Roberts CM, Levi M, McKee M, Schilling R, Lim WS, Grocott MPW. COVID-19: a complex multisystem disorder. Br J Anaesth. 2020;125(3):238–42. https://doi.org/10.1016/j.bja.2020.06.013.
Article
CAS
PubMed
Google Scholar
Wiersinga WJ, Rhodes A, Cheng AC, Peacock SJ, Prescott HC. Pathophysiology, transmission, diagnosis, and treatment of coronavirus disease 2019 (COVID-19): a review. Jama. 2020;324(8):782–93. https://doi.org/10.1001/jama.2020.12839.
Article
CAS
PubMed
Google Scholar
Sinjari B, D'Ardes D, Santilli M, Rexhepi I, D'Addazio G, Di Carlo P, et al. SARS-CoV-2 and Oral manifestation: an observational, human study. J Clin Med. 2020;9(10):3218. https://doi.org/10.3390/jcm9103218.
Article
CAS
PubMed Central
Google Scholar
Nuno-Gonzalez A, Martin-Carrillo P, Magaletsky K, Martin Rios MD, Herranz Mañas C, Artigas Almazan J, et al. Prevalence of mucocutaneous manifestations in 666 patients with COVID-19 in a field hospital in Spain: oral and palmoplantar findings. Br J Dermatol. 2021;184(1):184–5. https://doi.org/10.1111/bjd.19564.
Article
CAS
PubMed
Google Scholar
Wang D, Hu B, Hu C, Zhu F, Liu X, Zhang J, et al. Clinical Characteristics of 138 Hospitalized Patients With 2019 Novel Coronavirus–Infected Pneumonia in Wuhan, China. JAMA. 2020;323(11):1061–9. https://doi.org/10.1001/jama.2020.1585.
Article
CAS
PubMed
PubMed Central
Google Scholar
Xiao F, Tang M, Zheng X, Liu Y, Li X, Shan H. Evidence for gastrointestinal infection of SARS-CoV-2. Gastroenterology. 2020;158(6):1831–3.e3. https://doi.org/10.1053/j.gastro.2020.02.055.
Article
CAS
PubMed
Google Scholar
Ren Z, Wang H, Cui G, Lu H, Wang L, Luo H, et al. Alterations in the human oral and gut microbiomes and lipidomics in COVID-19. Gut. 2021:gutjnl-2020-323826. https://doi.org/10.1136/gutjnl-2020-323826.
Wu Y, Cheng X, Jiang G, Tang H, Ming S, Tang L, 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(1):61. https://doi.org/10.1038/s41522-021-00232-5.
Article
CAS
PubMed
PubMed Central
Google Scholar
Shen Z, Xiao Y, Kang L, Ma W, Shi L, Zhang L, et al. Genomic Diversity of Severe Acute Respiratory Syndrome–Coronavirus 2 in Patients With Coronavirus Disease 2019. Clin Infect Dis. 2020;71(15):713–20. https://doi.org/10.1093/cid/ciaa203.
Article
CAS
PubMed
Google Scholar
Hanada S, Pirzadeh M, Carver KY, Deng JC. Respiratory viral infection-induced microbiome alterations and secondary bacterial pneumonia. Front Immunol. 2018;9:2640. https://doi.org/10.3389/fimmu.2018.02640.
Article
CAS
PubMed
PubMed Central
Google Scholar
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;6(1):9. https://doi.org/10.1186/s40168-017-0386-z.
Article
PubMed
PubMed Central
Google Scholar
Ma S, Zhang F, Zhou F, Li H, Ge W, Gan R, et al. Metagenomic analysis reveals oropharyngeal microbiota alterations in patients with COVID-19. Signal Transduct Target Ther. 2021;6(1):191. https://doi.org/10.1038/s41392-021-00614-3.
Article
CAS
PubMed
PubMed Central
Google Scholar
Yeoh YK, Zuo T, Lui GC-Y, Zhang F, Liu Q, Li AYL, et al. Gut microbiota composition reflects disease severity and dysfunctional immune responses in patients with COVID-19. Gut. 2021;70(4):698. https://doi.org/10.1136/gutjnl-2020-323020.
Article
CAS
PubMed
Google Scholar
Xiong D, Muema C, Zhang X, Pan X, Xiong J, Yang H, et al. Enriched opportunistic pathogens revealed by metagenomic sequencing hint potential linkages between pharyngeal microbiota and COVID-19. Virol Sin. 2021. https://doi.org/10.1007/s12250-021-00391-x.
Rueca M, Fontana A, Bartolini B, Piselli P, Mazzarelli A, Copetti M, et al. Investigation of nasal/Oropharyngeal microbial community of COVID-19 patients by 16S rDNA sequencing. Int J Environ Res Public Health. 2021;18(4). https://doi.org/10.3390/ijerph18042174.
Takeuchi K, Matsumoto K, Furuta M, Fukuyama S, Takeshita T, Ogata H, et al. Periodontitis is associated with chronic obstructive pulmonary disease. J Dent Res. 2019;98(5):534–40. https://doi.org/10.1177/0022034519833630.
Article
CAS
PubMed
Google Scholar
van der Maarel-Wierink CD, Vanobbergen JNO, Bronkhorst EM, Schols JMGA, de Baat C. Oral health care and aspiration pneumonia in frail older people: a systematic literature review. Gerodontology. 2013;30(1):3–9. https://doi.org/10.1111/j.1741-2358.2012.00637.x.
Article
PubMed
Google Scholar
Terpenning MS, Taylor GW, Lopatin DE, Kerr CK, Dominguez BL, Loesche WJ. Aspiration pneumonia: dental and Oral risk factors in an older veteran population. J Am Geriatr Soc. 2001;49(5):557–63. https://doi.org/10.1046/j.1532-5415.2001.49113.x.
Article
CAS
PubMed
Google Scholar
Li Y, He J, He Z, Zhou Y, Yuan M, Xu X, et al. Phylogenetic and functional gene structure shifts of the oral microbiomes in periodontitis patients. ISME J. 2014;8(9):1879–91. https://doi.org/10.1038/ismej.2014.28.
Article
CAS
PubMed
PubMed Central
Google Scholar
Brennan CA, Garrett WS. Fusobacterium nucleatum — symbiont, opportunist and oncobacterium. Nat Rev Microbiol. 2019;17(3):156–66. https://doi.org/10.1038/s41579-018-0129-6.
Article
CAS
PubMed
PubMed Central
Google Scholar
Flanagan L, Schmid J, Ebert M, Soucek P, Kunicka T, Liska V, et al. Fusobacterium nucleatum associates with stages of colorectal neoplasia development, colorectal cancer and disease outcome. Eur J Clin Microbiol Infect Dis. 2014;33(8):1381–90.
Article
CAS
PubMed
Google Scholar
Guo S, Lu Y, Xu B, Wang W, Xu J, Zhang G. A simple fecal bacterial marker panel for the diagnosis of Crohn’s disease. Front Microbiol. 2019;10(1306). https://doi.org/10.3389/fmicb.2019.01306.
Takahashi Y, Watanabe N, Kamio N, Yokoe S, Suzuki R, Sato S, et al. Expression of the SARS-CoV-2 receptor ACE2 and Proinflammatory cytokines induced by the Periodontopathic bacterium Fusobacterium nucleatum in human respiratory epithelial cells. Int J Mol Sci. 2021;22(3):1352.
Article
CAS
PubMed
PubMed Central
Google Scholar
Takahashi Y, Watanabe N, Kamio N, Kobayashi R, Iinuma T, Imai K. Aspiration of periodontopathic bacteria due to poor oral hygiene potentially contributes to the aggravation of COVID-19. J Oral Sci. 2021;63(1):1–3. https://doi.org/10.2334/josnusd.20-0388.
Article
CAS
Google Scholar
Tang L, Gu S, Gong Y, Li B, Lu H, Li Q, et al. Clinical significance of the correlation between changes in the major intestinal Bacteria species and COVID-19 severity. Engineering (Beijing). 2020;6(10):1178–84. https://doi.org/10.1016/j.eng.2020.05.013.
Article
CAS
Google Scholar
Zuo T, Zhang F, Lui GCY, Yeoh YK, Li AYL, Zhan H, et al. Alterations in gut microbiota of patients with COVID-19 during time of hospitalization. Gastroenterology. 2020;159(3):944–55 e8. https://doi.org/10.1053/j.gastro.2020.05.048.
Article
CAS
PubMed
Google Scholar
Guo S, Li L, Xu B, Li M, Zeng Q, Xiao H, et al. A simple and novel fecal biomarker for colorectal Cancer: ratio of Fusobacterium Nucleatum to probiotics populations, based on their antagonistic effect. Clin Chem. 2018;64(9):1327–37. https://doi.org/10.1373/clinchem.2018.289728.
Article
PubMed
Google Scholar
Cao R, Bao L, Pan M, Zhang C, Liao H, Liu L, et al. Detection of SARS-CoV-2 in fecal samples with different pretreatment methods and PCR kits. BMC Microbiol. 2021;21(1):56. https://doi.org/10.1186/s12866-021-02118-0.
Article
CAS
PubMed
PubMed Central
Google Scholar
Abraham JP, Plourde BD, Cheng L. Using heat to kill SARS-CoV-2. Rev Med Virol 2020;30(5):e2115. doi:https://doi.org/https://doi.org/10.1002/rmv.2115.
National Health Commission of the People's Republic of China. The Protocol on Prevention and Control of COVID-19 (seventh edition) 2020 [updated September 15th; cited 2021 25, April]. Available from: http://www.nhc.gov.cn/jkj/s3577/202009/318683cbfaee4191aee29cd774b19d8d/files/f9ea38ce2c2d4352bf61ab0feada439f.pdf.
Google Scholar
General Office of the National Health Commission of the People’s Republic of China. Guidelines of diagnosis and treatment of COVID-19 (trial version 7) 2020 [cited 2020. Available from: http://www.nhc.gov.cn/yzygj/s7653p/202003/46c9294a7dfe4cef80dc7f5912eb1989/files/ce3e6945832a438eaae415350a8ce964.pdf.
Google Scholar
Zhang XM, Li Y, Gu YX, Zhang CN, Lai HC, Shi JY. Ta-coated titanium surface with superior Bacteriostasis and Osseointegration. Int J Nanomedicine. 2019;14:8693–706. https://doi.org/10.2147/ijn.S218640.
Article
CAS
PubMed
PubMed Central
Google Scholar
Sokol H, Pigneur B, Watterlot L, Lakhdari O, Bermúdez-Humarán LG, Gratadoux JJ, et al. Faecalibacterium prausnitzii is an anti-inflammatory commensal bacterium identified by gut microbiota analysis of Crohn disease patients. Proc Natl Acad Sci U S A. 2008;105(43):16731–6. https://doi.org/10.1073/pnas.0804812105.
Article
CAS
PubMed
PubMed Central
Google Scholar
Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Lozupone CA, Turnbaugh PJ, et al. Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. Proc Natl Acad Sci U S A. 2011;108(Suppl 1):4516–22. https://doi.org/10.1073/pnas.1000080107.
Article
PubMed
Google Scholar
Schmittgen TD, Livak KJ. Analyzing real-time PCR data by the comparative CT method. Nat Protoc. 2008;3(6):1101–8. https://doi.org/10.1038/nprot.2008.73.
Article
CAS
PubMed
Google Scholar
Kim YJ, Lee SM, Park BK, Kim SS, Yi J, Kim HH, et al. Evaluation of propidium monoazide real-time PCR for early detection of viable mycobacterium tuberculosis in clinical respiratory specimens. Ann Lab Med. 2014;34(3):203–9. https://doi.org/10.3343/alm.2014.34.3.203.
Article
CAS
PubMed
PubMed Central
Google Scholar
Uritskiy GV, DiRuggiero J, Taylor J. MetaWRAP—a flexible pipeline for genome-resolved metagenomic data analysis. Microbiome. 2018;6(1):158. https://doi.org/10.1186/s40168-018-0541-1.
Article
PubMed
PubMed Central
Google Scholar
Langmead B, Salzberg SL. Fast gapped-read alignment with bowtie 2. Nat Methods. 2012;9(4):357–9. https://doi.org/10.1038/nmeth.1923.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wood DE, Lu J, Langmead B. Improved metagenomic analysis with kraken 2. Genome Biol. 2019;20(1):257. https://doi.org/10.1186/s13059-019-1891-0.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lu J, Breitwieser FP, Thielen P, Salzberg SL. Bracken: estimating species abundance in metagenomics data. PeerJ Comput Sci. 2017;3:e104.
Article
Google Scholar
Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, et al. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol. 2009;75(23):7537. https://doi.org/10.1128/AEM.01541-09.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wu Z, McGoogan JM. Characteristics of and important lessons from the coronavirus disease 2019 (COVID-19) outbreak in China: summary of a report of 72 314 cases from the Chinese Center for Disease Control and Prevention. JAMA. 2020;323(13):1239–42. https://doi.org/10.1001/jama.2020.2648.
Article
CAS
PubMed
Google Scholar
Chen SL, Feng HY, Xu H, Huang SS, Sun JF, Zhou L, et al. Patterns of deterioration in moderate patients with COVID-19 from Jan 2020 to mar 2020: a multi-center, retrospective cohort study in China. Front Med (Lausanne). 2020;7:567296. https://doi.org/10.3389/fmed.2020.567296.
Article
Google Scholar
Huang C, Wang Y, Li X, Ren L, Zhao J, Hu Y, et al. Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China. Lancet. 2020;395(10223):497–506.
Article
CAS
PubMed
PubMed Central
Google Scholar
Mandrekar JN. Receiver operating characteristic curve in diagnostic test assessment. J Thorac Oncol. 2010;5(9):1315–6. https://doi.org/10.1097/JTO.0b013e3181ec173d.
Article
PubMed
Google Scholar
Mammen MJ, Scannapieco FA, Sethi S. Oral-lung microbiome interactions in lung diseases. Periodontology 2000. 2020;83(1):234–41. https://doi.org/10.1111/prd.12301.
Article
PubMed
Google Scholar
de Carvalho Baptista IM, Martinho FC, Nascimento GG, da Rocha Santos CE, Prado RFD, Valera MC. Colonization of oropharynx and lower respiratory tract in critical patients: risk of ventilator-associated pneumonia. Arch Oral Biol. 2018;85:64–9. https://doi.org/10.1016/j.archoralbio.2017.09.029.
Article
PubMed
Google Scholar
Kumar PS. From focal sepsis to periodontal medicine: a century of exploring the role of the oral microbiome in systemic disease. J Physiol. 2017;595(2):465–76. https://doi.org/10.1113/jp272427.
Article
CAS
PubMed
Google Scholar
Kinane DF, Stathopoulou PG, Papapanou PN, et al. Nat Rev Dis Primers. 2017;3(1):17038. https://doi.org/10.1038/nrdp.2017.38.
Article
PubMed
Google Scholar
Pradhan A, Olsson P-E. Sex differences in severity and mortality from COVID-19: are males more vulnerable? Biol Sex Differ. 2020;11(1):53. https://doi.org/10.1186/s13293-020-00330-7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhao Y, Zhao Z, Wang Y, Zhou Y, Ma Y, Zuo W. Single-cell RNA expression profiling of ACE2, the receptor of SARS-CoV-2. Am J Respir Crit Care Med. 2020;202(5):756–9. https://doi.org/10.1164/rccm.202001-0179LE.
Article
CAS
PubMed
PubMed Central
Google Scholar
Abe M, Mitani A, Hoshi K, Yanagimoto S. Large gender gap in Oral hygiene behavior and its impact on gingival health in late adolescence. Int J Environ Res Public Health. 2020;17(12). https://doi.org/10.3390/ijerph17124394.
Mamai-Homata E, Koletsi-Kounari H, Margaritis V. Gender differences in oral health status and behavior of Greek dental students: a meta-analysis of 1981, 2000, and 2010 data. J Int Soc Prev Community Dent. 2016;6(1):60–8. https://doi.org/10.4103/2231-0762.175411.
Article
PubMed
PubMed Central
Google Scholar
Furuta M, Ekuni D, Irie K, Azuma T, Tomofuji T, Ogura T, et al. Sex differences in gingivitis relate to interaction of Oral health behaviors in young people. J Periodontol. 2011;82(4):558–65. https://doi.org/10.1902/jop.2010.100444.
Article
PubMed
Google Scholar
Cevik M, Kuppalli K, Kindrachuk J, Peiris M. Virology, transmission, and pathogenesis of SARS-CoV-2. BMJ. 2020;371:m3862. https://doi.org/10.1136/bmj.m3862.
Article
PubMed
Google Scholar
Li J, Zhao F, Wang Y, Chen J, Tao J, Tian G, et al. Gut microbiota dysbiosis contributes to the development of hypertension. Microbiome. 2017;5(1):14. https://doi.org/10.1186/s40168-016-0222-x.
Article
PubMed
PubMed Central
Google Scholar
Ai J-W, Zhang H-C, Xu T, Wu J, Zhu M, Yu Y-Q, et al. Optimizing diagnostic strategy for novel coronavirus pneumonia, a multi-center study in Eastern China. medRxiv. 2020:2020.02.13.20022673. https://doi.org/10.1101/2020.02.13.20022673.
Wu F, Zhao S, Yu B, Chen YM, Wang W, Song ZG, et al. A new coronavirus associated with human respiratory disease in China. Nature. 2020;579(7798):265–9. https://doi.org/10.1038/s41586-020-2008-3.
Article
CAS
PubMed
PubMed Central
Google Scholar
Han Y, Jia Z, Shi J, Wang W, He K. The active lung microbiota landscape of COVID-19 patients. medRxiv. 2020:2020.08.20.20144014. https://doi.org/10.1101/2020.08.20.20144014.
Khan AA, Khan Z. COVID-2019-associated overexpressed Prevotella proteins mediated host-pathogen interactions and their role in coronavirus outbreak. Bioinformatics. 2020;36(13):4065–9. https://doi.org/10.1093/bioinformatics/btaa285.
Article
CAS
PubMed
Google Scholar
Maraki S, Papadakis IS. Rothia mucilaginosa pneumonia: a literature review. Infect Dis. 2015;47(3):125–9. https://doi.org/10.3109/00365548.2014.980843.
Article
CAS
Google Scholar
de Carvalho FM, Lemos LN, Ciapina LP, Moreira RG, Gerber A, Guimarães APC, et al. Prevalence of bacterial pathogens and potential role in COVID-19 severity in patients admitted to intensive care units in Brazil. medRxiv. 2020:2020.12.22.20248501. https://doi.org/10.1101/2020.12.22.20248501.
Yildiz H, Sünnetçioğlu A, Ekin S, Baran Aİ, Özgökçe M, Aşker S, et al. Delftia acidovorans pneumonia with lung cavities formation. Colomb Med (Cali). 2019;50(3):215–21. https://doi.org/10.25100/cm.v50i3.4025.
Article
Google Scholar
Patel D, Iqbal AM, Mubarik A, Vassa N, Godil R, Saad M, et al. Delftia acidovorans: a rare cause of septic pulmonary embolism from catheter-related infection: case report and literature review. Respir Med Case Rep. 2019;27:100835. https://doi.org/10.1016/j.rmcr.2019.100835.
Article
PubMed
PubMed Central
Google Scholar
Zhang X, Zhang D, Jia H, Feng Q, Wang D, Liang D, et al. The oral and gut microbiomes are perturbed in rheumatoid arthritis and partly normalized after treatment. Nat Med. 2015;21(8):895–905. https://doi.org/10.1038/nm.3914.
Article
CAS
PubMed
Google Scholar