Exploring substrate–microbe interactions: a metabiotic approach toward developing targeted synbiotic compositions

References

• Feng Q, Chen WD, Wang YD. Gut microbiota: an integral moderator in health and disease. Front Microbiol. 2018;9:151. doi:10.3389/fmicb.2018.00151.
   PubMed Web of Science ®Google Scholar
• Gonzalez-Sarrias A, Garcia-Villalba R, Romo-Vaquero M, Alasalvar C, Orem A, Zafrilla P, Tomás‐Barberán FA, Selma MV, Espín JC. Clustering according to urolithin metabotype explains the interindividual variability in the improvement of cardiovascular risk biomarkers in overweight-obese individuals consuming pomegranate: A randomized clinical trial. Mol Nutr Food Res. 2017;61(5):61. doi:10.1002/mnfr.201600830.
   Web of Science ®Google Scholar
• de Roos B, Aura AM, Bronze M, Cassidy A, Conesa MTG, Gibney MG, de Roos B, Greyling A, Kaput J, Kerem Z. et al. Targeting the delivery of dietary plant bioactives to those who would benefit most: from science to practical applications. Eur J Nutr. 2019;58(S2):65–31. doi:10.1007/s00394-019-02075-5.
   PubMedGoogle Scholar
• Morand C, De Roos B, Garcia-Conesa MT, Gibney ER, Landberg R, Manach C, Milenkovic D, Rodriguez-Mateos A, Van de Wiele T, Tomas-Barberan F. et al. Why interindividual variation in response to consumption of plant food bioactives matters for future personalised nutrition. Proc Nutr Soc. 2020;79(2):225–35. doi:10.1017/S0029665120000014.
   PubMed Web of Science ®Google Scholar
• Frankenfeld CL. Cardiometabolic risk and gut microbial phytoestrogen metabolite phenotypes. Mol Nutr Food Res. 2017;61(1):61. doi:10.1002/mnfr.201500900.
   Web of Science ®Google Scholar
• Dahan A, Miller JM, Amidon GL. Prediction of solubility and permeability class membership: provisional BCS classification of the world’s top oral drugs. AAPS J. 2009;11(4):740–6. doi:10.1208/s12248-009-9144-x.
   PubMed Web of Science ®Google Scholar
• Tintelnot J, Xu Y, Lesker TR, Schonlein M, Konczalla L, Giannou AD, Pelczar P, Kylies D, Puelles VG, Bielecka AA. et al. Microbiota-derived 3-IAA influences chemotherapy efficacy in pancreatic cancer. Nature. 2023;615(7950):168–74. doi:10.1038/s41586-023-05728-y.
   PubMed Web of Science ®Google Scholar
• Wu H, Esteve E, Tremaroli V, Khan MT, Caesar R, Manneras-Holm L, Ståhlman M, Olsson LM, Serino M, Planas-Fèlix M. et al. Metformin alters the gut microbiome of individuals with treatment-naive type 2 diabetes, contributing to the therapeutic effects of the drug. Nat Med. 2017;23(7):850–8. doi:10.1038/nm.4345.
   PubMed Web of Science ®Google Scholar
• Vich Vila A, Collij V, Sanna S, Sinha T, Imhann F, Bourgonje AR, Mujagic Z, Jonkers DMAE, Masclee AAM, Fu J. et al. Impact of commonly used drugs on the composition and metabolic function of the gut microbiota. Nat Commun. 2020;11(1):362. doi:10.1038/s41467-019-14177-z.
   PubMed Web of Science ®Google Scholar
• Wilck N, Matus MG, Kearney SM, Olesen SW, Forslund K, Bartolomaeus H, Haase S, Mähler A, Balogh A, Markó L. et al. Salt-responsive gut commensal modulates TH17 axis and disease. Nature. 2017;551(7682):585–9. doi:10.1038/nature24628.
   PubMed Web of Science ®Google Scholar
• Speckmann B, Steinbrenner H. Selenium and selenoproteins in inflammatory bowel diseases and experimental colitis. Inflamm Bowel Dis. 2014;20:1110–1119. doi:10.1097/MIB.0000000000000020.
   PubMed Web of Science ®Google Scholar
• Dostal A, Chassard C, Hilty FM, Zimmermann MB, Jaeggi T, Rossi S, Lacroix C. Iron depletion and repletion with ferrous sulfate or electrolytic iron modifies the composition and metabolic activity of the gut microbiota in rats. J Nutr. 2012;142(2):271–277. doi:10.3945/jn.111.148643.
   PubMed Web of Science ®Google Scholar
• Lehouritis P, Stanton M, McCarthy FO, Jeavons M, Tangney M. Activation of multiple chemotherapeutic prodrugs by the natural enzymolome of tumour-localised probiotic bacteria. J Control Release. 2016;222:9–17. doi:10.1016/j.jconrel.2015.11.030.
   PubMed Web of Science ®Google Scholar
• Wallace BD, Wang H, Lane KT, Scott JE, Orans J, Koo JS, Venkatesh M, Jobin C, Yeh L-A, Mani S. et al. Alleviating cancer drug toxicity by inhibiting a bacterial enzyme. Science. 2010;330(6005):831–5. doi:10.1126/science.1191175.
   PubMed Web of Science ®Google Scholar
• Zimmermann M, Zimmermann-Kogadeeva M, Wegmann R, Goodman AL. Separating host and microbiome contributions to drug pharmacokinetics and toxicity. Science. 2019;363(6427). doi:10.1126/science.aat9931.
   Web of Science ®Google Scholar
• Schroder H, Gustafsson BE. Azo reduction of salicyl-azo-sulphapyridine in germ-free and conventional rats. Xenobiotica. 1973;3(4):225–31. doi:10.3109/00498257309151518.
   PubMed Web of Science ®Google Scholar
• Oancea I, Movva R, Das I, Aguirre de Carcer D, Schreiber V, Yang Y, Purdon A, Harrington B, Proctor M, Wang R. et al. Colonic microbiota can promote rapid local improvement of murine colitis by thioguanine independently of T lymphocytes and host metabolism. Gut. 2017;66(1):59–69. doi:10.1136/gutjnl-2015-310874.
   PubMed Web of Science ®Google Scholar
• Becker HEF, Demers K, Derijks LJJ, Jonkers D, Penders J. Current evidence and clinical relevance of drug-microbiota interactions in inflammatory bowel disease. Front Microbiol. 2023;14:1107976. doi:10.3389/fmicb.2023.1107976.
   PubMed Web of Science ®Google Scholar
• Zhang X, Han Y, Huang W, Jin M, Gao Z. The influence of the gut microbiota on the bioavailability of oral drugs. Acta Pharm Sin B. 2021;11(7):1789–812. doi:10.1016/j.apsb.2020.09.013.
   PubMed Web of Science ®Google Scholar
• Dobkin JF, Saha JR Jr., Butler VP, Neu HC, Lindenbaum J. Digoxin-inactivating bacteria: identification in human gut flora. Science. 1983;220(4594):325–327. doi:10.1126/science.6836275.
   PubMed Web of Science ®Google Scholar
• Tierney BT, Yang Z, Luber JM, Beaudin M, Wibowo MC, Baek C, Mehlenbacher E, Patel CJ, Kostic AD. The landscape of genetic content in the gut and oral human microbiome. Cell Host Microbe. 2019;26(2):283–295.e8. doi:10.1016/j.chom.2019.07.008.
   PubMed Web of Science ®Google Scholar
• Visconti A, Le Roy CI, Rosa F, Rossi N, Martin TC, Mohney RP, Li W, de Rinaldis E, Bell JT, Venter JC. et al. Interplay between the human gut microbiome and host metabolism. Nat Commun. 2019;10(1):4505. doi:10.1038/s41467-019-12476-z.
   PubMed Web of Science ®Google Scholar
• Zamboni N, Saghatelian A, Patti GJ. Defining the metabolome: size, flux, and regulation. Mol Cell. 2015;58(4):699–706. doi:10.1016/j.molcel.2015.04.021.
   PubMed Web of Science ®Google Scholar
• Martin FP, Dumas ME, Wang Y, Legido-Quigley C, Yap IK, Tang H, Zirah S, Murphy GM, Cloarec O, Lindon JC. et al. A top-down systems biology view of microbiome-mammalian metabolic interactions in a mouse model. Mol Syst Biol. 2007;3(1):112. doi:10.1038/msb4100153.
   PubMedGoogle Scholar
• Matsumoto M, Kibe R, Ooga T, Aiba Y, Kurihara S, Sawaki E, Koga Y, Benno Y. Impact of intestinal microbiota on intestinal luminal metabolome. Sci Rep. 2012;2(1):233. doi:10.1038/srep00233.
   PubMedGoogle Scholar
• Moriya T, Satomi Y, Murata S, Sawada H, Kobayashi HJM. Effect of gut microbiota on host whole metabolome. Metabolomics. 2017;13(9). doi:10.1007/s11306-017-1240-9.
   Web of Science ®Google Scholar
• Chen L, Zhernakova DV, Kurilshikov A, Andreu-Sanchez S, Wang D, Augustijn HE, Vich Vila A, Weersma RK, Medema MH, Netea MG. et al. Influence of the microbiome, diet and genetics on inter-individual variation in the human plasma metabolome. Nat Med. 2022;28(11):2333–43. doi:10.1038/s41591-022-02014-8.
   PubMed Web of Science ®Google Scholar
• Singh V, Lee G, Son H, Koh H, Kim ES, Unno T, Shin J-H. Butyrate producers, “The Sentinel of Gut”: Their intestinal significance with and beyond butyrate, and prospective use as microbial therapeutics. Front Microbiol. 2022;13:1103836. doi:10.3389/fmicb.2022.1103836.
   PubMed Web of Science ®Google Scholar
• Nogal A, Valdes AM, Menni C. The role of short-chain fatty acids in the interplay between gut microbiota and diet in cardio-metabolic health. Gut Microbes. 2021;13(1):1–24. doi:10.1080/19490976.2021.1897212.
   PubMed Web of Science ®Google Scholar
• Gasaly N, Hermoso MA, Gotteland M. Butyrate and the fine-tuning of colonic homeostasis: Implication for inflammatory bowel diseases. Int J Mol Sci. 2021;22(6):22. doi:10.3390/ijms22063061.
   Web of Science ®Google Scholar
• Vital M, Karch A, Pieper DH, Shade A. Colonic butyrate-producing communities in humans: An overview using omics data. mSystems. 2017;2(6). doi:10.1128/mSystems.00130-17.
   PubMed Web of Science ®Google Scholar
• Perraudeau F, McMurdie P, Bullard J, Cheng A, Cutcliffe C, Deo A, Eid J, Gines J, Iyer M, Justice N. et al. Improvements to postprandial glucose control in subjects with type 2 diabetes: a multicenter, double blind, randomized placebo-controlled trial of a novel probiotic formulation. BMJ Open Diab Res Care. 2020;8(1):e001319. doi:10.1136/bmjdrc-2020-001319.
   PubMed Web of Science ®Google Scholar
• Kaminski M, Skonieczna-Zydecka K, Nowak JK, Stachowska E. Global and local diet popularity rankings, their secular trends, and seasonal variation in Google trends data. Nutrition. 2020;79-80:110759. doi:10.1016/j.nut.2020.110759.
   PubMed Web of Science ®Google Scholar
• Dodd D, Spitzer MH, Van Treuren W, Merrill BD, Hryckowian AJ, Higginbottom SK, Le A, Cowan TM, Nolan GP, Fischbach MA. et al. A gut bacterial pathway metabolizes aromatic amino acids into nine circulating metabolites. Nature. 2017;551(7682):648–52. doi:10.1038/nature24661.
   PubMed Web of Science ®Google Scholar
• Pan T, Pei Z, Fang Z, Wang H, Zhu J, Zhang H, Zhao J, Chen W, Lu W. Uncovering the specificity and predictability of tryptophan metabolism in lactic acid bacteria with genomics and metabolomics. Front Cell Infect Microbiol. 2023;13:1154346. doi:10.3389/fcimb.2023.1154346.
   PubMed Web of Science ®Google Scholar
• Lamas B, Richard ML, Leducq V, Pham HP, Michel ML, Da Costa G, Bridonneau C, Jegou S, Hoffmann TW, Natividad JM. et al. CARD9 impacts colitis by altering gut microbiota metabolism of tryptophan into aryl hydrocarbon receptor ligands. Nat Med. 2016;22(6):598–605. doi:10.1038/nm.4102.
   PubMed Web of Science ®Google Scholar
• Singer D, Camargo SM, Ramadan T, Schafer M, Mariotta L, Herzog B, Huggel K, Wolfer D, Werner S, Penninger JM. et al. Defective intestinal amino acid absorption in Ace2 null mice. Am J Physiol Gastrointest Liver Physiol. 2012;303(6):G686–95. doi:10.1152/ajpgi.00140.2012.
   PubMed Web of Science ®Google Scholar
• Chimerel C, Emery E, Summers DK, Keyser U, Gribble FM, Reimann F. Bacterial metabolite indole modulates incretin secretion from intestinal enteroendocrine L cells. Cell Rep. 2014;9(4):1202–8. doi:10.1016/j.celrep.2014.10.032.
   PubMed Web of Science ®Google Scholar
• Friedberg LM, Sen AK, Nguyen Q, Tonucci GP, Hellwarth EB, Gibbons WJ Jr., Jones, JA. In vivo biosynthesis of N,N-dimethyltryptamine, 5-MeO-N,N-dimethyltryptamine, and bufotenine in E.coli. Metab Eng. 2023;78:61–71.
   PubMed Web of Science ®Google Scholar
• Artusa V, Calabrone L, Mortara L, Peri F, Bruno A. Microbiota-derived natural products targeting cancer stem cells: inside the gut pharma factory. Int J Mol Sci. 2023;24(5):24. doi:10.3390/ijms24054997.
   Web of Science ®Google Scholar
• Sari Z, Miko E, Kovacs T, Janko L, Csonka T, Lente G, Sebő É, Tóth J, Tóth D, Árkosy P. et al. Indolepropionic acid, a metabolite of the microbiome, has cytostatic properties in breast cancer by activating AHR and PXR receptors and inducing oxidative stress. Cancers Basel. 2020;12(9):12. doi:10.3390/cancers12092411.
   Web of Science ®Google Scholar
• Ogyu K, Kubo K, Noda Y, Iwata Y, Tsugawa S, Omura Y, Wada M, Tarumi R, Plitman E, Moriguchi S. et al. Kynurenine pathway in depression: A systematic review and meta-analysis. Neurosci Biobehav Rev. 2018;90:16–25. doi:10.1016/j.neubiorev.2018.03.023.
   PubMed Web of Science ®Google Scholar
• Osadchiy V, Labus JS, Gupta A, Jacobs J, Ashe-McNalley C, Hsiao EY, Mayer EA. Correlation of tryptophan metabolites with connectivity of extended central reward network in healthy subjects. PLoS One. 2018;13(8):e0201772. doi:10.1371/journal.pone.0201772.
   PubMed Web of Science ®Google Scholar
• Rothhammer V, Mascanfroni ID, Bunse L, Takenaka MC, Kenison JE, Mayo L, Chao C-C, Patel B, Yan R, Blain M. et al. Type I interferons and microbial metabolites of tryptophan modulate astrocyte activity and central nervous system inflammation via the aryl hydrocarbon receptor. Nat Med. 2016;22(6):586–97. doi:10.1038/nm.4106.
   PubMed Web of Science ®Google Scholar
• Qi H, Li Y, Yun H, Zhang T, Huang Y, Zhou J, Yan H, Wei J, Liu Y, Zhang Z. et al. Lactobacillus maintains healthy gut mucosa by producing L-Ornithine. Commun Biol. 2019;2(1):171. doi:10.1038/s42003-019-0424-4.
   PubMedGoogle Scholar
• Cervantes-Barragan L, Chai JN, Tianero MD, Di Luccia B, Ahern PP, Merriman J, Cortez VS, Caparon MG, Donia MS, Gilfillan S. et al. Lactobacillus reuteri induces gut intraepithelial CD4 + CD8αα + T cells. Science. 2017;357(6353):806–810. doi:10.1126/science.aah5825.
   PubMed Web of Science ®Google Scholar
• Cheng Y, Jin UH, Allred CD, Jayaraman A, Chapkin RS, Safe S. Aryl Hydrocarbon Receptor Activity of Tryptophan Metabolites in Young Adult Mouse Colonocytes. Drug Metab Dispos. 2015;43(10):1536–43. doi:10.1124/dmd.115.063677.
   PubMed Web of Science ®Google Scholar
• Zelante T, Iannitti RG, Cunha C, De Luca A, Giovannini G, Pieraccini G, Zecchi R, D’Angelo C, Massi-Benedetti C, Fallarino F. et al. Tryptophan catabolites from microbiota engage aryl hydrocarbon receptor and balance mucosal reactivity via interleukin-22. Immunity. 2013;39(2):372–85. doi:10.1016/j.immuni.2013.08.003.
   PubMed Web of Science ®Google Scholar
• Krishnan S, Ding Y, Saedi N, Choi M, Sridharan GV, Sherr DH, Yarmush ML, Alaniz RC, Jayaraman A, Lee K. et al. Gut microbiota-derived tryptophan metabolites modulate inflammatory response in hepatocytes and macrophages. Cell Rep. 2018;23(4):1099–111. doi:10.1016/j.celrep.2018.03.109.
   PubMed Web of Science ®Google Scholar
• Bock KW. Human and rodent aryl hydrocarbon receptor (AHR): from mediator of dioxin toxicity to physiologic AHR functions and therapeutic options. Biol Chem. 2017;398(4):455–64. doi:10.1515/hsz-2016-0303.
   PubMed Web of Science ®Google Scholar
• Venkatesh M, Mukherjee S, Wang H, Li H, Sun K, Benechet AP, Qiu Z, Maher L, Redinbo M, Phillips R. et al. Symbiotic bacterial metabolites regulate gastrointestinal barrier function via the xenobiotic sensor PXR and Toll-like receptor 4. Immunity. 2014;41(2):296–310. doi:10.1016/j.immuni.2014.06.014.
   PubMed Web of Science ®Google Scholar
• Elsden SR, Hilton MG, Waller JM. The end products of the metabolism of aromatic amino acids by Clostridia. Arch Microbiol. 1976;107(3):283–8. doi:10.1007/BF00425340.
   PubMed Web of Science ®Google Scholar
• Mayo B, Vazquez L, Florez AB. Equol: A Bacterial Metabolite from The Daidzein Isoflavone and Its Presumed Beneficial Health Effects. Nutrients. 2019;11(9):11. doi:10.3390/nu11092231.
   Web of Science ®Google Scholar
• Tit DM, Bungau S, Iovan C, Nistor Cseppento DC, Endres L, Sava C, Sabau A, Furau G, Furau C. Effects of the hormone replacement therapy and of Soy Isoflavones on bone resorption in Postmenopause. J Clin Med. 2018;7(10):297. doi:10.3390/jcm7100297.
   PubMed Web of Science ®Google Scholar
• Ma L, Liu G, Ding M, Zong G, Hu FB, Willett WC, Rimm EB, Manson JE, Sun Q. Isoflavone Intake and the risk of coronary heart disease in US men and women: Results from 3 prospective cohort studies. Circulation. 2020;141(14):1127–1137. doi:10.1161/CIRCULATIONAHA.119.041306.
   PubMed Web of Science ®Google Scholar
• Wada K, Nakamura K, Tamai Y, Tsuji M, Kawachi T, Hori A, Takeyama N, Tanabashi S, Matsushita S, Tokimitsu N. et al. Soy isoflavone intake and breast cancer risk in Japan: from the Takayama study. Int J Cancer. 2013;133(4):952–60. doi:10.1002/ijc.28088.
   PubMed Web of Science ®Google Scholar
• Song KB, Atkinson C, Frankenfeld CL, Jokela T, Wahala K, Thomas WK, Lampe JW. Prevalence of daidzein-metabolizing phenotypes differs between Caucasian and Korean American women and girls. J Nutr. 2006;136(5):1347–1351. doi:10.1093/jn/136.5.1347.
   PubMed Web of Science ®Google Scholar
• Takahashi A, Kokubun M, Anzai Y, Kogre A, Ogata T, Imaizumi H, Fujita M, Hayashi M, Abe K, Ohira H. et al. Association between equol production and metabolic syndrome in Japanese women in their 50s-60s. Menopause. 2022;29(10):1196–9. doi:10.1097/GME.0000000000002052.
   PubMed Web of Science ®Google Scholar
• Zhang X, Fujiyoshi A, Ahuja V, Vishnu A, Barinas-Mitchell E, Kadota A, Miura K, Edmundowicz D, Ueshima H, Sekikawa A. et al. Association of equol producing status with aortic calcification in middle-aged Japanese men: The ERA JUMP study. Int J Cardiol. 2022;352:158–64. doi:10.1016/j.ijcard.2022.01.065.
   PubMed Web of Science ®Google Scholar
• Miller LM, Lampe JW, Newton KM, Gundersen G, Fuller S, Reed SD, Frankenfeld, CL. Being overweight or obese is associated with harboring a gut microbial community not capable of metabolizing the soy isoflavone daidzein to O-desmethylangolensin in peri- and post-menopausal women. Maturitas. 2017;99:37–42. doi:10.1016/j.maturitas.2017.02.006.
   PubMed Web of Science ®Google Scholar
• Clerici C, Setchell KD, Battezzati PM, Pirro M, Giuliano V, Asciutti S, Castellani D, Nardi E, Sabatino G, Orlandi S. et al. Pasta naturally enriched with isoflavone aglycons from soy germ reduces serum lipids and improves markers of cardiovascular risk. J Nutr. 2007;137(10):2270–8. doi:10.1093/jn/137.10.2270.
   PubMed Web of Science ®Google Scholar
• Dufault-Thompson K, Hall B, Jiang X. Taxonomic distribution and evolutionary analysis of the equol biosynthesis gene cluster. BMC Genom. 2022;23(1):182. doi:10.1186/s12864-022-08426-7.
   PubMed Web of Science ®Google Scholar
• Guo Y, Zhao L, Fang X, Zhong Q, Liang H, Liang W, Wang L. Isolation and identification of a human intestinal bacterium capable of daidzein conversion. FEMS Microbiol Lett. 2021;368(8). doi:10.1093/femsle/fnab046.
   Web of Science ®Google Scholar
• Yokoyama S, Suzuki T. Isolation and characterization of a novel equol-producing bacterium from human feces. Biosci Biotechnol Biochem. 2008;72(10):2660–6. doi:10.1271/bbb.80329.
   PubMed Web of Science ®Google Scholar
• Raimondi S, Roncaglia L, De Lucia M, Amaretti A, Leonardi A, Pagnoni UM, Rossi M. Bioconversion of soy isoflavones daidzin and daidzein by Bifidobacterium strains. Appl Microbiol Biotechnol. 2009;81(5):943–950. doi:10.1007/s00253-008-1719-4.
   PubMed Web of Science ®Google Scholar
• Usui T, Tochiya M, Sasaki Y, Muranaka K, Yamakage H, Himeno A, Shimatsu A, Inaguma A, Ueno T, Uchiyama S. et al. Effects of natural S-equol supplements on overweight or obesity and metabolic syndrome in the Japanese, based on sex and equol status. Clin Endocrinol (Oxf). 2013;78(3):365–72. doi:10.1111/j.1365-2265.2012.04400.x.
   PubMed Web of Science ®Google Scholar
• Hazim S, Curtis PJ, Schar MY, Ostertag LM, Kay CD, Minihane AM, Cassidy A. Acute benefits of the microbial-derived isoflavone metabolite equol on arterial stiffness in men prospectively recruited according to equol producer phenotype: a double-blind randomized controlled trial. Am J Clin Nutr. 2016;103(3):694–702. doi:10.3945/ajcn.115.125690.
   PubMed Web of Science ®Google Scholar
• Bapir M, Untracht GR, Cooke D, McVey JH, Skene SS, Campagnolo P, Whyte MB, Dikaios N, Rodriguez-Mateos A, Sampson DD. et al. Cocoa flavanol consumption improves lower extremity endothelial function in healthy individuals and people with type 2 diabetes. Food Funct. 2022;13(20):10439–48. doi:10.1039/D2FO02017C.
   PubMed Web of Science ®Google Scholar
• Heiss C, Istas G, Feliciano RP, Weber T, Wang B, Favari C, Mena P, Del Rio D, Rodriguez-Mateos A. Daily consumption of cranberry improves endothelial function in healthy adults: a double blind randomized controlled trial. Food Funct. 2022;13(7):3812–3824. doi:10.1039/D2FO00080F.
   PubMed Web of Science ®Google Scholar
• Sesso HD, Manson JE, Aragaki AK, Rist PM, Johnson LG, Friedenberg G, Copeland T, Clar A, Mora S, Moorthy MV. et al. Effect of cocoa flavanol supplementation for the prevention of cardiovascular disease events: the COcoa Supplement and Multivitamin Outcomes Study (COSMOS) randomized clinical trial. Am J Clin Nutr. 2022;115(6):1490–500. doi:10.1093/ajcn/nqac055.
   PubMed Web of Science ®Google Scholar
• Garcia-Diez E, Lopez-Oliva ME, Perez-Jimenez J, Martin MA, Ramos S. Metabolic regulation of (−)-epicatechin and the colonic metabolite 2,3-dihydroxybenzoic acid on the glucose uptake, lipid accumulation and insulin signalling in cardiac H9c2 cells. Food Funct. 2022;13(10):5602–5615. doi:10.1039/D2FO00182A.
   PubMed Web of Science ®Google Scholar
• Mena P, Favari C, Acharjee A, Chernbumroong S, Bresciani L, Curti C, Brighenti F, Heiss C, Rodriguez-Mateos A, Del Rio D. et al. Metabotypes of flavan-3-ol colonic metabolites after cranberry intake: elucidation and statistical approaches. Eur J Nutr. 2022;61(3):1299–317. doi:10.1007/s00394-021-02692-z.
   PubMed Web of Science ®Google Scholar
• Takagaki A, Nanjo F. Catabolism of (+)-Catechin and (−)-Epicatechin by Rat Intestinal Microbiota. J Agric Food Chem. 2013;61(20):4927–4935. doi:10.1021/jf304431v.
   PubMed Web of Science ®Google Scholar
• Sanchez-Patan F, Tabasco R, Monagas M, Requena T, Pelaez C, Moreno-Arribas MV, Bartolomé B. Capability of Lactobacillus plantarum IFPL935 to catabolize flavan-3-ol compounds and complex phenolic extracts. J Agric Food Chem. 2012;60(29):7142–7151. doi:10.1021/jf3006867.
   PubMed Web of Science ®Google Scholar
• Kutschera M, Engst W, Blaut M, Braune A. Isolation of catechin-converting human intestinal bacteria. J Appl Microbiol. 2011;111(1):165–75. doi:10.1111/j.1365-2672.2011.05025.x.
   PubMed Web of Science ®Google Scholar
• Rodriguez-Garcia C, Sanchez-Quesada C, Toledo E, Delgado-Rodriguez M, Gaforio JJ. Naturally Lignan-Rich Foods: A dietary tool for health promotion? Molecules. 2019;24(5):24. doi:10.3390/molecules24050917.
   Web of Science ®Google Scholar
• Koemel NA, Senior AM, Benmarhnia T, Holmes A, Okada M, Oulhote Y, Parker HM, Shah S, Simpson SJ, Raubenheimer D. et al. Diet quality, microbial lignan metabolites, and cardiometabolic health among US adults. Nutrients. 2023;15(6):15. doi:10.3390/nu15061412.
   Web of Science ®Google Scholar
• Mullens DA, Ivanov I, Hullar MAJ, Randolph TW, Lampe JW, Chapkin RS. Personalized nutrition using microbial metabolite phenotype to stratify participants and non-invasive host exfoliomics reveal the effects of flaxseed lignan supplementation in a Placebo-Controlled Crossover Trial. Nutrients. 2022;14(12):14. doi:10.3390/nu14122377.
   Web of Science ®Google Scholar
• Xu C, Liu Q, Zhang Q, Gu A, Jiang ZY. Urinary enterolactone is associated with obesity and metabolic alteration in men in the US national health and nutrition examination survey 2001–10. Br J Nutr. 2015;113(4):683–690. doi:10.1017/S0007114514004115.
   PubMed Web of Science ®Google Scholar
• Clavel T, Henderson G, Engst W, Dore J, Blaut M. Phylogeny of human intestinal bacteria that activate the dietary lignan secoisolariciresinol diglucoside. FEMS Microbiol Ecol. 2006;55(3):471–478. doi:10.1111/j.1574-6941.2005.00057.x.
   PubMed Web of Science ®Google Scholar
• Senizza A, Rocchetti G, Mosele JI, Patrone V, Callegari ML, Morelli L, Lucini L. Lignans and gut microbiota: An interplay revealing potential health implications. Molecules. 2020;25(23):25. doi:10.3390/molecules25235709.
   Web of Science ®Google Scholar
• Park S, Sim KS, Hwangbo Y, Park SJ, Kim YJ, Kim JH. Naringenin and Phytoestrogen 8-Prenylnaringenin Protect against Islet Dysfunction and Inhibit Apoptotic Signaling in Insulin-Deficient Diabetic Mice. Molecules. 2022;27(13):27. doi:10.3390/molecules27134227.
   Web of Science ®Google Scholar
• Yamashita M, Fukizawa S, Nonaka Y. Hop-derived prenylflavonoid isoxanthohumol suppresses insulin resistance by changing the intestinal microbiota and suppressing chronic inflammation in high fat diet-fed mice. Eur Rev Med Pharmacol Sci. 2020;24(3):1537–47. doi:10.26355/eurrev_202002_20212.
   PubMed Web of Science ®Google Scholar
• Possemiers S, Rabot S, Espin JC, Bruneau A, Philippe C, Gonzalez-Sarrias A, Heyerick A, Tomás-Barberán FA, De Keukeleire D, Verstraete W. et al. Eubacterium limosum activates isoxanthohumol from hops (Humulus lupulus L.) into the potent phytoestrogen 8-prenylnaringenin in vitro and in rat intestine. J Nutr. 2008;138(7):1310–6. doi:10.1093/jn/138.7.1310.
   PubMed Web of Science ®Google Scholar
• Paraiso IL, Plagmann LS, Yang L, Zielke R, Gombart AF, Maier CS, Sikora AE, Blakemore PR, Stevens JF. Reductive Metabolism of Xanthohumol and 8-Prenylnaringenin by the Intestinal Bacterium Eubacterium ramulus. Mol Nutr Food Res. 2019;63(2):e1800923. doi:10.1002/mnfr.201800923.
   PubMed Web of Science ®Google Scholar
• Tomas-Barberan FA, Garcia-Villalba R, Gonzalez-Sarrias A, Selma MV, Espin JC. Ellagic acid metabolism by human gut microbiota: consistent observation of three urolithin phenotypes in intervention trials, independent of food source, age, and health status. J Agric Food Chem. 2014;62(28):6535–6538. doi:10.1021/jf5024615.
   PubMed Web of Science ®Google Scholar
• Tomas-Barberan FA, Gonzalez-Sarrias A, Garcia-Villalba R, Nunez-Sanchez MA, Selma MV, Garcia-Conesa MT, Espín JC. Urolithins, the rescue of “old” metabolites to understand a “new” concept: Metabotypes as a nexus among phenolic metabolism, microbiota dysbiosis, and host health status. Mol Nutr Food Res. 2017;61(1):61. doi:10.1002/mnfr.201500901.
   Web of Science ®Google Scholar
• Gonzalez-Barrio R, Edwards CA, Crozier A. Colonic catabolism of ellagitannins, ellagic acid, and raspberry anthocyanins: in vivo and in vitro studies. Drug Metab Dispos. 2011;39(9):1680–8. doi:10.1124/dmd.111.039651.
   PubMed Web of Science ®Google Scholar
• Cortes-Martin A, Garcia-Villalba R, Gonzalez-Sarrias A, Romo-Vaquero M, Loria-Kohen V, Ramirez-de-Molina A, Tomás-Barberán FA, Selma MV, Espín JC. The gut microbiota urolithin metabotypes revisited: the human metabolism of ellagic acid is mainly determined by aging. Food Funct. 2018;9(8):4100–4106. doi:10.1039/C8FO00956B.
   PubMed Web of Science ®Google Scholar
• Cortes-Martin A, Romo-Vaquero M, Garcia-Mantrana I, Rodriguez-Varela A, Collado MC, Espin JC, Selma MV. Urolithin metabotypes can anticipate the different restoration of the gut microbiota and anthropometric profiles during the first year postpartum. Nutrients. 2019;11(9):11. doi:10.3390/nu11092079.
   Web of Science ®Google Scholar
• Cortes-Martin A, Colmenarejo G, Selma MV, Espin JC. Genetic polymorphisms, mediterranean diet and microbiota-associated urolithin metabotypes can predict obesity in childhood-adolescence. Sci Rep. 2020;10(1):7850. doi:10.1038/s41598-020-64833-4.
   PubMed Web of Science ®Google Scholar
• Selma MV, Beltran D, Garcia-Villalba R, Espin JC, Tomas-Barberan FA. Description of urolithin production capacity from ellagic acid of two human intestinal Gordonibacter species. Food Funct. 2014;5(8):1779–84. doi:10.1039/C4FO00092G.
   PubMed Web of Science ®Google Scholar
• Selma MV, Beltran D, Luna MC, Romo-Vaquero M, Garcia-Villalba R, Mira A, Espín, JC. Isolation of human intestinal bacteria capable of producing the bioactive metabolite isourolithin a from Ellagic Acid. Front Microbiol. 2017;8:1521. doi:10.3389/fmicb.2017.01521.
   PubMed Web of Science ®Google Scholar
• Garcia-Villalba R, Gimenez-Bastida JA, Cortes-Martin A, Avila-Galvez MÁ, Tomas-Barberan FA, Selma MV, Espín JC, González‐Sarrías A. Urolithins: A comprehensive update on their metabolism, bioactivity, and associated gut microbiota. Mol Nutr Food Res. 2022;66(21):e2101019. doi:10.1002/mnfr.202101019.
   PubMed Web of Science ®Google Scholar
• Andreux PA, Blanco-Bose W, Ryu D, Burdet F, Ibberson M, Aebischer P, Auwerx J, Singh A, Rinsch C. The mitophagy activator urolithin a is safe and induces a molecular signature of improved mitochondrial and cellular health in humans. Nat Metab. 2019;1(6):595–603. doi:10.1038/s42255-019-0073-4.
   PubMedGoogle Scholar
• Serhan CN, Levy BD. Resolvins in inflammation: emergence of the pro-resolving superfamily of mediators. J Clin Invest. 2018;128(7):2657–69. doi:10.1172/JCI97943.
   PubMed Web of Science ®Google Scholar
• Speckmann B, Kleinbolting J, Borner F, Jordan PM, Werz O, Pelzer S, Tom Dieck H, Wagner T, Schön C. Synbiotic compositions of bacillus megaterium and polyunsaturated fatty acid salt enable self-sufficient production of specialized pro-resolving mediators. Nutrients. 2022;14(11):14. doi:10.3390/nu14112265.
   Web of Science ®Google Scholar
• Miyata J, Arita M. Role of omega-3 fatty acids and their metabolites in asthma and allergic diseases. Allergol Int. 2015;64(1):27–34. doi:10.1016/j.alit.2014.08.003.
   PubMed Web of Science ®Google Scholar
• Mangino MJ, Brounts L, Harms B, Heise C. Lipoxin biosynthesis in inflammatory bowel disease. Prostaglandins Other Lipid Mediat. 2006;79(1–2):84–92. doi:10.1016/j.prostaglandins.2005.10.004.
   PubMed Web of Science ®Google Scholar
• Wang CW, Colas RA, Dalli J, Arnardottir HH, Nguyen D, Hasturk H, Chiang N, Van Dyke TE, Serhan CN. et al. Maresin 1 biosynthesis and proresolving anti-infective functions with human-localized aggressive periodontitis leukocytes. Infect Immun. 2015;84(3):658–665. doi:10.1128/IAI.01131-15.
   PubMed Web of Science ®Google Scholar
• Ajabnoor SM, Thorpe G, Abdelhamid A, Hooper L. Long-term effects of increasing omega-3, omega-6 and total polyunsaturated fats on inflammatory bowel disease and markers of inflammation: a systematic review and meta-analysis of randomized controlled trials. Eur J Nutr. 2021;60(5):2293–316. doi:10.1007/s00394-020-02413-y.
   PubMed Web of Science ®Google Scholar
• Calder PC. Marine omega-3 fatty acids and inflammatory processes: Effects, mechanisms and clinical relevance. Biochim Biophys Acta. 2015;1851(4):469–84. doi:10.1016/j.bbalip.2014.08.010.
   PubMed Web of Science ®Google Scholar
• Mullin GE, Limketkai BN, Parian AM. Fish oil for inflammatory bowel disease: Panacea or Placebo? Gastroenterol Clin North Am. 2021;50(1):169–82. doi:10.1016/j.gtc.2020.10.010.
   PubMed Web of Science ®Google Scholar
• Borner F, Pace S, Jordan PM, Gerstmeier J, Gomez M, Rossi A, Gilbert NC, Newcomer ME, Werz O. Allosteric Activation of 15-Lipoxygenase-1 by boswellic acid induces the lipid mediator class switch to promote resolution of inflammation. Adv Sci (Weinh). 2023;10(6):e2205604. doi:10.1002/advs.202205604.
   PubMedGoogle Scholar
• Norris PC, Skulas-Ray AC, Riley I, Richter CK, Kris-Etherton PM, Jensen GL, Serhan CN, Maddipati KR. Identification of specialized pro-resolving mediator clusters from healthy adults after intravenous low-dose endotoxin and omega-3 supplementation: a methodological validation. Sci Rep. 2018;8(1):18050. doi:10.1038/s41598-018-36679-4.
   PubMedGoogle Scholar
• Horn T, Adel S, Schumann R, Sur S, Kakularam KR, Polamarasetty A, Redanna P, Kuhn H, Heydeck D. Evolutionary aspects of lipoxygenases and genetic diversity of human leukotriene signaling. Prog Lipid Res. 2015;57:13–39. doi:10.1016/j.plipres.2014.11.001.
   PubMed Web of Science ®Google Scholar
• Furuya T, Shibata D, Kino K. Phylogenetic analysis of Bacillus P450 monooxygenases and evaluation of their activity towards steroids. Steroids. 2009;74(12):906–12. doi:10.1016/j.steroids.2009.06.005.
   PubMed Web of Science ®Google Scholar
• Capdevila JH, Wei S, Helvig C, Falck JR, Belosludtsev Y, Truan G, Graham-Lorence SE, Peterson JA. The highly stereoselective oxidation of polyunsaturated fatty acids by cytochrome P450BM-3. J Biol Chem. 1996;271(37):22663–22671. doi:10.1074/jbc.271.37.22663.
   PubMed Web of Science ®Google Scholar
• Piewngam P, Zheng Y, Nguyen TH, Dickey SW, Joo HS, Villaruz AE, Glose KA, Fisher EL, Hunt RL, Li B. et al. Pathogen elimination by probiotic Bacillus via signalling interference. Nature. 2018;562(7728):532–7. doi:10.1038/s41586-018-0616-y.
   PubMed Web of Science ®Google Scholar
• Zou D, Zhao Z, Li L, Min Y, Zhang D, Ji A, Jiang C, Wei X, Wu X. A comprehensive review of spermidine: Safety, health effects, absorption and metabolism, food materials evaluation, physical and chemical processing, and bioprocessing. Comp Rev Food Sci Food Safe. 2022;21(3):2820–2842. doi:10.1111/1541-4337.12963.
   PubMed Web of Science ®Google Scholar
• Rhodes CH, Zhu C, Agus J, Tang X, Li Q, Engebrecht J, Zivkovic AM. Human fasting modulates macrophage function and upregulates multiple bioactive metabolites that extend lifespan in Caenorhabditis elegans: a pilot clinical study. Am J Clin Nutr. 2023;117(2):286–297. doi:10.1016/j.ajcnut.2022.10.015.
   PubMed Web of Science ®Google Scholar
• Kiechl S, Pechlaner R, Willeit P, Notdurfter M, Paulweber B, Willeit K, Werner P, Ruckenstuhl C, Iglseder B, Weger S. et al. Higher spermidine intake is linked to lower mortality: a prospective population-based study. Am J Clin Nutr. 2018;108(2):371–80. doi:10.1093/ajcn/nqy102.
   PubMed Web of Science ®Google Scholar
• Schwarz C, Benson GS, Horn N, Wurdack K, Grittner U, Schilling R, Märschenz S, Köbe T, Hofer SJ, Magnes C. et al. Effects of spermidine supplementation on cognition and biomarkers in older adults with subjective cognitive decline: a randomized clinical trial. JAMA Netw Open. 2022;5(5):e2213875. doi:10.1001/jamanetworkopen.2022.13875.
   PubMed Web of Science ®Google Scholar
• Noack J, Kleessen B, Proll J, Dongowski G, Blaut M. Dietary guar gum and pectin stimulate intestinal microbial polyamine synthesis in rats. J Nutr. 1998;128(8):1385–91. doi:10.1093/jn/128.8.1385.
   PubMed Web of Science ®Google Scholar
• Xie SS, Wu HJ, Zang HY, Wu LM, Zhu QQ, Gao XW. Plant growth promotion by spermidine-producing Bacillus subtilis OKB105. Mol Plant Microbe Interact. 2014;27(7):655–63. doi:10.1094/MPMI-01-14-0010-R.
   PubMed Web of Science ®Google Scholar
• Caffaratti C, Plazy C, Cunin V, Toussaint B, Le Gouellec A. Bioengineering of Escherichia coli Nissle 1917 for production and excretion of spermidine, a key metabolite in human health. Metabolites. 2022;12(11):1061.
   PubMed Web of Science ®Google Scholar
• Button JE, Autran CA, Reens AL, Cosetta CM, Smriga S, Ericson M, Pierce JV, Cook DN, Lee ML, Sun AK. et al. Dosing a synbiotic of human milk oligosaccharides and B. infantis leads to reversible engraftment in healthy adult microbiomes without antibiotics. Cell Host Microbe. 2022;30(5):712–725.e7. doi:10.1016/j.chom.2022.04.001.
   PubMed Web of Science ®Google Scholar
• Gibson GR, Hutkins R, Sanders ME, Prescott SL, Reimer RA, Salminen SJ, Scott K, Stanton C, Swanson KS, Cani PD. et al. Expert consensus document: The International Scientific Association for Probiotics and Prebiotics (ISAPP) consensus statement on the definition and scope of prebiotics. Nat Rev Gastroenterol Hepatol. 2017;14(8):491–502. doi:10.1038/nrgastro.2017.75.
   PubMed Web of Science ®Google Scholar
• Swanson KS, Gibson GR, Hutkins R, Reimer RA, Reid G, Verbeke K, Scott KP, Holscher HD, Azad MB, Delzenne NM. et al. The International Scientific Association for Probiotics and Prebiotics (ISAPP) consensus statement on the definition and scope of synbiotics. Nat Rev Gastroenterol Hepatol. 2020;17(11):687–701. doi:10.1038/s41575-020-0344-2.
   PubMed Web of Science ®Google Scholar
• Louis P, Flint HJ, Michel C. How to Manipulate the Microbiota: Prebiotics. Adv Exp Med Biol. 2016;902:119–142.
   PubMed Web of Science ®Google Scholar
• Bindels LB, Delzenne NM, Cani PD, Walter J. Towards a more comprehensive concept for prebiotics. Nat Rev Gastroenterol Hepatol. 2015;12(5):303–10. doi:10.1038/nrgastro.2015.47.
   PubMed Web of Science ®Google Scholar
• Caviglia GP, De Blasio F, Vernero M, Armandi A, Rosso C, Saracco GM, Bugianesi E, Astegiano M, Ribaldone DG. Efficacy of a Preparation Based on Calcium Butyrate, Bifidobacterium bifidum, Bifidobacterium lactis, and Fructooligosaccharides in the Prevention of Relapse in Ulcerative Colitis: A Prospective Observational Study. J Clin Med. 2021;10(21):10. doi:10.3390/jcm10214961.
   Web of Science ®Google Scholar
• Roda A, Simoni P, Magliulo M, Nanni P, Baraldini M, Roda G, Roda E. A new oral formulation for the release of sodium butyrate in the ileo-cecal region and colon. World J Gastroenterol. 2007;13:1079–1084. doi:10.3748/wjg.v13.i7.1079.
   PubMed Web of Science ®Google Scholar
• Homann J, Suo J, Schmidt M, de Bruin N, Scholich K, Geisslinger G, Ferreirós N. In vivo availability of pro-resolving lipid mediators in oxazolone induced dermal inflammation in the mouse. PLoS One. 2015;10(11):e0143141. doi:10.1371/journal.pone.0143141.
   PubMed Web of Science ®Google Scholar
• Doyle R, Sadlier DM, Godson C. Pro-resolving lipid mediators: Agents of anti-ageing? Semin Immunol. 2018;40:36–48. doi:10.1016/j.smim.2018.09.002.
   PubMed Web of Science ®Google Scholar
• Cholkar K, Gilger BC, Mitra AK. Topical delivery of aqueous micellar resolvin E1 analog (RX-10045). Int J Pharm. 2016;498(1–2):326–34. doi:10.1016/j.ijpharm.2015.12.037.
   PubMed Web of Science ®Google Scholar
• de Molon RS, Thurlings RM, Walgreen B, Helsen MM, van der Kraan PM, Cirelli JA, Koenders MI. Systemic resolvin E1 (RvE1) treatment does not ameliorate the severity of Collagen-Induced Arthritis (CIA) in Mice: A randomized, prospective, and controlled proof of concept study. Mediators Inflamm. 2019;2019:1–14. doi:10.1155/2019/5689465.
   Web of Science ®Google Scholar
• Efsa Panel on Dietetic Products N, Allergies Turck D, Bresson JL, Burlingame B, Dean T, Heinonen M, Hirsch‐Ernst K-I, Mangelsdorf I, McArdle HJ, Naska A. et al. Safety of proline-specific oligopeptidase as a novel food pursuant to Regulation (EC) No 258/97. EFSA J. 2017;15(2):e04681. doi:10.2903/j.efsa.2017.4681.
   PubMed Web of Science ®Google Scholar
• Krishnareddy S, Stier K, Recanati M, Lebwohl B, Green PH. Commercially available glutenases: a potential hazard in coeliac disease. Therap Adv Gastroenterol. 2017;10(6):473–81. doi:10.1177/1756283X17690991.
   PubMed Web of Science ®Google Scholar
• Nettleton JA, Greany KA, Thomas W, Wangen KE, Adlercreutz H, Kurzer MS. Plasma phytoestrogens are not altered by probiotic consumption in postmenopausal women with and without a history of breast cancer. J Nutr. 2004;134(8):1998–2003. doi:10.1093/jn/134.8.1998.
   PubMed Web of Science ®Google Scholar
• Bonorden MJ, Greany KA, Wangen KE, Phipps WR, Feirtag J, Adlercreutz H, Kurzer MS. Consumption of Lactobacillus acidophilus and Bifidobacterium longum do not alter urinary equol excretion and plasma reproductive hormones in premenopausal women. Eur J Clin Nutr. 2004;58(12):1635–1642. doi:10.1038/sj.ejcn.1602020.
   PubMed Web of Science ®Google Scholar
• Decroos K, Eeckhaut E, Possemiers S, Verstraete W. Administration of equol-producing bacteria alters the equol production status in the Simulator of the Gastrointestinal Microbial Ecosystem (SHIME). J Nutr. 2006;136(4):946–52. doi:10.1093/jn/136.4.946.
   PubMed Web of Science ®Google Scholar
• Mustafa SE, Mustafa S, Abas F, Manap M, Ismail A, Amid M, Elzen S. Optimization of culture conditions of soymilk for equol production by Bifidobacterium breve 15700 and Bifidobacterium longum BB536. Food Chem. 2019;278:767–772. doi:10.1016/j.foodchem.2018.11.107.
   PubMed Web of Science ®Google Scholar
• Wang XL, Kim HJ, Kang SI, Kim SI, Hur HG. Production of phytoestrogen S-equol from daidzein in mixed culture of two anaerobic bacteria. Arch Microbiol. 2007;187(2):155–60. doi:10.1007/s00203-006-0183-8.
   PubMed Web of Science ®Google Scholar
• Kydd L, Shiveshwarkar P, Jaworski J. Engineering Escherichia coli for Conversion of Dietary Isoflavones in the Gut. ACS Synth Biol. 2022;11(11):3575–82. doi:10.1021/acssynbio.2c00277.
   PubMed Web of Science ®Google Scholar
• Pereira-Caro G, Oliver CM, Weerakkody R, Singh T, Conlon M, Borges G, Sanguansri L, Lockett T, Roberts SA, Crozier A. et al. Chronic administration of a microencapsulated probiotic enhances the bioavailability of orange juice flavanones in humans. Free Radic Biol Med. 2015;84:206–14. doi:10.1016/j.freeradbiomed.2015.03.010.
   PubMed Web of Science ®Google Scholar
• Shimojo Y, Ozawa Y, Toda T, Igami K, Shimizu T. Probiotic Lactobacillus paracasei A221 improves the functionality and bioavailability of kaempferol-glucoside in kale by its glucosidase activity. Sci Rep. 2018;8(1):9239. doi:10.1038/s41598-018-27532-9.
   PubMedGoogle Scholar
• Tom Dieck H, Schon C, Wagner T, Pankoke HC, Fluegel M, Speckmann B. A synbiotic formulation comprising Bacillus subtilis DSM 32315 and L-Alanyl-L-Glutamine improves intestinal butyrate levels and lipid metabolism in healthy humans. Nutrients. 2021;14(1):14. doi:10.3390/nu14010143.
   PubMed Web of Science ®Google Scholar
• Duysburgh C, Van den Abbeele P, Krishnan K, Bayne TF, Marzorati M. A synbiotic concept containing spore-forming Bacillus strains and a prebiotic fiber blend consistently enhanced metabolic activity by modulation of the gut microbiome in vitro. Int J Pharm X. 2019;1:100021. doi:10.1016/j.ijpx.2019.100021.
   PubMedGoogle Scholar
• Xu Y, Yu Y, Shen Y, Li Q, Lan J, Wu Y, Zhang R, Cao G, Yang C. Effects of Bacillus subtilis and Bacillus licheniformis on growth performance, immunity, short chain fatty acid production, antioxidant capacity, and cecal microflora in broilers. Poult Sci. 2021;100(9):101358. doi:10.1016/j.psj.2021.101358.
   PubMed Web of Science ®Google Scholar
• Stoeva MK, Garcia-So J, Justice N, Myers J, Tyagi S, Nemchek M, McMurdie PJ, Kolterman O, Eid J. Butyrate-producing human gut symbiont, Clostridium butyricum, and its role in health and disease. Gut Microbes. 2021;13(1):1–28. doi:10.1080/19490976.2021.1907272.
   PubMed Web of Science ®Google Scholar
• Ojo O, Feng QQ, Ojo OO, Wang XH. The role of dietary fibre in modulating gut microbiota dysbiosis in patients with type 2 diabetes: A systematic review and meta-analysis of randomised controlled trials. Nutrients. 2020;12(11):3239.
   PubMed Web of Science ®Google Scholar
• Matsumoto M, Kitada Y, Naito Y. Endothelial function is improved by inducing microbial polyamine production in the gut: A randomized placebo-controlled trial. Nutrients. 2019;11(5):11. doi:10.3390/nu11051188.
   Web of Science ®Google Scholar
• Wagh SK, Lammers KM, Padul MV, Rodriguez-Herrera A, Dodero VI. Celiac disease and possible dietary interventions: From enzymes and probiotics to postbiotics and viruses. Int J Mol Sci. 2022;23(19):23. doi:10.3390/ijms231911748.
   Web of Science ®Google Scholar
• Cristofori F, Francavilla R, Capobianco D, Dargenio VN, Filardo S, Mastromarino P. Bacterial-based strategies to hydrolyze gluten peptides and protect intestinal mucosa. Front Immunol. 2020;11:567801. doi:10.3389/fimmu.2020.567801.
   PubMed Web of Science ®Google Scholar
• De Angelis M, Cassone A, Rizzello CG, Gagliardi F, Minervini F, Calasso M, Di Cagno R, Francavilla R, Gobbetti M. Mechanism of degradation of immunogenic gluten epitopes from Triticum turgidum L. var. durum by sourdough lactobacilli and fungal proteases. Appl Environ Microbiol. 2010;76(2):508–518. doi:10.1128/AEM.01630-09.
   PubMed Web of Science ®Google Scholar
• De Angelis M, Siragusa S, Vacca M, Di Cagno R, Cristofori F, Schwarm M, Pelzer S, Flügel M, Speckmann B, Francavilla R. et al. Selection of Gut-Resistant Bacteria and Construction of Microbial Consortia for Improving Gluten Digestion under Simulated Gastrointestinal Conditions. Nutrients. 2021;13(3):992. doi:10.3390/nu13030992.
   PubMed Web of Science ®Google Scholar
• Mirza Alizadeh A, Hosseini H, Mollakhalili Meybodi N, Hashempour-Baltork F, Alizadeh-Sani M, Tajdar-Oranj B. Mitigation of potentially toxic elements in food products by probiotic bacteria: A comprehensive review. Food Res Int. 2022;152:110324. doi:10.1016/j.foodres.2021.110324.
   PubMed Web of Science ®Google Scholar
• Yi YJ, Lim JM, Gu S, Lee WK, Oh E, Lee SM, Oh B-T. Potential use of lactic acid bacteria Leuconostoc mesenteroides as a probiotic for the removal of Pb(II) toxicity. J Microbiol. 2017;55(4):296–303. doi:10.1007/s12275-017-6642-x.
   PubMed Web of Science ®Google Scholar
• Hu T, Song J, Zeng W, Li J, Wang H, Zhang Y, Suo H. Lactobacillus plantarum LP33 attenuates Pb-induced hepatic injury in rats by reducing oxidative stress and inflammation and promoting Pb excretion. Food Chem Toxicol. 2020;143:111533. doi:10.1016/j.fct.2020.111533.
   PubMed Web of Science ®Google Scholar
• Zhai Q, Wang G, Zhao J, Liu X, Tian F, Zhang H, Chen W. Protective effects of Lactobacillus plantarum CCFM8610 against acute cadmium toxicity in mice. Appl Environ Microbiol. 2013;79(5):1508–1515. doi:10.1128/AEM.03417-12.
   PubMed Web of Science ®Google Scholar
• Zhai Q, Liu Y, Wang C, Zhao J, Zhang H, Tian F, Lee Y-K, Chen W. Increased Cadmium Excretion Due to Oral Administration of Lactobacillus plantarum Strains by Regulating Enterohepatic Circulation in Mice. J Agric Food Chem. 2019;67(14):3956–3965. doi:10.1021/acs.jafc.9b01004.
   PubMed Web of Science ®Google Scholar
• Feng P, Yang J, Zhao S, Ling Z, Han R, Wu Y, Salama E-S, Kakade A, Khan A, Jin W. et al. Human supplementation with Pediococcus acidilactici GR-1 decreases heavy metals levels through modifying the gut microbiota and metabolome. NPJ Biofilms Microbio. 2022;8(1):63. doi:10.1038/s41522-022-00326-8.
   PubMed Web of Science ®Google Scholar
• Li Y, Zhu J, Lin G, Gao K, Yu Y, Chen S, Chen L, Chen Z, Li L. Probiotic effects of Lacticaseibacillus rhamnosus 1155 and Limosilactobacillus fermentum 2644 on hyperuricemic rats. Front Nutr. 2022;9:993951. doi:10.3389/fnut.2022.993951.
   PubMed Web of Science ®Google Scholar
• He L, Tang W, Huang L, Zhou W, Huang S, Zou L, Yuan L, Men D, Chen S, Hu Y. et al. Rational design of a genome-based insulated system in Escherichia coli facilitates heterologous uricase expression for hyperuricemia treatment. Bioeng Transl Med. 2023;8(2):e10449. doi:10.1002/btm2.10449.
   PubMed Web of Science ®Google Scholar
• Rodriguez JM, Garranzo M, Segura J, Orgaz B, Arroyo R, Alba C, Beltrán D, Fernández L. A randomized pilot trial assessing the reduction of gout episodes in hyperuricemic patients by oral administration of Ligilactobacillus salivarius CECT 30632, a strain with the ability to degrade purines. Front Microbiol. 2023;14:1111652. doi:10.3389/fmicb.2023.1111652.
   PubMed Web of Science ®Google Scholar
• Blasco T, Perez-Burillo S, Balzerani F, Hinojosa-Nogueira D, Lerma-Aguilera A, Pastoriza S, Cendoya X, Rubio Á, Gosalbes MJ, Jiménez-Hernández N. et al. An extended reconstruction of human gut microbiota metabolism of dietary compounds. Nat Commun. 2021;12(1):4728. doi:10.1038/s41467-021-25056-x.
   PubMed Web of Science ®Google Scholar
• Heinken A, Hertel J, Acharya G, Ravcheev DA, Nyga M, Okpala OE, Hogan M, Magnúsdóttir S, Martinelli F, Nap B. et al. Genome-scale metabolic reconstruction of 7,302 human microorganisms for personalized medicine. Nat Biotechnol. 2023;41(9):1320–1331. doi:10.1038/s41587-022-01628-0.
   PubMed Web of Science ®Google Scholar