Login Register Cart 0
Generic placeholder image

Current Protein & Peptide Science

Editor-in-Chief

ISSN (Print): 1389-2037
ISSN (Online): 1875-5550

Back
Journal Home About Journal Editorial Board Journal Insight Current Issue Volumes/Issues
Subscribe
Research Article

EHAI: Enhanced Human Microbe-Disease Association Identification

Author(s): Ruizhi Fan, Chenhua Dong, Hu Song, Yixin Xu, Linsen Shi, Teng Xu, Meng Cao, Tao Jiang and Jun Song*

Volume 21, Issue 11, 2020

Page: [1078 - 1084] Pages: 7

DOI: 10.2174/1389203721666200702150249

Price: $65

Abstract

Recently, an increasing number of biological and clinical reports have demonstrated that imbalance of microbial community has the ability to play important roles among several complex diseases concerning human health. Having a good knowledge of discovering potential of microbe-disease relationships, which provides the ability to having a better understanding of some issues, including disease pathology, further boosts disease diagnostics and prognostics, has been taken into account. Nevertheless, a few computational approaches can meet the need of huge scale of microbe-disease association discovery. In this work, we proposed the EHAI model, which is Enhanced Human microbe- disease Association Identification. EHAI employed the microbe-disease associations, and then Gaussian interaction profile kernel similarity has been utilized to enhance the basic microbe-disease association. Actually, some known microbe-disease associations and a large amount of associations are still unavailable among the datasets. The ‘super-microbe’ and ‘super-disease’ were employed to enhance the model. Computational results demonstrated that such super-classes have the ability to be helpful to the performance of EHAI. Therefore, it is anticipated that EHAI can be treated as an important biological tool in this field.

Keywords: Diseases, microbe, colorectal cancer, machine learning, EHAI, HMDAD.

« Previous Next »
Graphical Abstract

[1]
Human Microbiome Project Consortium. A framework for human microbiome research. Nature, 2012, 486(7402), 215-221.
[http://dx.doi.org/10.1038/nature11209] [PMID: 22699610]
[2]
Human Microbiome Project Consortium. Structure, function and diversity of the healthy human microbiome. Nature, 2012, 486(7402), 207-214.
[http://dx.doi.org/10.1038/nature11234] [PMID: 22699609]
[3]
Ventura, M.; O’Flaherty, S.; Claesson, M.J.; Turroni, F.; Klaenhammer, T.R.; van Sinderen, D.; O’Toole, P.W. Genome-scale analyses of health-promoting bacteria: probiogenomics. Nat. Rev. Microbiol., 2009, 7(1), 61-71.
[http://dx.doi.org/10.1038/nrmicro2047] [PMID: 19029955]
[4]
Sommer, F.; Bäckhed, F. The gut microbiota--masters of host development and physiology. Nat. Rev. Microbiol., 2013, 11(4), 227-238.
[http://dx.doi.org/10.1038/nrmicro2974] [PMID: 23435359]
[5]
Gill, S.R.; Pop, M.; Deboy, R.T.; Eckburg, P.B.; Turnbaugh, P.J.; Samuel, B.S.; Gordon, J.I.; Relman, D.A.; Fraser-Liggett, C.M.; Nelson, K.E. Metagenomic analysis of the human distal gut microbiome. Science, 2006, 312(5778), 1355-1359.
[http://dx.doi.org/10.1126/science.1124234] [PMID: 16741115]
[6]
Smith, K.; McCoy, K.D.; Macpherson, A.J. Use of axenic animals in studying the adaptation of mammals to their commensal intestinal microbiota. Semin. Immunol., 2007, 19(2), 59-69.
[http://dx.doi.org/10.1016/j.smim.2006.10.002] [PMID: 17118672]
[7]
Bäckhed, F.; Ley, R.E.; Sonnenburg, J.L.; Peterson, D.A.; Gordon, J.I. Host-bacterial mutualism in the human intestine. Science, 2005, 307(5717), 1915-1920.
[http://dx.doi.org/10.1126/science.1104816] [PMID: 15790844]
[8]
Turnbaugh, P.J.; Hamady, M.; Yatsunenko, T.; Cantarel, B.L.; Duncan, A.; Ley, R.E.; Sogin, M.L.; Jones, W.J.; Roe, B.A.; Affourtit, J.P.; Egholm, M.; Henrissat, B.; Heath, A.C.; Knight, R.; Gordon, J.I. A core gut microbiome in obese and lean twins. Nature, 2009, 457(7228), 480-484.
[http://dx.doi.org/10.1038/nature07540] [PMID: 19043404]
[9]
Goodrich, J.K.; Waters, J.L.; Poole, A.C.; Sutter, J.L.; Koren, O.; Blekhman, R.; Beaumont, M.; Van Treuren, W.; Knight, R.; Bell, J.T.; Spector, T.D.; Clark, A.G.; Ley, R.E. Human genetics shape the gut microbiome. Cell, 2014, 159(4), 789-799.
[http://dx.doi.org/10.1016/j.cell.2014.09.053] [PMID: 25417156]
[10]
Davenport, E.R.; Mizrahi-Man, O.; Michelini, K.; Barreiro, L.B.; Ober, C.; Gilad, Y. Seasonal variation in human gut microbiome composition. PLoS One, 2014, 9(3)e90731
[http://dx.doi.org/10.1371/journal.pone.0090731] [PMID: 24618913]
[11]
Donia, M.S.; Cimermancic, P.; Schulze, C.J.; Wieland Brown, L.C.; Martin, J.; Mitreva, M.; Clardy, J.; Linington, R.G.; Fischbach, M.A. A systematic analysis of biosynthetic gene clusters in the human microbiome reveals a common family of antibiotics. Cell, 2014, 158(6), 1402-1414.
[http://dx.doi.org/10.1016/j.cell.2014.08.032] [PMID: 25215495]
[12]
Walker, A.W.; Ince, J.; Duncan, S.H.; Webster, L.M.; Holtrop, G.; Ze, X.; Brown, D.; Stares, M.D.; Scott, P.; Bergerat, A.; Louis, P.; McIntosh, F.; Johnstone, A.M.; Lobley, G.E.; Parkhill, J.; Flint, H.J. Dominant and diet-responsive groups of bacteria within the human colonic microbiota. ISME J., 2011, 5(2), 220-230.
[http://dx.doi.org/10.1038/ismej.2010.118] [PMID: 20686513]
[13]
Wu, G.D.; Chen, J.; Hoffmann, C.; Bittinger, K.; Chen, Y.Y.; Keilbaugh, S.A.; Bewtra, M.; Knights, D.; Walters, W.A.; Knight, R.; Sinha, R.; Gilroy, E.; Gupta, K.; Baldassano, R.; Nessel, L.; Li, H.; Bushman, F.D.; Lewis, J.D. Linking long-term dietary patterns with gut microbial enterotypes. Science, 2011, 334(6052), 105-108.
[http://dx.doi.org/10.1126/science.1208344] [PMID: 21885731]
[14]
Henao-Mejia, J.; Elinav, E.; Thaiss, C.A.; Licona-Limon, P.; Flavell, R.A. Role of the intestinal microbiome in liver disease. J. Autoimmun., 2013, 46, 66-73.
[http://dx.doi.org/10.1016/j.jaut.2013.07.001] [PMID: 24075647]
[15]
Munoz-Garach, A.; Diaz-Perdigones, C.; Tinahones, F.J. Gut microbiota and type 2 diabetes mellitus. Endocrinologia y nutricion: organode la Sociedad Espanola de Endocrinologia y Nutricion., 2016,63(10), 560-568.
[http://dx.doi.org/10.1016/j.endoen.2016.07.004]
[16]
Wen, L.; Ley, R.E.; Volchkov, P.Y.; Stranges, P.B.; Avanesyan, L.; Stonebraker, A.C.; Hu, C.; Wong, F.S.; Szot, G.L.; Bluestone, J.A.; Gordon, J.I.; Chervonsky, A.V. Innate immunity and intestinal microbiota in the development of Type 1 diabetes. Nature, 2008, 455(7216), 1109-1113.
[http://dx.doi.org/10.1038/nature07336] [PMID: 18806780]
[17]
Noval Rivas, M.; Crother, T.R.; Arditi, M. The microbiome in asthma. Curr. Opin. Pediatr., 2016, 28(6), 764-771.
[http://dx.doi.org/10.1097/MOP.0000000000000419] [PMID: 27606957]
[18]
Sokol, H.; Seksik, P.; Rigottier-Gois, L.; Lay, C.; Lepage, P.; Podglajen, I.; Marteau, P.; Doré, J. Specificities of the fecal microbiota in inflammatory bowel disease. Inflamm. Bowel Dis., 2006, 12(2), 106-111.
[http://dx.doi.org/10.1097/01.MIB.0000200323.38139.c6] [PMID: 16432374]
[19]
Castellarin, M.; Warren, R.L.; Freeman, J.D.; Dreolini, L.; Krzywinski, M.; Strauss, J.; Barnes, R.; Watson, P.; Allen-Vercoe, E.; Moore, R.A.; Holt, R.A. Fusobacterium nucleatum infection is prevalent in human colorectal carcinoma. Genome Res., 2012, 22(2), 299-306.
[http://dx.doi.org/10.1101/gr.126516.111] [PMID: 22009989]
[20]
Schwabe, R.F.; Jobin, C. The microbiome and cancer. Nat. Rev. Cancer, 2013, 13(11), 800-812.
[http://dx.doi.org/10.1038/nrc3610] [PMID: 24132111]
[21]
Hilty, M.; Burke, C.; Pedro, H.; Cardenas, P.; Bush, A.; Bossley, C.; Davies, J.; Ervine, A.; Poulter, L.; Pachter, L.; Moffatt, M.F.; Cookson, W.O. Disordered microbial communities in asthmatic airways. PLoS One, 2010, 5(1)e8578
[http://dx.doi.org/10.1371/journal.pone.0008578] [PMID: 20052417]
[22]
Mondot, S.; Kang, S.; Furet, J.P.; Aguirre de Carcer, D.; McSweeney, C.; Morrison, M.; Marteau, P.; Doré, J.; Leclerc, M. Highlighting new phylogenetic specificities of Crohn’s disease microbiota. Inflamm. Bowel Dis., 2011, 17(1), 185-192.
[http://dx.doi.org/10.1002/ibd.21436] [PMID: 20722058]
[23]
Moore, W.E.; Moore, L.H. Intestinal floras of populations that have a high risk of colon cancer. Appl. Environ. Microbiol., 1995, 61(9), 3202-3207.
[http://dx.doi.org/10.1128/AEM.61.9.3202-3207.1995] [PMID: 7574628]
[24]
Chen, Y.; Yang, F.; Lu, H.; Wang, B.; Chen, Y.; Lei, D.; Wang, Y.; Zhu, B.; Li, L. Characterization of fecal microbial communities in patients with liver cirrhosis. Hepatology, 2011, 54(2), 562-572.
[http://dx.doi.org/10.1002/hep.24423] [PMID: 21574172]
[25]
Ma, W.; Zhang, L.; Zeng, P.; Huang, C.; Li, J.; Geng, B.; Yang, J.; Kong, W.; Zhou, X.; Cui, Q. An analysis of human microbe-disease associations. Brief. Bioinform., 2017, 18(1), 85-97.
[PMID: 26883326]
[26]
Chen, X.; Yan, G.Y. Semi-supervised learning for potential human microRNA-disease associations inference. Sci. Rep., 2014, 4, 5501.
[http://dx.doi.org/10.1038/srep05501] [PMID: 24975600]
[27]
Chen, X.; Yan, C.C.; Zhang, X.; You, Z.H.; Huang, Y.A.; Yan, G.Y. HGIMDA: Heterogeneous graph inference for miRNA-disease association prediction. Oncotarget, 2016, 7(40), 65257-65269.
[http://dx.doi.org/10.18632/oncotarget.11251] [PMID: 27533456]
[28]
Chen, X.; Yan, C.C.; Zhang, X.; You, Z.H.; Deng, L.; Liu, Y.; Zhang, Y.; Dai, Q. WBSMDA: Within and Between Score for MiRNA-Disease Association prediction. Sci. Rep., 2016, 6, 21106.
[http://dx.doi.org/10.1038/srep21106] [PMID: 26880032]
[29]
Chen, X.; Yan, C.C.; Zhang, X.; You, Z.H. Long non-coding RNAs and complex diseases: from experimental results to computational models. Brief. Bioinform., 2017, 18(4), 558-576.
[http://dx.doi.org/10.1093/bib/bbw060] [PMID: 27345524]
[30]
Chen, X.; You, Z.H.; Yan, G.Y.; Gong, D.W. IRWRLDA: improved random walk with restart for lncRNA-disease association prediction. Oncotarget, 2016, 7(36), 57919-57931.
[http://dx.doi.org/10.18632/oncotarget.11141] [PMID: 27517318]
[31]
Chen, X.; Huang, Y.A.; Wang, X.S.; You, Z.H.; Chan, K.C. FMLNCSIM: fuzzy measure-based lncRNA functional similarity calculation model. Oncotarget, 2016, 7(29), 45948-45958.
[http://dx.doi.org/10.18632/oncotarget.10008] [PMID: 27322210]
[32]
Chen, X.; Yan, C.C.; Zhang, X.; Zhang, X.; Dai, F.; Yin, J.; Zhang, Y. Drug-target interaction prediction: databases, web servers and computational models. Brief. Bioinform., 2016, 17(4), 696-712.
[http://dx.doi.org/10.1093/bib/bbv066] [PMID: 26283676]
[33]
Chen, X.; Ren, B.; Chen, M.; Wang, Q.; Zhang, L.; Yan, G. NLLSS: Predicting Synergistic Drug Combinations Based on Semi-supervised Learning. PLOS Comput. Biol., 2016, 12(7)e1004975
[http://dx.doi.org/10.1371/journal.pcbi.1004975] [PMID: 27415801]
[34]
Martinez, F.D. Genes, environments, development and asthma: a reappraisal. Eur. Respir. J., 2007, 29(1), 179-184.
[http://dx.doi.org/10.1183/09031936.00087906] [PMID: 17197483]
[35]
Vos, T.; Barber, R.M.; Bell, B.; Bertozzi-Villa, A.; Biryukov, S.; Bolliger, I.; Charlson, F.; Davis, A.; Degenhardt, L.; Dicker, D. Global Burden of Disease Study 2013 Collaborators. Global, regional, and national incidence, prevalence, and years lived with disability for 301 acute and chronic diseases and injuries in 188 countries, 1990-2013: a systematic analysis for the Global Burden of Disease Study 2013. Lancet, 2015, 386(9995), 743-800.
[http://dx.doi.org/10.1016/S0140-6736(15)60692-4] [PMID: 26063472]
[36]
Huang, YJ; Nelson, CE; Brodie, EL; Desantis, TZ; Baek, MS; Liu, J; Woyke, T; Allgaier, M; Bristow, J; Wiener-Kronish, JP; Sutherland, ER; King, TS; Icitovic, N; Martin, RJ; Calhoun, WJ; Castro, M Airway microbiota and bronchial hyperresponsiveness in patients with suboptimally controlled asthma.The Journal of allergy and clinical immunology., 2011, 127(2), 372-381.. e1-3..
[http://dx.doi.org/10.1016/j.jaci.2010.10.048]
[37]
Marri, P.R.; Stern, D.A.; Wright, A.L.; Billheimer, D.; Martinez, F.D. Asthma-associated differences in microbial composition of induced sputum. J. Allergy Clini. Immunolo., 2013, 131(2), 346-352. e3..
[http://dx.doi.org/10.1016/j.jaci.2012.11.013]
[38]
Park, H.; Shin, J.W.; Park, S.G.; Kim, W. Microbial communities in the upper respiratory tract of patients with asthma and chronic obstructive pulmonary disease. PLoS One, 2014, 9(10)e109710
[http://dx.doi.org/10.1371/journal.pone.0109710] [PMID: 25329665]
[39]
Vael, C.; Vanheirstraeten, L.; Desager, K.N.; Goossens, H. Denaturing gradient gel electrophoresis of neonatal intestinal microbiota in relation to the development of asthma. BMC Microbiol., 2011, 11, 68.
[http://dx.doi.org/10.1186/1471-2180-11-68] [PMID: 21477358]
[40]
Yu, J.; Jang, S.O.; Kim, B.J.; Song, Y.H.; Kwon, J.W.; Kang, M.J.; Choi, W.A.; Jung, H.D.; Hong, S.J. The Effects of Lactobacillus rhamnosus on the Prevention of Asthma in a Murine Model. Allergy Asthma Immunol. Res., 2010, 2(3), 199-205.
[http://dx.doi.org/10.4168/aair.2010.2.3.199] [PMID: 20592920]
[41]
Naghavi, M.; Wang, H.; Lozano, R.; Davis, A.; Liang, X.; Zhou, M.; Vollset, S.E.; Ozgoren, A.A.; Abdalla, S.; Abd-Allah, F. GBD 2013 Mortality and Causes of Death Collaborators. Global, regional, and national age-sex specific all-cause and cause-specific mortality for 240 causes of death, 1990-2013: a systematic analysis for the Global Burden of Disease Study 2013. Lancet, 2015, 385(9963), 117-171.
[http://dx.doi.org/10.1016/S0140-6736(14)61682-2] [PMID: 25530442]
[42]
Perz, J.F.; Armstrong, G.L.; Farrington, L.A.; Hutin, Y.J.; Bell, B.P. The contributions of hepatitis B virus and hepatitis C virus infections to cirrhosis and primary liver cancer worldwide. J. Hepatol., 2006, 45(4), 529-538.
[http://dx.doi.org/10.1016/j.jhep.2006.05.013] [PMID: 16879891]
[43]
Qin, N.; Yang, F.; Li, A.; Prifti, E.; Chen, Y.; Shao, L.; Guo, J.; Le Chatelier, E.; Yao, J.; Wu, L.; Zhou, J.; Ni, S.; Liu, L.; Pons, N.; Batto, J.M.; Kennedy, S.P.; Leonard, P.; Yuan, C.; Ding, W.; Chen, Y.; Hu, X.; Zheng, B.; Qian, G.; Xu, W.; Ehrlich, S.D.; Zheng, S.; Li, L. Alterations of the human gut microbiome in liver cirrhosis. Nature, 2014, 513(7516), 59-64.
[http://dx.doi.org/10.1038/nature13568] [PMID: 25079328]
[44]
Fouts, D.E.; Torralba, M.; Nelson, K.E.; Brenner, D.A.; Schnabl, B. Bacterial translocation and changes in the intestinal microbiome in mouse models of liver disease. J. Hepatol., 2012, 56(6), 1283-1292.
[http://dx.doi.org/10.1016/j.jhep.2012.01.019] [PMID: 22326468]
[45]
Zhao, H.Y.; Wang, H.J.; Lu, Z.; Xu, S.Z. Intestinal microflora in patients with liver cirrhosis. Chin. J. Dig. Dis., 2004, 5(2), 64-67.
[http://dx.doi.org/10.1111/j.1443-9573.2004.00157.x] [PMID: 15612659]
[46]
Shi, Y.; Hu, F.B. The global implications of diabetes and cancer. Lancet, 2014, 383(9933), 1947-1948.
[http://dx.doi.org/10.1016/S0140-6736(14)60886-2] [PMID: 24910221]
[47]
Atlas, D. International diabetes federation.Press Release, Cape Town, South Africa., 2006, 4.
[48]
Furet, J.P.; Kong, L.C.; Tap, J.; Poitou, C.; Basdevant, A.; Bouillot, J.L.; Mariat, D.; Corthier, G.; Doré, J.; Henegar, C.; Rizkalla, S.; Clément, K. Differential adaptation of human gut microbiota to bariatric surgery-induced weight loss: links with metabolic and low-grade inflammation markers. Diabetes, 2010, 59(12), 3049-3057.
[http://dx.doi.org/10.2337/db10-0253] [PMID: 20876719]
[49]
Larsen, N.; Vogensen, F.K.; van den Berg, F.W.; Nielsen, D.S.; Andreasen, A.S.; Pedersen, B.K.; Al-Soud, W.A.; Sørensen, S.J.; Hansen, L.H.; Jakobsen, M. Gut microbiota in human adults with type 2 diabetes differs from non-diabetic adults. PLoS One, 2010, 5(2)e9085
[http://dx.doi.org/10.1371/journal.pone.0009085] [PMID: 20140211]
[50]
He, C.; Yang, Z.; Lu, N.H. Helicobacter pylori infection and diabetes: is it a myth or fact? World J. Gastroenterol., 2014, 20(16), 4607-4617.
[http://dx.doi.org/10.3748/wjg.v20.i16.4607] [PMID: 24782613]
[51]
Zhou, M.; Rong, R.; Munro, D.; Zhu, C.; Gao, X.; Zhang, Q.; Dong, Q. Investigation of the effect of type 2 diabetes mellitus on subgingival plaque microbiota by high-throughput 16S rDNA pyrosequencing. PLoS One, 2013, 8(4)e61516
[http://dx.doi.org/10.1371/journal.pone.0061516] [PMID: 23613868]
[52]
Kampoo, K.; Teanpaisan, R.; Ledder, R.G.; McBain, A.J. Oral bacterial communities in individuals with type 2 diabetes who live in southern Thailand. Appl. Environ. Microbiol., 2014, 80(2), 662-671.
[http://dx.doi.org/10.1128/AEM.02821-13] [PMID: 24242241]
[53]
Nitzan, O.; Elias, M.; Chazan, B.; Saliba, W. Urinary tract infections in patients with type 2 diabetes mellitus: review of prevalence, diagnosis, and management. Diabetes Metab. Syndr. Obes., 2015, 8, 129-136.
[PMID: 25759592]
[54]
Chen, X.; Liu, M.X.; Yan, G.Y. RWRMDA: predicting novel human microRNA-disease associations. Mol. Biosyst., 2012, 8(10), 2792-2798.
[http://dx.doi.org/10.1039/c2mb25180a] [PMID: 22875290]
[55]
Chen, X.; Yan, C.C.; Luo, C.; Ji, W.; Zhang, Y.; Dai, Q. Constructing lncRNA functional similarity network based on lncRNA-disease associations and disease semantic similarity. Sci. Rep., 2015, 5, 11338.
[http://dx.doi.org/10.1038/srep11338] [PMID: 26061969]
[56]
Chen, X.; Yan, G.Y. Novel human lncRNA-disease association inference based on lncRNA expression profiles. Bioinformatics, 2013, 29(20), 2617-2624.
[http://dx.doi.org/10.1093/bioinformatics/btt426] [PMID: 24002109]
[57]
Wang, E.; Zaman, N.; Mcgee, S.; Milanese, J.S.; Masoudi-Nejad, A.; O’Connor-McCourt, M. Predictive genomics: a cancer hallmark network framework for predicting tumor clinical phenotypes using genome sequencing data. Semin. Cancer Biol., 2015, 30, 4-12.
[http://dx.doi.org/10.1016/j.semcancer.2014.04.002] [PMID: 24747696]
[58]
Wang, E. Understanding genomic alterations in cancer genomes using an integrative network approach. Cancer Lett., 2013, 340(2), 261-269.
[http://dx.doi.org/10.1016/j.canlet.2012.11.050] [PMID: 23266571]
[59]
van Laarhoven, T.; Nabuurs, S.B.; Marchiori, E. Gaussian interaction profile kernels for predicting drug-target interaction. Bioinformatics, 2011, 27(21), 3036-3043.
[http://dx.doi.org/10.1093/bioinformatics/btr500] [PMID: 21893517]
[60]
Ward, J.H., Jr Hierarchical grouping to optimize an objective function. J. Am. Stat. Assoc., 1963, 58(301), 236-244.
[http://dx.doi.org/10.1080/01621459.1963.10500845]
[61]
Zhang, M.L.; Zhou, Z.H. M L-KNN: A lazy learning approach to multi-label learning. Pattern Recognit., 2007, 40(7), 2038-2048.
[http://dx.doi.org/10.1016/j.patcog.2006.12.019]
[62]
Shi, J.Y.; Yiu, S.M.; Li, Y.; Leung, H.C.; Chin, F.Y. Predicting drug-target interaction for new drugs using enhanced similarity measures and super-target clustering. Methods, 2015, 83, 98-104.
[http://dx.doi.org/10.1016/j.ymeth.2015.04.036] [PMID: 25957673]
[63]
Dang, H.T.; Park, H.K.; Shin, J.W.; Park, S-G.; Kim, W. Analysis of Oropharyngeal Microbiota between the Patients with Bronchial Asthma and the Non-Asthmatic Persons. J. Bacteriol. Virol., 2013,43(4), 270-278..
[http://dx.doi.org/10.4167/jbv.2013.43.4.270]

Rights & Permissions Print Cite
Article Metrics
30
Wayfinder Image
© 2024 Bentham Science Publishers | Privacy Policy