Results and lessons learned from the sbv IMPROVER metagenomics diagnostics for inflammatory bowel disease challenge

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  • Baumgart, D. C. & Sandborn, W. J. Inflammatory bowel disease: Clinical aspects and established and evolving therapies. Lancet 369(9573), 1641–1657 (2007).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Baumgart, D. C. The diagnosis and treatment of Crohn’s disease and ulcerative colitis. Deutsches Aerzteblatt Online 106(8), 123–133 (2009).

    Google Scholar 

  • Conrad, K., Roggenbuck, D. & Laass, M. W. Diagnosis and classification of ulcerative colitis. Autoimmun. Rev. 13(4–5), 463–466 (2014).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Laass, M. W., Roggenbuck, D. & Conrad, K. Diagnosis and classification of Crohn’s disease. Autoimmun. Rev. 13(4), 467–471 (2014).

    Article 
    PubMed 

    Google Scholar 

  • Tontini, G. E. Differential diagnosis in inflammatory bowel disease colitis: State of the art and future perspectives. World J. Gastroenterol. 21(1), 21 (2015).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Bernstein, C. N. et al. World gastroenterology organization practice guidelines for the diagnosis and management of IBD in 2010. Inflamm. Bowel Dis. 16(1), 112–124 (2010).

    Article 
    PubMed 

    Google Scholar 

  • Annese, V. et al. European evidence based consensus for endoscopy in inflammatory bowel disease. J. Crohn’s Colitis 7(12), 982–1018 (2013).

    Article 

    Google Scholar 

  • Ott, S. J. Reduction in diversity of the colonic mucosa associated bacterial microflora in patients with active inflammatory bowel disease. Gut 53(5), 685–693 (2004).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Manichanh, C. Reduced diversity of faecal microbiota in Crohn’s disease revealed by a metagenomic approach. Gut 55(2), 205–211 (2006).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Frank, D. N. et al. Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases. Proc. Natl. Acad. Sci. 104(34), 13780–13785 (2007).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Lloyd-Price, J. et al. Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases. Nature 569(7758), 655–662 (2019).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Gubatan, J. et al. Artificial intelligence applications in inflammatory bowel disease: Emerging technologies and future directions. World J. Gastroenterol. 27(17), 1920–1935 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Meyer, P. et al. Industrial methodology for process verification in research (IMPROVER): Toward systems biology verification. Bioinformatics 28(9), 1193–1201 (2012).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • MEDIC. https://www.intervals.science/resources/sbv-improver/medic.

  • Belcastroa, V. et al. The sbv IMPROVER Systems Toxicology computational challenge: Identification of human and species-independent blood response markers as predictors of smoking exposure and cessation status. Comput. Toxicol. 5, 38–51 (2018).

    Article 

    Google Scholar 

  • Vich Vila, A. et al. Gut microbiota composition and functional changes in inflammatory bowel disease and irritable bowel syndrome. Science Translational Medicine. 10(472), 8914 (2018).

    Article 

    Google Scholar 

  • Parada Venegas, D., et al. Short chain fatty acids (SCFAs)-mediated gut epithelial and immune regulation and its relevance for inflammatory bowel diseases. Front. Immunol. 10, 277 (2019).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Machiels, K. et al. A decrease of the butyrate-producing species Roseburia hominis and Faecalibacterium prausnitziidefines dysbiosis in patients with ulcerative colitis. Gut 63(8), 1275–1283 (2013).

    Article 
    PubMed 

    Google Scholar 

  • Facchin, S., et al. Microbiota changes induced by microencapsulated sodium butyrate in patients with inflammatory bowel disease. Neurogastroenterol. Motil. 32(10), e13914 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Kang, S. et al. Dysbiosis of fecal microbiota in Crohnʼs disease patients as revealed by a custom phylogenetic microarray. Inflamm. Bowel Dis. 16(12), 2034–2042 (2010).

    Article 
    PubMed 

    Google Scholar 

  • Zhang, L. et al. Bacterial species associated with human inflammatory bowel disease and their pathogenic mechanisms. Front. Microbiol. 24, 13 (2022).

    Google Scholar 

  • Sorg, J. A. & Sonenshein, A. L. Bile salts and glycine as cogerminants for clostridium difficile spores. J. Bacteriol. 190(7), 2505–2512 (2008).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Xu, X., et al. The gut metagenomics and metabolomics signature in patients with inflammatory bowel disease. Gut Pathogens 14, 26 (2022).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Han, D. H., et al. Co-administration of Lactobacillus gasseri KBL697 and tumor necrosis factor-alpha inhibitor infliximab improves colitis in mice. Sci. Rep. 12(1), 9640 (2022).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Bjarnason, I., Sission, G. & Hayee, B. A randomised, double-blind, placebo-controlled trial of a multi-strain probiotic in patients with asymptomatic ulcerative colitis and Crohn’s disease. Inflammopharmacology 27(3), 465–473 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Baldelli, V., Scaldaferri, F., Putignani, L. & Del Chierico, F. The role of enterobacteriaceae in gut microbiota dysbiosis in inflammatory bowel diseases. Microorganisms 9(4), 697 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Garrett, W. S. et al. Enterobacteriaceae Act in concert with the gut microbiota to induce spontaneous and maternally transmitted colitis. Cell Host Microbe 8(3), 292–300 (2010).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Ruby, T., McLaughlin, L., Gopinath, S. & Monack, D. Salmonella’s long-term relationship with its host. FEMS Microbiol. Rev. 36(3), 600–615 (2012).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Geddes, K. et al. Nod1 and Nod2 regulation of inflammation in the salmonella colitis model. Infect. Immun. 78(12), 5107–5115 (2010).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Deng, Q. & Barbieri, J. T. Molecular mechanisms of the cytotoxicity of ADP-ribosylating toxins. Annu. Rev. Microbiol. 62(1), 271–288 (2008).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Mahendran, V. et al. Prevalence of campylobacter species in adult Crohn’s disease and the preferential colonization sites of campylobacter species in the human intestine. Heimesaat MM, editor. PLoS ONE 6(9), e25417 (2011).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Sun, D. et al. Angiogenin maintains gut microbe homeostasis by balancing α-Proteobacteria and Lachnospiraceae. Gut 70(4), 666–676 (2020).

    Article 
    PubMed 

    Google Scholar 

  • Jangid, A. et al. Association of colitis with gut-microbiota dysbiosis in clathrin adapter AP-1B knockout mice. Blachier F, editor. PLoS ONE 15(3), e0228358 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Stojanov, S., Berlec, A. & Štrukelj, B. The influence of probiotics on the firmicutes/bacteroidetes ratio in the treatment of obesity and inflammatory bowel disease. Microorganisms 8(11), 1715 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Alam, M. T., et al. Microbial imbalance in inflammatory bowel disease patients at different taxonomic levels. Gut Pathogens 12, 1 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Eckburg, P. B. Diversity of the human intestinal microbial flora. Science 308(5728), 1635–1638 (2005).

    Article 
    ADS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Brown, E. M. et al. Bacteroides-derived sphingolipids are critical for maintaining intestinal homeostasis and symbiosis. Cell Host Microbe 25(5), 668-680.e7 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Waidmann, M. et al. Bacteroides vulgatus protects against Escherichia coli-induced colitis in gnotobiotic interleukin-2-deficient mice. Gastroenterology 125(1), 162–177 (2003).

    Article 
    PubMed 

    Google Scholar 

  • Round, J. L. & Mazmanian, S. K. The gut microbiota shapes intestinal immune responses during health and disease. Nat. Rev. Immunol. 9(5), 313–323 (2009).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Rabizadeh, S. et al. Enterotoxigenic Bacteroides fragilis: A potential instigator of colitis. Inflamm. Bowel Dis. 13(12), 1475–1483 (2007).

    Article 
    PubMed 

    Google Scholar 

  • Yao, S., Zhao, Z., Wang, W. & Liu, X. Bifidobacterium longum: Protection against inflammatory bowel disease. Wang K, editor. J. Immunol. Res. 2021, 1–11 (2021).

    Article 

    Google Scholar 

  • Pompei, A. et al. Folate production by bifidobacteria as a potential probiotic property. Appl. Environ. Microbiol. 73(1), 179–185 (2006).

    Article 
    ADS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Zhao, X. et al. Response of gut microbiota to metabolite changes induced by endurance exercise. Front. Microbiol. 20(9), 765 (2018).

    Article 

    Google Scholar 

  • Clavel, T. et al. Intestinal microbiota in metabolic diseases. Gut Microbes. 5(4), 544–551 (2014).

    Article 
    PubMed 

    Google Scholar 

  • Mottawea, W., et al. Altered intestinal microbiota–host mitochondria crosstalk in new onset Crohn’s disease. Nat. Commun. 7(1), 13419 (2016).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Edwards, J.-A. et al. Role of regenerating islet-derived proteins in inflammatory bowel disease. World J. Gastroenterol. 26(21), 2702–2714 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Dharmani, P., Strauss, J., Ambrose, C., Allen-Vercoe, E. & Chadee, K. Fusobacterium nucleatum infection of colonic cells stimulates MUC2 mucin and tumor necrosis factor alpha. Bäumler AJ, editor. Infect. Immun. 79(7), 2597–2607 (2011).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Santoru, M. L., et al. Cross sectional evaluation of the gut-microbiome metabolome axis in an Italian cohort of IBD patients. Sci. Rep. 7(1), 9523 (2017).

    Article 
    ADS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Chen, T. et al. Akkermansia muciniphila protects against psychological disorder-induced gut microbiota-mediated colonic mucosal barrier damage and aggravation of colitis. Front. Cell. Infect. Microbiol. 14, 11 (2021).

    Google Scholar 

  • Qian, K. et al. A β-N-acetylhexosaminidase Amuc_2109 from Akkermansia muciniphila protects against dextran sulfate sodium-induced colitis in mice by enhancing intestinal barrier and modulating gut microbiota. Food Funct. 13, 2216–2227 (2022).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Lo Sasso, G. et al. Inflammatory bowel disease-associated changes in the gut: Focus on Kazan patients. Inflamm. Bowel Dis. 27(3), 418–433 (2020).

    Article 
    PubMed Central 

    Google Scholar 

  • Yi, S. K. M., Steyvers, M., Lee, M. D. & Dry, M. J. The wisdom of the crowd in combinatorial problems. Cogn. Sci. 36(3), 452–470 (2012).

    Article 
    PubMed 

    Google Scholar 

  • Good, B. M. & Su, A. I. Crowdsourcing for bioinformatics. Bioinformatics 29(16), 1925–1933 (2013).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Talikka, M. et al. Novel approaches to develop community-built biological network models for potential drug discovery. Expert Opin. Drug Discov. 12(8), 849–857 (2017).

    PubMed 

    Google Scholar 

  • Sparks, R., Lau, W. W. & Tsang, J. S. Expanding the immunology toolbox: Embracing public-data reuse and crowdsourcing. Immunity 45(6), 1191–1204 (2016).

    Article 
    PubMed 

    Google Scholar 

  • Shah, N., Levy, A. E., Moriates, C. & Arora, V. M. Wisdom of the crowd. Acad. Med. 90(5), 624–628 (2015).

    Article 
    PubMed 

    Google Scholar 

  • Linde, J., Schulze, S., Henke, S. G. & Guthke, R. Data- and knowledge-based modeling of gene regulatory networks: An update. EXCLI J. 2(14), 346–378 (2015).

    Google Scholar 

  • Bakir-Gungor, B. et al. Inflammatory bowel disease biomarkers of human gut microbiota selected via different feature selection methods. PeerJ 25(10), e13205 (2022).

    Article 

    Google Scholar 

  • LaPierre, N., Ju, C.J.-T., Zhou, G. & Wang, W. MetaPheno: A critical evaluation of deep learning and machine learning in metagenome-based disease prediction. Methods 166, 74–82 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Pasolli, E., Truong, D. T., Malik, F., Waldron, L. & Segata, N. Machine learning meta-analysis of large metagenomic datasets: Tools and biological insights. PLoS Comput. Biol. 12(7), e1004977 (2016).

    Article 
    ADS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Eck, A. et al. Robust microbiota-based diagnostics for inflammatory bowel disease. McAdam AJ, editor. J. Clin. Microbiol. 55(6), 1720–1732 (2017).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Mirsepasi-Lauridsen, H. C. et al. Substantial intestinal microbiota differences between patients with ulcerative colitis from Ghana and Denmark. Front. Cell. Infect. Microbiol. https://doi.org/10.3389/fcimb.2022.832500 (2022).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Mirsepasi-Lauridsen, H. C. et al. Disease-specific enteric microbiome dysbiosis in inflammatory bowel disease. Front. Med. 20, 5 (2018).

    Google Scholar 

  • Marbach, D. et al. Wisdom of crowds for robust gene network inference. Nat. Methods 9(8), 796–804 (2012).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Stolovitzky, G., Prill, R. J. & Califano, A. Lessons from the DREAM2 challenges. Ann. N. Y. Acad. Sci. 1158(1), 159–195 (2009).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar 

  • Papin, J. A. & Mac, G. F. Wisdom of crowds in computational biology. PLoS Comput. Biol. 15(5), e1007032 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Buisson, A. et al. Comparative Acceptability and Perceived Clinical Utility of Monitoring Tools. Inflamm. Bowel Dis. 23(8), 1425–1433 (2017).

    Article 
    PubMed 

    Google Scholar 

  • Kalla, R. et al. Patients’ perceptions of faecal calprotectin testing in inflammatory bowel disease: Results from a prospective multicentre patient-based survey*. Scand. J. Gastroenterol. 53(12), 1437–1442 (2018).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Maréchal, C. et al. Compliance with the faecal calprotectin test in patients with inflammatory bowel disease. United Eur. Gastroenterol. J. 5(5), 702–707 (2017).

    Article 

    Google Scholar 

  • Khakoo, N. S., et al. Patient adherence to fecal calprotectin testing is low compared to other commonly ordered tests in patients with inflammatory bowel disease. Crohn’s Colitis 360 3(3), otab028 (2021).

    Article 

    Google Scholar 

  • He, Q., et al. Two distinct metacommunities characterize the gut microbiota in Crohn’s disease patients. GigaScience 6(7), 1–11 (2017).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Schirmer, M. et al. Dynamics of metatranscription in the inflammatory bowel disease gut microbiome. Nat. Microbiol. 3(3), 337–346 (2018).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Li, H. Minimap2: Pairwise alignment for nucleotide sequences. Birol I, editor. Bioinformatics 34(18), 3094–3100 (2018).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Li, H. et al. The sequence alignment/map format and SAMtools. Bioinformatics 25(16), 2078–2079 (2009).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • BBMap. SourceForge. http://sourceforge.net/projects/bbmap.

  • Andrews, S. Babraham bioinformatics—FastQC A quality control tool for high throughput sequence data (2010). http://www.bioinformatics.babraham.ac.uk/projects/fastqc.

  • Ewels, P., Magnusson, M., Lundin, S. & Käller, M. MultiQC: Summarize analysis results for multiple tools and samples in a single report. Bioinformatics 32(19), 3047–3048 (2016).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Wood, D. E., Lu, J. & Langmead, B. Improved metagenomic analysis with Kraken 2. Genome Biol. 20(1), 257 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Lu, J., Breitwieser, F. P., Thielen, P. & Salzberg, S. L. Bracken: Estimating species abundance in metagenomics data. PeerJ Comput. Sci. 2(3), e104 (2017).

    Article 

    Google Scholar 

  • O’Leary, N. A. et al. Reference sequence (RefSeq) database at NCBI: Current status, taxonomic expansion, and functional annotation. Nucleic Acids Res. 44(D1), D733–D745 (2015).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • McIver, L. J. et al. bioBakery: A meta’omic analysis environment. Hancock J, editor. Bioinformatics 34(7), 1235–1237 (2017).

    Article 
    PubMed Central 

    Google Scholar 

  • Kuhn, M., et al. caret: Classification and Regression Training. R-Packages. 2020. https://cran.r-project.org/web/packages/caret/index.html.



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