. The placenta harbors a unique microbiome. Sci. Transl. Med.,  2014, 6(237), 237ra65.
 [http://dx.doi.org/10.1126/scitranslmed.3008599]

[23]
Rodríguez, J.M.; Murphy, K.; Stanton, C.; Ross, R.P.; Kober, O.I.; Juge, N.; Avershina, E.; Rudi, K.; Narbad, A.; Jenmalm, M.C.; Marchesi, J.R.; Collado, M.C. The composition of the gut microbiota throughout life, with an emphasis on early life. Microb. Ecol. Health Dis.,  2015, 26(1), 26050.
 [PMID: 25651996]

[24]
Koenig, J.E.; Spor, A.; Scalfone, N.; Fricker, A.D.; Stombaugh, J.; Knight, R.; Angenent, L.T.; Ley, R.E. Succession of microbial consortia in the developing infant gut microbiome. Proc. Natl. Acad. Sci. USA,  2011, 108(S1), 4578-4585.
 [http://dx.doi.org/10.1073/pnas.1000081107] [PMID: 20668239]

[25]
Avershina, E.; Storrø, O.; Øien, T.; Johnsen, R.; Pope, P.; Rudi, K. Major faecal microbiota shifts in composition and diversity with age in a geographically restricted cohort of mothers and their children. FEMS Microbiol. Ecol.,  2014, 87(1), 280-290.
 [http://dx.doi.org/10.1111/1574-6941.12223] [PMID: 24112053]

[26]
Aagaard, K.; Riehle, K.; Ma, J.; Segata, N.; Mistretta, T.A.; Coarfa, C.; Raza, S.; Rosenbaum, S.; den Veyver, V.I.; Milosavljevic, A.; Gevers, D.; Huttenhower, C.; Petrosino, J.; Versalovic, J. A metagenomic approach to characterization of the vaginal microbiome signature in pregnancy. PLoS One,  2012, 7(6), e36466.
 [http://dx.doi.org/10.1371/journal.pone.0036466] [PMID: 22719832]

[27]
Jakobsson, H.E.; Abrahamsson, T.R.; Jenmalm, M.C.; Harris, K.; Quince, C.; Jernberg, C.; Björkstén, B.; Engstrand, L.; Andersson, A.F. Decreased gut microbiota diversity, delayed bacteroidetes colonisation and reduced th1 responses in infants delivered by caesarean section. Gut,  2014, 63(4), 559-566.
 [http://dx.doi.org/10.1136/gutjnl-2012-303249] [PMID: 23926244]

[28]
Bäckhed, F.; Roswall, J.; Peng, Y.; Feng, Q.; Jia, H.; Datchary, K.P.; Li, Y.; Xia, Y.; Xie, H.; Zhong, H.; Khan, M.T.; Zhang, J.; Li, J.; Xiao, L.; Aama, A.J.; Zhang, D.; Lee, Y.S.; Kotowska, D.; Colding, C.; Tremaroli, V.; Yin, Y.; Bergman, S.; Xu, X.; Madsen, L.; Kristiansen, K.; Dahlgren, J.; Wang, J. Dynamics and stabilization of the human gut microbiome during the first year of life. Cell Host. Microbe.,  2015, 17(5), 690-703.
 [http://dx.doi.org/10.1016/j.chom.2015.04.004] [PMID: 25974306]

[29]
Bäckhed, F. Programming of host metabolism by the gut microbiota. Ann. Nutr. Metab.,  2011, 58(S2), 44-52.
 [http://dx.doi.org/10.1159/000328042] [PMID: 21846980]

[30]
Palmer, C.; Bik, E.M.; DiGiulio, D.B.; Relman, D.A.; Brown, P.O. Development of the human infant intestinal microbiota. PLoS Biol.,  2007, 5(7), e177.
 [http://dx.doi.org/10.1371/journal.pbio.0050177] [PMID: 17594176]

[31]
Dethlefsen, L.; Relman, D.A. Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation. Proc. Natl. Acad. Sci.,  2011, 108(Suppl. 1), 4554-4561.
 [http://dx.doi.org/10.1073/pnas.1000087107] [PMID: 20847294]

[32]
Claesson, M.J.; Cusack, S.; O’Sullivan, O.; Diniz, G.R.; de Weerd, H.; Flannery, E.; Marchesi, J.R.; Falush, D.; Dinan, T.; Fitzgerald, G.; Stanton, C.; van Sinderen, D.; O’Connor, M.; Harnedy, N.; O’Connor, K.; Henry, C.; O’Mahony, D.; Fitzgerald, A.P.; Shanahan, F.; Twomey, C.; Hill, C.; Ross, R.P.; O’Toole, P.W. Composition, variability, and temporal stability of the intestinal microbiota of the elderly. Proc. Natl. Acad. Sci.,  2011, 108(S1), 4586-4591.
 [http://dx.doi.org/10.1073/pnas.1000097107] [PMID: 20571116]

[33]
Biagi, E.; Nylund, L.; Candela, M.; Ostan, R.; Bucci, L.; Pini, E.; Nikkïla, J.; Monti, D.; Satokari, R.; Franceschi, C.; Brigidi, P.; De Vos, W. Through ageing, and beyond: Gut microbiota and inflammatory status in seniors and centenarians. PLoS One,  2010, 5(5), e10667.
 [http://dx.doi.org/10.1371/journal.pone.0010667] [PMID: 20498852]

[34]
Claesson, M.J.; Jeffery, I.B.; Conde, S.; Power, S.E.; O’Connor, E.M.; Cusack, S.; Harris, H.M.B.; Coakley, M.; Lakshminarayanan, B.; O’Sullivan, O.; Fitzgerald, G.F.; Deane, J.; O’Connor, M.; Harnedy, N.; O’Connor, K.; O’Mahony, D.; van Sinderen, D.; Wallace, M.; Brennan, L.; Stanton, C.; Marchesi, J.R.; Fitzgerald, A.P.; Shanahan, F.; Hill, C.; Ross, R.P.; O’Toole, P.W. Gut microbiota composition correlates with diet and health in the elderly. Nature,  2012, 488(7410), 178-184.
 [http://dx.doi.org/10.1038/nature11319] [PMID: 22797518]

[35]
Woodmansey, E.J.; McMurdo, M.E.T.; Macfarlane, G.T.; Macfarlane, S. Comparison of compositions and metabolic activities of fecal microbiotas in young adults and in antibiotic-treated and non-antibiotic-treated elderly subjects. Appl. Environ. Microbiol.,  2004, 70(10), 6113-6122.
 [http://dx.doi.org/10.1128/AEM.70.10.6113-6122.2004] [PMID: 15466557]

[36]
Biagi, E.; Candela, M.; Turroni, S.; Garagnani, P.; Franceschi, C.; Brigidi, P. Ageing and gut microbes: Perspectives for health maintenance and longevity. Pharmacol. Res.,  2013, 69(1), 11-20.
 [http://dx.doi.org/10.1016/j.phrs.2012.10.005] [PMID: 23079287]

[37]
Musso, G.; Gambino, R.; Cassader, M. Obesity, diabetes, and gut microbiota: The hygiene hypothesis expanded? Diabetes Care,  2010, 33(10), 2277-2284.
 [http://dx.doi.org/10.2337/dc10-0556] [PMID: 20876708]

[38]
Louis, P.; Hold, G.L.; Flint, H.J. The gut microbiota, bacterial metabolites and colorectal cancer. Nat. Rev. Microbiol.,  2014, 12(10), 661-672.
 [http://dx.doi.org/10.1038/nrmicro3344] [PMID: 25198138]

[39]
Louis, P.; Flint, H.J. Formation of propionate and butyrate by the human colonic microbiota. Environ. Microbiol.,  2017, 19(1), 29-41.
 [http://dx.doi.org/10.1111/1462-2920.13589] [PMID: 27928878]

[40]
Macfarlane, S.; Macfarlane, G.T. Regulation of short-chain fatty acid production. Proc. Nutr. Soc.,  2003, 62(1), 67-72.
 [http://dx.doi.org/10.1079/PNS2002207] [PMID: 12740060]

[41]
Morrison, D.J.; Preston, T. Formation of short chain fatty acids by the gut microbiota and their impact on human metabolism. Gut Microbes,  2016, 7(3), 189-200.
 [http://dx.doi.org/10.1080/19490976.2015.1134082] [PMID: 26963409]

[42]
Derrien, M.; Vaughan, E.E.; Plugge, C.M.; de Vos, W.M. Akkermansia muciniphila gen. nov., sp. nov., A human intestinal mucin-degrading bacterium. Int. J. Syst. Evol. Microbiol.,  2004, 54(5), 1469-1476.
 [http://dx.doi.org/10.1099/ijs.0.02873-0] [PMID: 15388697]

[43]
Guarner, F.; Malagelada, J.R. Gut flora in health and disease. Lancet,  2003, 361(9356), 512-519.
 [http://dx.doi.org/10.1016/S0140-6736(03)12489-0] [PMID: 12583961]

[44]
Lin, L.; Zhang, J. Role of intestinal microbiota and metabolites on gut homeostasis and human diseases. BMC Immunol.,  2017, 18(1), 2.
 [http://dx.doi.org/10.1186/s12865-016-0187-3] [PMID: 28061847]

[45]
Oliveira, C.R.; Fachi, J.L.; Vieira, A.; Sato, F.T.; Vinolo, M.A.R. Regulation of immune cell function by short‐chain fatty acids. Clin. Transl. Immunology,  2016, 5(4), e73.
 [http://dx.doi.org/10.1038/cti.2016.17] [PMID: 27195116]

[46]
Donohoe, D.R.; Collins, L.B.; Wali, A.; Bigler, R.; Sun, W.; Bultman, S.J. The Warburg effect dictates the mechanism of butyrate-mediated histone acetylation and cell proliferation. Mol. Cell,  2012, 48(4), 612-626.
 [http://dx.doi.org/10.1016/j.molcel.2012.08.033] [PMID: 23063526]

[47]
Chambers, E.S.; Morrison, D.J.; Frost, G. Control of appetite and energy intake by SCFA: What are the potential underlying mechanisms? Proc. Nutr. Soc.,  2015, 74(3), 328-336.
 [http://dx.doi.org/10.1017/S0029665114001657] [PMID: 25497601]

[48]
Pingitore, A.; Chambers, E.S.; Hill, T.; Maldonado, I.R.; Liu, B.; Bewick, G.; Morrison, D.J.; Preston, T.; Wallis, G.A.; Tedford, C.; González, C.R.; Huang, G.C.; Choudhary, P.; Frost, G.; Persaud, S.J. The diet-derived short chain fatty acid propionate improves beta-cell function in humans and stimulates insulin secretion from human islets in vitro. Diabetes Obes. Metab.,  2017, 19(2), 257-265.
 [http://dx.doi.org/10.1111/dom.12811] [PMID: 27761989]

[49]
Byrne, C.S.; Chambers, E.S.; Alhabeeb, H.; Chhina, N.; Morrison, D.J.; Preston, T.; Tedford, C.; Fitzpatrick, J.; Irani, C.; Busza, A.; Garcia-Perez, I.; Fountana, S.; Holmes, E.; Goldstone, A.P.; Frost, G.S. Increased colonic propionate reduces anticipatory reward responses in the human striatum to high-energy foods. Am. J. Clin. Nutr.,  2016, 104(1), 5-14.
 [http://dx.doi.org/10.3945/ajcn.115.126706] [PMID: 27169834]

[50]
LeBlanc, J.G.; Milani, C.; de Giori, G.S.; Sesma, F.; van Sinderen, D.; Ventura, M. Bacteria as vitamin suppliers to their host: A gut microbiota perspective. Curr. Opin. Biotechnol.,  2013, 24(2), 160-168.
 [http://dx.doi.org/10.1016/j.copbio.2012.08.005] [PMID: 22940212]

[51]
Pompei, A.; Cordisco, L.; Amaretti, A.; Zanoni, S.; Matteuzzi, D.; Rossi, M. Folate production by bifidobacteria as a potential probiotic property. Appl. Environ. Microbiol.,  2007, 73(1), 179-185.
 [http://dx.doi.org/10.1128/AEM.01763-06] [PMID: 17071792]

[52]
Hill, M.J. Intestinal flora and endogenous vitamin synthesis. Eur. J. Cancer Prev.,  1997, 6(2)(Suppl. 1), S43-S45.
 [http://dx.doi.org/10.1097/00008469-199703001-00009] [PMID: 9167138]

[53]
Staley, C.; Weingarden, A.R.; Khoruts, A.; Sadowsky, M.J. Interaction of gut microbiota with bile acid metabolism and its influence on disease states. Appl. Microbiol. Biotechnol.,  2017, 101(1), 47-64.
 [http://dx.doi.org/10.1007/s00253-016-8006-6] [PMID: 27888332]

[54]
Smith, K.; McCoy, K.D.; Macpherson, A.J. Use of axenic animals in studying the adaptation of mammals to their commensal intestinal microbiota. Semin Immunol,  2007, 19(2), 59-69.
 [http://dx.doi.org/10.1016/j.smim.2006.10.002]

[55]
Swanson, P.A., II; Kumar, A.; Samarin, S.; Kumar, V.M.; Kundu, K.; Murthy, N.; Hansen, J.; Nusrat, A.; Neish, A.S. Enteric commensal bacteria potentiate epithelial restitution via reactive oxygen species-mediated inactivation of focal adhesion kinase phosphatases. Proc. Natl. Acad. Sci.,  2011, 108(21), 8803-8808.
 [http://dx.doi.org/10.1073/pnas.1010042108] [PMID: 21555563]

[56]
Reunanen, J.; Kainulainen, V.; Huuskonen, L.; Ottman, N.; Belzer, C.; Huhtinen, H.; de Vos, W.M.; Satokari, R. Akkermansia muciniphila adheres to enterocytes and strengthens the integrity of the epithelial cell layer. Appl. Environ. Microbiol.,  2015, 81(11), 3655-3662.
 [http://dx.doi.org/10.1128/AEM.04050-14] [PMID: 25795669]

[57]
Chen, H.Q.; Yang, J.; Zhang, M.; Zhou, Y.K.; Shen, T.Y.; Chu, Z.X.; Zhang, M.; Hang, X.M.; Jiang, Y.Q.; Qin, H.L. Lactobacillus plantarum ameliorates colonic epithelial barrier dysfunction by modulating the apical junctional complex and PepT1 in IL-10 knockout mice. Am. J. Physiol. Gastrointest. Liver Physiol.,  2010, 299(6), G1287-G1297.
 [http://dx.doi.org/10.1152/ajpgi.00196.2010] [PMID: 20884889]

[58]
Petersson, J.; Schreiber, O.; Hansson, G.C.; Gendler, S.J.; Velcich, A.; Lundberg, J.O.; Roos, S.; Holm, L.; Phillipson, M. Importance and regulation of the colonic mucus barrier in a mouse model of colitis. Am. J. Physiol. Gastrointest. Liver Physiol.,  2011, 300(2), G327-G333.
 [http://dx.doi.org/10.1152/ajpgi.00422.2010] [PMID: 21109593]

[59]
Wrzosek, L.; Miquel, S.; Noordine, M.L.; Bouet, S.; Curt, C.M.J.; Robert, V.; Philippe, C.; Bridonneau, C.; Cherbuy, C.; Masselot, R.C.; Langella, P.; Thomas, M. Bacteroides thetaiotaomicron and Faecalibacterium prausnitziiinfluence the production of mucus glycans and the development of goblet cells in the colonic epithelium of a gnotobiotic model rodent. BMC Biol.,  2013, 11(1), 61.
 [http://dx.doi.org/10.1186/1741-7007-11-61] [PMID: 23692866]

[60]
Varyukhina, S.; Freitas, M.; Bardin, S.; Robillard, E.; Tavan, E.; Sapin, C.; Grill, J.P.; Trugnan, G. Glycan-modifying bacteria-derived soluble factors from Bacteroides thetaiotaomicron and Lactobacillus casei inhibit rotavirus infection in human intestinal cells. Microbes Infect.,  2012, 14(3), 273-278.
 [http://dx.doi.org/10.1016/j.micinf.2011.10.007] [PMID: 22079149]

[61]
Freitas, M.; Cayuela, C.; Antoine, J.M.; Piller, F.; Sapin, C.; Trugnan, G. A heat labile soluble factor from Bacteroides thetaiotaomicron VPI-5482 specifically increases the galactosylation pattern of HT29-MTX cells. Cell. Microbiol.,  2001, 3(5), 289-300.
 [http://dx.doi.org/10.1046/j.1462-5822.2001.00113.x] [PMID: 11298652]

[62]
Mazmanian, S.K.; Liu, C.H.; Tzianabos, A.O.; Kasper, D.L. An immunomodulatory molecule of symbiotic bacteria directs maturation of the host immune system. Cell,  2005, 122(1), 107-118.
 [http://dx.doi.org/10.1016/j.cell.2005.05.007] [PMID: 16009137]

[63]
Hevia, A.; Delgado, S.; Sánchez, B.; Margolles, A. Molecular players involved in the interaction between beneficial bacteria and the immune system. Front. Microbiol.,  2015, 6, 1285.
 [http://dx.doi.org/10.3389/fmicb.2015.01285] [PMID: 26635753]

[64]
Schnupf, P.; Routhiau, G.V.; Gros, M.; Friedman, R.; Nilges, M.M.; Nigro, G.; Bensussan, C.N.; Sansonetti, P.J. Growth and host interaction of mouse segmented filamentous bacteria in vitro. Nature,  2015, 520(7545), 99-103.
 [http://dx.doi.org/10.1038/nature14027] [PMID: 25600271]

[65]
Nagai, M.; Obata, Y.; Takahashi, D.; Hase, K. Fine-tuning of the mucosal barrier and metabolic systems using the diet-microbial metabolite axis. Int. Immunopharmacol.,  2016, 37, 79-86.
 [http://dx.doi.org/10.1016/j.intimp.2016.04.001] [PMID: 27133028]

[66]
Derrien, M.; Belzer, C.; de Vos, W.M. Akkermansia muciniphila and its role in regulating host functions. Microb. Pathog.,  2017, 106, 171-181.
 [http://dx.doi.org/10.1016/j.micpath.2016.02.005] [PMID: 26875998]

[67]
Sokol, H.; Seksik, P.; Furet, J.P.; Firmesse, O.; Larmurier, N.I.; Beaugerie, L.; Cosnes, J.; Corthier, G.; Marteau, P.; Doré, J. Low counts of Faecalibacterium prausnitzii in colitis microbiota. Inflamm. Bowel Dis.,  2009, 15(8), 1183-1189.
 [http://dx.doi.org/10.1002/ibd.20903] [PMID: 19235886]

[68]
Siles, L.M.; Duncan, S.H.; Gil, G.L.J.; Medina, M.M. Faecalibacterium prausnitzii : From microbiology to diagnostics and prognostics. ISME J.,  2017, 11(4), 841-852.
 [http://dx.doi.org/10.1038/ismej.2016.176] [PMID: 28045459]

[69]
Quévrain, E.; Maubert, M.A.; Michon, C.; Chain, F.; Marquant, R.; Tailhades, J.; Miquel, S.; Carlier, L.; Humarán, B.L.G.; Pigneur, B.; Lequin, O.; Kharrat, P.; Thomas, G.; Rainteau, D.; Aubry, C.; Breyner, N.; Afonso, C.; Lavielle, S.; Grill, J-P.; Chassaing, G.; Chatel, J.M.; Trugnan, G.; Xavier, R.; Langella, P.; Sokol, H.; Seksik, P. Identification of an anti-inflammatory protein from Faecalibacterium prausnitzii, A commensal bacterium deficient in Crohn’s disease. Gut,  2016, 65(3), 415-425.
 [http://dx.doi.org/10.1136/gutjnl-2014-307649] [PMID: 26045134]

[70]
Hooper, L.V.; Macpherson, A.J. Immune adaptations that maintain homeostasis with the intestinal microbiota. Nat. Rev. Immunol.,  2010, 10(3), 159-169.
 [http://dx.doi.org/10.1038/nri2710] [PMID: 20182457]

[71]
Mathias, A.; Pais, B.; Favre, L.; Benyacoub, J.; Corthésy, B. Role of secretory IgA in the mucosal sensing of commensal bacteria. Gut Microbes,  2014, 5(6), 688-695.
 [http://dx.doi.org/10.4161/19490976.2014.983763] [PMID: 25536286]

[72]
Rios, D.; Wood, M.B.; Li, J.; Chassaing, B.; Gewirtz, A.T.; Williams, I.R. Antigen sampling by intestinal M cells is the principal pathway initiating mucosal IgA production to commensal enteric bacteria. Mucosal Immunol.,  2016, 9(4), 907-916.
 [http://dx.doi.org/10.1038/mi.2015.121] [PMID: 26601902]

[73]
Rogier, E.; Frantz, A.; Bruno, M.; Kaetzel, C. Secretory IgA is concentrated in the outer layer of colonic mucus along with gut bacteria. Pathogens,  2014, 3(2), 390-403.
 [http://dx.doi.org/10.3390/pathogens3020390] [PMID: 25437806]

[74]
Jandhyala, S.M.; Talukdar, R.; Subramanyam, C.; Vuyyuru, H.; Sasikala, M.; Reddy, N.D. Role of the normal gut microbiota. World J. Gastroenterol.,  2015, 21(29), 8787-8803.
 [http://dx.doi.org/10.3748/wjg.v21.i29.8787] [PMID: 26269668]

[75]
Macfarlane, G.T.; Macfarlane, S. Bacteria, colonic fermentation, and gastrointestinal health. J. AOAC Int.,  2012, 95(1), 50-60.
 [http://dx.doi.org/10.5740/jaoacint.SGE_Macfarlane] [PMID: 22468341]

[76]
Walker, A.W.; Duncan, S.H.; Leitch, M.E.C.; Child, M.W.; Flint, H.J. pH and peptide supply can radically alter bacterial populations and short-chain fatty acid ratios within microbial communities from the human colon. Appl. Environ. Microbiol.,  2005, 71(7), 3692-3700.
 [http://dx.doi.org/10.1128/AEM.71.7.3692-3700.2005] [PMID: 16000778]

[77]
Macfarlane, G.T.; Cummings, J.H.; Allison, C. Protein degradation by human intestinal bacteria. J. Gen. Microbiol.,  1986, 132(6), 1647-1656.
 [PMID: 3543210]

[78]
Cummings, J.H.; Macfarlane, G.T. The control and consequences of bacterial fermentation in the human colon. J. Appl. Bacteriol.,  1991, 70(6), 443-459.
 [http://dx.doi.org/10.1111/j.1365-2672.1991.tb02739.x] [PMID: 1938669]

[79]
Hamer, H.M.; De Preter, V.; Windey, K.; Verbeke, K. Functional analysis of colonic bacterial metabolism: Relevant to health? Am. J. Physiol. Gastrointest. Liver Physiol.,  2012, 302(1), G1-G9.
 [http://dx.doi.org/10.1152/ajpgi.00048.2011] [PMID: 22016433]

[80]
Magee, E.A.; Richardson, C.J.; Hughes, R.; Cummings, J.H. Contribution of dietary protein to sulfide production in the large intestine: An in vitro and a controlled feeding study in humans. Am. J. Clin. Nutr.,  2000, 72(6), 1488-1494.
 [http://dx.doi.org/10.1093/ajcn/72.6.1488] [PMID: 11101476]

[81]
Guerville, M.; Boudry, G. Gastrointestinal and hepatic mechanisms limiting entry and dissemination of lipopolysaccharide into the systemic circulation. Am. J. Physiol. Gastrointest. Liver Physiol.,  2016, 311(1), G1-G15.
 [http://dx.doi.org/10.1152/ajpgi.00098.2016] [PMID: 27151941]

[82]
Blaut, M. Relationship of prebiotics and food to intestinal microflora. Eur. J. Nutr.,  2002, 41(S1), 1.
 [http://dx.doi.org/10.1007/s00394-002-1102-7] [PMID: 12420111]

[83]
Cummings, J.H.; Englyst, H.N. What is dietary fibre? Trends Food Sci. Technol.,  1991, 2, 99-103.
 [http://dx.doi.org/10.1016/0924-2244(91)90638-Y]

[84]
Respondek, F.; Swanson, K.S.; Belsito, K.R.; Vester, B.M.; Wagner, A.; Istasse, L.; Diez, M. Short-chain fructooligosaccharides influence insulin sensitivity and gene expression of fat tissue in obese dogs. J. Nutr.,  2008, 138(9), 1712-1718.
 [http://dx.doi.org/10.1093/jn/138.9.1712] [PMID: 18716174]

[85]
Gibson, G.R.; Roberfroid, M.B. Dietary modulation of the human colonic microbiota: Introducing the concept of prebiotics. J. Nutr.,  1995, 125(6), 1401-1412.
 [http://dx.doi.org/10.1093/jn/125.6.1401] [PMID: 7782892]

[86]
Vieira, A.T.; Teixeira, M.M.; Martins, F.S. The role of probiotics and prebiotics in inducing gut immunity. Front. Immunol.,  2013, 4, 445.
 [http://dx.doi.org/10.3389/fimmu.2013.00445] [PMID: 24376446]

[87]
Schnorr, S.L.; Candela, M.; Rampelli, S.; Centanni, M.; Consolandi, C.; Basaglia, G.; Turroni, S.; Biagi, E.; Peano, C.; Severgnini, M.; Fiori, J.; Gotti, R.; De Bellis, G.; Luiselli, D.; Brigidi, P.; Mabulla, A.; Marlowe, F.; Henry, A.G.; Crittenden, A.N. Gut microbiome of the Hadza hunter-gatherers. Nat. Commun.,  2014, 5(1), 3654.
 [http://dx.doi.org/10.1038/ncomms4654] [PMID: 24736369]

[88]
Marlow, G.; Ellett, S.; Ferguson, I.R.; Zhu, S.; Karunasinghe, N.; Jesuthasan, A.C.; Han, D.Y.; Fraser, A.G.; Ferguson, L.R. Transcriptomics to study the effect of a Mediterranean-inspired diet on inflammation in Crohn’s disease patients. Hum. Genomics,  2013, 7(1), 24.
 [http://dx.doi.org/10.1186/1479-7364-7-24] [PMID: 24283712]

[89]
Bauer, G.M.; Yeh, M.C. The health advantage of a vegan diet: Exploring the gut microbiota connection. Nutrients,  2014, 6(11), 4822-4838.
 [http://dx.doi.org/10.3390/nu6114822] [PMID: 25365383]

[90]
Matijašić, B.B.; Obermajer, T.; Lipoglavšek, L.; Grabnar, I.; Avguštin, G.; Rogelj, I. Association of dietary type with fecal microbiota in vegetarians and omnivores in Slovenia. Eur. J. Nutr.,  2014, 53(4), 1051-1064.
 [http://dx.doi.org/10.1007/s00394-013-0607-6] [PMID: 24173964]

[91]
Vors, C.; Pineau, G.; Gabert, L.; Drai, J.; Pélissier, L.C.; Defoort, C.; Lairon, D.; Désage, M.; Danthine, S.; Porcheron, L.S.; Vidal, H.; Laville, M.; Michalski, M.C. Modulating absorption and postprandial handling of dietary fatty acids by structuring fat in the meal: A randomized crossover clinical trial. Am. J. Clin. Nutr.,  2013, 97(1), 23-36.
 [http://dx.doi.org/10.3945/ajcn.112.043976] [PMID: 23235199]

[92]
Daniel, H.; Gholami, A.M.; Berry, D.; Desmarchelier, C.; Hahne, H.; Loh, G.; Mondot, S.; Lepage, P.; Rothballer, M.; Walker, A.; Böhm, C.; Wenning, M.; Wagner, M.; Blaut, M.; Kopplin, S.P.; Kuster, B.; Haller, D.; Clavel, T. High-fat diet alters gut microbiota physiology in mice. ISME J.,  2014, 8(2), 295-308.
 [http://dx.doi.org/10.1038/ismej.2013.155] [PMID: 24030595]

[93]
Clarke, S.F.; Murphy, E.F.; Nilaweera, K.; Ross, P.R.; Shanahan, F.; O’Toole, P.W.; Cotter, P.D. The gut microbiota and its relationship to diet and obesity. Gut Microbes,  2012, 3(3), 186-202.
 [http://dx.doi.org/10.4161/gmic.20168] [PMID: 22572830]

[94]
De Filippo, C.; Cavalieri, D.; Di Paola, M.; Ramazzotti, M.; Poullet, J.B.; Massart, S.; Collini, S.; Pieraccini, G.; Lionetti, P. Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa. Proc. Natl. Acad. Sci.,  2010, 107(33), 14691-14696.
 [http://dx.doi.org/10.1073/pnas.1005963107] [PMID: 20679230]

[95]
Riaz, M.S.; Shaheen, T.; Batool, N.; Saleem, S.; Haris, A.; Hayat, F. Modulation of immune system by taking probiotic bacteria: Especially focus on lactic acid bacteria. Asian J Agr Biol.,  2015, 3, 74-77.

[96]
Ndagijimana, M.; Laghi, L.; Vitali, B.; Placucci, G.; Brigidi, P.; Guerzoni, M.E. Effect of a synbiotic food consumption on human gut metabolic profiles evaluated by 1h nuclear magnetic resonance spectroscopy. Int. J. Food Microbiol.,  2009, 134(1-2), 147-153.
 [http://dx.doi.org/10.1016/j.ijfoodmicro.2009.04.016] [PMID: 19446905]

[97]
Sanz, Y.; De Palma, G. Gut microbiota and probiotics in modulation of epithelium and gut-associated lymphoid tissue function. Int. Rev. Immunol.,  2009, 28(6), 397-413.
 [http://dx.doi.org/10.3109/08830180903215613] [PMID: 19954356]

[98]
Chassaing, B.; Koren, O.; Goodrich, J.K.; Poole, A.C.; Srinivasan, S.; Ley, R.E.; Gewirtz, A.T. Dietary emulsifiers impact the mouse gut microbiota promoting colitis and metabolic syndrome. Nature,  2015, 519(7541), 92-96.
 [http://dx.doi.org/10.1038/nature14232] [PMID: 25731162]

[99]
Hogenová, T.H.; Štěpánková, R.; Hudcovic, T.; Tučková, L.; Cukrowska, B.; Žádníková, L.R.; Kozáková, H.; Rossmann, P.; Bártová, J.; Sokol, D.; Funda, D.P.; Borovská, D.; Řeháková, Z.; Šinkora, J.; Hofman, J.; Drastich, P.; Kokešová, A. Commensal bacteria (normal microflora), mucosal immunity and chronic inflammatory and autoimmune diseases. Immunol. Lett.,  2004, 93(2-3), 97-108.
 [http://dx.doi.org/10.1016/j.imlet.2004.02.005] [PMID: 15158604]

[100]
Rawls, J.F.; Samuel, B.S.; Gordon, J.I. Gnotobiotic zebrafish reveal evolutionarily conserved responses to the gut microbiota. Proc. Natl. Acad. Sci.,  2004, 101(13), 4596-4601.
 [http://dx.doi.org/10.1073/pnas.0400706101] [PMID: 15070763]

[101]
Sonnenburg, J.L.; Bäckhed, F. Diet–microbiota interactions as moderators of human metabolism. Nature,  2016, 535(7610), 56-64.
 [http://dx.doi.org/10.1038/nature18846] [PMID: 27383980]

[102]
Ley, R.E. Obesity and the human microbiome. Curr. Opin. Gastroenterol.,  2010, 26(1), 5-11.
 [http://dx.doi.org/10.1097/MOG.0b013e328333d751] [PMID: 19901833]

[103]
Zhao, L. The gut microbiota and obesity: From correlation to causality. Nat. Rev. Microbiol.,  2013, 11(9), 639-647.
 [http://dx.doi.org/10.1038/nrmicro3089] [PMID: 23912213]

[104]
Ley, R.E.; Bäckhed, F.; Turnbaugh, P.; Lozupone, C.A.; Knight, R.D.; Gordon, J.I. Obesity alters gut microbial ecology. Proc. Natl. Acad. Sci.,  2005, 102(31), 11070-11075.
 [http://dx.doi.org/10.1073/pnas.0504978102] [PMID: 16033867]

[105]
Turnbaugh, PJ; Hamady, M; Yatsunenko, T; Cantarel, BL; Duncan, A; Ley, RE A core gut microbiome in obese and lean twins. Nature.,  2009, 457(7228), 480-4.

[106]
Turnbaugh, PJ; Ley, RE; Mahowald, MA; Magrini, V; Mardis, ER; Gordon, JI An obesity-associated gut microbiome with increased capacity for energy harvest. Nature.,  2006, 444(7122), 1027-31.

[107]
Zhang, H.; DiBaise, J.K.; Zuccolo, A.; Kudrna, D.; Braidotti, M.; Yu, Y.; Parameswaran, P.; Crowell, M.D.; Wing, R.; Rittmann, B.E.; Brown, K.R. Human gut microbiota in obesity and after gastric bypass. Proc. Natl. Acad. Sci.,  2009, 106(7), 2365-2370.
 [http://dx.doi.org/10.1073/pnas.0812600106] [PMID: 19164560]

[108]
Gregor, M.F.; Hotamisligil, G.S. Inflammatory mechanisms in obesity. Annu. Rev. Immunol.,  2011, 29(1), 415-445.
 [http://dx.doi.org/10.1146/annurev-immunol-031210-101322] [PMID: 21219177]

[109]
Cani, P.D.; Possemiers, S.; de Wiele, V.T.; Guiot, Y.; Everard, A.; Rottier, O.; Geurts, L.; Naslain, D.; Neyrinck, A.; Lambert, D.M.; Muccioli, G.G.; Delzenne, N.M. Changes in gut microbiota control inflammation in obese mice through a mechanism involving GLP-2-driven improvement of gut permeability. Gut,  2009, 58(8), 1091-1103.
 [http://dx.doi.org/10.1136/gut.2008.165886] [PMID: 19240062]

[110]
Bäckhed, F.; Ding, H.; Wang, T.; Hooper, L.V.; Koh, G.Y.; Nagy, A.; Semenkovich, C.F.; Gordon, J.I. The gut microbiota as an environmental factor that regulates fat storage. Proc. Natl. Acad. Sci.,  2004, 101(44), 15718-15723.
 [http://dx.doi.org/10.1073/pnas.0407076101] [PMID: 15505215]

[111]
Hall, M.A.; Cole, C.B.; Smith, S.L.; Fuller, R.; Rolles, C.J. Factors influencing the presence of faecal lactobacilli in early infancy. Arch. Dis. Child.,  1990, 65(2), 185-188.
 [http://dx.doi.org/10.1136/adc.65.2.185] [PMID: 2317064]

[112]
Afrc, R.F. Probiotics in man and animals. J. Appl. Bacteriol.,  1989, 66(5), 365-378.
 [http://dx.doi.org/10.1111/j.1365-2672.1989.tb05105.x] [PMID: 2666378]

[113]
Fuller, R. Probiotics: the scientific basis. Intest. Microecol. Consultant, Reading; Springer Nature: UK, 1992. 

[114]
Fuller, R. Probiotics 2: applications and practical aspects; Springer Science & Business Media, 1997. 
 [http://dx.doi.org/10.1007/978-94-011-5860-2]

[115]
McFarland, L.V.; Surawicz, C.M.; Greenberg, R.N.; Elmer, G.W.; Moyer, K.A.; Melcher, S.A.; Bowen, K.E.; Cox, J.L. Prevention of beta-lactam-associated diarrhea by Saccharomyces boulardii compared with placebo. Am. J. Gastroenterol.,  1995, 90(3), 439-448.
 [PMID: 7872284]

[116]
Pothoulakis, C.; Kelly, C.P.; Joshi, M.A.; Gao, N.; O’Keane, C.J.; Castagliuolo, I.; Lamont, J.T. Saccharomyces boulardii inhibits clostridium difficile toxin a binding and enterotoxicity in rat ileum. Gastroenterology,  1993, 104(4), 1108-1115.
 [http://dx.doi.org/10.1016/0016-5085(93)90280-P] [PMID: 8462799]

[117]
Kennedy, M.J.; Volz, P.A. Ecology of candida albicans gut colonization: inhibition of candida adhesion, colonization, and dissemination from the gastrointestinal tract by bacterial antagonism. Infect. Immun.,  1985, 49(3), 654-663.
 [http://dx.doi.org/10.1128/iai.49.3.654-663.1985] [PMID: 3897061]

[118]
Ducluzeau, R.; Bensaada, M. Comparative effect of a single or continuous administration of" Saccharomyces boulardii" on the establishment of various strains of" candida" in the digestive tract of gnotobiotic mice Ann Microbiol.,  1982, 133(3), 491-501.

[119]
Tomoda, T.; Nakano, Y.; Kageyama, T. Variation of intestinal candida of patients with leukemia and the effect of Lactobacillus administration. Japanese J. Med. Mycol.,  1983, 24(4), 356-358.
 [http://dx.doi.org/10.3314/jjmm1960.24.356]

[120]
Isolauri, E.; Jalonen, T.; Juntunen, M.; Rautanen, T.; Koivula, T. A human lactobacillus strain (Lactobacillus GG) promotes recovery from acute diarrhoea in children. Pediatr. Res.,  1990, 27(5), 529.
 [http://dx.doi.org/10.1203/00006450-199005000-00026] [PMID: 2345682]

[121]
Bérézin, B.E. Treatment and prevention of antibiotic associated diarrhea. Int. J. Antimicrob. Agents,  2000, 16(4), 521-526.
 [http://dx.doi.org/10.1016/S0924-8579(00)00293-4] [PMID: 11118872]

[122]
Hotta, M.; Sato, Y.; Iwata, S.; Yamashita, N.; Sunakawa, K.; Oikawa, T.; Tanaka, R.; Watanabe, K.; Takayama, H.; Yajima, M.; Sekiguchi, S.; Arai, S.; Sakurai, T.; Mutai, M. Clinical effects of bifidobacterium preparations on pediatric intractable diarrhea. Keio J. Med.,  1987, 36(3), 298-314.
 [http://dx.doi.org/10.2302/kjm.36.298] [PMID: 3682553]

[123]
Saavedra, J.M.; Bauman, N.A.; Perman, J.A.; Yolken, R.H.; Saavedra, J.M.; Bauman, N.A.; Oung, I. Feeding of Bifidobacterium bifidum and Streptococcus thermophilus to infants in hospital for prevention of diarrhoea and shedding of rotavirus. Lancet,  1994, 344(8929), 1046-1049.
 [http://dx.doi.org/10.1016/S0140-6736(94)91708-6] [PMID: 7934445]

[124]
Buddington, R.K.; Williams, C.H.; Chen, S.C.; Witherly, S.A. Dietary supplement of neosugar alters the fecal flora and decreases activities of some reductive enzymes in human subjects. Am. J. Clin. Nutr.,  1996, 63(5), 709-716.
 [http://dx.doi.org/10.1093/ajcn/63.5.709] [PMID: 8615353]

[125]
Kleessen, B.; Sykura, B.; Zunft, H.J.; Blaut, M. Effects of inulin and lactose on fecal microflora, microbial activity, and bowel habit in elderly constipated persons. Am. J. Clin. Nutr.,  1997, 65(5), 1397-1402.
 [http://dx.doi.org/10.1093/ajcn/65.5.1397] [PMID: 9129468]

[126]
Rowland, I.R.; Tanaka, R. The effects of transgalactosylated oligosaccharides on gut flora metabolism in rats associated with a human faecal microflora. J. Appl. Bacteriol.,  1993, 74(6), 667-674.
 [http://dx.doi.org/10.1111/j.1365-2672.1993.tb05201.x] [PMID: 8349528]

[127]
Salminen, S; Salminen, E Lactulose, lactic acid bacteria, intestinal microecology and mucosal protection. Scand. J. Gastroenterol. Suppl.,  1997, 222, 45-8.
 [http://dx.doi.org/10.1080/00365521.1997.11720717]

[128]
Pan, S.; Chen, A.; Han, Z.; Wang, Y.; Lu, X.; Yang, Y. 1H NMR-based metabonomic study on the effects of Epimedium on glucocorticoid-induced osteoporosis. J. Chromatogr. B Analyt. Technol. Biomed. Life Sci.,  2016, 1038, 118-126.
 [http://dx.doi.org/10.1016/j.jchromb.2016.10.015] [PMID: 27810280]

[129]
Li, L. How does the microbiota affect human health? Engineering,  2017, 3(1), 1.
 [http://dx.doi.org/10.1016/J.ENG.2017.01.021]

[130]
Lv, G.; Cheng, N.; Wang, H. The gut microbiota, tumorigenesis, and liver diseases. Engineering,  2017, 3(1), 110-114.
 [http://dx.doi.org/10.1016/J.ENG.2017.01.017]

[131]
Patterson, E.; Ryan, P.M.; Cryan, J.F.; Dinan, T.G.; Ross, R.P.; Fitzgerald, G.F.; Stanton, C. Gut microbiota, obesity and diabetes. Postgrad. Med. J.,  2016, 92(1087), 286-300.
 [http://dx.doi.org/10.1136/postgradmedj-2015-133285] [PMID: 26912499]

[132]
Wang, Y.; Wang, B.; Wu, J.; Jiang, X.; Tang, H.; Nielsen, O.H. Modulation of gut microbiota in pathological states. Engineering,  2017, 3(1), 83-89.
 [http://dx.doi.org/10.1016/J.ENG.2017.01.013]

[133]
Trøseid, M.; Andersen, G.Ø.; Broch, K.; Hov, J.R. The gut microbiome in coronary artery disease and heart failure: Current knowledge and future directions. EBioMedicine,  2020, 52, 102649.
 [http://dx.doi.org/10.1016/j.ebiom.2020.102649] [PMID: 32062353]

[134]
Zhang, H.; Chen, Y.; Wang, Z.; Xie, G.; Liu, M.; Yuan, B.; Chai, H.; Wang, W.; Cheng, P. Implications of gut microbiota in neurodegenerative diseases. Front. Immunol.,  2022, 13, 785644.
 [http://dx.doi.org/10.3389/fimmu.2022.785644] [PMID: 35237258]

[135]
Novakovic, M.; Rout, A.; Kingsley, T.; Kirchoff, R.; Singh, A.; Verma, V.; Kant, R.; Chaudhary, R. Role of gut microbiota in cardiovascular diseases. World J. Cardiol.,  2020, 12(4), 110-122.
 [http://dx.doi.org/10.4330/wjc.v12.i4.110] [PMID: 32431782]

[136]
Walsh, J.; Griffin, B.T.; Clarke, G.; Hyland, N.P. Drug–gut microbiota interactions: Implications for neuropharmacology. Br. J. Pharmacol.,  2018, 175(24), 4415-4429.
 [http://dx.doi.org/10.1111/bph.14366] [PMID: 29782640]

[137]
Creely, S.J.; McTernan, P.G.; Kusminski, C.M.; Fisher, M.; Da Silva, N.F.; Khanolkar, M.; Evans, M.; Harte, A.L.; Kumar, S. Lipopolysaccharide activates an innate immune system response in human adipose tissue in obesity and type 2 diabetes. Am. J. Physiol. Endocrinol. Metab.,  2007, 292(3), E740-E747.
 [http://dx.doi.org/10.1152/ajpendo.00302.2006] [PMID: 17090751]

[138]
Qi, P.; Li, Z.; Chen, M.; Sun, Z.; Huang, C. Metabolism and tissue distribution study of Vaccaria seeds (Wang-Bu-Liu-Xing) in benign prostatic hyperplasia model rat: Toward an in-depth study for its bioactive components. J. Pharm. Biomed. Anal.,  2013, 85, 218-230.
 [http://dx.doi.org/10.1016/j.jpba.2013.07.037] [PMID: 23973757]

[139]
Zhou, J.; Ma, Y.H.; Zhou, Z.; Chen, Y.; Wang, Y.; Gao, X. Intestinal absorption and metabolism of epimedium flavonoids in osteoporosis rats. Drug Metab. Dispos.,  2015, 43(10), 1590-1600.
 [http://dx.doi.org/10.1124/dmd.115.064386] [PMID: 26135008]

[140]
Roca-Saavedra, P.; Vilabrille, M.V.; Miranda, J.M.; Nebot, C.; Cobas, C.A.; Franco, C.M.; Cepeda, A. Food additives, contaminants and other minor components: Effects on human gut microbiota—A review. J. Physiol. Biochem.,  2018, 74(1), 69-83.
 [http://dx.doi.org/10.1007/s13105-017-0564-2] [PMID: 28488210]

[141]
Zhai, L.; Shi, J.; Xu, W.; Heinrich, M.; Wang, J.; Deng, W. Ex vivo and in situ evaluation of ‘dispelling-wind’ chinese medicine herb-drugs on intestinal absorption of chlorogenic acid. Phytother. Res.,  2015, 29(12), 1974-1981.
 [http://dx.doi.org/10.1002/ptr.5492] [PMID: 26514546]

[142]
Liu, C.; Hu, M.; Guo, H.; Zhang, M.; Zhang, J.; Li, F.; Zhong, Z.; Chen, Y.; Li, Y.; Xu, P.; Li, J.; Liu, L.; Liu, X. Combined contribution of increased intestinal permeability and inhibited deglycosylation of ginsenoside Rb1 in the intestinal tract to the enhancement of ginsenoside Rb1 exposure in diabetic rats after oral administration. Drug Metab. Dispos.,  2015, 43(11), 1702-1710.
 [http://dx.doi.org/10.1124/dmd.115.064881] [PMID: 26265741]

[143]
Arai, M.; Yokosuka, O.; Fukai, K.; Kanda, T.; Kojima, H.; Kawai, S.; Imazeki, F.; Hirasawa, H.; Saisho, H. A case of severe acute hepatitis of unknown etiology treated with the chinese herbal medicine inchinko-to. Hepatol. Res.,  2004, 28(3), 161-165.
 [http://dx.doi.org/10.1016/j.hepres.2003.09.004] [PMID: 15036073]

[144]
Kato, M.; Ishige, A.; Anjiki, N.; Yamamoto, M.; Irie, Y.; Taniyama, M.; Kibe, R.; Oka, J.; Benno, Y.; Watanabe, K. Effect of herbal medicine Juzentaihoto on hepatic and intestinal heat shock gene expression requires intestinal microflora in mouse. World J. Gastroenterol.,  2007, 13(16), 2289-2297.
 [http://dx.doi.org/10.3748/wjg.v13.i16.2289] [PMID: 17511026]

[145]
Canfora, E.E.; Jocken, J.W.; Blaak, E.E. Short-chain fatty acids in control of body weight and insulin sensitivity. Nat. Rev. Endocrinol.,  2015, 11(10), 577-591.
 [http://dx.doi.org/10.1038/nrendo.2015.128] [PMID: 26260141]

[146]
Lam, W.; Jiang, Z.; Guan, F.; Hu, R.; Liu, S.H.; Chu, E.; Cheng, Y.C. The number of intestinal bacteria is not critical for the enhancement of antitumor activity and reduction of intestinal toxicity of irinotecan by the Chinese herbal medicine PHY906 (KD018). BMC Complement. Altern. Med.,  2014, 14(1), 490.
 [http://dx.doi.org/10.1186/1472-6882-14-490] [PMID: 25510341]

[147]
Ley, R.E.; Peterson, D.A.; Gordon, J.I. Ecological and evolutionary forces shaping microbial diversity in the human intestine. Cell,  2006, 124(4), 837-848.
 [http://dx.doi.org/10.1016/j.cell.2006.02.017] [PMID: 16497592]

[148]
Xu, J.; Chen, H.B.; Li, S.L. Understanding the molecular mechanisms of the interplay between herbal medicines and gut microbiota. Med. Res. Rev.,  2017, 37(5), 1140-1185.
 [http://dx.doi.org/10.1002/med.21431] [PMID: 28052344]

[149]
Peschlow, L.E. Acceleration of large intestine transit time in rats by sennosides and related compounds. J. Pharm. Pharmacol.,  2011, 38(5), 369-373.
 [http://dx.doi.org/10.1111/j.2042-7158.1986.tb04589.x] [PMID: 2872313]

[150]
Li, X.; Huo, C.; Wang, Q.; Zhang, X.; Sheng, X.; Zhang, L. Microbial metabolism of loganin by intestinal bacteria and identification of new metabolites in rat. Biomed. Chromatogr.,  2008, 22(4), 367-373.
 [http://dx.doi.org/10.1002/bmc.941] [PMID: 18059048]

[151]
Du, L.; Tao, J.; Jiang, S.; Qian, D.; Guo, J.; Duan, J. Metabolic profiles of the FlosAbelmoschus manihot extract by intestinal bacteria from the normal and CKD model rats based on UPLC‐Q‐TOF/MS. Biomed. Chromatogr.,  2017, 31(2), e3795.
 [http://dx.doi.org/10.1002/bmc.3795] [PMID: 27451133]

[152]
Wang, Y.F.; Liu, Y.N.; Xiong, W.; Yan, D.M.; Zhu, Y.; Gao, X.M.; Xu, Y.T.; Qi, A.D. A UPLC–MS/MS method for in vivo and in vitro pharmacokinetic studies of psoralenoside, isopsoralenoside, psoralen and isopsoralen from Psoralea corylifolia extract. J. Ethnopharmacol.,  2014, 151(1), 609-617.
 [http://dx.doi.org/10.1016/j.jep.2013.11.013] [PMID: 24315982]

[153]
Tao, J.; Zhao, M.; Jiang, S.; Pu, X.; Wei, X. Comparative metabolism of two major compounds in Fructus Corni extracts by gut microflora from normal and chronic nephropathy rats in vitro by UPLC-Q-TOF/MS. J. Chromatogr. B Analyt. Technol. Biomed. Life Sci.,  2018, 1073, 170-176.
 [http://dx.doi.org/10.1016/j.jchromb.2017.12.025] [PMID: 29276981]

[154]
Wang, M.; Hu, Q.; Shi, Q.; Yang, G.; Feng, F. Metabolic profile elucidation of Zhi–Zi–Da–Huang decoction in rat intestinal bacteria using high-resolution mass spectrometry combined with multiple analytical perspectives. Xenobiotica,  2019, 49(1), 1-12.
 [http://dx.doi.org/10.1080/00498254.2017.1414972] [PMID: 29219669]

[155]
Feng, R.; Shou, J.W.; Zhao, Z.X.; He, C.Y.; Ma, C.; Huang, M.; Fu, J.; Tan, X.S.; Li, X.Y.; Wen, B.Y.; Chen, X.; Yang, X.Y.; Ren, G.; Lin, Y.; Chen, Y.; You, X.F.; Wang, Y.; Jiang, J.D. Transforming berberine into its intestine-absorbable form by the gut microbiota. Sci. Rep.,  2015, 5(1), 12155.
 [http://dx.doi.org/10.1038/srep12155] [PMID: 26174047]

[156]
Fu, J.; Wu, S.; Wang, M.; Tian, Y.; Zhang, Z.; Song, R. Intestinal metabolism of Polygonum cuspidatum in vitro and in vivo. Biomed. Chromatogr.,  2018, 32(6), e4190.
 [http://dx.doi.org/10.1002/bmc.4190] [PMID: 29334690]

[157]
Zhao, M.; Du, L.; Tao, J.; Qian, D.; Guo, J.; Jiang, S.; Shang, E.; Duan, J.; Wu, C. Ultra-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry for rapid analysis of the metabolites of morroniside produced by human intestinal bacteria. J. Chromatogr. B Analyt. Technol. Biomed. Life Sci.,  2015, 976-977, 61-67.
 [http://dx.doi.org/10.1016/j.jchromb.2014.11.014] [PMID: 25482010]

[158]
Xu, J.; Zhao, M.; Qian, D.; Shang, E.; Jiang, S.; Guo, J.; Duan, J.; Du, L. Comparative metabolism of Radix scutellariae extract by intestinal bacteria from normal and type 2 diabetic mice in vitro. J. Ethnopharmacol.,  2014, 153(2), 368-374.
 [http://dx.doi.org/10.1016/j.jep.2014.02.020] [PMID: 24632019]

[159]
Wang, C.Z.; Zhang, C.F.; Chen, L.; Anderson, S.; Lu, F.; Yuan, C.S. Colon cancer chemopreventive effects of baicalein, an active enteric microbiome metabolite from baicalin. Int. J. Oncol.,  2015, 47(5), 1749-1758.
 [http://dx.doi.org/10.3892/ijo.2015.3173] [PMID: 26398706]

[160]
Khanal, T.; Kim, H.G.; Hwang, Y.P.; Kong, M.J.; Kang, M.J.; Yeo, H.K.; Kim, D.H.; Jeong, T.C.; Jeong, H.G. Role of metabolism by the human intestinal microflora in arbutin-induced cytotoxicity in HepG2 cell cultures. Biochem. Biophys. Res. Commun.,  2011, 413(2), 318-324.
 [http://dx.doi.org/10.1016/j.bbrc.2011.08.094] [PMID: 21889493]

[161]
Bae, E.A.; Shin, J.; Kim, D.H. Metabolism of ginsenoside Re by human intestinal microflora and its estrogenic effect. Biol. Pharm. Bull.,  2005, 28(10), 1903-1908.
 [http://dx.doi.org/10.1248/bpb.28.1903] [PMID: 16204943]

[162]
Bae, E.A.; Choo, M.K.; Park, E.K.; Park, S.Y.; Shin, H.Y.; Kim, D.H. Metabolism of ginsenoside R(c) by human intestinal bacteria and its related antiallergic activity. Biol. Pharm. Bull.,  2002, 25(6), 743-747.
 [http://dx.doi.org/10.1248/bpb.25.743] [PMID: 12081140]

[163]
Wang, H.Y.; Qi, L.W.; Wang, C.Z.; Li, P. Bioactivity enhancement of herbal supplements by intestinal microbiota focusing on ginsenosides. Am. J. Chin. Med.,  2011, 39(6), 1103-1115.
 [http://dx.doi.org/10.1142/S0192415X11009433] [PMID: 22083984]

[164]
Jin, M.; Qin, J.; Wu, W. [Clinical study on “sini” decoction in treating stenocardia for coronary heart disease]. Zhong Yao Cai,  2003, 26(1), 71-73.
 [PMID: 12858776]

[165]
Zhang, M.; Peng, Y.; Wang, M.; Gao, B.; Zhao, L.; Li, X. The influence of compatibility of Si-Ni decoction with metabolism in intestinal bacteria on transports of toxic diterpenoid alkaloids from processed aconite root across Caco-2 monolayers. J. Ethnopharmacol.,  2019, 228, 164-178.
 [http://dx.doi.org/10.1016/j.jep.2018.09.022] [PMID: 30223050]

[166]
Carter, J.H.; McLafferty, M.A.; Goldman, P. Role of the gastrointestinal microflora in amygdalin (laetrile)-induced cyanide toxicity. Biochem. Pharmacol.,  1980, 29(3), 301-304.
 [http://dx.doi.org/10.1016/0006-2952(80)90504-3] [PMID: 7362642]

[167]
Marchesi, J.R.; Dutilh, B.E.; Hall, N.; Peters, W.H.M.; Roelofs, R.; Boleij, A.; Tjalsma, H. Towards the human colorectal cancer microbiome. PLoS One,  2011, 6(5), e20447.
 [http://dx.doi.org/10.1371/journal.pone.0020447] [PMID: 21647227]

[168]
Everard, A; Lazarevic, V; Derrien, M; Girard, M; Muccioli, GG; Neyrinck, AM Responses of gut microbiota and glucose and lipid metabolism to prebiotics in genetic obese and diet-induced leptin-resistant mice. Diabetes.,  2011, 60(11), 2775-86.

[169]
Bottacini, F.; van Sinderen, D.; Ventura, M. Omics of bifidobacteria: Research and insights into their health-promoting activities. Biochem. J.,  2017, 474(24), 4137-4152.
 [http://dx.doi.org/10.1042/BCJ20160756] [PMID: 29212851]

[170]
Samuelson, D.R.; Welsh, D.A.; Shellito, J.E. Regulation of lung immunity and host defense by the intestinal microbiota. Front. Microbiol.,  2015, 6, 1085.
 [http://dx.doi.org/10.3389/fmicb.2015.01085] [PMID: 26500629]

[171]
Cani, P.D.; Neyrinck, A.M.; Fava, F.; Knauf, C.; Burcelin, R.G.; Tuohy, K.M.; Gibson, G.R.; Delzenne, N.M. Selective increases of bifidobacteria in gut microflora improve high-fat-diet-induced diabetes in mice through a mechanism associated with endotoxaemia. Diabetologia,  2007, 50(11), 2374-2383.
 [http://dx.doi.org/10.1007/s00125-007-0791-0] [PMID: 17823788]

[172]
Plovier, H.; Everard, A.; Druart, C.; Depommier, C.; Van Hul, M.; Geurts, L.; Chilloux, J.; Ottman, N.; Duparc, T.; Lichtenstein, L.; Myridakis, A.; Delzenne, N.M.; Klievink, J.; Bhattacharjee, A.; van der Ark, K.C.H.; Aalvink, S.; Martinez, L.O.; Dumas, M.E.; Maiter, D.; Loumaye, A.; Hermans, M.P.; Thissen, J.P.; Belzer, C.; de Vos, W.M.; Cani, P.D. A purified membrane protein from Akkermansia muciniphila or the pasteurized bacterium improves metabolism in obese and diabetic mice. Nat. Med.,  2017, 23(1), 107-113.
 [http://dx.doi.org/10.1038/nm.4236] [PMID: 27892954]

[173]
David, L.A.; Maurice, C.F.; Carmody, R.N.; Gootenberg, D.B.; Button, J.E.; Wolfe, B.E.; Ling, A.V.; Devlin, A.S.; Varma, Y.; Fischbach, M.A.; Biddinger, S.B.; Dutton, R.J.; Turnbaugh, P.J. Diet rapidly and reproducibly alters the human gut microbiome. Nature,  2014, 505(7484), 559-563.
 [http://dx.doi.org/10.1038/nature12820] [PMID: 24336217]

[174]
Eeckhaut, V.; Machiels, K.; Perrier, C.; Romero, C.; Maes, S.; Flahou, B.; Steppe, M.; Haesebrouck, F.; Sas, B.; Ducatelle, R.; Vermeire, S.; Immerseel, V.F. Butyricicoccus pullicaecorum in inflammatory bowel disease. Gut,  2013, 62(12), 1745-1752.
 [http://dx.doi.org/10.1136/gutjnl-2012-303611] [PMID: 23263527]

[175]
Tsilingiri, K.; Barbosa, T.; Penna, G.; Caprioli, F.; Sonzogni, A.; Viale, G.; Rescigno, M. Probiotic and postbiotic activity in health and disease: Comparison on a novel polarised ex-vivo organ culture model. Gut,  2012, 61(7), 1007-1015.
 [http://dx.doi.org/10.1136/gutjnl-2011-300971] [PMID: 22301383]

[176]
Duffy, M.; O’Mahony, L.; Coffey, J.C.; Collins, J.K.; Shanahan, F.; Redmond, H.P.; Kirwan, W.O. Sulfate-reducing bacteria colonize pouches formed for ulcerative colitis but not for familial adenomatous polyposis. Dis. Colon Rectum,  2002, 45(3), 384-388.
 [http://dx.doi.org/10.1007/s10350-004-6187-z] [PMID: 12068199]

[177]
Kaper, J.B.; Nataro, J.P.; Mobley, H.L.T. Pathogenic Escherichia coli. Nat. Rev. Microbiol.,  2004, 2(2), 123-140.
 [http://dx.doi.org/10.1038/nrmicro818] [PMID: 15040260]

[178]
De la Fuente, M.; Franchi, L.; Araya, D.; Jiménez, D.D.; Olivares, M.; Lobos, A.M.; Golenbock, D.; González, M.J.; Kostner, L.F.; Quera, R.; Núñez, G.; Vidal, R.; Hermoso, M.A. Escherichia coli isolates from inflammatory bowel diseases patients survive in macrophages and activate NLRP3 inflammasome. Int. J. Med. Microbiol.,  2014, 304(3-4), 384-392.
 [http://dx.doi.org/10.1016/j.ijmm.2014.01.002] [PMID: 24581881]

[179]
Feng, W.; Ao, H.; Peng, C.; Yan, D. Gut microbiota, A new frontier to understand traditional chinese medicines. Pharmacol. Res.,  2019, 142, 176-191.
 [http://dx.doi.org/10.1016/j.phrs.2019.02.024] [PMID: 30818043]

[180]
Yue, S.J.; Xin, L.T.; Fan, Y.C.; Li, S.J.; Tang, Y.P.; Duan, J.A.; Guan, H.S.; Wang, C.Y. Herb pair danggui-honghua: Mechanisms underlying blood stasis syndrome by system pharmacology approach. Sci. Rep.,  2017, 7(1), 40318.
 [http://dx.doi.org/10.1038/srep40318] [PMID: 28074863]

[181]
Sgouras, D.N.; Panayotopoulou, E.G.; Gonzalez, M.B.; Petraki, K.; Michopoulos, S.; Mentis, A. Lactobacillus johnsonii La1 attenuates Helicobacter pylori-associated gastritis and reduces levels of proinflammatory chemokines in C57BL/6 mice. Clin. Diagn. Lab. Immunol.,  2005, 12(12), 1378-1386.
 [PMID: 16339060]

[182]
Chiva, M.; Soriano, G.; Rochat, I.; Peralta, C.; Rochat, F.; Llovet, T.; Mirelis, B.; Schiffrin, E.J.; Guarner, C.; Balanzó, J. Effect of Lactobacillus johnsonii La1 and antioxidants on intestinal flora and bacterial translocation in rats with experimental cirrhosis. J. Hepatol.,  2002, 37(4), 456-462.
 [http://dx.doi.org/10.1016/S0168-8278(02)00142-3] [PMID: 12217598]

[183]
Luo, S.; Wen, R.; Wang, Q.; Zhao, Z.; Nong, F.; Fu, Y.; Huang, S.; Chen, J.; Zhou, L.; Luo, X. Rhubarb Peony Decoction ameliorates ulcerative colitis in mice by regulating gut microbiota to restoring Th17/Treg balance. J. Ethnopharmacol.,  2019, 231, 39-49.
 [http://dx.doi.org/10.1016/j.jep.2018.08.033] [PMID: 30170079]

[184]
Yin, X.; Peng, J.; Zhao, L.; Yu, Y.; Zhang, X.; Liu, P.; Feng, Q.; Hu, Y.; Pang, X. Structural changes of gut microbiota in a rat non-alcoholic fatty liver disease model treated with a Chinese herbal formula. Syst. Appl. Microbiol.,  2013, 36(3), 188-196.
 [http://dx.doi.org/10.1016/j.syapm.2012.12.009] [PMID: 23453736]

[185]
Li, M.; Gao, J.; Tang, Y.; Liu, M.; Wu, S.; Qu, K.; Long, X.; Li, H.; Liu, M.; Liu, Y.; Yuan, J.; Mao, L.; Liu, Y.; Zheng, X.; Wang, E.; Wang, J.; Yang, Y. Traditional herbal medicine-derived sulforaphene LFS-01 reverses colitis in mice by selectively altering the gut microbiota and promoting intestinal gamma-delta T cells. Front. Pharmacol.,  2018, 8, 959.
 [http://dx.doi.org/10.3389/fphar.2017.00959] [PMID: 29375374]

[186]
Chen, D.; Yang, X.; Yang, J.; Lai, G.; Yong, T.; Tang, X.; Shuai, O.; Zhou, G.; Xie, Y.; Wu, Q. Prebiotic effect of fructooligosaccharides from Morinda officinalis on Alzheimer’s disease in rodent models by targeting the microbiota-gut-brain axis. Front. Aging Neurosci.,  2017, 9, 403.
 [http://dx.doi.org/10.3389/fnagi.2017.00403] [PMID: 29276488]

[187]
Chen, L.; Brar, M.S.; Leung, F.C.C.; Hsiao, W.L.W. Triterpenoid herbal saponins enhance beneficial bacteria, decrease sulfate-reducing bacteria, modulate inflammatory intestinal microenvironment and exert cancer preventive effects in ApcMin/+ mice. Oncotarget,  2016, 7(21), 31226-31242.
 [http://dx.doi.org/10.18632/oncotarget.8886] [PMID: 27121311]

[188]
Ramiah, S.K.; Zulkifli, I.; Rahim, N.A.A.; Ebrahimi, M.; Meng, G.Y. Effects of two herbal extracts and virginiamycin supplementation on growth performance, intestinal microflora population and Fatty Acid composition in broiler chickens. Asian-Australas. J. Anim. Sci.,  2014, 27(3), 375-382.
 [http://dx.doi.org/10.5713/ajas.2013.13030] [PMID: 25049964]

[189]
Fujisaka, S.; Usui, I.; Nawaz, A.; Igarashi, Y.; Okabe, K.; Furusawa, Y.; Watanabe, S.; Yamamoto, S.; Sasahara, M.; Watanabe, Y.; Nagai, Y.; Yagi, K.; Nakagawa, T.; Tobe, K. Bofutsushosan improves gut barrier function with a bloom of Akkermansia muciniphila and improves glucose metabolism in mice with diet-induced obesity. Sci. Rep.,  2020, 10(1), 5544.
 [http://dx.doi.org/10.1038/s41598-020-62506-w] [PMID: 32218475]

[190]
Moradian, K.S.; Hakemi, G.M.; Andalib, A.; Yazdani, R.; Arasteh, J.; Kardar, G.A. The effect of licorice protein fractions on proliferation and apoptosis of gastrointestinal cancer cell lines. Nutr. Cancer,  2017, 69(2), 330-339.
 [http://dx.doi.org/10.1080/01635581.2017.1263347] [PMID: 28045565]

[191]
Zhang, X.; Zhao, S.; Song, X.; Jia, J.; Zhang, Z.; Zhou, H.; Fu, H.; Cui, H.; Hu, S.; Fang, M.; Liu, X.; Bian, Y. Inhibition effect of glycyrrhiza polysaccharide (GCP) on tumor growth through regulation of the gut microbiota composition. J. Pharmacol. Sci.,  2018, 137(4), 324-332.
 [http://dx.doi.org/10.1016/j.jphs.2018.03.006] [PMID: 30150145]

[192]
Hamer, H.M.; Jonkers, D.; Venema, K.; Vanhoutvin, S.; Troost, F.J.; Brummer, R.J. Review article: The role of butyrate on colonic function. Aliment. Pharmacol. Ther.,  2008, 27(2), 104-119.
 [http://dx.doi.org/10.1111/j.1365-2036.2007.03562.x] [PMID: 17973645]

[193]
Ohata, A.; Usami, M.; Miyoshi, M. Short-chain fatty acids alter tight junction permeability in intestinal monolayer cells via lipoxygenase activation. Nutrition,  2005, 21(7-8), 838-847.
 [http://dx.doi.org/10.1016/j.nut.2004.12.004] [PMID: 15975492]

[194]
Sanna, S.; van Zuydam, N.R.; Mahajan, A.; Kurilshikov, A.; Vila, V.A.; Võsa, U.; Mujagic, Z.; Masclee, A.A.M.; Jonkers, D.M.A.E.; Oosting, M.; Joosten, L.A.B.; Netea, M.G.; Franke, L.; Zhernakova, A.; Fu, J.; Wijmenga, C.; McCarthy, M.I. Causal relationships among the gut microbiome, short-chain fatty acids and metabolic diseases. Nat. Genet.,  2019, 51(4), 600-605.
 [http://dx.doi.org/10.1038/s41588-019-0350-x] [PMID: 30778224]

[195]
Rajendran, P.; Ho, E.; Williams, D.E.; Dashwood, R.H. Dietary phytochemicals, HDAC inhibition, and DNA damage/repair defects in cancer cells. Clin. Epigenetics,  2011, 3(1), 4.
 [http://dx.doi.org/10.1186/1868-7083-3-4] [PMID: 22247744]

[196]
Samuel, B.S.; Shaito, A.; Motoike, T.; Rey, F.E.; Backhed, F.; Manchester, J.K.; Hammer, R.E.; Williams, S.C.; Crowley, J.; Yanagisawa, M.; Gordon, J.I. Effects of the gut microbiota on host adiposity are modulated by the short-chain fatty-acid binding G protein-coupled receptor, Gpr41. Proc. Natl. Acad. Sci.,  2008, 105(43), 16767-16772.
 [http://dx.doi.org/10.1073/pnas.0808567105] [PMID: 18931303]

[197]
Tolhurst, G.; Heffron, H.; Lam, Y.S.; Parker, H.E.; Habib, A.M.; Diakogiannaki, E.; Cameron, J.; Grosse, J.; Reimann, F.; Gribble, F.M. Short-chain fatty acids stimulate glucagon-like peptide-1 secretion via the G-protein-coupled receptor FFAR2. Diabetes,  2012, 61(2), 364-371.
 [http://dx.doi.org/10.2337/db11-1019] [PMID: 22190648]

[198]
Arpaia, N.; Campbell, C.; Fan, X.; Dikiy, S.; van der Veeken, J.; deRoos, P.; Liu, H.; Cross, J.R.; Pfeffer, K.; Coffer, P.J.; Rudensky, A.Y. Metabolites produced by commensal bacteria promote peripheral regulatory T-cell generation. Nature,  2013, 504(7480), 451-455.
 [http://dx.doi.org/10.1038/nature12726] [PMID: 24226773]

[199]
Ahmed, K.; Tunaru, S.; Offermanns, S. GPR109A, GPR109B and GPR81, A family of hydroxy-carboxylic acid receptors. Trends Pharmacol. Sci.,  2009, 30(11), 557-562.
 [http://dx.doi.org/10.1016/j.tips.2009.09.001] [PMID: 19837462]

[200]
Morita, N.; Umemoto, E.; Fujita, S.; Hayashi, A.; Kikuta, J.; Kimura, I.; Haneda, T.; Imai, T.; Inoue, A.; Mimuro, H.; Maeda, Y.; Kayama, H.; Okumura, R.; Aoki, J.; Okada, N.; Kida, T.; Ishii, M.; Nabeshima, R.; Takeda, K. GPR31-dependent dendrite protrusion of intestinal CX3CR1+ cells by bacterial metabolites. Nature,  2019, 566(7742), 110-114.
 [http://dx.doi.org/10.1038/s41586-019-0884-1] [PMID: 30675063]

[201]
Wang, Y.; Shou, J.W.; Li, X.Y.; Zhao, Z.X.; Fu, J.; He, C.Y.; Feng, R.; Ma, C.; Wen, B.Y.; Guo, F.; Yang, X.Y.; Han, Y.X.; Wang, L.L.; Tong, Q.; You, X.F.; Lin, Y.; Kong, W.J.; Si, S.Y.; Jiang, J.D. Berberine-induced bioactive metabolites of the gut microbiota improve energy metabolism. Metabolism,  2017, 70, 72-84.
 [http://dx.doi.org/10.1016/j.metabol.2017.02.003] [PMID: 28403947]

[202]
Wei, X.; Tao, J.; Xiao, S.; Jiang, S.; Shang, E.; Zhu, Z.; Qian, D.; Duan, J. Xiexin Tang improves the symptom of type 2 diabetic rats by modulation of the gut microbiota. Sci. Rep.,  2018, 8(1), 3685.
 [http://dx.doi.org/10.1038/s41598-018-22094-2] [PMID: 29487347]

[203]
Lv, W.; Liu, C.; Ye, C.; Sun, J.; Tan, X.; Zhang, C.; Qu, Q.; Shi, D.; Guo, S. Structural modulation of gut microbiota during alleviation of antibiotic-associated diarrhea with herbal formula. Int. J. Biol. Macromol.,  2017, 105(Pt 3), 1622-1629.
 [http://dx.doi.org/10.1016/j.ijbiomac.2017.02.060] [PMID: 28219687]

[204]
Chang, C.J.; Lin, C.S.; Lu, C.C.; Martel, J.; Ko, Y.F.; Ojcius, D.M.; Tseng, S.F.; Wu, T.R.; Chen, Y.Y.M.; Young, J.D.; Lai, H.C. Ganoderma lucidum reduces obesity in mice by modulating the composition of the gut microbiota. Nat. Commun.,  2015, 6(1), 7489.
 [http://dx.doi.org/10.1038/ncomms8489] [PMID: 26102296]

[205]
Dumas, M.E.; Barton, R.H.; Toye, A.; Cloarec, O.; Blancher, C.; Rothwell, A.; Fearnside, J.; Tatoud, R.; Blanc, V.; Lindon, J.C.; Mitchell, S.C.; Holmes, E.; McCarthy, M.I.; Scott, J.; Gauguier, D.; Nicholson, J.K. Metabolic profiling reveals a contribution of gut microbiota to fatty liver phenotype in insulin-resistant mice. Proc. Natl. Acad. Sci.,  2006, 103(33), 12511-12516.
 [http://dx.doi.org/10.1073/pnas.0601056103] [PMID: 16895997]

[206]
Pignanelli, M.; Just, C.; Bogiatzi, C.; Dinculescu, V.; Gloor, G.; Vercoe, A.E.; Reid, G.; Urquhart, B.; Ruetz, K.; Velenosi, T.; Spence, J. Mediterranean diet score: Associations with metabolic products of the intestinal microbiome, carotid plaque burden, and renal function. Nutrients,  2018, 10(6), 779.
 [http://dx.doi.org/10.3390/nu10060779] [PMID: 29914158]

[207]
Oellgaard, J.; Winther, S.A.; Hansen, T.S.; Rossing, P.; von Scholten, B.J. Trimethylamine N-oxide (TMAO) as a new potential therapeutic target for insulin resistance and cancer. Curr. Pharm. Des.,  2017, 23(25), 3699-3712.
 [PMID: 28641532]

[208]
Liu, C.C.; Wu, Y.F.; Feng, G.M.; Gao, X.X.; Zhou, Y.Z.; Hou, W.J.; Qin, X.M.; Du, G.H.; Tian, J.S. Plasma-metabolite-biomarkers for the therapeutic response in depressed patients by the traditional Chinese medicine formula Xiaoyaosan: A 1H NMR-based metabolomics approach. J. Affect. Disord.,  2015, 185, 156-163.
 [http://dx.doi.org/10.1016/j.jad.2015.05.005] [PMID: 26186531]

[209]
Tian, J.; Peng, G.; Gao, X.; Zhou, Y.; Xing, J.; Qin, X.; Du, G. Dynamic analysis of the endogenous metabolites in depressed patients treated with TCM formula Xiaoyaosan using urinary 1H NMR-based metabolomics. J. Ethnopharmacol.,  2014, 158(Pt A), 1-10.
 [http://dx.doi.org/10.1016/j.jep.2014.10.005] [PMID: 25448502]

[210]
Zou, Z.J.; Liu, Z.H.; Gong, M.J.; Han, B.; Wang, S.M.; Liang, S.W. Intervention effects of puerarin on blood stasis in rats revealed by a 1H NMR-based metabonomic approach. Phytomedicine,  2015, 22(3), 333-343.
 [http://dx.doi.org/10.1016/j.phymed.2015.01.006] [PMID: 25837270]

[211]
Wei, L.; Liao, P.; Wu, H.; Li, X.; Pei, F.; Li, W.; Wu, Y. Metabolic profiling studies on the toxicological effects of realgar in rats by 1H NMR spectroscopy. Toxicol. Appl. Pharmacol.,  2009, 234(3), 314-325.
 [http://dx.doi.org/10.1016/j.taap.2008.11.010] [PMID: 19073202]

[212]
Claus, S.P.; Tsang, T.M.; Wang, Y.; Cloarec, O.; Skordi, E.; Martin, F.P.; Rezzi, S.; Ross, A.; Kochhar, S.; Holmes, E.; Nicholson, J.K. Systemic multicompartmental effects of the gut microbiome on mouse metabolic phenotypes. Mol. Syst. Biol.,  2008, 4(1), 219.
 [http://dx.doi.org/10.1038/msb.2008.56] [PMID: 18854818]

[213]
Pallister, T.; Jackson, M.A.; Martin, T.C.; Zierer, J.; Jennings, A.; Mohney, R.P.; MacGregor, A.; Steves, C.J.; Cassidy, A.; Spector, T.D.; Menni, C. Hippurate as a metabolomic marker of gut microbiome diversity: Modulation by diet and relationship to metabolic syndrome. Sci. Rep.,  2017, 7(1), 13670.
 [http://dx.doi.org/10.1038/s41598-017-13722-4] [PMID: 29057986]

[214]
Xing, H.; Zhang, K.; Zhang, R.; Zhang, Y.; Gu, L.; Shi, H.; Bi, K.; Chen, X. Determination of depression biomarkers in rat plasma by liquid chromatography-mass spectrometry for the study of the antidepressant effect of Zhi-Zi-Hou-Po decoction on rat model of chronic unpredictable mild stress. J. Chromatogr. B Analyt. Technol. Biomed. Life Sci.,  2015, 988, 135-142.
 [http://dx.doi.org/10.1016/j.jchromb.2015.02.037] [PMID: 25770791]

[215]
Guan, Y.; Tang, G.; Li, L.; Shu, J.; Zhao, Y.; Huang, L.; Tang, J. Herbal medicine and gut microbiota: Exploring untapped therapeutic potential in neurodegenerative disease management. Arch. Pharm. Res.,  2024, 47(2), 146-164.
 [http://dx.doi.org/10.1007/s12272-023-01484-9] [PMID: 38225532]

[216]
Han, B; Huang, H; Li, Z; Gong, M; Shi, W; Zhu, C Therapeutic effects of chinese medicine herb pair, huzhang and guizhi, on monosodium urate crystal-induced gouty arthritis in rats revealed by anti-inflammatory assessments and NMR-based metabonomics. Evid Based Complement Alternat Med.,  2016, 2016, 9398435.

[217]
Troy, EB; Kasper, DL Beneficial effects of Bacteroides fragilis polysaccharides on the immune system. Front Biosci,  2010, 15(1), 25-34.
 [http://dx.doi.org/10.2741/3603]

[218]
Wisnewsky, A.J.; Gaborit, B.; Dutour, A.; Clement, K. Gut microbiota and non-alcoholic fatty liver disease: New insights. Clin. Microbiol. Infect.,  2013, 19(4), 338-348.
 [http://dx.doi.org/10.1111/1469-0691.12140] [PMID: 23452163]

[219]
Miura, K; Seki, E; Ohnishi, H; Brenner, DA Role of toll-like receptors and their downstream molecules in the development of nonalcoholic fatty liver disease. Gastroenterol Res Pract.,  2010, 2010, 362847.
 [http://dx.doi.org/10.1155/2010/362847]

[220]
Frasinariu, O.E.; Ceccarelli, S.; Alisi, A.; Moraru, E.; Nobili, V. Gut-liver axis and fibrosis in nonalcoholic fatty liver disease: An input for novel therapies. Dig. Liver Dis.,  2013, 45(7), 543-551.
 [http://dx.doi.org/10.1016/j.dld.2012.11.010] [PMID: 23280158]

[221]
Jiang, D.; Kang, A.; Yao, W.; Lou, J.; Zhang, Q.; Bao, B.; Cao, Y.; Yu, S.; Guo, S.; Zhang, Y.; Tang, Y.; Zhang, L. Euphorbia kansui fry-baked with vinegar modulates gut microbiota and reduces intestinal toxicity in rats. J. Ethnopharmacol.,  2018, 226, 26-35.
 [http://dx.doi.org/10.1016/j.jep.2018.07.029] [PMID: 30059729]

[222]
Ni, Y.; Su, M.; Qiu, Y.; Chen, M.; Liu, Y.; Zhao, A.; Jia, W. Metabolic profiling using combined GC–MS and LC–MS provides a systems understanding of aristolochic acid‐induced nephrotoxicity in rat. FEBS Lett.,  2007, 581(4), 707-711.
 [http://dx.doi.org/10.1016/j.febslet.2007.01.036] [PMID: 17274990]

[223]
Zhao, M.; Xu, J.; Qian, D.; Guo, J.; Jiang, S.; Shang, E.; Duan, J. Identification of astilbin metabolites produced by human intestinal bacteria using UPLC‐Q‐TOF/MS. Biomed. Chromatogr.,  2014, 28(7), 1024-1029.
 [http://dx.doi.org/10.1002/bmc.3111] [PMID: 24399635]

[224]
Wen, J.; Teng, B.; Yang, P.; Chen, X.; Li, C.; Jing, Y.; Wei, J.; Zhang, C. The potential mechanism of Bawei Xileisan in the treatment of dextran sulfate sodium-induced ulcerative colitis in mice. J. Ethnopharmacol.,  2016, 188, 31-38.
 [http://dx.doi.org/10.1016/j.jep.2016.04.054] [PMID: 27132718]

[225]
Chen, Y.; Xiao, S.; Gong, Z.; Zhu, X.; Yang, Q.; Li, Y.; Gao, S.; Dong, Y.; Shi, Z.; Wang, Y.; Weng, X.; Li, Q.; Cai, W.; Qiang, W. Wuji Wan formula ameliorates diarrhea and disordered colonic motility in post-inflammation irritable bowel syndrome rats by modulating the gut microbiota. Front. Microbiol.,  2017, 8, 2307.
 [http://dx.doi.org/10.3389/fmicb.2017.02307] [PMID: 29218037]

[226]
Holmes, D. Medicinal mushroom reduces obesity by modulating microbiota. Nat. Rev. Endocrinol.,  2015, 11(9), 504.
 [http://dx.doi.org/10.1038/nrendo.2015.114] [PMID: 26170024]

[227]
Ko, S-J; Han, G; Kim, S-K; Seo, J-G; Chung, W-S; Ryu, B Effect of Korean herbal medicine combined with a probiotic mixture on diarrhea-dominant irritable bowel syndrome: A double-blind, randomized, placebo-controlled trial. Evid. Based Complement. Alternat. Med.,  2013, 2013, 824605.
 [http://dx.doi.org/10.1155/2013/824605]

[228]
Wenzig, P.E.M.; Koskinen, K.; Eichinger, M.C.; Bauer, R. A Combined LC-MS Metabolomics-and 16S rRNA sequencing platform to assess interactions between herbal medicinal products and human gut bacteria in vitro: A pilot study on willow bark extract. Front. Pharmacol.,  2017, 8, 893.
 [http://dx.doi.org/10.3389/fphar.2017.00893] [PMID: 29326584]

[229]
Zhou, S.S.; Xu, J.; Zhu, H.; Wu, J.; Xu, J.D.; Yan, R.; Li, X.Y.; Liu, H.H.; Duan, S.M.; Wang, Z.; Chen, H.B.; Shen, H.; Li, S.L. Gut microbiota-involved mechanisms in enhancing systemic exposure of ginsenosides by coexisting polysaccharides in ginseng decoction. Sci. Rep.,  2016, 6(1), 22474.
 [http://dx.doi.org/10.1038/srep22474] [PMID: 26932472]

[230]
Zhang, W.; Jiang, S.; Qian, D.; Shang, E.; Duan, J. Effect of liquiritin on human intestinal bacteria growth: Metabolism and modulation. Biomed. Chromatogr.,  2014, 28(9), 1271-1277.
 [http://dx.doi.org/10.1002/bmc.3160] [PMID: 24616071]

[231]
Cai, H.; Su, S.; Li, Y.; Zhu, Z.; Guo, J.; Zhu, Y.; Guo, S.; Qian, D.; Duan, J. Danshen can interact with intestinal bacteria from normal and chronic renal failure rats. Biomed. Pharmacother.,  2019, 109, 1758-1771.
 [http://dx.doi.org/10.1016/j.biopha.2018.11.047] [PMID: 30551430]
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DOI https://dx.doi.org/10.2174/0113892002287336240328083220	Print ISSN 1389-2002
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Current Drug Metabolism

Regulation of Gut Microbiota by Herbal Medicines

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Current Drug Metabolism

Regulation of Gut Microbiota by Herbal Medicines

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