Evaluation of gut microbiota predictive potential associated with phenotypic characteristics to identify multifactorial diseases

References

• Dekaboruah E, Suryavanshi MV, Chettri D, Verma AK. Human microbiome: an academic update on human body site specific surveillance and its possible role. Arch Microbiol. 2020;202(8):2147–18. doi: 10.1007/s00203-020-01931-x.
   PubMed Web of Science ®Google Scholar
• Gupta VK, Kim M, Bakshi U, Cunningham KY, Davis JM, Lazaridis KN, Nelson H, Chia N, Sung J. A predictive index for health status using species-level gut microbiome profiling. Nat Commun. 2020;11(1). doi: 10.1038/s41467-020-18476-8.
   Web of Science ®Google Scholar
• Bielka W, Przezak A, Pawlik A. The role of the gut microbiota in the pathogenesis of diabetes. Int J Mol Sci. 2022;23(1):480. doi: 10.3390/ijms23010480.
   PubMed Web of Science ®Google Scholar
• Pascal V, Pozuelo M, Borruel N, Casellas F, Campos D, Santiago A, Martinez X, Varela E, Sarrabayrouse G, Machiels K, et al. A microbial signature for Crohn's disease. Gut. 2017;66(5):813–822. doi: 10.1136/gutjnl-2016-313235.
   PubMed Web of Science ®Google Scholar
• Sankarasubramanian J, Ahmad R, Avuthu N, Singh AB, Guda C. Gut microbiota and metabolic specificity in ulcerative colitis and crohn’s disease. Front Med. 2020;7. doi:10.3389/fmed.2020.606298.
   Web of Science ®Google Scholar
• He Z, Shao T, Li H, Xie Z, Wen C. Alterations of the gut microbiome in Chinese patients with systemic lupus erythematosus. Gut Pathog. 2016;8(1). doi: 10.1186/s13099-016-0146-9.
   PubMedGoogle Scholar
• Shilo S, Godneva A, Rachmiel M, Korem T, Bussi Y, Kolobkov D, Karady T, Bar N, Wolf BC, Glantz-Gashai Y, et al. The gut microbiome of adults with type 1 diabetes and its association with the host glycemic control. Diab Care. 2022;45(3):555–563. doi: 10.2337/dc21-1656.
   PubMed Web of Science ®Google Scholar
• Doumatey AP, Adeyemo A, Zhou J, Lei L, Adebamowo SN, Adebamowo C, Rotimi CN. Gut microbiome profiles are associated with type 2 diabetes in urban Africans. Front Cell Infect Microbiol. 2020;10:10. doi:10.3389/fcimb.2020.00063.
   PubMed Web of Science ®Google Scholar
• Metwaly A, Reitmeier S, Haller D. Microbiome risk profiles as biomarkers for inflammatory and metabolic disorders. Nature Reviews Gastroenterol Mathsemicol Hepatol. 2022;19(6):383–397. doi: 10.1038/s41575-022-00581-2.
   PubMed Web of Science ®Google Scholar
• Poussin C, Sierro N, Boué S, Battey J, Scotti E, Belcastro V, Peitsch MC, Ivanov NV, Hoeng J. Interrogating the microbiome: experimental and computational considerations in support of study reproducibility. Drug Discov Today. 2018;23(9):1644–1657. doi: 10.1016/j.drudis.2018.06.005.
   PubMed Web of Science ®Google Scholar
• Vila AV, Imhann F, Collij V, Jankipersadsing SA, Gurry T, Mujagic Z, Kurilshikov A, Bonder MJ, Jiang X, Tigchelaar EF, et al. Gut microbiota composition and functional changes in inflammatory bowel disease and irritable bowel syndrome. Sci Transl Med. 2018;10(472). doi: 10.1126/scitranslmed.aap8914.
   Web of Science ®Google Scholar
• Marcos-Zambrano LJ, Karaduzovic-Hadziabdic K, Turukalo TL, Przymus P, Trajkovik V, Aasmets O, Berland M, Gruca A, Hasic J, Hron K, et al. Applications of machine learning in human microbiome studies: a review on feature selection, biomarker identification, disease prediction and treatment. Front Microbiol. 2021;12:12. doi:10.3389/fmicb.2021.634511.
   Web of Science ®Google Scholar
• Aronson JK, Ferner RE. Biomarkers—a general review. CP Pharmacol. 2017;76(1). doi: 10.1002/cpph.19.
   Google Scholar
• Yang L, Chen J. A comprehensive evaluation of microbial differential abundance analysis methods: current status and potential solutions. Microbiome. 2022;10(1). doi: 10.1186/s40168-022-01320-0.
   Web of Science ®Google Scholar
• Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJA, Holmes SP. DADA2: high-resolution sample inference from Illumina amplicon data. Nat Methods. 2016;13(7):581–583. doi: 10.1038/nmeth.3869.
   PubMed Web of Science ®Google Scholar
• Pires DEV, Oliveira FS, Correa FB, Morais DK, Fernandes GR. TAG.ME: taxonomic assignment of genetic markers for ecology bioRxiv 263293. 2018. doi:10.1101/263293.
   Google Scholar
• Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15(12). doi: 10.1186/s13059-014-0550-8.
   Web of Science ®Google Scholar
• Kuhn M. Building predictive models in R using the caret package. J Stat Soft. 2008;28(5). doi: 10.18637/jss.v028.i05.
   PubMed Web of Science ®Google Scholar
• Han H, Guo X, Yu H. Variable selection using mean decrease accuracy and mean decrease gini based on random forest. In: 2016 7th IEEE International Conference on Software Engineering and Service Science (ICSESS); Beijing,China. IEEE; 2016.
   Google Scholar
• Hosmer DW, Lemesbow S. Goodness of fit tests for the multiple logistic regression model. Communicat Statist Theory Meth. 1980;9(10):1043–1069. doi: 10.1080/03610928008827941.
   Web of Science ®Google Scholar
• Ghannam RB, Techtmann SM. Machine learning applications in microbial ecology human microbiome studies, and environmental monitoring. Comput Struct Biotechnol J. 2021;19:1092–1107. doi:10.1016/j.csbj.2021.01.028.
   PubMed Web of Science ®Google Scholar
• Kohli A, Holzwanger EA, Levy AN. Emerging use of artificial intelligence in inflammatory bowel disease. World J Gastroentero. 2020;26(44):6923–6928. doi: 10.3748/wjg.v26.i44.6923.
   PubMed Web of Science ®Google Scholar
• Olesen SW, Alm EJ. Dysbiosis is not an answer. Nat Microbiol. 2016;1(12). doi: 10.1038/nmicrobiol.2016.228.
   Web of Science ®Google Scholar
• Ahmad A, Yang W, Chen G, Shafiq M, Javed S, Zaidi SSA, Shahid R, Liu C, Bokhari H, Jacobs J. Analysis of gut microbiota of obese individuals with type 2 diabetes and healthy individuals. PLoS ONE. 2019;14(12):e0226372. doi: 10.1371/journal.pone.0226372.
   PubMed Web of Science ®Google Scholar
• Ley RE, Turnbaugh PJ, Klein S, Gordon JI. Human gut microbes associated with obesity. Nature. 2006;444(7122):1022–1023. doi: 10.1038/4441022a.
   PubMed Web of Science ®Google Scholar
• Scher JU, Ubeda C, Artacho A, Attur M, Isaac S, Reddy SM, Marmon S, Neimann A, Brusca S, Patel T, et al. Decreased bacterial diversity characterizes the altered gut microbiota in patients with psoriatic arthritis, resembling dysbiosis in inflammatory bowel disease. Arthritis Rheumatol. 2014;67(1):128–139. doi: 10.1002/art.38892.
   Web of Science ®Google Scholar
• Rinninella E, Raoul P, Cintoni M, Franceschi F, Miggiano G, Gasbarrini A, Mele M. What is the healthy gut microbiota composition? A changing ecosystem across age environment, diet, and diseases. Microorgan. 2019;7(1):14. doi: 10.3390/microorganisms7010014.
   PubMed Web of Science ®Google Scholar
• Vujkovic-Cvijin I, Sklar J, Jiang L, Natarajan L, Knight R, Belkaid Y. Host variables confound gut microbiota studies of human disease. Nature. 2020;587(7834):448–454. doi: 10.1038/s41586-020-2881-9.
   PubMed Web of Science ®Google Scholar
• Wilkinson JE, Franzosa EA, Everett C, Li C, Bae S, Berzansky I, Bhosle A, Bjørnevik K, Brennan CA, Cao YG, et al. A framework for microbiome science in public health. Nat Med. 2021;27(5):766–774. doi:10.1038/s41591-021-01258-0.
   PubMed Web of Science ®Google Scholar
• Kurilshikov A, Medina-Gomez C, Bacigalupe R, Radjabzadeh D, Wang J, Demirkan A, Roy CIL, Garay JAR, Finnicum CT, Liu X, et al. Large-scale association analyses identify host factors influencing human gut microbiome composition. Nat Genet. 2021;53(2):156–165. doi: 10.1038/s41588-020-00763-1.
   PubMed Web of Science ®Google Scholar
• Li P, Luo H, Ji B, Nielsen J. Machine learning for data integration in human gut microbiome. Microb Cell Fact. 2022;21(1). doi: 10.1186/s12934-022-01973-4.
   Web of Science ®Google Scholar
• Salim F, Mizutani S, Zolfo M, Yamada T. Recent advances of machine learning applications in human gut microbiota study: from observational analysis toward causal inference and clinical intervention. Curr Opin Biotechnol. 2023;79:102884. doi:10.1016/j.copbio.2022.102884.
   PubMed Web of Science ®Google Scholar
• Schloss PD, Ravel J. Identifying and overcoming threats to reproducibility, replicability, robustness, and generalizability in microbiome research. mBio. 2018;9(3). doi: 10.1128/mBio.00525-18.
   Web of Science ®Google Scholar
• Douglas GM, Hansen R, Jones CMA, Dunn KA, Comeau AM, Bielawski JP, Tayler R, El-Omar EM, Russell RK, Hold GL, et al. Multi-omics differentially classify disease state and treatment outcome in pediatric Crohn’s disease. Microbiome. 2018;6(1). doi: 10.1186/s40168-018-0398-3.
   PubMedGoogle Scholar
• Dhaliwal J, Erdman L, Drysdale E, Rinawi F, Muir J, Walters TD, Siddiqui I, Griffiths AM, Church PC. Accurate classification of pediatric colonic inflammatory bowel disease subtype using a random forest machine learning classifier. J Pediatr Gastroenterol Nutr. 2021;72(2):262–269. doi: 10.1097/MPG.0000000000002956.
   PubMed Web of Science ®Google Scholar
• Zuo W, Wang B, Bai X, Luan Y, Fan Y, Michail S, Sun F. 16S rRNA and metagenomic shotgun sequencing data revealed consistent patterns of gut microbiome signature in pediatric ulcerative colitis. Sci Rep. 2022;12(1). doi: 10.1038/s41598-022-07995-7.
   Web of Science ®Google Scholar
• Ananthakrishnan AN, Luo C, Yajnik V, Khalili H, Garber JJ, Stevens BW, Cleland T, Xavier RJ. Gut microbiome function predicts response to anti-integrin biologic therapy in inflammatory bowel diseases. Cell Host & Microbe. 2017;21(5):603–610.e3. doi: 10.1016/j.chom.2017.04.010.
   PubMed Web of Science ®Google Scholar
• da Rocha IMG, Torrinhas R, Fonseca D, de Oliveira Lyra C, de Sousa Alves Neri JL, Balmant BD, Callado L, Charlton K, Queiroz N, Waitzberg DL. Pro-inflammatory diet is correlated with high veillonella rogosae gut inflammation and clinical relapse of inflammatory bowel disease. Nutrients. 2023;15(19):4148. doi: 10.3390/nu15194148.
   PubMed Web of Science ®Google Scholar
• Wu H, Cai L, Li D, Wang X, Zhao S, Zou F, Zhou K. Metagenomics biomarkers selected for prediction of three different diseases in Chinese population. Biomed Res Int. 2018;2018:1–7. doi:10.1155/2018/2936257.
   Web of Science ®Google Scholar
• Wei F, Xu H, Yan C, Rong C, Liu B, Zhou H, Zhou XJ. Changes of intestinal flora in patients with systemic lupus erythematosus in northeast China. PLoS ONE. 2019;14(3):e0213063. doi: 10.1371/journal.pone.0213063.
   PubMed Web of Science ®Google Scholar
• Li Y, Wang HF, Li X, Li HX, Zhang Q, Zhou HW, He Y, Li P, Fu C, Zhang XH, et al. Disordered intestinal microbes are associated with the activity of systemic lupus erythematosus. Clin Sci. 2019;133(7):821–838. doi:10.1042/CS20180841.
   Web of Science ®Google Scholar
• Balmant BD, Fonseca DC, Prudêncio APA, Rocha IM, Callado L, Alves JTM, de Miranda Torrinhas RSM, Borba EF, Waitzberg DL. Megamonas funiformis plasma zonulin, and sodium intake affect C3 complement levels in inactive systemic lupus erythematosus. Nutri. 2023;15(8):1999. doi: 10.3390/nu15081999.
   Google Scholar
• Smart CEM, Evans M, O’Connell SM, McElduff P, Lopez PE, Jones TW, Davis EA, King BR. Both dietary protein and fat increase postprandial glucose excursions in children with type 1 diabetes and the effect is additive. Diab Care. 2013;36(12):3897–3902. doi: 10.2337/dc13-1195.
   PubMed Web of Science ®Google Scholar
• Chávez-Carbajal A, Pizano-Zárate ML, Hernández-Quiroz F, Ortiz-Luna GF, Morales-Hernández RM, Sales-Millán AD, Hernández-Trejo M, García-Vite A, Beltrán-Lagunes L, Hoyo-Vadillo C, et al. Characterization of the gut microbiota of individuals at different T2D stages reveals a complex relationship with the host. Microorgan. 2020;8(1):94. doi: 10.3390/microorganisms8010094.
   PubMed Web of Science ®Google Scholar
• Li Q, Chang Y, Zhang K, Chen H, Tao S, Zhang Z. Implication of the gut microbiome composition of type 2 diabetic patients from northern China. Sci Rep. 2020;10(1). doi: 10.1038/s41598-020-62224-3.
   Web of Science ®Google Scholar
• Gou W, Ling CW, He Y, Jiang Z, Fu Y, Xu F, Miao Z, Sun TY, Lin JS, Zhu HL, et al. Interpretable machine learning framework reveals robust gut microbiome features associated with type 2 diabetes. Diab Care. 2020;44(2):358–366. doi: 10.2337/dc20-1536.
   PubMed Web of Science ®Google Scholar
• Castellarin M, Warren RL, Freeman JD, Dreolini L, Krzywinski M, Strauss J, Barnes R, Watson P, Allen-Vercoe E, Moore RA, et al. Fusobacterium nucleatum infection is prevalent in human colorectal carcinoma. Genome Res. 2011;22(2):299–306. doi: 10.1101/gr.126516.111.
   PubMed Web of Science ®Google Scholar
• Osman MA, Neoh HM, Mutalib NSA, Chin SF, Mazlan L, Ali RAR, Zakaria AD, Ngiu CS, Ang MY, Jamal R. Parvimonas micra, Peptostreptococcus stomatis, Fusobacterium nucleatum and Akkermansia muciniphila as a four-bacteria biomarker panel of colorectal cancer. Sci Rep. 2021;11(1). doi: 10.1038/s41598-021-82465-0.
   Web of Science ®Google Scholar
• Shariati A, Razavi S, Ghaznavi-Rad E, Jahanbin B, Akbari A, Norzaee S, Darban-Sarokhalil D. Association between colorectal cancer and Fusobacterium nucleatum and bacteroides fragilis bacteria in Iranian patients: a preliminary study. Infect Agent Cancer. 2021;16(1). doi: 10.1186/s13027-021-00381-4.
   PubMed Web of Science ®Google Scholar