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
Items 401–500 of 998
Outer membrane vesicles in gram-negative bacteria and its correlation with pathogenesis
Abolhasani, F. S., Vaghefinanekaran, N., Yarahmadi, A., Akrami, S., Mirmahdavi, S., Yousefi, M. H., Afkhami, H., & Shafiei, M. (2025) · Frontiers in Immunology · doi:10.3389/fimmu.2025.1541636 · Cited by 33
Grobbee, E. J., Lam, S. Y., Fuhler, G. M., Blakaj, B., Konstantinov, S. R., Bruno, M. J., Peppelenbosch, M. P., Kuipers, E. J., & Spaander, M. C. W. (2019) · United European Gastroenterology Journal · doi:10.1177/2050640619890732 · Cited by 42
Pan, H., Du, L., Li, W., Yang, Y., Zhang, Y., & Wang, C. (2020) · Research in Microbiology · doi:10.1016/j.resmic.2020.01.001 · Cited by 32
Seyfried, F., Phetcharaburanin, J., Glymenaki, M., Nordbeck, A., Hankir, M. K., Nicholson, J. K., Holmes, E. C., Marchesi, J. R., & Li, J. V. (2021) · Gut Microbes · doi:10.1080/19490976.2021.1875108 · Cited by 33
Eisele, Y., Mallea, P. M., Gigic, B., Stephens, W. Z., Warby, C. A., Buhrke, K., Lin, T., Boehm, J., Schrotz‐King, P., Hardikar, S. S., et al. (2021) · Clinical Colorectal Cancer · doi:10.1016/j.clcc.2021.02.007 · Cited by 32
Self-citationGastrectomy impact on the gut microbiome in patients with gastric cancer: A comprehensive review
Maksimaityte, V., Baušys, A., Kryžauskas, M., Lukšta, M., Stundienė, I., Bičkaitė, K., Baušys, B., Poškus, T., Baušys, R., & Strupas, K. (2021) · World Journal of Gastrointestinal Surgery · doi:10.4240/wjgs.v13.i7.678 · Cited by 32
Casimiro‐Soriguer, C. S., Loucera, C., Peña-Chilet, M., & Dopazo, J. (2022) · Scientific Reports · doi:10.1038/s41598-021-04182-y · Cited by 38
Shen, J., Li, P., Liu, S., Liu, Q., Li, Y., Zhang, Z., Yang, C., Hu, M., Sun, Y., He, C., et al. (2020) · Food & Function · doi:10.1039/d0fo01731k · Cited by 31
Bile acid distributions, sex-specificity, and prognosis in colorectal cancer
Cai, Y. A., Shen, X., Lu, L., Yan, H. Y., Huang, H., Gaule, P., Muca, E., Theriot, C. M., Rattray, Z., Rattray, N. J. W., et al. (2022) · Biology of Sex Differences · doi:10.1186/s13293-022-00473-9 · Cited by 32
Wirbel, J., Zych, K., Essex, M., Karcher, N., Kartal, E., Salazar, G., Peer Bork, B., Sunagawa, S., & Zeller, G. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.02.06.931808 · Cited by 33
Self-citationObón‐Santacana, M., Mas-Lloret, J., Bars‐Cortina, D., Criado‐Mesas, L., Carreras‐Torres, R., Díez-Villanueva, A., Moratalla-Navarro, F., Guinó, E., Ibáñez‐Sanz, G., Alonso, L. R., et al. (2022) · Cancers · doi:10.3390/cancers14174214 · Cited by 31
Gut Microbiome–Colorectal Cancer Relationship
Yadav, D., Sainatham, C., Filippov, E., Kanagala, S. G., Ishaq, S. M., & Jayakrishnan, T. (2024) · Microorganisms · doi:10.3390/microorganisms12030484 · Cited by 33
Tian, K., Jing, D., Lan, J., Lv, M., & Wang, T. (2024) · Immunity Inflammation and Disease · doi:10.1002/iid3.1316 · Cited by 35
Nooij, S., Plomp, N., Sanders, I. M. J. G., Schout, L., van der Meulen, A. E., Terveer, E. M., Norman, J. M., Karcher, N., Larralde, M., Vossen, R. H. A. M., et al. (2025) · Nature Communications · doi:10.1038/s41467-025-56449-x · Cited by 35
Self-citationPersonalized colorectal cancer risk assessment through explainable AI and Gut microbiome profiling
Novielli, P., Baldi, S., Romano, D., Magarelli, M., Diacono, D., Bitonto, P. D., Nannini, G., Gloria, L. D., Bellotti, R., Amedei, A., et al. (2025) · Gut Microbes · doi:10.1080/19490976.2025.2543124 · Cited by 34
Bikaeva, I., Popenko, A., Klimenko, N. S., Игоревич, К. С., Chuprikova, L., Филипенко, М. Л., Tyakht, A., & Alexeev, D. G. (2020) · Molecular and Cellular Probes · doi:10.1016/j.mcp.2020.101570 · Cited by 36
Method development for cross-study microbiome data mining: Challenges and opportunities
Su, X., Jing, G., Zhang, Y., & Wu, S. (2020) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2020.07.020 · Cited by 31
de Jesus, V. C., Khan, M. W., Mittermuller, B.-A., Duan, K., Hu, P., Schroth, R. J., & Chelikani, P. (2021) · Frontiers in Microbiology · doi:10.3389/fmicb.2021.683685 · Cited by 32
Robust cross-cohort gut microbiome associations with COVID-19 severity
Li, J., Ghosh, T. S., MacCann, R., Mallon, P. W. G., Hill, C., Draper, L. A., Schult, D., Fanning, L. J., Shannon, R., Sadlier, C., et al. (2023) · Gut Microbes · doi:10.1080/19490976.2023.2242615 · Cited by 32
Liu, C., Li, Z., Ding, J., Zhen, H., Fang, M., & Nie, C. (2021) · Frontiers in Microbiology · doi:10.3389/fmicb.2021.765291 · Cited by 31
Mutignani, M., Penagini, R., Gargari, G., Guglielmetti, S., Cintolo, M., Airoldi, A., Leone, P., Carnevali, P., Ciafardini, C., Petrocelli, G., et al. (2021) · Cancers · doi:10.3390/cancers13246363 · Cited by 34
Privitera, G., Rana, N., Scaldaferri, F., Armuzzi, A., & Pizarro, T. T. (2022) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2021.806680 · Cited by 30
Tumour microbiomes and Fusobacterium genomics in Vietnamese colorectal cancer patients
Tran, H. N. H., Thu, T. N. H., Nguyen, P. H., Vo, C. N., Doan, K. V., Minh, C. N. N., Nguyễn, N. T., Ta, V. N. D., Vu, K. A., Hua, T. D., et al. (2022) · npj Biofilms and Microbiomes · doi:10.1038/s41522-022-00351-7 · Cited by 31
van Elsland, D. M., Duijster, J. W., Zhang, J., Stévenin, V., Zhang, Y., Zha, L., Xia, Y., Franz, E., Sun, J., Mughini‐Gras, L., et al. (2022) · Cell Reports Medicine · doi:10.1016/j.xcrm.2022.100852 · Cited by 31
How Diet and Lifestyle Can Fine-Tune Gut Microbiomes for Healthy Aging
Tamayo, M., Olivares, M., Ruas‐Madiedo, P., Margollés, A., Espı́n, J. C., Medina, I., Moreno-Arribas, M. V., Canals, S., Mirasso, C. R., Ortín, S., et al. (2024) · Annual Review of Food Science and Technology · doi:10.1146/annurev-food-072023-034458 · Cited by 33
Zhang, C., Wang, Y., Cheng, L., Cao, X., & Liu, C. (2025) · Frontiers in Oncology · doi:10.3389/fonc.2025.1557959 · Cited by 33
Towards multi-label classification: Next step of machine learning for microbiome research
Wu, S., Chen, Y., Li, Z., Li, J., Zhao, F., & Su, X. (2021) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2021.04.054 · Cited by 29
Molina‐Vega, M., César, M. J. P., Gutiérrez‐Repiso, C., Fernández‐Valero, A., Lima-Rubio, F., González‐Romero, S., Moreno‐Indias, I., & Tinahones, F. J. (2021) · Biomedicine & Pharmacotherapy · doi:10.1016/j.biopha.2021.112465 · Cited by 29
Löwenmark, T., Li, X., Löfgren‐Burström, A., Zingmark, C., Ling, A., Kellgren, T. G., Larsson, P. G., Ljuslinder, I., Wai, S. N., Edin, S., et al. (2022) · Cancer Immunology Immunotherapy · doi:10.1007/s00262-022-03179-4 · Cited by 29
The Role of the Microbiome on the Pathogenesis and Treatment of Colorectal Cancer
Yu, I., Wu, R., Tokumaru, Y., Terracina, K. P., & Takabe, K. (2022) · Cancers · doi:10.3390/cancers14225685 · Cited by 30
Löwenmark, T., Löfgren‐Burström, A., Zingmark, C., Ljuslinder, I., Dahlberg, M. L., Edin, S., & Palmqvist, R. (2022) · Cancers · doi:10.3390/cancers14235937 · Cited by 30
Microbiome in Cancer Development and Treatment
Čierniková, S., Ševčíková, A., Mladosievičová, B., & Mego, M. (2023) · Microorganisms · doi:10.3390/microorganisms12010024 · Cited by 29
Richardson, M., Ren, J., Rubinstein, M. R., Taylor, J. A., Friedman, R. A., Shen, B., & Han, Y. W. (2020) · Gut Microbes · doi:10.1080/19490976.2020.1814120 · Cited by 28
Biological invasions alter environmental microbiomes: A meta-analysis
Malacrinò, A., Sadowski, V. A., Martin, T. K., de Oliveira, N. C., Brackett, I. J., Feller, J. D., Harris, K. J., Cómbita-Heredia, O., Vescio, R., & Bennett, A. E. (2020) · PLoS ONE · doi:10.1371/journal.pone.0240996 · Cited by 28
Mulenga, M., Kareem, S. A., Sabri, A. Q. M., & Seera, M. (2021) · IEEE Access · doi:10.1109/access.2021.3094529 · Cited by 27
The gut microbiota and gut disease
Fehily, S. R., Basnayake, C., Wright, E. K., & Kamm, M. A. (2021) · Internal Medicine Journal · doi:10.1111/imj.15520 · Cited by 30
Cheng, K.-W., Tseng, C.-H., Chen, I., Huang, B.-C., Liu, H.-J., Ho, K., Lin, W., Chuang, C.-H., Huang, M., Leu, Y.-L., et al. (2022) · Pharmacological Research · doi:10.1016/j.phrs.2022.106115 · Cited by 28
The potential of fecal microbiota and amino acids to detect and monitor patients with adenoma
Bosch, S., Acharjee, A., Quraishi, M. N., Rojas, P., Bakkali, A., Jansen, E. E. W., Brentar, M. B., Kuijvenhoven, J. P., Stokkers, P. C. F., Struys, E. A., et al. (2022) · Gut Microbes · doi:10.1080/19490976.2022.2038863 · Cited by 28
Giuffrè, M., Moretti, R., & Tiribelli, C. (2023) · International Journal of Molecular Sciences · doi:10.3390/ijms24065229 · Cited by 32
A hidden confounder for microbiome studies: medications used years before sample collection
Aasmets, O., Taba, N., Krigul, K. L., Andreson, R., Estonian Biobank Research Team, Org, E., Metspalu, M., Metspalu, A., Milani, L., & Esko, T. (2025) · mSystems · doi:10.1128/msystems.00541-25 · Cited by 30
Microbiomes, Their Function, and Cancer: How Metatranscriptomics Can Close the Knowledge Gap
Aitmanaitė, L., Širmonaitis, K., & Russo, G. (2023) · International Journal of Molecular Sciences · doi:10.3390/ijms241813786 · Cited by 28
Gut microbiota in colorectal cancer: From pathogenesis to clinic
Fusco, W., Bricca, L., Kaitsas, F., Tartaglia, M., Venturini, I., Rugge, M., Gasbarrini, A., Cammarota, G., & Ianiro, G. (2024) · Best Practice & Research Clinical Gastroenterology · doi:10.1016/j.bpg.2024.101941 · Cited by 32
Wang, K., Lo, C., Mehta, R. S., Nguyen, L. H., Wang, Y., Ma, W., Ugai, T., Kawamura, H., Ugai, S., Takashima, Y., et al. (2024) · Gastroenterology · doi:10.1053/j.gastro.2024.07.040 · Cited by 28
Self-citationRetractedInhibition of autotrophic nitrifiers in a nitrogen-rich paddy soil by elevated CO2
Zhang, K., Lei, W., Zhang, H., Xu, C., Xiao, J., Li, S., Liang, M., He, J., Lai, Y., Li, R., et al. (2024) · Nature Geoscience · doi:10.1038/s41561-024-01583-2 · Cited by 28
Nutrition and gut health: the impact of specific dietary components – it's not just five-a-day
Rhodes, J. M. (2020) · Proceedings of The Nutrition Society · doi:10.1017/s0029665120000026 · Cited by 30
Nutritional Interventions Targeting Gut Microbiota during Cancer Therapies
Rinninella, E., Raoul, P. C., Cintoni, M., Palombaro, M., Pulcini, G., Gasbarrini, A., & Mele, M. C. (2021) · Microorganisms · doi:10.3390/microorganisms9071469 · Cited by 28
Effect of gut microbiota in the colorectal cancer and potential target therapy
Li, J., Zhu, Y., Yang, L., & Wang, Z. (2022) · Discover Oncology · doi:10.1007/s12672-022-00517-x · Cited by 29
Dietrich, A., Matchado, M. S., Zwiebel, M., Ölke, B., Lauber, M., Lagkouvardos, I., Baumbach, J., Haller, D., Brandl, B., Skurk, T., et al. (2022) · Microbial Genomics · doi:10.1099/mgen.0.000852 · Cited by 31
Current understandings of colibactin regulation
Addington, E., Sandalli, S., & Roe, A. J. (2024) · Microbiology · doi:10.1099/mic.0.001427 · Cited by 27
Exploring the Gut Microbiota–Retina Axis: Implications for Health and Disease
Schiavone, N., Isoldi, G., Calcagno, S., Rovida, E., Antiga, E., Almeida, C. V. D., & Lulli, M. (2025) · Microorganisms · doi:10.3390/microorganisms13051101 · Cited by 27
Langheinrich, M. C., Wirtz, S. J., Kneis, B., Gittler, M. M., Tyc, O., Schierwagen, R., Brunner, M., Krautz, C., Weber, G. F., Pilarsky, C. P., et al. (2020) · Journal of Clinical Medicine · doi:10.3390/jcm9092785 · Cited by 27
Sinha, R. R., Zhao, N., Goedert, J. J., Byrd, D. A., Wan, Y., Hua, X., Hullings, A. G., Knight, R. D., van Breda, S. G., Mathijs, K., et al. (2021) · Environmental Research · doi:10.1016/j.envres.2021.111084 · Cited by 28
Self-citationGoelz, H., Wetzel, S., Mehrbarzin, N., Utzolino, S., Häcker, G. A., & Badr, M. T. (2021) · Cells · doi:10.3390/cells10113226 · Cited by 26
Abu-Humaidan, A. H. A., Alrawabdeh, J. A., Theeb, L. S., Hamadneh, Y. I., & Omari, M. B. (2021) · International Journal of Environmental Research and Public Health · doi:10.3390/ijerph182413324 · Cited by 30
The Tissue-Associated Microbiota in Colorectal Cancer: A Systematic Review
da Costa, C. P., Vieira, P. F., Mendes-Rocha, M., Pereira‐Marques, J., Ferreira, R. M., & Figueiredo, C. (2022) · Cancers · doi:10.3390/cancers14143385 · Cited by 29
Silvestri, A., Gil‐Gómez, A., Vitale, M., Braga, D., Demitri, C., Brescia, P., Madaghiele, M., Spadoni, I., Jones, B., Fornasa, G., et al. (2023) · Cell Reports Medicine · doi:10.1016/j.xcrm.2023.101235 · Cited by 28
Xu, Z., Yeoh, Y. K., Tun, H. M., Fei, N., Zhang, J., Morrison, M., Kamm, M. A., Yu, J., Chan, F. K. L., & Ng, S. C. (2024) · Microbiology Spectrum · doi:10.1128/spectrum.01516-24 · Cited by 26
Bosák, J., Lexa, M., Fiedorová, K., Gadara, D. C., Micenková, L., Spáčil, Z., Litzman, J., Freiberger, T., & Šmajs, D. (2021) · Frontiers in Immunology · doi:10.3389/fimmu.2021.671239 · Cited by 24
Next steps after 15 stimulating years of human gut microbiome research
Clavel, T., Horz, H., Segata, N., & Vehreschild, M. J. G. T. (2021) · Microbial Biotechnology · doi:10.1111/1751-7915.13970 · Cited by 26
Self-citationIntestinal microbiota research from a global perspective
Wallenborn, J. T., & Vonaesch, P. (2022) · Gastroenterology report · doi:10.1093/gastro/goac010 · Cited by 26
Yuan, D., Tao, Y., Wang, H., Wang, J., Cao, Y., Cao, G., Pan, S., & Yu, Z. (2022) · Investigational New Drugs · doi:10.1007/s10637-022-01263-1 · Cited by 27
Implication of gut microbes and its metabolites in colorectal cancer
Kumar, A., Ali, A., Kapardar, R. K., Dar, G. M., Nimisha, Apurva, A., Sharma, A. K., Verma, R., Sattar, R. S. A., Ahmad, E., et al. (2022) · Journal of Cancer Research and Clinical Oncology · doi:10.1007/s00432-022-04422-2 · Cited by 26
HIV, Cancer, and the Microbiota: Common Pathways Influencing Different Diseases
Herrera, S., Martínez‐Sanz, J., & Villar, S. S. (2019) · Frontiers in Immunology · doi:10.3389/fimmu.2019.01466 · Cited by 25
Computational Metagenomics: State of the Art
Pita-Galeana, M. A., Ruhle, M., López-Vázquez, L., de Anda‐Jáuregui, G., & Lemus, E. H. (2025) · International Journal of Molecular Sciences · doi:10.3390/ijms26189206 · Cited by 28
Manghi, P., Antonello, G., Schiffer, L., Golzato, D., Wokaty, A., Beghini, F., Mirzayi, C. A., Long, K., Gravel-Pucillo, K., Piccinno, G., et al. (2025) · Nature Communications · doi:10.1038/s41467-025-66888-1 · Cited by 26
Self-citationGut microbiota imbalance in colorectal cancer patients, the risk factor of COVID-19 mortality
Cai, C., Zhang, X., Liu, Y., Shen, E., Feng, Z., Guo, C., Han, Y., Ouyang, Y., & Shen, H. (2021) · Gut Pathogens · doi:10.1186/s13099-021-00466-w · Cited by 23
Polychronidis, G., Siddiqi, H., Ahmed, F. A., Papatheodorou, S., Giovannucci, E. L., & Song, M. (2023) · International Journal of Epidemiology · doi:10.1093/ije/dyad042 · Cited by 27
How Can the Microbiome Induce Carcinogenesis and Modulate Drug Resistance in Cancer Therapy?
Mendes, I., & Vale, N. (2023) · International Journal of Molecular Sciences · doi:10.3390/ijms241411855 · Cited by 24
Gut Microbial Signatures in Sporadic and Hereditary Colorectal Cancer
Mori, G., & Pasca, M. R. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms22031312 · Cited by 28
Topçuoğlu, B. D., Lesniak, N. A., Ruffin, M. T., Wiens, J., & Schloss, P. D. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/816090 · Cited by 26
Smart Microbiomes: How AI Is Revolutionizing Personalized Medicine
Alexandrescu, L., Tofolean, I. T., Condur, L., Tofolean, D. E., Nicoara, A. D., Șerbănescu, L., Rusu, E. E., Twakor, A. N., Dumitru, E., Dumitru, A., et al. (2025) · Bioengineering · doi:10.3390/bioengineering12090944 · Cited by 28
Modeling cancer–microbiome interactions in vitro: A guide to co‐culture platforms
Moskal, K., Khurana, N., Siegert, L., Lee, Y., Clevers, H. C., Elinav, E., & Puschhof, J. (2024) · International Journal of Cancer · doi:10.1002/ijc.35298 · Cited by 24
Austin, G. I., Kav, A. B., ElNaggar, S., Park, H., Biermann, J., Uhlemann, A., Pe’er, I., & Korem, T. (2025) · Nature Microbiology · doi:10.1038/s41564-025-01954-4 · Cited by 24
Schöpf, F., Marongiu, G. L., Milaj, K., Sprink, T., Kikhney, J., Moter, A., & Roderer, D. (2025) · Nature Communications · doi:10.1038/s41467-025-63451-w · Cited by 23
Secondary bile acid production by gut bacteria promotes Western diet-associated colorectal cancer
Oßwald, A., Wortmann, E., Wylensek, D., Kuhls, S., Coleman, O. I., Peuker, K., Strigli, A., Ducarmon, Q. R., Larralde, M., Liang, W., et al. (2025) · Gut · doi:10.1136/gutjnl-2024-332243 · Cited by 33
Self-citationComparative metagenomic analysis of the vaginal microbiome in healthy women
Liu, F., Zhou, Y., Zhu, L., Wang, Z., Ma, L., He, Y., & Fu, P. (2021) · Synthetic and Systems Biotechnology · doi:10.1016/j.synbio.2021.04.002 · Cited by 23
Wolf, P. G., Byrd, D. A., Cares, K., Dai, H., Odoms‐Young, A. M., Gaskins, H. R., Ridlon, J. M., & Tussing-Humphreys, L. M. (2022) · mSystems · doi:10.1128/msystems.01174-21 · Cited by 28
Pozzi, C., Levi, R., Braga, D., Carli, F., Darwich, A., Spadoni, I., Oresta, B., Dioguardi, C. C., Peano, C., Ubaldi, L., et al. (2022) · Gastro Hep Advances · doi:10.1016/j.gastha.2021.12.006 · Cited by 23
Gupta, I., Pedersen, S., Vranić, S., & Moustafa, A. A. (2022) · Cancers · doi:10.3390/cancers14122964 · Cited by 25
Differences in the gut microbiome by physical activity and BMI among colorectal cancer patients.
Himbert, C., Stephens, W. Z., Gigic, B., Hardikar, S. S., Holowatyj, A. N., Lin, T., Ose, J., Swanson, E., Ashworth, A., Warby, C. A., et al. (2022) · PubMed Central · Cited by 24
Self-citationThe Gut Microbiome, Microsatellite Status and the Response to Immunotherapy in Colorectal Cancer
Sillo, T. O., Beggs, A. D., Middleton, G., & Akingboye, A. A. (2023) · International Journal of Molecular Sciences · doi:10.3390/ijms24065767 · Cited by 25
Jie, Z., Zhu, Q., Zou, Y., Wu, Q., Qin, M., He, D., Lin, X., Tong, X., Zhang, J., Zhu, J., et al. (2023) · iScience · doi:10.1016/j.isci.2023.106960 · Cited by 24
Zhu, X., Xu, P., Zhu, R., Gao, W., Yin, W., Lan, P., Zhu, L., & Jiao, N. (2024) · Communications Biology · doi:10.1038/s42003-023-05714-0 · Cited by 25
Epidemiology and early screening strategies for colorectal cancer in China
Yang, Y., Gao, Z., Huang, A., Shi, J., Sun, Z. Z., Hong, H., & Gu, J. (2023) · Chinese Journal of Cancer Research · doi:10.21147/j.issn.1000-9604.2023.06.05 · Cited by 23
Wang, B., Sun, F., & Luan, Y. (2024) · Scientific Reports · doi:10.1038/s41598-024-57670-2 · Cited by 26
Intratumoral and fecal microbiota reveals microbial markers associated with gastric carcinogenesis
Wang, Y., Wang, Y., Han, W., Han, M., Liu, X., Dai, J., Dong, Y., Sun, T., & Xu, J. (2024) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2024.1397466 · Cited by 23
A tale of two bacteria – Bacteroides fragilis, Escherichia coli, and colorectal cancer
Lichtenstern, C. R., & Lamichhane-Khadka, R. (2023) · Frontiers in Bacteriology · doi:10.3389/fbrio.2023.1229077 · Cited by 23
Jin, D.-M., Morton, J. T., & Bonneau, R. (2024) · mSystems · doi:10.1128/msystems.00295-24 · Cited by 27
Mancinetti, F., Marinelli, A., Boccardi, V., & Mecocci, P. (2024) · Mechanisms of Ageing and Development · doi:10.1016/j.mad.2024.111998 · Cited by 25
Wen, Q., Qiu, L., Qiu, C., Che, K., Zeng, R., Wang, X., Cao, P., Xing, L., Yang, Z., & Yu, J. (2025) · Cancer Letters · doi:10.1016/j.canlet.2025.217881 · Cited by 24
Gut microbiome-mediated transformation of dietary phytonutrients is associated with health outcomes
Zhang, L., Marfil-Sánchez, A., Kuo, T.-H., Seelbinder, B., van Dam, L., Depetris-Chauvin, A., Jahn, L. J., Sommer, M. O. A., Zimmermann, M., Ni, Y., et al. (2025) · Nature Microbiology · doi:10.1038/s41564-025-02197-z · Cited by 28
Sadaiappan, B., Prasannakumar, C., Nambiar, U. V., Subramanian, M., & Gauns, M. (2021) · Scientific Reports · doi:10.1038/s41598-021-82482-z · Cited by 22
Serrano, D., Pozzi, C., Guglietta, S., Fosso, B., Suppa, M., Gnagnarella, P., Corso, F., Bellerba, F., Macis, D., Aristarco, V., et al. (2021) · Nutrients · doi:10.3390/nu13020363 · Cited by 24
Self-citationPratt, M., Forbes, J. D., Knox, N., Bernstein, C. N., & Domselaar, G. V. (2021) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2021.716604 · Cited by 23
The crosstalk of the human microbiome in breast and colon cancer: A metabolomics analysis
Mukherjee, A. G., Wanjari, U. R., Bradu, P., Murali, R., Kannampuzha, S., Loganathan, T., Doss, C. G. P., Arun Prakash, B. P., Renu, K., Dey, A., et al. (2022) · Critical Reviews in Oncology/Hematology · doi:10.1016/j.critrevonc.2022.103757 · Cited by 22
Li, J., Gillilland, M. G., Lee, A. A., Wu, X., Zhou, S.-Y., & Owyang, C. (2022) · JCI Insight · doi:10.1172/jci.insight.148309 · Cited by 22
RetractedLamaudière, M. T. F., Arasaradnam, R. P., Weedall, G. D., & Morozov, I. Y. (2023) · mSphere · doi:10.1128/msphere.00626-22 · Cited by 22
Phage Interactions with the Nervous System in Health and Disease
Jędrusiak, A., Fortuna, W., Majewska, J., Górski, A., & Jończyk‐Matysiak, E. (2023) · Cells · doi:10.3390/cells12131720 · Cited by 25
Geistlinger, L., Mirzayi, C. A., Zohra, F., Azhar, R., Elsafoury, S., Grieve, C., Wokaty, J., Gamboa-Tuz, S. D., Sengupta, P., Hecht, I., et al. (2023) · Nature Biotechnology · doi:10.1038/s41587-023-01872-y · Cited by 23
Self-citationPark, R., Umar, S., & Kasi, A. (2020) · Current Colorectal Cancer Reports · doi:10.1007/s11888-020-00456-1 · Cited by 21
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
