Zhu N, Zhang D, Wang W, Li X, Yang B, Song J, Zhao X, Huang B, Shi W, Lu R, et al. China Novel Coronavirus investigating and Research Team. A novel coronavirus from patients with Pneumonia in China, 2019. N Engl J Med. 2020 Feb;20(8):727–33. https://doi.org/10.1056/NEJMoa2001017
Guan WJ, Ni ZY, Hu Y, Liang WH, Ou CQ, He JX, Liu L, Shan H, Lei CL, Hui DSC, et al. China Medical Treatment Expert Group for Covid-19. Clinical characteristics of Coronavirus Disease 2019 in China. N Engl J Med. 2020 Apr;30(18):1708–20. https://doi.org/10.1056/NEJMoa2002032
Bergwerk M, Gonen T, Lustig Y, Amit S, Lipsitch M, Cohen C, Mandelboim M, Levin EG, Rubin C, Indenbaum V, et al. Covid-19 breakthrough infections in Vaccinated Health Care Workers. N Engl J Med. 2021 Oct;14(16):1474–84. https://doi.org/10.1056/NEJMoa2109072
Edara VV, Pinsky BA, Suthar MS, Lai L, Davis-Gardner ME, Floyd K, Flowers MW, Wrammert J, Hussaini L, Ciric CR et al. Infection and Vaccine-Induced Neutralizing-Antibody Responses to the SARS-CoV-2 B.1.617 Variants. N Engl J Med. 2021 Aug 12;385(7):664–666. doi: https://doi.org/10.1056/NEJMc2107799
Mehta P, McAuley DF, Brown M, Sanchez E, Tattersall RS, Manson JJ, HLH Across Speciality Collaboration, UK. COVID-19: consider cytokine storm syndromes and immunosuppression. Lancet. 2020 Mar;28(10229):1033–4. https://doi.org/10.1016/S0140-6736(20)30628-0
Bandopadhyay P, D’Rozario R, Lahiri A, Sarif J, Ray Y, Paul SR, Roy R, Maiti R, Chaudhuri K, Bagchi S et al. Nature and Dimensions of Systemic Hyperinflammation and its Attenuation by Convalescent Plasma in Severe COVID-19. J Infect Dis 2021 Aug 16;224(4):565–74. doi: https://doi.org/10.1093/infdis/jiab010
Li H, Liu L, Zhang D, Xu J, Dai H, Tang N, Su X, Cao B. SARS-CoV-2 and viral sepsis: observations and hypotheses. Lancet. 2020 May;9(10235):1517–20. https://doi.org/10.1016/S0140-6736(20)30920-X
Combes AJ, Courau T, Kuhn NF, Hu KH, Ray A, Chen WS, Chew NW, Cleary SJ, Kushnoor D, Reeder GC et al. Global absence and targeting of protective immune states in severe COVID-19. Nature. 2021 Mar;591(7848):124–30. doi: https://doi.org/10.1038/s41586-021-03234-7
Sarif J, Raychaudhuri D, D’Rozario R, Bandopadhyay P, Singh P, Mehta P, Hoque MA, Sinha BP, Kushwaha M, Sahni S et al. Plasma Gradient of Soluble Urokinase-Type Plasminogen Activator Receptor Is Linked to Pathogenic Plasma Proteome and Immune Transcriptome and Stratifies Outcomes in Severe COVID-19. Front Immunol 2021 Oct 28;12:738093. doi: https://doi.org/10.3389/fimmu.2021.738093
RECOVERY Collaborative Group, Horby P, Lim WS, Emberson JR, Mafham M, Bell JL, Linsell L, Staplin N, Brightling C, Ustianowski A, et al. Dexamethasone in hospitalized patients with Covid-19. N Engl J Med. 2021 Feb;25(8):693–704. https://doi.org/10.1056/NEJMoa2021436
Dequin PF, Heming N, Meziani F, Plantefève G, Voiriot G, Badié J, François B, Aubron C, Ricard JD, Ehrmann S, et al. Effect of hydrocortisone on 21-Day mortality or respiratory support among critically ill patients with COVID-19: a Randomized Clinical Trial. JAMA. 2020 Oct;6(13):1298–306. https://doi.org/10.1001/jama.2020.16761
Investigators REMAP-CAP, Gordon AC, Mouncey PR, Al-Beidh F, Rowan KM, Nichol AD, Arabi YM, Annane D, Beane A, van Bentum-Puijk W, et al. Interleukin-6 receptor antagonists in critically ill patients with Covid-19. N Engl J Med. 2021 Apr;22(16):1491–502. https://doi.org/10.1056/NEJMoa2100433
Salvarani C, Dolci G, Massari M, Merlo DF, Cavuto S, Savoldi L, Bruzzi P, Boni F, Braglia L, Turrà C, et al. Effect of Tocilizumab vs Standard Care on Clinical worsening in patients hospitalized with COVID-19 pneumonia: a Randomized Clinical Trial. JAMA Intern Med. 2021 Jan;181(1):24–31. https://doi.org/10.1001/jamainternmed.2020.6615
Cao B, Wang Y, Wen D, Liu W, Wang J, Fan G, Ruan L, Song B, Cai Y, Wei M, et al. A trial of lopinavir-ritonavir in adults hospitalized with severe Covid-19. N Engl J Med. 2020 May;7(19):1787–99. https://doi.org/10.1056/NEJMoa2001282
Beigel JH, Tomashek KM, Dodd LE, Mehta AK, Zingman BS, Kalil AC, Hohmann E, Chu HY, Luetkemeyer A, Kline S, et al. Remdesivir for the treatment of Covid-19 - final report. N Engl J Med. 2020 Nov;5(19):1813–26. https://doi.org/10.1056/NEJMoa2007764
Dougan M, Nirula A, Azizad M, Mocherla B, Gottlieb RL, Chen P, Hebert C, Perry R, Boscia J, Heller B, et al. Bamlanivimab plus Etesevimab in mild or moderate Covid-19. N Engl J Med. 2021 Oct;7(15):1382–92. https://doi.org/10.1056/NEJMoa2102685
Gomes MGM, Ferreira MU, Corder RM, King JG, Souto-Maior C, Penha-Gonçalves C, Gonçalves G, Chikina M, Pegden W, Aguas R. Individual variation in susceptibility or exposure to SARS-CoV-2 lowers the herd immunity threshold. J Theor Biol 2022 May 7;540:111063. doi: https://doi.org/10.1016/j.jtbi.2022.111063
Cho I, Blaser MJ. The human microbiome: at the interface of health and disease. Nat Rev Genet. 2012 Mar 13;13(4):260 – 70. doi: https://doi.org/10.1038/nrg3182
Byndloss MX, Bäumler AJ. The germ-organ theory of non-communicable diseases. Nat Rev Microbiol. 2018 Feb;16(2):103–10. https://doi.org/10.1038/nrmicro.2017.158
Libertucci J, Young VB. The role of the microbiota in infectious diseases. Nat Microbiol 2019 Jan;4(1):35–45. doi: https://doi.org/10.1038/s41564-018-0278-4
Velazquez EM, Nguyen H, Heasley KT, Saechao CH, Gil LM, Rogers AWL, Miller BM, Rolston MR, Lopez CA, Litvak Y, et al. Endogenous Enterobacteriaceae underlie variation in susceptibility to Salmonella infection. Nat Microbiol. 2019 Jun;4(6):1057–64. https://doi.org/10.1038/s41564-019-0407-8
Villarino NF, LeCleir GR, Denny JE, Dearth SP, Harding CL, Sloan SS, Gribble JL, Campagna SR, Wilhelm SW, Schmidt NW. Composition of the gut microbiota modulates the severity of malaria. Proc Natl Acad Sci U S A. 2016 Feb 23;113(8):2235-40. doi: https://doi.org/10.1073/pnas.1504887113
Yildiz S, Mazel-Sanchez B, Kandasamy M, Manicassamy B, Schmolke M. Influenza A virus infection impacts systemic microbiota dynamics and causes quantitative enteric dysbiosis. Microbiome 2018 Jan 10;6(1):9. doi: https://doi.org/10.1186/s40168-017-0386-z
Harding JN, Siefker D, Vu L, You D, DeVincenzo J, Pierre JF, Cormier SA. Altered gut microbiota in infants is associated with respiratory syncytial virus disease severity. BMC Microbiol. 2020 Jun 1;20(1):140. doi: https://doi.org/10.1186/s12866-020-01816-5
Rooks MG, Garrett WS. Gut microbiota, metabolites and host immunity. Nat Rev Immunol. 2016 May 27;16(6):341 – 52. doi: https://doi.org/10.1038/nri.2016.42
Budden KF, Gellatly SL, Wood DL, Cooper MA, Morrison M, Hugenholtz P, Hansbro PM. Emerging pathogenic links between microbiota and the gut-lung axis. Nat Rev Microbiol 2017 Jan;15(1):55–63. doi: https://doi.org/10.1038/nrmicro.2016.142
Sarkar A, Harty S, Moeller AH, Klein SL, Erdman SE, Friston KJ, Carmody RN. The gut microbiome as a biomarker of differential susceptibility to SARS-CoV-2. Trends Mol Med. 2021 Dec;27(12):1115–34. https://doi.org/10.1016/j.molmed.2021.09.009
Ren Z, Wang H, Cui G, Lu H, Wang L, Luo H, Chen X, Ren H, Sun R, Liu W, et al. Alterations in the human oral and gut microbiomes and lipidomics in COVID-19. Gut. 2021 Jul;70(7):1253–65. https://doi.org/10.1136/gutjnl-2020-323826
Nagata N, Takeuchi T, Masuoka H, Aoki R, Ishikane M, Iwamoto N, Sugiyama M, Suda W, Nakanishi Y, Terada-Hirashima J, Kimura M, Nishijima T, et al. Human gut microbiota and its metabolites Impact Immune responses in COVID-19 and its complications. Gastroenterology. 2023 Feb;164(2):272–88. https://doi.org/10.1053/j.gastro.2022.09.024
Parada Venegas D, De la Fuente MK, Landskron G, González MJ, Quera R, Dijkstra G, Harmsen HJM, Faber KN, Hermoso MA. Short Chain Fatty Acids (SCFAs)-Mediated Gut Epithelial and Immune Regulation and Its Relevance for Inflammatory Bowel Diseases. Front Immunol. 2019 Mar 11;10:277. doi: 10.3389/fimmu.2019.00277. Erratum in: Front Immunol. 2019 Jun 28;10:1486.
Kot B, Piechota M, Jakubczak A, Gryzińska M, Witeska M, Grużewska A, Baran K, Denkiewicz P. The prevalence of virulence determinants in methicillin-resistant Staphylococcus aureus isolated from different infections in hospitalized patients in Poland. Sci Rep. 2022 Mar 31;12(1):5477. doi: https://doi.org/10.1038/s41598-022-09517-x
Dubin K, Pamer EG. Enterococci and Their Interactions with the Intestinal Microbiome. Microbiol Spectr. 2014 Nov;5(6):https://doi.org/10.1128/microbiolspec.BAD-0014-2016. doi: 10.1128/microbiolspec.BAD-0014-2016.
Balakrishnan B, Luckey D, Taneja V. Autoimmunity-Associated Gut Commensals Modulate Gut Permeability and Immunity in Humanized Mice. Mil Med. 2019 Mar 1;184(Suppl 1):529–536. doi: https://doi.org/10.1093/milmed/usy309
Kalinkovich A, Livshits G. A cross talk between dysbiosis and gut-associated immune system governs the development of inflammatory arthropathies. Semin Arthritis Rheum. 2019 Dec;49(3):474–84. https://doi.org/10.1016/j.semarthrit.2019.05.007
Alexander M, Ang QY, Nayak RR, Bustion AE, Sandy M, Zhang B, Upadhyay V, Pollard KS, Lynch SV, Turnbaugh PJ. Human gut bacterial metabolism drives Th17 activation and colitis. Cell Host Microbe. 2022 Jan 12;30(1):17–30.e9. doi: https://doi.org/10.1016/j.chom.2021.11.001
Vacca M, Celano G, Calabrese FM, Portincasa P, Gobbetti M, De Angelis M. The Controversial Role of Human Gut Lachnospiraceae. Microorganisms 2020 Apr 15;8(4):573. doi: https://doi.org/10.3390/microorganisms8040573
Ryan MP, Pembroke JT. The Genus Ochrobactrum as Major Opportunistic Pathogens. Microorganisms 2020 Nov 16;8(11):1797. doi: https://doi.org/10.3390/microorganisms8111797
Thomas CM, Hong T, van Pijkeren JP, Hemarajata P, Trinh DV, Hu W, Britton RA, Kalkum M, Versalovic J. Histamine derived from probiotic Lactobacillus reuteri suppresses TNF via modulation of PKA and ERK signaling. PLoS ONE. 2012;7(2):e31951. https://doi.org/10.1371/journal.pone.0031951
Article CAS PubMed PubMed Central Google Scholar
Elenkov IJ, Webster E, Papanicolaou DA, Fleisher TA, Chrousos GP, Wilder RL. Histamine potently suppresses human IL-12 and stimulates IL-10 production via H2 receptors. J Immunol. 1998 Sep 1;161(5):2586-93.
Barker HA. Amino acid degradation by anaerobic bacteria. Annu Rev Biochem. 1981;50:23–40. https://doi.org/10.1146/annurev.bi.50.070181.000323
Article CAS PubMed Google Scholar
Spence JD, Bang H, Chambless LE, Stampfer MJ. Vitamin intervention for Stroke Prevention trial: an efficacy analysis. Stroke. 2005 Nov;36(11):2404–9. https://doi.org/10.1161/01.STR.0000185929.38534.f3
Ling L, Chen Z, Lui G, Wong CK, Wong WT, Ng RWY, Tso EYK, Fung KSC, Chan V, Yeung ACM, Hui DSC, et al. Longitudinal Cytokine Profile in patients with mild to critical COVID-19. Front Immunol. 2021 Dec;6:12:763292. https://doi.org/10.3389/fimmu.2021.763292
Vaninov N. In the eye of the COVID-19 cytokine storm. Nat Rev Immunol. 2020 May;20(5):277. https://doi.org/10.1038/s41577-020-0305-6
Mangalmurti N, Hunter CA. Cytokine Storms: Understanding COVID-19. Immunity. 2020 Jul 14;53(1):19–25. doi: https://doi.org/10.1016/j.immuni.2020.06.017
Mokhtari T, Hassani F, Ghaffari N, Ebrahimi B, Yarahmadi A, Hassanzadeh G. COVID-19 and multiorgan failure: a narrative review on potential mechanisms. J Mol Histol. 2020 Dec;51(6):613–28. https://doi.org/10.1007/s10735-020-09915-3
Jose RJ, Manuel A. COVID-19 cytokine storm: the interplay between inflammation and coagulation. Lancet Respir Med. 2020 Jun;8(6):e46–7. https://doi.org/10.1016/S2213-2600(20)30216-2
Alkan A, Uncu A, Taşkıran I, Tanrıverdi Ö. Double-edged sword: Granulocyte colony stimulating factors in cancer patients during the COVID-19 era. Clinics (Sao Paulo). 2020;75:e2033. doi: https://doi.org/10.6061/clinics/2020/e2033
Álvarez-Mercado AI, Navarro-Oliveros M, Robles-Sánchez C, Plaza-Díaz J, Sáez-Lara MJ, Muñoz-Quezada S, Fontana L, Abadía-Molina F. Microbial Population Changes and Their Relationship with Human Health and Disease. Microorganisms. 2019 Mar 3;7(3):68. doi: https://doi.org/10.3390/microorganisms7030068
Ray Y, Paul SR, Bandopadhyay P, D’Rozario R, Sarif J, Raychaudhuri D, Bhowmik D, Lahiri A, Vasudevan JS, Maurya R et al. A phase 2 single center open label randomised control trial for convalescent plasma therapy in patients with severe COVID-19. Nat Commun. 2022 Jan 19;13(1):383. doi: https://doi.org/10.1038/s41467-022-28064-7
Raychaudhuri D, Bandopadhyay P, D’Rozario R, Sarif J, Ray Y, Paul SR, Singh P, Chaudhuri K, Bhaduri R, Pandey R et al. Clinical Trial Sub-Group Analyses to Investigate Clinical and Immunological Outcomes of Convalescent Plasma Therapy in Severe COVID-19. Mayo Clin Proc Innov Qual Outcomes. 2022 Sep 14. doi: https://doi.org/10.1016/j.mayocpiqo.2022.09.001
Nogal A, Valdes AM, Menni C. The role of short-chain fatty acids in the interplay between gut microbiota and diet in cardio-metabolic health. Gut Microbes 2021 Jan-Dec;13(1):1–24. doi: https://doi.org/10.1080/19490976.2021.1897212
Van Hul M, Le Roy T, Prifti E, Dao MC, Paquot A, Zucker JD, Delzenne NM, Muccioli G, Clément K, Cani PD. From correlation to causality: the case of Subdoligranulum. Gut Microbes 2020 Nov 9;12(1):1–13. doi: https://doi.org/10.1080/19490976.2020.1849998
De Maesschalck C, Van Immerseel F, Eeckhaut V, De Baere S, Cnockaert M, Croubels S, Haesebrouck F, Ducatelle R, Vandamme P. Faecalicoccus acidiformans gen. nov., sp. nov., isolated from the chicken caecum, and reclassification of Streptococcus pleomorphus (Barnes 1977), Eubacterium biforme (Eggerth 1935) and Eubacterium cylindroides (Cato 1974) as Faecalicoccus pleomorphus comb. nov., Holdemanella biformis gen. nov., comb. nov. and Faecalitalea cylindroides gen. nov., comb. nov., respectively, within the family Erysipelotrichaceae. Int J Syst Evol Microbiol. 2014 Nov;64(Pt 11):3877–3884. doi: https://doi.org/10.1099/ijs.0.064626-0
Lee MR, Huang YT, Liao CH, Chuang TY, Lin CK, Lee SW, Lai CC, Yu CJ, Hsueh PR. Bacteremia caused by Brevundimonas species at a tertiary care hospital in Taiwan, 2000–2010. Eur J Clin Microbiol Infect Dis. 2011 Oct;30(10):1185–91. https://doi.org/10.1007/s10096-011-1210-5
Idrees M, Mohammad AR, Karodia N, Rahman A. Multimodal Role of Amino Acids in Microbial Control and Drug Development. Antibiotics (Basel). 2020 Jun 17;9(6):330. doi: https://doi.org/10.3390/antibiotics9060330
Cumming BM, Chinta KC, Reddy VP, Steyn AJC. Role of Ergothioneine in Microbial Physiology and Pathogenesis. Antioxid Redox Signal 2018 Feb 20;28(6):431–44. doi: https://doi.org/10.1089/ars.2017.7300
Lin SJ, Guarente L. Nicotinamide adenine dinucleotide, a metabolic regulator of transcription, longevity and disease. Curr Opin Cell Biol. 2003 Apr;15(2):241–6. https://doi.org/10.1016/s0955-0674(03)00006-1
Randazzo A, Kornreich A, Lissoir B. A Clostridium hathewayi isolate in blood culture of a patient with an acute appendicitis. Anaerobe. 2015 Oct;35(Pt B):44 – 7. doi: https://doi.org/10.1016/j.anaerobe.2015.07.003
Deriu E, Boxx GM, He X, Pan C, Benavidez SD, Cen L, Rozengurt N, Shi W, Cheng G. Influenza Virus Affects Intestinal Microbiota and Secondary Salmonella Infection in the Gut through Type I Interferons. PLoS Pathog. 2016 May 5;12(5):e1005572. doi: https://doi.org/10.1371/journal.ppat.1005572
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 Jun 2;165(6):1332–1345. doi: https://doi.org/10.1016/j.cell.2016.05.041
Tai N, Wong FS, Wen L. The role of gut microbiota in the development of type 1, type 2 diabetes mellitus and obesity. Rev Endocr Metab Disord. 2015 Mar;16(1):55–65. https://doi.org/10.1007/s11154-015-9309-0
McLean MH, Dieguez D Jr, Miller LM, Young HA. Does the microbiota play a role in the pathogenesis of autoimmune diseases? Gut. 2015 Feb;64(2):332–41. doi: https://doi.org/10.1136/gutjnl-2014-308514. Epub 2014 Nov 21.
Wilmanski T, Diener C, Rappaport N, Patwardhan S, Wiedrick J, Lapidus J, Earls JC, Zimmer A, Glusman G, Robinson M, Yurkovich JT, et al. Gut microbiome pattern reflects healthy ageing and predicts survival in humans. Nat Metab. 2021 Feb;3(2):274–86. https://doi.org/10.1038/s42255-021-00348-0
Avendaño-Solá C, Ramos-Martínez A, Muñez-Rubio E, Ruiz-Antorán B, Malo de Molina R, Torres F, Fernández-Cruz A, Calderón-Parra J, Payares-Herrera C, de Díaz A et al. A multicenter randomized open-label clinical trial for convalescent plasma in patients hospitalized with COVID-19 pneumonia. J Clin Invest 2021 Oct 15;131(20):e152740. doi: https://doi.org/10.1172/JCI152740
Nagy E. Anaerobic infections: update on treatment considerations. Drugs. 2010 May 7;70(7):841 – 58. doi: https://doi.org/10.2165/11534490-000000000-00000
Antunes LC, Visca P, Towner KJ. Acinetobacter baumannii: evolution of a global pathogen. Pathog Dis. 2014 Aug;71(3):292–301. https://doi.org/10.1111/2049-632X.12125
Sridharan GV, Choi K, Klemashevich C, Wu C, Prabakaran D, Pan LB, Steinmeyer S, Mueller C, Yousofshahi M, Alaniz RC et al. Prediction and quantification of bioactive microbiota metabolites in the mouse gut. Nat Commun 2014 Nov 20;5:5492. doi: https://doi.org/10.1038/ncomms6492
Frei R, Ferstl R, Konieczna P, Ziegler M, Simon T, Rugeles TM, Mailand S, Watanabe T, Lauener R, Akdis CA, et al. Histamine receptor 2 modifies dendritic cell responses to microbial ligands. J Allergy Clin Immunol. 2013 Jul;132(1):194–204. https://doi.org/10.1016/j.jaci.2013.01.013
Yeoh YK, Zuo T, Lui GC, Zhang F, Liu Q, Li AY, Chung AC, Cheung CP, Tso EY, Fung KS, et al. Gut microbiota composition reflects disease severity and dysfunctional immune responses in patients with COVID-19. Gut. 2021 Apr;70(4):698–706. https://doi.org/10.1136/gutjnl-2020-323020
Klindworth A, Pruesse E, Schweer T, Peplies J, Quast C, Horn M, Glöckner FO. Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies. Nucleic Acids Res 2013 Jan 7;41(1):e1. doi: https://doi.org/10.1093/nar/gks808
Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014 Aug 1;30(15):2114-20. doi: https://doi.org/10.1093/bioinformatics/btu170
Bolyen E, Rideout JR, Dillon MR, Bokulich NA, Abnet CC, Al-Ghalith GA, Alexander H, Alm EJ, Arumugam M, Asnicar F et al. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat Biotechnol. 2019 Aug;37(8):852–857. doi: https://doi.org/10.1038/s41587-019-0209-9. Erratum in: Nat Biotechnol. 2019 Sep;37(9):1091.
Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJ, Holmes SP. DADA2: High-resolution sample inference from Illumina amplicon data. Nat Methods 2016 Jul;13(7):581–3. doi: https://doi.org/10.1038/nmeth.3869
Bokulich NA, Kaehler BD, Rideout JR, Dillon M, Bolyen E, Knight R, Huttley GA, Gregory Caporaso J. Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2’s q2-feature-classifier plugin. Microbiome 2018 May 17;6(1):90. doi: https://doi.org/10.1186/s40168-018-0470-z
Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, Peplies J, Glöckner FO. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 2013 Jan;41(Database issue):D590–6. https://doi.org/10.1093/nar/gks1219
Dhariwal A, Chong J, Habib S, King IL, Agellon LB, Xia J. MicrobiomeAnalyst: a web-based tool for comprehensive statistical, visual and meta-analysis of microbiome data. Nucleic Acids Res. 2017 Jul 3;45(W1):W180-W188. doi: https://doi.org/10.1093/nar/gkx295
Chong J, Liu P, Zhou G, Xia J. Using MicrobiomeAnalyst for comprehensive statistical, functional, and meta-analysis of microbiome data. Nat Protoc. 2020 Mar;15(3):799–821. https://doi.org/10.1038/s41596-019-0264-1
Oksanen J, Blanchet FG, Friendly M et al. Vegan: community ecology package, https://CRAN.R-project.org/package=vegan (2020, accessed 28 January 2021).
Hughes JB, Hellmann JJ, Ricketts TH, Bohannan BJM. Counting the Uncountable: Statistical Approaches to Estimating Microbial Diversity. Appl Environ Microbiol. 2002 Jan;68(1):448. doi: https://doi.org/10.1128/AEM.68.1.448. Erratum for: Appl Environ Microbiol. 67:4399.
Haegeman B, Hamelin J, Moriarty J, Neal P, Dushoff J, Weitz JS. Robust estimation of microbial diversity in theory and in practice. ISME J. 2013 Jun;7(6):1092–101. https://doi.org/10.1038/ismej.2013.10
Faust K, Sathirapongsasuti JF, Izard J, Segata N, Gevers D, Raes J, Huttenhower C. Microbial co-occurrence relationships in the human microbiome. PLoS Comput Biol. 2012;8(7):e1002606. https://doi.org/10.1371/journal.pcbi.1002606
Article CAS PubMed PubMed Central Google Scholar
Matchado MS, Lauber M, Reitmeier S, Kacprowski T, Baumbach J, Haller D, List M. Network analysis methods for studying microbial communities: A mini review. Comput Struct Biotechnol J 2021 May 4;19:2687–98. doi: https://doi.org/10.1016/j.csbj.2021.05.001
Douglas GM, Maffei VJ, Zaneveld JR, Yurgel SN, Brown JR, Taylor CM, Huttenhower C, Langille MGI. PICRUSt2 for prediction of metagenome functions. Nat Biotechnol. 2020 Jun;38(6):685–8. https://doi.org/10.1038/s41587-020-0548-6
Barbera P, Kozlov AM, Czech L, Morel B, Darriba D, Flouri T, Stamatakis A. EPA-ng: Massively Parallel Evolutionary Placement of Genetic Sequences. Syst Biol. 2019 Mar 1;68(2):365–369. doi: https://doi.org/10.1093/sysbio/syy054
Czech L, Stamatakis A. Scalable methods for analyzing and visualizing phylogenetic placement of metagenomic samples. PLoS One. 2019 May 28;14(5):e0217050. doi: https://doi.org/10.1371/journal.pone.0217050. Erratum in: PLoS One. 2019 Jul 11;14(7):e0219925.
Louca S, Doebeli M. Efficient comparative phylogenetics on large trees. Bioinf 2018 Mar 15;34(6):1053–5. doi: https://doi.org/10.1093/bioinformatics/btx701
Ye Y, Doak TG. A parsimony approach to biological pathway reconstruction/inference for genomes and metagenomes. PLoS Comput Biol. 2009 Aug;5(8):e1000465. https://doi.org/10.1371/journal.pcbi.1000465
Kanehisa M, Goto S, Sato Y, Furumichi M, Tanabe M. KEGG for integration and interpretation of large-scale molecular data sets. Nucleic Acids Res. 2012 Jan;40(Database issue):D109–14. https://doi.org/10.1093/nar/gkr988
Segata N, Izard J, Waldron L, Gevers D, Miropolsky L, Garrett WS, et al. Metagenomic biomarker discovery and explanation. Genome Biol. 2011;12(6):R60.
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