REFERENCES
1. Fan Y, Pedersen O. Gut microbiota in human metabolic health and disease. Nat Rev Microbiol 2021;19:55-71.
3. Sencio V, Machado MG, Trottein F. The lung-gut axis during viral respiratory infections: the impact of gut dysbiosis on secondary disease outcomes. Mucosal Immunol 2021;14:296-304.
4. Arpaia N, Campbell C, Fan X, et al. Metabolites produced by commensal bacteria promote peripheral regulatory T-cell generation. Nature 2013;504:451-5.
6. Zuo T, Zhang F, Lui GCY, et al. Alterations in gut microbiota of patients with COVID-19 during time of hospitalization. Gastroenterology 2020;159:944-55.e8.
7. Gomaa EZ. Human gut microbiota/microbiome in health and diseases: a review. Antonie Van Leeuwenhoek 2020;113:2019-40.
8. Wu Y, Cheng X, Jiang G, et al. Altered oral and gut microbiota and its association with SARS-CoV-2 viral load in COVID-19 patients during hospitalization. NPJ Biofilms Microbiomes 2021;7:61.
9. He F, Zhang T, Xue K, et al. Fecal multi-omics analysis reveals diverse molecular alterations of gut ecosystem in COVID-19 patients. Anal Chim Acta 2021;1180:338881.
10. Zuo T, Zhan H, Zhang F, et al. Alterations in fecal fungal microbiome of patients with COVID-19 during time of hospitalization until discharge. Gastroenterology 2020;159:1302-10.e5.
11. Shen Y, Yu F, Zhang D, et al. Dynamic alterations in the respiratory tract microbiota of patients with COVID-19 and its association with microbiota in the gut. Adv Sci 2022;9:e2200956.
12. Gu S, Chen Y, Wu Z, et al. Alterations of the gut microbiota in patients with coronavirus disease 2019 or H1N1 influenza. Clin Infect Dis 2020;71:2669-78.
13. Zhang F, Wan Y, Zuo T, et al. Prolonged impairment of short-chain fatty acid and L-isoleucine biosynthesis in gut microbiome in patients with COVID-19. Gastroenterology 2022;162:548-61.e4.
14. Lv W, He J, Shao J, Chen Y, Xia L, Zhang L. Causal relationships between short-chain fatty acids and L-isoleucine biosynthesis and susceptibility and severity of COVID-19: evidence from Mendelian randomization. J Infect 2023;87:e16-8.
15. Lv L, Jiang H, Chen Y, et al. The faecal metabolome in COVID-19 patients is altered and associated with clinical features and gut microbes. Anal Chim Acta 2021;1152:338267.
16. Yelin D, Margalit I, Yahav D, Runold M, Bruchfeld J. Long COVID-19-it’s not over until? Clin Microbiol Infect 2021;27:506-8.
17. Vestad B, Ueland T, Lerum TV, et al. Respiratory dysfunction three months after severe COVID-19 is associated with gut microbiota alterations. J Intern Med 2022;291:801-12.
18. Cui GY, Rao BC, Zeng ZH, et al. Characterization of oral and gut microbiome and plasma metabolomics in COVID-19 patients after 1-year follow-up. Mil Med Res 2022;9:32.
19. Su Q, Lau RI, Liu Q, Chan FKL, Ng SC. Post-acute COVID-19 syndrome and gut dysbiosis linger beyond 1 year after SARS-CoV-2 clearance. Gut 2023;72:1230-2.
20. Dumas A, Bernard L, Poquet Y, Lugo-Villarino G, Neyrolles O. The role of the lung microbiota and the gut-lung axis in respiratory infectious diseases. Cell Microbiol 2018;20:e12966.
21. Wang J, Li F, Wei H, Lian ZX, Sun R, Tian Z. Respiratory influenza virus infection induces intestinal immune injury via microbiota-mediated Th17 cell-dependent inflammation. J Exp Med 2014;211:2397-410.
22. Groves HT, Higham SL, Moffatt MF, Cox MJ, Tregoning JS. Respiratory viral infection alters the gut microbiota by inducing inappetence. mBio 2020;11:e03236-19.
23. Merad M, Martin JC. Pathological inflammation in patients with COVID-19: a key role for monocytes and macrophages. Nat Rev Immunol 2020;20:355-62.
24. Cerf-Bensussan N, Gaboriau-Routhiau V. The immune system and the gut microbiota: friends or foes? Nat Rev Immunol 2010;10:735-44.
25. Liang W, Feng Z, Rao S, et al. Diarrhoea may be underestimated: a missing link in 2019 novel coronavirus. Gut 2020;69:1141-3.
26. Qi F, Qian S, Zhang S, Zhang Z. Single cell RNA sequencing of 13 human tissues identify cell types and receptors of human coronaviruses. Biochem Biophys Res Commun 2020;526:135-40.
27. Hoffmann M, Kleine-Weber H, Schroeder S, et al. SARS-CoV-2 cell entry depends on ACE2 and TMPRSS2 and is blocked by a clinically proven protease inhibitor. Cell 2020;181:271-80.e8.
28. Walls AC, Park YJ, Tortorici MA, Wall A, McGuire AT, Veesler D. Structure, function, and antigenicity of the SARS-CoV-2 spike glycoprotein. Cell 2020;183:1735.
29. Lin L, Jiang X, Zhang Z, et al. Gastrointestinal symptoms of 95 cases with SARS-CoV-2 infection. Gut 2020;69:997-1001.
30. Jiang X, Luo M, Zou Z, Wang X, Chen C, Qiu J. Asymptomatic SARS-CoV-2 infected case with viral detection positive in stool but negative in nasopharyngeal samples lasts for 42 days. J Med Virol 2020;92:1807-9.
31. Bradley BT, Maioli H, Johnston R, et al. Histopathology and ultrastructural findings of fatal COVID-19 infections in Washington State: a case series. Lancet 2020;396:320-32.
32. Jiao L, Li H, Xu J, et al. The gastrointestinal tract is an alternative route for SARS-CoV-2 infection in a nonhuman primate model. Gastroenterology 2021;160:1647-61.
33. Lamers MM, Beumer J, van der Vaart J, et al. SARS-CoV-2 productively infects human gut enterocytes. Science 2020;369:50-4.
34. Katz-Agranov N, Zandman-Goddard G. Autoimmunity and COVID-19 - The microbiotal connection. Autoimmun Rev 2021;20:102865.
35. de Oliveira AP, Lopes ALF, Pacheco G, de Sá Guimarães Nolêto IR, Nicolau LAD, Medeiros JVR. Premises among SARS-CoV-2, dysbiosis and diarrhea: walking through the ACE2/mTOR/autophagy route. Med Hypotheses 2020;144:110243.
36. Patel P, Roper J. Gut microbiome composition is associated with COVID-19 disease severity. Gastroenterology 2021;161:722-4.
37. Rawson TM, Moore LSP, Zhu N, et al. Bacterial and fungal coinfection in individuals with coronavirus: a rapid review to support COVID-19 antimicrobial prescribing. Clin Infect Dis 2020;71:2459-68.
38. Chen N, Zhou M, Dong X, et al. Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study. Lancet 2020;395:507-13.
39. Cox MJ, Loman N, Bogaert D, O’Grady J. Co-infections: potentially lethal and unexplored in COVID-19. Lancet Microbe 2020;1:e11.
40. Martins-Filho PR, Tavares CSS, Santos VS. Factors associated with mortality in patients with COVID-19. A quantitative evidence synthesis of clinical and laboratory data. Eur J Intern Med 2020;76:97-9.
41. Li J, Richards EM, Handberg EM, Pepine CJ, Raizada MK. Butyrate regulates COVID-19-relevant genes in gut epithelial organoids from normotensive rats. Hypertension 2021;77:e13-6.
42. Liu XF, Shao JH, Liao YT, et al. Regulation of short-chain fatty acids in the immune system. Front Immunol 2023;14:1186892.
43. Fan L, Xia Y, Wang Y, et al. Gut microbiota bridges dietary nutrients and host immunity. Sci China Life Sci 2023;66:2466-514.
44. Zuo T, Liu Q, Zhang F, et al. Depicting SARS-CoV-2 faecal viral activity in association with gut microbiota composition in patients with COVID-19. Gut 2021;70:276-84.
45. Stefan KL, Kim MV, Iwasaki A, Kasper DL. Commensal microbiota modulation of natural resistance to virus infection. Cell 2020;183:1312-24.e10.
46. Tang L, Gu S, Gong Y, et al. Clinical significance of the correlation between changes in the major intestinal bacteria species and COVID-19 severity. Engineering 2020;6:1178-84.
47. Ma N, He T, Johnston LJ, Ma X. Host-microbiome interactions: the aryl hydrocarbon receptor as a critical node in tryptophan metabolites to brain signaling. Gut Microbes 2020;11:1203-19.
48. Tsay JCJ, Wu BG, Sulaiman I, et al. Lower airway dysbiosis affects lung cancer progression. Cancer Discov 2021;11:293-307.
49. Dhar D, Mohanty A. Gut microbiota and Covid-19- possible link and implications. Virus Res 2020;285:198018.
50. Mendes de Almeida V, Engel DF, Ricci MF, et al. Gut microbiota from patients with COVID-19 cause alterations in mice that resemble post-COVID symptoms. Gut Microbes 2023;15:2249146.
51. Lau HCH, Ng SC, Yu J. Targeting the gut microbiota in coronavirus disease 2019: hype or hope? Gastroenterology 2022;162:9-16.
52. Troisi J, Venutolo G, Pujolassos Tanyà M, Delli Carri M, Landolfi A, Fasano A. COVID-19 and the gastrointestinal tract: source of infection or merely a target of the inflammatory process following SARS-CoV-2 infection? World J Gastroenterol 2021;27:1406-18.
53. Wu D, Zhang Y, Dong S, Zhong C. Mutual interaction of microbiota and host immunity during health and diseases. Biophys Rep 2021;7:326-40.
54. Mozaffari SA, Salehi A, Mousavi E, et al. SARS-CoV-2-associated gut microbiome alteration; A new contributor to colorectal cancer pathogenesis. Pathol Res Pract 2022;239:154131.
55. McNabney SM, Henagan TM. Short chain fatty acids in the colon and peripheral tissues: a focus on butyrate, colon cancer, obesity and insulin resistance. Nutrients 2017;9:1348.
56. Lo BC, Shin SB, Canals Hernaez D, et al. IL-22 preserves gut epithelial integrity and promotes disease remission during chronic salmonella infection. J Immunol 2019;202:956-65.
57. Maruyama D, Liao WI, Tian X, et al. Regulation of lung immune tone by the gut-lung axis via dietary fiber, gut microbiota, and short-chain fatty acids. bioRxiv 2023;In press.
58. Cryan JF, O’Riordan KJ, Sandhu K, Peterson V, Dinan TG. The gut microbiome in neurological disorders. Lancet Neurol 2020;19:179-94.
59. Hashimoto K. Detrimental effects of COVID-19 in the brain and therapeutic options for long COVID: the role of Epstein-Barr virus and the gut-brain axis. Mol Psychiatry 2023;In press.
60. Luo J, Liang S, Jin F. Gut microbiota in antiviral strategy from bats to humans: a missing link in COVID-19. Sci China Life Sci 2021;64:942-56.
61. Ghannoum MA, Ford M, Bonomo RA, Gamal A, McCormick TS. A microbiome-driven approach to combating depression during the COVID-19 pandemic. Front Nutr 2021;8:672390.
62. Nakov R, Dimitrova-Yurukova D, Snegarova V, Nakov V, Fox M, Heinrich H. Increased prevalence of gastrointestinal symptoms and disorders of gut-brain interaction during the COVID-19 pandemic: an internet-based survey. Neurogastroenterol Motil 2022;34:e14197.
