Tang CH. Research of pathogenesis and novel therapeutics in arthritis. Int J Mol Sci. 2019;20:1646.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Glyn-Jones S, Palmer AJ, Agricola R, Price AJ, Vincent TL, Weinans H, Carr AJ. Osteoarthritis. Lancet. 2015;386:376–87.

Article  CAS  PubMed  Google Scholar 

Wilson L, Saseen JJ. Gouty arthritis: a review of acute management and prevention. Pharmacotherapy. 2016;36:906–22.

Article  CAS  PubMed  Google Scholar 

Neogi T. The epidemiology and impact of pain in osteoarthritis. Osteoarthr Cartil. 2013;21:1145–53.

Article  CAS  Google Scholar 

Favazzo LJ, Hendesi H, Villani DA, Soniwala S, Dar QA, Schott EM, Gill SR, Zuscik MJ. The gut microbiome-joint connection: implications in osteoarthritis. Curr Opin Rheumatol. 2020;32:92–101.

Article  PubMed  Google Scholar 

Lin X, Shao T, Huang L, Wen X, Wang M, Wen C, He Z. Simiao decoction alleviates gouty arthritis by modulating proinflammatory cytokines and the gut ecosystem. Front Pharmacol. 2020;11:955.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Lee KA, Luong MK, Shaw H, Nathan P, Bataille V, Spector TD. The gut microbiome: what the oncologist ought to know. Br J Cancer. 2021;125:1197–209.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Camarillo-Guerrero LF, Almeida A, Rangel-Pineros G, Finn RD, Lawley TD. Massive expansion of human gut bacteriophage diversity. Cell. 2021;184:1098-1109.e1099.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Tomofuji Y, Kishikawa T, Maeda Y, Ogawa K, Nii T, Okuno T, Oguro-Igashira E, Kinoshita M, Yamamoto K, Sonehara K, et al. Whole gut virome analysis of 476 Japanese revealed a link between phage and autoimmune disease. Ann Rheum Dis. 2022;81:278–88.

Article  PubMed  Google Scholar 

Li C, Zhang Y, Yan Q, Guo R, Chen C, Li S, Zhang Y, Meng J, Ma J, You W. Alterations in the gut virome in patients with ankylosing spondylitis. Front Immunol. 2023;14:1154380.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Chen C, Zhang Y, Yao X, Li S, Wang G, Huang Y, Yang Y, Zhang A, Liu C, Zhu D. Characterizations of the gut bacteriome, mycobiome, and virome in patients with osteoarthritis. Microbiol Spect. 2023;11:e01711-01722.

Google Scholar 

Chen C, Yan Q, Yao X, Li S, Lv Q, Wang G, Zhong Q, Tang F, Liu Z, Huang Y. Alterations of the gut virome in patients with systemic lupus erythematosus. Front Immunol. 2023;13:1050895.

Article  PubMed  PubMed Central  Google Scholar 

de Jonge PA, Wortelboer K, Scheithauer TP, van den Born BJH, Zwinderman AH, Nobrega FL, Dutilh BE, Nieuwdorp M, Herrema H. Gut virome profiling identifies a widespread bacteriophage family associated with metabolic syndrome. Nat Commun. 2022;13:1–15.

Article  Google Scholar 

Ezzatpour S, Mondragon Portocarrero ADC, Cardelle-Cobas A, Lamas A, Lopez-Santamarina A, Miranda JM, Aguilar HC. The human gut virome and its relationship with nontransmissible chronic diseases. Nutrients. 2023;15:977.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Tun HM, Peng Y, Massimino L, Sin ZY, Parigi TL, Facoetti A, Rahman S, Danese S, Ungaro F. Gut virome in inflammatory bowel disease and beyond. Gut. 2024;73:350–60.

Article  CAS  PubMed  Google Scholar 

Guo R, Li S, Zhang Y, Zhang Y, Wang G, Ullah H, Ma Y, Yan Q. Dysbiotic oral and gut viromes in untreated and treated rheumatoid arthritis patients. Microbiol Spectr. 2022;2022: e0034822.

Article  Google Scholar 

Mangalea MR, Paez-Espino D, Kieft K, Chatterjee A, Chriswell ME, Seifert JA, Feser ML, Demoruelle MK, Sakatos A, Anantharaman K, et al. Individuals at risk for rheumatoid arthritis harbor differential intestinal bacteriophage communities with distinct metabolic potential. Cell Host Microbe. 2021;29(726–739): e725.

Google Scholar 

Neogi T, Jansen TL, Dalbeth N, Fransen J, Schumacher HR, Berendsen D, Brown M, Choi H, Edwards NL, Janssens HJ, et al. 2015 Gout classification criteria: an American College of Rheumatology/European League Against Rheumatism collaborative initiative. Ann Rheum Dis. 2015;74:1789–98.

Article  CAS  PubMed  Google Scholar 

Chen C, Zhang Y, Yao X, Li S, Wang G, Huang Y, Yang Y, Zhang A, Liu C, Zhu D, et al. Characterizations of the gut bacteriome, mycobiome, and virome in patients with osteoarthritis. Microbiol Spectr. 2023;11: e0171122.

Article  PubMed  Google Scholar 

Yan Q, Wang Y, Chen X, Jin H, Wang G, Guan K, Zhang Y, Zhang P, Ayaz T, Liang Y, et al. Characterization of the gut DNA and RNA Viromes in a Cohort of Chinese Residents and Visiting Pakistanis. Virus Evol. 2021;7: veab022.

Article  PubMed  PubMed Central  Google Scholar 

Li D, Liu CM, Luo R, Sadakane K, Lam TW. MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. Bioinformatics. 2015;31:1674–6.

Article  CAS  PubMed  Google Scholar 

Li S, Guo R, Zhang Y, Li P, Chen F, Wang X, Li J, Jie Z, Lv Q, Jin H. A catalogue of 48,425 nonredundant viruses from oral metagenomes expands the horizon of the human oral virome. iScience. 2022;2022: 104418.

Article  Google Scholar 

Wang G, Li S, Yan Q, Guo R, Zhang Y, Chen F, Tian X, Lv Q, Jin H, Ma X, Ma Y. Optimization and evaluation of viral metagenomic amplification and sequencing procedures toward a genome-level resolution of the human fecal DNA virome. J Adv Res. 2022;48:75–86.

Article  PubMed  PubMed Central  Google Scholar 

Nayfach S, Camargo AP, Schulz F, Eloe-Fadrosh E, Roux S, Kyrpides NC. CheckV assesses the quality and completeness of metagenome-assembled viral genomes. Nat Biotechnol. 2020;39:578.

Article  PubMed  PubMed Central  Google Scholar 

Ren J, Ahlgren NA, Lu YY, Fuhrman JA, Sun F. VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data. Microbiome. 2017;5:69.

Article  PubMed  PubMed Central  Google Scholar 

Kieft K, Zhou Z, Anantharaman K. VIBRANT: automated recovery, annotation and curation of microbial viruses, and evaluation of viral community function from genomic sequences. Microbiome. 2020;8:90.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Gregory AC, Zablocki O, Zayed AA, Howell A, Bolduc B, Sullivan MB. The gut virome database reveals age-dependent patterns of virome diversity in the human gut. Cell Host Microbe. 2020;28(724–740): e728.

Google Scholar 

Boratyn GM, Camacho C, Cooper PS, Coulouris G, Fong A, Ma N, Madden TL, Matten WT, McGinnis SD, Merezhuk Y. BLAST: a more efficient report with usability improvements. Nucleic Acids Res. 2013;41:W29–33.

Article  PubMed  PubMed Central  Google Scholar 

Mihara T, Nishimura Y, Shimizu Y, Nishiyama H, Yoshikawa G, Uehara H, Hingamp P, Goto S, Ogata H. Linking virus genomes with host taxonomy. Viruses. 2016;8:66.

Article  PubMed  PubMed Central  Google Scholar 

Kanehisa M, Furumichi M, Tanabe M, Sato Y, Morishima K. KEGG: new perspectives on genomes, pathways, diseases and drugs. Nucleic Acids Res. 2017;45:D353–61.

Article  CAS  PubMed  Google Scholar 

Dixon P. VEGAN, a package of R functions for community ecology. J Veg Sci. 2003;14:927–30.

Article  Google Scholar 

Nayfach S, Paez-Espino D, Call L, Low SJ, Sberro H, Ivanova NN, Proal AD, Fischbach MA, Bhatt AS, Hugenholtz P, Kyrpides NC. Metagenomic compendium of 189,680 DNA viruses from the human gut microbiome. Nat Microbiol. 2021;6:960–70.

Article  CAS  PubMed