Long-term dysbiosis of the gut microbiome has a significant impact on colorectal cancer (CRC) progression and explains part of the observed heterogeneity of the disease. Even though the shifts in gut microbiome in the normal-adenoma-carcinoma sequence were described, the landscape of the microbiome within CRC and its associations with clinical variables remain under-explored. We performed 16S rRNA gene sequencing of paired tumour tissue, adjacent visually normal mucosa and stool swabs of 178 patients with stage 0-IV CRC to describe the tumour microbiome and its association with clinical variables. We identified new genera associated either with CRC tumour mucosa or CRC in general. The tumour mucosa was dominated by genera belonging to oral pathogens. Based on the tumour microbiome, we stratified CRC patients into three subtypes, significantly associated with prognostic factors such as tumour grade, sidedness and TNM staging, BRAF mutation and MSI status. We found that the CRC microbiome is strongly correlated with the grade, location and stage, but these associations are dependent on the microbial environment. Our study opens new research avenues in the microbiome CRC biomarker detection of disease progression while identifying its limitations, suggesting the need for combining several sampling sites (e.g., stool and tumour swabs).

Department of Laboratory Medicine Clinical Microbiology and Immunology University Hospital Brno 625 00 Brno Czech Republic

Department of Pharmacology Faculty of Medicine Masaryk University 625 00 Brno Czech Republic

Institute of Biostatistics and Analyses Faculty of Medicine Masaryk University 625 00 Brno Czech Republic

Research Centre for Applied Molecular Oncology Masaryk Memorial Cancer Institute 656 53 Brno Czech Republic

Research Centre for Toxic Compounds in the Environment Faculty of Science Masaryk University 625 00 Brno Czech Republic

Research Centre of Information Technology IT4Innovations Centre of Excellence Brno University of Technology 601 90 Brno Czech Republic

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Ferlay J., Colombet M., Soerjomataram I., Dyba T., Randi G., Bettio M., Gavin A., Visser O., Bray F. Cancer incidence and mortality patterns in Europe: Estimates for 40 countries and 25 major cancers in 2018. Eur. J. Cancer. 2018;103:356–387. doi: 10.1016/j.ejca.2018.07.005. PubMed DOI

Punt C.J.A., Koopman M., Vermeulen L. From tumour heterogeneity to advances in precision treatment of colorectal cancer. Nat. Rev. Clin. Oncol. 2017;14:235–246. doi: 10.1038/nrclinonc.2016.171. PubMed DOI

Van Der Jeught K., Xu H.-C., Li Y.-J., Lu X.-B., Ji G. Drug resistance and new therapies in colorectal cancer. World J. Gastroenterol. 2018;24:3834–3848. doi: 10.3748/wjg.v24.i34.3834. PubMed DOI PMC

Ahn J., Sinha R., Pei Z., Dominianni C., Wu J., Shi J., Goedert J.J., Hayes R., Yang L. Human Gut Microbiome and Risk for Colorectal Cancer. J. Natl. Cancer Inst. 2013;105:1907–1911. doi: 10.1093/jnci/djt300. PubMed DOI PMC

Arthur J., Perez-Chanona E., Mühlbauer M., Tomkovich S., Uronis J.M., Fan T.-J., Campbell B.J., Abujamel T., Dogan B., Rogers A.B., et al. Intestinal Inflammation Targets Cancer-Inducing Activity of the Microbiota. Science. 2012;338:120–123. doi: 10.1126/science.1224820. PubMed DOI PMC

Balamurugan R., Rajendiran E., George S., Samuel G.V., Ramakrishna B. Real-time polymerase chain reaction quantification of specific butyrate-producing bacteria, DesulfovibrioandEnterococcus faecalisin the feces of patients with colorectal cancer. J. Gastroenterol. Hepatol. 2008;23:1298–1303. doi: 10.1111/j.1440-1746.2008.05490.x. PubMed DOI

Chen J., Young S.M., Allen C., Seeber A., Péli-Gulli M.-P., Panchaud N., Waller A., Ursu O., Yao T., Golden J.E., et al. Identification of a Small Molecule Yeast TORC1 Inhibitor with a Multiplex Screen Based on Flow Cytometry. ACS Chem. Biol. 2012;7:715–722. doi: 10.1021/cb200452r. PubMed DOI PMC

Chen W., Liu F., Ling Z., Tong X., Xiang C. Human Intestinal Lumen and Mucosa-Associated Microbiota in Patients with Colorectal Cancer. PLoS ONE. 2012;7:e39743. doi: 10.1371/journal.pone.0039743. PubMed DOI PMC

Cipe G., Idiz U.O., Firat D., Bektasoglu H. Relationship between intestinal microbiota and colorectal cancer. World J. Gastrointest. Oncol. 2015;7:233–240. doi: 10.4251/wjgo.v7.i10.233. PubMed DOI PMC

Kostic A., Chun E., Robertson L., Glickman J.N., Gallini C.A., Michaud M., Clancy T.E., Chung D.C., Lochhead P., Hold G., et al. Fusobacterium nucleatum Potentiates Intestinal Tumorigenesis and Modulates the Tumor-Immune Microenvironment. Cell Host Microbe. 2013;14:207–215. doi: 10.1016/j.chom.2013.07.007. PubMed DOI PMC

Lu Y., Chen J., Zheng J., Hu G., Wang J., Huang C., Lou L., Wang X., Zeng Y. Mucosal adherent bacterial dysbiosis in patients with colorectal adenomas. Sci. Rep. 2016;6:26337. doi: 10.1038/srep26337. PubMed DOI PMC

Marchesi J.R., Dutilh B.E., Hall N., Peters W.H.M., Roelofs R., Boleij A., Tjalsma H. Towards the Human Colorectal Cancer Microbiome. PLoS ONE. 2011;6:e20447. doi: 10.1371/journal.pone.0020447. PubMed DOI PMC

Nakatsu G., Li X., Zhou H., Sheng J., Wong S.H., Wu W.K.K., Ng S.C., Tsoi H., Dong Y., Zhang N., et al. Gut mucosal microbiome across stages of colorectal carcinogenesis. Nat. Commun. 2015;6:8727. doi: 10.1038/ncomms9727. PubMed DOI PMC

Rubinstein M.R., Wang X., Liu W., Hao Y., Cai G., Han Y.W. Fusobacterium nucleatum Promotes Colorectal Carcinogenesis by Modulating E-Cadherin/β-Catenin Signaling via its FadA Adhesin. Cell Host Microbe. 2013;14:195–206. doi: 10.1016/j.chom.2013.07.012. PubMed DOI PMC

Sobhani I., Tap J., Roudot-Thoraval F., Roperch J.P., Letulle S., Langella P., Corthier G., Van Nhieu J.T., Furet J.-P. Microbial Dysbiosis in Colorectal Cancer (CRC) Patients. PLoS ONE. 2011;6:e16393. doi: 10.1371/journal.pone.0016393. PubMed DOI PMC

Viljoen K.S., Dakshinamurthy A., Goldberg P., Blackburn J.M. Quantitative Profiling of Colorectal Cancer-Associated Bacteria Reveals Associations between Fusobacterium spp., Enterotoxigenic Bacteroides fragilis (ETBF) and Clinicopathological Features of Colorectal Cancer. PLoS ONE. 2015;10:e0119462. doi: 10.1371/journal.pone.0119462. PubMed DOI PMC

Wang T., Cai G., Qiu Y., Fei N., Zhang M., Pang X., Jia W., Cai S., Zhao L. Structural segregation of gut microbiota between colorectal cancer patients and healthy volunteers. ISME J. 2011;6:320–329. doi: 10.1038/ismej.2011.109. PubMed DOI PMC

Wu N., Yang X., Zhang R., Li J., Xiao X., Hu Y., Chen Y., Yang F., Lu N., Wang Z., et al. Dysbiosis Signature of Fecal Microbiota in Colorectal Cancer Patients. Microb. Ecol. 2013;66:462–470. doi: 10.1007/s00248-013-0245-9. PubMed DOI

Yang J., McDowell A., Kim E.K., Seo H., Lee W.H., Moon C.-M., Kym S.-M., Lee D.H., Park Y.S., Jee Y.-K., et al. Development of a colorectal cancer diagnostic model and dietary risk assessment through gut microbiome analysis. Exp. Mol. Med. 2019;51:1–15. doi: 10.1038/s12276-019-0313-4. PubMed DOI PMC

Yu J., Feng Q., Wong S.H., Zhang D., Liang Q.Y., Qin Y., Tang L., Zhao H., Stenvang J., Li Y., et al. Metagenomic analysis of faecal microbiome as a tool towards targeted non-invasive biomarkers for colorectal cancer. Gut. 2017;66:70–78. doi: 10.1136/gutjnl-2015-309800. PubMed DOI

Zackular J.P., Baxter N., Iverson K.D., Sadler W.D., Petrosino J.F., Chen G.Y., Schloss P.D. The Gut Microbiome Modulates Colon Tumorigenesis. mBio. 2013;4:e00692-13. doi: 10.1128/mBio.00692-13. PubMed DOI PMC

Zackular J., Rogers M., Ruffin M., Schloss P.D. The Human Gut Microbiome as a Screening Tool for Colorectal Cancer. Cancer Prev. Res. 2014;7:1112–1121. doi: 10.1158/1940-6207.CAPR-14-0129. PubMed DOI PMC

Vaupel P., Harrison L. Tumor Hypoxia: Causative Factors, Compensatory Mechanisms, and Cellular Response. Oncologist. 2004;9((Suppl. S5)):4–9. doi: 10.1634/theoncologist.9-90005-4. PubMed DOI

Louis P., Hold G., Flint H.J. The gut microbiota, bacterial metabolites and colorectal cancer. Nat. Rev. Microbiol. 2014;12:661–672. doi: 10.1038/nrmicro3344. PubMed DOI

Tlaskalova-Hogenova H., Vannucci L., Klimesova K., Stepankova R., Krizan J., Kverka M. Microbiome and Colorectal Carcinoma. Cancer J. 2014;20:217–224. doi: 10.1097/PPO.0000000000000052. PubMed DOI

Xiao Y., Freeman G.J. The Microsatellite Instable Subset of Colorectal Cancer Is a Particularly Good Candidate for Checkpoint Blockade Immunotherapy. Cancer Discov. 2015;5:16–18. doi: 10.1158/2159-8290.CD-14-1397. PubMed DOI PMC

Tjalsma H., Boleij A., Marchesi J.R., Dutilh B.E. A bacterial driver–passenger model for colorectal cancer: Beyond the usual suspects. Nat. Rev. Genet. 2012;10:575–582. doi: 10.1038/nrmicro2819. PubMed DOI

Pennisi E. Cancer Therapies Use a Little Help from Microbial Friends. Science. 2013;342:921. doi: 10.1126/science.342.6161.921. PubMed DOI

Thomas A.M., Manghi P., Asnicar F., Pasolli E., Armanini F., Zolfo M., Beghini F., Manara S., Karcher N., Pozzi C., et al. Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation. Nat. Med. 2019;25:667–678. doi: 10.1038/s41591-019-0405-7. PubMed DOI PMC

Feng Q., Liang S., Jia H., Stadlmayr A., Tang L., Lan Z., Zhang D., Xia H., Xu X., Jie Z., et al. Gut microbiome development along the colorectal adenoma–carcinoma sequence. Nat. Commun. 2015;6:6528. doi: 10.1038/ncomms7528. PubMed DOI

Dejea C.M., Wick E.C., Hechenbleikner E.M., White J.R., Welch J.L.M., Rossetti B.J., Peterson S.N., Snesrud E.C., Borisy G.G., Lazarev M., et al. Microbiota organization is a distinct feature of proximal colorectal cancers. Proc. Natl. Acad. Sci. USA. 2014;111:18321–18326. doi: 10.1073/pnas.1406199111. PubMed DOI PMC

Zeller G., Tap J., Voigt A.Y., Sunagawa S., Kultima J.R., Costea P.I., Amiot A., Böhm J., Brunetti F., Habermann N., et al. Potential of fecal microbiota for early-stage detection of colorectal cancer. Mol. Syst. Biol. 2014;10:766. doi: 10.15252/msb.20145645. PubMed DOI PMC

Yang Y., Cai Q., Shu X., Steinwandel M.D., Blot W.J., Zheng W., Long J. Prospective study of oral microbiome and colorectal cancer risk in low-income and African American populations. Int. J. Cancer. 2019;144:2381–2389. doi: 10.1002/ijc.31941. PubMed DOI PMC

Liu C., Zhang Y., Shang Y., Wu B., Yang E., Luo Y.-Y., Li X. Intestinal bacteria detected in cancer and adjacent tissue from patients with colorectal cancer. Oncol. Lett. 2018;17:1115–1127. doi: 10.3892/ol.2018.9714. PubMed DOI PMC

Pu L.Z.C.T., Yamamoto K., Honda T., Nakamura M., Yamamura T., Hattori S., Burt A.D., Singh R., Hirooka Y., Fujishiro M. Microbiota profile is different for early and invasive colorectal cancer and is consistent throughout the colon. J. Gastroenterol. Hepatol. 2020;35:433–437. doi: 10.1111/jgh.14868. PubMed DOI

Flemer B., Lynch D.B., Brown J.M.R., Jeffery I., Ryan F., Claesson M., O’Riordain M., Shanahan F., O’Toole P.W. Tumour-associated and non-tumour-associated microbiota in colorectal cancer. Gut. 2017;66:633–643. doi: 10.1136/gutjnl-2015-309595. PubMed DOI PMC

Egao Z., Eguo B., Egao R., Ezhu Q., Eqin H. Microbiota disbiosis is associated with colorectal cancer. Front. Microbiol. 2015;6:20. doi: 10.3389/fmicb.2015.00020. PubMed DOI PMC

Li E., Hamm C.M., Gulati A.S., Sartor R.B., Chen H., Wu X., Zhang T., Rohlf F.J., Zhu W., Gu C., et al. Inflammatory Bowel Diseases Phenotype, C. difficile and NOD2 Genotype Are Associated with Shifts in Human Ileum Associated Microbial Composition. PLoS ONE. 2012;7:e26284. doi: 10.1371/journal.pone.0026284. PubMed DOI PMC

Han S., Wu W., Da M., Xu J., Zhuang J., Zhang L., Zhang X., Yang X. Adequate Lymph Node Assessments and Investigation of Gut Microorganisms and Microbial Metabolites in Colorectal Cancer. OTT. 2020;13:1893–1906. doi: 10.2147/OTT.S242017. PubMed DOI PMC

Wu Y., Shi L., Li Q., Wu J., Peng W., Li H., Chen K., Ren Y., Fu X. Microbiota Diversity in Human Colorectal Cancer Tissues Is Associated with Clinicopathological Features. Nutr. Cancer. 2019;71:214–222. doi: 10.1080/01635581.2019.1578394. PubMed DOI

Apprill A., McNally S., Parsons R., Weber L. Minor revision to V4 region SSU rRNA 806R gene primer greatly increases detection of SAR11 bacterioplankton. Aquat. Microb. Ecol. 2015;75:129–137. doi: 10.3354/ame01753. DOI

Caporaso J.G., Lauber C.L., Walters W.A., Berg-Lyons D., Lozupone C.A., Turnbaugh P.J., Fierer N., Knight R. Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. Proc. Natl. Acad. Sci. USA. 2011;108:4516–4522. doi: 10.1073/pnas.1000080107. PubMed DOI PMC

Callahan B.J., McMurdie P., Rosen M.J., Han A.W., Johnson A.J.A., Holmes S. DADA2: High-resolution sample inference from Illumina amplicon data. Nat. Methods. 2016;13:581–583. doi: 10.1038/nmeth.3869. PubMed DOI PMC

Aronesty E. Comparison of Sequencing Utility Programs. TOBIOIJ. 2013;7:1–8. doi: 10.2174/1875036201307010001. DOI

Pruesse E., Quast C., Knittel K., Fuchs B.M., Ludwig W., Peplies J., Glöckner F.O. SILVA: A comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res. 2007;35:7188–7196. doi: 10.1093/nar/gkm864. PubMed DOI PMC

Edgar R.C. Search and clustering orders of magnitude faster than BLAST. Bioinformatics. 2010;26:2460–2461. doi: 10.1093/bioinformatics/btq461. PubMed DOI

Caporaso J.G., Kuczynski J., Stombaugh J., Bittinger K., Bushman F., Costello E.K., Fierer N., Peña A.G., Goodrich J.K., Gordon J.I., et al. QIIME allows analysis of high-throughput community sequencing data. Nat. Methods. 2010;7:335–336. doi: 10.1038/nmeth.f.303. PubMed DOI PMC

Altschul S.F., Gish W., Miller W., Myers E.W., Lipman D.J. Basic local alignment search tool. J. Mol. Biol. 1990;215:403–410. doi: 10.1016/S0022-2836(05)80360-2. PubMed DOI

Lozupone C., Knight R. UniFrac: A New Phylogenetic Method for Comparing Microbial Communities. Appl. Environ. Microbiol. 2005;71:8228–8235. doi: 10.1128/AEM.71.12.8228-8235.2005. PubMed DOI PMC

Douglas G.M., Maffei V.J., Zaneveld J.R., Yurgel S.N., Brown J.R., Taylor C.M., Huttenhower C., Langille M.G.I. PICRUSt2 for prediction of metagenome functions. Nat. Biotechnol. 2020;38:685–688. doi: 10.1038/s41587-020-0548-6. PubMed DOI PMC

Aitchison J. The Statistical Analysis of Compositional Data. J. R. Stat. Soc. Ser. B Methodol. 1982;44:139–160. doi: 10.1111/j.2517-6161.1982.tb01195.x. DOI

Gloor G.B., Wu J.R., Pawlowsky-Glahn V., Egozcue J.J. It’s all relative: Analyzing microbiome data as compositions. Ann. Epidemiol. 2016;26:322–329. doi: 10.1016/j.annepidem.2016.03.003. PubMed DOI

Martín-Fernández J.-A., Hron K., Templ M., Filzmoser P., Palarea-Albaladejo J. Bayesian-multiplicative treatment of count zeros in compositional data sets. Stat. Model. Int. J. 2015;15:134–158. doi: 10.1177/1471082X14535524. DOI

Tsilimigras M.C., Fodor A.A. Compositional data analysis of the microbiome: Fundamentals, tools, and challenges. Ann. Epidemiol. 2016;26:330–335. doi: 10.1016/j.annepidem.2016.03.002. PubMed DOI

Oaksen J., Blanchet F.G., Friendly M., Kindt R., Legendre P., McGlinn D., Minchin P.R., O’Hara R.B., Simpson G.L., Solymos P., et al. Vegan: Community Ecology Package. R Package. 2019. [(accessed on 4 July 2020)]. Available online: http://cran.rproject.org/package=vegan.

Comas-Cufí M. R Package. coda.base: A Basic Set of Functions for Compositional Data Analysis. 2020. [(accessed on 4 July 2020)]. Available online: https://rdrr.io/cran/coda.base/

Kloke J.D., McKean J.W. Rfit: Rank-Based Estimation for Linear Models. R J. 2012;4:57–64. doi: 10.32614/RJ-2012-014. DOI

Benjamini Y., Hochberg Y. Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing. J. R. Stat. Soc. Ser. B Methodol. 1995;57:289–300. doi: 10.1111/j.2517-6161.1995.tb02031.x. DOI

Gu Z., Gu L., Eils R., Schlesner M., Brors B. circlize implements and enhances circular visualization in R. Bioinformatics. 2014;30:2811–2812. doi: 10.1093/bioinformatics/btu393. PubMed DOI

Gu Z., Eils R., Schlesner M. Complex heatmaps reveal patterns and correlations in multidimensional genomic data. Bioinformatics. 2016;32:2847–2849. doi: 10.1093/bioinformatics/btw313. PubMed DOI

Warnes G.R., Bolker B., Bonebakker L., Gentleman R., Liaw W.H.A., Lumley T., Maechler M., Magnusson A., Moeller S., Schwartz M., et al. Gplots: Various R Programming Tools for Plotting Data; R Package. 2020. [(accessed on 4 July 2020)]. Available online: https://rdrr.io/cran/gplots/

Wickham H. Ggplot2: Elegant Graphics for Data Analysis. 2nd ed. Springer; Cham, Switzerland: 2016.

Wray C.M., Ziogas A., Hinojosa M.W., Le H., Stamos M.J., Zell J.A. Tumor Subsite Location Within the Colon Is Prognostic for Survival After Colon Cancer Diagnosis. Dis. Colon Rectum. 2009;52:1359–1366. doi: 10.1007/DCR.0b013e3181a7b7de. PubMed DOI

Pasolli E., Schiffer L., Manghi P., Renson A., Obenchain V., Truong D.T., Beghini F., Malik F., Ramos M., Dowd J., et al. Accessible, curated metagenomic data through ExperimentHub. Nat. Methods. 2017;14:1023–1024. doi: 10.1038/nmeth.4468. PubMed DOI PMC

De Almeida C.V., Lulli M., Di Pilato V., Schiavone N., Russo E., Nannini G., Baldi S., Borrelli R., Bartolucci G., Menicatti M., et al. Differential Responses of Colorectal Cancer Cell Lines to Enterococcus faecalis’ Strains Isolated from Healthy Donors and Colorectal Cancer Patients. JCM. 2019;8:388. doi: 10.3390/jcm8030388. PubMed DOI PMC

Gupta A., Dhakan D.B., Maji A., Saxena R., Visnu Prasoodanan P.K., Mahajan S., Pulikkan J., Kurian J., Gomez A.M., Scaria J., et al. Association of Flavonifractor plautii, a Flavonoid-Degrading Bacterium, with the Gut Microbiome of Colorectal Cancer Patients in India. mSystems. 2019;4 doi: 10.1128/mSystems.00438-19. PubMed DOI PMC

Ai D., Pan H., Li X., Gao Y., Liu G., Xia L.C. Identifying Gut Microbiota Associated with Colorectal Cancer Using a Zero-Inflated Lognormal Model. Front. Microbiol. 2019;10:826. doi: 10.3389/fmicb.2019.00826. PubMed DOI PMC

Ito M., Kanno S., Nosho K., Sukawa Y., Mitsuhashi K., Kurihara H., Igarashi H., Takahashi T., Tachibana M., Takahashi H., et al. Association ofFusobacterium nucleatumwith clinical and molecular features in colorectal serrated pathway. Int. J. Cancer. 2015;137:1258–1268. doi: 10.1002/ijc.29488. PubMed DOI

Bahmani S., Azarpira N., Moazamian E. Anti-colon cancer activity of Bifidobacterium metabolites on colon cancer cell line SW742. Turk. J. Gastroenterol. 2019;30:835–842. doi: 10.5152/tjg.2019.18451. PubMed DOI PMC

Mangifesta M., Mancabelli L., Milani C., Gaiani F., De’Angelis N., De’Angelis G.L., Van Sinderen D., Ventura M., Turroni F. Mucosal microbiota of intestinal polyps reveals putative biomarkers of colorectal cancer. Sci. Rep. 2018;8:1–9. doi: 10.1038/s41598-018-32413-2. PubMed DOI PMC

Parisa A., Roya G., Mahdi R., Shabnam R., Maryam E., Malihe T. Anti-cancer effects of Bifidobacterium species in colon cancer cells and a mouse model of carcinogenesis. PLoS ONE. 2020;15:e0232930. doi: 10.1371/journal.pone.0232930. PubMed DOI PMC

Sivan A., Corrales L., Hubert N., Williams J.B., Aquino-Michaels K., Earley Z.M., Benyamin F.W., Lei Y.M., Jabri B., Alegre M.-L., et al. Commensal Bifidobacterium promotes antitumor immunity and facilitates anti-PD-L1 efficacy. Science. 2015;350:1084–1089. doi: 10.1126/science.aac4255. PubMed DOI PMC

Koncina E., Haan S., Rauh S., Letellier E. Prognostic and Predictive Molecular Biomarkers for Colorectal Cancer: Updates and Challenges. Cancers. 2020;12:319. doi: 10.3390/cancers12020319. PubMed DOI PMC

Guinney J., Dienstmann R., Wang X., De Reyniès A., Schlicker A., Soneson C., Marisa L., Roepman P., Nyamundanda G., Angelino P., et al. The consensus molecular subtypes of colorectal cancer. Nat. Med. 2015;21:1350–1356. doi: 10.1038/nm.3967. PubMed DOI PMC

Koliarakis I., Messaritakis I., Nikolouzakis T.K., Hamilos G., Souglakos J., Tsiaoussis J. Oral Bacteria and Intestinal Dysbiosis in Colorectal Cancer. Int. J. Mol. Sci. 2019;20:4146. doi: 10.3390/ijms20174146. PubMed DOI PMC

Long X., Wong C.C., Tong L., Chu E.S.H., Szeto C.H., Go M.Y.Y., Coker O.O., Chan A.W.H., Chan F.K., Sung J.J.Y., et al. Peptostreptococcus anaerobius promotes colorectal carcinogenesis and modulates tumour immunity. Nat. Microbiol. 2019;4:2319–2330. doi: 10.1038/s41564-019-0541-3. PubMed DOI

Abed J., Emgård J.E., Zamir G., Faroja M., Almogy G., Grenov A., Sol A., Naor R., Pikarsky E., Atlan K.A., et al. Fap2 Mediates Fusobacterium nucleatum Colorectal Adenocarcinoma Enrichment by Binding to Tumor-Expressed Gal-GalNAc. Cell Host Microbe. 2016;20:215–225. doi: 10.1016/j.chom.2016.07.006. PubMed DOI PMC

Zou X., Feng B., Dong T., Yan G., Tan B., Shen H., Huang A., Zhang X., Zhang M., Yang P., et al. Up-regulation of type I collagen during tumorigenesis of colorectal cancer revealed by quantitative proteomic analysis. J. Proteom. 2013;94:473–485. doi: 10.1016/j.jprot.2013.10.020. PubMed DOI

Takahashi N. Microbial ecosystem in the oral cavity: Metabolic diversity in an ecological niche and its relationship with oral diseases. Int. Congr. Ser. 2005;1284:103–112. doi: 10.1016/j.ics.2005.06.071. DOI

Eley B.M., Cox S.W. Proteolytic and hydrolytic enzymes from putative periodontal pathogens: Characterization, molecular genetics, effects on host defenses and tissues and detection in gingival crevice fluid. Periodontol. 2000. 2003;31:105–124. doi: 10.1034/j.1600-0757.2003.03107.x. PubMed DOI

Potempa J., Sroka A., Imamura T., Travis J. Gingipains, the major cysteine proteinases and virulence factors of Porphyromonas gingivalis: Structure, function and assembly of multidomain protein complexes. Curr. Protein Pept. Sci. 2003;4:397–407. doi: 10.2174/1389203033487036. PubMed DOI

Gonçalves L.F.H., Fermiano D., Feres M., Figueiredo L.C., Teles F.R.P., Mayer M.P.A., Faveri M. Levels ofSelenomonasspecies in generalized aggressive periodontitis. J. Periodontal Res. 2012;47:711–718. doi: 10.1111/j.1600-0765.2012.01485.x. PubMed DOI PMC

Scher J.U., Ubeda C., Equinda M., Khanin R., Buischi Y., Viale A., Lipuma L., Attur M., Pillinger M., Weissmann G., et al. Periodontal disease and the oral microbiota in new-onset rheumatoid arthritis. Arthritis Rheum. 2012;64:3083–3094. doi: 10.1002/art.34539. PubMed DOI PMC

Herbert B.A., Novince C.M., Kirkwood K.L. Aggregatibacter actinomycetemcomitans, a potent immunoregulator of the periodontal host defense system and alveolar bone homeostasis. Mol. Oral Microbiol. 2016;31:207–227. doi: 10.1111/omi.12119. PubMed DOI PMC

Lin W.-R., Chen Y.-S., Liu Y.-C. Cellulitis and Bacteremia Caused by Bergeyella zoohelcum. J. Formos. Med. Assoc. 2007;106:573–576. doi: 10.1016/S0929-6646(07)60008-4. PubMed DOI

Peel M.M., Hornidge K.A., Luppino M., Stacpoole A.M., Weaver R.E. Actinobacillus spp. and related bacteria in infected wounds of humans bitten by horses and sheep. J. Clin. Microbiol. 1991;29:2535–2538. doi: 10.1128/jcm.29.11.2535-2538.1991. PubMed DOI PMC

Sohn K.M., Huh K., Baek J.-Y., Kim Y.-S., Kang C.-I., Peck K.R., Lee N.Y., Song J.-H., Ko K.S., Chung D.R. A new causative bacteria of infective endocarditis, Bergeyella cardium sp. nov. Diagn. Microbiol. Infect. Dis. 2015;81:213–216. doi: 10.1016/j.diagmicrobio.2014.12.001. PubMed DOI

Friis-Møller A., Christensen J.J., Fussing V., Hesselbjerg A., Christiansen J., Bruun B. Clinical Significance and Taxonomy of Actinobacillus hominis. J. Clin. Microbiol. 2001;39:930–935. doi: 10.1128/JCM.39.3.930-935.2001. PubMed DOI PMC

Zha Z., Lv Y., Tang H., Li T., Miao Y., Cheng J., Wang G., Tan Y., Zhu Y., Xing X., et al. An orally administered butyrate-releasing xylan derivative reduces inflammation in dextran sulphate sodium-induced murine colitis. Int. J. Biol. Macromol. 2020;156:1217–1233. doi: 10.1016/j.ijbiomac.2019.11.159. PubMed DOI

Kelly T.N., Bazzano L.A., Ajami N.J., He H., Zhao J., Petrosino J.F., Correa A., He J. Gut Microbiome Associates with Lifetime Cardiovascular Disease Risk Profile Among Bogalusa Heart Study Participants. Circ. Res. 2016;119:956–964. doi: 10.1161/CIRCRESAHA.116.309219. PubMed DOI PMC

Niederseer D., Bracher I., Stadlmayr A., Huber-Schönauer U., Plöderl M., Obeid S., Schmied C., Hammerl S., Stickel F., Lederer D., et al. Association between Cardiovascular Risk and Diabetes with Colorectal Neoplasia: A Site-Specific Analysis. J. Clin. Med. 2018;7:484. doi: 10.3390/jcm7120484. PubMed DOI PMC

Mei Q.-X., Huang C.-L., Luo S.-Z., Zhang X.-M., Zeng Y., Lu Y.-Y. Characterization of the duodenal bacterial microbiota in patients with pancreatic head cancer vs. healthy controls. Pancreatology. 2018;18:438–445. doi: 10.1016/j.pan.2018.03.005. PubMed DOI

Gao R., Kong C., Huang L., Li H., Qu X., Liu Z., Lan P., Wang J., Qin H. Mucosa-associated microbiota signature in colorectal cancer. Eur. J. Clin. Microbiol. Infect. Dis. 2017;36:2073–2083. doi: 10.1007/s10096-017-3026-4. PubMed DOI

Xi Y., Yuefen P., Wei W., Quan Q., Jing Z., Jiamin X., Shuwen H. Analysis of prognosis, genome, microbiome, and microbial metabolome in different sites of colorectal cancer. J. Transl. Med. 2019;17:1–22. doi: 10.1186/s12967-019-2102-1. PubMed DOI PMC

Kamphuis J., Mercier-Bonin M., Eutamène H., Théodorou V. Mucus organisation is shaped by colonic content; a new view. Sci. Rep. 2017;7:1–13. doi: 10.1038/s41598-017-08938-3. PubMed DOI PMC

Paone P., Cani P.D. Mucus barrier, mucins and gut microbiota: The expected slimy partners? Gut. 2020;69:2232–2243. doi: 10.1136/gutjnl-2020-322260. PubMed DOI PMC

Luu T.H., Michel C., Bard J.-M., Dravet F., Nazih H., Bobin-Dubigeon C. Intestinal Proportion ofBlautiasp. is Associated with Clinical Stage and Histoprognostic Grade in Patients with Early-Stage Breast Cancer. Nutr. Cancer. 2017;69:267–275. doi: 10.1080/01635581.2017.1263750. PubMed DOI

Wu A.H., Tseng C., Vigen C., Yu Y., Cozen W., Garcia A.A., Spicer D. Gut microbiome associations with breast cancer risk factors and tumor characteristics: A pilot study. Breast Cancer Res. Treat. 2020;182:451–463. doi: 10.1007/s10549-020-05702-6. PubMed DOI PMC

Zhuang H., Cheng L., Wang Y., Zhang Y.-K., Zhao M.-F., Liang G.-D., Zhang M.-C., Li Y.-G., Zhao J.-B., Gao Y.-N., et al. Dysbiosis of the Gut Microbiome in Lung Cancer. Front. Cell. Infect. Microbiol. 2019;9:112. doi: 10.3389/fcimb.2019.00112. PubMed DOI PMC

Budinska E., Popovici V., Tejpar S., D’Ario G., Lapique N., Sikora K.O., Di Narzo A.F., Yan P., Hodgson J.G., Weinrich S., et al. Gene expression patterns unveil a new level of molecular heterogeneity in colorectal cancer. J. Pathol. 2013;231:63–76. doi: 10.1002/path.4212. PubMed DOI PMC

He Z., Gharaibeh R.Z., Newsome R.C., Pope J.L., Dougherty M., Tomkovich S., Pons B., Mirey G., Vignard J., Hendrixson D.R., et al. Campylobacter jejuni promotes colorectal tumorigenesis through the action of cytolethal distending toxin. Gut. 2019;68:289–300. doi: 10.1136/gutjnl-2018-317200. PubMed DOI PMC

Drewes J.L., White J.R., Dejea C.M., Fathi P., Iyadorai T., Vadivelu J., Roslani A.C., Wick E.C., Mongodin E.F., Loke M.F., et al. High-resolution bacterial 16S rRNA gene profile meta-analysis and biofilm status reveal common colorectal cancer consortia. Npj Biofilms Microbiomes. 2017;3:1–12. doi: 10.1038/s41522-017-0040-3. PubMed DOI PMC

Kaplan C.W., Lux R., Haake S.K., Shi W. TheFusobacterium nucleatumouter membrane protein RadD is an arginine-inhibitable adhesin required for inter-species adherence and the structured architecture of multispecies biofilm. Mol. Microbiol. 2009;71:35–47. doi: 10.1111/j.1365-2958.2008.06503.x. PubMed DOI PMC

Tomkovich S., Dejea C.M., Winglee K., Drewes J.L., Chung L., Housseau F., Pope J.L., Gauthier J., Sun X., Mühlbauer M., et al. Human colon mucosal biofilms from healthy or colon cancer hosts are carcinogenic. J. Clin. Investig. 2019;129:1699–1712. doi: 10.1172/JCI124196. PubMed DOI PMC

Jorth P., Turner K.H., Gumus P., Nizam N., Buduneli N., Whiteley M. Metatranscriptomics of the Human Oral Microbiome during Health and Disease. mBio. 2014;5:e01012-14. doi: 10.1128/mBio.01012-14. PubMed DOI PMC

Liu Y., Geng R., Liu L., Jin X., Yan W., Zhao F., Wang S., Guo X., Ghimire G., Wei Y. Gut Microbiota-Based Algorithms in the Prediction of Metachronous Adenoma in Colorectal Cancer Patients Following Surgery. Front. Microbiol. 2020;11:1106. doi: 10.3389/fmicb.2020.01106. PubMed DOI PMC

Alexander J.L., Wilson I.D., Teare J., Marchesi J., Nicholson J.K., Kinross J. Gut microbiota modulation of chemotherapy efficacy and toxicity. Nat. Rev. Gastroenterol. Hepatol. 2017;14:356–365. doi: 10.1038/nrgastro.2017.20. PubMed DOI

Chew S.-S., Tan L.T.-H., Law J.W.-F., Pusparajah P., Goh B.-H., Ab Mutalib N.S., Lee L.-H. Targeting Gut Microbial Biofilms—A Key to Hinder Colon Carcinogenesis? Cancers. 2020;12:2272. doi: 10.3390/cancers12082272. PubMed DOI PMC

Kim G.W., Kim Y.-S., Lee S.H., Park S.G., Kim D.H., Cho J.Y., Hahm K.B., Hong S.P., Yoo J.-H. Periodontitis is associated with an increased risk for proximal colorectal neoplasms. Sci. Rep. 2019;9:7528. doi: 10.1038/s41598-019-44014-8. PubMed DOI PMC

Horz H.-P., Scheer S., Huenger F., Vianna M.E., Conrads G. Selective isolation of bacterial DNA from human clinical specimens. J. Microbiol. Methods. 2008;72:98–102. doi: 10.1016/j.mimet.2007.10.007. PubMed DOI

Walker S.P., Tangney M., Claesson M. Sequence-Based Characterization of Intratumoral Bacteria—A Guide to Best Practice. Front. Oncol. 2020;10:179. doi: 10.3389/fonc.2020.00179. PubMed DOI PMC

Heravi F.S., Zakrzewski M., Vickery K., Hu H. Host DNA depletion efficiency of microbiome DNA enrichment methods in infected tissue samples. J. Microbiol. Methods. 2020;170:105856. doi: 10.1016/j.mimet.2020.105856. PubMed DOI

Multiple regulatory events contribute to a widespread circular RNA downregulation in precancer and early stage of colorectal cancer development