Integrated analysis of gut microbiome and host immune responses in COVID-19

Abstract

Emerging evidence indicates that the gut microbiome contributes to the host immune response to infectious diseases. Here, to explore the role of the gut microbiome in the host immune responses in COVID-19, we conducted shotgun metagenomic sequencing and immune profiling of 14 severe/critical and 24 mild/moderate COVID-19 cases as well as 31 healthy control samples. We found that the diversity of the gut microbiome was reduced in severe/critical COVID-19 cases compared to mild/moderate ones. We identified the abundance of some gut microbes altered post-SARS-CoV-2 infection and related to disease severity, such as Enterococcus faecium, Coprococcus comes, Roseburia intestinalis, Akkermansia muciniphila, Bacteroides cellulosilyticus and Blautia obeum. We further analyzed the correlation between the abundance of gut microbes and host responses, and obtained a correlation map between clinical features of COVID-19 and 16 severity-related gut microbe, including Coprococcus comes that was positively correlated with CD3⁺/CD4⁺/CD8⁺ lymphocyte counts. In addition, an integrative analysis of gut microbiome and the transcriptome of peripheral blood mononuclear cells (PBMCs) showed that genes related to viral transcription and apoptosis were up-regulated in Coprococcus comes low samples. Moreover, a number of metabolic pathways in gut microbes were also found to be differentially enriched in severe/critical or mild/moderate COVID-19 cases, including the superpathways of polyamine biosynthesis II and sulfur oxidation that were suppressed in severe/critical COVID-19. Together, our study highlighted a potential regulatory role of severity related gut microbes in the immune response of host.

Keywords

COVID-19 / SARS-COV-2 / gut microbiome / immune response

References

[1] Shen Y, Zheng F, Sun D, Ling Y, Chen J, Li F, Li T, Qian Z, Zhang Y, Xu Q, Liu L, Huang Q, Shan F, Xu L, Wu J, Zhu Z, Song Z, Li S, Shi Y, Zhang J, Wu X, Mendelsohn JB, Zhu T, Lu H. Epidemiology and clinical course of COVID-19 in Shanghai, China. Emerg Microbes Infect 2020; 9(1): 1537–1545

[2] Taleghani N, Taghipour F. Diagnosis of COVID-19 for controlling the pandemic: a review of the state-of-the-art. Biosens Bioelectron 2021; 174: 112830

[3] D’Arienzo M, Coniglio A. Assessment of the SARS-CoV-2 basic reproduction number, R₀, based on the early phase of COVID-19 outbreak in Italy. Biosaf Health 2020; 2(2): 57–59

[4] Zhang X, Tan Y, Ling Y, Lu G, Liu F, Yi Z, Jia X, Wu M, Shi B, Xu S, Chen J, Wang W, Chen B, Jiang L, Yu S, Lu J, Wang J, Xu M, Yuan Z, Zhang Q, Zhang X, Zhao G, Wang S, Chen S, Lu H. Viral and host factors related to the clinical outcome of COVID-19. Nature 2020; 583(7816): 437–440

[5] Tan Y, Zhang W, Zhu Z, Qiao N, Ling Y, Guo M, Yin T, Fang H, Xu X, Lu G, Zhang P, Yang S, Fu Z, Liang D, Xie Y, Zhang R, Jiang L, Yu S, Lu J, Jiang F, Chen J, Xiao C, Wang S, Chen S, Bian XW, Lu H, Liu F, Chen S. Integrating longitudinal clinical laboratory tests with targeted proteomic and transcriptomic analyses reveal the landscape of host responses in COVID-19. Cell Discov 2021; 7(1): 42

[6] Jin A, Yan B, Hua W, Feng D, Xu B, Liang L, Guo C. Clinical characteristics of patients diagnosed with COVID-19 in Beijing. Biosaf Health 2020; 2(2): 104–111

[7] Kok L, Masopust D, Schumacher TN. The precursors of CD8⁺ tissue resident memory T cells: from lymphoid organs to infected tissues. Nat Rev Immunol 2021; [Epub ahead of print] doi: 10.1038/s41577-021-00590-3

[8] Krautkramer KA, Fan J, Bäckhed F. Gut microbial metabolites as multi-kingdom intermediates. Nat Rev Microbiol 2021; 19(2): 77–94

[9] Fan Y, Pedersen O. Gut microbiota in human metabolic health and disease. Nat Rev Microbiol 2021; 19(1): 55–71

[10] Martinez-Guryn K, Leone V, Chang EB. Regional diversity of the gastrointestinal microbiome. Cell Host Microbe 2019; 26(3): 314–324

[11] Falony G, Joossens M, Vieira-Silva S, Wang J, Darzi Y, Faust K, Kurilshikov A, Bonder MJ, Valles-Colomer M, Vandeputte D, Tito RY, Chaffron S, Rymenans L, Verspecht C, De Sutter L, Lima-Mendez G, D’hoe K, Jonckheere K, Homola D, Garcia R, Tigchelaar EF, Eeckhaudt L, Fu J, Henckaerts L, Zhernakova A, Wijmenga C, Raes J. Population-level analysis of gut microbiome variation. Science 2016; 352(6285): 560–564

[12] Abt MC, Osborne LC, Monticelli LA, Doering TA, Alenghat T, Sonnenberg GF, Paley MA, Antenus M, Williams KL, Erikson J, Wherry EJ, Artis D. Commensal bacteria calibrate the activation threshold of innate antiviral immunity. Immunity 2012; 37(1): 158–170

[13] Ganal SC, Sanos SL, Kallfass C, Oberle K, Johner C, Kirschning C, Lienenklaus S, Weiss S, Staeheli P, Aichele P, Diefenbach A. Priming of natural killer cells by nonmucosal mononuclear phagocytes requires instructive signals from commensal microbiota. Immunity 2012; 37(1): 171–186

[14] Yeoh YK, Zuo T, Lui GC, Zhang F, Liu Q, Li AY, Chung AC, Cheung CP, Tso EY, Fung KS, Chan V, Ling L, Joynt G, Hui DS, Chow KM, Ng SSS, Li TC, Ng RW, Yip TC, Wong GL, Chan FK, Wong CK, Chan PK, Ng SC. Gut microbiota composition reflects disease severity and dysfunctional immune responses in patients with COVID-19. Gut 2021; 70(4): 698–706

[15] Chen Y, Gu S, Chen Y, Lu H, Shi D, Guo J, Wu WR, Yang Y, Li Y, Xu KJ, Ding C, Luo R, Huang C, Yu L, Xu M, Yi P, Liu J, Tao JJ, Zhang H, Lv L, Wang B, Sheng J, Li L. Six-month follow-up of gut microbiota richness in patients with COVID-19. Gut 2022; 71(1): 222–225

[16] Zuo T, Zhang F, Lui GCY, Yeoh YK, Li AYL, Zhan H, Wan Y, Chung ACK, Cheung CP, Chen N, Lai CKC, Chen Z, Tso EYK, Fung KSC, Chan V, Ling L, Joynt G, Hui DSC, Chan FKL, Chan PKS, Ng SC. Alterations in gut microbiota of patients with COVID-19 during time of hospitalization. Gastroenterology 2020; 159(3): 944–955.e8

[17] Cao J, Wang C, Zhang Y, Lei G, Xu K, Zhao N, Lu J, Meng F, Yu L, Yan J, Bai C, Zhang S, Zhang N, Gong Y, Bi Y, Shi Y, Chen Z, Dai L, Wang J, Yang P. Integrated gut virome and bacteriome dynamics in COVID-19 patients. Gut Microbes 2021; 13(1): 1–21

[18] Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 2014; 30(15): 2114–2120

[19] Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods 2012; 9(4): 357–359

[20] Wood DE, Lu J, Langmead B. Improved metagenomic analysis with Kraken 2. Genome Biol 2019; 20(1): 257

[21] Robinson MD, McCarthy DJ, Smyth GK. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 2010; 26(1): 139–140

[22] Hall M, Beiko RG. 16S rRNA gene analysis with QIIME2. Methods Mol Biol 2018; 1849: 113–129

[23] Segata N, Izard J, Waldron L, Gevers D, Miropolsky L, Garrett WS, Huttenhower C. Metagenomic biomarker discovery and explanation. Genome Biol 2011; 12(6): R60

[24] Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol 2014; 15(12): 550

[25] Beghini F, McIver LJ, Blanco-Míguez A, Dubois L, Asnicar F, Maharjan S, Mailyan A, Manghi P, Scholz M, Thomas AM, Valles-Colomer M, Weingart G, Zhang Y, Zolfo M, Huttenhower C, Franzosa EA, Segata N. Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3. eLife 2021; 10: e65088

[26] Newsome RC, Gauthier J, Hernandez MC, Abraham GE, Robinson TO, Williams HB, Sloan M, Owings A, Laird H, Christian T, Pride Y, Wilson KJ, Hasan M, Parker A, Senitko M, Glover SC, Gharaibeh RZ, Jobin C. The gut microbiome of COVID-19 recovered patients returns to uninfected status in a minority-dominated United States cohort. Gut Microbes 2021; 13(1): 1–15

[27] Gu S, Chen Y, Wu Z, Chen Y, Gao H, Lv L, Guo F, Zhang X, Luo R, Huang C, Lu H, Zheng B, Zhang J, Yan R, Zhang H, Jiang H, Xu Q, Guo J, Gong Y, Tang L, Li L. Alterations of the gut microbiota in patients with coronavirus disease 2019 or H1N1 influenza. Clin Infect Dis 2020; 71(10): 2669–2678

[28] Tao W, Zhang G, Wang X, Guo M, Zeng W, Xu Z, Cao D, Pan A, Wang Y, Zhang K, Ma X, Chen Z, Jin T, Liu L, Weng J, Zhu S. Analysis of the intestinal microbiota in COVID-19 patients and its correlation with the inflammatory factor IL-18. Med Microecol 2020; 5: 100023

[29] Zuo T, Liu Q, Zhang F, Lui GC, Tso EY, Yeoh YK, Chen Z, Boon SS, Chan FK, Chan PK, Ng SC. Depicting SARS-CoV-2 faecal viral activity in association with gut microbiota composition in patients with COVID-19. Gut 2021; 70(2): 276–284

[30] Tan Y, Liu F, Xu X, Ling Y, Huang W, Zhu Z, Guo M, Lin Y, Fu Z, Liang D, Zhang T, Fan J, Xu M, Lu H, Chen S. Durability of neutralizing antibodies and T-cell response post SARS-CoV-2 infection. Front Med 2020; 14(6): 746–751

[31] Zhu C, Song K, Shen Z, Quan Y, Tan B, Luo W, Wu S, Tang K, Yang Z, Wang X. Roseburia intestinalis inhibits interleukin17 excretion and promotes regulatory T cells differentiation in colitis. Mol Med Rep 2018; 17(6): 7567–7574

[32] Schirmer M, Smeekens SP, Vlamakis H, Jaeger M, Oosting M, Franzosa EA, Ter Horst R, Jansen T, Jacobs L, Bonder MJ, Kurilshikov A, Fu J, Joosten LAB, Zhernakova A, Huttenhower C, Wijmenga C, Netea MG, Xavier RJ. Linking the human gut microbiome to inflammatory cytokine production capacity. Cell 2016; 167(4): 1125–1136.e8

[33] Naidoo CC, Nyawo GR, Sulaiman I, Wu BG, Turner CT, Bu K, Palmer Z, Li Y, Reeve BWP, Moodley S, Jackson JG, Limberis J, Diacon AH, van Helden PD, Clemente JC, Warren RM, Noursadeghi M, Segal LN, Theron G. Anaerobe-enriched gut microbiota predicts pro-inflammatory responses in pulmonary tuberculosis. EBioMedicine 2021; 67: 103374

[34] Loomba R, Seguritan V, Li W, Long T, Klitgord N, Bhatt A, Dulai PS, Caussy C, Bettencourt R, Highlander SK, Jones MB, Sirlin CB, Schnabl B, Brinkac L, Schork N, Chen CH, Brenner DA, Biggs W, Yooseph S, Venter JC, Nelson KE. Gut microbiome-based metagenomic signature for non-invasive detection of advanced fibrosis in human nonalcoholic fatty liver disease. Cell Metab 2017; 25(5): 1054–1062.e5

[35] Solé C, Guilly S, Da Silva K, Llopis M, Le-Chatelier E, Huelin P, Carol M, Moreira R, Fabrellas N, De Prada G, Napoleone L, Graupera I, Pose E, Juanola A, Borruel N, Berland M, Toapanta D, Casellas F, Guarner F, Doré J, Solà E, Ehrlich SD, Ginès P. Alterations in gut microbiome in cirrhosis as assessed by quantitative metagenomics: relationship with acute-on-chronic liver failure and prognosis. Gastroenterology 2021; 160(1): 206–218.e13

[36] Jie Z, Xia H, Zhong SL, Feng Q, Li S, Liang S, Zhong H, Liu Z, Gao Y, Zhao H, Zhang D, Su Z, Fang Z, Lan Z, Li J, Xiao L, Li J, Li R, Li X, Li F, Ren H, Huang Y, Peng Y, Li G, Wen B, Dong B, Chen JY, Geng QS, Zhang ZW, Yang H, Wang J, Wang J, Zhang X, Madsen L, Brix S, Ning G, Xu X, Liu X, Hou Y, Jia H, He K, Kristiansen K. The gut microbiome in atherosclerotic cardiovascular disease. Nat Commun 2017; 8(1): 845

[37] Depommier C, Everard A, Druart C, Plovier H, Van Hul M, Vieira-Silva S, Falony G, Raes J, Maiter D, Delzenne NM, de Barsy M, Loumaye A, Hermans MP, Thissen JP, de Vos WM, Cani PD. Supplementation with Akkermansia muciniphila in overweight and obese human volunteers: a proof-of-concept exploratory study. Nat Med 2019; 25(7): 1096–1103

[38] Rasmussen M, Johansson D, Söbirk SK, Mörgelin M, Shannon O. Clinical isolates of Enterococcus faecalis aggregate human platelets. Microbes Infect 2010; 12(4): 295–301

[39] Ahmadrajabi R, Dalfardi MS, Farsinejad A, Saffari F. Distribution of Ebp pili among clinical and fecal isolates of Enterococcus faecalis and evaluation for human platelet activation. APMIS 2018; 126(4): 314–319

[40] Lee W, Lim S, Son HH, Bae KS. Sonicated extract of Enterococcus faecalis induces irreversible cell cycle arrest in phytohemagglutinin-activated human lymphocytes. J Endod 2004; 30(4): 209–212

[41] Nakamura A, Kurihara S, Takahashi D, Ohashi W, Nakamura Y, Kimura S, Onuki M, Kume A, Sasazawa Y, Furusawa Y, Obata Y, Fukuda S, Saiki S, Matsumoto M, Hase K. Symbiotic polyamine metabolism regulates epithelial proliferation and macrophage differentiation in the colon. Nat Commun 2021; 12(1): 2105

[42] Proietti E, Rossini S, Grohmann U, Mondanelli G. Polyamines and kynurenines at the intersection of immune modulation. Trends Immunol 2020; 41(11): 1037–1050

[43] Zhang M, Caragine T, Wang H, Cohen PS, Botchkina G, Soda K, Bianchi M, Ulrich P, Cerami A, Sherry B, Tracey KJ. Spermine inhibits proinflammatory cytokine synthesis in human mononuclear cells: a counterregulatory mechanism that restrains the immune response. J Exp Med 1997; 185(10): 1759–1768

[44] Wang Q, Zhang M, Ding Y, Wang Q, Zhang W, Song P, Zou MH. Activation of NAD(P)H oxidase by tryptophan-derived 3-hydroxykynurenine accelerates endothelial apoptosis and dysfunction in vivo. Circ Res 2014; 114(3): 480–492

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