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Multi-omics analyses of the ulcerative colitis gut microbiome link Bacteroides vulgatus proteases with disease severity
Open accessAbstract
Ulcerative colitis (UC) is driven by disruptions in host-microbiota homoeostasis, but current treatments exclusively target host inflammatory pathways. To understand how host-microbiota interactions become disrupted in UC, we collected and analysed six faecal- or serum-based omic datasets (metaproteomic, metabolomic, metagenomic, metapeptidomic and amplicon sequencing profiles of faecal samples and proteomic profiles of serum samples) from 40 UC patients at a single inflammatory bowel disease centre, as well as various clinical, endoscopic and histologic measures of disease activity. A validation cohort of 210 samples (73 UC, 117 Crohn's disease, 20 healthy controls) was collected and analysed separately and independently. Data integration across both cohorts showed that a subset of the clinically active UC patients had an overabundance of proteases that originated from the bacterium Bacteroides vulgatus. To test whether B. vulgatus proteases contribute to UC disease activity, we first profiled B. vulgatus proteases found in patients and bacterial cultures. Use of a broad-spectrum protease inhibitor improved B. vulgatus-induced barrier dysfunction in vitro, and prevented colitis in B. vulgatus monocolonized, IL10-deficient mice. Furthermore, transplantation of faeces from UC patients with a high abundance of B. vulgatus proteases into germfree mice induced colitis dependent on protease activity. These results, stemming from a multi-omics approach, improve understanding of functional microbiota alterations that drive UC and provide a resource for identifying other pathways that could be inhibited as a strategy to treat this disease.
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“Some of the correlated proteases included serine and metalloproteases that largely function in the extracellular space and may exacerbate disease activity.”
From The emerging roles of bacterial proteases in intestinal diseases (2023) · cites this paper as [33]
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“A subset of the clinically active UC patients had an overabundance of proteases derived from the bacterium Bacteroides vulgatus.”
From The emerging roles of bacterial proteases in intestinal diseases (2023) · cites this paper as [33]
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Metadata
- Authors
- Mills, R. H., Dulai, P. S., Vázquez-Baeza, Y., Sauceda, C., Daniel, N., Gerner, R. R., Batachari, L. E., Malfavon, M., Zhu, Q., Weldon, K., Humphrey, G., Carrillo-Terrazas, M., Goldasich, L. D., Bryant, M., Raffatellu, M., Quinn, R. A., Gewirtz, A. T., Chassaing, B., Chu, H., Sandborn, W. J., Dorrestein, P. C., Knight, R., & Gonzalez, D. J.
- Affiliations
- University of California San Diego (US)
- Centre National de la Recherche Scientifique (FR)
- Michigan State University (US)
- Georgia State University (US)
- Corresponding author
- Knight, Rob
- Gonzalez, David J.
- ORCID
- Mills, Robert H.
- Dulai, Parambir S.
- Vázquez-Baeza, Yoshiki
- Sauceda, Consuelo
- Daniel, Noëmie
- Gerner, Romana R.
- Batachari, Lakshmi E.
- Malfavon, Mario
- Zhu, Qiyun
- Weldon, Kelly
- Goldasich, Lindsay DeRight
- Bryant, MacKenzie
- Raffatellu, Manuela
- Quinn, Robert A.
- Gewirtz, Andrew T.
- Chu, Hiutung
- Sandborn, William J.
- Dorrestein, Pieter C.
- Knight, Rob
- Gonzalez, David J.
- Venue
- Nature Microbiology
- Published
- 2022-01-27
- Volume
- 7
- Issue
- 2
- Pages
- 262-276
- ISSN
- 2058-5276 (ISSN-L)
- PMC
- PMC8852248
- OpenAlex
- W4213182271
- Cited by
- 385
- References
- 111
- Citations by year
- 2026: 79 · 2025: 100 · 2024: 113 · 2023: 61 · 2022: 32
- FWCI
- 25.05
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Nature Microbiology (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- Funders
- U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (T32 DK007202, P30 DK120515)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Health Sciences › Medicine › Gastroenterology › Inflammatory Bowel Disease
- Health Sciences › Medicine › Gastroenterology › Microscopic Colitis
- Keywords
- ulcerative colitis, Bacteroides vulgatus, bacterial proteases, gut microbiota, host-microbiota interactions, disease severity, Crohn's disease, intestinal barrier dysfunction, protease inhibitors, IL-10-deficient mice, germ-free mice, fecal microbiota transplantation, multi-omics integration, metaproteomics, metabolomics, metagenomics, serum proteomics
- MeSH terms
- Gastrointestinal Microbiome, Adult, Animals, Bacterial Proteins, Bacteroides, Colitis, Ulcerative, Feces, Female, Humans, Longitudinal Studies, Male, Middle Aged, Peptide Hydrolases, Severity of Illness Index, Cohort Studies, Proteomics, Mice, Metagenome, Metagenomics
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
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