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Current Bioinformatics

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ISSN (Print): 1574-8936
ISSN (Online): 2212-392X

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Research Article

The Human OncoBiome Database: A Database of Cancer Microbiome Datasets

Author(s): Nadia and Jayashree Ramana*

Volume 15, Issue 5, 2020

Page: [472 - 477] Pages: 6

DOI: 10.2174/1574893614666190902152727

Price: $65

Abstract

Background: The microbiome plays a very important role in many physiological processes including metabolism, inflammation, homeostasis and many biological pathways. Therefore, dysbiosis of the microbiome disrupts these pathways in different ways that may result in causing cancer. There is a complex connection between the microbiome and cancer. The human bodies are continuously exposed to microbial cells, both resident and transient, as well as their byproducts, including toxic metabolites.

Objective: To develop the manually curated, searchable and metagenomic resource to facilitate the investigation of Human Cancer microbiota and make it publicly accessible through a web interface which will help further in metagenomic studies.

Methods: In HOBD, the information on different cancers (Oral Cancer, Breast Cancer, Liver Cancer, and Colorectal Cancer) has been compiled. The main purpose of creating HOBD was to provide the scientific community with comprehensive information on the species that play a crucial role in various Human Cancers.

Result: Over time, this resource will grow to become a unique community resource of human cancer bacteria, providing an extra level of annotation for the analysis of metagenomic datasets.

Conclusion: The HOBD site offers easy to use tools for viewing all publicly available Human Cancer microbiota. The freely accessible website is available at http://www.juit.ac.in/hcmd/home.

Keywords: Microbiome, cancer, database, metagenomics, HOBD, metabolism.

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[1]
Fulbright LE, Ellermann M. The microbiome and the hallmarks of cancer. PLoS Pathog 2017; 3 e1006480
[http://dx.doi.org/10.1371/journal.ppat.1006480]
[2]
Goodman B, Gardner H. The microbiome and cancer. J Pathol 2018; 244(5): 667-76.
[http://dx.doi.org/10.1002/path.5047] [PMID: 29377130]
[3]
Ohtani N. Microbiome and cancer. Semin Immunopathol 2015; 37(1): 65-72.
[http://dx.doi.org/10.1007/s00281-014-0457-1] [PMID: 25404117]
[4]
Meng S, Chen B, Yang J, et al. Study of microbiomes in aseptically collected samples of human breast tissue using needle biopsy and the potential role of in situ tissue microbiomes for promoting malignancy. Front Oncol 2018; 8: 318.
[http://dx.doi.org/10.3389/fonc.2018.00318] [PMID: 30175072]
[5]
Human Microbiome Project Consortium. Structure, function and diversity of the healthy human microbiome. Nature 2012; 486(7402): 207-14.
[http://dx.doi.org/10.1038/nature11234] [PMID: 22699609]
[6]
Ravel J, Blaser MJ, Braun J, et al. Human microbiome science: vision for the future, Bethesda, MD, July 24 to 26, 2013. Microbiome 2014; 2: 16-6.
[http://dx.doi.org/10.1186/2049-2618-2-16]
[7]
Sellner KG, Doucette GJ, Kirkpatrick GJ. Harmful algal blooms: causes, impacts and detection. J Ind Microbiol Biotechnol 2003; 30(7): 383-406.
[http://dx.doi.org/10.1007/s10295-003-0074-9] [PMID: 12898390]
[8]
Zeller G, Tap J, Voigt AY, et al. Potential of fecal microbiota for early-stage detection of colorectal cancer. Mol Syst Biol 2014; 10: 766.
[http://dx.doi.org/10.15252/msb.20145645] [PMID: 25432777]
[9]
Kinross J, Mirnezami R, Alexander J, et al. A prospective analysis of mucosal microbiome-metabonome interactions in colorectal cancer using a combined MAS 1HNMR and metataxonomic strategy. Sci Rep 2017; 7(1): 8979.
[http://dx.doi.org/10.1038/s41598-017-08150-3] [PMID: 28827587]
[10]
Burns MB, Montassier E, Abrahante J, et al. Colorectal cancer mutational profiles correlate with defined microbial communities in the tumor microenvironment. PLoS Genet 2018; 14(6) e1007376
[http://dx.doi.org/10.1371/journal.pgen.1007376] [PMID: 29924794]
[11]
Park CH, Eun CS, Han DS. Intestinal microbiota, chronic inflammation, and colorectal cancer. Intest Res 2018; 16(3): 338-45.
[http://dx.doi.org/10.5217/ir.2018.16.3.338] [PMID: 30090032]
[12]
Farhana L, Banerjee HN, Verma M, Majumdar APN. Role of Microbiome in Carcinogenesis Process and Epigenetic Regulation of Colorectal Cancer. Methods Mol Biol 2018; 1856: 35-55.
[http://dx.doi.org/10.1007/978-1-4939-8751-1_3] [PMID: 30178245]
[13]
Mendonça LABM, Dos Santos Ferreira R, de Cássia Avellaneda Guimarães R, et al. The complex puzzle of interactions among functional food, gut microbiota, and colorectal cancer. Front Oncol 2018; 8: 325.
[http://dx.doi.org/10.3389/fonc.2018.00325] [PMID: 30234008]
[14]
Loo TM, Kamachi F, Watanabe Y, et al. Gut microbiota promotes obesity-associated liver cancer through pge2-mediated suppression of antitumor immunity. Cancer Discov 2017; 7(5): 522-38.
[http://dx.doi.org/10.1158/2159-8290.CD-16-0932] [PMID: 28202625]
[15]
Ma C, Han M, Heinrich B. Gut microbiome-mediated bile acid metabolism regulates liver cancer via NKT cells. Science 2018; 360 eaan5931
[http://dx.doi.org/10.1126/science.aan5931]
[16]
Morgan XC, Huttenhower C. Chapter 12: Human microbiome analysis. PLOS Comput Biol 2012; 8(12) e1002808
[http://dx.doi.org/10.1371/journal.pcbi.1002808] [PMID: 23300406]
[17]
Fernández MF, Reina-Pérez I, Astorga JM, Rodríguez-Carrillo A, Plaza-Díaz J, Fontana L. Breast cancer and its relationship with the microbiota. int j environ res public health 2018; 15(8): 1747.
[http://dx.doi.org/10.3390/ijerph15081747] [PMID: 30110974]
[18]
Gianoulis TA, Raes J, Patel PV, et al. Quantifying environmental adaptation of metabolic pathways in metagenomics. Proc Natl Acad Sci USA
[http://dx.doi.org/10.1073/pnas.0808022106]]
[19]
Vogtmann E, Hua X, Zeller G, et al. Colorectal Cancer and the Human Gut Microbiome: Reproducibility with Whole-Genome Shotgun Sequencing. PLoS One 2016; 11(5) e0155362
[http://dx.doi.org/10.1371/journal.pone.0155362] [PMID: 27171425]
[20]
Lozupone C, Lladser ME, Knights D, Stombaugh J, Knight R. UniFrac: an effective distance metric for microbial community comparison. ISME J 2011; 5(2): 169-72.
[http://dx.doi.org/10.1038/ismej.2010.133] [PMID: 20827291]
[21]
Lee W-H, Chen H-M, Yang S-F, et al. Bacterial alterations in salivary microbiota and their association in oral cancer. Sci Rep 2017; 7(1): 16540.
[http://dx.doi.org/10.1038/s41598-017-16418-x] [PMID: 29184122]
[22]
Dahmus JD, Kotler DL, Kastenberg DM, Kistler CA. The gut microbiome and colorectal cancer: a review of bacterial pathogenesis. J Gastrointest Oncol 2018; 9(4): 769-77.
[http://dx.doi.org/10.21037/jgo.2018.04.07] [PMID: 30151274]
[23]
Asmaa Ezzat MNMI, Irni Suhayu Sapian, et al. Metagenomic Study of the Liver Microbiota in Liver Cancer-Metagenomic and Metatranscriptomic Analyses of the Hepatocellular Carcinoma- Associated Microbial Communities and the Potential Role of Microbial Communities in Liver Cancer. J Gastrointest Dig Syst 2014; 4: 228.
[http://dx.doi.org/10.4172/2161-069X.1000228]
[24]
Thompson KJ, Ingle JN, Tang X, et al. A comprehensive analysis of breast cancer microbiota and host gene expression. PLoS One 2017; 12(11) e0188873
[http://dx.doi.org/10.1371/journal.pone.0188873] [PMID: 29190829]
[25]
Seshadri R, Kravitz SA, Smarr L, Gilna P, Frazier M. CAMERA: a community resource for metagenomics. PLoS Biol 2007; 5(3) e75
[http://dx.doi.org/10.1371/journal.pbio.0050075] [PMID: 17355175]
[26]
Amer A, Galvin S, Healy CM, Moran GP. The Microbiome of Potentially Malignant Oral Leukoplakia Exhibits Enrichment for Fusobacterium, Leptotrichia, Campylobacter, and Rothia Species. Front Microbiol 2017; 8: 2391.
[http://dx.doi.org/10.3389/fmicb.2017.02391] [PMID: 29250055]

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