Microbiome

Introduction

Microbiota is the sum total of all organisms present in the human body. It includes bacteria, fungi, viruses, and other unicellular organisms. Microbiome is the combined genetic material from all microorganisms in a given host. The terms microbiome and microbiota are generally used interchangeably. As per the Human Microbiome Project, human microbiota harbors 10 to 100 trillion organisms. It means for every human cell, there are 10 times more microbes present. The microbiome is present in all parts of the body with the preponderance at the skin, oral cavity, lower gastrointestinal tract, upper respiratory tract, and genitourinary tract.[1] [2]

As per the International Cancer Microbiome Consortium Meeting, various terms used in the study of microbiome are tabulated as in [Table 1].

Table 1 Definitions used in the study of microbiome

Term	Definition
Microbiome	The combined genetic material from all microorganisms in a specified niche
Microbiota	All the microorganisms in a specified niche
Dysbiosis	Departure from the healthy microbiome state
Symbiont	An organism living closely with another
Mutualistic	An organism living closely with another and both organism benefit
Commensalistic	An organism living closely with another and one benefits while others are not benefited
Parasitic	An organism living closely with another and benefits by harming another
Amensalistic	An organism living closely with another and no benefit by harming another
Pathogen	A microorganism that can cause disease
Pathobiont	Microorganisms present in the microbiota that can cause disease
Pharmacomicrobiomics	The study of the interaction of host microbiome and drugs

Publication History

Article published online:
24 December 2021

• References

• 1 Human Microbiome Project Consortium. Structure, function and diversity of the healthy human microbiome. Nature 2012; 486 (7402): 207-214
• 2 Rosner JL. Ten times more microbial cells than body cells in humans?. Microbe 2014; 9: 47
• 3 Penders J, Gerhold K, Thijs C. et al. New insights into the hygiene hypothesis in allergic diseases: mediation of sibling and birth mode effects by the gut microbiota. Gut Microbes 2014; 5 (02) 239-244
• 4 Penders J, Thijs C, Vink C. et al. Factors influencing the composition of the intestinal microbiota in early infancy. Pediatrics 2006; 118 (02) 511-521
• 5 Chen L, Zhang YH, Huang T, Cai YD. Gene expression profiling gut microbiota in different races of humans. Sci Rep 2016; 6: 23075
• 6 Nougayrède JP, Homburg S, Taieb F. et al. Escherichia coli induces DNA double-strand breaks in eukaryotic cells. Science 2006; 313 (5788): 848-851
• 7 Cougnoux A, Dalmasso G, Martinez R. et al. Bacterial genotoxin colibactin promotes colon tumour growth by inducing a senescence-associated secretory phenotype. Gut 2014; 63 (12) 1932-1942
• 8 Polk DB, Peek Jr RM. Helicobacter pylori: gastric cancer and beyond. Nat Rev Cancer 2010; 10 (06) 403-414
• 9 Wu S, Rhee KJ, Albesiano E. et al. A human colonic commensal promotes colon tumorigenesis via activation of T helper type 17 T cell responses. Nat Med 2009; 15 (09) 1016-1022
• 10 Williams VM, Filippova M, Soto U, Duerksen-Hughes PJ. HPV-DNA integration and carcinogenesis: putative roles for inflammation and oxidative stress. Future Virol 2011; 6 (01) 45-57
• 11 Gaines S, Williamson AJ, Hyman N, Kandel J. How the microbiome is shaping our understanding of cancer biology and its treatment. Semin Colon Rectal Surg 2018; 29: 12-16
• 12 Wynendaele E, Verbeke F, D'Hondt M. et al. Crosstalk between the microbiome and cancer cells by quorum sensing peptides. Peptides 2015; 64: 40-48
• 13 Furusawa Y, Obata Y, Fukuda S. et al. Commensal microbe-derived butyrate induces the differentiation of colonic regulatory T cells. Nature 2013; 504 (7480): 446-450
• 14 Liang L, Ai L, Qian J, Fang JY, Xu J. Long noncoding RNA expression profiles in gut tissues constitute molecular signatures that reflect the types of microbes. Sci Rep 2015; 5: 11763
• 15 Ríos-Covián D, Ruas-Madiedo P, Margolles A, Gueimonde M, de Los Reyes-Gavilán CG, Salazar N. Intestinal short chain fatty acids and their link with diet and human health. Front Microbiol 2016; 7: 185
• 16 Li F, Hullar MA, Schwarz Y, Lampe JW. Human gut bacterial communities are altered by addition of cruciferous vegetables to a controlled fruit- and vegetable-free diet. J Nutr 2009; 139 (09) 1685-1691
• 17 Russell WR, Gratz SW, Duncan SH. et al. High-protein, reduced-carbohydrate weight-loss diets promote metabolite profiles likely to be detrimental to colonic health. Am J Clin Nutr 2011; 93 (05) 1062-1072
• 18 Bashiardes S, Tuganbaev T, Federici S, Elinav E. The microbiome in anti-cancer therapy. Semin Immunol 2017; 32: 74-81
• 19 Fulbright LE, Ellermann M, Arthur JC. The microbiome and the hallmarks of cancer. PLoS Pathog 2017; 13 (09) e1006480
• 20 Cox G, Koteva K, Wright GD. An unusual class of anthracyclines potentiate Gram-positive antibiotics in intrinsically resistant Gram-negative bacteria. J Antimicrob Chemother 2014; 69 (07) 1844-1855
• 21 Yang J, Liu KX, Qu JM, Wang XD. The changes induced by cyclophosphamide in intestinal barrier and microflora in mice. Eur J Pharmacol 2013; 714 (1-3): 120-124
• 22 Luxo C, Jurado AS, Custódio JB, Madeira VM. Toxic effects of tamoxifen on the growth and respiratory activity of Bacillus stearothermophilus. Toxicol In Vitro 2001; 15 (4-5): 303-305
• 23 Zhou DJ, Pan J, Yu HL, Zheng GW, Xu JH. Target-oriented discovery of a new esterase-producing strain Enterobacter sp. ECU1107 for whole cell-catalyzed production of (2S,3R)-3-phenylglycidate as a chiral synthon of Taxol. Appl Microbiol Biotechnol 2013; 97 (14) 6293-6300
• 24 Vanlancker E, Vanhoecke B, Smet R, Props R, Van de Wiele T. 5-Fluorouracil sensitivity varies among oral micro-organisms. J Med Microbiol 2016; 65 (08) 775-783
• 25 Vande Voorde J, Sabuncuoğlu S, Noppen S. et al. Nucleoside-catabolizing enzymes in mycoplasma-infected tumor cell cultures compromise the cytostatic activity of the anticancer drug gemcitabine. J Biol Chem 2014; 289 (19) 13054-13065
• 26 Vida A, Kardos G, Kovács T, Bodrogi BL, Bai P. Deletion of poly(ADP—ribose) polymerase-1 changes the composition of the microbiome in the gut. Mol Med Rep 2018; 18 (05) 4335-4341
• 27 Zhu XX, Yang XJ, Chao YL. et al. The potential effect of oral microbiota in the prediction of mucositis during radiotherapy for nasopharyngeal carcinoma. EBioMedicine 2017; 18: 23-31
• 28 Vétizou M, Pitt JM, Daillère R. et al. Anticancer immunotherapy by CTLA-4 blockade relies on the gut microbiota. Science 2015; 350 (6264): 1079-1084
• 29 Gopalakrishnan V, Spencer CN, Nezi L. et al. Gut microbiome modulates response to anti-PD-1 immunotherapy in melanoma patients. Science 2018; 359 (6371): 97-103