Cirrhosis related functionality characteristic of the fecal microbiota as revealed by a metaproteomic approach
Open accessAbstract
BACKGROUND: Intestinal microbiota operated as a whole and was closely related with human health. Previous studies had suggested close relationship between liver cirrhosis (LC) and gut microbiota. METHODS: To determine the functional characteristic of the intestinal microbiota specific for liver cirrhosis, the fecal metaproteome of three LC patients with Child-Turcotte-Pugh (CTP) score of A, B, and C, and their spouse were first compared using high-throughput approach based on denaturing polyacrylamide gel electrophoresis and liquid chromatography-tandem mass spectrometry in our study. RESULTS: A total of 5,020 proteins (88 % from bacteria, 12 % form human) were identified and annotated based on the GO and KEGG classification. Our results indicated that the LC patients possessed a core metaproteome including 119 proteins, among which 14 proteins were enhanced expressed and 7 proteins were unique for LC patients compared with the normal, which were dominant at the function of carbohydrate metabolism. In addition, LC patients have unique biosynthesis of branched chain amino acid (BCAA), pantothenate, and CoA, enhanced as CTP scores increased. Those three substances were all important in a wide array of key and essential biological roles of life. CONCLUSIONS: We observed a highly comparable cirrhosis-specific metaproteome clustering of fecal microbiota and provided the first supportive evidence for the presence of a LC-related substantial functional core mainly involved in carbohydrate, BCAA, pantothenate, and CoA metabolism, suggesting the compensation of intestinal microbiota for the fragile and innutritious body of cirrhotic patients.
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
Cites
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?
The gut microbiomes of patients with advanced liver disease and cirrhosis are characterized by increased potentially pathogenic bacteria and reduced beneficial bacteria.
“The gut microbiomes of patients with advanced liver disease and cirrhosis are characterized by an increase in potentially pathogenic bacteria, along with reduced numbers of bacteria with beneficial properties32,84,85.”
From The gut microbiome and liver cancer: mechanisms and clinical translation (2017) · cites this paper as [84]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
Altschul, S. (1997) · Nucleic Acids Research · doi:10.1093/nar/25.17.3389 · Cited by 73,302 · see citing works
A human gut microbial gene catalogue established by metagenomic sequencing
MetaHIT Consortium, Qin, J., Li, R., Raes, J., Arumugam, M., Burgdorf, K. S., Manichanh, C., Nielsen, T., Pons, N., Levenez, F., et al. (2010) · Nature · doi:10.1038/nature08821 · Cited by 11,624 · see citing works
SignalP 4.0: discriminating signal peptides from transmembrane regions
Petersen, T. N., Brunak, S., von Heijne, G., & Nielsen, H. (2011) · Nature Methods · doi:10.1038/nmeth.1701 · Cited by 8,847 · see citing works
Turnbaugh, P. J., Ley, R. E., Hamady, M., Fraser-Liggett, C. M., Knight, R., & Gordon, J. I. (2007) · Nature · doi:10.1038/nature06244 · Cited by 6,091 · see citing works
Signals from chloroplasts converge to regulate nuclear gene expression.
Koussevitzky, S., Nott, A., Mockler, T. C., Hong, F., Sachetto‐Martins, G., Surpin, M. A., Lim, J. C.-S., Mittler, R., & Chory, J. (2007) · PubMed · doi:10.1126/science.1140516 · Cited by 5,076 · see citing works
In-gel digestion for mass spectrometric characterization of proteins and proteomes
Shevchenko, A., Tomas, H., Havli, J., Olsen, J. V., & Mann, M. (2006) · Nature Protocols · doi:10.1038/nprot.2006.468 · Cited by 4,867 · see citing works
Metagenomic Analysis of the Human Distal Gut Microbiome
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. (2006) · Science · doi:10.1126/science.1124234 · Cited by 4,699 · see citing works
The COG database: a tool for genome-scale analysis of protein functions and evolution
Tatusov, R. L. (2000) · Nucleic Acids Research · doi:10.1093/nar/28.1.33 · Cited by 4,480 · see citing works
Yu, N., Wagner, J. R., Laird, M. R., Melli, G., Rey, S., Lo, R., Dao, P., Şahinalp, S. C., Ester, M., Foster, L. J., et al. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq249 · Cited by 2,496 · see citing works
Reduced diversity of faecal microbiota in Crohn’s disease revealed by a metagenomic approach
Manichanh, C., Rigottier-Gois, L., Bonnaud, E., Gloux, K., Pelletier, E., Frangeul, L., Nalin, R., Jarrin, C., Chardon, P., Marteau, P., et al. (2006) · Gut · doi:10.1136/gut.2005.073817 · Cited by 2,277 · see citing works
Characterization of fecal microbial communities in patients with liver cirrhosis
Chen, Y., Yang, F., Lu, H., Wang, B., Chen, Y., Lei, D., Wang, Y., Zhu, B., & Li, L. (2011) · Hepatology · doi:10.1002/hep.24423 · Cited by 1,038 · see citing works
Self-citationBragulla, H. H., & Homberger, D. G. (2009) · Journal of Anatomy · doi:10.1111/j.1469-7580.2009.01066.x · Cited by 780 · see citing works
High-throughput diversity and functionality analysis of the gastrointestinal tract microbiota
Zoetendal, E. G., Rajilić-Stojanović, M. D., & de Vos, W. M. (2008) · Gut · doi:10.1136/gut.2007.133603 · Cited by 672 · see citing works
Community Proteomics of a Natural Microbial Biofilm
Ram, R. J., VerBerkmoes, N. C., Thelen, M. P., Tyson, G. W., Baker, B. J., Blake, R. C., Shah, M. B., Hettich, R. L., & Banfield, J. F. (2005) · Science · doi:10.1126/science.1109070 · Cited by 659 · see citing works
Gut microbiota disturbance during antibiotic therapy: a multi-omic approach
Pérez‐Cobas, A. E., Gosalbes, M. J., Friedrichs, A. K., Knecht, H., Artacho, A., Eismann, K., Otto, W., Rojo, D., Bargiela, R., von Bergen�, M., et al. (2012) · Gut · doi:10.1136/gutjnl-2012-303184 · Cited by 603 · see citing works
Wilmes, P., & Bond, P. L. (2004) · Environmental Microbiology · doi:10.1111/j.1462-2920.2004.00687.x · Cited by 391 · see citing works
iPath: interactive exploration of biochemical pathways and networks
Letunić, I., Yamada, T., Kanehisa, M. I., & Peer Bork, B. (2008) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2008.01.001 · Cited by 201 · see citing works
Kolmeder, C. A., de Been, M., Nikkilä, J., Ritamo, I., Mättö, J., Valmu, L., Salojärvi, J., Palva, A., Salonen, A., & de Vos, W. M. (2012) · PLoS ONE · doi:10.1371/journal.pone.0029913 · Cited by 199 · see citing works
Gut microflora in the pathogenesis of the complications of cirrhosis
García–Tsao, G., & Wiest, R. (2004) · Best Practice & Research Clinical Gastroenterology · doi:10.1016/j.bpg.2003.10.005 · Cited by 190 · see citing works
Klaassens, E. S., de Vos, W. M., & Vaughan, E. E. (2006) · Applied and Environmental Microbiology · doi:10.1128/aem.01921-06 · Cited by 172 · see citing works
Wei, X., Yan, X., Zou, D., Yang, Z., Wang, X., Liu, W., Wang, S., Li, X., Han, J., Huang, L., et al. (2013) · BMC Gastroenterology · doi:10.1186/1471-230x-13-175 · Cited by 156 · see citing works
Self-citationGut microbiota and host metabolism in liver cirrhosis
Usami, M. (2015) · World Journal of Gastroenterology · doi:10.3748/wjg.v21.i41.11597 · Cited by 148 · see citing works
Gut microbiota disturbance during antibiotic therapy
Ferrer, M., dos Santos, V. A. P. M., Ott, S. J., & Moyá, A. (2013) · Gut Microbes · doi:10.4161/gmic.27128 · Cited by 112 · see citing works
Hernández, E., Bargiela, R., Diez, M. S., Friedrichs, A. K., Pérez‐Cobas, A. E., Gosalbes, M. J., Knecht, H., Martínez‐Martínez, M., Seifert, J., von Bergen�, M., et al. (2013) · Gut Microbes · doi:10.4161/gmic.25321 · Cited by 91 · see citing works
Subnuclear Proteomics in Colorectal Cancer
Albrethsen, J., Knol, J. C., Piersma, S. R., et al. (2010) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m900546-mcp200 · Cited by 70 · see citing works
Pantothenate Utilization by Plasmodium as a Target for Antimalarial Chemotherapy
Spry, C., van Schalkwyk, D. A., Strauss, E., et al. (2010) · Infectious Disorders - Drug Targets · doi:10.2174/187152610791163390 · Cited by 51 · see citing works
Gut microbiome and intestinal barrier failure – The “Achilles heel” in hepatology?
Benten, D., & Wiest, R. (2012) · Journal of Hepatology · doi:10.1016/j.jhep.2012.03.003 · Cited by 41 · see citing works
Bernal, V., Masdemont-Hernández, B., Arense, P., Cánovas, M., & Iborra, J. L. (2007) · Journal of Biotechnology · doi:10.1016/j.jbiotec.2007.05.034 · Cited by 12 · see citing works
Flagged first, then by citations
Cited by
Sorted by citations
The gut microbiome and liver cancer: mechanisms and clinical translation
Yu, L.-X., & Schwabe, R. F. (2017) · Nature Reviews Gastroenterology & Hepatology · doi:10.1038/nrgastro.2017.72 · Cited by 634 · see citing works
- Authors
- Wei, X., Jiang, S., Chen, Y., Zhao, X., Li, H., Lin, W., Li, B., Wang, X., Yuan, J., & Sun, Y.
- Affiliations
- Academy of Military Medical Sciences (CN)
- Corresponding author
- Yuan, Jing
- Sun, Yansong
- Venue
- BMC Gastroenterology
- Published
- 2016-10-04
- Volume
- 16
- Issue
- 1
- Pages
- 121-121
- ISSN
- 1471-230X (ISSN-L)
- PMC
- PMC5051048
- OpenAlex
- W2529534298
- Cited by
- 45
- References
- 28
- Citations by year
- 2026: 1 · 2025: 4 · 2024: 3 · 2023: 5 · 2022: 2 · 2021: 5 · 2020: 9 · 2019: 8 · 2018: 3 · 2017: 5
- FWCI
- 2.77
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- cc-by
- Locations
- BMC Gastroenterology (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Funders
- Deutscher Akademischer Austauschdienst (D/09/04778, Grant D/09/04778)
- National Natural Science Foundation of China (2011ZX10004-001, 31370093, 863 Program)
- Bundesministerium für Bildung und Forschung
- National High-tech Research and Development Program (SS2014AA022210)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Health Sciences › Medicine › Hepatology › Liver Disease and Transplantation
- Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
- Keywords
- liver cirrhosis, gut microbiota, carbohydrate metabolism, branched-chain amino acid biosynthesis, pantothenate and CoA biosynthesis, Child-Pugh score
- MeSH terms
- Gastrointestinal Microbiome, Amino Acids, Branched-Chain, Coenzyme A, Feces, Female, Humans, Liver Cirrhosis, Male, Middle Aged, Pantothenic Acid, Severity of Illness Index, Spouses, Proteomics, Carbohydrate Metabolism, Metagenome
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
