[1]

Bray F, Laversanne M, Sung H, Ferlay J, Siegel RL, et al. 2024. Global cancer statistics 2022: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries. CA: A Cancer Journal for Clinicians 74:229−263

doi: 10.3322/caac.21834
[2]

Feng Q, Liang S, Jia H, Stadlmayr A, Tang L, et al. 2015. Gut microbiome development along the colorectal adenoma–carcinoma sequence. Nature Communications 6:6528

doi: 10.1038/ncomms7528
[3]

Leslie A, Carey FA, Pratt NR, Steele RC. 2002. The colorectal adenoma–carcinoma sequence. British Journal of Surgery 89:845−860

doi: 10.1046/j.1365-2168.2002.02120.x
[4]

Silinskaite U, Valciukiene J, Jakubauskas M, Poskus T. 2025. The immune environment in colorectal adenoma: a systematic review. Biomedicines 13:699

doi: 10.3390/biomedicines13030699
[5]

Mizutani T, Boretto M, Lim S, Drost J, González DM, et al. 2024. Recapitulating the adenoma–carcinoma sequence by selection of four spontaneous oncogenic mutations in mismatch-repair-deficient human colon organoids. Nature Cancer 5:1852−1867

doi: 10.1038/s43018-024-00841-x
[6]

Pino MS, Chung DC. 2010. The chromosomal instability pathway in colon cancer. Gastroenterology 138:2059−2072

doi: 10.1053/j.gastro.2009.12.065
[7]

Boland CR, Goel A. 2010. Microsatellite instability in colorectal cancer. Gastroenterology 138:2073−2087.e3

doi: 10.1053/j.gastro.2009.12.064
[8]

Tilg H, Adolph TE, Gerner RR, Moschen AR. 2018. The intestinal microbiota in colorectal cancer. Cancer Cell 33:954−964

doi: 10.1016/j.ccell.2018.03.004
[9]

Lam TJ, Ye Y. 2022. Meta-analysis of microbiome association networks reveal patterns of dysbiosis in diseased microbiomes. Scientific Reports 12:17482

doi: 10.1038/s41598-022-22541-1
[10]

Kim M, Vogtmann E, Ahlquist DA, Devens ME, Kisiel JB, et al. 2020. Fecal metabolomic signatures in colorectal adenoma patients are associated with gut microbiota and early events of colorectal cancer pathogenesis. mBio 11:e03186-19

doi: 10.1128/mbio.03186-19
[11]

Vacante M, Ciuni R, Basile F, Biondi A. 2020. Gut microbiota and colorectal cancer development: a closer look to the adenoma-carcinoma sequence. Biomedicines 8:489

doi: 10.3390/biomedicines8110489
[12]

Ghafouri-Fard S, Safarzadeh A, Taheri M, Jamali E. 2023. Identification of diagnostic biomarkers via weighted correlation network analysis in colorectal cancer using a system biology approach. Scientific Reports 13:13637

doi: 10.1038/s41598-023-40953-5
[13]

Lugo-Martinez J, Ruiz-Perez D, Narasimhan G, Bar-Joseph Z. 2019. Dynamic interaction network inference from longitudinal microbiome data. Microbiome 7:54

doi: 10.1186/s40168-019-0660-3
[14]

Chen C, Jiang L, Fu G, Wang M, Wang Y, et al. 2019. An omnidirectional visualization model of personalized gene regulatory networks. npj Systems Biology and Applications 5:38

doi: 10.1038/s41540-019-0116-1
[15]

Shingleton A. 2010. Allometry: The Study of Biological Scaling. Nature Education Knowledge 3:2

[16]

Wu R, Jiang L. 2021. Recovering dynamic networks in big static datasets. Physics Reports 912:1−57

doi: 10.1016/j.physrep.2021.01.003
[17]

Dong A, Wu S, Che J, Wang Y, Wu R. 2023. idopNetwork: a network tool to dissect spatial community ecology. Methods in Ecology and Evolution 14:2272−2283

doi: 10.1111/2041-210X.14172
[18]

Bholowalia P, Kumar A. 2014. EBK-means: a clustering technique based on elbow method and k-means in WSN. International Journal of Computer Applications 105(9):17−24

[19]

Syakur MA, Khotimah BK, Rochman EMS, Satoto BD. 2018. Integration k-means clustering method and elbow method for identification of the best customer profile cluster. IOP Conference Series: Materials Science and Engineering 336:012017

doi: 10.1088/1757-899X/336/1/012017
[20]

Grigor'yan A, Lin Y, Muranov Y, Yau ST. 2012. Homologies of path complexes and digraphs. arXiv:1207.2834

doi: 10.48550/arXiv.1207.2834
[21]

Wu S, Liu X, Dong A, Gragnoli C, Griffin C, et al. 2023. The metabolomic physics of complex diseases. Proceedings of the National Academy of Sciences of the United States of America 120:e2308496120

doi: 10.1073/pnas.2308496120
[22]

Chen YJ, Leung PM, Wood JL, Bay SK, Hugenholtz P, et al. 2021. Metabolic flexibility allows bacterial habitat generalists to become dominant in a frequently disturbed ecosystem. The ISME Journal 15:2986−3004

doi: 10.1038/s41396-021-00988-w
[23]

Nakatsu G, Li X, Zhou H, Sheng J, Wong SH, et al. 2015. Gut mucosal microbiome across stages of colorectal carcinogenesis. Nature Communications 6:8727

doi: 10.1038/ncomms9727
[24]

Zhou X, Shen X, Johnson JS, Spakowicz DJ, Agnello M, et al. 2024. Longitudinal profiling of the microbiome at four body sites reveals core stability and individualized dynamics during health and disease. Cell Host & Microbe 32:506−526.e9

doi: 10.1016/j.chom.2024.02.012
[25]

Abbas-Egbariya H, Haberman Y, Braun T, Hadar R, Denson L, et al. 2022. Meta-analysis defines predominant shared microbial responses in various diseases and a specific inflammatory bowel disease signal. Genome Biology 23:61

doi: 10.1186/s13059-022-02637-7
[26]

Kadelka C, Wheeler M, Veliz-Cuba A, Murrugarra D, Laubenbacher R. 2023. Modularity of biological systems: a link between structure and function. Journal of the Royal Society Interface 20:20230505

doi: 10.1098/rsif.2023.0505
[27]

Segal E, Shapira M, Regev A, Pe'er D, Botstein D, et al. 2003. Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data. Nature Genetics 34:166−176

doi: 10.1038/ng1165
[28]

Manipur I, Granata I, Maddalena L, Guarracino MR. 2020. Clustering analysis of tumor metabolic networks. BMC Bioinformatics 21:349

doi: 10.1186/s12859-020-03564-9
[29]

Ferro S, Azevedo-Silva J, Casal M, Côrte-Real M, Baltazar F, et al. 2016. Characterization of acetate transport in colorectal cancer cells and potential therapeutic implications. Oncotarget 7:70639−70653

doi: 10.18632/oncotarget.12156
[30]

Venema K, Vermunt SHF, Brink EJ. 2005. D-Tagatose increases butyrate production by the colonic microbiota in healthy men and women. Microbial Ecology in Health and Disease 17:47−57

doi: 10.1080/08910600510035093
[31]

Park GB, Chung YH, Kim D. 2017. 2-Deoxy-D-glucose suppresses the migration and reverses the drug resistance of colon cancer cells through ADAM expression regulation. Anti-Cancer Drugs 28:410−420

doi: 10.1097/CAD.0000000000000472
[32]

Szilagyi A, Nathwani U, Vinokuroff C, Correa JA, Shrier I. 2006. The effect of lactose maldigestion on the relationship between dairy food intake and colorectal cancer: a systematic review. Nutrition and Cancer 55:141−150

doi: 10.1207/s15327914nc5502_4
[33]

Pöschel L, Gehr E, Buchhaupt M. 2022. Improvement of dicarboxylic acid production with Methylorubrum extorquens by reduction of product reuptake. Applied Microbiology and Biotechnology 106:6713−6731

doi: 10.1007/s00253-022-12161-0
[34]

Lee S. 2025. Influence of pH on the cytotoxic activity of organic acids against breast cancer cells. Bioorganic & Medicinal Chemistry 129:118330

doi: 10.1016/j.bmc.2025.118330
[35]

Mingrone G, Castagneto-Gissey L, Macé K. 2013. Use of dicarboxylic acids in type 2 diabetes. British Journal of Clinical Pharmacology 75:671−676

doi: 10.1111/j.1365-2125.2012.04177.x
[36]

Zhang C, Zhou S, Chang H, Zhuang F, Shi Y, et al. 2021. Metabolomic profiling identified serum metabolite biomarkers and related metabolic pathways of colorectal cancer. Disease Markers 2021:6858809

doi: 10.1155/2021/6858809
[37]

Meziti A, Mathou N, Paraskeva K, Kountouras J, Floudaras I, et al. 2022. Differences in bacterial community composition between healthy and polyps related gut biopsies. Public Health and Toxicology 2:A75

doi: 10.18332/pht/149811
[38]

Yang Y, Dai D, Jin W, Huang Y, Zhang Y, et al. 2022. Microbiota and metabolites alterations in proximal and distal gastric cancer patients. Journal of Translational Medicine 20:439

doi: 10.1186/s12967-022-03650-x
[39]

Ahmed S, Singh S, Singh V, Roberts KD, Zaidi A, et al. 2022. The Weissella genus: clinically treatable bacteria with antimicrobial/probiotic effects on inflammation and cancer. Microorganisms 10:2427

doi: 10.3390/microorganisms10122427
[40]

Du Y, Liu L, Yan W, Li Y, Li Y, et al. 2023. The anticancer mechanisms of exopolysaccharide from Weissella cibaria D-2 on colorectal cancer via apoptosis induction. Scientific Reports 13:21117

doi: 10.1038/s41598-023-47943-7
[41]

Hao Q, Huang F, Chang L, Dai H, Chen W, et al. 2025. Weissella cibaria suppresses colitis-associated colorectal cancer by modulating the gut microbiota-bile acid-FXR axis. mSystems 10:e0028825

doi: 10.1128/msystems.00288-25
[42]

Mahoney-Kurpe SC, Palevich N, Gagic D, Biggs PJ, Reid PM, et al. 2024. Transcriptomic and proteomic changes associated with cobalamin-dependent propionate production by the rumen bacterium Xylanibacter ruminicola. mSystems 9:e00864-24

doi: 10.1128/msystems.00864-24
[43]

Huang G, Khan I, Li X, Chen L, Leong W, et al. 2017. Ginsenosides Rb3 and Rd reduce polyps formation while reinstate the dysbiotic gut microbiota and the intestinal microenvironment in ApcMin/+ mice. Scientific Reports 7:12552

doi: 10.1038/s41598-017-12644-5
[44]

Hamilton AL, Kamm MA, Ng SC, Morrison M. 2018. Proteus spp. as putative gastrointestinal pathogens. Clinical Microbiology Reviews 31:e00085-17

doi: 10.1128/cmr.00085-17
[45]

Brodin P. 2022. Immune-microbe interactions early in life: a determinant of health and disease long term. Science 376:945−950

doi: 10.1126/science.abk2189
[46]

Wallen ZD. 2021. Comparison study of differential abundance testing methods using two large Parkinson disease gut microbiome datasets derived from 16S amplicon sequencing. BMC Bioinformatics 22:265

doi: 10.1186/s12859-021-04193-6
[47]

Srinivasan S, Jnana A, Murali TS. 2024. Modeling microbial community networks: methods and tools for studying microbial interactions. Microbial Ecology 87:56

doi: 10.1007/s00248-024-02370-7
[48]

Oña L, Shreekar SK, Kost C. 2025. Disentangling microbial interaction networks. Trends in Microbiology 33:619−634

doi: 10.1016/j.tim.2025.01.013
[49]

Wu D, Wang AJ, Bu DC, Sun YY, Li CH, et al. 2025. The interplay between tissue-resident microbiome and host proteins by integrated multi-omics during progression of colorectal adenoma to carcinoma. iMeta 4:e70090

doi: 10.1002/imt2.70090
[50]

Mousa WK, Chehadeh F, Husband S. 2022. Microbial dysbiosis in the gut drives systemic autoimmune diseases. Frontiers in Immunology 13:906258

doi: 10.3389/fimmu.2022.906258
[51]

Dovrolis N, Gazouli M, Rigal F, Whittaker RJ, Matthews TJ, et al. 2024. Power-law scaling in intratumoral microbiota of colorectal cancer. Gut Pathogens 16:34

doi: 10.1186/s13099-024-00631-x
[52]

Joos R, Boucher K, Lavelle A, Arumugam M, Blaser MJ, et al. 2025. Examining the healthy human microbiome concept. Nature Reviews Microbiology 23:192−205

doi: 10.1038/s41579-024-01107-0
[53]

Chen Z, Zhang Z, Nie BN, Huang W, Zhu Y, et al. 2025. Temporal network analysis of gut microbiota unveils aging trajectories associated with colon cancer. mSystems 10:e01188-24

doi: 10.1128/msystems.01188-24
[54]

Li J, Convertino M. 2019. Optimal microbiome networks: macroecology and criticality. Entropy 21:506

doi: 10.3390/e21050506
[55]

O'Malley MA. 2024. The concept of balance in microbiome research. BioEssays 46:2400050

doi: 10.1002/bies.202400050
[56]

Lupatini M, Suleiman AKA, Jacques RJS, Antoniolli ZI, de Siqueira Ferreira A, et al. 2014. Network topology reveals high connectance levels and few key microbial genera within soils. Frontiers in Environmental Science 2:10

doi: 10.3389/fenvs.2014.00010
[57]

Peura S, Bertilsson S, Jones RI, Eiler A. 2015. Resistant microbial cooccurrence patterns inferred by network topology. Applied and Environmental Microbiology 81:2090−2097

doi: 10.1128/AEM.03660-14
[58]

Ai D, Pan H, Li X, Wu M, Xia LC. 2019. Association network analysis identifies enzymatic components of gut microbiota that significantly differ between colorectal cancer patients and healthy controls. PeerJ 7:e7315

doi: 10.7717/peerj.7315