REFERENCES
1. NIH. Cancer stat facts: female breast cancer subtypes. Available from: https://seer.cancer.gov/statfacts/html/breast-subtypes.html. [Last accessed on 26 Oct 2024].
2. Rugo HS, Delord JP, Im SA, et al. Safety and antitumor activity of pembrolizumab in patients with estrogen receptor-positive/human epidermal growth factor receptor 2-negative advanced breast cancer. Clin Cancer Res 2018;24:2804-11.
3. Nanda R, Liu MC, Yau C, et al. Effect of pembrolizumab plus neoadjuvant chemotherapy on pathologic complete response in women with early-stage breast cancer: an analysis of the ongoing phase 2 adaptively randomized I-SPY2 trial. JAMA Oncol 2020;6:676-84.
4. Pérez-García JM, Llombart-Cussac A, G Cortés M, et al. Pembrolizumab plus eribulin in hormone-receptor-positive, HER2-negative, locally recurrent or metastatic breast cancer (KELLY): an open-label, multicentre, single-arm, phase II trial. Eur J Cancer 2021;148:382-94.
5. Cortes J, O’Shaughnessy J, Loesch D, et al; EMBRACE (Eisai Metastatic Breast Cancer Study Assessing Physician’s Choice Versus E7389) investigators. Eribulin monotherapy versus treatment of physician’s choice in patients with metastatic breast cancer (EMBRACE): a phase 3 open-label randomised study. Lancet 2011;377:914-23.
6. Lee SH, Cho SY, Yoon Y, et al. Bifidobacterium bifidum strains synergize with immune checkpoint inhibitors to reduce tumour burden in mice. Nat Microbiol 2021;6:277-88.
7. Sivan A, Corrales L, Hubert N, et al. Commensal Bifidobacterium promotes antitumor immunity and facilitates anti-PD-L1 efficacy. Science 2015;350:1084-9.
8. Tanoue T, Morita S, Plichta DR, et al. A defined commensal consortium elicits CD8 T cells and anti-cancer immunity. Nature 2019;565:600-5.
9. Viaud S, Saccheri F, Mignot G, et al. The intestinal microbiota modulates the anticancer immune effects of cyclophosphamide. Science 2013;342:971-6.
10. Iida N, Dzutsev A, Stewart CA, et al. Commensal bacteria control cancer response to therapy by modulating the tumor microenvironment. Science 2013;342:967-70.
11. Gopalakrishnan V, Spencer CN, Nezi L, et al. Gut microbiome modulates response to anti-PD-1 immunotherapy in melanoma patients. Science 2018;359:97-103.
12. Davar D, Dzutsev AK, McCulloch JA, et al. Fecal microbiota transplant overcomes resistance to anti-PD-1 therapy in melanoma patients. Science 2021;371:595-602.
13. Routy B, Le Chatelier E, Derosa L, et al. Gut microbiome influences efficacy of PD-1-based immunotherapy against epithelial tumors. Science 2018;359:91-7.
14. Vétizou M, Pitt JM, Daillère R, et al. Anticancer immunotherapy by CTLA-4 blockade relies on the gut microbiota. Science 2015;350:1079-84.
15. Routy B, Gopalakrishnan V, Daillère R, Zitvogel L, Wargo JA, Kroemer G. The gut microbiota influences anticancer immunosurveillance and general health. Nat Rev Clin Oncol 2018;15:382-96.
16. Burugu S, Asleh-Aburaya K, Nielsen TO. Immune infiltrates in the breast cancer microenvironment: detection, characterization and clinical implication. Breast Cancer 2017;24:3-15.
17. Kitamoto S, Nagao-Kitamoto H, Hein R, Schmidt TM, Kamada N. The bacterial connection between the oral cavity and the gut diseases. J Dent Res 2020;99:1021-9.
18. Dore J, Ehrlich SD, Levenez F, et al.
19. Caporaso JG, Lauber CL, Walters WA, et al. Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. ISME J 2012;6:1621-4.
20. Kiu R, Brown J, Bedwell H, et al. Genomic analysis on broiler-associated Clostridium perfringens strains and exploratory caecal microbiome investigation reveals key factors linked to poultry necrotic enteritis. Anim Microbiome 2019;1:12.
21. Huson DH, Beier S, Flade I, et al. MEGAN community edition - interactive exploration and analysis of large-scale microbiome sequencing data. PLoS Comput Biol 2016;12:e1004957.
22. The comprehensive R archive network. https://cran.r-project.org/. [Last accessed on 26 Oct 2024]
23. Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol 2014;15:550.
24. Chen S, Zhou Y, Chen Y, Gu J. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 2018;34:i884-90.
25. Beghini F, McIver LJ, Blanco-Míguez A, et al. Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3. Elife 2021;10:e65088.
26. Li D, Liu CM, Luo R, Sadakane K, Lam TW. MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. Bioinformatics 2015;31:1674-6.
27. Uritskiy GV, DiRuggiero J, Taylor J. MetaWRAP-a flexible pipeline for genome-resolved metagenomic data analysis. Microbiome 2018;6:158.
28. Wood DE, Lu J, Langmead B. Improved metagenomic analysis with Kraken 2. Genome Biol 2019;20:257.
29. Lu J, Breitwieser FP, Thielen P, Salzberg SL. Bracken: estimating species abundance in metagenomics data. PeerJ Computer Science 2017;3:e104.
30. Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 2015;25:1043-55.
31. Finn RD, Clements J, Eddy SR. HMMER web server: interactive sequence similarity searching. Nucleic Acids Res 2011;39:W29-37.
32. Hyatt D, LoCascio PF, Hauser LJ, Uberbacher EC. Gene and translation initiation site prediction in metagenomic sequences. Bioinformatics 2012;28:2223-30.
33. Wu YW, Simmons BA, Singer SW. MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets. Bioinformatics 2016;32:605-7.
34. Kang DD, Li F, Kirton E, et al. MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies. PeerJ 2019;7:e7359.
35. Chaumeil PA, Mussig AJ, Hugenholtz P, Parks DH. GTDB-Tk: a toolkit to classify genomes with the genome taxonomy database. Bioinformatics 2019;36:1925-7.
36. vegan: an R package for community ecologists. Available from: https://github.com/vegandevs/vegan/. [Last accessed on 26 Oct 2024].
37. Segata N, Izard J, Waldron L, et al. Metagenomic biomarker discovery and explanation. Genome Biol 2011;12:R60.
38. Zhou Z, Tran PQ, Breister AM, et al. METABOLIC: high-throughput profiling of microbial genomes for functional traits, metabolism, biogeochemistry, and community-scale functional networks. Microbiome 2022;10:33.
39. Florensa AF, Kaas RS, Clausen PTLC, Aytan-Aktug D, Aarestrup FM. ResFinder - an open online resource for identification of antimicrobial resistance genes in next-generation sequencing data and prediction of phenotypes from genotypes. Microb Genom 2022;8:000748.
40. Zankari E, Hasman H, Cosentino S, et al. Identification of acquired antimicrobial resistance genes. J Antimicrob Chemother 2012;67:2640-4.
41. Franco AA, Mundy LM, Trucksis M, Wu S, Kaper JB, Sears CL. Cloning and characterization of the Bacteroides fragilis metalloprotease toxin gene. Infect Immun 1997;65:1007-13.
42. Seemann T. ABRicate. 1.0.1 ed. Available from: https://github.com/tseemann/abricate. [Last accessed on 26 Oct 2024].
43. Dybdal-Hargreaves NF, Risinger AL, Mooberry SL. Eribulin mesylate: mechanism of action of a unique microtubule-targeting agent. Clin Cancer Res 2015;21:2445-52.
44. Swami U, Chaudhary I, Ghalib MH, Goel S. Eribulin - a review of preclinical and clinical studies. Crit Rev Oncol Hematol 2012;81:163-84.
45. Zhang ZY, King BM, Pelletier RD, Wong YN. Delineation of the interactions between the chemotherapeutic agent eribulin mesylate (E7389) and human CYP3A4. Cancer Chemother Pharmacol 2008;62:707-16.
46. Mazmanian SK, Liu CH, Tzianabos AO, Kasper DL. An immunomodulatory molecule of symbiotic bacteria directs maturation of the host immune system. Cell 2005;122:107-18.
47. Dasgupta S, Erturk-Hasdemir D, Ochoa-Reparaz J, Reinecker HC, Kasper DL. Plasmacytoid dendritic cells mediate anti-inflammatory responses to a gut commensal molecule via both innate and adaptive mechanisms. Cell Host Microbe 2014;15:413-23.
48. Barton LL, Ritz NL, Fauque GD, Lin HC. Sulfur cycling and the intestinal microbiome. Dig Dis Sci 2017;62:2241-57.
49. Krinos CM, Coyne MJ, Weinacht KG, Tzianabos AO, Kasper DL, Comstock LE. Extensive surface diversity of a commensal microorganism by multiple DNA inversions. Nature 2001;414:555-8.
50. Baruch EN, Youngster I, Ben-Betzalel G, et al. Fecal microbiota transplant promotes response in immunotherapy-refractory melanoma patients. Science 2021;371:602-9.
51. Dizman N, Meza L, Bergerot P, et al. Nivolumab plus ipilimumab with or without live bacterial supplementation in metastatic renal cell carcinoma: a randomized phase 1 trial. Nat Med 2022;28:704-12.
52. Iida N, Stewart C, Goldszmid R, Dzutsev A, Trinchieri G. Gut commensal bacteria promote anti-tumor innate immune responses in distant tumors after immunotherapy and chemotherapy (162.5). J Immunol 2012;188:162.5.
53. Li Y, Tinoco R, Elmén L, et al. Gut microbiota dependent anti-tumor immunity restricts melanoma growth in Rnf5-/- mice. Nat Commun 2019;10:1492.
54. Mager LF, Burkhard R, Pett N, et al. Microbiome-derived inosine modulates response to checkpoint inhibitor immunotherapy. Science 2020;369:1481-9.
55. McKee AM, Kirkup BM, Madgwick M, et al. Antibiotic-induced disturbances of the gut microbiota result in accelerated breast tumor growth. iScience 2021;24:103012.
56. Roy S, Trinchieri G. Microbiota: a key orchestrator of cancer therapy. Nat Rev Cancer 2017;17:271-85.
57. Teng NMY, Price CA, McKee AM, Hall LJ, Robinson SD. Exploring the impact of gut microbiota and diet on breast cancer risk and progression. Int J Cancer 2021;149:494-504.
58. Latorre-Pérez A, Hernández M, Iglesias JR, et al. The Spanish gut microbiome reveals links between microorganisms and Mediterranean diet. Sci Rep 2021;11:21602.
59. Han YW. Fusobacterium nucleatum: a commensal-turned pathogen. Curr Opin Microbiol 2015;23:141-7.
60. Castellarin M, Warren RL, Freeman JD, et al. Fusobacterium nucleatum infection is prevalent in human colorectal carcinoma. Genome Res 2012;22:299-306.
61. Kostic AD, Gevers D, Pedamallu CS, et al. Genomic analysis identifies association of Fusobacterium with colorectal carcinoma. Genome Res 2012;22:292-8.
62. Parhi L, Alon-Maimon T, Sol A, et al. Breast cancer colonization by Fusobacterium nucleatum accelerates tumor growth and metastatic progression. Nat Commun 2020;11:3259.
63. Sulyanto RM, Thompson ZA, Beall CJ, Leys EJ, Griffen AL. The predominant oral microbiota is acquired early in an organized pattern. Sci Rep 2019;9:10550.
64. Kawasaki M, Ikeda Y, Ikeda E, et al. Oral infectious bacteria in dental plaque and saliva as risk factors in patients with esophageal cancer. Cancer 2021;127:512-9.
65. Mukherjee PK, Wang H, Retuerto M, et al. Bacteriome and mycobiome associations in oral tongue cancer. Oncotarget 2017;8:97273-89.
66. Zhou CB, Pan SY, Jin P, et al. Fecal signatures of Streptococcus anginosus and Streptococcus constellatus for noninvasive screening and early warning of gastric cancer. Gastroenterology 2022;162:1933-47.e18.
67. Perdigon G, Nader de Macias ME, Alvarez S, Oliver G, Pesce de Ruiz Holgado AA. Enhancement of immune response in mice fed with Streptococcus thermophilus and Lactobacillus acidophilus. J Dairy Sci 1987;70:919-26.
68. Kaci G, Goudercourt D, Dennin V, et al. Anti-inflammatory properties of Streptococcus salivarius, a commensal bacterium of the oral cavity and digestive tract. Appl Environ Microbiol 2014;80:928-34.
69. Nearing JT, Douglas GM, Hayes MG, et al. Microbiome differential abundance methods produce different results across 38 datasets. Nat Commun 2022;13:342.
70. Chen F, Dai X, Zhou CC, et al. Integrated analysis of the faecal metagenome and serum metabolome reveals the role of gut microbiome-associated metabolites in the detection of colorectal cancer and adenoma. Gut 2022;71:1315-25.
71. Hezaveh K, Shinde RS, Klötgen A, et al. Tryptophan-derived microbial metabolites activate the aryl hydrocarbon receptor in tumor-associated macrophages to suppress anti-tumor immunity. Immunity 2022;55:324-40.e8.
72. Neff CP, Rhodes ME, Arnolds KL, et al. Diverse intestinal bacteria contain putative zwitterionic capsular polysaccharides with anti-inflammatory properties. Cell Host Microbe 2016;20:535-47.
73. Gul L, Modos D, Fonseca S, et al. Extracellular vesicles produced by the human commensal gut bacterium Bacteroides thetaiotaomicron affect host immune pathways in a cell-type specific manner that are altered in inflammatory bowel disease. J Extracell Vesicles 2022;11:e12189.
74. Zhang M, Zhou Q, Dorfman RG, et al. Butyrate inhibits interleukin-17 and generates tregs to ameliorate colorectal colitis in rats. BMC Gastroenterol 2016;16:84.
75. Kovács T, Mikó E, Vida A, et al. Cadaverine, a metabolite of the microbiome, reduces breast cancer aggressiveness through trace amino acid receptors. Sci Rep 2019;9:1300.
76. Mikó E, Vida A, Kovács T, et al. Lithocholic acid, a bacterial metabolite reduces breast cancer cell proliferation and aggressiveness. Biochim Biophys Acta Bioenerg 2018;1859:958-74.
77. Corander J, Hanage WP, Pensar J. Causal discovery for the microbiome. Lancet Microbe 2022;3:e881-7.
