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Alterations of the human gut microbiome in liver cirrhosis
Abstract
Liver cirrhosis occurs as a consequence of many chronic liver diseases that are prevalent worldwide. Here we characterize the gut microbiome in liver cirrhosis by comparing 98 patients and 83 healthy control individuals. We build a reference gene set for the cohort containing 2.69 million genes, 36.1% of which are novel. Quantitative metagenomics reveals 75,245 genes that differ in abundance between the patients and healthy individuals (false discovery rate < 0.0001) and can be grouped into 66 clusters representing cognate bacterial species; 28 are enriched in patients and 38 in control individuals. Most (54%) of the patient-enriched, taxonomically assigned species are of buccal origin, suggesting an invasion of the gut from the mouth in liver cirrhosis. Biomarkers specific to liver cirrhosis at gene and function levels are revealed by a comparison with those for type 2 diabetes and inflammatory bowel disease. On the basis of only 15 biomarkers, a highly accurate patient discrimination index is created and validated on an independent cohort. Thus microbiota-targeted biomarkers may be a powerful tool for diagnosis of different diseases.
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“Studies in the past few years have demonstrated profound alterations of the intestinal microbiota in patients with cirrhosis, showing increased Enterobacteriacea as well as strains that are typically found in the oral microbiota, such as Veillonellaceae and Streptococcaceae, consistent with an invasion of microorganisms from the mouth to the gut in liver cirrhosis32,33.”
From The gut microbiome and liver cancer: mechanisms and clinical translation (2017) · cites this paper as [32]
In the citing paper
“Metagenomic studies have revealed substantial alterations in the composition of the gut microbiota in a range of CLD as well as in patients with cirrhosis12,32.”
From The gut microbiome and liver cancer: mechanisms and clinical translation (2017) · cites this paper as [32]
In the citing paper
“Key changes in the composition of the intestinal microbiota in cirrhosis include enrichment of Veillonella or Streptococcus as well as decreased bacteria from the order Clostridiales32.”
From The gut microbiome and liver cancer: mechanisms and clinical translation (2017) · cites this paper as [32]
In the citing paper
“Of note, the majority of the patient-enriched species were of buccal origin, suggesting an invasion of the gut from the mouth in liver cirrhosis32.”
From The gut microbiome and liver cancer: mechanisms and clinical translation (2017) · cites this paper as [32]
In the citing paper
“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 [32]
In the citing paper
“Changes in the composition of the oral microbiome and the colonisation of the lower intestinal tract by oral-specific bacteria has been related to cirrhosis49.”
From Cholestasis induced by bile duct ligation promotes changes in the intestinal microbiome in mice (2019) · cites this paper as [49]
In the citing paper
“Increased presence of Prevotella has been found in cirrhotics49”
From Cholestasis induced by bile duct ligation promotes changes in the intestinal microbiome in mice (2019) · cites this paper as [49]
Citations
Cites
Fast and accurate short read alignment with Burrows-Wheeler transform
Li, H., & Durbin, R. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp324 · Cited by 58,607
An obesity-associated gut microbiome with increased capacity for energy harvest
Turnbaugh, P. J., Ley, R. E., Mahowald, M. A., Magrini, V., Mardis, E. R., & Gordon, J. I. (2006) · Nature · doi:10.1038/nature05414 · Cited by 12,444
Structure, function and diversity of the healthy human microbiome
The Human Microbiome Project Consortium (2012) · Nature · doi:10.1038/nature11234 · Cited by 11,726
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
Self-citationPrincipal components analysis corrects for stratification in genome-wide association studies
Price, A. L., Patterson, N. J., Plenge, R. M., Weinblatt, M. E., Shadick, N. A., & Reich, D. (2006) · Nature Genetics · doi:10.1038/ng1847 · Cited by 10,248
Human gut microbes associated with obesity
Ley, R. E., Turnbaugh, P. J., Klein, S., & Gordon, J. I. (2006) · Nature · doi:10.1038/4441022a · Cited by 8,785
A core gut microbiome in obese and lean twins
Turnbaugh, P. J., Hamady, M., Yatsunenko, T., Cantarel, B. L., Duncan, A., Ley, R. E., Sogin, M. L., Jones, W. J., Roe, B. A., Affourtit, J. P., et al. (2009) · Nature · doi:10.1038/nature07540 · Cited by 7,823
Human gut microbiome viewed across age and geography
Yatsunenko, T., Rey, F. E., Manary, M. J., Trehan, I., Dominguez-Bello, M. G., Contreras, M., Magris, M., Hidalgo, G., Baldassano, R. N., Anokhin, A. P., et al. (2012) · Nature · doi:10.1038/nature11053 · Cited by 7,815
A metagenome-wide association study of gut microbiota in type 2 diabetes
Qin, J., Li, Y., Cai, Z., Li, S., Zhu, J., Zhang, F., Liang, S., Zhang, W., Guan, Y., Shen, D., et al. (2012) · Nature · doi:10.1038/nature11450 · Cited by 6,762
Self-citationLinking long-term dietary patterns with gut microbial enterotypes
Wu, G. D., Chen, J., Hoffmann, C., Bittinger, K., Chen, Y.-Y., Keilbaugh, S. A., Bewtra, M., Knights, D., Walters, W. A., Knight, R., et al. (2011) · Science · doi:10.1126/science.1208344 · Cited by 6,513
Self-citation
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Changes of Intestinal Functions in Liver Cirrhosis
Fukui, H., & Wiest, R. (2016) · Inflammatory Intestinal Diseases · doi:10.1159/000444436 · Cited by 6,820
Gut microbiota in human metabolic health and disease
Fan, Y., & Pedersen, O. (2021) · Nature Reviews Microbiology · doi:10.1038/s41579-020-0433-9 · Cited by 4,724
The Human Intestinal Microbiome in Health and Disease
Lynch, S. V., & Pedersen, O. (2016) · New England Journal of Medicine · doi:10.1056/nejmra1600266 · Cited by 3,637
Shotgun metagenomics, from sampling to analysis
Quince, C., Walker, A. W., Simpson, J. T., Loman, N. J., & Segata, N. (2017) · Nature Biotechnology · doi:10.1038/nbt.3935 · Cited by 2,202
The gut-liver axis in liver disease: Pathophysiological basis for therapy
Albillos, A., de Gottardi, A., & Rescigno, M. (2020) · Journal of Hepatology · doi:10.1016/j.jhep.2019.10.003 · Cited by 2,166
Local and systemic mechanisms linking periodontal disease and inflammatory comorbidities
Hajishengallis, G., & Chavakis, T. (2021) · Nature Reviews Immunology · doi:10.1038/s41577-020-00488-6 · Cited by 1,871
Gut microbiota dysbiosis contributes to the development of hypertension
Li, J., Zhao, F., Wang, Y., Chen, J., Tao, J., Tian, G., Wu, S., Liu, W., Cui, Q., Geng, B., et al. (2017) · Microbiome · doi:10.1186/s40168-016-0222-x · Cited by 1,685
The gut microbiome in atherosclerotic cardiovascular disease
Jie, Z., Xia, H., Zhong, S.-L., Feng, Q., Li, S., Liang, S., Zhong, H., Liu, Z., Gao, Y., Zhao, H., et al. (2017) · Nature Communications · doi:10.1038/s41467-017-00900-1 · Cited by 1,638
SCFA: mechanisms and functional importance in the gut
Martin‐Gallausiaux, C., Marinelli, L., Blottière, H. M., Larraufie, P., & Lapaque, N. (2020) · Proceedings of The Nutrition Society · doi:10.1017/s0029665120006916 · Cited by 1,585
Hepatic stellate cells as key target in liver fibrosis
Higashi, T., Friedman, S. L., & Hoshida, Y. (2017) · Advanced Drug Delivery Reviews · doi:10.1016/j.addr.2017.05.007 · Cited by 1,485
The gut-liver axis and the intersection with the microbiome
Tripathi, A., Debelius, J., Brenner, D. A., Karin, M., Loomba, R., Schnabl, B., & Knight, R. (2018) · Nature Reviews Gastroenterology & Hepatology · doi:10.1038/s41575-018-0011-z · Cited by 1,480
Blanco-Míguez, A., Beghini, F., Cumbo, F., McIver, L. J., Thompson, K. N., Zolfo, M., Manghi, P., Dubois, L., Huang, K. D., Thomas, A. M., et al. (2023) · Nature Biotechnology · doi:10.1038/s41587-023-01688-w · Cited by 1,442
Liver Fibrosis: Mechanistic Concepts and Therapeutic Perspectives
Roehlen, N., Crouchet, E., & Baumert, T. F. (2020) · Cells · doi:10.3390/cells9040875 · Cited by 1,237
Immunology in the liver — from homeostasis to disease
Heymann, F., & Tacke, F. (2016) · Nature Reviews Gastroenterology & Hepatology · doi:10.1038/nrgastro.2015.200 · Cited by 1,180
Gut microbiota and human NAFLD: disentangling microbial signatures from metabolic disorders
Aron‐Wisnewsky, J., Vigliotti, C., Witjes, J. J., Le, P. T., Holleboom, A. G., Verheij, J., Nieuwdorp, M., & Clément, K. (2020) · Nature Reviews Gastroenterology & Hepatology · doi:10.1038/s41575-020-0269-9 · Cited by 1,132
Loomba, R., Seguritan, V., Li, W., Long, T., Klitgord, N., Bhatt, A., Dulai, P. S., Caussy, C., Bettencourt, R., Highlander, S. K., et al. (2017) · Cell Metabolism · doi:10.1016/j.cmet.2017.04.001 · Cited by 1,123
The intestinal microbiota fuelling metabolic inflammation
Tilg, H., Zmora, N., Adolph, T. E., & Elinav, E. (2020) · Nature Reviews Immunology · doi:10.1038/s41577-019-0198-4 · Cited by 1,089
Yassour, M., Vatanen, T., Siljander, H., Hämäläinen, A.-M., Härkönen, T., Ryhänen, S. J., Franzosa, E. A., Vlamakis, H., Huttenhower, C., Gevers, D., et al. (2016) · Science Translational Medicine · doi:10.1126/scitranslmed.aad0917 · Cited by 1,043
Ghosh, T. S., Rampelli, S., Jeffery, I. B., Santoro, A., Neto, M., Capri, M., Giampieri, E., Jennings, A., Candela, M., Turroni, S., et al. (2020) · Gut · doi:10.1136/gutjnl-2019-319654 · Cited by 991
Ectopic colonization of oral bacteria in the intestine drives T H 1 cell induction and inflammation
Atarashi, K., Suda, W., Luo, C., Kawaguchi, T., Motoo, I., Narushima, S., Kiguchi, Y., Yasuma, K., Watanabe, E., Tanoue, T., et al. (2017) · Science · doi:10.1126/science.aan4526 · Cited by 957
The Human Microbiota in Health and Disease
Wang, B., Yao, M., Lv, L., Ling, Z., & Li, L. (2017) · Engineering · doi:10.1016/j.eng.2017.01.008 · Cited by 916
Self-citationHill‐Burns, E. M., Debelius, J. W., Morton, J. T., Wissemann, W. T., Lewis, M. R., Wallen, Z. D., Peddada, S. D., Factor, S. A., Molho, E., Zabetian, C. P., et al. (2017) · Movement Disorders · doi:10.1002/mds.26942 · Cited by 874
Alcoholic liver disease: mechanisms of injury and targeted treatment
Louvet, A., & Mathurin, P. (2015) · Nature Reviews Gastroenterology & Hepatology · doi:10.1038/nrgastro.2015.35 · Cited by 867
Gut-liver axis: Pathophysiological concepts and clinical implications
Tilg, H., Adolph, T. E., & Trauner, M. (2022) · Cell Metabolism · doi:10.1016/j.cmet.2022.09.017 · Cited by 843
Microbial strain-level population structure and genetic diversity from metagenomes
Truong, D. T., Tett, A., Pasolli, E., Huttenhower, C., & Segata, N. (2017) · Genome Research · doi:10.1101/gr.216242.116 · Cited by 839
Ren, Z., Li, A., Jiang, J., Zhou, L., Yu, Z., Lu, H., Xie, H., Chen, X., Shao, L., Zhang, R., et al. (2018) · Gut · doi:10.1136/gutjnl-2017-315084 · Cited by 782
Self-citationInsights from 20 years of bacterial genome sequencing
Land, M., Hauser, L., Jun, S., Nookaew, I., Leuze, M. R., Ahn, T.-H., Karpinets, T. V., Lund, O., Kora, G., Wassenaar, T. M., et al. (2015) · Functional & Integrative Genomics · doi:10.1007/s10142-015-0433-4 · Cited by 771
Oral microbiomes: more and more importance in oral cavity and whole body
Gao, L., Xu, T., Huang, G., Jiang, S., Gu, Y., & Chen, F. (2018) · Protein & Cell · doi:10.1007/s13238-018-0548-1 · Cited by 770
New insights from uncultivated genomes of the global human gut microbiome
Nayfach, S., Shi, Z. J., Seshadri, R., Pollard, K. S., & Kyrpides, N. C. (2019) · Nature · doi:10.1038/s41586-019-1058-x · Cited by 737
Mukherjee, A., Lordan, C., Ross, R. P., & Cotter, P. D. (2020) · Gut Microbes · doi:10.1080/19490976.2020.1802866 · Cited by 726
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Peng, X., Cheng, L., You, Y., Tang, C., Ren, B., Li, Y., Xu, X., & Zhou, X. (2022) · International Journal of Oral Science · doi:10.1038/s41368-022-00163-7 · Cited by 707
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Moya, A., & Ferrer, M. (2016) · Trends in Microbiology · doi:10.1016/j.tim.2016.02.002 · Cited by 690
Ponziani, F. R., Bhoori, S., Castelli, C., Putignani, L., Rivoltini, L., CHIERICO, F. D., Sanguinetti, M., Morelli, D., Sterbini, F. P., Petito, V., et al. (2018) · Hepatology · doi:10.1002/hep.30036 · Cited by 684
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Early life dynamics of the human gut virome and bacterial microbiome in infants
Lim, E. S., Zhou, Y., Zhao, G., Bauer, I. K., Droit, L., Ndao, I. M., Warner, B. B., Tarr, P. I., Wang, D., & Holtz, L. R. (2015) · Nature Medicine · doi:10.1038/nm.3950 · Cited by 670
Liu, P., Wu, L., Peng, G., Han, Y., Tang, R., Ge, J., Zhang, L., Jia, L., Yue, S., Zhou, K., et al. (2019) · Brain, Behavior, and Immunity · doi:10.1016/j.bbi.2019.05.008 · Cited by 669
Self-citationThe oral microbiome: diversity, biogeography and human health
Baker, J. L., Mark Welch, J. L., Kauffman, K. M., McLean, J. S., & He, X. (2024) · Nature Reviews Microbiology · doi:10.1038/s41579-023-00963-6 · Cited by 661
Machine Learning Meta-analysis of Large Metagenomic Datasets: Tools and Biological Insights
Pasolli, E., Truong, D. T., Malik, F., Waldron, L., & Segata, N. (2016) · PLOS Computational Biology · doi:10.1371/journal.pcbi.1004977 · Cited by 659
Antibiotics as deep modulators of gut microbiota: between good and evil
Ianiro, G., Tilg, H., & Gasbarrini, A. (2016) · Gut · doi:10.1136/gutjnl-2016-312297 · Cited by 653
VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data
Ren, J., Ahlgren, N. A., Lu, Y. Y., Fuhrman, J. A., & Sun, F. (2017) · Microbiome · doi:10.1186/s40168-017-0283-5 · Cited by 653
Bernardi, M., Moreau, R., Angeli, P., Schnabl, B., & Arroyo, V. (2015) · Journal of Hepatology · doi:10.1016/j.jhep.2015.07.004 · Cited by 645
MicroRNAs and complex diseases: from experimental results to computational models
Chen, X., Xie, D., Zhao, Q., & You, Z. (2017) · Briefings in Bioinformatics · doi:10.1093/bib/bbx130 · Cited by 641
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
Microbiome–host systems interactions: protective effects of propionate upon the blood–brain barrier
Hoyles, L., Snelling, T., Umlai, U.-K., Nicholson, J. K., Carding, S. R., Glen, R. C., & McArthur, S. (2018) · Microbiome · doi:10.1186/s40168-018-0439-y · Cited by 591
Intestinal microbiota contributes to individual susceptibility to alcoholic liver disease
Llopis, M., Cassard, A., Wrzosek, L., Boschat, L., Bruneau, A., Ferrere, G., Puchois, V., Martin, J., Lepage, P., Roy, T. L., et al. (2015) · Gut · doi:10.1136/gutjnl-2015-310585 · Cited by 578
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Yao, M., Xie, J., Du, H., McClements, D. J., Xiao, H., & Li, L. (2020) · Comprehensive Reviews in Food Science and Food Safety · doi:10.1111/1541-4337.12532 · Cited by 571
Self-citationJu, C., & Tacke, F. (2016) · Cellular & Molecular Immunology · doi:10.1038/cmi.2015.104 · Cited by 554
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Wang, X., Yang, S., Li, S., Zhao, L., Hao, Y., Qin, J., Zhang, L., Zhang, C., Bian, W., Zuo, L., et al. (2020) · Gut · doi:10.1136/gutjnl-2019-319766 · Cited by 553
Self-citationMilosevic, I., Vujovic, A., Barac, A., Djelic, M., Korac, M., Radovanovic Spurnic, A., Gmizic, I., Stevanovic, O., Djordjevic, V., Lekic, N., et al. (2019) · International Journal of Molecular Sciences · doi:10.3390/ijms20020395 · Cited by 551
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Tilg, H., Cani, P. D., & Mayer, E. A. (2016) · Gut · doi:10.1136/gutjnl-2016-312729 · Cited by 525
Accessible, curated metagenomic data through ExperimentHub
Pasolli, E., Schiffer, L., Manghi, P., Renson, A., Obenchain, V., Truong, D. T., Beghini, F., Malik, F., Ramos, M., Dowd, J. B., et al. (2017) · Nature Methods · doi:10.1038/nmeth.4468 · Cited by 514
The gut microbiome of healthy Japanese and its microbial and functional uniqueness
Nishijima, S., Suda, W., Oshima, K., Kim, S.-W., Hirose, Y., Morita, H., & Hattori, M. (2016) · DNA Research · doi:10.1093/dnares/dsw002 · Cited by 513
Identification of antimicrobial peptides from the human gut microbiome using deep learning
Ma, Y., Guo, Z., Xia, B., Zhang, Y., Liu, X., Yu, Y., Tang, N., Tong, X., Wang, M., Ye, X., et al. (2022) · Nature Biotechnology · doi:10.1038/s41587-022-01226-0 · Cited by 512
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Hrncir, T. (2022) · Microorganisms · doi:10.3390/microorganisms10030578 · Cited by 512
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Yan, Q., Gu, Y., Li, X., Yang, W. Q., Jia, L., Chen, C., Han, X., Huang, Y., Zhao, L., Li, P., et al. (2017) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2017.00381 · Cited by 511
Self-citationHepatic encephalopathy: Novel insights into classification, pathophysiology and therapy
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Song, Z., Cai, Y., Lao, X., Wang, X., Lin, X., Cui, Y., Kalavagunta, P. K., Liao, J., Jin, L., Shang, J., et al. (2019) · Microbiome · doi:10.1186/s40168-019-0628-3 · Cited by 505
Contribution of the Intestinal Microbiome and Gut Barrier to Hepatic Disorders
Chopyk, D. M., & Grakoui, A. (2020) · Gastroenterology · doi:10.1053/j.gastro.2020.04.077 · Cited by 504
Colonic Butyrate-Producing Communities in Humans: an Overview Using Omics Data
Vital, M., Karch, A., & Pieper, D. H. (2017) · mSystems · doi:10.1128/msystems.00130-17 · Cited by 502
Arroyo, V., Angeli, P., Moreau, R., Jalan, R., Clària, J., Trebicka, J., Fernández, J., Gustot, T., Caraceni, P., & Bernardi, M. (2020) · Journal of Hepatology · doi:10.1016/j.jhep.2020.11.048 · Cited by 494
Cirrhosis-associated immune dysfunction
Albillos, A., Martín‐Mateos, R., der Merwe, V., Wiest, R., Jalan, R., & Álvarez‐Mon, M. (2021) · Nature Reviews Gastroenterology & Hepatology · doi:10.1038/s41575-021-00520-7 · Cited by 485
Behary, J., Amorim, N. M. L., Jiang, X., Raposo, A. E., Gong, L., McGovern, E., Ibrahim, R., Chu, F., Stephens, C., Jebeili, H., et al. (2021) · Nature Communications · doi:10.1038/s41467-020-20422-7 · Cited by 483
EASL Clinical Practice Guidelines on the management of hepatic encephalopathy
Montagnese, S., Rautou, P., Romero‐Gómez, M., Larsen, F. S., Shawcross, D. L., Thabut, D., Vilstrup, H., & Weißenborn, K. (2022) · Journal of Hepatology · doi:10.1016/j.jhep.2022.06.001 · Cited by 481
Tett, A., Huang, K. D., Asnicar, F., Fehlner-Peach, H., Pasolli, E., Karcher, N., Armanini, F., Manghi, P., Bonham, K., Zolfo, M., et al. (2019) · Cell Host & Microbe · doi:10.1016/j.chom.2019.08.018 · Cited by 476
Links of gut microbiota composition with alcohol dependence syndrome and alcoholic liver disease
Dubinkina, V. B., Tyakht, A., Odintsova, V. Y., Yarygin, K. S., Kovarsky, B. A., Pavlenko, A. V., Ischenko, D. S., Popenko, A., Alexeev, D. G., Taraskina, A. Y., et al. (2017) · Microbiome · doi:10.1186/s40168-017-0359-2 · Cited by 472
Gut microbiome, liver immunology, and liver diseases
Wang, R., Tang, R., Li, B., Ma, X., Schnabl, B., & Tilg, H. (2021) · Cellular & Molecular Immunology · doi:10.1038/s41423-020-00592-6 · Cited by 466
Acute-on-chronic liver failure in cirrhosis
Arroyo, V., Moreau, R., Kamath, P. S., Jalan, R., Ginès, P., Nevens, F., Fernández, J., To, U. K., García–Tsao, G., & Schnabl, B. (2016) · Nature Reviews Disease Primers · doi:10.1038/nrdp.2016.41 · Cited by 450
Low diversity gut microbiota dysbiosis: drivers, functional implications and recovery
Kriss, M. S., Hazleton, K. Z., Nusbacher, N. M., Martin, C. G., & Lozupone, C. (2018) · Current Opinion in Microbiology · doi:10.1016/j.mib.2018.07.003 · Cited by 435
Tang, R., Wei, Y., Li, Y., Chen, W., Chen, H., Wang, Q., Yang, F., Miao, Q., Xiao, X., Zhang, H., et al. (2018) · Gut · doi:10.1136/gutjnl-2016-313332 · Cited by 434
Self-citationAdaptive Evolution within Gut Microbiomes of Healthy People
Zhao, S., Lieberman, T. D., Poyet, M., Kauffman, K. M., Gibbons, S. M., Groussin, M., Xavier, R. J., & Alm, E. J. (2019) · Cell Host & Microbe · doi:10.1016/j.chom.2019.03.007 · Cited by 434
The native microbiome of the nematode Caenorhabditis elegans: gateway to a new host-microbiome model
Dirksen, P., Marsh, S., Braker, I., Heitland, N., Wagner, S., Nakad, R., Mäder, S., Petersen, C., Kowallik, V., Rosenstiel, P. C., et al. (2016) · BMC Biology · doi:10.1186/s12915-016-0258-1 · Cited by 434
Païssé, S., Valle, C., Servant, F., Courtney, M., Burcelin, R., Amar, J., & Lelouvier, B. (2016) · Transfusion · doi:10.1111/trf.13477 · Cited by 431
Engelmann, C., Clària, J., Szabó, G., Bosch, J., & Bernardi, M. (2021) · Journal of Hepatology · doi:10.1016/j.jhep.2021.01.002 · Cited by 431
Metagenome-wide association studies: fine-mining the microbiome
Wang, J., & Jia, H. (2016) · Nature Reviews Microbiology · doi:10.1038/nrmicro.2016.83 · Cited by 429
Quantifying Diet-Induced Metabolic Changes of the Human Gut Microbiome
Shoaie, S., Ghaffari, P., Kovatcheva‐Datchary, P., Mardinoğlu, A., Sen, P., Pujos‐Guillot, E., de Wouters, T., Juste, C., Rizkalla, S. W., Chilloux, J., et al. (2015) · Cell Metabolism · doi:10.1016/j.cmet.2015.07.001 · Cited by 428
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Mills, S., Stanton, C., Lane, J. A., Smith, G., & Ross, R. P. (2019) · Nutrients · doi:10.3390/nu11040923 · Cited by 426
Application of metagenomics in the human gut microbiome
Wang, W., Xu, S., Ren, Z., Tao, L., Jiang, J., & Zheng, S. (2015) · World Journal of Gastroenterology · doi:10.3748/wjg.v21.i3.803 · Cited by 419
Self-citationRole of the gut microbiota in type 2 diabetes and related diseases
Yang, G., Wei, J., Liu, P., Zhang, Q., Tian, Y., Hou, G., Meng, L., Xin, Y., & Jiang, X. (2021) · Metabolism · doi:10.1016/j.metabol.2021.154712 · Cited by 418
Primary sclerosing cholangitis is characterised by intestinal dysbiosis independent from IBD
Sabino, J., Vieira-Silva, S., Machiels, K., Joossens, M., Falony, G., Ballet, V., Ferrante, M., Van Assche, G., Van der Merwe, S., Vermeire, S., et al. (2016) · Gut · doi:10.1136/gutjnl-2015-311004 · Cited by 413
Li, W., Wu, X., Hu, X., Wang, T., Liang, S., Duan, Y., Jin, F., & Qin, B. (2017) · Science China Life Sciences · doi:10.1007/s11427-016-9001-4 · Cited by 406
Self-citationNakajima, M., Arimatsu, K., Kato, T., Matsuda, Y., Minagawa, T., Takahashi, N., Ohno, H., & Yamazaki, K. (2015) · PLoS ONE · doi:10.1371/journal.pone.0134234 · Cited by 403
Lee, G., You, H. J., Bajaj, J. S., Joo, S. K., Yu, J., Park, S., Kang, H., Park, J. H., Kim, J. H., Lee, D. H., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-18754-5 · Cited by 395
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Guo, Z., Zhang, J., Wang, Z., Ang, K. Y., Huang, S. W., Hou, Q., Su, X., Qiao, J., Zheng, Y., Wang, L., et al. (2016) · Scientific Reports · doi:10.1038/srep20602 · Cited by 389
Strain-level microbial epidemiology and population genomics from shotgun metagenomics
Scholz, M., Ward, D. V., Pasolli, E., Tolio, T., Zolfo, M., Asnicar, F., Truong, D. T., Tett, A., Morrow, A. L., & Segata, N. (2016) · Nature Methods · doi:10.1038/nmeth.3802 · Cited by 389
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Nakatsu, G., Zhou, H., Wu, W. K. K., Wong, S. H., Coker, O. O., Dai, Z., Li, X., Szeto, C.-H., Sugimura, N., Lam, T. Y.-T., et al. (2018) · Gastroenterology · doi:10.1053/j.gastro.2018.04.018 · Cited by 386
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Wen, C., Zheng, Z., Shao, T., Liu, L., Xie, Z., Chatelier, E. L., He, Z., Zhong, W., Fan, Y., Zhang, L., et al. (2017) · Genome biology · doi:10.1186/s13059-017-1271-6 · Cited by 386
Self-citationCui, X., Ye, L., Li, J., Jin, L., Wang, W., Li, S., Bao, M., Wu, S., Li, L., Geng, B., et al. (2018) · Scientific Reports · doi:10.1038/s41598-017-18756-2 · Cited by 380
Self-citationModeling microbial abundances and dysbiosis with beta-binomial regression
Martin, B. D., Witten, D., & Willis, A. D. (2020) · The Annals of Applied Statistics · doi:10.1214/19-aoas1283 · Cited by 379
Breast cancer in postmenopausal women is associated with an altered gut metagenome
Zhu, J., Liao, M., Yao, Z., Liang, W., Li, Q., Liu, J., Yang, H., Ji, Y., Wei, W., Tan, A., et al. (2018) · Microbiome · doi:10.1186/s40168-018-0515-3 · Cited by 377
Self-citationBajer, L., Kverka, M., Kostovčík, M., Mačinga, P., Dvořák, J., Stehlíková, Z., Březina, J., Wohl, P., Špičák, J., & Drastich, P. (2017) · World Journal of Gastroenterology · doi:10.3748/wjg.v23.i25.4548 · Cited by 376
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Schwabe, R. F., & Greten, T. F. (2020) · Journal of Hepatology · doi:10.1016/j.jhep.2019.08.016 · Cited by 375
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Ahlawat, S., Asha, A., & Sharma, K. K. (2020) · Letters in Applied Microbiology · doi:10.1111/lam.13333 · Cited by 372
Alzheimer’s disease and gut microbiota
Hu, X., Wang, T., & Jin, F. (2016) · Science China Life Sciences · doi:10.1007/s11427-016-5083-9 · Cited by 371
Self-citationEndocannabinoids–at the crossroads between the gut microbiota and host metabolism
Cani, P. D., Plovier, H., Van Hul, M., Geurts, L., Delzenne, N. M., Druart, C., & Everard, A. (2016) · Nature Reviews Endocrinology · doi:10.1038/nrendo.2015.211 · Cited by 367
Honey bees as models for gut microbiota research
Zheng, H., Steele, M. I., Leonard, S. P., Motta, E. V. S., & Moran, N. A. (2018) · Lab Animal · doi:10.1038/s41684-018-0173-x · Cited by 348
Interchange of entire communities: microbial community coalescence
Rillig, M. C., Antonovics, J., Caruso, T., Lehmann, A., Powell, J. R., Veresoglou, S. D., & Verbruggen, E. (2015) · Trends in Ecology & Evolution · doi:10.1016/j.tree.2015.06.004 · Cited by 345
A Universal Gut-Microbiome-Derived Signature Predicts Cirrhosis
Oh, T. G., Kim, S. M., Caussy, C., Fu, T., Guo, J. P., Bassirian, S., Singh, S., Madamba, E. V., Bettencourt, R., Richards, L., et al. (2020) · Cell Metabolism · doi:10.1016/j.cmet.2020.06.005 · Cited by 344
Self-citationXie, H., Guo, R., Zhong, H., Feng, Q., Lan, Z., Qin, B., Ward, K. J., Jackson, M. A., Xia, Y., Chen, X., et al. (2016) · Cell Systems · doi:10.1016/j.cels.2016.10.004 · Cited by 341
Metadata
- Authors
- Qin, N., Yang, F., Li, A., Prifti, E., Chen, Y., Shao, L., Guo, J., Le Chatelier, E., Yao, J., Wu, L., Zhou, J., Ni, S., Liu, L., Pons, N., Batto, J. M., Kennedy, S. P., Leonard, P., Yuan, C., Ding, W., Chen, Y., Hu, X., Zheng, B., Qian, G., Xu, W., Ehrlich, S. D., Zheng, S., & Li, L.
- Affiliations
- First Affiliated Hospital Zhejiang University (CN)
- Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (FR)
- Guy's Hospital (GB)
- Corresponding author
- Ehrlich, S. Dusko
- Zheng, Shusen
- Li, Lanjuan
- ORCID
- Venue
- Nature
- Published
- 2014-07-23
- Volume
- 513
- Issue
- 7516
- Pages
- 59-64
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- OpenAlex
- W1964027278
- Cited by
- 2,177
- References
- 56
- Citations by year
- 2026: 136 · 2025: 174 · 2024: 215 · 2023: 214 · 2022: 226 · 2021: 283 · 2020: 235 · 2019: 201 · 2018: 161 · 2017: 136 · 2016: 98 · 2015: 83 · 2014: 10
- FWCI
- 44.66
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Nature (publishedVersion)
- PubMed (publishedVersion)
- HAL (submittedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- Research Portal (King's College London) (submittedVersion)
- Funders
- Agence Nationale de la Recherche (ANR-11-DPBS-0001)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Health Sciences › Medicine › Hepatology › Liver Disease and Transplantation
- Health Sciences › Dentistry › Periodontics › Oral microbiology and periodontitis research
- Keywords
- liver cirrhosis, gut microbiota, microbiome biomarkers, oral bacteria, Veillonella, Streptococcus, diagnostic biomarkers, novel genes, type 2 diabetes, inflammatory bowel disease
- MeSH terms
- Chronic Disease, Diabetes Mellitus, Type 2, Feces, Genetic Markers, Health, Humans, Liver Cirrhosis, Mouth, Phylogeny, Reproducibility of Results, Inflammatory Bowel Diseases, Case-Control Studies, Gastrointestinal Tract, Metagenomics, Microbiota
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