The DOI matches its Crossref record; 49 of the 49 references it cites were found in a registry or an index.
Longitudinal Multi-omics Reveals Subset-Specific Mechanisms Underlying Irritable Bowel Syndrome
Open accessAbstract
The gut microbiome has been implicated in multiple human chronic gastrointestinal (GI) disorders. Determining its mechanistic role in disease has been difficult due to apparent disconnects between animal and human studies and lack of an integrated multi-omics view of disease-specific physiological changes. We integrated longitudinal multi-omics data from the gut microbiome, metabolome, host epigenome, and transcriptome in the context of irritable bowel syndrome (IBS) host physiology. We identified IBS subtype-specific and symptom-related variation in microbial composition and function. A subset of identified changes in microbial metabolites correspond to host physiological mechanisms that are relevant to IBS. By integrating multiple data layers, we identified purine metabolism as a novel host-microbial metabolic pathway in IBS with translational potential. Our study highlights the importance of longitudinal sampling and integrating complementary multi-omics data to identify functional mechanisms that can serve as therapeutic targets in a comprehensive treatment strategy for chronic GI diseases. VIDEO ABSTRACT.
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“However, an integrated longitudinal multi-omics analysis of the gut microbiome, metabolome, host epigenome and transcriptome, in the context of host symptoms and physiology in patients with IBS-D and IBS-C, identified subtype-specific and symptom-related variations in microbial composition and function.76”
From British Society of Gastroenterology guidelines on the management of irritable bowel syndrome (2021) · cites this paper as [76]
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Robinson, M. D., McCarthy, D. J., & Smyth, G. K. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btp616 · Cited by 41,364
BLAST+: architecture and applications
Camacho, C., Coulouris, G., Avagyan, V., Ma, N., Papadopoulos, J., Bealer, K., & Madden, T. L. (2009) · BMC Bioinformatics · doi:10.1186/1471-2105-10-421 · Cited by 22,074 · cited 1×
“pBLAST analysis (Camacho et al., 2009) perfectly matched the coding sequence (CDS) with topoisomerase III (E = 0).”
Kim, D., Pertea, G., Trapnell, C., Pimentel, H., Kelley, R., & Salzberg, S. L. (2013) · Genome Biology · doi:10.1186/gb-2013-14-4-r36 · Cited by 12,668 · cited 1×
“12 (Kim et al., 2013) against the human hg19 genome build and gene counts with the Subread package 1.”
Adjusting batch effects in microarray expression data using empirical Bayes methods
Johnson, W. E., Li, C., & Rabinovic, A. (2007) · Biostatistics · doi:10.1093/biostatistics/kxj037 · Cited by 8,658 · cited 1×
“Potential batch effects were corrected by the Combat method (Johnson et al., 2007; Sun et al., 2011).”
Skyline: an open source document editor for creating and analyzing targeted proteomics experiments
MacLean, B., Tomazela, D. M., Shulman, N., Chambers, M., Finney, G. L., Frewen, B., Kern, R., Tabb, D. L., Liebler, D. C., & MacCoss, M. J. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq054 · Cited by 4,697 · cited 1×
“Raw data files were imported into Skyline software (MacLean et al., 2010).”
Shrivastava, A., & Gupta, V. B. (2011) · Chronicles of young scientists · doi:10.4103/2229-5186.79345 · Cited by 3,237 · cited 1×
“Limits of detection (LOD) and limits of quantification (LOQ) were calculated as 3× or 10× the standard deviation of the blank divided by the slope of the calibration curve respectively (Broccardo et al., 2013; Shrivastava and Gupta, 2011).”
Liao, Y., Smyth, G. K., & Shi, W. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz114 · Cited by 2,878
Reigstad, C. S., Salmonson, C. E., III, J. F. R., Szurszewski, J. H., Linden, D. R., Sonnenburg, J. L., Farrugia, G., & Kashyap, P. C. (2015) · The FASEB Journal · doi:10.1096/fj.14-259598 · Cited by 1,335 · cited 1×
“We have previously described the role of SCFAs in modulating the serotonergic pathway in host GI tissue (Bhattarai et al., 2017b; Reigstad et al., 2015).”
Self-citationChAMP: updated methylation analysis pipeline for Illumina BeadChips
Tian, Y., Morris, T. J., Webster, A. P., Yang, Z., Beck, S., Feber, A., & Teschendorff, A. E. (2017) · Bioinformatics · doi:10.1093/bioinformatics/btx513 · Cited by 1,091
Cloarec, O., Dumas, M., Craig, A., Barton, R. H., Trygg, J., Hudson, J., Blancher, C., Gauguier, D., Lindon, J. C., Holmes, E. C., et al. (2005) · Analytical Chemistry · doi:10.1021/ac048630x · Cited by 912 · cited 2×
“Discriminatory spectral features were annotated using statistical total correlation spectroscopy (STOCSY) (Cloarec et al., 2005) and a combination of in-house and online databases (https://hmdb.”
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Small molecule metabolites: discovery of biomarkers and therapeutic targets
Qiu, S., Cai, Y., Yao, H., Lin, C., Xie, Y., Tang, S., & Zhang, A. (2023) · Signal Transduction and Targeted Therapy · doi:10.1038/s41392-023-01399-3 · Cited by 993
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Cunningham, M., Azcarate-Peril, M. A., Barnard, A., Benoit, V., Grimaldi, R., Guyonnet, D., Holscher, H. D., Hunter, K., Manurung, S., Obis, D., et al. (2021) · Trends in Microbiology · doi:10.1016/j.tim.2021.01.003 · Cited by 637
British Society of Gastroenterology guidelines on the management of irritable bowel syndrome
Vasant, D. H., Paine, P. A., Black, C. J., Houghton, L. A., Everitt, H. A., Corsetti, M., Agrawal, A., Aziz, I., Farmer, A. D., Eugenicos, M. P., et al. (2021) · Gut · doi:10.1136/gutjnl-2021-324598 · Cited by 592
Comprehensive Review of Uterine Fibroids: Developmental Origin, Pathogenesis, and Treatment
Yang, Q., Ciebiera, M., Bariani, M. V., Ali, M. K., Elkafas, H., Boyer, T., & Al-Hendy, A. A. (2021) · Endocrine Reviews · doi:10.1210/endrev/bnab039 · Cited by 497
Metadata
- Authors
- Mars, R. A. T., Yang, Y., Ward, T., Houtti, M., Priya, S., Lekatz, H. R., Tang, X., Sun, Z., Kalari, K. R., Korem, T., Bhattarai, Y., Zheng, T., Bar, N., Frost, G., Johnson, A. J., van Treuren, W., Han, S., Ordog, T., Grover, M., Sonnenburg, J., D’Amato, M., Camilleri, M., Elinav, E., Segal, E., Blekhman, R., Farrugia, G., Swann, J. R., Knights, D., & Kashyap, P. C.
- Affiliations
- Mayo Clinic (US)
- Imperial College London (GB)
- University of Minnesota (US)
- Canadian Institute for Advanced Research (CA)
- Monash University (AU)
- Weizmann Institute of Science (IL)
- Stanford University (US)
- German Cancer Research Center (DE)
- University of Southampton (GB)
- Corresponding author
- Knights, Dan
- Kashyap, Purna C.
- ORCID
- Mars, Ruben A.T.
- Houtti, Mo
- Priya, Sambhawa
- Tang, Xiaojia
- Sun, Zhifu
- Kalari, Krishna R.
- Korem, Tal
- Bhattarai, Yogesh
- Zheng, Tenghao
- Frost, Gary
- Johnson, Abigail J.
- Han, Shuo
- Ordog, Tamas
- Grover, Madhusudan
- Sonnenburg, Justin
- D’Amato, Mauro
- Camilleri, Michael
- Elinav, Eran
- Segal, Eran
- Blekhman, Ran
- Farrugia, Gianrico
- Swann, Jonathan R.
- Knights, Dan
- Kashyap, Purna C.
- Venue
- Cell
- Publisher
- Elsevier BV
- Published
- 2020-09
- Volume
- 182
- Issue
- 6
- Pages
- 1460-1473.e17
- ISSN
- 0092-8674 (ISSN-L)
- PMC
- PMC8109273
- OpenAlex
- W3084404023
- Cited by
- 456
- References
- 49
- Citations by year
- 2026: 59 · 2025: 69 · 2024: 99 · 2023: 78 · 2022: 92 · 2021: 53 · 2020: 5
- FWCI
- 18.48
- Type
- journal article
- Language
- en
- Update notices
- erratum (2020-11-12)
- Open access
- bronze
- doi.org
- Licence
- Locations
- Cell (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- ePrints Soton (University of Southampton) (acceptedVersion)
- ePrints Soton (University of Southampton) (submittedVersion)
- Funders
- Foundation for the National Institutes of Health
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Health Sciences › Medicine › Gastroenterology › Gastrointestinal motility and disorders
- Health Sciences › Medicine › Gastroenterology › Inflammatory Bowel Disease
- Keywords
- irritable bowel syndrome, gut microbiota, microbial metabolites, purine metabolism, host-microbe interactions, IBS subtypes, host transcriptome, host metabolome, chronic gastrointestinal diseases, therapeutic target
- MeSH terms
- Gastrointestinal Microbiome, Host Microbial Interactions, Animals, Bile Acids and Salts, Biopsy, Butyrates, Chromatography, Liquid, Cross-Sectional Studies, Feces, Female, Gene Expression Regulation, Humans, Longitudinal Studies, Male, Prospective Studies, Purines, Software, Hypoxanthine, Irritable Bowel Syndrome, Mice, Tandem Mass Spectrometry, Metabolome, Epigenomics, Transcriptome, Observational Studies as Topic
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