Fajgenbaum, D. C. & June, C. H. Cytokine storm. N. Engl. J. Med. 383, 2255–2273 (2020).
Lucas, C. et al. Longitudinal analyses reveal immunological misfiring in extreme COVID-19. Nature 584, 463–469 (2020).
Zuo, T. et al. Alterations in intestine microbiota of sufferers with COVID-19 throughout time of hospitalization. Gastroenterology 159, 944–955.e8 (2020).
Yeoh, Y. Okay. et al. Intestine microbiota composition displays illness severity and dysfunctional immune responses in sufferers with COVID-19. Intestine 70, 698–706 (2021).
Gu, S. et al. Alterations of the intestine microbiota in sufferers with coronavirus illness 2019 or H1N1 influenza. Clin. Infect. Dis. 71, 2669–2678 (2020).
Liu, Q. et al. Intestine microbiota dynamics in a potential cohort of sufferers with post-acute COVID-19 syndrome. Intestine 71, 544–552 (2022).
Zhang, F. et al. Extended impairment of short-chain fatty acid and L-isoleucine biosynthesis in intestine microbiome in sufferers with COVID-19. Gastroenterology 162, 548–561.e4 (2022).
Vestad, B. et al. Respiratory dysfunction three months after extreme COVID-19 is related to intestine microbiota alterations. J. Intern. Med.https://doi.org/10.1111/joim.13458 (2022).
Nori, P. et al. Bacterial and fungal coinfections in COVID-19 sufferers hospitalized through the New York Metropolis pandemic surge. Infect. Management Hosp. Epidemiol. 42, 84–88 (2021).
Grasselli, G. et al. Hospital-acquired infections in critically Sick sufferers With COVID-19. Chest 160, 454–465 (2021).
Yu, D. et al. Low prevalence of bloodstream an infection and excessive blood tradition contamination charges in sufferers with COVID-19. PLoS One 15, e0242533 (2020).
Langford, B. J. et al. Bacterial co-infection and secondary an infection in sufferers with COVID-19: a residing fast evaluation and meta-analysis. Clin. Microbiol. Infect. 26, 1622–1629 (2020).
Shafran, N. et al. Secondary bacterial an infection in COVID-19 sufferers is a stronger predictor for dying in comparison with influenza sufferers. Sci. Rep. 11, 12703 (2021).
Kumar, N. P. et al. Systemic irritation and microbial translocation are attribute options of SARS-CoV-2-related multisystem inflammatory syndrome in youngsters.Open Discussion board Infect. Dis. 8, ofab279 (2021).
Buffie, C. G. et al. Precision microbiome reconstitution restores bile acid mediated resistance to Clostridium difficile. Nature 517, 205–208 (2015).
Buffie, C. G. & Pamer, E. G. Microbiota-mediated colonization resistance in opposition to intestinal pathogens. Nat. Rev. Immunol. 13, 790–801 (2013).
Modi, S. R., Collins, J. J. & Relman, D. A. Antibiotics and the intestine microbiota. J. Clin. Investig. 124, 4212–4218 (2014).
Shimasaki, T. et al. Elevated relative abundance of Klebsiella pneumoniaecarbapenemase-producing klebsiella pneumoniae throughout the intestine microbiota is related to threat of bloodstream an infection in long-term acute care hospital sufferers. Clin. Infect. Dis. 68, 2053–2059 (2019).
Kim, S., Covington, A. & Pamer, E. G. The intestinal microbiota: Antibiotics, colonization resistance, and enteric pathogens. Immunol. Rev. 279, 90–105 (2017).
Morjaria, S. et al. Antibiotic-induced shifts in fecal microbiota density and composition throughout hematopoietic stem cell transplantation. Infect. Immun. 87, e00206-19 (2019).
Niehus, R. et al. Quantifying antibiotic affect on within-patient dynamics of extended-spectrum beta-lactamase resistance. Elife 9, e49206 (2020).
Taur, Y. et al. Intestinal domination and the chance of bacteremia in sufferers present process allogeneic hematopoietic stem cell transplantation. Clin. Infect. Dis. 55, 905–914 (2012).
Taur, Y. et al. Reconstitution of the intestine microbiota of antibiotic-treated sufferers by autologous fecal microbiota transplant. Sci. Transl. Med. 10, eaap9489 (2018).
Liao, C. et al. Compilation of longitudinal microbiota knowledge and hospitalome from hematopoietic cell transplantation sufferers. Sci. Information 8, 71 (2021).
Peled, J. U. et al. Microbiota as predictor of mortality in allogeneic hematopoietic-cell transplantation. N. Engl. J. Med. 382, 822–834 (2020).
Pamer, E. G., Taur, Y., Jenq, R. & van den Brink, M. R. M. Affect of the intestinal microbiota on infections and survival following hematopoietic stem cell transplantation. Blood 124, SCI-48-SCI-48 (2014).
Chanderraj, R. et al. The bacterial density of scientific rectal swabs is very variable, correlates with sequencing contamination, and predicts affected person threat of extraintestinal an infection. Microbiome 10, 2 (2022).
McCullers, J. A. The co-pathogenesis of influenza viruses with micro organism within the lung. Nat. Rev. Microbiol. 12, 252–262 (2014).
Wang, D. et al. Medical traits of 138 hospitalized sufferers with 2019 novel coronavirus-infected pneumonia in Wuhan, China. JAMA 323, 1061–1069 (2020).
Westblade, L. F., Simon, M. S. & Satlin, M. J. Bacterial coinfections in coronavirus illness 2019. Tendencies Microbiol 29, 930–941 (2021).
Sepulveda, J. et al. Bacteremia and blood tradition utilization throughout COVID-19 surge in New York Metropolis. J. Clin. Microbiol. 58, e00875-20 (2020).
Lansbury, L., Lim, B., Baskaran, V. & Lim, W. S. Co-infections in individuals with COVID-19: a scientific evaluation and meta-analysis. J. Infect. 81, 266–275 (2020).
Sieswerda, E. et al. Suggestions for antibacterial remedy in adults with COVID-19 – an proof primarily based guideline. Clin. Microbiol. Infect. 27, 61–66 (2021).
Zhai, B. et al. Excessive-resolution mycobiota evaluation reveals dynamic intestinal translocation previous invasive candidiasis. Nat. Med. 26, 59–64 (2020).
Gago, J. et al. Pathogen species is related to mortality in nosocomial bloodstream an infection in sufferers with COVID-19. Open Discussion board Infect. Dis. 9, ofac083 (2022).
Haak, B. W. et al. Affect of intestine colonization with butyrate-producing microbiota on respiratory viral an infection following allo-HCT. Blood 131, 2978–2986 (2018).
Deriu, E. et al. Influenza virus impacts intestinal microbiota and secondary Salmonella an infection within the intestine by sort i interferons. PLoS Pathog. 12, e1005572 (2016).
Yildiz, S., Mazel-Sanchez, B., Kandasamy, M., Manicassamy, B. & Schmolke, M. Influenza A virus an infection impacts systemic microbiota dynamics and causes quantitative enteric dysbiosis. Microbiome 6, 9 (2018).
Sencio, V. et al. Intestine dysbiosis throughout influenza contributes to pulmonary pneumococcal superinfection by altered short-chain fatty acid manufacturing. Cell Rep. 30, 2934–2947.e6 (2020).
Steed, A. L. et al. The microbial metabolite desaminotyrosine protects from influenza by sort I interferon. Science 357, 498–502 (2017).
Abt, M. C. et al. Commensal micro organism calibrate the activation threshold of innate antiviral immunity. Immunity 37, 158–170 (2012).
Ichinohe, T. et al. Microbiota regulates immune protection in opposition to respiratory tract influenza A virus an infection. Proc. Natl Acad. Sci. USA 108, 5354–5359 (2011).
Sencio, V. et al. Influenza virus an infection impairs the intestine’s barrier properties and favors secondary enteric bacterial an infection by lowered manufacturing of short-chain fatty acids. Infect. Immun. 89, e0073420 (2021).
Wang, J. et al. Respiratory influenza virus an infection induces intestinal immune damage by way of microbiota-mediated Th17 cell-dependent irritation. J. Exp. Med. 211, 2397–2410 (2014).
Winkler, E. S. et al. SARS-CoV-2 causes lung an infection with out extreme illness in human ACE2 knock-in mice. J. Virol. 96, e0151121 (2022).
Yinda, C. Okay. et al. K18-hACE2 mice develop respiratory illness resembling extreme COVID-19. PLoS Pathog. 17, e1009195 (2021).
Zheng, J. et al. COVID-19 therapies and pathogenesis together with anosmia in K18-hACE2 mice. Nature 589, 603–607 (2021).
Golden, J. W. et al. Human angiotensin-converting enzyme 2 transgenic mice contaminated with SARS-CoV-2 develop extreme and deadly respiratory illness. JCI Perception 5, e142032 (2020).
Bao, L. et al. The pathogenicity of SARS-CoV-2 in hACE2 transgenic mice. Nature 583, 830–833 (2020).
Cadwell, Okay. et al. A key position for autophagy and the autophagy gene Atg16l1 in mouse and human intestinal Paneth cells. Nature 456, 259–263 (2008).
Cadwell, Okay. et al. Virus-plus-susceptibility gene interplay determines Crohn’s illness gene Atg16L1 phenotypes in gut. Cell 141, 1135–1145 (2010).
Matsuzawa-Ishimoto, Y. et al. Autophagy protein ATG16L1 prevents necroptosis within the intestinal epithelium. J. Exp. Med. 214, 3687–3705 (2017).
Schluter, J. et al. The intestine microbiota is related to immune cell dynamics in people. Nature 588, 303–307 (2020).
Gopalakrishnan, V. et al. Intestine microbiome modulates response to anti-PD-1 immunotherapy in melanoma sufferers. Science 359, 97–103 (2018).
Diefenbach, C. S. et al. Microbial dysbiosis is related to aggressive histology and opposed scientific end result in B-cell non-Hodgkin lymphoma. Blood Adv. 5, 1194–1198 (2021).
Sokol, H. et al. Faecalibacterium prausnitzii is an anti-inflammatory commensal bacterium recognized by intestine microbiota evaluation of Crohn illness sufferers. Proc. Natl Acad. Sci. USA 105, 16731–16736 (2008).
Wrzosek, L. et al. Bacteroides thetaiotaomicron and Faecalibacterium prausnitzii affect the manufacturing of mucus glycans and the event of goblet cells within the colonic epithelium of a gnotobiotic mannequin rodent. BMC Biol. 11, 61 (2013).
Seibert, B. et al. Delicate and extreme SARS-CoV-2 an infection induces respiratory and intestinal microbiome adjustments within the K18-hACE2 transgenic mouse mannequin. Microbiol. Spectr. 9, e0053621 (2021).
Sencio, V. et al. Alteration of the intestine microbiota following SARS-CoV-2 an infection correlates with illness severity in hamsters. Intestine Microbes 14, 2018900 (2022).
Sokol, H. et al. SARS-CoV-2 an infection in nonhuman primates alters the composition and useful exercise of the intestine microbiota. Intestine Microbes 13, 1–19 (2021).
Gaebler, C. et al. Evolution of antibody immunity to SARS-CoV-2. Nature 591, 639–644 (2021).
Park, S.-Okay. et al. Detection of SARS-CoV-2 in fecal samples from sufferers with asymptomatic and Delicate COVID-19 in Korea. Clin. Gastroenterol. Hepatol. 19, 1387–1394.e2 (2021).
Xiao, F. et al. Proof for gastrointestinal an infection of SARS-CoV-2. Gastroenterology 158, 1831–1833.e3 (2020).
Cheung, Okay. S. et al. Gastrointestinal manifestations of SARS-CoV-2 an infection and virus load in fecal samples from a Hong Kong Cohort: systematic evaluation and meta-analysis. Gastroenterology 159, 81–95 (2020).
Lamers, M. M. et al. SARS-CoV-2 productively infects human intestine enterocytes. Science 369, 50–54 (2020).
Cao, J. et al. Built-in intestine virome and bacteriome dynamics in COVID-19 sufferers. Intestine Microbes 13, 1–21 (2021).
Klag, T., Stange, E. F. & Wehkamp, J. Faulty antibacterial barrier in inflammatory bowel illness. Dig. Dis. 31, 310–316 (2013).
Ramanan, D. & Cadwell, Okay. Intrinsic protection mechanisms of the intestinal epithelium. Cell Host Microbe 19, 434–441 (2016).
Schluter, J. & Foster, Okay. R. The evolution of mutualism in intestine microbiota by way of host epithelial choice. PLoS Biol. 10, e1001424 (2012).
McLoughlin, Okay., Schluter, J., Rakoff-Nahoum, S., Smith, A. L. & Foster, Okay. R. Host choice of microbiota by way of differential adhesion. Cell Host Microbe 19, 550–559 (2016).
Fernandez-Castañer, M. et al. Analysis of B-cell perform in diabetics by C-peptide willpower in basal and postprandial urine. Diabete Metab. 13, 538–542 (1987).
Yu, S. et al. Paneth cell-derived lysozyme defines the composition of mucolytic microbiota and the inflammatory tone of the gut. Immunity 53, 398–416.e8 (2020).
Salzman, N. H. et al. Enteric defensins are important regulators of intestinal microbial ecology. Nat. Immunol. 11, 76–83 (2010).
van der Lugt, B. et al. Akkermansia muciniphila ameliorates the age-related decline in colonic mucus thickness and attenuates immune activation in accelerated growing older Ercc1-/Δ7 mice. Immun. Ageing 16, 6 (2019).
Routy, B. et al. Intestine microbiome influences efficacy of PD-1-based immunotherapy in opposition to epithelial tumors. Science 359, 91–97 (2018).
Wang, C., Hu, J., Blaser, M. J. & Li, H. Estimating and testing the microbial causal mediation impact with high-dimensional and compositional microbiome knowledge. Bioinformatics 36, 347–355 (2020).
Zhang, X.-S. et al. Antibiotic-induced acceleration of sort 1 diabetes alters maturation of innate intestinal immunity. Elife 7, e37816 (2018).
Schulfer, A. F. et al. The affect of early-life sub-therapeutic antibiotic therapy (STAT) on extreme weight is powerful regardless of switch of intestinal microbes. ISME J. 13, 1280–1292 (2019).
Wang, L. et al. An observational cohort research of bacterial co-infection and implications for empirical antibiotic remedy in sufferers presenting with COVID-19 to hospitals in North West London. J. Antimicrob. Chemother. 76, 796–803 (2021).
Labarta-Bajo, L. et al. Kind I IFNs and CD8 T cells improve intestinal barrier permeability after continual viral an infection. J. Exp. Med. 217, e20192276 (2020).
Karki, R. et al. Synergism of TNF-α and IFN-γ triggers inflammatory cell dying, tissue injury, and mortality in SARS-CoV-2 an infection and cytokine shock syndromes. Cell 184, 149–168.e17 (2021).
Giron, L. B. et al. Plasma markers of disrupted intestine permeability in extreme COVID-19 sufferers. Entrance. Immunol. 12, 686240 (2021).
Ubeda, C. et al. Vancomycin-resistant Enterococcus domination of intestinal microbiota is enabled by antibiotic therapy in mice and precedes bloodstream invasion in people. J. Clin. Investig. 120, 4332–4341 (2010).
Dickson, R. P. et al. Enrichment of the lung microbiome with intestine micro organism in sepsis and the acute respiratory misery syndrome. Nat. Microbiol. 1, 16113 (2016).
Yelin, I. et al. Genomic and epidemiological proof of bacterial transmission from probiotic capsule to blood in ICU sufferers. Nat. Med. 25, 1728–1732 (2019).
Xie, X. et al. An Infectious cDNA Clone of SARS-CoV-2. Cell Host Microbe 27, 841–848.e3 (2020).
Gohl, D. M. et al. Systematic enchancment of amplicon marker gene strategies for elevated accuracy in microbiome research. Nat. Biotechnol. 34, 942–949 (2016).
Wang, Q., Garrity, G. M., Tiedje, J. M. & Cole, J. R. Naive Bayesian classifier for fast project of rRNA sequences into the brand new bacterial taxonomy. Appl. Environ. Microbiol. 73, 5261–5267 (2007).
Pawlowsky-Glahn, V., Egozcue, J. J. & Tolosana-Delgado, R. Modelling and Evaluation of Compositional Information. (John Wiley & Sons, Ltd, 2015). https://doi.org/10.1002/9781119003144
Kruschke, J. Okay. Bayesian estimation supersedes the t take a look at. J. Exp. Psychol. Gen. 142, 573–603 (2013).
Homan, M. D. & Gelman, A. The No-U-Flip sampler: adaptively setting path lengths in Hamiltonian Monte Carlo. J. Mach. Study. Res. 15, 1593–1623 (2014).
