Allergy Asthma Respir Dis.  2016 Sep;4(5):311-320. 10.4168/aard.2016.4.5.311.

Human microbiome studies in Korea

Affiliations
  • 1Department of Public Health Sciences, Graduate School, Korea University, Seoul, Korea. hanayi@korea.ac.kr
  • 2Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Korea.
  • 3School of Biosystem and Biomedical Science, Korea University, Seoul, Korea.

Abstract

During the second half of the 2000s, the significant impact of human microbiome on human diseases and health conditions was found. Since the Human Microbiome Project, many microbiome studies have been reported in domestic and international references. Gastrointestinal tract microbiome has been most investigated so far, and the association with illness has been demonstrated in many diseases. Recently, the range of study was extended to multiple human organs, such as the respiratory tract, skin, and urogenital tract. Given the scale and speed of research and development in recent years, the role of microbiome in many diseases would be established before long. In this review, we aimed to summarize the current status of microbiome studies in Korea and foreign countries with an emphasis on respiratory tract microbiome. The main concept and analytical methods for microbiome research, associations of microbiome and diseases, and research projects on Korean microbiome are reviewed.

Keyword

Microbiota; Gastrointestinal microbiome; Metagenomics; Respiratory airflow; Korea

MeSH Terms

Gastrointestinal Microbiome
Gastrointestinal Tract
Humans*
Korea*
Metagenomics
Microbiota*
Pulmonary Ventilation
Respiratory System
Skin

Figure

  • Fig. 1 Number of the publications by National Institutes of Health (NIH) Human Microbiome Project (HMP), USA. Distribution of the publications depending on calendar year (A), and depending on associated organs or diseases (B). Data from the NIH HMP website (http://hmpdacc.org).

  • Fig. 2 Count of microbiome research funding and publications in Korea.


Cited by  2 articles

Research trends in obesity & obesogenic environments in Korea
Myoungsook Lee
Nutr Res Pract. 2019;13(6):461-472.    doi: 10.4162/nrp.2019.13.6.461.

Microbiome research in food allergy and atopic dermatitis
Min-Hye Kim, Dong In Suh, Soo-Young Lee, Yoon-Keun Kim, Young-Joo Cho, Sang-Heon Cho
Allergy Asthma Respir Dis. 2016;4(6):389-398.    doi: 10.4168/aard.2016.4.6.389.


Reference

1. Collins FS, Morgan M, Patrinos A. The Human Genome Project: lessons from large-scale biology. Science. 2003; 300:286–290.
Article
2. Turnbaugh PJ, Ley RE, Hamady M, Fraser-Liggett CM, Knight R, Gordon JI. The human microbiome project. Nature. 2007; 449:804–810.
Article
3. Davies J. In a map for human life, count the microbes, too. Science. 2001; 291:2316.
Article
4. Relman DA, Falkow S. The meaning and impact of the human genome sequence for microbiology. Trends Microbiol. 2001; 9:206–208.
Article
5. Lederberg J, McCray AT. 'Ome sweet' omics: a genealogical treasury of words. Scientist. 2001; 15:8–10.
6. Ursell LK, Metcalf JL, Parfrey LW, Knight R. Defining the human microbiome. Nutr Rev. 2012; 70:Suppl 1. S38–S44.
Article
7. Savage DC. Microbial ecology of the gastrointestinal tract. Annu Rev Microbiol. 1977; 31:107–133.
Article
8. Grice EA, Segre JA. The human microbiome: our second genome. Annu Rev Genomics Hum Genet. 2012; 13:151–170.
Article
9. O'Hara AM, Shanahan F. The gut flora as a forgotten organ. EMBO Rep. 2006; 7:688–693.
10. Staley JT, Konopka A. Measurement of in situ activities of nonphotosynthetic microorganisms in aquatic and terrestrial habitats. Annu Rev Microbiol. 1985; 39:321–346.
Article
11. Ward DM, Weller R, Bateson MM. 16S rRNA sequences reveal numerous uncultured microorganisms in a natural community. Nature. 1990; 345:63–65.
Article
12. Pace NR. A molecular view of microbial diversity and the biosphere. Science. 1997; 276:734–740.
Article
13. Torsvik V, Goksøyr J, Daae FL. High diversity in DNA of soil bacteria. Appl Environ Microbiol. 1990; 56:782–787.
Article
14. NIH HMP Working Group. Peterson J, Garges S, Giovanni M, McInnes P, Wang L, et al. The NIH Human Microbiome Project. Genome Res. 2009; 19:2317–2323.
Article
15. Handelsman J, Rondon MR, Brady SF, Clardy J, Goodman RM. Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products. Chem Biol. 1998; 5:R245–R249.
Article
16. Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, et al. QIIME allows analysis of high-throughput community sequencing data. Nat Methods. 2010; 7:335–336.
Article
17. Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, et al. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol. 2009; 75:7537–7541.
Article
18. Cole JR, Wang Q, Fish JA, Chai B, McGarrell DM, Sun Y, et al. Ribosomal Database Project: data and tools for high throughput rRNA analysis. Nucleic Acids Res. 2014; 42(Database issue):D633–D642.
Article
19. Abarenkov K, Tedersoo L, Nilsson RH, Vellak K, Saar I, Veldre V, et al. PlutoF: a web based workbench for ecological and taxonomic research, with an online implementation for fungal ITS sequences. Evol Bioinform. 2010; 6:189–196.
20. Bocci V. The neglected organ: bacterial flora has a crucial immunostimulatory role. Perspect Biol Med. 1992; 35:251–260.
Article
21. Wold AE. The hygiene hypothesis revised: is the rising frequency of allergy due to changes in the intestinal flora? Allergy. 1998; 53:46 Suppl. 20–25.
Article
22. Bäckhed F, Ding H, Wang T, Hooper LV, Koh GY, Nagy A, et al. The gut microbiota as an environmental factor that regulates fat storage. Proc Natl Acad Sci U S A. 2004; 101:15718–15723.
Article
23. Carmody RN, Turnbaugh PJ. Host-microbial interactions in the metabolism of therapeutic and diet-derived xenobiotics. J Clin Invest. 2014; 124:4173–4181.
Article
24. Johnson CH, Patterson AD, Idle JR, Gonzalez FJ. Xenobiotic metabolomics: major impact on the metabolome. Annu Rev Pharmacol Toxicol. 2012; 52:37–56.
Article
25. Saad R, Rizkallah MR, Aziz RK. Gut Pharmacomicrobiomics: the tip of an iceberg of complex interactions between drugs and gut-associated microbes. Gut Pathog. 2012; 4:16.
Article
26. Sousa T, Paterson R, Moore V, Carlsson A, Abrahamsson B, Basit AW. The gastrointestinal microbiota as a site for the biotransformation of drugs. Int J Pharm. 2008; 363:1–25.
Article
27. Miller AW, Dearing D. The metabolic and ecological interactions of oxalate-degrading bacteria in the Mammalian gut. Pathogens. 2013; 2:636–652.
Article
28. Siva S, Barrack ER, Reddy GP, Thamilselvan V, Thamilselvan S, Menon M, et al. A critical analysis of the role of gut Oxalobacter formigenes in oxalate stone disease. BJU Int. 2009; 103:18–21.
Article
29. Jones ML, Tomaro-Duchesneau C, Prakash S. The gut microbiome, probiotics, bile acids axis, and human health. Trends Microbiol. 2014; 22:306–308.
Article
30. Ridlon JM, Kang DJ, Hylemon PB, Bajaj JS. Bile acids and the gut microbiome. Curr Opin Gastroenterol. 2014; 30:332–338.
Article
31. Sagar NM, Cree IA, Covington JA, Arasaradnam RP. The interplay of the gut microbiome, bile acids, and volatile organic compounds. Gastroenterol Res Pract. 2015; 2015:398585.
Article
32. Round JL, Mazmanian SK. The gut microbiota shapes intestinal immune responses during health and disease. Nat Rev Immunol. 2009; 9:313–323.
Article
33. Hooper LV, Littman DR, Macpherson AJ. Interactions between the microbiota and the immune system. Science. 2012; 336:1268–1273.
Article
34. Hanski I, von Hertzen L, Fyhrquist N, Koskinen K, Torppa K, Laatikainen T, et al. Environmental biodiversity, human microbiota, and allergy are interrelated. Proc Natl Acad Sci U S A. 2012; 109:8334–8339.
Article
35. Sampson TR, Mazmanian SK. Control of brain development, function, and behavior by the microbiome. Cell Host Microbe. 2015; 17:565–576.
Article
36. Diaz Heijtz R, Wang S, Anuar F, Qian Y, Björkholm B, Samuelsson A, et al. Normal gut microbiota modulates brain development and behavior. Proc Natl Acad Sci U S A. 2011; 108:3047–3052.
Article
37. Messaoudi M, Lalonde R, Violle N, Javelot H, Desor D, Nejdi A, et al. Assessment of psychotropic-like properties of a probiotic formulation (Lactobacillus helveticus R0052 and Bifidobacterium longum R0175) in rats and human subjects. Br J Nutr. 2011; 105:755–764.
Article
38. Steenbergen L, Sellaro R, van Hemert S, Bosch JA, Colzato LS. A randomized controlled trial to test the effect of multispecies probiotics on cognitive reactivity to sad mood. Brain Behav Immun. 2015; 48:258–264.
Article
39. Kau AL, Ahern PP, Griffin NW, Goodman AL, Gordon JI. Human nutrition, the gut microbiome and the immune system. Nature. 2011; 474:327–336.
Article
40. Newburg DS, Walker WA. Protection of the neonate by the innate immune system of developing gut and of human milk. Pediatr Res. 2007; 61:2–8.
Article
41. Pop M, Walker AW, Paulson J, Lindsay B, Antonio M, Hossain MA, et al. Diarrhea in young children from low-income countries leads to largescale alterations in intestinal microbiota composition. Genome Biol. 2014; 15:R76.
Article
42. Youmans BP, Ajami NJ, Jiang ZD, Campbell F, Wadsworth WD, Petrosino JF, et al. Characterization of the human gut microbiome during travelers' diarrhea. Gut Microbes. 2015; 6:110–119.
Article
43. Arumugam M, Raes J, Pelletier E, Le Paslier D, Yamada T, Mende DR, et al. Enterotypes of the human gut microbiome. Nature. 2011; 473:174–180.
Article
44. Ley RE, Turnbaugh PJ, Klein S, Gordon JI. Microbial ecology: human gut microbes associated with obesity. Nature. 2006; 444:1022–1023.
45. Turnbaugh PJ, Bäckhed F, Fulton L, Gordon JI. Diet-induced obesity is linked to marked but reversible alterations in the mouse distal gut microbiome. Cell Host Microbe. 2008; 3:213–223.
Article
46. Turnbaugh PJ, Hamady M, Yatsunenko T, Cantarel BL, Duncan A, Ley RE, et al. A core gut microbiome in obese and lean twins. Nature. 2009; 457:480–484.
Article
47. Turnbaugh PJ, Ley RE, Mahowald MA, Magrini V, Mardis ER, Gordon JI. An obesity-associated gut microbiome with increased capacity for energy harvest. Nature. 2006; 444:1027–1031.
Article
48. Everard A, Belzer C, Geurts L, Ouwerkerk JP, Druart C, Bindels LB, et al. Cross-talk between Akkermansia muciniphila and intestinal epithelium controls diet-induced obesity. Proc Natl Acad Sci U S A. 2013; 110:9066–9071.
Article
49. Shin NR, Lee JC, Lee HY, Kim MS, Whon TW, Lee MS, et al. An increase in the Akkermansia spp. population induced by metformin treatment improves glucose homeostasis in diet-induced obese mice. Gut. 2014; 63:727–735.
Article
50. Qin J, Li Y, Cai Z, Li S, Zhu J, Zhang F, et al. A metagenome-wide association study of gut microbiota in type 2 diabetes. Nature. 2012; 490:55–60.
Article
51. Wlodarska M, Kostic AD, Xavier RJ. An integrative view of microbiomehost interactions in inflammatory bowel diseases. Cell Host Microbe. 2015; 17:577–591.
Article
52. Bouma G, Strober W. The immunological and genetic basis of inflammatory bowel disease. Nat Rev Immunol. 2003; 3:521–533.
Article
53. Willing BP, Dicksved J, Halfvarson J, Andersson AF, Lucio M, Zheng Z, et al. A pyrosequencing study in twins shows that gastrointestinal microbial profiles vary with inflammatory bowel disease phenotypes. Gastroenterology. 2010; 139:1844–1854.e1.
Article
54. Bhattacharjee S, Lukiw WJ. Alzheimer's disease and the microbiome. Front Cell Neurosci. 2013; 7:153.
Article
55. Gatz M, Pedersen NL. Study of dementia in Swedish twins. Twin Res Hum Genet. 2013; 16:313–316.
Article
56. Miklossy J. Alzheimer's disease: a neurospirochetosis. Analysis of the evidence following Koch's and Hill's criteria. J Neuroinflammation. 2011; 8:90.
Article
57. Shoemark DK, Allen SJ. The microbiome and disease: reviewing the links between the oral microbiome, aging, and Alzheimer's disease. J Alzheimers Dis. 2015; 43:725–738.
Article
58. Koeth RA, Wang Z, Levison BS, Buffa JA, Org E, Sheehy BT, et al. Intestinal microbiota metabolism of L-carnitine, a nutrient in red meat, promotes atherosclerosis. Nat Med. 2013; 19:576–585.
Article
59. Yi H, Yong D, Lee K, Cho YJ, Chun J. Profiling bacterial community in upper respiratory tracts. BMC Infect Dis. 2014; 14:583.
Article
60. Park H, Shin JW, Park SG, Kim W. Microbial communities in the upper respiratory tract of patients with asthma and chronic obstructive pulmonary disease. PLoS One. 2014; 9:e109710.
Article
61. Choi EB, Hong SW, Kim DK, Jeon SG, Kim KR, Cho SH, et al. Decreased diversity of nasal microbiota and their secreted extracellular vesicles in patients with chronic rhinosinusitis based on a metagenomic analysis. Allergy. 2014; 69:517–526.
Article
62. Jung WH, Croll D, Cho JH, Kim YR, Lee YW. Analysis of the nasal vestibule mycobiome in patients with allergic rhinitis. Mycoses. 2015; 58:167–172.
Article
63. Griffin JL, Wang X, Stanley E. Does our gut microbiome predict cardiovascular risk? A review of the evidence from metabolomics. Circ Cardiovasc Genet. 2015; 8:187–191.
Article
64. Tang WH, Hazen SL. The contributory role of gut microbiota in cardiovascular disease. J Clin Invest. 2014; 124:4204–4211.
Article
65. DiGiulio DB, Callahan BJ, McMurdie PJ, Costello EK, Lyell DJ, Robaczewska A, et al. Temporal and spatial variation of the human microbiota during pregnancy. Proc Natl Acad Sci U S A. 2015; 112:11060–11065.
Article
66. Metcalf JL, Xu ZZ, Weiss S, Lax S, Van Treuren W, Hyde ER, et al. Microbial community assembly and metabolic function during mammalian corpse decomposition. Science. 2016; 351:158–162.
Article
67. Emanuelsson F, Claesson BE, Ljungström L, Tvede M, Ung KA. Faecal microbiota transplantation and bacteriotherapy for recurrent Clostridium difficile infection: a retrospective evaluation of 31 patients. Scand J Infect Dis. 2014; 46:89–97.
Article
68. Gough E, Shaikh H, Manges AR. Systematic review of intestinal microbiota transplantation (fecal bacteriotherapy) for recurrent Clostridium difficile infection. Clin Infect Dis. 2011; 53:994–1002.
Article
69. Suwantarat N, Bobak DA. Fecal bacteriotherapy for recurrent Clostridium difficile infection: What's Old Is New Again? Curr Infect Dis Rep. 2013; 15:101–103.
Article
70. Delzenne NM, Neyrinck AM, Bäckhed F, Cani PD. Targeting gut microbiota in obesity: effects of prebiotics and probiotics. Nat Rev Endocrinol. 2011; 7:639–646.
Article
Full Text Links
  • AARD
Actions
Cited
CITED
export Copy
Close
Share
  • Twitter
  • Facebook
Similar articles
Copyright © 2024 by Korean Association of Medical Journal Editors. All rights reserved.     E-mail: koreamed@kamje.or.kr