Metagenomics: A New Horizon in Cancer Research

Overview

Journal Meta Gene

Publisher Elsevier

Specialty Genetics

Date 2015 Jun 26

PMID 26110115

Citations 9

Authors

Joyita Banerjee

Neetu Mishra

Yogita Dhas

Affiliations

Soon will be listed here.

Abstract

Metagenomics has broadened the scope of targeting microbes responsible for inducing various types of cancers. About 16.1% of cancers are associated with microbial infection. Metagenomics is an equitable way of identifying and studying micro-organisms within their habitat. In cancer research, this approach has revolutionized the way of identifying, analyzing and targeting the microbial diversity present in the tissue specimens of cancer patients. The genomic analyses of these micro-organisms through next generation sequencing techniques invariably facilitate in recognizing the microbial population in biopsies and their evolutionary relationships with each other. In this review an attempt has been made to generate current metagenomic view on cancer microbiota. Different types of micro-organisms have been found to be linked to various types of cancers, thus, contributing significantly in understanding the disease at molecular level.

Citing Articles

Human papillomavirus, vaginal microbiota and metagenomics: the interplay between development and progression of cervical cancer.

Leon-Gomez P, Romero V Front Microbiol. 2025; 15:1515258.

PMID: 39911706 PMC: 11794528. DOI: 10.3389/fmicb.2024.1515258.

Power-law scaling in intratumoral microbiota of colorectal cancer.

Dovrolis N, Gazouli M, Rigal F, Whittaker R, Matthews T, Georgiou K Gut Pathog. 2024; 16(1):34.

PMID: 38972996 PMC: 11229225. DOI: 10.1186/s13099-024-00631-x.

Finding phylogeny-aware and biologically meaningful averages of metagenomic samples: L2UniFrac.

Wei W, Millward A, Koslicki D Bioinformatics. 2023; 39(39 Suppl 1):i57-i65.

PMID: 37387190 PMC: 10311324. DOI: 10.1093/bioinformatics/btad238.

Bioinformatic Tools for NGS-Based Metagenomics to Improve the Clinical Diagnosis of Emerging, Re-Emerging and New Viruses.

Ibanez-Lligona M, Colomer-Castell S, Gonzalez-Sanchez A, Gregori J, Campos C, Garcia-Cehic D Viruses. 2023; 15(2).

PMID: 36851800 PMC: 9965957. DOI: 10.3390/v15020587.

Finding phylogeny-aware and biologically meaningful averages of metagenomic samples: UniFrac.

Wei W, Millward A, Koslicki D bioRxiv. 2023; .

PMID: 36778267 PMC: 9915697. DOI: 10.1101/2023.02.02.526854.

References

de Martel C, Ferlay J, Franceschi S, Vignat J, Bray F, Forman D . Global burden of cancers attributable to infections in 2008: a review and synthetic analysis. Lancet Oncol. 2012; 13(6):607-15. DOI: 10.1016/S1470-2045(12)70137-7. View

Polissi A, Soria M . Functional genomics of bacterial pathogens: from post-genomics to therapeutic targets. Mol Microbiol. 2005; 57(2):307-12. DOI: 10.1111/j.1365-2958.2005.04480.x. View

McCOY W, MASON 3rd J . Enterococcal endocarditis associated with carcinoma of the sigmoid; report of a case. J Med Assoc State Ala. 1951; 21(6):162-6. View

Yooseph S, Andrews-Pfannkoch C, Tenney A, McQuaid J, Williamson S, Thiagarajan M . A metagenomic framework for the study of airborne microbial communities. PLoS One. 2013; 8(12):e81862. PMC: 3859506. DOI: 10.1371/journal.pone.0081862. View

Chen K, Pachter L . Bioinformatics for whole-genome shotgun sequencing of microbial communities. PLoS Comput Biol. 2005; 1(2):106-12. PMC: 1185649. DOI: 10.1371/journal.pcbi.0010024. View

Paulino L, Tseng C, Strober B, Blaser M . Molecular analysis of fungal microbiota in samples from healthy human skin and psoriatic lesions. J Clin Microbiol. 2006; 44(8):2933-41. PMC: 1594634. DOI: 10.1128/JCM.00785-06. View

Butel J, Lednicky J . Cell and molecular biology of simian virus 40: implications for human infections and disease. J Natl Cancer Inst. 1999; 91(2):119-34. DOI: 10.1093/jnci/91.2.119. View

Barete S, Calvez V, Mouquet C, Barrou B, Kreis H, Dantal J . Clinical features and contribution of virological findings to the management of Kaposi sarcoma in organ-allograft recipients. Arch Dermatol. 2000; 136(12):1452-8. DOI: 10.1001/archderm.136.12.1452. View

Dejea C, Wick E, Sears C . Bacterial oncogenesis in the colon. Future Microbiol. 2013; 8(4):445-60. PMC: 4052711. DOI: 10.2217/fmb.13.17. View

10.

Zheng Z, Andersson A, Ye W, Nyren O, Normark S, Engstrand L . A method for metagenomics of Helicobacter pylori from archived formalin-fixed gastric biopsies permitting longitudinal studies of carcinogenic risk. PLoS One. 2011; 6(10):e26442. PMC: 3198776. DOI: 10.1371/journal.pone.0026442. View

11.

Gao Z, Tseng C, Pei Z, Blaser M . Molecular analysis of human forearm superficial skin bacterial biota. Proc Natl Acad Sci U S A. 2007; 104(8):2927-32. PMC: 1815283. DOI: 10.1073/pnas.0607077104. View

12.

Pushalkar S, Mane S, Ji X, Li Y, Evans C, Crasta O . Microbial diversity in saliva of oral squamous cell carcinoma. FEMS Immunol Med Microbiol. 2011; 61(3):269-77. PMC: 3078631. DOI: 10.1111/j.1574-695X.2010.00773.x. View

13.

de Sanjose S, Quint W, Alemany L, Geraets D, Klaustermeier J, Lloveras B . Human papillomavirus genotype attribution in invasive cervical cancer: a retrospective cross-sectional worldwide study. Lancet Oncol. 2010; 11(11):1048-56. DOI: 10.1016/S1470-2045(10)70230-8. View

14.

Mardis E . Next-generation DNA sequencing methods. Annu Rev Genomics Hum Genet. 2008; 9:387-402. DOI: 10.1146/annurev.genom.9.081307.164359. View

15.

Strauss J, Kaplan G, Beck P, Rioux K, Panaccione R, DeVinney R . Invasive potential of gut mucosa-derived Fusobacterium nucleatum positively correlates with IBD status of the host. Inflamm Bowel Dis. 2011; 17(9):1971-8. DOI: 10.1002/ibd.21606. View

16.

Dicksved J, Lindberg M, Rosenquist M, Enroth H, Jansson J, Engstrand L . Molecular characterization of the stomach microbiota in patients with gastric cancer and in controls. J Med Microbiol. 2009; 58(Pt 4):509-516. DOI: 10.1099/jmm.0.007302-0. View

17.

Till A, Goulden V, Cunliffe W, Holland K . The cutaneous microflora of adolescent, persistent and late-onset acne patients does not differ. Br J Dermatol. 2000; 142(5):885-92. DOI: 10.1046/j.1365-2133.2000.03467.x. View

18.

Xie G, Chain P, Lo C, Liu K, Gans J, Merritt J . Community and gene composition of a human dental plaque microbiota obtained by metagenomic sequencing. Mol Oral Microbiol. 2010; 25(6):391-405. PMC: 2975940. DOI: 10.1111/j.2041-1014.2010.00587.x. View

19.

zur Hausen H . Papillomavirus infections--a major cause of human cancers. Biochim Biophys Acta. 1996; 1288(2):F55-78. DOI: 10.1016/0304-419x(96)00020-0. View

20.

Rous P . A SARCOMA OF THE FOWL TRANSMISSIBLE BY AN AGENT SEPARABLE FROM THE TUMOR CELLS. J Exp Med. 2009; 13(4):397-411. PMC: 2124874. DOI: 10.1084/jem.13.4.397. View