The DOI matches its Crossref record; 83 of the 85 references it cites were found in a registry or an index.
Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer
Open accessAbstract
Association studies have linked microbiome alterations with many human diseases. However, they have not always reported consistent results, thereby necessitating cross-study comparisons. Here, a meta-analysis of eight geographically and technically diverse fecal shotgun metagenomic studies of colorectal cancer (CRC, n = 768), which was controlled for several confounders, identified a core set of 29 species significantly enriched in CRC metagenomes (false discovery rate (FDR) < 1 × 10−5). CRC signatures derived from single studies maintained their accuracy in other studies. By training on multiple studies, we improved detection accuracy and disease specificity for CRC. Functional analysis of CRC metagenomes revealed enriched protein and mucin catabolism genes and depleted carbohydrate degradation genes. Moreover, we inferred elevated production of secondary bile acids from CRC metagenomes, suggesting a metabolic link between cancer-associated gut microbes and a fat- and meat-rich diet. Through extensive validations, this meta-analysis firmly establishes globally generalizable, predictive taxonomic and functional microbiome CRC signatures as a basis for future diagnostics. Cross-study analysis defines fecal microbial species associated with colorectal cancer.
Overview
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
Verification
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 cited source says what the claim attributes to it.
In the citing paper
“The lack of solid cross-study reproducible microbial biomarkers of ICI response is not attributable to analytical choices, as applying the same meta-analysis methods in the context of colorectal cancer confirmed the strong and consistent biomarkers across cohorts described elsewhere13,14.”
From Cross-cohort gut microbiome associations with immune checkpoint inhibitor response in advanced melanoma (2022) · cites this paper as [13]
In the citing paper
“This signature, identified using both supervised machine learning and a meta-analysis, included the bacterial species Solobacterium moorei, Fusobacterium nucleatum, Parvimonas micra, Peptostreptococcus stomatis, Peptostreptococcus anaerobius and Gemella morbillorum”
From Gut OncoMicrobiome Signatures (GOMS) as next-generation biomarkers for cancer immunotherapy (2023) · cites this paper as [49]
In the citing paper
“Several taxonomic features associated with sequence variants of cutC were also found to be enriched in patients with CRC, including Hungatella hathewayi, Clostridium asparagiforme, Klebsiella oxytoca, and E coli.”
From Influence of the Gut Microbiome, Diet, and Environment on Risk of Colorectal Cancer (2020) · cites this paper as [146]
In the citing paper
“A meta-analysis of metagenomes of fecal samples146 found patients with CRC to have higher levels of 2 bacterial genes that regulate TMA synthesis: choline TMA-lyase (cutC) and choline TMA-lyase-activating enzyme (cutD).”
From Influence of the Gut Microbiome, Diet, and Environment on Risk of Colorectal Cancer (2020) · cites this paper as [146]
In the citing paper
“Moreover, the bai operon, encoding 7α-dehydroxylation in Clostridium spp. required for synthesis of secondary bile acids, was found to be enriched in metagenomes of fecal samples from patients with CRC.146”
From Influence of the Gut Microbiome, Diet, and Environment on Risk of Colorectal Cancer (2020) · cites this paper as [146]
In the citing paper
“A recent analysis of 8 geographically and technically diverse fecal shotgun metagenomic studies found evidence for increased production of secondary bile acids in patients with CRC, indicating a metabolic link between cancer-associated microbes and a fat- and meat-rich diet. 146”
From Influence of the Gut Microbiome, Diet, and Environment on Risk of Colorectal Cancer (2020) · cites this paper as [146]
In the citing paper
“This pattern has been found previously both with MetaPhlAn 2 (Thomas et al., 2019) and with mOTUs2 (Wirbel et al., 2019), in large part due to low-level detection of typically oral microbes in addition to the baseline gut microbiome during CRC.”
From Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3 (2021) · cites this paper as Wirbel et al., 2019
In the citing paper
“Nearly all microbial-based cancer diagnostics are sequencing-based and have focused on tumors within the aerodigestive tract (31), such as colorectal (118–121), pancreatic (122, 123), and lung cancer (124–126).”
From The microbiome and human cancer (2021) · cites this paper as [118]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing
Benjamini, Y., & Hochberg, Y. (1995) · Journal of the Royal Statistical Society Series B: Statistical Methodology · doi:10.1111/j.2517-6161.1995.tb02031.x · Cited by 109,482
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
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
Regression shrinkage and selection via the lasso
Tibshirani, R. (1996) · Journal of the Royal Statistical Society Series B: Statistical Methodology · doi:10.1111/j.2517-6161.1996.tb02080.x · Cited by 51,482
MUSCLE: multiple sequence alignment with high accuracy and high throughput
Edgar, R. C. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh340 · Cited by 44,662
The Elements of Statistical Learning
Hastie, T., Tibshirani, R., & Friedman, J. (2009) · Springer Series in Statistics · doi:10.1007/978-0-387-84858-7 · Cited by 25,970
pROC: an open-source package for R and S+ to analyze and compare ROC curves
Robin, X., Turck, N., Hainard, A., Tiberti, N., Lisacek, F., Sanchez, J.-C., & Müller, M. (2011) · BMC Bioinformatics · doi:10.1186/1471-2105-12-77 · Cited by 13,697
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-citationPeng, H., Long, F., & Ding, C. (2005) · IEEE Transactions on Pattern Analysis and Machine Intelligence · doi:10.1109/tpami.2005.159 · Cited by 10,818
Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample
Caporaso, J. G., Lauber, C. L., Walters, W. A., Berg-Lyons, D., Lozupone, C., Turnbaugh, P. J., Fierer, N., & Knight, R. D. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1000080107 · Cited by 9,944
Cited by
Sorted by citations
Cryan, J. F., O'Riordan, K. J., Cowan, C. S. M., Sandhu, K. V., Bastiaanssen, T. F. S., Boehme, M., Codagnone, M. G., Cussotto, S., Fulling, C., Golubeva, A. V., et al. (2019) · Physiological Reviews · doi:10.1152/physrev.00018.2018 · Cited by 5,286
Beghini, F., McIver, L. J., Blanco-Míguez, A., Dubois, L., Asnicar, F., Maharjan, S., Mailyan, A., Manghi, P., Scholz, M., Thomas, A. M., et al. (2021) · eLife · doi:10.7554/elife.65088 · Cited by 2,303
Self-citationLocal 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
Chong, J., Liu, P., Zhou, G., & Xia, J. (2020) · Nature Protocols · doi:10.1038/s41596-019-0264-1 · Cited by 1,708
The microbiome and human cancer
Sepich-Poore, G. D., Zitvogel, L., Straussman, R., Hasty, J., Wargo, J. A., & Knight, R. (2021) · Science · doi:10.1126/science.abc4552 · Cited by 1,332
Gut microbiota in colorectal cancer: mechanisms of action and clinical applications
Wong, S. H., & Yu, J. (2019) · Nature Reviews Gastroenterology & Hepatology · doi:10.1038/s41575-019-0209-8 · Cited by 1,392
Mutational signature in colorectal cancer caused by genotoxic pks+ E. coli
Pleguezuelos-Manzano, C., Puschhof, J., Rosendahl Huber, A., van Hoeck, A., Wood, H. M., Nomburg, J., Gurjao, C., Manders, F., Dalmasso, G., Stege, P. B., et al. (2020) · Nature · doi:10.1038/s41586-020-2080-8 · Cited by 1,208
Gut Microbiome: Profound Implications for Diet and Disease
Hills, R. D., Pontefract, B., Mishcon, H. R., Black, C. A., Sutton, S. C., & Theberge, C. R. (2019) · Nutrients · doi:10.3390/nu11071613 · Cited by 1,143
Thomas, A. M., Manghi, P., Asnicar, F., Pasolli, E., Armanini, F., Zolfo, M., Beghini, F., Manara, S., Karcher, N., Pozzi, C., et al. (2019) · Nature Medicine · doi:10.1038/s41591-019-0405-7 · Cited by 1,030
Self-citationAntibiotics as Major Disruptors of Gut Microbiota
Ramirez, J., Guarner, F., Fernández, L. B., Saito, A. M., Sdepanian, V. L., & Cohen, H. (2020) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2020.572912 · Cited by 981
Gut microbiota-derived bile acids in intestinal immunity, inflammation, and tumorigenesis
Cai, J., Sun, L., & Gonzalez, F. J. (2022) · Cell Host & Microbe · doi:10.1016/j.chom.2022.02.004 · Cited by 892
Patel, S. G., Karlitz, J. J., Yen, T., Lieu, C. H., & Boland, C. R. (2022) · The Lancet Gastroenterology & Hepatology · doi:10.1016/s2468-1253(21)00426-x · Cited by 812
The gut microbiome as a modulator of healthy ageing
Ghosh, T. S., Shanahan, F., & O’Toole, P. W. (2022) · Nature Reviews Gastroenterology & Hepatology · doi:10.1038/s41575-022-00605-x · Cited by 817
Influence of the Gut Microbiome, Diet, and Environment on Risk of Colorectal Cancer
Song, M., Chan, A. T., & Sun, J. (2020) · Gastroenterology · doi:10.1053/j.gastro.2019.06.048 · Cited by 752
Prevotella Diversity, Niches and Interactions with the Human Host
Tett, A., Pasolli, E., Masetti, G., Ercolini, D., & Segata, N. (2021) · Nature Reviews Microbiology · doi:10.1038/s41579-021-00559-y · Cited by 748
Self-citationRising incidence of early-onset colorectal cancer — a call to action
Akimoto, N., Ugai, T., Zhong, R., Hamada, T., Fujiyoshi, K., Giannakis, M., Wu, K., Cao, Y., Ng, K., & Ogino, S. (2020) · Nature Reviews Clinical Oncology · doi:10.1038/s41571-020-00445-1 · Cited by 771
Gut microbiota in colorectal cancer development and therapy
Wong, C. C., & Yu, J. (2023) · Nature Reviews Clinical Oncology · doi:10.1038/s41571-023-00766-x · Cited by 779
Romano, S., Savva, G. M., Bedarf, J. R., Charles, I. G., Hildebrand, F., & Narbad, A. (2021) · npj Parkinson's Disease · doi:10.1038/s41531-021-00156-z · Cited by 707
Cullin, N., Azevedo Antunes, C., Straussman, R., Stein-Thoeringer, C. K., & Elinav, E. (2021) · Cancer Cell · doi:10.1016/j.ccell.2021.08.006 · Cited by 578
The Intestinal Microbiota and Colorectal Cancer
Cheng, Y., Ling, Z., & Li, L. (2020) · Frontiers in Immunology · doi:10.3389/fimmu.2020.615056 · Cited by 609
Federici, S., Kredo-Russo, S., Valdés-Mas, R., Kviatcovsky, D., Weinstock, E., Matiuhin, Y., Silberberg, Y., Atarashi, K., Furuichi, M., Oka, A., et al. (2022) · Cell · doi:10.1016/j.cell.2022.07.003 · Cited by 542
Reporting guidelines for human microbiome research: the STORMS checklist
Mirzayi, C. A., Renson, A., Massive Analysis and Quality Control Society, Furlanello, C., Sansone, S., Zohra, F., Elsafoury, S., Geistlinger, L., Kasselman, L. J., Eckenrode, K. B., et al. (2021) · Nature Medicine · doi:10.1038/s41591-021-01552-x · Cited by 587
Self-citationSignaling pathways involved in colorectal cancer: pathogenesis and targeted therapy
Li, Q., Geng, S., Luo, H., Wang, W., Mo, Y.-Q., Luo, Q., Wang, L., Song, G.-B., Sheng, J.-P., & Xu, B. (2024) · Signal Transduction and Targeted Therapy · doi:10.1038/s41392-024-01953-7 · Cited by 546
Lee, K. A., Thomas, A. M., Bolte, L. A., Björk, J. R., de Ruijter, L. K., Armanini, F., Asnicar, F., Blanco-Miguez, A., Board, R., Calbet-Llopart, N., et al. (2022) · Nature Medicine · doi:10.1038/s41591-022-01695-5 · Cited by 464
Self-citationNext-generation sequencing: insights to advance clinical investigations of the microbiome
Wensel, C. R., Pluznick, J. L., Salzberg, S. L., & Sears, C. L. (2022) · Journal of Clinical Investigation · doi:10.1172/jci154944 · Cited by 437
Host–microbiota maladaptation in colorectal cancer
Janney, A., Powrie, F., & Mann, E. H. (2020) · Nature · doi:10.1038/s41586-020-2729-3 · Cited by 445
The Bacterial Connection between the Oral Cavity and the Gut Diseases
Kitamoto, S., Nagao‐Kitamoto, H., Hein, R., Schmidt, T. M., & Kamada, N. (2020) · Journal of Dental Research · doi:10.1177/0022034520924633 · Cited by 474
The role of farnesoid X receptor in metabolic diseases, and gastrointestinal and liver cancer
Sun, L., Cai, J., & Gonzalez, F. J. (2021) · Nature Reviews Gastroenterology & Hepatology · doi:10.1038/s41575-020-00404-2 · Cited by 459
Colorectal Cancer: Epidemiology, Risk Factors, and Prevention
Roshandel, G., Ghasemi‐Kebria, F., & Malekzadeh, R. (2024) · Cancers · doi:10.3390/cancers16081530 · Cited by 476
Metagenome-wide association of gut microbiome features for schizophrenia
Zhu, F., Ju, Y., Wang, W., Wang, Q., Guo, R., Ma, Q., Sun, Q., Fan, Y., Xie, Y., Yang, Z., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-15457-9 · Cited by 409
Marcos-Zambrano, L. J., Karađuzović-Hadžiabdić, K., Lončar-Turukalo, T., Przymus, P., Trajkovik, V., Aasmets, O., Berland, M., Gruca, A., Telalović, J. H., Hron, K., et al. (2021) · Frontiers in Microbiology · doi:10.3389/fmicb.2021.634511 · Cited by 447
Unravelling the collateral damage of antibiotics on gut bacteria
Maier, L., Goemans, C., Wirbel, J., Kuhn, M., Eberl, C., Pruteanu, M., Müller, P., García‐Santamarina, S., Cacace, E., Zhang, B., et al. (2021) · Nature · doi:10.1038/s41586-021-03986-2 · Cited by 405
Self-citationKang, X., Liu, C., Ding, Y., Ni, Y., Ji, F., Lau, H. C. H., Jiang, L., Sung, J. J., Wong, S. H., & Yu, J. (2023) · Gut · doi:10.1136/gutjnl-2023-330291 · Cited by 394
Fusobacterium nucleatum, a key pathogenic factor and microbial biomarker for colorectal cancer
Wang, N., & Fang, J. (2022) · Trends in Microbiology · doi:10.1016/j.tim.2022.08.010 · Cited by 405
The role of gut microbiota in cancer treatment: friend or foe?
Cheng, W. Y., Wu, C.-Y., & Yu, J. (2020) · Gut · doi:10.1136/gutjnl-2020-321153 · Cited by 384
The Healthy Microbiome—What Is the Definition of a Healthy Gut Microbiome?
Shanahan, F., Ghosh, T. S., & O’Toole, P. W. (2021) · Gastroenterology · doi:10.1053/j.gastro.2020.09.057 · Cited by 383
A predictive index for health status using species-level gut microbiome profiling
Gupta, V. K., Kim, M., Bakshi, U., Cunningham, K. Y., Davis, J. M., Lazaridis, K. N., Nelson, H., Chia, N., & Sung, J. (2020) · Nature Communications · doi:10.1038/s41467-020-18476-8 · Cited by 338
Bacteria in cancer initiation, promotion and progression
Tekle, G. E., & Garrett, W. S. (2023) · Nature reviews. Cancer · doi:10.1038/s41568-023-00594-2 · Cited by 361
Advancing functional and translational microbiome research using meta-omics approaches
Zhang, X., Li, L., Butcher, J., Stintzi, A., & Figeys, D. (2019) · Microbiome · doi:10.1186/s40168-019-0767-6 · Cited by 357
Liu, N.-N., Jiao, N., Tan, J.-C., Wang, Z., Wu, D., Wang, A.-J., Chen, J., Tao, L., Zhou, C., Fang, W., et al. (2022) · Nature Microbiology · doi:10.1038/s41564-021-01030-7 · Cited by 306
Gut microbiome, big data and machine learning to promote precision medicine for cancer
Cammarota, G., Ianiro, G., Ahern, A., Carbone, C., Temko, A., Claesson, M. J., Gasbarrini, A., & Tortora, G. (2020) · Nature Reviews Gastroenterology & Hepatology · doi:10.1038/s41575-020-0327-3 · Cited by 324
MicrobiotaProcess: A comprehensive R package for deep mining microbiome
Xu, S., Zhan, L., Tang, W., Dai, Z., Zhou, L., Feng, T., Chen, M., Liu, S., Wu, T., Hu, E., et al. (2023) · The Innovation · doi:10.1016/j.xinn.2023.100388 · Cited by 312
Cong, J., Liu, P., Han, Z., Ying, W., Li, C., Yang, Y., Wang, S., Yang, J., Cao, F., Shen, J., et al. (2024) · Immunity · doi:10.1016/j.immuni.2024.02.014 · Cited by 333
A faecal microbiota signature with high specificity for pancreatic cancer
Kartal, E., Schmidt, T. S. B., Molina-Montes, E., Rodríguez-Perales, S., Wirbel, J., Maistrenko, O. M., Akanni, W. A., Alashkar Alhamwe, B., Alves, R. J., Carrato, A., et al. (2022) · Gut · doi:10.1136/gutjnl-2021-324755 · Cited by 290
Self-citationBell, H. N., Rebernick, R. J., Goyert, J. W., Singhal, R., Kuljanin, M., Kerk, S. A., Huang, W., Das, N. K., Andren, A. C., Solanki, S. A., et al. (2021) · Cancer Cell · doi:10.1016/j.ccell.2021.12.001 · Cited by 310
Genome-scale metabolic reconstruction of 7,302 human microorganisms for personalized medicine
Heinken, A., Hertel, J., Acharya, G., Ravcheev, D. A., Nyga, M., Okpala, O. E., Hogan, M., Magnúsdóttir, S., Martinelli, F., Nap, B., et al. (2023) · Nature Biotechnology · doi:10.1038/s41587-022-01628-0 · Cited by 310
Ning, L., Zhou, Y., Sun, H. L., Zhang, Y., Shen, C., Wang, Z., Xuan, B., Zhao, Y., Ma, Y., Yan, Y., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-42788-0 · Cited by 334
Topçuoğlu, B. D., Lesniak, N. A., Ruffin, M. T., Wiens, J., & Schloss, P. D. (2020) · mBio · doi:10.1128/mbio.00434-20 · Cited by 295
Dietary fat, bile acid metabolism and colorectal cancer
Ocvirk, S., & O’Keefe, S. J. (2020) · Seminars in Cancer Biology · doi:10.1016/j.semcancer.2020.10.003 · Cited by 266
Machine learning for microbiologists
Asnicar, F., Thomas, A. M., Passerini, A., Waldron, L., & Segata, N. (2023) · Nature Reviews Microbiology · doi:10.1038/s41579-023-00984-1 · Cited by 284
Self-citationGut bacteria identified in colorectal cancer patients promote tumourigenesis via butyrate secretion
Okumura, S., Konishi, Y., Narukawa, M., Sugiura, Y., Yoshimoto, S., Arai, Y., Sato, S., Yoshida, Y., Tsuji, S., Uemura, K., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-25965-x · Cited by 273
Wirbel, J., Zych, K., Essex, M., Karcher, N., Kartal, E., Salazar, G., Bork, P., Sunagawa, S., & Zeller, G. (2021) · Genome Biology · doi:10.1186/s13059-021-02306-1 · Cited by 269
Self-citationIdentification of microbial markers across populations in early detection of colorectal cancer
Wu, Y., Jiao, N., Zhu, R., Zhang, Y., Wu, D., Wang, A.-J., Fang, S., Tao, L., Li, Y., Cheng, S., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-23265-y · Cited by 266
Intratumoural microbiota: a new frontier in cancer development and therapy
Cao, Y., Xia, H., Tan, X., Shi, C., Ma, Y., Meng, D., Zhou, M., Lv, Z., Wang, S., & Jin, Y. (2024) · Signal Transduction and Targeted Therapy · doi:10.1038/s41392-023-01693-0 · Cited by 269
Zhang, Z., Tang, H., Chen, P., Xie, H., & Tao, Y. (2019) · Signal Transduction and Targeted Therapy · doi:10.1038/s41392-019-0074-5 · Cited by 263
Rethinking healthy eating in light of the gut microbiome
Armet, A. M., Deehan, E. C., O’Sullivan, A. F., Mota, J. F., Field, C. J., Prado, C. M., Lucey, A. J., & Walter, J. (2022) · Cell Host & Microbe · doi:10.1016/j.chom.2022.04.016 · Cited by 252
A core microbiome signature as an indicator of health
Wu, G., Xu, T., Zhao, N., Lam, Y. Y., Ding, X., Wei, D., Fan, J., Shi, Y., Li, X., Li, M., et al. (2024) · Cell · doi:10.1016/j.cell.2024.09.019 · Cited by 250
A comprehensive framework for early-onset colorectal cancer research
Eng, C., Jacome, A. A. D. A., Agarwal, R., Hayat, M. H., Byndloss, M. X., Holowatyj, A. N., Bailey, C., & Lieu, C. H. (2022) · The Lancet Oncology · doi:10.1016/s1470-2045(21)00588-x · Cited by 264
Commensal microbiota from patients with inflammatory bowel disease produce genotoxic metabolites
Cao, Y., Oh, J., Xue, M., Huh, W. J., Wang, J., González-Hernández, J. A., Rice, T., Martin, A. L., Song, D., Crawford, J. M., et al. (2022) · Science · doi:10.1126/science.abm3233 · Cited by 259
Microbiome-based interventions to modulate gut ecology and the immune system
Hitch, T. C. A., Hall, L. J., Walsh, S. K., Leventhal, G. E., Slack, E. M. C., de Wouters, T., Walter, J., & Clavel, T. (2022) · Mucosal Immunology · doi:10.1038/s41385-022-00564-1 · Cited by 268
Microbiota Metabolites in Health and Disease
McCarville, J. L., Chen, G. Y., Cuevas, V. D., Troha, K., & Ayres, J. S. (2020) · Annual Review of Immunology · doi:10.1146/annurev-immunol-071219-125715 · Cited by 255
Rühlemann, M. C., Hermes, B. M., Bang, C., Doms, S., Moitinho‐Silva, L., Thingholm, L. B., Frost, F., Degenhardt, F. C., Wittig, M., Kässens, J. C., et al. (2021) · Nature Genetics · doi:10.1038/s41588-020-00747-1 · Cited by 252
Adjusting for age improves identification of gut microbiome alterations in multiple diseases
Ghosh, T. S., Das, M., Jeffery, I. B., & O'Toole, P. W. (2020) · eLife · doi:10.7554/elife.50240 · Cited by 233
Scorletti, E., Afolabi, P. R., Miles, E. A., Smith, D. E., Almehmadi, A., Alshathry, A., Childs, C. E., Del Fabbro, S., Bilson, J., Moyses, H. E., et al. (2020) · Gastroenterology · doi:10.1053/j.gastro.2020.01.031 · Cited by 237
A collection of bacterial isolates from the pig intestine reveals functional and taxonomic diversity
Wylensek, D., Hitch, T. C. A., Riedel, T., Afrizal, A., Kumar, N., Wortmann, E., Liu, T., Devendran, S., Lesker, T. R., Hernández, S. B., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-19929-w · Cited by 238
Self-citationBaldini, F., Hertel, J., Sandt, E., Thinnes, C. C., Neuberger-Castillo, L., Pavelka, L., Betsou, F., Krüger, R., Thiele, I., Aguayo, G., et al. (2020) · BMC Biology · doi:10.1186/s12915-020-00775-7 · Cited by 229
Metabolic syndrome, metabolic comorbid conditions and risk of early-onset colorectal cancer
Chen, H., Zheng, X., Zong, X., Li, Z., Li, N., Hur, J., Fritz, C. D. L., Chapman, W. C., Nickel, K. B., Tipping, A. D., et al. (2020) · Gut · doi:10.1136/gutjnl-2020-321661 · Cited by 238
Nagata, N., Nishijima, S., Kojima, Y., Hisada, Y., Imbe, K., Miyoshi-Akiyama, T., Suda, W., Kimura, M., Aoki, R., Sekine, K., et al. (2022) · Gastroenterology · doi:10.1053/j.gastro.2022.03.054 · Cited by 209
Self-citationMorton, J. T., Jin, D.-M., Mills, R. H., Shao, Y., Rahman, G., McDonald, D. T., Zhu, Q., Balaban, M., Jiang, Y., Cantrell, K., et al. (2023) · Nature Neuroscience · doi:10.1038/s41593-023-01361-0 · Cited by 246
Colorectal cancer-associated microbiota contributes to oncogenic epigenetic signatures
Sobhani, I., Bergsten, E., Couffin, S., Amiot, A., Nebbad, B., Barau, C., de’Angelis, N., Rabot, S., Canouï‐Poitrine, F., Mestivier, D., et al. (2019) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1912129116 · Cited by 221
Xia, Y. (2020) · Progress in molecular biology and translational science · doi:10.1016/bs.pmbts.2020.04.003 · Cited by 239
Colorectal Cancer: From Risk Factors to Oncogenesis
Ionescu, V. A., Gheorghe, G., Bacalbaşa, N., Chiotoroiu, A. L., & Diaconu, C. C. (2023) · Medicina · doi:10.3390/medicina59091646 · Cited by 225
Pan, S., Zhao, X., & Coelho, L. P. (2023) · Bioinformatics · doi:10.1093/bioinformatics/btad209 · Cited by 227
Self-citationGut Bacteriophage: Current Understanding and Challenges
Sutton, T., & Hill, C. (2019) · Frontiers in Endocrinology · doi:10.3389/fendo.2019.00784 · Cited by 199
Utilizing the gut microbiome in decompensated cirrhosis and acute-on-chronic liver failure
Trebicka, J., Bork, P., Krag, A. A., & Arumugam, M. (2020) · Nature Reviews Gastroenterology & Hepatology · doi:10.1038/s41575-020-00376-3 · Cited by 204
Self-citationCommensal Clostridiales strains mediate effective anti-cancer immune response against solid tumors
Montalban‐Arques, A., Katkeviciutė, E., Busenhart, P., Bircher, A., Wirbel, J., Zeller, G., Morsy, Y., Borsig, L., Garzon, J. F. G., Mueller, A., et al. (2021) · Cell Host & Microbe · doi:10.1016/j.chom.2021.08.001 · Cited by 200
Self-citationPan, S., Zhu, C., Zhao, X., & Coelho, L. P. (2022) · Nature Communications · doi:10.1038/s41467-022-29843-y · Cited by 203
Self-citationWestern diets and chronic diseases
Adolph, T. E., & Tilg, H. (2024) · Nature Medicine · doi:10.1038/s41591-024-03165-6 · Cited by 224
Sharpton, S. R., Schnabl, B., Knight, R., & Loomba, R. (2021) · Cell Metabolism · doi:10.1016/j.cmet.2020.11.010 · Cited by 194
Dahiya, D., & Nigam, P. S. N. (2023) · International Journal of Molecular Sciences · doi:10.3390/ijms24043074 · Cited by 223
Applications of organoids for cancer biology and precision medicine
Lo, Y.-H., Karlsson, K., & Kuo, C. J. (2020) · Nature Cancer · doi:10.1038/s43018-020-0102-y · Cited by 182
Another renaissance for bile acid gastrointestinal microbiology
Ridlon, J. M., & Gaskins, H. R. (2024) · Nature Reviews Gastroenterology & Hepatology · doi:10.1038/s41575-024-00896-2 · Cited by 205
Osman, M. A., Neoh, H., Mutalib, N. A., Chin, S., Mazlan, L., Ali, R. A. R., Zakaria, A. D., Ngiu, C. S., Ang, M. Y., & Jamal, R. (2021) · Scientific Reports · doi:10.1038/s41598-021-82465-0 · Cited by 190
Radiotherapy and the gut microbiome: facts and fiction
Liu, J., Liu, C., & Yue, J. (2021) · Radiation Oncology · doi:10.1186/s13014-020-01735-9 · Cited by 194
Nguyen, L. H., Ma, W., Wang, D. D., Cao, Y., Mallick, H., Gerbaba, T. K., Lloyd‐Price, J., Abu-Ali, G., Hall, A. B., Sikavi, D. R., et al. (2020) · Gastroenterology · doi:10.1053/j.gastro.2019.12.029 · Cited by 186
Dai, D., Zhu, J., Sun, C., Li, M., Liu, J., Wu, S., Ning, K., He, L., Zhao, X., & Chen, W.-H. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkab1019 · Cited by 182
Iftekhar, A., Berger, H., Bouznad, N., Heuberger, J., Boccellato, F., Dobrindt, U., Hermeking, H., Sigal, M. J., & Meyer, T. F. (2021) · Nature Communications · doi:10.1038/s41467-021-21162-y · Cited by 188
Gut Microbial Signatures Can Discriminate Unipolar from Bipolar Depression
Zheng, P., Yang, J., Li, Y., Wu, J., Liang, W., Yin, B., Tan, X., Huang, Y., Chai, T., Zhang, H., et al. (2020) · Advanced Science · doi:10.1002/advs.201902862 · Cited by 177
Genetic manipulation of gut microbes enables single-gene interrogation in a complex microbiome
Jin, W., Li, T., Huo, D., Qu, S., Li, X. V., Arifuzzaman, M., Lima, S. F., Shi, H., Wang, A., Putzel, G., et al. (2022) · Cell · doi:10.1016/j.cell.2021.12.035 · Cited by 183
LaCourse, K. D., Zepeda‐Rivera, M. A., Kempchinsky, A. G., Baryiames, A. A., Minot, S. S., Johnston, C. D., & Bullman, S. (2022) · Cell Reports · doi:10.1016/j.celrep.2022.111625 · Cited by 179
Utilization of the microbiome in personalized medicine
Ratiner, K., Ciocan, D. M., Abdeen, S. K., & Elinav, E. (2023) · Nature Reviews Microbiology · doi:10.1038/s41579-023-00998-9 · Cited by 189
The microbial landscape of colorectal cancer
White, M., & Sears, C. L. (2023) · Nature Reviews Microbiology · doi:10.1038/s41579-023-00973-4 · Cited by 173
Karcher, N., Nigro, E., Punčochář, M., Blanco-Míguez, A., Ciciani, M., Manghi, P., Zolfo, M., Cumbo, F., Manara, S., Golzato, D., et al. (2021) · Genome Biology · doi:10.1186/s13059-021-02427-7 · Cited by 159
Self-citationAgudelo-Ochoa, G. M., Valdés-Duque, B. E., Giraldo-Giraldo, N. A., Jaillier-Ramírez, A. M., Giraldo-Villa, A., Acevedo-Castaño, I., Yepes-Molina, M. A., Barbosa-Barbosa, J., & Benítez-Paéz, A. (2020) · Gut Microbes · doi:10.1080/19490976.2019.1707610 · Cited by 166
Molecular mechanisms of postbiotics in colorectal cancer prevention and treatment
Rad, A. H., Maleki, L. A., Kafil, H. S., & Abbasi, A. (2020) · Critical Reviews in Food Science and Nutrition · doi:10.1080/10408398.2020.1765310 · Cited by 172
Influence of gastrectomy for gastric cancer treatment on faecal microbiome and metabolome profiles
Erawijantari, P. P., Mizutani, S., Shiroma, H., Shiba, S., Nakajima, T., Sakamoto, T., Saito, Y., Fukuda, S., Yachida, S., & Yamada, T. (2020) · Gut · doi:10.1136/gutjnl-2019-319188 · Cited by 168
Self-citationMa, S., Shungin, D., Mallick, H., Schirmer, M., Nguyen, L. H., Kolde, R., Franzosa, E., Vlamakis, H., Xavier, R., & Huttenhower, C. (2022) · Genome biology · doi:10.1186/s13059-022-02753-4 · Cited by 164
Gut Microbiota in Colorectal Cancer: Biological Role and Therapeutic Opportunities
Pandey, H., Tang, D. W. T., Wong, S. H., & Lal, D. (2023) · Cancers · doi:10.3390/cancers15030866 · Cited by 171
Armour, C. R., Nayfach, S., Pollard, K. S., & Sharpton, T. J. (2019) · mSystems · doi:10.1128/msystems.00332-18 · Cited by 163
GMrepo: a database of curated and consistently annotated human gut metagenomes
Wu, S., Sun, C., Li, Y., Wang, T., Jia, L., Lai, S., Yang, Y., Luo, P., Dai, D., Yang, Y.-Q., et al. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz764 · Cited by 158
Metadata
- Authors
- Wirbel, J., Pyl, P. T., Kartal, E., Zych, K., Kashani, A., Milanese, A., Fleck, J. S., Voigt, A. Y., Palleja, A., Ponnudurai, R., Sunagawa, S., Coelho, L. P., Schrotz-King, P., Vogtmann, E., Habermann, N., Niméus, E., Thomas, A. M., Manghi, P., Gandini, S., Serrano, D., Mizutani, S., Shiroma, H., Shiba, S., Shibata, T., Yachida, S., Yamada, T., Waldron, L., Naccarati, A., Segata, N., Sinha, R., Ulrich, C. M., Brenner, H., Arumugam, M., Bork, P., & Zeller, G.
- Affiliations
- European Molecular Biology Laboratory (DE)
- University of Copenhagen (DK)
- ETH Zurich (CH)
- Shanghai Medical College of Fudan University (CN)
- National Cancer Institute (US)
- Lund University (SE)
- Universidade de São Paulo (BR)
- University of Trento (IT)
- European Institute of Oncology (IT)
- Tokyo Institute of Technology (JP)
- National Cancer Center Research Institute (JP)
- Institute of Medical Science, The University of Tokyo (JP)
- City University of New York (US)
- Italian institute for Genomic Medicine (IT)
- University of Utah (US)
- German Cancer Research Center (DE)
- Corresponding author
- Arumugam, Manimozhiyan
- Zeller, Georg
- ORCID
- Wirbel, Jakob
- Pyl, Paul Theodor
- Kartal, Ece
- Zych, Konrad
- Milanese, Alessio
- Fleck, Jonas S.
- Voigt, Anita Y.
- Palleja, Albert
- Sunagawa, Shinichi
- Coelho, Luis Pedro
- Schrotz-King, Petra
- Vogtmann, Emily
- Niméus, Emma
- Thomas, Andrew M.
- Manghi, Paolo
- Gandini, Sara
- Serrano, Davide
- Mizutani, Sayaka
- Shiroma, Hirotsugu
- Shiba, Satoshi
- Shibata, Tatsuhiro
- Yachida, Shinichi
- Yamada, Takuji
- Waldron, Levi
- Naccarati, Alessio
- Segata, Nicola
- Sinha, Rashmi
- Ulrich, Cornelia M.
- Brenner, Hermann
- Arumugam, Manimozhiyan
- Bork, Peer
- Zeller, Georg
- Venue
- Nature Medicine
- Published
- 2019-04
- Volume
- 25
- Issue
- 4
- Pages
- 679-689
- ISSN
- 1078-8956 (ISSN-L)
- 1546-170X
- PMC
- PMC7984229
- OpenAlex
- W2927453907
- Semantic Scholar
- 62b9cf8262232a54b36b08e6822fc0e815ce909a
- Cited by
- 1,373
- References
- 85
- Citations by year
- 2026: 214 · 2025: 215 · 2024: 224 · 2023: 189 · 2022: 176 · 2021: 169 · 2020: 143 · 2019: 41
- FWCI
- 11.74
- Type
- journal article
- Language
- en
- Open access
- Licence
- other-oa
- www.springer.com/tdm (tdm)
- Locations
- Nature Medicine (publishedVersion)
- PubMed (publishedVersion)
- Research at the University of Copenhagen (University of Copenhagen) (publishedVersion, other-oa)
- University of Southern Denmark Research Portal (University of Southern Denmark) (publishedVersion, other-oa)
- PubMed Central (acceptedVersion)
- Iris (University of Trento) (submittedVersion, other-oa)
- MDC Repository (Max-Delbrueck-Center for Molecular Medicine) (submittedVersion)
- QUT ePrints (Queensland University of Technology) (submittedVersion)
- Lund University Publications (Lund University) (submittedVersion)
- The Mouseion at the JAXlibrary (Jackson Laboratory) (submittedVersion)
- Funders
- Deutsches Krebsforschungszentrum
- Huntsman Cancer Foundation
- Eidgenössische Technische Hochschule Zürich
- Novo Nordisk
- Helmut Horten Stiftung
- National Institutes of Health
- Japan Society for the Promotion of Science (16H06279, 18K15800)
- National Cancer Institute (R01CA189184, R01CA207371, ZIACP010198, P30CA042014, U01CA206110)
- H2020 European Research Council (669830, 716575)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Health Sciences › Medicine › Infectious Diseases › Clostridium difficile and Clostridium perfringens research
- Health Sciences › Medicine › Oncology › Colorectal Cancer Treatments and Studies
- Keywords
- colorectal cancer, gut microbiota, fecal metagenome, microbial signatures, cross-study comparison, protein degradation, carbohydrate degradation, secondary bile acids, cancer diagnosis
- MeSH terms
- Gastrointestinal Microbiome, Adenoma, Aged, Feces, Female, Humans, Male, Middle Aged, Models, Biological, Species Specificity, Biomarkers, Tumor, Colorectal Neoplasms, Reproducibility of Results, Cohort Studies, Databases, Genetic, 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
