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. 2023 Jun 5:1–49. Online ahead of print. doi: 10.1007/s11427-023-2346-1

Gut microbiota bridges dietary nutrients and host immunity

Lijuan Fan 1,#, Yaoyao Xia 1,#, Youxia Wang 1,#, Dandan Han 2,#, Yanli Liu 3,#, Jiahuan Li 4,#, Jie Fu 5,#, Leli Wang 6,#, Zhending Gan 1, Bingnan Liu 1, Jian Fu 1, Congrui Zhu 1, Zhenhua Wu 2, Jinbiao Zhao 2, Hui Han 7, Hao Wu 4, Yiwen He 6,8, Yulong Tang 6, Qingzhuo Zhang 1, Yibin Wang 3, Fan Zhang 3, Xin Zong 5,, Jie Yin 9,, Xihong Zhou 6,, Xiaojun Yang 3,, Junjun Wang 2,, Yulong Yin 6,9,, Wenkai Ren 1,
PMCID: PMC10247344  PMID: 37286860

Abstract

Dietary nutrients and the gut microbiota are increasingly recognized to cross-regulate and entrain each other, and thus affect host health and immune-mediated diseases. Here, we systematically review the current understanding linking dietary nutrients to gut microbiota-host immune interactions, emphasizing how this axis might influence host immunity in health and diseases. Of relevance, we highlight that the implications of gut microbiota-targeted dietary intervention could be harnessed in orchestrating a spectrum of immune-associated diseases.

Keywords: amino acid, carbohydrate, lipid, trace element, vitamin, gut microbiota, immunity

Acknowledgements

This work was supported by the National Key Research and Development Program of China (2021YFD1300700, 2021YFD1300201, 2022YFA1304201), the National Natural Science Foundation of China (32225047, U22A20510, 32125036, 32172750, 31972596, 31902170, 31630074, 32272916, 32102567), the Laboratory of Lingnan Modern Agriculture Project (NT2021005), the China Agricultural Research System of MOF and MARA (CARS-35), the Key Research and Development Project of Hainan Province (ZDYF2021XDNY177), the 111 Project (B16044), the Program for Shaanxi Science and Technology (2022KJXX-13). Our profound admiration and respect go to researchers in this field and in our laboratories, for their dedication and hard work. We apologize to scientists whose work is in this field if their papers are not cited owing to space limitations.

Footnotes

Compliance and ethics

The author(s) declare that they have no conflict of interest.

Contributed equally to this work

Contributor Information

Xin Zong, Email: zongxin@zju.edu.cn.

Jie Yin, Email: yinjie@hunau.edu.cn.

Xihong Zhou, Email: xhzhou@isa.ac.cn.

Xiaojun Yang, Email: yangxj@nwsuaf.edu.cn.

Junjun Wang, Email: wangjj@cau.edu.cn.

Yulong Yin, Email: yinyulong@isa.ac.cn.

Wenkai Ren, Email: renwenkai19@scau.edu.cn.

References

  1. Abdalkareem Jasim S, Jade Catalan Opulencia M, Alexis Ramírez-Coronel A, Kamal Abdelbasset W, Hasan Abed M, Markov A, Raheem Lateef Al-Awsi G, Azamatovich Shamsiev J, Thaeer Hammid A, Nader Shalaby M, et al. The emerging role of microbiota-derived short-chain fatty acids in immunometabolism. Int Immunopharmacol. 2022;110:108983. doi: 10.1016/j.intimp.2022.108983. [DOI] [PubMed] [Google Scholar]
  2. Abe RAM, Masroor A, Khorochkov A, Prieto J, Singh KB, Nnadozie MC, Abdal M, Shrestha N, Mohammed L. The role of vitamins in non-alcoholic fatty liver disease: a systematic review. Cureus. 2021;13:e16855. doi: 10.7759/cureus.16855. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Abidin MZ, Saravanan T, Zhang J, Tepper PG, Strauss E, Poelarends GJ. Modular enzymatic cascade synthesis of vitamin B5 and its derivatives. Chem Eur J. 2018;24:17434–17438. doi: 10.1002/chem.201804151. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Akiba, Y., Maruta, K., Takajo, T., Narimatsu, K., Said, H., Kato, I., Kuwahara, A., and Kaunitz, J.D. (2020). Lipopolysaccharides transport during fat absorption in rodent small intestine. Am J Physiol Gastrointest Liver Physiol 318, G1070–G1087. [DOI] [PMC free article] [PubMed]
  5. Akkerman R, Faas MM, de Vos P. Non-digestible carbohydrates in infant formula as substitution for human milk oligosaccharide functions: effects on microbiota and gut maturation. Crit Rev Food Sci Nutr. 2019;59:1486–1497. doi: 10.1080/10408398.2017.1414030. [DOI] [PubMed] [Google Scholar]
  6. Al-Bulish MSM, Cao W, Yang R, Wang Y, Xue C, Tang Q. Docosahexaenoic acid-rich fish oil alleviates hepatic steatosis in association with regulation of gut microbiome in ob/ob mice. Food Res Int. 2022;157:111373. doi: 10.1016/j.foodres.2022.111373. [DOI] [PubMed] [Google Scholar]
  7. Alamir OF, Oladele RO, Ibe C. Nutritional immunity: targeting fungal zinc homeostasis. Heliyon. 2021;7:e07805. doi: 10.1016/j.heliyon.2021.e07805. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Alexeev EE, Lanis JM, Kao DJ, Campbell EL, Kelly CJ, Battista KD, Gerich ME, Jenkins BR, Walk ST, Kominsky DJ, et al. Microbiota-derived indole metabolites promote human and murine intestinal homeostasis through regulation of interleukin-10 receptor. Am J Pathol. 2018;188:1183–1194. doi: 10.1016/j.ajpath.2018.01.011. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Amato KR, Leigh SR, Kent A, Mackie RI, Yeoman CJ, Stumpf R M, Wilson BA, Nelson KE, White BA, Garber PA. The gut microbiota appears to compensate for seasonal diet variation in the wild black howler monkey (Alouatta pigra) Microb Ecol. 2015;69:434–443. doi: 10.1007/s00248-014-0554-7. [DOI] [PubMed] [Google Scholar]
  10. Amir Shaghaghi M, Bernstein CN, Serrano León A, El-Gabalawy H, Eck P. Polymorphisms in the sodium-dependent ascorbate transporter gene SLC23A1 are associated with susceptibility to Crohn disease. Am J Clin Nutr. 2014;99:378–383. doi: 10.3945/ajcn.113.068015. [DOI] [PubMed] [Google Scholar]
  11. Anhê FF, Barra NG, Cavallari JF, Henriksbo BD, Schertzer J D. Metabolic endotoxemia is dictated by the type of lipopolysaccharide. Cell Rep. 2021;36:109691. doi: 10.1016/j.celrep.2021.109691. [DOI] [PubMed] [Google Scholar]
  12. Anzilotti C, Swan DJ, Boisson B, Deobagkar-Lele M, Oliveira C, Chabosseau P, Engelhardt KR, Xu X, Chen R, Alvarez L, et al. An essential role for the Zn2+ transporter ZIP7 in B cell development. Nat Immunol. 2019;20:350–361. doi: 10.1038/s41590-018-0295-8. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Araújo JR, Tazi A, Burlen-Defranoux O, Vichier-Guerre S, Nigro G, Licandro H, Demignot S, Sansonetti PJ. Fermentation products of commensal bacteria alter enterocyte lipid metabolism. Cell Host Microbe 27. 2020;358–375:e7. doi: 10.1016/j.chom.2020.01.028. [DOI] [PubMed] [Google Scholar]
  14. Arendsen, L.P., Thakar, R., and Sultan, A.H. (2019). The use of copper as an antimicrobial agent in health care, including obstetrics and gynecology. Clin Microbiol Rev 32. [DOI] [PMC free article] [PubMed]
  15. Arias-Borrego A, Callejón-Leblic B, Calatayud M, Gómez-Ariza JL, Collado MC, García-Barrera T. Insights into cancer and neurodegenerative diseases through selenoproteins and the connection with gut microbiota—current analytical methodologies. Expert Rev Proteomics. 2019;16:805–814. doi: 10.1080/14789450.2019.1664292. [DOI] [PubMed] [Google Scholar]
  16. Armet AM, Deehan EC, O’Sullivan AF, Mota JF, Field CJ, Prado CM, Lucey AJ, Walter J. Rethinking healthy eating in light of the gut microbiome. Cell Host Microbe. 2022;30:764–785. doi: 10.1016/j.chom.2022.04.016. [DOI] [PubMed] [Google Scholar]
  17. Arpaia N, Campbell C, Fan X, Dikiy S, van der Veeken J, Deroos P, Liu H, Cross JR, Pfeffer K, Coffer PJ, et al. Metabolites produced by commensal bacteria promote peripheral regulatory T-cell generation. Nature. 2013;504:451–455. doi: 10.1038/nature12726. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Arrieta MC, Stiemsma LT, Dimitriu PA, Thorson L, Russell S, Yurist-Doutsch S, Kuzeljevic B, Gold MJ, Britton HM, Lefebvre DL, et al. Early infancy microbial and metabolic alterations affect risk of childhood asthma. Sci Transl Med. 2015;7:307ra152. doi: 10.1126/scitranslmed.aab2271. [DOI] [PubMed] [Google Scholar]
  19. Badawy AAB. Tryptophan availability for kynurenine pathway metabolism across the life span: control mechanisms and focus on aging, exercise, diet and nutritional supplements. Neuropharmacology. 2017;112:248–263. doi: 10.1016/j.neuropharm.2015.11.015. [DOI] [PubMed] [Google Scholar]
  20. Bai R, Cui F, Li W, Wang Y, Wang Z, Gao Y, Wang N, Xu Q, Hu F, Zhang Y. Codonopsis pilosula oligosaccharides modulate the gut microbiota and change serum metabolomic profiles in high-fat diet-induced obese mice. Food Funct. 2022;13:8143–8157. doi: 10.1039/D2FO01119K. [DOI] [PubMed] [Google Scholar]
  21. Bai Y, Wang R, Yang Y, Li R, Wu X. Folic acid absorption characteristics and effect on cecal microbiota of laying hens. Front Vet Sci. 2021;8:720851. doi: 10.3389/fvets.2021.720851. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Bai Y, Zhou X, Li N, Zhao J, Ye H, Zhang S, Yang H, Pi Y, Tao S, Han D, et al. In vitro fermentation characteristics and fiber-degrading enzyme kinetics of cellulose, arabinoxylan, β-glucan and glucomannan by pig fecal microbiota. Microorganisms. 2021;9:1071. doi: 10.3390/microorganisms9051071. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Balabanova L, Averianova L, Marchenok M, Son O, Tekutyeva L. Microbial and genetic resources for cobalamin (Vitamin B12) biosynthesis: from ecosystems to industrial biotechnology. Int J Mol Sci. 2021;22:4522. doi: 10.3390/ijms22094522. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Balfegó M, Canivell S, Hanzu FA, Sala-Vila A, Martínez-Medina M, Murillo S, Mur T, Ruano EG, Linares F, Porras N, et al. Effects of sardine-enriched diet on metabolic control, inflammation and gut microbiota in drug-naïve patients with type 2 diabetes: a pilot randomized trial. Lipids Health Dis. 2016;15:78. doi: 10.1186/s12944-016-0245-0. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Balzano T, Dadsetan S, Forteza J, Cabrera-Pastor A, Taoro-Gonzalez L, Malaguarnera M, Gil-Perotin S, Cubas-Nuñez L, Casanova B, Castro-Quintas A, et al. Chronic hyperammonemia induces peripheral inflammation that leads to cognitive impairment in rats: reversed by anti-TNF-α treatment. J Hepatol. 2020;73:582–592. doi: 10.1016/j.jhep.2019.01.008. [DOI] [PubMed] [Google Scholar]
  26. Bansal T, Alaniz RC, Wood TK, Jayaraman A. The bacterial signal indole increases epithelial-cell tight-junction resistance and attenuates indicators of inflammation. Proc Natl Acad Sci USA. 2010;107:228–233. doi: 10.1073/pnas.0906112107. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Barcik W, Pugin B, Westermann P, Perez NR, Ferstl R, Wawrzyniak M, Smolinska S, Jutel M, Hessel EM, Michalovich D, et al. Histamine-secreting microbes are increased in the gut of adult asthma patients. J Allergy Clin Immunol. 2016;138:1491–1494. doi: 10.1016/j.jaci.2016.05.049. [DOI] [PubMed] [Google Scholar]
  28. Battistini C, Ballan R, Herkenhoff ME, Saad SMI, Sun J. Vitamin D modulates intestinal microbiota in inflammatory bowel diseases. Int J Mol Sci. 2020;22:362. doi: 10.3390/ijms22010362. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Beaumont M, Blachier F. Amino acids in intestinal physiology and health. In: Wu G, editor. Amino Acids in Nutrition and Health. Cham: Springer; 2020. pp. 1–20. [DOI] [PubMed] [Google Scholar]
  30. Bellono NW, Bayrer JR, Leitch DB, Castro J, Zhang C, O’Donnell TA, Brierley SM, Ingraham HA, Julius D. Enterochromaffin cells are gut chemosensors that couple to sensory neural pathways. Cell. 2017;170:185–198. doi: 10.1016/j.cell.2017.05.034. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Belzer, C., Chia, L.W., Aalvink, S., Chamlagain, B., Piironen, V., Knol, J., and de Vos, W.M. (2017). Microbial metabolic networks at the mucus layer lead to diet-independent butyrate and vitamin B(12) production by intestinal symbionts. mBio 8. [DOI] [PMC free article] [PubMed]
  32. Bering S, Suchdev S, Sjøltov L, Berggren A, Tetens I, Bukhave K. A lactic acid-fermented oat gruel increases non-haem iron absorption from a phytate-rich meal in healthy women of childbearing age. br j nutr. 2006;96:80–85. doi: 10.1079/BJN20061683. [DOI] [PubMed] [Google Scholar]
  33. Berndt BE, Zhang M, Owyang SY, Cole TS, Wang TW, Luther J, Veniaminova NA, Merchant JL, Chen CC, Huffnagle GB, et al. Butyrate increases IL-23 production by stimulated dendritic cells. Am J Physiol Gastrointest Liver Physiol. 2012;303:G1384–G1392. doi: 10.1152/ajpgi.00540.2011. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Bersch-Ferreira C, Sampaio GR, Gehringer MO, Ross-Fernandes MB, Kovacs C, Alves R, Pereira JL, Magnoni CD, Weber B, Rogero MM. Association between polyunsaturated fatty acids and inflammatory markers in patients in secondary prevention of cardiovascular disease. Nutrition. 2017;37:30–36. doi: 10.1016/j.nut.2016.12.006. [DOI] [PubMed] [Google Scholar]
  35. Bhattarai Y, Williams BB, Battaglioli EJ, Whitaker WR, Till L, Grover M, Linden DR, Akiba Y, Kandimalla KK, Zachos NC, et al. Gut microbiota-produced tryptamine activates an epithelial G-protein-coupled receptor to increase colonic secretion. Cell Host Microbe. 2018;23:775–785. doi: 10.1016/j.chom.2018.05.004. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. Bidu C, Escoula Q, Bellenger S, Spor A, Galan M, Geissler A, Bouchot A, Dardevet D, Morio B, Cani PD, et al. The transplantation of ω3 PUFA-altered gut microbiota of fat-1 mice to wild-type littermates prevents obesity and associated metabolic disorders. Diabetes. 2018;67:1512–1523. doi: 10.2337/db17-1488. [DOI] [PubMed] [Google Scholar]
  37. Bielik V, Kolisek M. Bioaccessibility and bioavailability of minerals in relation to a healthy gut microbiome. Int J Mol Sci. 2021;22:6803. doi: 10.3390/ijms22136803. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. Bouter KE, Bakker GJ, Levin E, Hartstra AV, Kootte RS, Udayappan SD, Katiraei S, Bahler L, Gilijamse PW, Tremaroli V, et al. Differential metabolic effects of oral butyrate treatment in lean versus metabolic syndrome subjects. Clin Transl Gastroenterol. 2018;9:e155. doi: 10.1038/s41424-018-0025-4. [DOI] [PMC free article] [PubMed] [Google Scholar]
  39. Brütting C, Lara Bisch M, Brandsch C, Hirche F, Stangl GI. Impact of dietary propionate on fructose-induced changes in lipid metabolism, gut microbiota and short-chain fatty acids in mice. Int J Food Sci Nutr. 2021;72:160–173. doi: 10.1080/09637486.2020.1773415. [DOI] [PubMed] [Google Scholar]
  40. Bugianesi E, Petta S. NAFLD/NASH. J Hepatol. 2022;77:549–550. doi: 10.1016/j.jhep.2022.02.006. [DOI] [PubMed] [Google Scholar]
  41. Caesar R, Tremaroli V, Kovatcheva-Datchary P, Cani PD, Bäckhed F. Crosstalk between gut microbiota and dietary lipids aggravates WAT inflammation through TLR signaling. Cell Metab. 2015;22:658–668. doi: 10.1016/j.cmet.2015.07.026. [DOI] [PMC free article] [PubMed] [Google Scholar]
  42. Cai X, Deng L, Ma X, Guo Y, Feng Z, Liu M, Guan Y, Huang Y, Deng J, Li H, et al. Altered diversity and composition of gut microbiota in Wilson’s disease. Sci Rep. 2020;10:21825. doi: 10.1038/s41598-020-78988-7. [DOI] [PMC free article] [PubMed] [Google Scholar]
  43. Cai Y, Folkerts J, Folkerts G, Maurer M, Braber S. Microbiota-dependent and -independent effects of dietary fibre on human health. Br J Pharmacol. 2020;177:1363–1381. doi: 10.1111/bph.14871. [DOI] [PMC free article] [PubMed] [Google Scholar]
  44. Callejón-Leblic B, Selma-Royo M, Collado MC, Abril N, García-Barrera T. Impact of antibiotic-induced depletion of gut microbiota and selenium supplementation on plasma selenoproteome and metal homeostasis in a mice model. J Agric Food Chem. 2021;69:7652–7662. doi: 10.1021/acs.jafc.1c02622. [DOI] [PMC free article] [PubMed] [Google Scholar]
  45. Cani PD, Amar J, Iglesias MA, Poggi M, Knauf C, Bastelica D, Neyrinck AM, Fava F, Tuohy KM, Chabo C, et al. Metabolic endotoxemia initiates obesity and insulin resistance. Diabetes. 2007;56:1761–1772. doi: 10.2337/db06-1491. [DOI] [PubMed] [Google Scholar]
  46. Cantorna MT, Lin YD, Arora J, Bora S, Tian Y, Nichols RG, Patterson AD. Vitamin D regulates the microbiota to control the numbers of RORγt/FoxP3+ regulatory T cells in the colon. Front Immunol. 2019;10:1772. doi: 10.3389/fimmu.2019.01772. [DOI] [PMC free article] [PubMed] [Google Scholar]
  47. Cantu-Jungles TM, Bulut N, Chambry E, Ruthes A, Iacomini M, Keshavarzian A, Johnson TA, Hamaker BR. Dietary fiber hierarchical specificity: the missing link for predictable and strong shifts in gut bacterial communities. mBio. 2021;12:e0102821. doi: 10.1128/mBio.01028-21. [DOI] [PMC free article] [PubMed] [Google Scholar]
  48. Castaneda M, Strong JM, Alabi DA, Hernandez CJ. The gut microbiome and bone strength. Curr Osteoporos Rep. 2020;18:677–683. doi: 10.1007/s11914-020-00627-x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  49. Cervantes-Barragan L, Chai JN, Tianero MD, Di Luccia B, Ahern P P, Merriman J, Cortez VS, Caparon MG, Donia MS, Gilfillan S, et al. Lactobacillus reuteri induces gut intraepithelial CD4+ CD8αα+ T cells. Science. 2017;357:806–810. doi: 10.1126/science.aah5825. [DOI] [PMC free article] [PubMed] [Google Scholar]
  50. Cha HR, Chang SY, Chang JH, Kim JO, Yang JY, Kim CH, Kweon MN. Downregulation of Th17 cells in the small intestine by disruption of gut flora in the absence of retinoic acid. J Immunol. 2010;184:6799–6806. doi: 10.4049/jimmunol.0902944. [DOI] [PubMed] [Google Scholar]
  51. Chadaideh KS, Carmody RN. Host-microbial interactions in the metabolism of different dietary fats. Cell Metab. 2021;33:857–872. doi: 10.1016/j.cmet.2021.04.011. [DOI] [PubMed] [Google Scholar]
  52. Chandel NS. Carbohydrate metabolism. Cold Spring Harb Perspect Biol. 2021;13:a040568. doi: 10.1101/cshperspect.a040568. [DOI] [PMC free article] [PubMed] [Google Scholar]
  53. Chen L, Lin YL, Peng G, Li F. Structural basis for multifunctional roles of mammalian aminopeptidase N. Proc Natl Acad Sci USA. 2012;109:17966–17971. doi: 10.1073/pnas.1210123109. [DOI] [PMC free article] [PubMed] [Google Scholar]
  54. Chen L, Wang Z, Wang P, Yu X, Ding H, Wang Z, Feng J. Effect of long-term and short-term imbalanced Zn manipulation on gut microbiota and screening for microbial markers sensitive to zinc status. Microbiol Spectr. 2021;9:e0048321. doi: 10.1128/Spectrum.00483-21. [DOI] [PMC free article] [PubMed] [Google Scholar]
  55. Chen P, Torralba M, Tan J, Embree M, Zengler K, Stärkel P, van Pijkeren JP, DePew J, Loomba R, Ho SB, et al. Supplementation of saturated long-chain fatty acids maintains intestinal eubiosis and reduces ethanol-induced liver injury in mice. Gastroenterology. 2015;148:203–214. doi: 10.1053/j.gastro.2014.09.014. [DOI] [PMC free article] [PubMed] [Google Scholar]
  56. Chen R, Xu Y, Wu P, Zhou H, Lasanajak Y, Fang Y, Tang L, Ye L, Li X, Cai Z, et al. Transplantation of fecal microbiota rich in short chain fatty acids and butyric acid treat cerebral ischemic stroke by regulating gut microbiota. Pharmacol Res. 2019;148:104403. doi: 10.1016/j.phrs.2019.104403. [DOI] [PubMed] [Google Scholar]
  57. Chen S, Xia Y, He F, Fu J, Xin Z, Deng B, He L, Zhou X, Ren W. Serine supports IL-1β production in macrophages through mTOR signaling. Front Immunol. 2020;11:1866. doi: 10.3389/fimmu.2020.01866. [DOI] [PMC free article] [PubMed] [Google Scholar]
  58. Chen S, Yang M, Wang R, Fan X, Tang T, Li P, Zhou X, Qi K. Suppression of high-fat-diet-induced obesity in mice by dietary folic acid supplementation is linked to changes in gut microbiota. Eur J Nutr. 2022;61:2015–2031. doi: 10.1007/s00394-021-02769-9. [DOI] [PubMed] [Google Scholar]
  59. Chen Z, Ruan J, Li D, Wang M, Han Z, Qiu W, Wu G. The role of intestinal bacteria and gut-brain axis in hepatic encephalopathy. Front Cell Infect Microbiol. 2020;10:595759. doi: 10.3389/fcimb.2020.595759. [DOI] [PMC free article] [PubMed] [Google Scholar]
  60. Chitrakar I, Ahmed SF, Torelli AT, French JB. Structure of the E. coli agmatinase, SPEB. PLoS ONE. 2021;16:e0248991. doi: 10.1371/journal.pone.0248991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  61. Choi H, Rao MC, Chang EB. Gut microbiota as a transducer of dietary cues to regulate host circadian rhythms and metabolism. Nat Rev Gastroenterol Hepatol. 2021;18:679–689. doi: 10.1038/s41575-021-00452-2. [DOI] [PMC free article] [PubMed] [Google Scholar]
  62. Choi Y, Lee S, Kim S, Lee J, Ha J, Oh H, Lee Y, Kim Y, Yoon Y. Vitamin E (α-tocopherol) consumption influences gut microbiota composition. Int J Food Sci Nutr. 2020;71:221–225. doi: 10.1080/09637486.2019.1639637. [DOI] [PubMed] [Google Scholar]
  63. Ciesielska A, Matyjek M, Kwiatkowska K. TLR4 and CD14 trafficking and its influence on LPS-induced pro-inflammatory signaling. Cell Mol Life Sci. 2021;78:1233–1261. doi: 10.1007/s00018-020-03656-y. [DOI] [PMC free article] [PubMed] [Google Scholar]
  64. Coker JK, Moyne O, Rodionov DA, Zengler K. Carbohydrates great and small, from dietary fiber to sialic acids: How glycans influence the gut microbiome and affect human health. Gut Microbes. 2021;13:1–8. doi: 10.1080/19490976.2020.1869502. [DOI] [PMC free article] [PubMed] [Google Scholar]
  65. Corrêa-Oliveira R, Fachi JL, Vieira A, Sato FT, Vinolo MAR. Regulation of immune cell function by short-chain fatty acids. Clin Trans Immunol. 2016;5:e73. doi: 10.1038/cti.2016.17. [DOI] [PMC free article] [PubMed] [Google Scholar]
  66. Costantini L, Molinari R, Farinon B, Merendino N. Impact of omega-3 fatty acids on the gut microbiota. Int J Mol Sci. 2017;18:2645. doi: 10.3390/ijms18122645. [DOI] [PMC free article] [PubMed] [Google Scholar]
  67. Cronin P, Joyce SA, O’Toole PW, O’Connor EM. Dietary fibre modulates the gut microbiota. Nutrients. 2021;13:1655. doi: 10.3390/nu13051655. [DOI] [PMC free article] [PubMed] [Google Scholar]
  68. da Silva Ferreira AR, Wardill HR, Havinga R, Tissing WJE, Harmsen HJM. Prophylactic treatment with vitamins C and B2 for methotrexate-induced gastrointestinal mucositis. Biomolecules. 2021;11:34. doi: 10.3390/biom11010034. [DOI] [PMC free article] [PubMed] [Google Scholar]
  69. Dai J, Yang X, Yuan Y, Jia Y, Liu G, Lin N, Xiao H, Zhang L, Chen J. Toxicity, gut microbiota and metabolome effects after copper exposure during early life in SD rats. Toxicology. 2020;433–434:152395. doi: 10.1016/j.tox.2020.152395. [DOI] [PubMed] [Google Scholar]
  70. Daïen CI, Pinget GV, Tan JK, Macia L. Detrimental impact of microbiota-accessible carbohydrate-deprived diet on gut and immune homeostasis: an overview. Front Immunol. 2017;8:548. doi: 10.3389/fimmu.2017.00548. [DOI] [PMC free article] [PubMed] [Google Scholar]
  71. Dalile B, Van Oudenhove L, Vervliet B, Verbeke K. The role of short-chain fatty acids in microbiota-gut-brain communication. Nat Rev Gastroenterol Hepatol. 2019;16:461–478. doi: 10.1038/s41575-019-0157-3. [DOI] [PubMed] [Google Scholar]
  72. Daniel H, Gholami AM, Berry D, Desmarchelier C, Hahne H, Loh G, Mondot S, Lepage P, Rothballer M, Walker A, et al. High-fat diet alters gut microbiota physiology in mice. ISME J. 2014;8:295–308. doi: 10.1038/ismej.2013.155. [DOI] [PMC free article] [PubMed] [Google Scholar]
  73. Danneskiold-Samsøe NB, Andersen D, Radulescu ID, Normann-Hansen A, Brejnrod A, Kragh M, Madsen T, Nielsen C, Josefsen K, Fretté X, et al. A safflower oil based high-fat/high-sucrose diet modulates the gut microbiota and liver phospholipid profiles associated with early glucose intolerance in the absence of tissue inflammation. Mol Nutr Food Res. 2017;61:1600528. doi: 10.1002/mnfr.201600528. [DOI] [PubMed] [Google Scholar]
  74. Das NK, Schwartz AJ, Barthel G, Inohara N, Liu Q, Sankar A, Hill DR, Ma X, Lamberg O, Schnizlein MK, et al. Microbial metabolite signaling is required for systemic iron homeostasis. Cell Metab. 2020;31:115–130. doi: 10.1016/j.cmet.2019.10.005. [DOI] [PMC free article] [PubMed] [Google Scholar]
  75. De Filippis F, Pellegrini N, Vannini L, Jeffery IB, La Storia A, Laghi L, Serrazanetti DI, Di Cagno R, Ferrocino I, Lazzi C, et al. High-level adherence to a Mediterranean diet beneficially impacts the gut microbiota and associated metabolome. Gut. 2016;65:1812–1821. doi: 10.1136/gutjnl-2015-309957. [DOI] [PubMed] [Google Scholar]
  76. de Souza AZ, Zambom AZ, Abboud KY, Reis SK, Tannihão F, Guadagnini D, Saad MJA, Prada PO. Oral supplementation with l-glutamine alters gut microbiota of obese and overweight adults: a pilot study. Nutrition. 2015;31:884–889. doi: 10.1016/j.nut.2015.01.004. [DOI] [PubMed] [Google Scholar]
  77. de Vos WM, Tilg H, Van Hul M, Cani PD. Gut microbiome and health: mechanistic insights. Gut. 2022;71:1020–1032. doi: 10.1136/gutjnl-2021-326789. [DOI] [PMC free article] [PubMed] [Google Scholar]
  78. Delzenne NM, Bindels LB. Food for thought about manipulating gut bacteria. Nature. 2020;577:32–34. doi: 10.1038/d41586-019-03704-z. [DOI] [PubMed] [Google Scholar]
  79. Derrien M, Belzer C, de Vos WM. Akkermansia muciniphila and its role in regulating host functions. Microb Pathog. 2017;106:171–181. doi: 10.1016/j.micpath.2016.02.005. [DOI] [PubMed] [Google Scholar]
  80. Desai MS, Seekatz AM, Koropatkin NM, Kamada N, Hickey CA, Wolter M, Pudlo NA, Kitamoto S, Terrapon N, Muller A, et al. A dietary fiber-deprived gut microbiota degrades the colonic mucus barrier and enhances pathogen susceptibility. Cell. 2016;167:1339–1353. doi: 10.1016/j.cell.2016.10.043. [DOI] [PMC free article] [PubMed] [Google Scholar]
  81. Di Giancamillo A, Rossi R, Martino PA, Aidos L, Maghin F, Domeneghini C, Corino C. Copper sulphate forms in piglet diets: microbiota, intestinal morphology and enteric nervous system glial cells. Anim Sci J. 2018;89:616–624. doi: 10.1111/asj.12948. [DOI] [PubMed] [Google Scholar]
  82. Dickert S, Pierik AJ, Linder D, Buckel W. The involvement of coenzyme A esters in the dehydration of (R)-phenyllactate to (E)-cinnamate by Clostridium sporogenes. Eur J Biochem. 2000;267:3874–3884. doi: 10.1046/j.1432-1327.2000.01427.x. [DOI] [PubMed] [Google Scholar]
  83. Ding C, Festa RA, Chen YL, Espart A, Palacios Ò, Espín J, Capdevila M, Atrian S, Heitman J, Thiele DJ. Cryptococcus neoformans copper detoxification machinery is critical for fungal virulence. Cell Host Microbe. 2013;13:265–276. doi: 10.1016/j.chom.2013.02.002. [DOI] [PMC free article] [PubMed] [Google Scholar]
  84. Djoko KY, Ong CY, Walker MJ, McEwan AG. The role of copper and zinc toxicity in innate immune defense against bacterial pathogens. J Biol Chem. 2015;290:18954–18961. doi: 10.1074/jbc.R115.647099. [DOI] [PMC free article] [PubMed] [Google Scholar]
  85. Dodd D, Spitzer MH, van Treuren W, Merrill BD, Hryckowian AJ, Higginbottom SK, Le A, Cowan TM, Nolan GP, Fischbach M A, et al. A gut bacterial pathway metabolizes aromatic amino acids into nine circulating metabolites. Nature. 2017;551:648–652. doi: 10.1038/nature24661. [DOI] [PMC free article] [PubMed] [Google Scholar]
  86. Dong XY, Azzam MMM, Zou XT. Effects of dietary threonine supplementation on intestinal barrier function and gut microbiota of laying hens. Poultry Sci. 2017;96:3654–3663. doi: 10.3382/ps/pex185. [DOI] [PubMed] [Google Scholar]
  87. 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;142:271–277. doi: 10.3945/jn.111.148643. [DOI] [PMC free article] [PubMed] [Google Scholar]
  88. Dostal A, Fehlbaum S, Chassard C, Zimmermann MB, Lacroix C. Low iron availability in continuous in vitro colonic fermentations induces strong dysbiosis of the child gut microbial consortium and a decrease in main metabolites. FEMS Microbiol Ecol. 2013;83:161–175. doi: 10.1111/j.1574-6941.2012.01461.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  89. Du L, Liu B, Han Z, Xia Y, Wu M, Liu S. Melatonin shapes bacterial clearance function of porcine macrophages during enterotoxigenic Escherichia coli infection. Anim Nutr. 2022;11:242–251. doi: 10.1016/j.aninu.2022.06.018. [DOI] [PMC free article] [PubMed] [Google Scholar]
  90. Duan, Y., Zheng, C., Zheng, J., Ma, L., Ma, X., Zhong, Y., Zhao, X., Li, F., Guo, Q., and Yin, Y. (2022). Profiles of muscular amino acids, fatty acids, and metabolites in Shaziling pigs of different ages and relation to meat quality. Sci China Life Sci doi: 10.1007/s11427-022-2227-6. [DOI] [PubMed]
  91. Egerton S, Donoso F, Fitzgerald P, Gite S, Fouhy F, Whooley J, Dinan TG, Cryan JF, Culloty SC, Ross RP, et al. Investigating the potential of fish oil as a nutraceutical in an animal model of early life stress. Nutral Neurosci. 2022;25:356–378. doi: 10.1080/1028415X.2020.1753322. [DOI] [PubMed] [Google Scholar]
  92. Ellis JL, Karl JP, Oliverio AM, Fu X, Soares JW, Wolfe BE, Hernandez CJ, Mason JB, Booth SL. Dietary vitamin K is remodeled by gut microbiota and influences community composition. Gut Microbes. 2021;13:1–6. doi: 10.1080/19490976.2021.1887721. [DOI] [PMC free article] [PubMed] [Google Scholar]
  93. Fagundes RR, Bourgonje AR, Saeed A, Vich Vila A, Plomp N, Blokzijl T, Sadaghian Sadabad M, von Martels JZH, van Leeuwen SS, Weersma RK, et al. Inulin-grown Faecalibacterium prausnitzii cross-feeds fructose to the human intestinal epithelium. Gut Microbes. 2021;13:1993582. doi: 10.1080/19490976.2021.1993582. [DOI] [PMC free article] [PubMed] [Google Scholar]
  94. Fakhoury HMA, Kvietys PR, AlKattan W, Anouti FA, Elahi MA, Karras SN, Grant WB. Vitamin D and intestinal homeostasis: barrier, microbiota, and immune modulation. J Steroid Biochem Mol Biol. 2020;200:105663. doi: 10.1016/j.jsbmb.2020.105663. [DOI] [PubMed] [Google Scholar]
  95. Fan L, Liu B, Han Z, Ren W. Insights into host-microbe interaction: what can we do for the swine industry. Anim Nutr. 2021;7:17–23. doi: 10.1016/j.aninu.2020.10.003. [DOI] [PMC free article] [PubMed] [Google Scholar]
  96. Fang H, Li Z, Graff EC, McCafferty KJ, Judd RL. Niacin increases diet-induced hepatic steatosis in B6129 mice. Biochim Biophys Acta. 2020;1865:158731. doi: 10.1016/j.bbalip.2020.158731. [DOI] [PubMed] [Google Scholar]
  97. Fang W, Xue H, Chen X, Chen K, Ling W. Supplementation with sodium butyrate modulates the composition of the gut microbiota and ameliorates high-fat diet-induced obesity in mice. J Nutr. 2019;149:747–754. doi: 10.1093/jn/nxy324. [DOI] [PubMed] [Google Scholar]
  98. Fang, Z., Pan, T., Li, L., Wang, H., Zhu, J., Zhang, H., Zhao, J., Chen, W., and Lu, W. (2022). Bifidobacterium longum mediated tryptophan metabolism to improve atopic dermatitis via the gut-skin axis. Gut Microbes 14. [DOI] [PMC free article] [PubMed]
  99. Feng P, Yang Q, Luo L, Sun Y, Lv W, Wan S, Guan Z, Xiao Z, Liu F, Li Z, et al. The kinase PDK1 regulates regulatory T cell survival via controlling redox homeostasis. Theranostics. 2021;11:9503–9518. doi: 10.7150/thno.63992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  100. Feng ZM, Li TJ, Wu L, Xiao DF, Blachier F, Yin YL. Monosodium L-glutamate and dietary fat differently modify the composition of the intestinal microbiota in growing pigs. Obes Facts. 2015;8:87–100. doi: 10.1159/000380889. [DOI] [PMC free article] [PubMed] [Google Scholar]
  101. Fernández-Gallego N, Sánchez-Madrid F, Jiménez-Saiz R. Thinking small: zinc sensing by the gut epithelium. Allergy. 2021;76:411–413. doi: 10.1111/all.14531. [DOI] [PubMed] [Google Scholar]
  102. Fernandez-Julia PJ, Munoz-Munoz J, van Sinderen D. A comprehensive review on the impact of β-glucan metabolism by Bacteroides and Bifidobacterium species as members of the gut microbiota. Int J Biol Macromol. 2021;181:877–889. doi: 10.1016/j.ijbiomac.2021.04.069. [DOI] [PubMed] [Google Scholar]
  103. Ferreira RLU, Sena-Evangelista KCM, de Azevedo EP, Pinheiro F I, Cobucci RN, Pedrosa LFC. Selenium in human health and gut microflora: bioavailability of selenocompounds and relationship with diseases. Front Nutr. 2021;8:685317. doi: 10.3389/fnut.2021.685317. [DOI] [PMC free article] [PubMed] [Google Scholar]
  104. Figliuolo VR, dos Santos LM, Abalo A, Nanini H, Santos A, Brittes NM, Bernardazzi C, de Souza HSP, Vieira LQ, Coutinho-Silva R, et al. Sulfate-reducing bacteria stimulate gut immune responses and contribute to inflammation in experimental colitis. Life Sci. 2017;189:29–38. doi: 10.1016/j.lfs.2017.09.014. [DOI] [PubMed] [Google Scholar]
  105. Fischer F, Romero R, Hellhund A, Linne U, Bertrams W, Pinkenburg O, Eldin HS, Binder K, Jacob R, Walker A, et al. Dietary cellulose induces anti-inflammatory immunity and transcriptional programs via maturation of the intestinal microbiota. Gut Microbes. 2020;12:1829962. doi: 10.1080/19490976.2020.1829962. [DOI] [PMC free article] [PubMed] [Google Scholar]
  106. Flint HJ, Scott KP, Duncan SH, Louis P, Forano E. Microbial degradation of complex carbohydrates in the gut. Gut Microbes. 2012;3:289–306. doi: 10.4161/gmic.19897. [DOI] [PMC free article] [PubMed] [Google Scholar]
  107. Fontecha-Barriuso M, Lopez-Diaz AM, Carriazo S, Ortiz A, Sanz AB. Nicotinamide and acute kidney injury. Clin Kidney J. 2021;14:2453–2462. doi: 10.1093/ckj/sfab173. [DOI] [PMC free article] [PubMed] [Google Scholar]
  108. Frazier K, Kambal A, Zale EA, Pierre JF, Hubert N, Miyoshi S, Miyoshi J, Ringus DL, Harris D, Yang K, et al. High-fat diet disrupts REG3γ and gut microbial rhythms promoting metabolic dysfunction. Cell Host Microbe. 2022;30:809–823. doi: 10.1016/j.chom.2022.03.030. [DOI] [PMC free article] [PubMed] [Google Scholar]
  109. Fritsch J, Garces L, Quintero MA, Pignac-Kobinger J, Santander A M, Fernández I, Ban YJ, Kwon D, Phillips MC, Knight K, et al. Low-fat, high-fiber diet reduces markers of inflammation and dysbiosis and improves quality of life in patients with ulcerative colitis. Clin Gastroenterol Hepatol. 2021;19:1189–1199. doi: 10.1016/j.cgh.2020.05.026. [DOI] [PubMed] [Google Scholar]
  110. Fu X, Liu Z, Zhu C, Mou H, Kong Q. Nondigestible carbohydrates, butyrate, and butyrate-producing bacteria. Crit Rev Food Sci Nutr. 2019;59:S130–S152. doi: 10.1080/10408398.2018.1542587. [DOI] [PubMed] [Google Scholar]
  111. Gangadoo S, Dinev I, Chapman J, Hughes RJ, Van TTH, Moore R J, Stanley D. Selenium nanoparticles in poultry feed modify gut microbiota and increase abundance of Faecalibacterium prausnitzii. Appl Microbiol Biotechnol. 2018;102:1455–1466. doi: 10.1007/s00253-017-8688-4. [DOI] [PubMed] [Google Scholar]
  112. Geng H, Shu S, Dong J, Li H, Xu C, Han Y, Hu J, Han Y, Yang R, Cheng N. Association study of gut flora in Wilson’s disease through high-throughput sequencing. Medicine. 2018;97:e11743. doi: 10.1097/MD.0000000000011743. [DOI] [PMC free article] [PubMed] [Google Scholar]
  113. Ghaisas S, Maher J, Kanthasamy A. Gut microbiome in health and disease: linking the microbiome-gut-brain axis and environmental factors in the pathogenesis of systemic and neurodegenerative diseases. Pharmacol Ther. 2016;158:52–62. doi: 10.1016/j.pharmthera.2015.11.012. [DOI] [PMC free article] [PubMed] [Google Scholar]
  114. Ghezzal S, Postal BG, Quevrain E, Brot L, Seksik P, Leturque A, Thenet S, Carrière V. Palmitic acid damages gut epithelium integrity and initiates inflammatory cytokine production. Biochim Biophys Acta. 2020;1865:158530. doi: 10.1016/j.bbalip.2019.158530. [DOI] [PubMed] [Google Scholar]
  115. Ghosh TS, Rampelli S, Jeffery IB, Santoro A, Neto M, Capri M, Giampieri E, Jennings A, Candela M, Turroni S, et al. Mediterranean diet intervention alters the gut microbiome in older people reducing frailty and improving health status: the NU-AGE 1-year dietary intervention across five European countries. Gut. 2020;69:1218–1228. doi: 10.1136/gutjnl-2019-319654. [DOI] [PMC free article] [PubMed] [Google Scholar]
  116. Gielda LM, DiRita VJ. Zinc competition among the intestinal microbiota. mBio. 2012;3:e00171–00112. doi: 10.1128/mBio.00171-12. [DOI] [PMC free article] [PubMed] [Google Scholar]
  117. Glassner KL, Abraham BP, Quigley EMM. The microbiome and inflammatory bowel disease. J Allergy Clin Immunol. 2020;145:16–27. doi: 10.1016/j.jaci.2019.11.003. [DOI] [PubMed] [Google Scholar]
  118. Gnauck A, Lentle RG, Kruger MC. The characteristics and function of bacterial lipopolysaccharides and their endotoxic potential in humans. Int Rev Immunol. 2016;35:189–218. doi: 10.3109/08830185.2015.1087518. [DOI] [PubMed] [Google Scholar]
  119. González A, Gálvez N, Martín J, Reyes F, Pérez-Victoria I, Dominguez-Vera JM. Identification of the key excreted molecule by Lactobacillus fermentum related to host iron absorption. Food Chem. 2017;228:374–380. doi: 10.1016/j.foodchem.2017.02.008. [DOI] [PubMed] [Google Scholar]
  120. Grieneisen L, Dasari M, Gould TJ, Björk JR, Grenier JC, Yotova V, Jansen D, Gottel N, Gordon JB, Learn NH, et al. Gut microbiome heritability is nearly universal but environmentally contingent. Science. 2021;373:181–186. doi: 10.1126/science.aba5483. [DOI] [PMC free article] [PubMed] [Google Scholar]
  121. Gropper SS, Smith JL. Advanced Nutrition and Human Metabolism. Sixth Ed. Belmont: Wadsworth; 2012. [Google Scholar]
  122. Gu C, Suleria HAR, Dunshea FR, Howell K. Dietary lipids influence bioaccessibility of polyphenols from black carrots and affect microbial diversity under simulated gastrointestinal digestion. Antioxidants. 2020;9:762. doi: 10.3390/antiox9080762. [DOI] [PMC free article] [PubMed] [Google Scholar]
  123. Guetterman HM, Huey SL, Knight R, Fox AM, Mehta S, Finkelstein JL. Vitamin B-12 and the gastrointestinal microbiome: a systematic review. Adv Nutr. 2022;13:530–558. doi: 10.1093/advances/nmab123. [DOI] [PMC free article] [PubMed] [Google Scholar]
  124. Guo, C.J., Allen, B.M., Hiam, K.J., Dodd, D., Van Treuren, W., Higginbottom, S., Nagashima, K., Fischer, C.R., Sonnenburg, J.L., Spitzer, M.H., et al. (2019). Depletion of microbiome-derived molecules in the host using Clostridium genetics. Science 366. [DOI] [PMC free article] [PubMed]
  125. Hajam IA, Dar PA, Shahnawaz I, Jaume JC, Lee JH. Bacterial flagellin—a potent immunomodulatory agent. Exp Mol Med. 2017;49:e373. doi: 10.1038/emm.2017.172. [DOI] [PMC free article] [PubMed] [Google Scholar]
  126. Hasan R, Rink L, Haase H. Chelation of free Zn2+ impairs chemotaxis, phagocytosis, oxidative burst, degranulation, and cytokine production by neutrophil granulocytes. Biol Trace Elem Res. 2016;171:79–88. doi: 10.1007/s12011-015-0515-0. [DOI] [PubMed] [Google Scholar]
  127. Hayashi A, Mikami Y, Miyamoto K, Kamada N, Sato T, Mizuno S, Naganuma M, Teratani T, Aoki R, Fukuda S, et al. Intestinal dysbiosis and biotin deprivation induce alopecia through overgrowth of Lactobacillus murinus in mice. Cell Rep. 2017;20:1513–1524. doi: 10.1016/j.celrep.2017.07.057. [DOI] [PubMed] [Google Scholar]
  128. He W, Hu S, Du X, Wen Q, Zhong XP, Zhou X, Zhou C, Xiong W, Gao Y, Zhang S, et al. Vitamin B5 reduces bacterial growth via regulating innate immunity and adaptive immunity in mice infected with Mycobacterium tuberculosis. Front Immunol. 2018;9:365. doi: 10.3389/fimmu.2018.00365. [DOI] [PMC free article] [PubMed] [Google Scholar]
  129. He X, Slupsky CM. Metabolic fingerprint of dimethyl sulfone (DMSO2) in microbial-mammalian co-metabolism. J Proteome Res. 2014;13:5281–5292. doi: 10.1021/pr500629t. [DOI] [PubMed] [Google Scholar]
  130. He Y, Liu Y, Guan P, He L, Zhou X. Serine administration improves selenium status, oxidative stress, and mitochondrial function in longissimus dorsi muscle of piglets with intrauterine growth retardation. Biol Trace Elem Res. 2023;201:1740–1747. doi: 10.1007/s12011-022-03304-5. [DOI] [PubMed] [Google Scholar]
  131. He Z, Li X, Yang H, Wu P, Wang S, Cao D, Guo X, Xu Z, Gao J, Zhang W, et al. Effects of oral vitamin C supplementation on liver health and associated parameters in patients with non-alcoholic fatty liver disease: a randomized clinical trial. Front Nutr. 2021;8:745609. doi: 10.3389/fnut.2021.745609. [DOI] [PMC free article] [PubMed] [Google Scholar]
  132. Heimann E, Nyman M, Pålbrink AK, Lindkvist-Petersson K, Degerman E. Branched short-chain fatty acids modulate glucose and lipid metabolism in primary adipocytes. Adipocyte. 2016;5:359–368. doi: 10.1080/21623945.2016.1252011. [DOI] [PMC free article] [PubMed] [Google Scholar]
  133. Herrero del Valle A, Seip B, Cervera-Marzal I, Sacheau G, Seefeldt AC, Innis CA. Ornithine capture by a translating ribosome controls bacterial polyamine synthesis. Nat Microbiol. 2020;5:554–561. doi: 10.1038/s41564-020-0669-1. [DOI] [PMC free article] [PubMed] [Google Scholar]
  134. Hersoug LG, Møller P, Loft S. Gut microbiota-derived lipopolysaccharide uptake and trafficking to adipose tissue: implications for inflammation and obesity. Obesity Rev. 2016;17:297–312. doi: 10.1111/obr.12370. [DOI] [PubMed] [Google Scholar]
  135. Hezaveh K, Shinde RS, Klötgen A, Halaby MJ, Lamorte S, Ciudad MT, Quevedo R, Neufeld L, Liu ZQ, Jin R, et al. Tryptophan-derived microbial metabolites activate the aryl hydrocarbon receptor in tumor-associated macrophages to suppress anti-tumor immunity. Immunity. 2022;55:324–340. doi: 10.1016/j.immuni.2022.01.006. [DOI] [PMC free article] [PubMed] [Google Scholar]
  136. Hibberd, M.C., Wu, M., Rodionov, D.A., Li, X., Cheng, J., Griffin, N.W., Barratt, M.J., Giannone, R.J., Hettich, R.L., Osterman, A.L., et al. (2017). The effects of micronutrient deficiencies on bacterial species from the human gut microbiota. Sci Transl Med 9. [DOI] [PMC free article] [PubMed]
  137. Hills R, Pontefract B, Mishcon H, Black C, Sutton S, Theberge C. Gut microbiome: profound implications for diet and disease. Nutrients. 2019;11:1613. doi: 10.3390/nu11071613. [DOI] [PMC free article] [PubMed] [Google Scholar]
  138. Hirata A, Kishino S, Park SB, Takeuchi M, Kitamura N, Ogawa J. A novel unsaturated fatty acid hydratase toward C16 to C22 fatty acids from Lactobacillus acidophilus. J Lipid Res. 2015;56:1340–1350. doi: 10.1194/jlr.M059444. [DOI] [PMC free article] [PubMed] [Google Scholar]
  139. Hirmas B, Gasaly N, Orellana G, Vega-Sagardía M, Saa P, Gotteland M, Garrido D. Metabolic modeling and bidirectional culturing of two gut microbes reveal cross-feeding interactions and protective effects on intestinal cells. mSystems. 2022;7:e0064622. doi: 10.1128/msystems.00646-22. [DOI] [PMC free article] [PubMed] [Google Scholar]
  140. Ho Do M, Seo YS, Park HY. Polysaccharides: bowel health and gut microbiota. Crit Rev Food Sci Nutr. 2021;61:1212–1224. doi: 10.1080/10408398.2020.1755949. [DOI] [PubMed] [Google Scholar]
  141. Hojyo S, Miyai T, Fujishiro H, Kawamura M, Yasuda T, Hijikata A, Bin BH, Irié T, Tanaka J, Atsumi T, et al. Zinc transporter SLC39A10/ZIP10 controls humoral immunity by modulating B-cell receptor signal strength. Proc Natl Acad Sci USA. 2014;111:11786–11791. doi: 10.1073/pnas.1323557111. [DOI] [PMC free article] [PubMed] [Google Scholar]
  142. Holbert CE, Cullen MT, Casero RA, Stewart TM. Polyamines in cancer: integrating organismal metabolism and antitumour immunity. Nat Rev Cancer. 2022;22:467–480. doi: 10.1038/s41568-022-00473-2. [DOI] [PMC free article] [PubMed] [Google Scholar]
  143. Holscher HD. Dietary fiber and prebiotics and the gastrointestinal microbiota. Gut Microbes. 2017;8:172–184. doi: 10.1080/19490976.2017.1290756. [DOI] [PMC free article] [PubMed] [Google Scholar]
  144. Huang R, Xiang J, Zhou P. Vitamin D, gut microbiota, and radiation-related resistance: a love-hate triangle. J Exp Clin Cancer Res. 2019;38:493. doi: 10.1186/s13046-019-1499-y. [DOI] [PMC free article] [PubMed] [Google Scholar]
  145. Huang S, Li N, Liu C, Li T, Wang W, Jiang L, Li Z, Han D, Tao S, Wang J. Characteristics of the gut microbiota colonization, inflammatory profile, and plasma metabolome in intrauterine growth restricted piglets during the first 12 hours after birth. J Microbiol. 2019;57:748–758. doi: 10.1007/s12275-019-8690-x. [DOI] [PubMed] [Google Scholar]
  146. Huang S, Rong X, Liu M, Liang Z, Geng Y, Wang X, Zhang J, Ji C, Zhao L, Ma Q. Intestinal mucosal immunity-mediated modulation of the gut microbiome by oral delivery of Enterococcus faecium against Salmonella enteritidis pathogenesis in a laying hen model. Front Immunol. 2022;13:853954. doi: 10.3389/fimmu.2022.853954. [DOI] [PMC free article] [PubMed] [Google Scholar]
  147. Huang, W., Ma, T., Liu, Y., Kwok, L.Y., Li, Y., Jin, H., Zhao, F., Shen, X., Shi, X., Sun, Z., et al. (2022b). Spraying compound probiotics improves growth performance and immunity and modulates gut microbiota and blood metabolites of suckling piglets. Sci China Life Sci doi: 10.1007/s11427-022-2229-1. [DOI] [PubMed]
  148. Huang Y, Ding Y, Xu H, Shen C, Chen X, Li C. Effects of sodium butyrate supplementation on inflammation, gut microbiota, and short-chain fatty acids in Helicobacter pylori-infected mice. Helicobacter. 2021;26:e12785. doi: 10.1111/hel.12785. [DOI] [PubMed] [Google Scholar]
  149. Ijssennagger N, van der Meer R, van Mil SWC. Sulfide as a mucus barrier-breaker in inflammatory bowel disease. Trends Mol Med. 2016;22:190–199. doi: 10.1016/j.molmed.2016.01.002. [DOI] [PubMed] [Google Scholar]
  150. Iwao M, Gotoh K, Arakawa M, Endo M, Honda K, Seike M, Murakami K, Shibata H. Supplementation of branched-chain amino acids decreases fat accumulation in the liver through intestinal microbiota-mediated production of acetic acid. Sci Rep. 2020;10:18768. doi: 10.1038/s41598-020-75542-3. [DOI] [PMC free article] [PubMed] [Google Scholar]
  151. Jaacks LM, Vandevijvere S, Pan A, McGowan CJ, Wallace C, Imamura F, Mozaffarian D, Swinburn B, Ezzati M. The obesity transition: stages of the global epidemic. Lancet Diabetes Endocrinol. 2019;7:231–240. doi: 10.1016/S2213-8587(19)30026-9. [DOI] [PMC free article] [PubMed] [Google Scholar]
  152. Jabara HH, Boyden SE, Chou J, Ramesh N, Massaad MJ, Benson H, Bainter W, Fraulino D, Rahimov F, Sieff C, et al. A missense mutation in TFRC, encoding transferrin receptor 1, causes combined immunodeficiency. Nat Genet. 2016;48:74–78. doi: 10.1038/ng.3465. [DOI] [PMC free article] [PubMed] [Google Scholar]
  153. Jaeggi T, Kortman GAM, Moretti D, Chassard C, Holding P, Dostal A, Boekhorst J, Timmerman HM, Swinkels DW, Tjalsma H, et al. Iron fortification adversely affects the gut microbiome, increases pathogen abundance and induces intestinal inflammation in Kenyan infants. Gut. 2015;64:731–742. doi: 10.1136/gutjnl-2014-307720. [DOI] [PubMed] [Google Scholar]
  154. Ji Y, Fan X, Zhang Y, Li J, Dai Z, Wu Z. Glycine regulates mucosal immunity and the intestinal microbial composition in weaned piglets. Amino Acids. 2022;54:385–398. doi: 10.1007/s00726-021-02976-y. [DOI] [PubMed] [Google Scholar]
  155. Jiang Y, Liu Y, Gao M, Xue M, Wang Z, Liang H. Nicotinamide riboside alleviates alcohol-induced depression-like behaviours in C57BL/6J mice by altering the intestinal microbiota associated with microglial activation and BDNF expression. Food Funct. 2020;11:378–391. doi: 10.1039/C9FO01780A. [DOI] [PubMed] [Google Scholar]
  156. Jin L, Huang Y, Yang S, Wu D, Li C, Deng W, Zhao K, He Y, Li B, Zhang G, et al. Diet, habitat environment and lifestyle conversion affect the gut microbiomes of giant pandas. Sci Total Environ. 2021;770:145316. doi: 10.1016/j.scitotenv.2021.145316. [DOI] [PubMed] [Google Scholar]
  157. Johnson CH, Dejea CM, Edler D, Hoang LT, Santidrian AF, Felding BH, Ivanisevic J, Cho K, Wick EC, Hechenbleikner E M, et al. Metabolism links bacterial biofilms and colon carcinogenesis. Cell Metab. 2015;21:891–897. doi: 10.1016/j.cmet.2015.04.011. [DOI] [PMC free article] [PubMed] [Google Scholar]
  158. Kaliannan K, Wang B, Li XY, Kim KJ, Kang JX. A host-microbiome interaction mediates the opposing effects of omega-6 and omega-3 fatty acids on metabolic endotoxemia. Sci Rep. 2015;5:11276. doi: 10.1038/srep11276. [DOI] [PMC free article] [PubMed] [Google Scholar]
  159. Kang K, Sun Y, Pan D, Chang B, Sang LX. Nicotinamide ameliorates dextran sulfate sodium-induced chronic colitis in mice through its anti-inflammatory properties and modulates the gut micro-biota. J Immunol Res. 2021;2021:5084713. doi: 10.1155/2021/5084713. [DOI] [PMC free article] [PubMed] [Google Scholar]
  160. Kang M, Yin J, Ma J, Wu X, Huang K, Li T, Ouyang L. Effects of dietary histidine on growth performance, serum amino acids, and intestinal morphology and microbiota communities in low protein diet-fed piglets. Mediators Inflamm. 2020;2020:1240152. doi: 10.1155/2020/1240152. [DOI] [PMC free article] [PubMed] [Google Scholar]
  161. Katsarou MS, Papasavva M, Latsi R, Drakoulis N. Hemochromatosis: hereditary hemochromatosis and HFE gene. Vitamins Hormones. 2019;110:201–222. doi: 10.1016/bs.vh.2019.01.010. [DOI] [PubMed] [Google Scholar]
  162. Kayama H, Okumura R, Takeda K. Interaction between the microbiota, epithelia, and immune cells in the intestine. Annu Rev Immunol. 2020;38:23–48. doi: 10.1146/annurev-immunol-070119-115104. [DOI] [PubMed] [Google Scholar]
  163. Khan MT, Browne WR, van Dijl JM, Harmsen HJM. How can Faecalibacterium prausnitzii employ riboflavin for extracellular electron transfer. Antioxid Redox Signal. 2012;17:1433–1440. doi: 10.1089/ars.2012.4701. [DOI] [PubMed] [Google Scholar]
  164. Kibe R, Kurihara S, Sakai Y, Suzuki H, Ooga T, Sawaki E, Muramatsu K, Nakamura A, Yamashita A, Kitada Y, et al. Upregulation of colonic luminal polyamines produced by intestinal microbiota delays senescence in mice. Sci Rep. 2014;4:4548. doi: 10.1038/srep04548. [DOI] [PMC free article] [PubMed] [Google Scholar]
  165. Kim CH. Control of lymphocyte functions by gut microbiota-derived short-chain fatty acids. Cell Mol Immunol. 2021;18:1161–1171. doi: 10.1038/s41423-020-00625-0. [DOI] [PMC free article] [PubMed] [Google Scholar]
  166. Kim M, Cho JH, Seong PN, Jung H, Jeong JY, Kim S, Kim H, Kim ES, Keum GB, Guevarra RB, et al. Fecal microbiome shifts by different forms of copper supplementations in growing pigs. J Anim Sci Technol. 2021;63:1386–1396. doi: 10.5187/jast.2021.e118. [DOI] [PMC free article] [PubMed] [Google Scholar]
  167. Kim Y, Hwang SW, Kim S, Lee YS, Kim TY, Lee SH, Kim SJ, Yoo HJ, Kim EN, Kweon MN. Dietary cellulose prevents gut inflammation by modulating lipid metabolism and gut microbiota. Gut Microbes. 2020;11:944–961. doi: 10.1080/19490976.2020.1730149. [DOI] [PMC free article] [PubMed] [Google Scholar]
  168. Kishino S, Takeuchi M, Park SB, Hirata A, Kitamura N, Kunisawa J, Kiyono H, Iwamoto R, Isobe Y, Arita M, et al. Polyunsaturated fatty acid saturation by gut lactic acid bacteria affecting host lipid composition. Proc Natl Acad Sci USA. 2013;110:17808–17813. doi: 10.1073/pnas.1312937110. [DOI] [PMC free article] [PubMed] [Google Scholar]
  169. Kitada Y, Muramatsu K, Toju H, Kibe R, Benno Y, Kurihara S, Matsumoto M. Bioactive polyamine production by a novel hybrid system comprising multiple indigenous gut bacterial strategies. Sci Adv. 2018;4:eaat0062. doi: 10.1126/sciadv.aat0062. [DOI] [PMC free article] [PubMed] [Google Scholar]
  170. Kjølbæk L, Benítez-Páez A, Gómez del Pulgar EM, Brahe LK, Liebisch G, Matysik S, Rampelli S, Vermeiren J, Brigidi P, Larsen LH, et al. Arabinoxylan oligosaccharides and polyunsaturated fatty acid effects on gut microbiota and metabolic markers in overweight individuals with signs of metabolic syndrome: A randomized cross-over trial. Clin Nutr. 2020;39:67–79. doi: 10.1016/j.clnu.2019.01.012. [DOI] [PubMed] [Google Scholar]
  171. Knorr S, Sinn M, Galetskiy D, Williams RM, Wang C, Müller N, Mayans O, Schleheck D, Hartig JS. Widespread bacterial lysine degradation proceeding via glutarate and L-2-hydroxyglutarate. Nat Commun. 2018;9:5071. doi: 10.1038/s41467-018-07563-6. [DOI] [PMC free article] [PubMed] [Google Scholar]
  172. Kociova S, Dolezelikova K, Horky P, Skalickova S, Baholet D, Bozdechova L, Vaclavkova E, Belkova J, Nevrkla P, Skladanka J, et al. Zinc phosphate-based nanoparticles as alternatives to zinc oxide in diet of weaned piglets. J Anim Sci Biotechnol. 2020;11:59. doi: 10.1186/s40104-020-00458-x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  173. Koh A, De Vadder F, Kovatcheva-Datchary P, Bäckhed F. From dietary fiber to host physiology: short-chain fatty acids as key bacterial metabolites. Cell. 2016;165:1332–1345. doi: 10.1016/j.cell.2016.05.041. [DOI] [PubMed] [Google Scholar]
  174. Kramer J, Özkaya Ö, Kümmerli R. Bacterial siderophores in community and host interactions. Nat Rev Microbiol. 2020;18:152–163. doi: 10.1038/s41579-019-0284-4. [DOI] [PMC free article] [PubMed] [Google Scholar]
  175. Krautkramer KA, Fan J, Bäckhed F. Gut microbial metabolites as multi-kingdom intermediates. Nat Rev Microbiol. 2021;19:77–94. doi: 10.1038/s41579-020-0438-4. [DOI] [PubMed] [Google Scholar]
  176. Kreuzer-Redmer S, Arends D, Schulte JN, Karweina D, Korkuc P, Wöltje N, Hesse D, Pieper R, Gerdts V, Zentek J, et al. High dosage of zinc modulates T-cells in a time-dependent manner within porcine gut-associated lymphatic tissue. Br J Nutr. 2018;120:1349–1358. doi: 10.1017/S0007114518002908. [DOI] [PubMed] [Google Scholar]
  177. Kumagai S, Koyama S, Itahashi K, Tanegashima T, Lin Y, Togashi Y, Kamada T, Irie T, Okumura G, Kono H, et al. Lactic acid promotes PD-1 expression in regulatory T cells in highly glycolytic tumor microenvironments. Cancer Cell. 2022;40:201–218. doi: 10.1016/j.ccell.2022.01.001. [DOI] [PubMed] [Google Scholar]
  178. La Carpia F, Wojczyk BS, Annavajhala MK, Rebbaa A, Culp-Hill R, D’Alessandro A, Freedberg DE, Uhlemann AC, Hod EA. Transfusional iron overload and intravenous iron infusions modify the mouse gut microbiota similarly to dietary iron. npj Biofilms Microbiomes. 2019;5:26. doi: 10.1038/s41522-019-0097-2. [DOI] [PMC free article] [PubMed] [Google Scholar]
  179. Lai Y, Masatoshi H, Ma Y, Guo Y, Zhang B. Role of vitamin K in intestinal health. Front Immunol. 2021;12:791565. doi: 10.3389/fimmu.2021.791565. [DOI] [PMC free article] [PubMed] [Google Scholar]
  180. Lam YY, Ha CWY, Hoffmann JMA, Oscarsson J, Dinudom A, Mather TJ, Cook DI, Hunt NH, Caterson ID, Holmes AJ, et al. Effects of dietary fat profile on gut permeability and microbiota and their relationships with metabolic changes in mice. Obesity. 2015;23:1429–1439. doi: 10.1002/oby.21122. [DOI] [PubMed] [Google Scholar]
  181. Landete JM, Arena ME, Pardo I, Manca de Nadra MC, Ferrer S. The role of two families of bacterial enzymes in putrescine synthesis from agmatine via agmatine deiminase. Int Microbiol. 2010;13:169–177. doi: 10.2436/20.1501.01.123. [DOI] [PubMed] [Google Scholar]
  182. Larsen N, Vogensen FK, van den Berg FW, Nielsen DS, Andreasen AS, Pedersen BK, Al-Soud WA, Sorensen SJ, Hansen LH, Jakobsen M. Gut microbiota in human adults with type 2 diabetes differs from non-diabetic adults. PLoS ONE. 2010;5:e9085. doi: 10.1371/journal.pone.0009085. [DOI] [PMC free article] [PubMed] [Google Scholar]
  183. Lee C, Kim BG, Kim JH, Chun J, Im JP, Kim JS. Sodium butyrate inhibits the NF-kappa B signaling pathway and histone deacetylation, and attenuates experimental colitis in an IL-10 independent manner. Int Immunopharmacol. 2017;51:47–56. doi: 10.1016/j.intimp.2017.07.023. [DOI] [PubMed] [Google Scholar]
  184. Lee HC, Yu SC, Lo YC, Lin IH, Tung TH, Huang SY. A high linoleic acid diet exacerbates metabolic responses and gut microbiota dysbiosis in obese rats with diabetes mellitus. Food Funct. 2019;10:786–798. doi: 10.1039/C8FO02423E. [DOI] [PubMed] [Google Scholar]
  185. Lee PC, Hsieh YC, Huo TI, Yang UC, Lin CH, Li CP, Huang Y H, Hou MC, Lin HC, Lee KC. Active vitamin D3 treatment attenuated bacterial translocation via improving intestinal barriers in cirrhotic rats. Mol Nutr Food Res. 2021;65:2000937. doi: 10.1002/mnfr.202000937. [DOI] [PubMed] [Google Scholar]
  186. Lee T, Clavel T, Smirnov K, Schmidt A, Lagkouvardos I, Walker A, Lucio M, Michalke B, Schmitt-Kopplin P, Fedorak R, et al. Oral versus intravenous iron replacement therapy distinctly alters the gut microbiota and metabolome in patients with IBD. Gut. 2017;66:863–871. doi: 10.1136/gutjnl-2015-309940. [DOI] [PMC free article] [PubMed] [Google Scholar]
  187. Li H, Zhu Y, Zhao F, Song S, Li Y, Xu X, Zhou G, Li C. Fish oil, lard and soybean oil differentially shape gut microbiota of middle-aged rats. Sci Rep. 2017;7:826. doi: 10.1038/s41598-017-00969-0. [DOI] [PMC free article] [PubMed] [Google Scholar]
  188. Li JM, Yu R, Zhang LP, Wen SY, Wang SJ, Zhang XY, Xu Q, Kong LD. Dietary fructose-induced gut dysbiosis promotes mouse hippocampal neuroinflammation: a benefit of short-chain fatty acids. Microbiome. 2019;7:98. doi: 10.1186/s40168-019-0713-7. [DOI] [PMC free article] [PubMed] [Google Scholar]
  189. Li KH, Yu YH, Dong HJ, Zhang WB, Ma JC, Wang HH. Biological functions of ilvC in branched-chain fatty acid synthesis and diffusible signal factor family production in Xanthomonas campestris. Front Microbiol. 2017;8:2486. doi: 10.3389/fmicb.2017.02486. [DOI] [PMC free article] [PubMed] [Google Scholar]
  190. Li S, You J, Wang Z, Liu Y, Wang B, Du M, Zou T. Curcumin alleviates high-fat diet-induced hepatic steatosis and obesity in association with modulation of gut microbiota in mice. Food Res Int. 2021;143:110270. doi: 10.1016/j.foodres.2021.110270. [DOI] [PubMed] [Google Scholar]
  191. Li Y, Han H, Yin J, He X, Tang Z, Li T, Yao K, Yin Y. D- and L-aspartate regulates growth performance, inflammation and intestinal microbial community in young pigs. Food Funct. 2019;10:1028–1037. doi: 10.1039/C8FO01410H. [DOI] [PubMed] [Google Scholar]
  192. Li Y, Salih Ibrahim RM, Chi HL, Xiao T, Xia WJ, Li HB, Kang YM. Altered gut microbiota is involved in the anti-hypertensive effects of vitamin C in spontaneously hypertensive rat. Mol Nutr Food Res. 2021;65:2000885. doi: 10.1002/mnfr.202000885. [DOI] [PubMed] [Google Scholar]
  193. Li Z, Dong Y, Chen S, Jia X, Jiang X, Che L, Lin Y, Li J, Feng B, Fang Z, et al. Organic selenium increased gilts antioxidant capacity, immune function, and changed intestinal microbiota. Front Microbiol. 2021;12:723190. doi: 10.3389/fmicb.2021.723190. [DOI] [PMC free article] [PubMed] [Google Scholar]
  194. Liang H, Dai Z, Liu N, Ji Y, Chen J, Zhang Y, Yang Y, Li J, Wu Z, Wu G. Dietary L-tryptophan modulates the structural and functional composition of the intestinal microbiome in weaned piglets. Front Microbiol. 2018;9:1736. doi: 10.3389/fmicb.2018.01736. [DOI] [PMC free article] [PubMed] [Google Scholar]
  195. Liang L, Xiong Q, Kong J, Tian C, Miao L, Zhang X, Du H. Intraperitoneal supplementation of iron alleviates dextran sodium sulfate-induced colitis by enhancing intestinal barrier function. Biomed Pharmacother. 2021;144:112253. doi: 10.1016/j.biopha.2021.112253. [DOI] [PubMed] [Google Scholar]
  196. Liao Y, Fan L, Bin P, Zhu C, Chen Q, Cai Y, Duan J, Cai Q, Han W, Ding S, et al. GABA signaling enforces intestinal germinal center B cell differentiation. Proc Natl Acad Sci USA. 2022;119:e2215921119. doi: 10.1073/pnas.2215921119. [DOI] [PMC free article] [PubMed] [Google Scholar]
  197. Lin R, Liu W, Piao M, Zhu H. A review of the relationship between the gut microbiota and amino acid metabolism. Amino Acids. 2017;49:2083–2090. doi: 10.1007/s00726-017-2493-3. [DOI] [PubMed] [Google Scholar]
  198. Lindstad LJ, Lo G, Leivers S, Lu Z, Michalak L, Pereira GV, RøhrÅ K, Martens EC, McKee LS, Louis P, et al. Human gut Faecalibacterium prausnitzii deploys a highly efficient conserved system to cross-feed on β-mannan-derived oligosaccharides. mBio. 2021;12:e0362820. doi: 10.1128/mBio.03628-20. [DOI] [PMC free article] [PubMed] [Google Scholar]
  199. Ling C, Miao Z, Xiao M, Zhou H, Jiang Z, Fu Y, Xiong F, Zuo L, Liu Y, Wu Y, et al. The association of gut microbiota with osteoporosis is mediated by amino acid metabolism: multiomics in a large cohort. J Clin Endocrinol Metab. 2021;106:e3852–e3864. doi: 10.1210/clinem/dgab492. [DOI] [PubMed] [Google Scholar]
  200. Liu B, Yu D, Sun J, Wu X, Xin Z, Deng B, Fan L, Fu J, Ge L, Ren W. Characterizing the influence of gut microbiota on host tryptophan metabolism with germ-free pigs. Anim Nutr. 2022;11:190–200. doi: 10.1016/j.aninu.2022.07.005. [DOI] [PMC free article] [PubMed] [Google Scholar]
  201. Liu F, Smith AD, Solano-Aguilar G, Wang TTY, Pham Q, Beshah E, Tang Q, Urban JF, Jr, Xue C, Li RW. Mechanistic insights into the attenuation of intestinal inflammation and modulation of the gut microbiome by krill oil using in vitro and in vivo models. Microbiome. 2020;8:83. doi: 10.1186/s40168-020-00843-8. [DOI] [PMC free article] [PubMed] [Google Scholar]
  202. Liu H, Li X, Zhu Y, Huang Y, Zhang Q, Lin S, Fang C, Li L, Lv Y, Mei W, et al. Effect of plant-derived n-3 polyunsaturated fatty acids on blood lipids and gut microbiota: a double-blind randomized controlled trial. Front Nutr. 2022;9:830960. doi: 10.3389/fnut.2022.830960. [DOI] [PMC free article] [PubMed] [Google Scholar]
  203. Liu HQ, Qiu Y, Mu Y, Zhang XJ, Liu L, Hou XH, Zhang L, Xu XN, Ji AL, Cao R, et al. A high ratio of dietary n-3/n-6 polyunsaturated fatty acids improves obesity-linked inflammation and insulin resistance through suppressing activation of TLR4 in SD rats. Nutr Res. 2013;33:849–858. doi: 10.1016/j.nutres.2013.07.004. [DOI] [PubMed] [Google Scholar]
  204. Liu KY, Nakatsu CH, Jones-Hall Y, Kozik A, Jiang Q. Vitamin E alpha- and gamma-tocopherol mitigate colitis, protect intestinal barrier function and modulate the gut microbiota in mice. Free Radic Biol Med. 2021;163:180–189. doi: 10.1016/j.freeradbiomed.2020.12.017. [DOI] [PubMed] [Google Scholar]
  205. Liu L, Fu C, Li F. Acetate affects the process of lipid metabolism in rabbit liver, skeletal muscle and adipose tissue. Animals. 2019;9:799. doi: 10.3390/ani9100799. [DOI] [PMC free article] [PubMed] [Google Scholar]
  206. Liu S, Yu H, Li P, Wang C, Liu G, Zhang X, Zhang C, Qi M, Ji H. Dietary nano-selenium alleviated intestinal damage of juvenile grass carp (Ctenopharyngodon idella) induced by high-fat diet: Insight from intestinal morphology, tight junction, inflammation, anti-oxidization and intestinal microbiota. Anim Nutr. 2022;8:235–248. doi: 10.1016/j.aninu.2021.07.001. [DOI] [PMC free article] [PubMed] [Google Scholar]
  207. Liu T, Li J, Liu Y, Xiao N, Suo H, Xie K, Yang C, Wu C. Short-chain fatty acids suppress lipopolysaccharide-induced production of nitric oxide and proinflammatory cytokines through inhibition of NF-κB pathway in RAW264.7 cells. Inflammation. 2012;35:1676–1684. doi: 10.1007/s10753-012-9484-z. [DOI] [PubMed] [Google Scholar]
  208. Liu W, Crott JW, Lyu L, Pfalzer AC, Li J, Choi SW, Yang Y, Mason JB, Liu Z. Diet- and genetically-induced obesity produces alterations in the microbiome, inflammation and Wnt pathway in the intestine of Apc+/1638N mice: comparisons and contrasts. J Cancer. 2016;7:1780–1790. doi: 10.7150/jca.15792. [DOI] [PMC free article] [PubMed] [Google Scholar]
  209. Liu Y, Hou Y, Wang G, Zheng X, Hao H. Gut microbial metabolites of aromatic amino acids as signals in host-microbe interplay. Trends Endocrinol Metab. 2020;31:818–834. doi: 10.1016/j.tem.2020.02.012. [DOI] [PubMed] [Google Scholar]
  210. Liu Y, Jia Y, Yang K, Tong Z, Shi J, Li R, Xiao X, Ren W, Hardeland R, Reiter RJ, et al. Melatonin overcomes MCR-mediated colistin resistance in Gram-negative pathogens. Theranostics. 2020;10:10697–10711. doi: 10.7150/thno.45951. [DOI] [PMC free article] [PubMed] [Google Scholar]
  211. Liu Y, Yang J, Liu X, Liu R, Wang Y, Huang X, Li Y, Liu R, Yang X. Dietary folic acid addition reduces abdominal fat deposition mediated by alterations in gut microbiota and SCFA production in broilers. Anim Nutr. 2023;12:54–62. doi: 10.1016/j.aninu.2022.08.013. [DOI] [PMC free article] [PubMed] [Google Scholar]
  212. Lloyd-Price J, Arze C, Ananthakrishnan AN, Schirmer M, Avila-Pacheco J, Poon TW, Andrews E, Ajami NJ, Bonham KS, Brislawn CJ, et al. Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases. Nature. 2019;569:655–662. doi: 10.1038/s41586-019-1237-9. [DOI] [PMC free article] [PubMed] [Google Scholar]
  213. Lombard V, Golaconda Ramulu H, Drula E, Coutinho PM, Henrissat B. The carbohydrate-active enzymes database (CAZy) in 2013. Nucl Acids Res. 2014;42:D490–D495. doi: 10.1093/nar/gkt1178. [DOI] [PMC free article] [PubMed] [Google Scholar]
  214. López-Colom P, Castillejos L, Rodríguez-Sorrento A, Puyalto M, Mallo JJ, Martín-Orúe SM. Efficacy of medium-chain fatty acid salts distilled from coconut oil against two enteric pathogen challenges in weanling piglets. J Anim Sci Biotechnol. 2019;10:89. doi: 10.1186/s40104-019-0393-y. [DOI] [PMC free article] [PubMed] [Google Scholar]
  215. Lozada-Fernandez VV, deLeon O, Kellogg SL, Saravia FL, Hadiono MA, Atkinson SN, Grobe JL, Kirby JR. Nicotinamide riboside-conditioned microbiota deflects high-fat diet-induced weight gain in mice. mSystems. 2022;7:e0023021. doi: 10.1128/msystems.00230-21. [DOI] [PMC free article] [PubMed] [Google Scholar]
  216. Lu X, Wang F. Lactobacillus acidophilus and vitamin C attenuate ethanol-induced intestinal and liver injury in mice. Exp Ther Med. 2021;22:1005. doi: 10.3892/etm.2021.10438. [DOI] [PMC free article] [PubMed] [Google Scholar]
  217. Luisi MLE, Lucarini L, Biffi B, Rafanelli E, Pietramellara G, Durante M, Vidali S, Provensi G, Madiai S, Gheri CF, et al. Effect of mediterranean diet enriched in high quality extra virgin olive oil on oxidative stress, inflammation and gut microbiota in obese and normal weight adult subjects. Front Pharmacol. 2019;10:1366. doi: 10.3389/fphar.2019.01366. [DOI] [PMC free article] [PubMed] [Google Scholar]
  218. Luu M, Visekruna A. Short-chain fatty acids: bacterial messengers modulating the immunometabolism of T cells. Eur J Immunol. 2019;49:842–848. doi: 10.1002/eji.201848009. [DOI] [PubMed] [Google Scholar]
  219. Lv Z, Wang Y, Yang T, Zhan X, Li Z, Hu H, Li T, Chen J. Vitamin A deficiency impacts the structural segregation of gut microbiota in children with persistent diarrhea. J Clin Biochem Nutr. 2016;59:113–121. doi: 10.3164/jcbn.15-148. [DOI] [PMC free article] [PubMed] [Google Scholar]
  220. Ma, J., Zhu, Y., Wang, Z., Yu, X., Hu, R., Wang, X., Cao, G., Zou, H., Shah, A.M., Peng, Q., et al. (2021a). Glutamine supplementation affected the gut bacterial community and fermentation leading to improved nutrient digestibility in growth-retarded yaks. FEMS Microbiol Ecol 97. [DOI] [PubMed]
  221. Ma N, Ma X. Dietary amino acids and the gut-microbiome-immune axis: physiological metabolism and therapeutic prospects. Compr Rev Food Sci Food Saf. 2019;18:221–242. doi: 10.1111/1541-4337.12401. [DOI] [PubMed] [Google Scholar]
  222. Ma Y, Wang C, Zhang H, Yu L, Dong L, Gong D, Yao J, Wang H. Illumina sequencing and metabolomics analysis reveal thiamine modulation of ruminal microbiota and metabolome characteristics in goats fed a high-concentrate diet. Front Microbiol. 2021;12:653283. doi: 10.3389/fmicb.2021.653283. [DOI] [PMC free article] [PubMed] [Google Scholar]
  223. Maares M, Haase H. Zinc and immunity: An essential interrelation. Arch Biochem Biophys. 2016;611:58–65. doi: 10.1016/j.abb.2016.03.022. [DOI] [PubMed] [Google Scholar]
  224. Macias-Ceja DC, Ortiz-Masiá D, Salvador P, Gisbert-Ferrándiz L, Hernández C, Hausmann M, Rogler G, Esplugues JV, Hinojosa J, Alós R, et al. Succinate receptor mediates intestinal inflammation and fibrosis. Mucosal Immunol. 2019;12:178–187. doi: 10.1038/s41385-018-0087-3. [DOI] [PubMed] [Google Scholar]
  225. Magnúsdóttir S, Ravcheev D, de Crécy-Lagard V, Thiele I. Systematic genome assessment of B-vitamin biosynthesis suggests cooperation among gut microbes. Front Genet. 2015;6:148. doi: 10.3389/fgene.2015.00148. [DOI] [PMC free article] [PubMed] [Google Scholar]
  226. Mahalhal A, Williams JM, Johnson S, Ellaby N, Duckworth CA, Burkitt MD, Liu X, Hold GL, Campbell BJ, Pritchard DM, et al. Oral iron exacerbates colitis and influences the intestinal microbiome. PLoS ONE. 2018;13:e0202460. doi: 10.1371/journal.pone.0202460. [DOI] [PMC free article] [PubMed] [Google Scholar]
  227. Maharshak N, Ryu HS, Fan TJ, Onyiah JC, Schulz S, Otterbein S L, Wong R, Hansen JJ, Otterbein LE, Carroll IM, et al. Escherichia coli heme oxygenase modulates host innate immune responses. Microbiol Immunol. 2015;59:452–465. doi: 10.1111/1348-0421.12282. [DOI] [PMC free article] [PubMed] [Google Scholar]
  228. Makki K, Deehan EC, Walter J, Bäckhed F. The impact of dietary fiber on gut microbiota in host health and disease. Cell Host Microbe. 2018;23:705–715. doi: 10.1016/j.chom.2018.05.012. [DOI] [PubMed] [Google Scholar]
  229. Malerba M, Louis S, Cuvellier S, Shambat SM, Hua C, Gomart C, Fouet A, Ortonne N, Decousser JW, Zinkernagel AS, et al. Epidermal hepcidin is required for neutrophil response to bacterial infection. J Clin Invest. 2020;130:329–334. doi: 10.1172/JCI126645. [DOI] [PMC free article] [PubMed] [Google Scholar]
  230. Mandal S, Godfrey KM, McDonald D, Treuren WV, Bjørnholt JV, Midtvedt T, Moen B, Rudi K, Knight R, Brantsæter AL, et al. Fat and vitamin intakes during pregnancy have stronger relations with a pro-inflammatory maternal microbiota than does carbohydrate intake. Microbiome. 2016;4:55. doi: 10.1186/s40168-016-0200-3. [DOI] [PMC free article] [PubMed] [Google Scholar]
  231. Manukhov IV, Mamaeva DV, Rastorguev SM, Faleev NG, Morozova EA, Demidkina TV, Zavilgelsky GB. A gene encoding L-methionine γ-lyase is present in Enterobacteriaceae family genomes: identification and characterization of Citrobacter freundii L-methionine γ-Lyase. J Bacteriol. 2005;187:3889–3893. doi: 10.1128/JB.187.11.3889-3893.2005. [DOI] [PMC free article] [PubMed] [Google Scholar]
  232. Mardinoglu A, Shoaie S, Bergentall M, Ghaffari P, Zhang C, Larsson E, Bäckhed F, Nielsen J. The gut microbiota modulates host amino acid and glutathione metabolism in mice. Mol Syst Biol. 2015;11:834. doi: 10.15252/msb.20156487. [DOI] [PMC free article] [PubMed] [Google Scholar]
  233. Mardinoglu A, Wu H, Bjornson E, Zhang C, Hakkarainen A, Räsänen SM, Lee S, Mancina RM, Bergentall M, Pietiläinen K H, et al. An integrated understanding of the rapid metabolic benefits of a carbohydrate-restricted diet on hepatic steatosis in humans. Cell Metab 27. 2018;559–571:e5. doi: 10.1016/j.cmet.2018.01.005. [DOI] [PMC free article] [PubMed] [Google Scholar]
  234. Martín-Peláez S, Mosele JI, Pizarro N, Farràs M, de la Torre R, Subirana I, Pérez-Cano FJ, Castañer O, Solà R, Fernandez-Castillejo S, et al. Effect of virgin olive oil and thyme phenolic compounds on blood lipid profile: implications of human gut microbiota. Eur J Nutr. 2017;56:119–131. doi: 10.1007/s00394-015-1063-2. [DOI] [PubMed] [Google Scholar]
  235. Martinez-Guryn K, Hubert N, Frazier K, Urlass S, Musch MW, Ojeda P, Pierre JF, Miyoshi J, Sontag TJ, Cham CM, et al. Small intestine microbiota regulate host digestive and absorptive adaptive responses to dietary lipids. Cell Host Microbe. 2018;23:458–469. doi: 10.1016/j.chom.2018.03.011. [DOI] [PMC free article] [PubMed] [Google Scholar]
  236. Matsumoto M, Kurihara S, Kibe R, Ashida H, Benno Y. Longevity in mice is promoted by probiotic-induced suppression of colonic senescence dependent on upregulation of gut bacterial polyamine production. PLoS ONE. 2011;6:e23652. doi: 10.1371/journal.pone.0023652. [DOI] [PMC free article] [PubMed] [Google Scholar]
  237. Mayengbam S, Chleilat F, Reimer RA. Dietary vitamin B6 deficiency impairs gut microbiota and host and microbial metabolites in rats. Biomedicines. 2020;8:469. doi: 10.3390/biomedicines8110469. [DOI] [PMC free article] [PubMed] [Google Scholar]
  238. Mayneris-Perxachs J, Bolick DT, Leng J, Medlock GL, Kolling G L, Papin JA, Swann JR, Guerrant RL. Protein- and zinc-deficient diets modulate the murine microbiome and metabolic phenotype. Am J Clin Nutr. 2016;104:1253–1262. doi: 10.3945/ajcn.116.131797. [DOI] [PMC free article] [PubMed] [Google Scholar]
  239. Mayneris-Perxachs J, Castells-Nobau A, Arnoriaga-Rodríguez M, Martin M, de la Vega-Correa L, Zapata C, Burokas A, Blasco G, Coll C, Escrichs A, et al. Microbiota alterations in proline metabolism impact depression. Cell Metab. 2022;34:681–701. doi: 10.1016/j.cmet.2022.04.001. [DOI] [PubMed] [Google Scholar]
  240. Melkebeek V, Rasschaert K, Bellot P, Tilleman K, Favoreel H, Deforce D, De Geest BG, Goddeeris BM, Cox E. Targeting aminopeptidase N, a newly identified receptor for F4ac fimbriae, enhances the intestinal mucosal immune response. Mucosal Immunol. 2012;5:635–645. doi: 10.1038/mi.2012.37. [DOI] [PMC free article] [PubMed] [Google Scholar]
  241. Merra G, Noce A, Marrone G, Cintoni M, Tarsitano MG, Capacci A, De Lorenzo A. Influence of mediterranean diet on human gut microbiota. Nutrients. 2021;13:7. doi: 10.3390/nu13010007. [DOI] [PMC free article] [PubMed] [Google Scholar]
  242. Miller KA, Vicentini FA, Hirota SA, Sharkey KA, Wieser ME. Antibiotic treatment affects the expression levels of copper transporters and the isotopic composition of copper in the colon of mice. Proc Natl Acad Sci USA. 2019;116:5955–5960. doi: 10.1073/pnas.1814047116. [DOI] [PMC free article] [PubMed] [Google Scholar]
  243. Miyamoto J, Igarashi M, Watanabe K, Karaki S, Mukouyama H, Kishino S, Li X, Ichimura A, Irie J, Sugimoto Y, et al. Gut microbiota confers host resistance to obesity by metabolizing dietary polyunsaturated fatty acids. Nat Commun. 2019;10:4007. doi: 10.1038/s41467-019-11978-0. [DOI] [PMC free article] [PubMed] [Google Scholar]
  244. Mjaaseth UN, Norris JC, Aardema NDJ, Bunnell ML, Ward RE, Hintze KJ, Cho CE. Excess vitamins or imbalance of folic acid and choline in the gestational diet alter the gut microbiota and obesogenic effects in Wistar rat offspring. Nutrients. 2021;13:4510. doi: 10.3390/nu13124510. [DOI] [PMC free article] [PubMed] [Google Scholar]
  245. Moscoviz R, Kleerebezem R, Rombouts JL. Directing carbohydrates toward ethanol using mesophilic microbial communities. Curr Opin Biotechnol. 2021;67:175–183. doi: 10.1016/j.copbio.2021.01.016. [DOI] [PubMed] [Google Scholar]
  246. Mou Z, Yang Y, Hall AB, Jiang X. The taxonomic distribution of histamine-secreting bacteria in the human gut microbiome. BMC Genomics. 2021;22:695. doi: 10.1186/s12864-021-08004-3. [DOI] [PMC free article] [PubMed] [Google Scholar]
  247. Mousavi S, Bereswill S, Heimesaat MM. Immunomodulatory and antimicrobial effects of vitamin C. Eur J Microbiol Immunol. 2019;9:73–79. doi: 10.1556/1886.2019.00016. [DOI] [PMC free article] [PubMed] [Google Scholar]
  248. Muckenthaler MU, Rivella S, Hentze MW, Galy B. A red carpet for iron metabolism. Cell. 2017;168:344–361. doi: 10.1016/j.cell.2016.12.034. [DOI] [PMC free article] [PubMed] [Google Scholar]
  249. Nagashimada M, Ota T. Role of vitamin E in nonalcoholic fatty liver disease. IUBMB Life. 2019;71:516–522. doi: 10.1002/iub.1991. [DOI] [PubMed] [Google Scholar]
  250. Nairz M, Ferring-Appel D, Casarrubea D, Sonnweber T, Viatte L, Schroll A, Haschka D, Fang FC, Hentze MW, Weiss G, et al. Iron regulatory proteins mediate host resistance to Salmonella infection. Cell Host Microbe. 2015;18:254–261. doi: 10.1016/j.chom.2015.06.017. [DOI] [PMC free article] [PubMed] [Google Scholar]
  251. Nakamura A, Kurihara S, Takahashi D, Ohashi W, Nakamura Y, Kimura S, Onuki M, Kume A, Sasazawa Y, Furusawa Y, et al. Symbiotic polyamine metabolism regulates epithelial proliferation and macrophage differentiation in the colon. Nat Commun. 2021;12:2105. doi: 10.1038/s41467-021-22212-1. [DOI] [PMC free article] [PubMed] [Google Scholar]
  252. Naraoka Y, Yamaguchi T, Hu A, Akimoto K, Kobayashi H. Short chain fatty acids upregulate adipokine production in type 2 diabetes derived human adipocytes. Acta Endo (Buc) 2018;14:287–293. doi: 10.4183/aeb.2018.287. [DOI] [PMC free article] [PubMed] [Google Scholar]
  253. Narayan V, Kudva AK, Prabhu KS. Reduction of tetrathionate by mammalian thioredoxin reductase. Biochemistry. 2015;54:5121–5124. doi: 10.1021/acs.biochem.5b00620. [DOI] [PMC free article] [PubMed] [Google Scholar]
  254. Nastasi C, Fredholm S, Willerslev-Olsen A, Hansen M, Bonefeld C M, Geisler C, Andersen MH, Ødum N, Woetmann A. Butyrate and propionate inhibit antigen-specific CD8+ T cell activation by suppressing IL-12 production by antigen-presenting cells. Sci Rep. 2017;7:14516. doi: 10.1038/s41598-017-15099-w. [DOI] [PMC free article] [PubMed] [Google Scholar]
  255. Nayak S, Al Ashhab A, Zilberg D, Khozin-Goldberg I. Dietary supplementation with omega-6 LC-PUFA-rich microalgae regulates mucosal immune response and promotes microbial diversity in the zebrafish gut. Biology. 2020;9:119. doi: 10.3390/biology9060119. [DOI] [PMC free article] [PubMed] [Google Scholar]
  256. Needham BD, Funabashi M, Adame MD, Wang Z, Boktor JC, Haney J, Wu WL, Rabut C, Ladinsky MS, Hwang SJ, et al. A gut-derived metabolite alters brain activity and anxiety behaviour in mice. Nature. 2022;602:647–653. doi: 10.1038/s41586-022-04396-8. [DOI] [PMC free article] [PubMed] [Google Scholar]
  257. Neis E, Dejong C, Rensen S. The role of microbial amino acid metabolism in host metabolism. Nutrients. 2015;7:2930–2946. doi: 10.3390/nu7042930. [DOI] [PMC free article] [PubMed] [Google Scholar]
  258. Neophytou C, Pitsouli C. Biotin controls intestinal stem cell mitosis and host-microbiome interactions. Cell Rep. 2022;38:110505. doi: 10.1016/j.celrep.2022.110505. [DOI] [PubMed] [Google Scholar]
  259. Nettleford S, Prabhu K. Selenium and selenoproteins in gut inflammation—a review. Antioxidants. 2018;7:36. doi: 10.3390/antiox7030036. [DOI] [PMC free article] [PubMed] [Google Scholar]
  260. Nettleford SK, Zhao L, Qian F, Herold M, Arner B, Desai D, Amin S, Xiong N, Singh V, Carlson BA, et al. The essential role of selenoproteins in the resolution of citrobacter rodentium-induced intestinal inflammation. Front Nutr. 2020;7:96. doi: 10.3389/fnut.2020.00096. [DOI] [PMC free article] [PubMed] [Google Scholar]
  261. Nichenametla SN, Mattocks DAL, Midya V, Shneyder J. Differential effects of sulfur amino acid-restricted and low-calorie diets on gut microbiome profile and bile acid composition in male C57BL6/J mice. J Gerontol A Biol Sci Med Sci. 2021;76:1922–1929. doi: 10.1093/gerona/glaa270. [DOI] [PMC free article] [PubMed] [Google Scholar]
  262. Nogal A, Valdes AM, Menni C. The role of short-chain fatty acids in the interplay between gut microbiota and diet in cardiometabolic health. Gut Microbes. 2021;13:1–24. doi: 10.1080/19490976.2021.1897212. [DOI] [PMC free article] [PubMed] [Google Scholar]
  263. O’Grady J, O’Connor EM, Shanahan F. Review article: dietary fibre in the era of microbiome science. Aliment Pharmacol Ther. 2019;49:506–515. doi: 10.1111/apt.15129. [DOI] [PubMed] [Google Scholar]
  264. O’Keefe SJD. Diet, microorganisms and their metabolites, and colon cancer. Nat Rev Gastroenterol Hepatol. 2016;13:691–706. doi: 10.1038/nrgastro.2016.165. [DOI] [PMC free article] [PubMed] [Google Scholar]
  265. Oh SF, Praveena T, Song H, Yoo JS, Jung DJ, Erturk-Hasdemir D, Hwang YS, Lee CWC, Le Nours J, Kim H, et al. Host immunomodulatory lipids created by symbionts from dietary amino acids. Nature. 2021;600:302–307. doi: 10.1038/s41586-021-04083-0. [DOI] [PMC free article] [PubMed] [Google Scholar]
  266. Ohashi W, Fukada T. Contribution of zinc and zinc transporters in the pathogenesis of inflammatory bowel diseases. J Immunol Res. 2019;2019:1–11. doi: 10.1155/2019/8396878. [DOI] [PMC free article] [PubMed] [Google Scholar]
  267. Oliphant K, Allen-Vercoe E. Macronutrient metabolism by the human gut microbiome: major fermentation by-products and their impact on host health. Microbiome. 2019;7:91. doi: 10.1186/s40168-019-0704-8. [DOI] [PMC free article] [PubMed] [Google Scholar]
  268. Oliver A, Chase AB, Weihe C, Orchanian SB, Riedel SF, Hendrickson CL, Lay M, Sewall JM, Martiny JBH, Whiteson K. High-fiber, whole-food dietary intervention alters the human gut microbiome but not fecal short-chain fatty acids. mSystems. 2021;6:e00115–21. doi: 10.1128/mSystems.00115-21. [DOI] [PMC free article] [PubMed] [Google Scholar]
  269. Org E, Blum Y, Kasela S, Mehrabian M, Kuusisto J, Kangas AJ, Soininen P, Wang Z, Ala-Korpela M, Hazen SL, et al. Relationships between gut microbiota, plasma metabolites, and metabolic syndrome traits in the METSIM cohort. Genome Biol. 2017;18:70. doi: 10.1186/s13059-017-1194-2. [DOI] [PMC free article] [PubMed] [Google Scholar]
  270. Ortega-Hernández A, Martínez-Martínez E, Gómez-Gordo R, López-Andrés N, Fernández-Celis A, Gutiérrrez-Miranda B, Nieto ML, Alarcón T, Alba C, Gómez-Garre D, et al. The interaction between mitochondrial oxidative stress and gut microbiota in the cardiometabolic consequences in diet-induced obese rats. Antioxidants. 2020;9:640. doi: 10.3390/antiox9070640. [DOI] [PMC free article] [PubMed] [Google Scholar]
  271. Otten AT, Bourgonje AR, Peters V, Alizadeh BZ, Dijkstra G, Harmsen HJM. Vitamin C supplementation in healthy individuals leads to shifts of bacterial populations in the gut—a pilot study. Antioxidants. 2021;10:1278. doi: 10.3390/antiox10081278. [DOI] [PMC free article] [PubMed] [Google Scholar]
  272. Oyagbemi AA, Ajibade TO, Aboua YG, Gbadamosi IT, Adedapo ADA, Aro AO, Adejumobi OA, Thamahane-Katengua E, Omobowale TO, Falayi OO, et al. Potential health benefits of zinc supplementation for the management of COVID-19 pandemic. J Food Biochem. 2021;45:e13604. doi: 10.1111/jfbc.13604. [DOI] [PMC free article] [PubMed] [Google Scholar]
  273. Pajarillo EAB, Lee E, Kang DK. Trace metals and animal health: Interplay of the gut microbiota with iron, manganese, zinc, and copper. Anim Nutr. 2021;7:750–761. doi: 10.1016/j.aninu.2021.03.005. [DOI] [PMC free article] [PubMed] [Google Scholar]
  274. Pan F, Zhang LL, Luo HJ, Chen Y, Long L, Wang X, Zhuang PT, Li EM, Xu LY. Dietary riboflavin deficiency induces ariboflavinosis and esophageal epithelial atrophy in association with modification of gut microbiota in rats. Eur J Nutr. 2021;60:807–820. doi: 10.1007/s00394-020-02283-4. [DOI] [PubMed] [Google Scholar]
  275. Pan X, Xue F, Nan X, Tang Z, Wang K, Beckers Y, Jiang L, Xiong B. Illumina sequencing approach to characterize thiamine metabolism related bacteria and the impacts of thiamine supplementation on ruminal microbiota in dairy cows fed high-grain diets. Front Microbiol. 2017;8:1818. doi: 10.3389/fmicb.2017.01818. [DOI] [PMC free article] [PubMed] [Google Scholar]
  276. Pan Z, Hu Y, Huang Z, Han N, Li Y, Zhuang X, Yin J, Peng H, Gao Q, Zhang W, et al. Alterations in gut microbiota and metabolites associated with altitude-induced cardiac hypertrophy in rats during hypobaric hypoxia challenge. Sci China Life Sci. 2022;65:2093–2113. doi: 10.1007/s11427-021-2056-1. [DOI] [PubMed] [Google Scholar]
  277. Panagiotakos DB, Georgousopoulou EN, Pitsavos C, Chrysohoou C, Skoumas I, Pitaraki E, Georgiopoulos GA, Ntertimani M, Christou A, Stefanadis C. Exploring the path of Mediterranean diet on 10-year incidence of cardiovascular disease: The ATTICA study (2002–2012) Nutr Metab Cardiovasc Dis. 2015;25:327–335. doi: 10.1016/j.numecd.2014.09.006. [DOI] [PubMed] [Google Scholar]
  278. Pang J, Wang S, Wang Z, Wu Y, Zhang X, Pi Y, Han D, Zhang S, Wang J. Xylo-oligosaccharide alleviates Salmonella induced inflammation by stimulating Bifidobacterium animalis and inhibiting Salmonella colonization. FASEB J. 2021;35:e21977. doi: 10.1096/fj.202100919RR. [DOI] [PubMed] [Google Scholar]
  279. Paoli A, Mancin L, Bianco A, Thomas E, Mota JF, Piccini F. Ketogenic diet and microbiota: friends or enemies. Genes. 2019;10:534. doi: 10.3390/genes10070534. [DOI] [PMC free article] [PubMed] [Google Scholar]
  280. Park J, Cheon JH. Incidence and prevalence of inflammatory bowel disease across Asia. Yonsei Med J. 2021;62:99–108. doi: 10.3349/ymj.2021.62.2.99. [DOI] [PMC free article] [PubMed] [Google Scholar]
  281. Park J, Kim M, Kang SG, Jannasch AH, Cooper B, Patterson J, Kim CH. Short-chain fatty acids induce both effector and regulatory T cells by suppression of histone deacetylases and regulation of the mTOR-S6K pathway. Mucosal Immunol. 2015;8:80–93. doi: 10.1038/mi.2014.44. [DOI] [PMC free article] [PubMed] [Google Scholar]
  282. Parra M, Stahl S, Hellmann H. Vitamin B6 and its role in cell metabolism and physiology. Cells. 2018;1:84. doi: 10.3390/cells7070084. [DOI] [PMC free article] [PubMed] [Google Scholar]
  283. Parséus A, Sommer N, Sommer F, Caesar R, Molinaro A, Ståhlman M, Greiner TU, Perkins R, Bäckhed F. Microbiota-induced obesity requires farnesoid X receptor. Gut. 2017;66:429–437. doi: 10.1136/gutjnl-2015-310283. [DOI] [PMC free article] [PubMed] [Google Scholar]
  284. Peppone LJ, Inglis JE, Mustian KM, Heckler CE, Padula GDA, Mohile SG, Kamen CS, Culakova E, Lin PJ, Kerns SL, et al. Multicenter randomized controlled trial of omega-3 fatty acids versus omega-6 fatty acids for the control of cancer-related fatigue among breast cancer survivors. JNCI Cancer Spectrum. 2019;3:kz005. doi: 10.1093/jncics/pkz005. [DOI] [PMC free article] [PubMed] [Google Scholar]
  285. Peyssonnaux C, Zinkernagel AS, Datta V, Lauth X, Johnson RS, Nizet V. TLR4-dependent hepcidin expression by myeloid cells in response to bacterial pathogens. Blood. 2006;107:3727–3732. doi: 10.1182/blood-2005-06-2259. [DOI] [PMC free article] [PubMed] [Google Scholar]
  286. Pham VT, Dold S, Rehman A, Bird JK, Steinert RE. Vitamins, the gut microbiome and gastrointestinal health in humans. Nutr Res. 2021;95:35–53. doi: 10.1016/j.nutres.2021.09.001. [DOI] [PubMed] [Google Scholar]
  287. Pham VT, Fehlbaum S, Seifert N, Richard N, Bruins MJ, Sybesma W, Rehman A, Steinert RE. Effects of colon-targeted vitamins on the composition and metabolic activity of the human gut microbiome—a pilot study. Gut Microbes. 2021;13:1–20. doi: 10.1080/19490976.2021.1875774. [DOI] [PMC free article] [PubMed] [Google Scholar]
  288. Pieper R, Dadi TH, Pieper L, Vahjen W, Franke A, Reinert K, Zentek J. Concentration and chemical form of dietary zinc shape the porcine colon microbiome, its functional capacity and antibiotic resistance gene repertoire. ISME J. 2020;14:2783–2793. doi: 10.1038/s41396-020-0730-3. [DOI] [PMC free article] [PubMed] [Google Scholar]
  289. Popovic A, Bourdon C, Wang PW, Guttman DS, Soofi S, Bhutta Z A, Bandsma RHJ, Parkinson J, Pell LG. Micronutrient supplements can promote disruptive protozoan and fungal communities in the developing infant gut. Nat Commun. 2021;12:6729. doi: 10.1038/s41467-021-27010-3. [DOI] [PMC free article] [PubMed] [Google Scholar]
  290. Porter NT, Martens EC. The critical roles of polysaccharides in gut microbial ecology and physiology. Annu Rev Microbiol. 2017;71:349–369. doi: 10.1146/annurev-micro-102215-095316. [DOI] [PubMed] [Google Scholar]
  291. Prasad AS. Effects of zinc deficiency on Th1 and Th2 cytokine shifts. J Infect Dis. 2000;182:S62–S68. doi: 10.1086/315916. [DOI] [PubMed] [Google Scholar]
  292. Putnam EE, Goodman AL. B vitamin acquisition by gut commensal bacteria. PLoS Pathog. 2020;16:e1008208. doi: 10.1371/journal.ppat.1008208. [DOI] [PMC free article] [PubMed] [Google Scholar]
  293. Q.S., Medeiros PH, Ledwaba SE, Bolick DT, Giallourou N, Yum L K, Costa DVS, Oriá RB, Barry EM, Swann JR, Lima AM, et al. A murine model of diarrhea, growth impairment and metabolic disturbances with Shigella flexneri infection and the role of zinc deficiency. Gut Microbes. 2019;10:615–630. doi: 10.1080/19490976.2018.1564430. [DOI] [PMC free article] [PubMed] [Google Scholar]
  294. Ramos GP, Papadakis KA. Mechanisms of disease: inflammatory bowel diseases. Mayo Clin Proc. 2019;94:155–165. doi: 10.1016/j.mayocp.2018.09.013. [DOI] [PMC free article] [PubMed] [Google Scholar]
  295. Rankin LC, Kaiser KA, de los Santos-Alexis K, Park H, Uhlemann AC, Gray DHD, Arpaia N. Dietary tryptophan deficiency promotes gut RORγt+ Treg cells at the expense of Gata3+ Treg cells and alters commensal microbiota metabolism. Cell Rep. 2023;42:112135. doi: 10.1016/j.celrep.2023.112135. [DOI] [PMC free article] [PubMed] [Google Scholar]
  296. Ray K. Filling up on fibre for a healthy gut. Nat Rev Gastroenterol Hepatol. 2018;15:67. doi: 10.1038/nrgastro.2018.2. [DOI] [PubMed] [Google Scholar]
  297. Reddy BS, Pleasants JR, Wostmann BS. Effect of intestinal microflora on iron and zinc metabolism, and on activities of metalloenzymes in rats. J Nutr. 1972;102:101–107. doi: 10.1093/jn/102.1.101. [DOI] [PubMed] [Google Scholar]
  298. Reed S, Knez M, Uzan A, Stangoulis JCR, Glahn RP, Koren O, Tako E. Alterations in the gut (Gallus gallus) microbiota following the consumption of zinc biofortified wheat (Triticum aestivum)-based diet. J Agric Food Chem. 2018;66:6291–6299. doi: 10.1021/acs.jafc.8b01481. [DOI] [PubMed] [Google Scholar]
  299. Reed S, Neuman H, Moscovich S, Glahn R, Koren O, Tako E. Chronic zinc deficiency alters chick gut microbiota composition and function. Nutrients. 2015;7:9768–9784. doi: 10.3390/nu7125497. [DOI] [PMC free article] [PubMed] [Google Scholar]
  300. Ren W, Bin P, Yin Y, Wu G. Impacts of amino acids on the intestinal defensive system. In: Wu G, editor. Amino Acids in Nutrition and Health. Cham: Springer; 2020. pp. 133–151. [DOI] [PubMed] [Google Scholar]
  301. Ren W, Duan J, Yin J, Liu G, Cao Z, Xiong X, Chen S, Li T, Yin Y, Hou Y, et al. Dietary L-glutamine supplementation modulates microbial community and activates innate immunity in the mouse intestine. Amino Acids. 2014;46:2403–2413. doi: 10.1007/s00726-014-1793-0. [DOI] [PubMed] [Google Scholar]
  302. Ren W, Liao Y, Ding X, Jiang Y, Yan J, Xia Y, Tan B, Lin Z, Duan J, Jia X, et al. Slc6a13 deficiency promotes Th17 responses during intestinal bacterial infection. Mucosal Immunol. 2019;12:531–544. doi: 10.1038/s41385-018-0111-7. [DOI] [PubMed] [Google Scholar]
  303. Robertson RC, Kaliannan K, Strain CR, Ross RP, Stanton C, Kang JX. Maternal omega-3 fatty acids regulate offspring obesity through persistent modulation of gut microbiota. Microbiome. 2018;6:95. doi: 10.1186/s40168-018-0476-6. [DOI] [PMC free article] [PubMed] [Google Scholar]
  304. Robertson RC, Seira Oriach C, Murphy K, Moloney GM, Cryan JF, Dinan TG, Paul Ross R, Stanton C. Omega-3 polyunsaturated fatty acids critically regulate behaviour and gut microbiota development in adolescence and adulthood. Brain Behav Immun. 2017;59:21–37. doi: 10.1016/j.bbi.2016.07.145. [DOI] [PubMed] [Google Scholar]
  305. Robles-Vera I, Callejo M, Ramos R, Duarte J, Perez-Vizcaino F. Impact of vitamin D deficit on the rat gut microbiome. Nutrients. 2019;11:2564. doi: 10.3390/nu11112564. [DOI] [PMC free article] [PubMed] [Google Scholar]
  306. Rocha DM, Caldas AP, Oliveira LL, Bressan J, Hermsdorff H H. Saturated fatty acids trigger TLR4-mediated inflammatory response. Atherosclerosis. 2016;244:211–215. doi: 10.1016/j.atherosclerosis.2015.11.015. [DOI] [PubMed] [Google Scholar]
  307. Rodrigues HG, Takeo Sato F, Curi R, Vinolo MAR. Fatty acids as modulators of neutrophil recruitment, function and survival. Eur J Pharmacol. 2016;785:50–58. doi: 10.1016/j.ejphar.2015.03.098. [DOI] [PubMed] [Google Scholar]
  308. Rohr MW, Narasimhulu CA, Rudeski-Rohr TA, Parthasarathy S. Negative effects of a high-fat diet on intestinal permeability: a review. Adv Nutr. 2020;11:77–91. doi: 10.1093/advances/nmz061. [DOI] [PMC free article] [PubMed] [Google Scholar]
  309. Rom, O., Liu, Y., Liu, Z., Zhao, Y., Wu, J., Ghrayeb, A., Villacorta, L., Fan, Y., Chang, L., Wang, L., et al. (2020). Glycine-based treatment ameliorates NAFLD by modulating fatty acid oxidation, glutathione synthesis, and the gut microbiome. Sci Transl Med 12. [DOI] [PMC free article] [PubMed]
  310. Rosenkranz E, Maywald M, Hilgers RD, Brieger A, Clarner T, Kipp M, Plümäkers B, Meyer S, Schwerdtle T, Rink L. Induction of regulatory T cells in Th1-/Th17-driven experimental autoimmune encephalomyelitis by zinc administration. J Nutr Biochem. 2016;29:116–123. doi: 10.1016/j.jnutbio.2015.11.010. [DOI] [PubMed] [Google Scholar]
  311. Rosser EC, Piper CJM, Matei DE, Blair PA, Rendeiro AF, Orford M, Alber DG, Krausgruber T, Catalan D, Klein N, et al. Microbiota-derived metabolites suppress arthritis by amplifying arylhydrocarbon receptor activation in regulatory B cells. Cell Metab. 2020;31:837–851. doi: 10.1016/j.cmet.2020.03.003. [DOI] [PMC free article] [PubMed] [Google Scholar]
  312. Ruan D, Fouad AM, Fan QL, Huo XH, Kuang ZX, Wang H, Guo CY, Deng YF, Zhang C, Zhang JH, et al. Dietary L-arginine supplementation enhances growth performance, intestinal antioxidative capacity, immunity and modulates gut microbiota in yellow-feathered chickens. Poultry Sci. 2020;99:6935–6945. doi: 10.1016/j.psj.2020.09.042. [DOI] [PMC free article] [PubMed] [Google Scholar]
  313. Ryan PJ, Riechman SE, Fluckey JD, Wu G. Interorgan metabolism of amino acids in human health and disease. In: Wu G, editor. Amino Acids in Nutrition and Health. Cham: Springer; 2021. pp. 129–149. [DOI] [PubMed] [Google Scholar]
  314. Saito, Y., Sato, T., Nomoto, K., and Tsuji, H. (2018). Identification of phenol- and p-cresol-producing intestinal bacteria by using media supplemented with tyrosine and its metabolites. FEMS Microbiol Ecol 94. [DOI] [PMC free article] [PubMed]
  315. Samanovic MI, Ding C, Thiele DJ, Darwin KH. Copper in microbial pathogenesis: meddling with the met al. Cell Host Microbe. 2012;11:106–115. doi: 10.1016/j.chom.2012.01.009. [DOI] [PMC free article] [PubMed] [Google Scholar]
  316. Sang LX, Chang B, Zhu JF, Yang FL, Li Y, Jiang XF, Wang D N, Lu CL, Sun X. Sodium selenite ameliorates dextran sulfate sodium-induced chronic colitis in mice by decreasing Th1, Th17, and γδT and increasing CD4(+)CD25(+) regulatory T-cell responses. World J Gastroenterol. 2017;23:3850–3863. doi: 10.3748/wjg.v23.i21.3850. [DOI] [PMC free article] [PubMed] [Google Scholar]
  317. Santamaria L, Reveron I, de Felipe FL, de Las Rivas B, Munoz R. Ethylphenol formation by Lactobacillus plantarum: identification of the enzyme involved in the reduction of vinylphenols. Appl Environ Microbiol. 2018;84:e01064–18. doi: 10.1128/AEM.01064-18. [DOI] [PMC free article] [PubMed] [Google Scholar]
  318. Santos L, Neves C, Melo M, Soares P. Selenium and selenoproteins in immune mediated thyroid disorders. Diagnostics. 2018;8:70. doi: 10.3390/diagnostics8040070. [DOI] [PMC free article] [PubMed] [Google Scholar]
  319. Sargeant HR, McDowall KJ, Miller HM, Shaw MA. Dietary zinc oxide affects the expression of genes associated with inflammation: transcriptome analysis in piglets challenged with ETEC K88. Vet Immunol Immunopathol. 2010;137:120–129. doi: 10.1016/j.vetimm.2010.05.001. [DOI] [PubMed] [Google Scholar]
  320. Sato H, Zhang LS, Martinez K, Chang EB, Yang Q, Wang F, Howles PN, Hokari R, Miura S, Tso P. Antibiotics suppress activation of intestinal mucosal mast cells and reduce dietary lipid absorption in Sprague-Dawley rats. Gastroenterology. 2016;151:923–932. doi: 10.1053/j.gastro.2016.07.009. [DOI] [PMC free article] [PubMed] [Google Scholar]
  321. Sauer AK, Grabrucker AM. Zinc deficiency during pregnancy leads to altered microbiome and elevated inflammatory markers in mice. Front Neurosci. 2019;13:1295. doi: 10.3389/fnins.2019.01295. [DOI] [PMC free article] [PubMed] [Google Scholar]
  322. Saulnier DM, Riehle K, Mistretta T, Diaz M, Mandal D, Raza S, Weidler EM, Qin X, Coarfa C, Milosavljevic A, et al. Gastrointestinal microbiome signatures of pediatric patients with irritable bowel syndrome. Gastroenterology. 2011;141:1782–1791. doi: 10.1053/j.gastro.2011.06.072. [DOI] [PMC free article] [PubMed] [Google Scholar]
  323. Schoeler M, Caesar R. Dietary lipids, gut microbiota and lipid metabolism. Rev Endocr Metab Disord. 2019;20:461–472. doi: 10.1007/s11154-019-09512-0. [DOI] [PMC free article] [PubMed] [Google Scholar]
  324. Schwalm ND, Groisman EA. Navigating the gut buffet: control of polysaccharide utilization in Bacteroides spp. Trends Microbiol. 2017;25:1005–1015. doi: 10.1016/j.tim.2017.06.009. [DOI] [PubMed] [Google Scholar]
  325. Seal CJ, Courtin CM, Venema K, Vries J. Health benefits of whole grain: effects on dietary carbohydrate quality, the gut microbiome, and consequences of processing. Compr Rev Food Sci Food Saf. 2021;20:2742–2768. doi: 10.1111/1541-4337.12728. [DOI] [PubMed] [Google Scholar]
  326. Selmin OI, Papoutsis AJ, Hazan S, Smith C, Greenfield N, Donovan MG, Wren SN, Doetschman TC, Snider JM, Snider AJ, et al. n-6 high fat diet induces gut microbiome dysbiosis and colonic inflammation. Int J Mol Sci. 2021;22:6919. doi: 10.3390/ijms22136919. [DOI] [PMC free article] [PubMed] [Google Scholar]
  327. Shahidi F, Ambigaipalan P. Omega-3 polyunsaturated fatty acids and their health benefits. Annu Rev Food Sci Technol. 2018;9:345–381. doi: 10.1146/annurev-food-111317-095850. [DOI] [PubMed] [Google Scholar]
  328. Shang Q, Jiang H, Cai C, Hao J, Li G, Yu G. Gut microbiota fermentation of marine polysaccharides and its effects on intestinal ecology: An overview. Carbohydr Polyms. 2018;179:173–185. doi: 10.1016/j.carbpol.2017.09.059. [DOI] [PubMed] [Google Scholar]
  329. Shanmugam NKN, Trebicka E, Fu L, Shi HN, Cherayil BJ. Intestinal inflammation modulates expression of the iron-regulating hormone hepcidin depending on erythropoietic activity and the commensal microbiota. J Immunol. 2014;193:1398–1407. doi: 10.4049/jimmunol.1400278. [DOI] [PMC free article] [PubMed] [Google Scholar]
  330. Sheng Y, Fan F, Jensen O, Zhong Z, Kan B, Wang H, Zhu J. Dual zinc transporter systems in Vibrio cholerae promote competitive advantages over gut microbiome. Infect Immun. 2015;83:3902–3908. doi: 10.1128/IAI.00447-15. [DOI] [PMC free article] [PubMed] [Google Scholar]
  331. Shiba T, Kawakami K, Sasaki T, Makino I, Kato I, Kobayashi T, Uchida K, Kaneko K. Effects of intestinal bacteria-derived p-cresyl sulfate on Th1-type immune response in vivo and in vitro. Toxicol Appl Pharmacol. 2014;274:191–199. doi: 10.1016/j.taap.2013.10.016. [DOI] [PubMed] [Google Scholar]
  332. Shimada Y, Kinoshita M, Harada K, Mizutani M, Masahata K, Kayama H, Takeda K. Commensal bacteria-dependent indole production enhances epithelial barrier function in the colon. PLoS ONE. 2013;8:e80604. doi: 10.1371/journal.pone.0080604. [DOI] [PMC free article] [PubMed] [Google Scholar]
  333. Shin BS, Katoh T, Gutierrez E, Kim JR, Suga H, Dever TE. Amino acid substrates impose polyamine, eIF5A, or hypusine requirement for peptide synthesis. Nucleic Acids Res. 2017;45:8392–8402. doi: 10.1093/nar/gkx532. [DOI] [PMC free article] [PubMed] [Google Scholar]
  334. Short SP, Pilat JM, Barrett CW, Reddy VK, Haberman Y, Hendren JR, Marsh BJ, Keating CE, Motley AK, Hill KE, et al. Colonic epithelial-derived selenoprotein P is the source for antioxidant-mediated protection in colitis-associated cancer. Gastroenterology. 2021;160:1694–1708. doi: 10.1053/j.gastro.2020.12.059. [DOI] [PMC free article] [PubMed] [Google Scholar]
  335. Shrimali RK, Irons RD, Carlson BA, Sano Y, Gladyshev VN, Park JM, Hatfield DL. Selenoproteins mediate T cell immunity through an antioxidant mechanism. J Biol Chem. 2008;283:20181–20185. doi: 10.1074/jbc.M802559200. [DOI] [PMC free article] [PubMed] [Google Scholar]
  336. Si J, Kang H, You HJ, Ko GP. Revisiting the role of Akkermansia muciniphila as a therapeutic bacterium. Gut Microbes. 2022;14:2078619. doi: 10.1080/19490976.2022.2078619. [DOI] [PMC free article] [PubMed] [Google Scholar]
  337. Simonyté Sjödin K, Domellöf M, Lagerqvist C, Hernell O, Lönnerdal B, Szymlek-Gay EA, Sjödin A, West CE, Lind T. Administration of ferrous sulfate drops has significant effects on the gut microbiota of iron-sufficientinfants: a randomised controlled study. Gut. 2019;68:2095.1–2097. doi: 10.1136/gutjnl-2018-316988. [DOI] [PMC free article] [PubMed] [Google Scholar]
  338. Singh N, Gurav A, Sivaprakasam S, Brady E, Padia R, Shi H, Thangaraju M, Prasad PD, Manicassamy S, Munn DH, et al. Activation of Gpr109a, receptor for niacin and the commensal metabolite butyrate, suppresses colonic inflammation and carcinogenesis. Immunity. 2014;40:128–139. doi: 10.1016/j.immuni.2013.12.007. [DOI] [PMC free article] [PubMed] [Google Scholar]
  339. Sivaprakasam S, Ristic B, Mudaliar N, Hamood AN, Colmer-Hamood J, Wachtel MS, Nevels AG, Kottapalli KR, Ganapathy V. Hereditary hemochromatosis promotes colitis and colon cancer and causes bacterial dysbiosis in mice. Biochem J. 2020;477:3867–3883. doi: 10.1042/BCJ20200392. [DOI] [PMC free article] [PubMed] [Google Scholar]
  340. Skalny AV, Aschner M, Lei XG, Gritsenko VA, Santamaria A, Alekseenko SI, Prakash NT, Chang JS, Sizova EA, Chao JCJ, et al. Gut microbiota as a mediator of essential and toxic effects of zinc in the intestines and other tissues. Int J Mol Sci. 2021;22:13074. doi: 10.3390/ijms222313074. [DOI] [PMC free article] [PubMed] [Google Scholar]
  341. Song B, Zheng C, Zha C, Hu S, Yang X, Wang L, Xiao H. Dietary leucine supplementation improves intestinal health of mice through intestinal SIgA secretion. J Appl Microbiol. 2020;128:574–583. doi: 10.1111/jam.14464. [DOI] [PubMed] [Google Scholar]
  342. Song Q, Wang Y, Huang L, Shen M, Yu Y, Yu Q, Chen Y, Xie J. Review of the relationships among polysaccharides, gut microbiota, and human health. Food Res Int. 2021;140:109858. doi: 10.1016/j.foodres.2020.109858. [DOI] [PubMed] [Google Scholar]
  343. Sonnenburg ED, Smits SA, Tikhonov M, Higginbottom SK, Wingreen NS, Sonnenburg JL. Diet-induced extinctions in the gut microbiota compound over generations. Nature. 2016;529:212–215. doi: 10.1038/nature16504. [DOI] [PMC free article] [PubMed] [Google Scholar]
  344. Srinivasan K, Buys EM. Insights into the role of bacteria in vitamin A biosynthesis: Future research opportunities. Crit Rev Food Sci Nutr. 2019;59:3211–3226. doi: 10.1080/10408398.2018.1546670. [DOI] [PubMed] [Google Scholar]
  345. Stacchiotti V, Rezzi S, Eggersdorfer M, Galli F. Metabolic and functional interplay between gut microbiota and fat-soluble vitamins. Crit Rev Food Sci Nutr. 2021;61:3211–3232. doi: 10.1080/10408398.2020.1793728. [DOI] [PubMed] [Google Scholar]
  346. Steinert RE, Lee YK, Sybesma W. Vitamins for the gut microbiome. Trends Mol Med. 2020;26:137–140. doi: 10.1016/j.molmed.2019.11.005. [DOI] [PubMed] [Google Scholar]
  347. Strandwitz P, Kim KH, Terekhova D, Liu JK, Sharma A, Levering J, McDonald D, Dietrich D, Ramadhar TR, Lekbua A, et al. GABA-modulating bacteria of the human gut microbiota. Nat Microbiol. 2019;4:396–403. doi: 10.1038/s41564-018-0307-3. [DOI] [PMC free article] [PubMed] [Google Scholar]
  348. Sun CY, Li JR, Wang YY, Lin SY, Ou YC, Lin CJ, Wang JD, Liao SL, Chen CJ. p-Cresol sulfate caused behavior disorders and neurodegeneration in mice with unilateral nephrectomy involving oxidative stress and neuroinflammation. Int J Mol Sci. 2020;21:6687. doi: 10.3390/ijms21186687. [DOI] [PMC free article] [PubMed] [Google Scholar]
  349. Sun M, Wu W, Liu Z, Cong Y. Microbiota metabolite short chain fatty acids, GPCR, and inflammatory bowel diseases. J Gastroenterol. 2017;52:1–8. doi: 10.1007/s00535-016-1242-9. [DOI] [PMC free article] [PubMed] [Google Scholar]
  350. Sun Z, Yue Z, Liu E, Li X, Li C. Assessment of the bifidogenic and antibacterial activities of xylooligosaccharide. Front Nutr. 2022;9:858949. doi: 10.3389/fnut.2022.858949. [DOI] [PMC free article] [PubMed] [Google Scholar]
  351. Takahashi K, Suzuki N, Ogra Y. Effect of gut microflora on nutritional availability of selenium. Food Chem. 2020;319:126537. doi: 10.1016/j.foodchem.2020.126537. [DOI] [PubMed] [Google Scholar]
  352. Tan J, Ni D, Taitz J, Pinget GV, Read M, Senior A, Wali JA, Elnour R, Shanahan E, Wu H, et al. Dietary protein increases T-cell-independent sIgA production through changes in gut microbiota-derived extracellular vesicles. Nat Commun. 2022;13:4336. doi: 10.1038/s41467-022-31761-y. [DOI] [PMC free article] [PubMed] [Google Scholar]
  353. Taormina VM, Unger AL, Schiksnis MR, Torres-Gonzalez M, Kraft J. Branched-chain fatty acids—an underexplored class of dairy-derived fatty acids. Nutrients. 2020;12:2875. doi: 10.3390/nu12092875. [DOI] [PMC free article] [PubMed] [Google Scholar]
  354. Thompson MG, Blake-Hedges JM, Cruz-Morales P, Barajas JF, Curran SC, Eiben CB, Harris NC, Benites VT, Gin JW, Sharpless WA, et al. Massively parallel fitness profiling reveals multiple novel enzymes in Pseudomonas putida lysine metabolism. mBio 10. 2019;e02577:18. doi: 10.1128/mBio.02577-18. [DOI] [PMC free article] [PubMed] [Google Scholar]
  355. Tian Y, Nichols RG, Cai J, Patterson AD, Cantorna MT. Vitamin A deficiency in mice alters host and gut microbial metabolism leading to altered energy homeostasis. J Nutr Biochem. 2018;54:28–34. doi: 10.1016/j.jnutbio.2017.10.011. [DOI] [PMC free article] [PubMed] [Google Scholar]
  356. Trapecar M, Communal C, Velazquez J, Maass CA, Huang YJ, Schneider K, Wright CW, Butty V, Eng G, Yilmaz O, et al. Gut-liver physiomimetics reveal paradoxical modulation of IBD-related inflammation by short-chain fatty acids. Cell Syst. 2020;10:223–239. doi: 10.1016/j.cels.2020.02.008. [DOI] [PMC free article] [PubMed] [Google Scholar]
  357. Trompette A, Gollwitzer ES, Yadava K, Sichelstiel AK, Sprenger N, Ngom-Bru C, Blanchard C, Junt T, Nicod LP, Harris NL, et al. Gut microbiota metabolism of dietary fiber influences allergic airway disease and hematopoiesis. Nat Med. 2014;20:159–166. doi: 10.1038/nm.3444. [DOI] [PubMed] [Google Scholar]
  358. Tsutsumi R, Yamasaki Y, Takeo J, Miyahara H, Sebe M, Bando M, Tanba Y, Mishima Y, Takeji K, Ueshima N, et al. Long-chain monounsaturated fatty acids improve endothelial function with altering microbial flora. Transl Res. 2021;237:16–30. doi: 10.1016/j.trsl.2021.03.016. [DOI] [PubMed] [Google Scholar]
  359. 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;444:1027–1031. doi: 10.1038/nature05414. [DOI] [PubMed] [Google Scholar]
  360. Turroni F, Milani C, Duranti S, Mahony J, van Sinderen D, Ventura M. Glycan utilization and cross-feeding activities by Bifidobacteria. Trends Microbiol. 2018;26:339–350. doi: 10.1016/j.tim.2017.10.001. [DOI] [PubMed] [Google Scholar]
  361. van der Hee B, Wells JM. Microbial regulation of host physiology by short-chain fatty acids. Trends Microbiol. 2021;29:700–712. doi: 10.1016/j.tim.2021.02.001. [DOI] [PubMed] [Google Scholar]
  362. Venkatesh M, Mukherjee S, Wang H, Li H, Sun K, Benechet AP, Qiu Z, Maher L, Redinbo MR, Phillips RS, et al. Symbiotic bacterial metabolites regulate gastrointestinal barrier function via the xenobiotic sensor PXR and Toll-like receptor 4. Immunity. 2014;41:296–310. doi: 10.1016/j.immuni.2014.06.014. [DOI] [PMC free article] [PubMed] [Google Scholar]
  363. Verbeke KA, Boobis AR, Chiodini A, Edwards CA, Franck A, Kleerebezem M, Nauta A, Raes J, van Tol EAF, Tuohy KM. Towards microbial fermentation metabolites as markers for health benefits of prebiotics. Nutr Res Rev. 2015;28:42–66. doi: 10.1017/S0954422415000037. [DOI] [PMC free article] [PubMed] [Google Scholar]
  364. Villagómez-Estrada, S., Pérez, J.F., Darwich, L., Vidal, A., van Kuijk, S., Melo-Durán, D., and Solà-Oriol, D. (2020). Effects of copper and zinc sources and inclusion levels of copper on weanling pig performance and intestinal microbiota. J Anim Sci 98. [DOI] [PMC free article] [PubMed]
  365. Vinolo MAR, Rodrigues HG, Hatanaka E, Sato FT, Sampaio SC, Curi R. Suppressive effect of short-chain fatty acids on production of proinflammatory mediators by neutrophils. J Nutr Biochem. 2011;22:849–855. doi: 10.1016/j.jnutbio.2010.07.009. [DOI] [PubMed] [Google Scholar]
  366. Vinolo MAR, Rodrigues HG, Nachbar RT, Curi R. Regulation of inflammation by short chain fatty acids. Nutrients. 2011;3:858–876. doi: 10.3390/nu3100858. [DOI] [PMC free article] [PubMed] [Google Scholar]
  367. Vogt NM, Kerby RL, Dill-McFarland KA, Harding SJ, Merluzzi A P, Johnson SC, Carlsson CM, Asthana S, Zetterberg H, Blennow K, et al. Gut microbiome alterations in Alzheimer’s disease. Sci Rep. 2017;7:13537. doi: 10.1038/s41598-017-13601-y. [DOI] [PMC free article] [PubMed] [Google Scholar]
  368. Wagatsuma K, Yamada S, Ao M, Matsuura M, Tsuji H, Iida T, Miyamoto K, Oka K, Takahashi M, Tanaka K, et al. Diversity of gut microbiota affecting serum level of undercarboxylated osteocalcin in patients with Crohn’s disease. Nutrients. 2019;11:1541. doi: 10.3390/nu11071541. [DOI] [PMC free article] [PubMed] [Google Scholar]
  369. Walker A, Schmitt-Kopplin P. The role of fecal sulfur metabolome in inflammatory bowel diseases. Int J Med Microbiol. 2021;311:151513. doi: 10.1016/j.ijmm.2021.151513. [DOI] [PubMed] [Google Scholar]
  370. Wan Y, Wang F, Yuan J, Li J, Jiang D, Zhang J, Li H, Wang R, Tang J, Huang T, et al. Effects of dietary fat on gut microbiota and faecal metabolites, and their relationship with cardiometabolic risk factors: a 6-month randomised controlled-feeding trial. Gut. 2019;68:1417–1429. doi: 10.1136/gutjnl-2018-317609. [DOI] [PubMed] [Google Scholar]
  371. Wang B, Kong Q, Li X, Zhao J, Zhang H, Chen W, Wang G. A high-fat diet increases gut microbiota biodiversity and energy expenditure due to nutrient difference. Nutrients. 2020;12:3197. doi: 10.3390/nu12103197. [DOI] [PMC free article] [PubMed] [Google Scholar]
  372. Wang J, Wang J. Blood group-gut microbiome-health axis gains further support from landmark multi-omics study in swines. Sci China Life Sci. 2022;65:2338–2340. doi: 10.1007/s11427-022-2145-1. [DOI] [PMC free article] [PubMed] [Google Scholar]
  373. Wang L, Nong Q, Zhou Y, Sun Y, Chen W, Xie J, Zhu X, Shan T. Changes in serum fatty acid composition and metabolome-microbiome responses of Heigai Pigs induced by dietary n-6/n-3 polyunsaturated fatty acid ratio. Front Microbiol. 2022;13:917558. doi: 10.3389/fmicb.2022.917558. [DOI] [PMC free article] [PubMed] [Google Scholar]
  374. Wang R, Bai Y, Yang Y, Wu X, Li R. A comparison of production performance, egg quality, and cecal microbiota in laying hens receiving graded levels of vitamin B12. Front Vet Sci. 2021;8:712183. doi: 10.3389/fvets.2021.712183. [DOI] [PMC free article] [PubMed] [Google Scholar]
  375. Wang S, De Paepe K, Van de Wiele T, Fu X, Yuan Y, Zhang B, Huang Q. Starch microspheres entrapped with chitosan delay in vitro fecal fermentation and regulate human gut microbiota composition. J Agric Food Chem. 2021;69:12323–12332. doi: 10.1021/acs.jafc.1c04039. [DOI] [PubMed] [Google Scholar]
  376. Wang X, Li X, Dong Y. Vitamin D decreases plasma trimethylamine-N-oxide level in mice by regulating gut microbiota. Biomed Res Int. 2020;2020:9896743. doi: 10.1155/2020/9896743. [DOI] [PMC free article] [PubMed] [Google Scholar]
  377. Wang Y, Qi W, Guo X, Song G, Pang S, Fang W, Peng Z. Effects of oats, tartary buckwheat, and foxtail millet supplementation on lipid metabolism, oxido-inflammatory responses, gut microbiota, and colonic SCFA composition in high-fat diet fed rats. Nutrients. 2022;14:2760. doi: 10.3390/nu14132760. [DOI] [PMC free article] [PubMed] [Google Scholar]
  378. Wang Z, Bai Y, Pi Y, Gerrits WJJ, de Vries S, Shang L, Tao S, Zhang S, Han D, Zhu Z, et al. Xylan alleviates dietary fiber deprivation-induced dysbiosis by selectively promoting Bifidobacterium pseudocatenulatum in pigs. Microbiome. 2021;9:227. doi: 10.1186/s40168-021-01175-x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  379. Wang Z, Zhang X, Zhu L, Yang X, He F, Wang T, Bao T, Lu H, Wang H, Yang S. Inulin alleviates inflammation of alcoholic liver disease via SCFAs-inducing suppression of M1 and facilitation of M2 macrophages in mice. Int Immunopharmacol. 2020;78:106062. doi: 10.1016/j.intimp.2019.106062. [DOI] [PubMed] [Google Scholar]
  380. Wardman JF, Bains RK, Rahfeld P, Withers SG. Carbohydrate-active enzymes (CAZymes) in the gut microbiome. Nat Rev Microbiol. 2022;20:542–556. doi: 10.1038/s41579-022-00712-1. [DOI] [PubMed] [Google Scholar]
  381. Watson H, Mitra S, Croden FC, Taylor M, Wood HM, Perry SL, Spencer JA, Quirke P, Toogood GJ, Lawton CL, et al. A randomised trial of the effect of omega-3 polyunsaturated fatty acid supplements on the human intestinal microbiota. Gut. 2018;67:1974–1983. doi: 10.1136/gutjnl-2017-314968. [DOI] [PubMed] [Google Scholar]
  382. Wei M, Huang F, Zhao L, Zhang Y, Yang W, Wang S, Li M, Han X, Ge K, Qu C, et al. A dysregulated bile acid-gut microbiota axis contributes to obesity susceptibility. Ebiomedicine. 2020;55:102766. doi: 10.1016/j.ebiom.2020.102766. [DOI] [PMC free article] [PubMed] [Google Scholar]
  383. Wen K, Zhao MM, Liu L, Khogali MK, Geng TY, Wang HR, Gong DQ. Thiamine modulates intestinal morphological structure and microbiota under subacute ruminal acidosis induced by a high-concentrate diet in Saanen goats. Animal. 2021;15:100370. doi: 10.1016/j.animal.2021.100370. [DOI] [PubMed] [Google Scholar]
  384. White PJ, Newgard CB. Branched-chain amino acids in disease. Science. 2019;363:582–583. doi: 10.1126/science.aav0558. [DOI] [PMC free article] [PubMed] [Google Scholar]
  385. Williams BB, Van Benschoten AH, Cimermancic P, Donia MS, Zimmermann M, Taketani M, Ishihara A, Kashyap PC, Fraser J S, Fischbach MA. Discovery and characterization of gut microbiota decarboxylases that can produce the neurotransmitter tryptamine. Cell Host Microbe. 2014;16:495–503. doi: 10.1016/j.chom.2014.09.001. [DOI] [PMC free article] [PubMed] [Google Scholar]
  386. Wlodarska M, Luo C, Kolde R, d’Hennezel E, Annand JW, Heim C E, Krastel P, Schmitt EK, Omar AS, Creasey EA, et al. Indoleacrylic acid produced by commensal Peptostreptococcus species suppresses inflammation. Cell Host Microbe. 2017;22:25–37. doi: 10.1016/j.chom.2017.06.007. [DOI] [PMC free article] [PubMed] [Google Scholar]
  387. Wolschendorf F, Ackart D, Shrestha TB, Hascall-Dove L, Nolan S, Lamichhane G, Wang Y, Bossmann SH, Basaraba RJ, Niederweis M. Copper resistance is essential for virulence of Mycobacterium tuberculosis. Proc Natl Acad Sci USA. 2011;108:1621–1626. doi: 10.1073/pnas.1009261108. [DOI] [PMC free article] [PubMed] [Google Scholar]
  388. Wu CH, Ko JL, Liao JM, Huang SS, Lin MY, Lee LH, Chang LY, Ou CC. D-methionine alleviates cisplatin-induced mucositis by restoring the gut microbiota structure and improving intestinal inflammation. Ther Adv Med Oncol. 2019;11:175883591882102. doi: 10.1177/1758835918821021. [DOI] [PMC free article] [PubMed] [Google Scholar]
  389. Wu G, Bazer FW, Dai Z, Li D, Wang J, Wu Z. Amino acid nutrition in animals: protein synthesis and beyond. Annu Rev Anim Biosci. 2014;2:387–417. doi: 10.1146/annurev-animal-022513-114113. [DOI] [PubMed] [Google Scholar]
  390. Wu GD, Chen J, Hoffmann C, Bittinger K, Chen YY, Keilbaugh S A, Bewtra M, Knights D, Walters WA, Knight R, et al. Linking long-term dietary patterns with gut microbial enterotypes. Science. 2011;334:105–108. doi: 10.1126/science.1208344. [DOI] [PMC free article] [PubMed] [Google Scholar]
  391. Wu HM, Zhang J, Wang C, Liu Q, Guo G, Huo WJ, Chen L, Zhang YL, Pei CX, Zhang SL. Effects of riboflavin supplementation on performance, nutrient digestion, rumen microbiota composition and activities of Holstein bulls. Br J Nutr. 2021;126:1288–1295. doi: 10.1017/S0007114520005243. [DOI] [PubMed] [Google Scholar]
  392. Wu W, Sun M, Chen F, Cao AT, Liu H, Zhao Y, Huang X, Xiao Y, Yao S, Zhao Q, et al. Microbiota metabolite short-chain fatty acid acetate promotes intestinal IgA response to microbiota which is mediated by GPR43. Mucosal Immunol. 2017;10:946–956. doi: 10.1038/mi.2016.114. [DOI] [PMC free article] [PubMed] [Google Scholar]
  393. Wu Z, Pan D, Jiang M, Sang L, Chang B. Selenium-enriched Lactobacillus acidophilus ameliorates dextran sulfate sodium-induced chronic colitis in mice by regulating inflammatory cytokines and intestinal microbiota. Front Med. 2021;8:716816. doi: 10.3389/fmed.2021.716816. [DOI] [PMC free article] [PubMed] [Google Scholar]
  394. Xia P, Lian S, Wu Y, Yan L, Quan G, Zhu G. Zinc is an important inter-kingdom signal between the host and microbe. Vet Res. 2021;52:39. doi: 10.1186/s13567-021-00913-1. [DOI] [PMC free article] [PubMed] [Google Scholar]
  395. Xia Y, Chen S, Zhao Y, Chen S, Huang R, Zhu G, Yin Y, Ren W, Deng J. GABA attenuates ETEC-induced intestinal epithelial cell apoptosis involving GABAAR signaling and the AMPK-autophagy pathway. Food Funct. 2019;10:7509–7522. doi: 10.1039/C9FO01863H. [DOI] [PubMed] [Google Scholar]
  396. Xia Y, Ding X, Wang S, Ren W. Circadian orchestration of host and gut microbiota in infection. Biol Rev. 2023;98:115–131. doi: 10.1111/brv.12898. [DOI] [PubMed] [Google Scholar]
  397. Xia Y, He F, Wu X, Tan B, Chen S, Liao Y, Qi M, Chen S, Peng Y, Yin Y, et al. GABA transporter sustains IL-1β production in macrophages. Sci Adv. 2021;7:eabe9274. doi: 10.1126/sciadv.abe9274. [DOI] [PMC free article] [PubMed] [Google Scholar]
  398. Xia Y, Li Y, Wu X, Zhang Q, Chen S, Ma X, Yu M. Ironing out the details: how iron orchestrates macrophage polarization. Front Immunol. 2021;12:669566. doi: 10.3389/fimmu.2021.669566. [DOI] [PMC free article] [PubMed] [Google Scholar]
  399. Xia Y, Zhang Q, Ye Y, Wu X, He F, Peng Y, Yin Y, Ren W. Melatonergic signalling instructs transcriptional inhibition of IFNGR2 to lessen interleukin-1β-dependent inflammation. Clin Transl Med. 2022;12:e716. doi: 10.1002/ctm2.716. [DOI] [PMC free article] [PubMed] [Google Scholar]
  400. Xin FZ, Zhao ZH, Zhang RN, Pan Q, Gong ZZ, Sun C, Fan JG. Folic acid attenuates high-fat diet-induced steatohepatitis via deacetylase SIRT1-dependent restoration of PPARα. World J Gastroenterol. 2020;26:2203–2220. doi: 10.3748/wjg.v26.i18.2203. [DOI] [PMC free article] [PubMed] [Google Scholar]
  401. Xu AA, Kennedy LK, Hoffman K, White DL, Kanwal F, El-Serag HB, Petrosino JF, Jiao L. Dietary fatty acid intake and the colonic gut microbiota in humans. Nutrients. 2022;14:2722. doi: 10.3390/nu14132722. [DOI] [PMC free article] [PubMed] [Google Scholar]
  402. Xu Y, Xiang S, Ye K, Zheng Y, Feng X, Zhu X, Chen J, Chen Y. Cobalamin (vitamin B12) induced a shift in microbial composition and metabolic activity in an in vitro colon simulation. Front Microbiol. 2018;9:2780. doi: 10.3389/fmicb.2018.02780. [DOI] [PMC free article] [PubMed] [Google Scholar]
  403. Xu Z, Tang H, Huang F, Qiao Z, Wang X, Yang C, Deng Q. Algal oil rich in n-3 PUFA alleviates DSS-induced colitis via regulation of gut microbiota and restoration of intestinal barrier. Front Microbiol. 2020;11:615404. doi: 10.3389/fmicb.2020.615404. [DOI] [PMC free article] [PubMed] [Google Scholar]
  404. Xue F, Nan X, Li Y, Pan X, Guo Y, Jiang L, Xiong B. Metagenomic insights into effects of thiamine supplementation on ruminal non-methanogen archaea in high-concentrate diets feeding dairy cows. BMC Vet Res. 2019;15:7. doi: 10.1186/s12917-018-1745-0. [DOI] [PMC free article] [PubMed] [Google Scholar]
  405. Yamada S, Kamada N, Amiya T, Nakamoto N, Nakaoka T, Kimura M, Saito Y, Ejima C, Kanai T, Saito H. Gut microbiota-mediated generation of saturated fatty acids elicits inflammation in the liver in murine high-fat diet-induced steatohepatitis. BMC Gastroenterol. 2017;17:136. doi: 10.1186/s12876-017-0689-3. [DOI] [PMC free article] [PubMed] [Google Scholar]
  406. Yamamoto EA, Jørgensen TN. Relationships between vitamin D, gut microbiome, and systemic autoimmunity. Front Immunol. 2019;10:3141. doi: 10.3389/fimmu.2019.03141. [DOI] [PMC free article] [PubMed] [Google Scholar]
  407. Yamashiro Y. Gut microbiota in health and disease. Ann Nutr Metab. 2017;71:242–246. doi: 10.1159/000481627. [DOI] [PubMed] [Google Scholar]
  408. Yang S, Gao X, Meng J, Zhang A, Zhou Y, Long M, Li B, Deng W, Jin L, Zhao S, et al. Metagenomic analysis of bacteria, fungi, bacteriophages, and helminths in the gut of giant pandas. Front Microbiol. 2018;9:1717. doi: 10.3389/fmicb.2018.01717. [DOI] [PMC free article] [PubMed] [Google Scholar]
  409. Yang S, Li L, Yu L, Sun L, Li K, Tong C, Xu W, Cui G, Long M, Li P. Selenium-enriched yeast reduces caecal pathological injuries and intervenes changes of the diversity of caecal microbiota caused by Ochratoxin-A in broilers. Food Chem Toxicol. 2020;137:111139. doi: 10.1016/j.fct.2020.111139. [DOI] [PubMed] [Google Scholar]
  410. Yang Z, Huang S, Zou D, Dong D, He X, Liu N, Liu W, Huang L. Metabolic shifts and structural changes in the gut microbiota upon branched-chain amino acid supplementation in middle-aged mice. Amino Acids. 2016;48:2731–2745. doi: 10.1007/s00726-016-2308-y. [DOI] [PubMed] [Google Scholar]
  411. Yano JM, Yu K, Donaldson GP, Shastri GG, Ann P, Ma L, Nagler CR, Ismagilov RF, Mazmanian SK, Hsiao EY. Indigenous bacteria from the gut microbiota regulate host serotonin biosynthesis. Cell. 2015;161:264–276. doi: 10.1016/j.cell.2015.02.047. [DOI] [PMC free article] [PubMed] [Google Scholar]
  412. Yasuma T, Toda M, Abdel-Hamid AM, D’Alessandro-Gabazza C, Kobayashi T, Nishihama K, D’Alessandro VF, Pereira GV, Mackie RI, Gabazza EC, et al. Degradation products of complex arabinoxylans by Bacteroides intestinalis enhance the host immune response. Microorganisms. 2021;9:1126. doi: 10.3390/microorganisms9061126. [DOI] [PMC free article] [PubMed] [Google Scholar]
  413. Ye L, Bae M, Cassilly CD, Jabba SV, Thorpe DW, Martin AM, Lu HY, Wang J, Thompson JD, Lickwar CR, et al. Enteroendocrine cells sense bacterial tryptophan catabolites to activate enteric and vagal neuronal pathways. Cell Host Microbe. 2021;29:179–196. doi: 10.1016/j.chom.2020.11.011. [DOI] [PMC free article] [PubMed] [Google Scholar]
  414. Ye S, Shah BR, Li J, Liang H, Zhan F, Geng F, Li B. A critical review on interplay between dietary fibers and gut microbiota. Trends Food Sci Tech. 2022;124:237–249. doi: 10.1016/j.tifs.2022.04.010. [DOI] [Google Scholar]
  415. Yin J, Han H, Li Y, Liu Z, Zhao Y, Fang R, Huang X, Zheng J, Ren W, Wu F, et al. Lysine restriction affects feed intake and amino acid metabolism via gut microbiome in piglets. Cell Physiol Biochem. 2017;44:1749–1761. doi: 10.1159/000485782. [DOI] [PubMed] [Google Scholar]
  416. Yin J, Li Y, Han H, Chen S, Gao J, Liu G, Wu X, Deng J, Yu Q, Huang X, et al. Melatonin reprogramming of gut microbiota improves lipid dysmetabolism in high-fat diet-fed mice. J Pineal Res. 2018;65:e12524. doi: 10.1111/jpi.12524. [DOI] [PubMed] [Google Scholar]
  417. Yin J, Zhang B, Yu Z, Hu Y, Lv H, Ji X, Wang J, Peng B, Wang S. Ameliorative effect of dietary tryptophan on neurodegeneration and inflammation in d-galactose-induced aging mice with the potential mechanism relying on AMPK/SIRT1/PGC-1α pathway and gut microbiota. J Agric Food Chem. 2021;69:4732–4744. doi: 10.1021/acs.jafc.1c00706. [DOI] [PubMed] [Google Scholar]
  418. Yiu JHC, Chan KS, Cheung J, Li J, Liu Y, Wang Y, Fung WWL, Cai J, Cheung SWM, Dorweiler B, et al. Gut microbiota-associated activation of TLR5 induces apolipoprotein A1 production in the liver. Circ Res. 2020;127:1236–1252. doi: 10.1161/CIRCRESAHA.120.317362. [DOI] [PMC free article] [PubMed] [Google Scholar]
  419. York A. Your microbiome is what you eat. Nat Rev Microbiol. 2019;17:721. doi: 10.1038/s41579-019-0287-1. [DOI] [PubMed] [Google Scholar]
  420. Yue Q, Cai M, Xiao B, Zhan Q, Zeng C. A high-tryptophan diet reduces seizure-induced respiratory arrest and alters the gut microbiota in DBA/1 mice. Front Neurol. 2021;12:762323. doi: 10.3389/fneur.2021.762323. [DOI] [PMC free article] [PubMed] [Google Scholar]
  421. Zackular JP, Moore JL, Jordan AT, Juttukonda LJ, Noto MJ, Nicholson MR, Crews JD, Semler MW, Zhang Y, Ware LB, et al. Dietary zinc alters the microbiota and decreases resistance to Clostridium difficile infection. Nat Med. 2016;22:1330–1334. doi: 10.1038/nm.4174. [DOI] [PMC free article] [PubMed] [Google Scholar]
  422. Zackular JP, Skaar EP. The role of zinc and nutritional immunity in Clostridium difficile infection. Gut Microbes. 2018;9:469–476. doi: 10.1080/19490976.2018.1448354. [DOI] [PMC free article] [PubMed] [Google Scholar]
  423. 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;39:372–385. doi: 10.1016/j.immuni.2013.08.003. [DOI] [PubMed] [Google Scholar]
  424. Zelante T, Puccetti M, Giovagnoli S, Romani L. Regulation of host physiology and immunity by microbial indole-3-aldehyde. Curr Opin Immunol. 2021;70:27–32. doi: 10.1016/j.coi.2020.12.004. [DOI] [PubMed] [Google Scholar]
  425. Zentek J, Ferrara F, Pieper R, Tedin L, Meyer W, Vahjen W. Effects of dietary combinations of organic acids and medium chain fatty acids on the gastrointestinal microbial ecology and bacterial metabolites in the digestive tract of weaning piglets. J Anim Sci. 2013;91:3200–3210. doi: 10.2527/jas.2012-5673. [DOI] [PubMed] [Google Scholar]
  426. Zhai Q, Cen S, Li P, Tian F, Zhao J, Zhang H, Chen W. Effects of dietary selenium supplementation on intestinal barrier and immune responses associated with its modulation of gut microbiota. Environ Sci Technol Lett. 2018;5:724–730. doi: 10.1021/acs.estlett.8b00563. [DOI] [Google Scholar]
  427. Zhai Q, Li T, Yu L, Xiao Y, Feng S, Wu J, Zhao J, Zhang H, Chen W. Effects of subchronic oral toxic metal exposure on the intestinal microbiota of mice. Sci Bull. 2017;62:831–840. doi: 10.1016/j.scib.2017.01.031. [DOI] [PubMed] [Google Scholar]
  428. Zhai, S., Qin, S., Li, L., Zhu, L., Zou, Z., and Wang, L. (2019). Dietary butyrate suppresses inflammation through modulating gut microbiota in high-fat diet-fed mice. FEMS Microbiol Lett 366. [DOI] [PubMed]
  429. Zhai X, Wang N, Jiao H, Zhang J, Li C, Ren W, Reiter RJ, Su S. Melatonin and other indoles show antiviral activities against swine coronaviruses in vitro at pharmacological concentrations. J Pineal Res. 2021;71:e12754. doi: 10.1111/jpi.12754. [DOI] [PubMed] [Google Scholar]
  430. Zhang D, Gao X, Li H, Borger DK, Wei Q, Yang E, Xu C, Pinho S, Frenette PS. The microbiota regulates hematopoietic stem cell fate decisions by controlling iron availability in bone marrow. Cell Stem Cell 29. 2022;232–247:e7. doi: 10.1016/j.stem.2021.12.009. [DOI] [PMC free article] [PubMed] [Google Scholar]
  431. Zhang M, Gao C, Guo X, Guo S, Kang Z, Xiao D, Yan J, Tao F, Zhang W, Dong W, et al. Increased glutarate production by blocking the glutaryl-CoA dehydrogenation pathway and a catabolic pathway involving L-2-hydroxyglutarate. Nat Commun. 2018;9:2114. doi: 10.1038/s41467-018-04513-0. [DOI] [PMC free article] [PubMed] [Google Scholar]
  432. Zhang R, Gu J, Wang X, Li Y, Liu J, Lu C, Qiu L. Response of antibiotic resistance genes abundance by graphene oxide during the anaerobic digestion of swine manure with copper pollution. Sci Total Environ. 2019;654:292–299. doi: 10.1016/j.scitotenv.2018.11.094. [DOI] [PubMed] [Google Scholar]
  433. Zhang T, Zhu X, Guo J, Gu AZ, Li D, Chen J. Toxicity assessment of nano-ZnO exposure on the human intestinal microbiome, metabolic functions, and resistome using an in vitro colon simulator. Environ Sci Technol. 2021;55:6884–6896. doi: 10.1021/acs.est.1c00573. [DOI] [PubMed] [Google Scholar]
  434. Zhang X, Coker OO, Chu ES, Fu K, Lau HCH, Wang YX, Chan AWH, Wei H, Yang X, Sung JJY, et al. Dietary cholesterol drives fatty liver-associated liver cancer by modulating gut microbiota and metabolites. Gut. 2021;70:761–774. doi: 10.1136/gutjnl-2019-319664. [DOI] [PMC free article] [PubMed] [Google Scholar]
  435. Zhang X, Shang X, Jin S, Ma Z, Wang H, Ao N, Yang J, Du J. Vitamin D ameliorates high-fat-diet-induced hepatic injury via inhibiting pyroptosis and alters gut microbiota in rats. Arch Biochem Biophys. 2021;705:108894. doi: 10.1016/j.abb.2021.108894. [DOI] [PubMed] [Google Scholar]
  436. Zhang XL, Chen L, Yang J, Zhao SS, Jin S, Ao N, Yang J, Liu H X, Du J. Vitamin D alleviates non-alcoholic fatty liver disease via restoring gut microbiota and metabolism. Front Microbiol. 2023;14:1117644. doi: 10.3389/fmicb.2023.1117644. [DOI] [PMC free article] [PubMed] [Google Scholar]
  437. Zhang Y, He X, Qian Y, Xu S, Mo C, Yan Z, Yang X, Xiao Q. Plasma branched-chain and aromatic amino acids correlate with the gut microbiota and severity of Parkinson’s disease. NPJ Parkinsons Dis. 2022;8:48. doi: 10.1038/s41531-022-00312-z. [DOI] [PMC free article] [PubMed] [Google Scholar]
  438. Zhang Y, Lu T, Han L, Zhao L, Niu Y, Chen H. L-glutamine supplementation alleviates constipation during late gestation of mini sows by modifying the microbiota composition in feces. Biomed Res Int. 2017;2017:1–9. doi: 10.1155/2017/4862861. [DOI] [PMC free article] [PubMed] [Google Scholar]
  439. Zhao Y, Gong C, Xu J, Chen D, Yang B, Chen Z, Wei L. Research progress of fecal microbiota transplantation in liver diseases. J Clin Med. 2023;12:1683. doi: 10.3390/jcm12041683. [DOI] [PMC free article] [PubMed] [Google Scholar]
  440. Zhao Z, Shi A, Wang Q, Zhou J. High oleic acid peanut oil and extra virgin olive oil supplementation attenuate metabolic syndrome in rats by modulating the gut microbiota. Nutrients. 2019;11:3005. doi: 10.3390/nu11123005. [DOI] [PMC free article] [PubMed] [Google Scholar]
  441. Zhirnova IG, Kuznetsova AV, Rebrova OY, Labunsky DA, Komelkova LV, Poleshchuk VV, Senko OV. logical and statistical approach for the analysis of immunological parameters in patients with Wilson’s disease. Russ J Immunol. 1998;3:173–184. [PubMed] [Google Scholar]
  442. Zhou S, Wang Y, Jacoby JJ, Jiang Y, Zhang Y, Yu LL. Effects of medium- and long-chain triacylglycerols on lipid metabolism and gut microbiota composition in C57BL/6J Mice. J Agric Food Chem. 2017;65:6599–6607. doi: 10.1021/acs.jafc.7b01803. [DOI] [PubMed] [Google Scholar]
  443. Zhu H, Zhou Y, Qi Y, Ji R, Zhang J, Qian Z, Wu C, Tan J, Shao L, Chen D. Preparation and characterization of selenium enriched-Bifidobacterium longum DD98, and its repairing effects on antibiotic-induced intestinal dysbacteriosis in mice. Food Funct. 2019;10:4975–4984. doi: 10.1039/C9FO00960D. [DOI] [PubMed] [Google Scholar]
  444. Zhuang P, Shou Q, Lu Y, Wang G, Qiu J, Wang J, He L, Chen J, Jiao J, Zhang Y. Arachidonic acid sex-dependently affects obesity through linking gut microbiota-driven inflammation to hypothalamus-adipose-liver axis. Biochim Biophys Acta. 2017;1863:2715–2726. doi: 10.1016/j.bbadis.2017.07.003. [DOI] [PubMed] [Google Scholar]
  445. Zmora N, Suez J, Elinav E. You are what you eat: diet, health and the gut microbiota. Nat Rev Gastroenterol Hepatol. 2019;16:35–56. doi: 10.1038/s41575-018-0061-2. [DOI] [PubMed] [Google Scholar]

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