Cited by 386Gut microbiota and healthInflammatory Bowel DiseaseMicroscopic Colitis

The DOI matches its Crossref record; 111 of the 111 references it cites were found in a registry or an index.

Multi-omics analyses of the ulcerative colitis gut microbiome link Bacteroides vulgatus proteases with disease severity

Open access

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, Humphrey, Greg, Carrillo-Terrazas, Marvic, Goldasich, Lindsay DeRight, Bryant, MacKenzie, Raffatellu, Manuela, Quinn, Robert A., Gewirtz, Andrew T., Chassaing, Benoit, Chu, Hiutung, Sandborn, William J., Dorrestein, Pieter C., Knight, Rob, Gonzalez, David J.·2022·Nature Microbiology

DOI 10.1038/s41564-021-01050-3PMC PMC8852248

Open this paper in CoChat — free account

Abstract

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.

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

Integrity signals

Registry

Crossref · 10.1038/s41564-021-01050-3

Cites

111 of 111 references verified0 citation errors · 0 not checkable

Statistics

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Trimmomatic: a flexible trimmer for Illumina sequence data
Bolger, A. M., Lohse, M., & Usadel, B. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu170 · Cited by 65,548
Fast gapped-read alignment with Bowtie 2
Langmead, B., & Salzberg, S. L. (2012) · Nature Methods · doi:10.1038/nmeth.1923 · Cited by 56,400
Cytoscape: A software Environment for integrated models of biomolecular interaction networks
Shannon, P., Markiel, A., Ozier, O., Baliga, N. S., Wang, J. T., Ramage, D., Amin, N., Schwikowski, B., & Ideker, T. (2003) · Genome Research · doi:10.1101/gr.1239303 · Cited by 51,888
QIIME allows analysis of high-throughput community sequencing data
Caporaso, J. G., Kuczynski, J., Stombaugh, J., Bittinger, K., Bushman, F. D., Costello, E. K., Fierer, N., Peña, A. G., Goodrich, J. K., Gordon, J. I., et al. (2010) · Nature Methods · doi:10.1038/nmeth.f.303 · Cited by 34,887
Self-citation
Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2
Bolyen, E., Rideout, J. R., Dillon, M. R., Bokulich, N. A., Abnet, C. C., Al-Ghalith, G. A., Alexander, H., Alm, E. J., Arumugam, M., Asnicar, F., et al. (2019) · Nature Biotechnology · doi:10.1038/s41587-019-0209-9 · Cited by 23,742
Self-citation
Fast and sensitive protein alignment using DIAMOND
Buchfink, B., Xie, C., & Huson, D. H. (2015) · Nature Methods · doi:10.1038/nmeth.3176 · Cited by 14,201
Salmon provides fast and bias-aware quantification of transcript expression
Patro, R., Duggal, G., Love, M. I., Irizarry, R. A., & Kingsford, C. (2017) · Nature Methods · doi:10.1038/nmeth.4197 · Cited by 12,700
Prodigal: prokaryotic gene recognition and translation initiation site identification
Hyatt, D., Chen, G.-L., LoCascio, P. F., Land, M., Larimer, F. W., & Hauser, L. (2010) · BMC Bioinformatics · doi:10.1186/1471-2105-11-119 · Cited by 12,692
STRING v10: protein–protein interaction networks, integrated over the tree of life
Szklarczyk, D., Franceschini, A., Wyder, S., Forslund, K., Heller, D., Huerta-Cepas, J., Simonovic, M., Roth, A., Santos, A., Tsafou, K. P., et al. (2015) · Nucleic Acids Research · doi:10.1093/nar/gku1003 · Cited by 10,436
MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph
Li, D., Liu, C.-M., Luo, R., Sadakane, K., & Lam, T. (2015) · Bioinformatics · doi:10.1093/bioinformatics/btv033 · Cited by 10,133

Show all 111 references

Sorted by citations

Items 301–386 of 386

Integrating multi-omics technologies to decipher microbiome functions
Bossche, T. V. D., Lazau, E., Aho, V. T. E., Blakeley‐Ruiz, J. A., Wolf, M., Kunath, B. J., Valentin-Alvarado, L. E., Hellwig, P., Verschaffelt, P., Rajczewski, A. T., et al. (2026) · Nature Communications · doi:10.1038/s41467-026-77539-4 · Cited by 1
Assessment of the Inflammatory Effects of Gut Microbiota from Human Twins Discordant for Ulcerative Colitis on Germ-free Mice
Knudsen, L. A., Zachariassen, L. F., Strube, M. L., Havelund, J. F., Pilecki, B., Nexøe, A. B., Møller, F. T., Sørensen, S. B., Marcussen, N., Færgeman, N. J., et al. (2024) · Comparative Medicine · doi:10.30802/aalas-cm-23-000065 · Cited by 2
Bioinformatics Databases and Tools for Analysis of Multi-omics
Pham, C. A., Ngo, A. D., Bui, N. L., & Chu, D. (2024) · Springer eBooks · doi:10.1007/978-981-97-1844-3_4 · Cited by 1
Influence of micronutrient deficiency and dietary habits on the immune response and intestinal microbiocenosis in patients with inflammatory bowel disease
Романуха, В., & Гринів, О. І. (2024) · Reports of Vinnytsia National Medical University · doi:10.31393/reports-vnmedical-2024-28(3)-23 · Cited by 1
MASP1 modulation as a novel therapeutic target in severe pediatric pertussis: insights from a multi-omics approach
Xu, L., Wang, C., Liu, Y., Zhang, Y., Li, Z., & Pang, L. (2025) · Infection and Immunity · doi:10.1128/iai.00271-24 · Cited by 1
In Vitro Assessment of Bacillus thuringiensis Exopolysaccharides and Their Effects on Gut Microbiota from Ulcerative Colitis In Vitro
Gao, Z., Tang, J., Wu, C., Ding, W., Wang, X., Long, Y., Wang, Y., & Liu, H. (2025) · International Journal of Molecular Sciences · doi:10.3390/ijms26041692 · Cited by 1
An exploratory study on the metagenomic and proteomic characterization of hypothyroidism in the first half of pregnancy and correlation with Th1/Th2 balance
Zhang, C., Xu, Y., Zhang, M., Li, J., Sun, Z., Wang, Y., & Lin, P. (2025) · Frontiers in Immunology · doi:10.3389/fimmu.2025.1500866 · Cited by 1
The Influence of the Microbiome and Genetic Associations on Immune Functions and on Autoimmune and Autoinflammatory Diseases
Moreno, J. G., & Pacheco‐Tena, C. (2022) · Springer eBooks · doi:10.1007/978-981-19-4800-8_23 · Cited by 1
WITHDRAWN: SETD2 deficiency promotes the transition from PKD to ccRCC by dysregulation of sphingomyelin metabolismPreprint
Zhang, Y., Liu, C., Ye, T., Chen, L., Yang, X., Zhou, L., & An, H. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.11.10.515911 · Cited by 1
Chemoproteomic identification of a dipeptidyl peptidase 4 (DPP4) homolog in Bacteroides thetaiotaomicron important for envelope integrity and fitnessPreprint
Keller, L. J., Nguyen, T. H., Liu, L., Lakemeyer, M., Gelsinger, D. J., Chanin, R. B., Ngo, N., Lum, K. M., Faucher, F. F., Ipock, P., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.07.25.501481
Identification of a Key Genetic Factor Governing Arabinan Utilization in the Gut Microbiome Suggests a Novel Therapeutic Target for ConstipationPreprint
Zhang, C., Yu, L., Ma, C., Jiang, S., Wang, S., Tian, F., Xue, Y., Zhao, J., Zhang, H., Liu, L., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.12.15.518621
Eating our way to gut microbiome characterization
Sun, L., Lin, J., & Jiang, C. (2023) · Cell Host & Microbe · doi:10.1016/j.chom.2023.06.003
Microbiota intestinal associada à inflamação e permeabilidade intestinal em pacientes com doenças inflamatórias intestinais em remissão clínica
da Rocha, I. M. G. (2023) · Digital Library of Theses and Dissertations (Universidade de São Paulo) · doi:10.11606/t.5.2023.tde-23082023-154649
Additional file 2 of Altered intestinal microbiome and metabolome correspond to the clinical outcome of sepsis
Sun, S., Wang, D., Dong, D., Xu, L., Xie, M., Wang, Y., Ni, T., Jiang, W., Zhu, X., Ning, N., et al. (2023) · Figshare · doi:10.6084/m9.figshare.22623866
Composition and Pathogenic Potential of Mucosal Microbiota in Ulcerative Colitis
Tsvetikova, S. A., Круглов, Е. Е., Danilov, L. G., Zilov, D. S., Myakisheva, Y. V., Макарова, М. А., Кафтырева, Л. А., & Koshel, E. I. (2024) · Russian Journal of Bioorganic Chemistry · doi:10.1134/s1068162024110463
Gut Microbiota-Derived Proline-Leucine Dipeptide Alleviated Sepsis-Induced Ali Via Activating Nod2 Signaling Pathway Through the Gut-Lung AxisPreprint
何, 思., yang, L., Wei, A., Wang, X., He, L., Cui, L., Zhang, S., Zhong, C., zhuo, Y., & Wang, X. (2024) · SSRN Electronic Journal · doi:10.2139/ssrn.4805739
Metaanalysis of Public Wastewater Metagenomes: Revealing the Influence of Climatic Variations on the Abundance of the Bacterial Members
Karmakar, R., Mondal, K., & Ghosh, M. M. (2024) · Current World Environment · doi:10.12944/cwe.19.1.11
Funktionelle Charakterisierung der Darmflora und ihrerhydrolytisch aktiven Enzyme ‐Trendbericht Biochemie 2024 (2/3)
Lakemeyer, M., & Seidel, J. (2024) · Nachrichten aus der Chemie · doi:10.1002/nadc.20244143493
Integration of metagenomics and metaproteomics in the intestinal lavage fluids benefits construction of discriminative model and discovery of biomarkers for HBV liver diseases
Xu, H., Zhang, J., Wang, F., Chen, Y., Chen, H., Yang, F., Hou, G., Zi, J., Zhang, M., Zhou, J., et al. (2024) · PROTEOMICS · doi:10.1002/pmic.202400002
Spotted hyena gut cross-talks: Symbionts modulate mucosal immunityPreprint
Soares, S. P. V., Jarquín‐Díaz, V. H., Veiga, M. M., Karl, S., Czirják, G. Á., Weyrich, A., Metzger, S., East, M. L., Hofer, H., Heitlinger, E. G., et al. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.07.25.605121
Gut colonization of Enterococcus species is associated with COVID-19 disease in UgandaPreprint
Agudelo, C., Kateete, D. P., Nasinghe, E., Kamulegeya, R., Lubega, C., Mbabazi, M., Baker, N., Lin, K. Y., Liu, C. C., Kasambula, A. S., et al. (2024) · medRxiv · doi:10.1101/2024.09.28.24314457
Comparison of clinical characteristics, risk factors, and outcomes of patients infected with Bacteroides fragilis group at a tertiary care hospital in central China between 2017 and March 2024
Li, Y., Zhao, J., Ma, Q., Xu, J., Yuan, Y., Zhang, Q., Yan, W., Xu, W., Yang, Z., Li, G., et al. (2024) · Anaerobe · doi:10.1016/j.anaerobe.2024.102922
Die intestinale Mikrobiota bei chronisch-entzündlichen Darmerkrankungen
Misselwitz, B., & Haller, D. (2025) · Die Innere Medizin · doi:10.1007/s00108-024-01845-6
The Role of Bacterial Proteases From the Microbiome in Human Disease
Lee, Y.-C. J. (2025) · Cellular Microbiology · doi:10.1155/cmi/8860329
Fecal Microbial and Metabolic Signatures in VEO-IBD: Implications for Unique PathophysiologyPreprint
Kvitne, K. E., Zuffa, S., Charron‐Lamoureux, V., Mohanty, I., Patan, A., Mannochio-Russo, H., Zemlin, J., Burnett, L. A., Zhang, L. S., Cecala, M. C., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.04.26.650779
Self-citation
Comprehensive Analysis of Maternal and Infant Microbiome Profiles: Maternal Microbial Transmission Shapes Offspring Somatic Growth TrajectoryPreprint
Wang, K., Zhai, Q., Liu, J., Li, X., Chen, J., Wang, L., Ren, F., Liu, X., Wang, J., Chen, B., et al. (2025) · SSRN Electronic Journal · doi:10.2139/ssrn.5251553
Shared and Distinctive Microbial Biomarkers Enhance Precision Diagnostics of Inflammatory Bowel Disease and its SubtypesPreprint
Li, Y., Chen, Y., Shen, K., Feng, Y. X., Xie, Z., Wang, H., & Lu, C. (2025) · SSRN Electronic Journal · doi:10.2139/ssrn.5356128
Molecular weight-dependent therapeutic efficacy of guluronic alginate oligosaccharides in ulcerative colitis: insights into intestinal flora modulation and NF-κB pathway
Li, J., Yang, Q., Sun, L., Zong, W., Gao, X., Jiang, X., & Shen, Z. (2025) · Carbohydrate Polymer Technologies and Applications · doi:10.1016/j.carpta.2025.100991
A microbiome meta-transcriptomics pipeline identifies a novel human neutrophil elastase inhibitor that protects the colonic epithelial barrierPreprint
Stojkovic, B., Bekkers, M., Violi, J. P., Neilan, B. A., Keely, S., Donald, W. A., Riveros, C., & Kaiko, G. E. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.09.11.675725
Additional file 1 of The gut microbiome and HLA-B27-associated anterior uveitis: a case-control study
Morandi, S. C., Herzog, E. L., Munk, M., Kreuzer, M., Largiadèr, C. R., Wolf, S., Zinkernagel, M. S., & Zysset‐Burri, D. C. (2024) · Figshare · doi:10.6084/m9.figshare.25770398
Additional file 1 of Effect of ginsenoside compound K on alleviating colitis via modulating gut microbiota
Wang, L., Shao, L., Chen, M.-Y., Wang, L., Zhang, W., Tan, F.-B., & Huang, W.-H. (2022) · Figshare · doi:10.6084/m9.figshare.22609723
Additional file 3 of Altered intestinal microbiome and metabolome correspond to the clinical outcome of sepsis
Sun, S., Wang, D., Dong, D., Xu, L., Xie, M., Wang, Y., Ni, T., Jiang, W., Zhu, X., Ning, N., et al. (2023) · Figshare · doi:10.6084/m9.figshare.22623872
Additional file 11 of Altered intestinal microbiome and metabolome correspond to the clinical outcome of sepsis
Sun, S., Wang, D., Dong, D., Xu, L., Xie, M., Wang, Y., Ni, T., Jiang, W., Zhu, X., Ning, N., et al. (2023) · Figshare · doi:10.6084/m9.figshare.22623899
Additional file 5 of Altered intestinal microbiome and metabolome correspond to the clinical outcome of sepsis
Sun, S., Wang, D., Dong, D., Xu, L., Xie, M., Wang, Y., Ni, T., Jiang, W., Zhu, X., Ning, N., et al. (2023) · Figshare · doi:10.6084/m9.figshare.22623878
Additional file 1 of Altered intestinal microbiome and metabolome correspond to the clinical outcome of sepsis
Sun, S., Wang, D., Dong, D., Xu, L., Xie, M., Wang, Y., Ni, T., Jiang, W., Zhu, X., Ning, N., et al. (2023) · Figshare · doi:10.6084/m9.figshare.22623863
Additional file 8 of Altered intestinal microbiome and metabolome correspond to the clinical outcome of sepsis
Sun, S., Wang, D., Dong, D., Xu, L., Xie, M., Wang, Y., Ni, T., Jiang, W., Zhu, X., Ning, N., et al. (2023) · Figshare · doi:10.6084/m9.figshare.22623890
Additional file 7 of Altered intestinal microbiome and metabolome correspond to the clinical outcome of sepsis
Sun, S., Wang, D., Dong, D., Xu, L., Xie, M., Wang, Y., Ni, T., Jiang, W., Zhu, X., Ning, N., et al. (2023) · Figshare · doi:10.6084/m9.figshare.22623887
Additional file 6 of Altered intestinal microbiome and metabolome correspond to the clinical outcome of sepsis
Sun, S., Wang, D., Dong, D., Xu, L., Xie, M., Wang, Y., Ni, T., Jiang, W., Zhu, X., Ning, N., et al. (2023) · Figshare · doi:10.6084/m9.figshare.22623881
Additional file 10 of Altered intestinal microbiome and metabolome correspond to the clinical outcome of sepsis
Sun, S., Wang, D., Dong, D., Xu, L., Xie, M., Wang, Y., Ni, T., Jiang, W., Zhu, X., Ning, N., et al. (2023) · Figshare · doi:10.6084/m9.figshare.22623896
Additional file 1 of Constituents of stable commensal microbiota imply diverse colonic epithelial cell reactivity in patients with ulcerative colitis
Inčiūraitė, R., Gedgaudas, R., Lukoševičius, R., Tilinde, D., Ramonaitė, R., Link, A., Kašėtienė, N., Malakauskas, M., Kiudelis, G., Jonaitis, L. V., et al. (2024) · Figshare · doi:10.6084/m9.figshare.25466582
Additional file 2 of Gut microbiota DPP4-like enzymes are increased in type-2 diabetes and contribute to incretin inactivation
Olivares, M., Hernández-Calderón, P., Cárdenas-Brito, S., Liébana-García, R., Sanz, Y., & Benítez‐Páez, A. (2024) · Figshare · doi:10.6084/m9.figshare.26170649
Additional file 4 of Altered intestinal microbiome and metabolome correspond to the clinical outcome of sepsis
Sun, S., Wang, D., Dong, D., Xu, L., Xie, M., Wang, Y., Ni, T., Jiang, W., Zhu, X., Ning, N., et al. (2023) · Figshare · doi:10.6084/m9.figshare.22623875
Additional file 9 of Altered intestinal microbiome and metabolome correspond to the clinical outcome of sepsis
Sun, S., Wang, D., Dong, D., Xu, L., Xie, M., Wang, Y., Ni, T., Jiang, W., Zhu, X., Ning, N., et al. (2023) · Figshare · doi:10.6084/m9.figshare.22623893
Additional file 1 of Gut microbiota DPP4-like enzymes are increased in type-2 diabetes and contribute to incretin inactivation
Olivares, M., Hernández-Calderón, P., Cárdenas-Brito, S., Liébana-García, R., Sanz, Y., & Benítez-Páez, A. (2024) · Figshare · doi:10.6084/m9.figshare.26170489
Additional file 2 of Effect of ginsenoside compound K on alleviating colitis via modulating gut microbiota
Wang, L., Shao, L., Chen, M.-Y., Wang, L., Zhang, W., Tan, F.-B., & Huang, W.-H. (2023) · Figshare · doi:10.6084/m9.figshare.22609726
The Serine Protease-Serine Protease Inhibitor Regulatory Network in Inflammatory Bowel Disease: From Molecular Mechanisms to Novel Therapeutic Horizons
Li, Q., Ye, H., Chen, R., Zhou, G., & Zhang, S. (2026) · Journal of Advanced Research · doi:10.1016/j.jare.2026.01.002
Temporal dynamics of the fecal microbiome in wintering seagulls: a One Health perspective
Wang, M. Q., Qu, Y., Ma, X., Fan, Y., Zhang, C., Li, J., Liu, X., Wang, Z., Li, J., Wang, Y., et al. (2026) · BMC Genomics · doi:10.1186/s12864-026-12629-7
Comparative Genomic and Functional Profiling of ECM-Targeting Enzymes in Bacteroides, a Key Genus of the Human Gut MicrobiomePreprint
Azamar, K. M. M., Rajesh, K., Downing, B., Javith, M., Yamhure, I., & Porras, A. (2026) · bioRxiv · doi:10.64898/2026.03.04.709643
Escherichia coli extract (OM-89) preserves gut microbial balance more effectively than antibiotics in a healthy mouse model
Jung, J., Won, S. D., & Han, H. (2026) · Heliyon · doi:10.1016/j.heliyon.2026.e44741
Bifidobacterium animalis ssp. lactis BX-245-fermented milk alleviates inflammatory bowel disease by modulating the gut microbiota and metabolite profile
Si, H., Gao, Y., Li, H., Li, X., He, Q., Wang, J., Na, C., Borjihan, Q., & Chen, Y. (2026) · Journal of Dairy Science · doi:10.3168/jds.2025-28051
Investigating the shared genetic architecture between inflammatory bowel disease and pancreatitis: a genome-wide cross-trait analysis
Qi, H.-M., Liu, T.-T., Chen, J.-Y., Wang, Y.-H., Mao, X., Wang, Y., Jin, J., Lin, X., Yang, J., Zou, W., et al. (2026) · Molecular Genetics and Genomics · doi:10.1007/s00438-026-02406-2
Implication des protéases du microbiote intestinal dans les maladies inflammatoires digestives humaines
Mariaule, V. (2024) · theses.fr (ABES) · doi:10.70675/1d41e841zf788z4dd7z8784zc26304e24ea1
Zein-Coated Eicosapentaenoic Acid-Based Glibenclamide Nanocarriers for Treating Ulcerative Colitis
Mahajan, S., Kanika, Kumar, J. S., Kumar, A., Joshi, A., Ali, A., Jori, C., Ahmad, A., Ali, N., Son, Y., et al. (2026) · ACS Applied Nano Materials · doi:10.1021/acsanm.6c00223
Artesunate ameliorates experimental colitis by suppressing intestinal inflammation and modulating the gut microbiota
Haiyang, S. U. N., Jiang, R., Jingjing, J. I. N. G., Xinying, W. A. N. G., Ning, W. A. N. G., Guo, M., & Tang, C. (2026) · EXPERIMENTAL ANIMALS · doi:10.1538/expanim.26-0048
Antibiotic disruption of the gut microbiome triggers IBD-like proteolytic activity
Werner, L., Nissenbaum, T., Fibelman, M., Leibovitzh, H., Cohen, N. A., Brenner, M., Lobel, L., & Maharshak, N. (2026) · Cell Reports · doi:10.1016/j.celrep.2026.117478
Synthesis and Application of a Suite of 2,5-Aryl Tetrazole Photoaffinity-Based Probes for Profiling Microbial Carbohydrate and Mucin Metabolism in Gut Microbiota
Russo, J., Hudson, L. A., Relangi, T. R., Pitts, A. R., & Wright, A. (2026) · ACS Chemical Biology · doi:10.1021/acschembio.6c00268
An opposite pH-responsiveness “gating” strategy: Intelligent sporopollenin exine armor for targeted therapy of colitis
(42548), J. L., Ding, Z., Wei, J., Li, Y., Wang, X., Yan, X., (106345), D. L., Ye, T., Wang, S., & Sun, J. (2026) · Asian Journal of Pharmaceutical Sciences · doi:10.1016/j.ajps.2026.101172
Diversity of the instestinal microbiota of patients with different clinical profiles
Danelus, L. P., Magrini, F. E., Sophiatti, I. V. M., Dutra, P. H., Brambilla, E., & Paesi, S. (2026) · Gene Reports · doi:10.1016/j.genrep.2026.102566
Perinatal ampicillin exposure alters murine maternal fecal bile acid and acylcarnitine profiles
Zuffa, S., Thomas, S. P., Patan, A., Mohanty, I., Abiead, Y. E., Deleray, V., Kvitne, K. E., Kousha, A., Suzuki, E., Tsai, C. M., et al. (2026) · Gut Microbes · doi:10.1080/19490976.2026.2690698 · Cited by 4
Self-citation
Integrative metagenomics and structural bioinformatics identify explainable gut microbial variants associated with Crohn’s disease
Khan, N., Nasir, M. M., Aziz, U., Manzoor, H., Raziq, M. F., Hussain, Z., Jabeen, I., & Kayani, M. U. R. (2026) · PLoS ONE · doi:10.1371/journal.pone.0340748
Data-driven subphenotyping uncovers ulcerative colitis subtype with high risk for relapse in Japan: a prospective multicenter cohort study
Mikami, Y., Yamazaki, H., Hisamatsu, T., Nagahori, M., Kobayashi, T., Yonezawa, M., Shinzaki, S., Fujii, T., Saruta, M., Motoya, S., et al. (2026) · The Lancet Regional Health - Western Pacific · doi:10.1016/j.lanwpc.2026.101932
Multi-omics analyses of facial skin in acne identify distinct microbial and metabolic features at lesional and non-lesional sites
Chen, Y., Pessemier, B. D., Myers, T. D., Zuffa, S., Zemlin, J., Pourhamidi, S., Belo, S. E. D., Woo, A. C., Moreau, M., Idkowiak‐Baldys, J., et al. (2026) · npj Biofilms and Microbiomes · doi:10.1038/s41522-026-01086-5
Self-citation
Joint-RPCA: domain-aware multi-omics integration for systems microbiology
Vargas, B. C., Martino, C., Dilmore, A. H., Metcalf, J. L., Burcham, Z. M., Lahti, L., Bektanov, A., Borman, T., Salomaa, V. V., Niiranen, T., et al. (2026) · Molecular Systems Biology · doi:10.1038/s44320-026-00236-3
Self-citation
Evaluation of the substrate profile of microbial-host-isozyme reveals the role of BvDPP4 in inflammatory bowel disease
Zhuo, Y., Yan, S., Zhang, Z., Dong, B., Yin, D., Wen, Y., Mao, Y., Zhang, Z., Wang, K., & Jiang, C. (2026) · Science China Life Sciences · doi:10.1007/s11427-025-3377-9
The gut microbiome organ
Bi, Y., Song, W., Glymenaki, M., Hu, J., Li, X., Huang, H., Peng, Y., Ni, S., Haonon, O., Liu, Z., et al. (2026) · iMeta · doi:10.1002/imt2.70144 · Cited by 1
Protease-Activated Receptor-2 as a Proteolytic Rheostat in Colorectal and Pancreatic Cancer: From Mechanism to Biomarker-Guided Therapy
Yeganeh, H. T., Sellat, M., Anis, Z., Chiri, R., Patnaik, R., Gambhir, S., & Banerjee, Y. (2026) · International Journal of Molecular Sciences · doi:10.3390/ijms27177526
Baseline gut microbiome and metabolome profiles predict weight loss after a structured lifestyle intervention
Seethaler, B., Basrai, M., Delzenne, N. M., Walter, J., Nguyen, N. K., & Bischoff, S. C. (2026) · Microbiome · doi:10.1186/s40168-026-02501-x
From triggers to interfaces: polymer-stabilized nano-co-crystals for robust mesalazine delivery in UC.
khan, A., Kumar, S., Singh, A. R., Agarwal, M., Kailasiya, A., & Qureshi, J. (2026) · DARU Journal of Pharmaceutical Sciences · doi:10.1007/s40199-026-00648-4
Composition and Function of the Human Gut Microbiome
Hitch, T. C. A., & Clavel, T. (2026) · Springer eBooks · doi:10.1007/978-3-032-26410-7_2
Hydroxy-α-sanshool from Zanthoxylum bungeanum attenuates DSS-induced colitis through the modulation of gut microbiota and improvement of intestinal metabolism homeostasis
Nie, L., Xia, Y., Zhang, Z., Dong, Y., Huang, L., Lv, Y., Kuda, T., & He, Q. (2026) · Food Bioscience · doi:10.1016/j.fbio.2026.110003
Distinct Evolutionary Selection Patterns in Temperate and Filamentous Phages of Phocaeicola vulgatus in Health and IBDPreprint
Baldridge, M. T., Campbell, D. E., Wu, X., Emerson, O., Jin, H., & Grambo, S. (2026) · Research Square · doi:10.21203/rs.3.rs-10845320/v1
A prospective randomized controlled pilot study of gut microbiome modulation by Nigella sativa seed oil and thymoquinone metabolism in healthy volunteers: implications for gastrointestinal surgery
El-Banna, A. F., Junca, H., Steube, A., Wissenbach, D. K., Settmacher, U., Schneider, C., & Tekbaş, A. (2026) · Scientific Reports · doi:10.1038/s41598-026-69567-3
Differential Signature of Gut Microbiota in Female Patients with Condyloma Acuminatum and Its Association with Persistent Human Papillomavirus Infection
Wu, Y., Zhou, Q., Wang, C., & Liu, X. (2026) · Journal of Clinical Medicine · doi:10.3390/jcm15187265
Comparative Genomic and Functional Profiling of ECM-Associated Enzymes in Bacteroides, a Key Genus of the Human Gut Microbiome
Azamar, K. M. M., Rajesh, K., Garner, J., Downing, B., Javith, M., Yamhure, I., & Porras, A. (2026) · Cellular and Molecular Bioengineering · doi:10.1007/s12195-026-00938-6
Targeting gut microbial metabolism with Chinese herbal medicine in ulcerative colitis: A narrative review
Cai, Y., Liang, K., Li, Y., Du, Y., Dong, X., He, P., Wang, S., Zhang, S., & Zhao, L. (2026) · Journal of Traditional Chinese Medical Sciences · doi:10.1016/j.jtcms.2026.09.011
Gut microbiota and systemic sclerosis: Mechanistic insights and microbial therapies
Liu, Q., Wang, Y., Pei, M., Li, R., Gao, R., Gao, M., Chen, M., Gong, Y., Li, M., & Ni, B. (2026) · Autoimmunity Reviews · doi:10.1016/j.autrev.2026.104192
Lactobacillus reuteri attenuates chronic diarrhea by modulating microbiota homeostasis and macrophage polarization through the cGAS/STING pathway dependent on D-lactate-mediated mitochondrial function
Cheng, X., Zhang, Y., Li, C., Jiang, M., Song, J., Fang, F., Chang, K., Zhu, X., Jian, C., Chen, J., et al. (2026) · Microbiological Research · doi:10.1016/j.micres.2026.128750
High-fat diet induces an adaptive dysbiosis in the gut microbiota, associated with oxidative stress and the gut resistome profile in a rat model
Figueroa-Ajraz, F., Bongcam‐Rudloff, E., González-Pizarro, K., Dinamarca, M. A., Osses-Lobos, L., Sotomayor‐Zárate, R., & Ibacache‐Quiroga, C. (2026) · Frontiers in Microbiology · doi:10.3389/fmicb.2026.1935516
Microbiota-mediated naringenin release limits postoperative acute gastrointestinal injury by suppressing ferroptosis
Deng, F., Hu, J., Min, Y., Xie, S., Lin, Z., Sun, Q., Liu, H., He, S., Feng, S., Wu, L., et al. (2026) · Cell Reports Medicine · doi:10.1016/j.xcrm.2026.103101
Lactiplantibacillus plantarum HYY-DB36 alleviated dextran sulfate sodium (DSS)-induced ulcerative colitis through regulation of intestinal flora
Wu, W.-T., Huang, J.-Y., Lai, Y.-S., Tan, H.-L., Wang, L.-H., Zeng, X.-A., & Huang, Y. (2026) · Journal of Food Science and Technology · doi:10.1007/s13197-026-06910-6
Research Progress on Short-Chain Fatty Acids Regulating Treg/Th17 Immune Imbalance in the Inflammation-Associated Carcinogenesis of Ulcerative Colitis
徐, 丽. (2026) · Journal of Clinical Personalized Medicine · doi:10.12677/jcpm.2026.55356
Microbiota–host crosstalk in ulcerative colitis: mechanistic evidence and translational prospects for traditional Chinese medicine
Chen, J., Du, J., Mu, B., Zhang, J., 尚广彬, & Xiaojun, Y. (2026) · Frontiers in Pharmacology · doi:10.3389/fphar.2026.1956353
Receptor-Side Neuroimmune Remodeling in IBD: Participant-Level Associations with Metabolite-Sensing Programs and Colorectal Neoplasia Context
Hu, H., Xu, K., Yuan, X., Lei, Z., & Lu, Y. (2026) · International Journal of Molecular Sciences · doi:10.3390/ijms27209179
Evaluation of the effect of the probiotic bacterium Streptococcus salivarius on the human intestine
Burakova, I. Y., Dmitrievna, M. P., Pogorelova, S. V., Dmitrievna, S. Y., Kislova, T. A., & Syromyatnikov, M. (2026) · Proceedings of the Voronezh State University of Engineering Technologies · doi:10.20914/2310-1202-2026-2-238-244
Gut microbiota developmental trajectories in min and DLY pigs during lactation and nursery stages and the alleviation of ETEC-induced diarrhea by fecal microbiota transplantation
Xie, W., Li, Z., Lin, J., Bai, H., Li, J., Wen, C., Jiang, Y., Song, B., Wang, X., & 唐丽杰 (2026) · Frontiers in Microbiology · doi:10.3389/fmicb.2026.1939230
DUF6383-domain containing protein from Parabacteroides distasonis predicts survival in patients with alcohol-associated hepatitis
Kreimeyer, H., Gonzalez, C., Fondevila, M. F., AlcHepNet Investigators, Canbay, A. E., Stärkel, P., Gonzalez, D. J., & Schnabl, B. (2026) · Gut Microbes Reports · doi:10.1080/29933935.2026.2728306
Self-citation

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
Publisher: Springer Science and Business Media LLC
Published: 2022-01-27
Volume: 7
Issue: 2
Pages: 262-276
ISSN: 2058-5276 (ISSN-L)
DOI: 10.1038/s41564-021-01050-3
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
Licence: www.springer.com/tdm (tdm)
www.springer.com/tdm (vor)
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.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review

Multi-omics analyses of the ulcerative colitis gut microbiome link Bacteroides vulgatus proteases with disease severity

Abstract

Overview

Integrity signals

Verification

Claims the paper makes

Claims other papers make about this one

Self-check

Citations

Cites

Cited by

Related

Metadata

Record

About these checks