Publicado

2016-01-01

The human microbiota: the role of microbial communities in health and disease

La microbiota humana: comunidades microbianas en la salud y en la enfermedad

Palabras clave:

16S rRNA gene, microbial diversity, microbiome, diversidad microbiana, microbioma (en)
16S ARNr, diversidad microbiana, microbioma, Mycobacterium tuberculosis (es)

Autores/as

  • Luz Elena Botero Palacio Universidad Pontificia Bolivariana
  • Luisa Delgado Serrano Corporación Corpogen
  • Martha Lucía Cepeda Hernández Corporación Corpogen
  • Patricia Del Portillo Obando Corporación Corpogen
  • María Mercedes Zambrano Eder Corporación Corpogen

During the last decade, there has been increasing awareness of the massive number of microorganisms, collectively known as the human microbiota, that are associated with humans. This microbiota outnumbers the host cells by approximately a factor of ten and contains a large repertoire of microbial genome-encoded metabolic processes. The diverse human microbiota and its associated metabolic potential can provide the host with novel functions that can influence host health and disease status in ways that still need to be analyzed. The microbiota varies with age, with features that depend on the body site, host lifestyle and health status. The challenge is therefore to identify and characterize these microbial communities and use this information to learn how they function and how they can influence the host in terms of health and well-being. Here we provide an overview of some of the recent studies involving the human microbiota and about how these communities might affect host health and disease. A special emphasis is given to studies related to tuberculosis, a disease that claims over one million lives each year worldwide and still represents a challenge for control in many countries, including Colombia.

En las últimas décadas ha incrementado nuestro conocimiento sobre la gran cantidad de microorganismos que conviven con nosotros, comunidades que colectivamente se conocen como la microbiota humana. El número de microorganismos que conforman la microbiota supera el número de células del cuerpo humano por un factor de diez aproximadamente y aporta un gran repertorio de genes y procesos metabólicos. La diversidad de la microbiota humana y su potencial metabólico brindan al hospedero una serie de funciones que complementan sus procesos y a su vez pueden influir sobre la salud del ser humano en formas que apenas se empiezan a conocer. La microbiota varía desde el nacimiento hasta la vejez del individuo, con características que dependen del sitio corporal, del estilo de vida y del estado de salud del hospedero. El reto actual es aprovechar el conocimiento derivado de la identificación y caracterización de estas comunidades microbianas para entender cómo funcionan estos microorganismos y cómo pueden influir de forma positiva o negativa sobre la salud del humano. En este documento ofrecemos una revisión general de algunos estudios recientes sobre la microbiota humana y su posible efecto en el hospedero en términos de salud y bienestar. Igualmente, se mencionan estudios sobre microbiota y su posible asociación con la tuberculosis, una enfermedad que todavía cobra más de un millón de vidas anualmente a nivel mundial y cuyo control todavía representa un gran reto en varios países del mundo, incluido Colombia.

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Arumugam M, Raes J, Pelletier E, Le Paslier D, Yamada T, Mende DR, et al. Enterotypes of the human gut microbiome. Nature. 2011;473(7346):174-180. Doi: 10.1038/nature09944.

Bassis CM, Erb-Downward JR, Dickson RP, Freeman CM, Schmidt TM, Young VB, et al. Analysis of the upper respiratory tract microbiotas as the source of the lung and gastric microbiotas in healthy individuals. mBio. 2015;6(2):e00037. Doi: 10.1128/mBio.00037-15.

Beck JM, Young VB, Huffnagle GB. The microbiome of the lung. Transl Res. 2012;160(4):258-266. Doi: 10.1016/j.trsl.2012.02.005.

Belkaid Y, Hand TW. Role of the microbiota in immunity and inflammation. Cell. 2014;157(1):121-141. Doi: 10.1016/j.cell.2014.03.011.

Bik EM, Long CD, Armitage GC, Loomer P, Emerson J, Mongodin EF, et al. Bacterial diversity in the oral cavity of 10 healthy individuals. ISME J. 2010;4(8):962-974. Doi: 10.1038/ismej.2010.30.

Blaser MJ, Dominguez-Bello MG, Contreras M, Magris M, Hidalgo G, Estrada I, et al. Distinct cutaneous bacterial assemblages in a sampling of South American Amerindians and US residents. ISME J. 2013;7(1):85-95. Doi: 10.1038/ismej.2012.81.

Botero LE, Delgado-Serrano L, Cepeda ML, Bustos JR, Anzola JM, Del Portillo P, et al. Respiratory tract clinical sample selection for microbiota analysis in patients with pulmonary tuberculosis. Microbiome. 2014;2:29. Doi: 10.1186/2049-2618-2-29.

Brook I, Gober AE. Recovery of potential pathogens and interfering bacteria in the nasopharynx of smokers and nonsmokers. Chest. 2005;127(6):2072-2075. Doi: 10.1378/chest.127.6.2072.

Brotman RM, Bradford LL, Conrad M, Gajer P, Ault K, Peralta L, et al. Association between Trichomonas vaginalis and vaginal bacterial community composition among reproductive-age women. Sex Transm Dis. 2012;39(10):807-812. Doi: 10.1097/OLQ.0b013e3182631c79.

Cabrera-Rubio R, Garcia-Nunez M, Seto L, Anto JM, Moya A, Monso E, et al. Microbiome diversity in the bronchial tracts of patients with chronic obstructive pulmonary disease. J Clin Microbiol. 2012;50(11):3562-3568. Doi: 10.1128/JCM.00767-12.

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(5):335-336. Doi: 10.1038/nmeth.f.303.

Clemente JC, Ursell LK, Parfrey LW, Knight R. The impact of the gut microbiota on human health: an integrative view. Cell. 2012;148(6):1258-1270. Doi: 10.1016/j.cell.2012.01.035.

Cole JR, Wang Q, Cardenas E, Fish J, Chai B, Farris RJ, et al. The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res. 2009;37(suppl 1):D141-D145. Doi: 10.1093/nar/gkn879.

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(D1):D633-D642. Doi: 10.1093/nar/gkt1244.

Costello EK, Stagaman K, Dethlefsen L, Bohannan BJ, Relman DA. The application of ecological theory toward an understanding of the human microbiome. Science. 2012;336(6086):1255-1262. Doi: 10.1126/science.1224203.

Cox LM, Blaser MJ. Antibiotics in early life and obesity. Nat Rev Endocrinol. 2015;11:182-190. Doi: 10.1038/nrendo.2014.210.

Cui Z, Zhou Y, Li H, Zhang Y, Zhang S, Tang S, et al. Complex sputum microbial composition in patients with pulmonary tuberculosis. BMC Microbiol. 2012;12:276. Doi: 10.1186/1471-2180-12-276.

Chaban B, Albert A, Links MG, Gardy J, Tang P, Hill JE. Characterization of the upper respiratory tract microbiomes of patients with pandemic H1N1 influenza. PLoS One. 2013;8(7):e69559. Doi: 10.1371/journal.pone.0069559.

Charlson ES, Bittinger K, Haas AR, Fitzgerald AS, Frank I, Yadav A, et al. Topographical continuity of bacterial populations in the healthy human respiratory tract. Am J Respir Crit Care Med. 2011;184(8):957-63. Doi: 10.1164/rccm.201104-0655OC.

Charlson ES, Chen J, Custers-Allen R, Bittinger K, Li H, Sinha R, et al. Disordered microbial communities in the upper respiratory tract of cigarette smokers. PLoS One. 2010;5(12):e15216. Doi: 10.1371/journal.pone.0015216.

Chen H, Jiang W. Application of high-throughput sequencing in understanding human oral microbiome related with health and disease. Front Microbiol. 2014;5:508. Doi: 10.3389/fmicb.2014.00508.

Cheung MK, Lam WY, Fung WY, Law PT, Au CH, Nong W, et al. Sputum microbiota in tuberculosis as revealed by 16S rRNA pyrosequencing. PLoS One. 2013;8(1):e54574. Doi: 10.1371/journal.pone.0054574.

Delhaes L, Monchy S, Frealle E, Hubans C, Salleron J, Leroy S, et al. The airway microbiota in cystic fibrosis: a complex fungal and bacterial community—implications for therapeutic management. PLoS One. 2012;7(4):e36313. Doi: 10.1371/journal.pone.0036313.

DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K, et al. Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol. 2006;72(7):5069-5072. Doi: 10.1128/AEM.03006-05.

Dethlefsen L, McFall-Ngai M, Relman DA. An ecological and evolutionary perspective on human-microbe mutualism and disease. Nature. 2007;449(7164):811-818. Doi: 10.1038/nature06245.

Dore J, Blottiere H. The influence of diet on the gut microbiota and its consequences for health. Curr Opin Biotechy. 2015;32:195-199. Doi: 10.1016/j.copbio.2015.01.002.

Erb-Downward JR, Thompson DL, Han MK, Freeman CM, McCloskey L, Schmidt LA, et al. Analysis of the lung microbiome in the "healthy" smoker and in COPD. PLoS One. 2011;6(2):e16384. Doi:10.1371/journal.pone.0016384.

Fierer N, Hamady M, Lauber CL, Knight R. The influence of sex, handedness, and washing on the diversity of hand surface bacteria. Proc Natl Acad Sci USA. 2008;105(46):17994-17999. Doi: 10.1073/pnas.0807920105.

Filkins LM, Hampton TH, Gifford AH, Gross MJ, Hogan DA, Sogin ML, et al. Prevalence of streptococci and increased polymicrobial diversity associated with cystic fibrosis patient stability. J Bacteriol. 2012;194(17):4709-4717. Doi: 10.1128/JB.00566-12.

Fredricks DN. Molecular methods to describe the spectrum and dynamics of the vaginal microbiota. Anaerobe. 2011;17(4):191-195. Doi: 10.1016/j.anaerobe.2011.01.001.

Gevers D, Cohan FM, Lawrence JG, Spratt BG, Coenye T, Feil EJ, et al. Opinion: Re-evaluating prokaryotic species. Nat Rev Microbiol. 2005;3(9):733-739. Doi: 10.1038/nrmicro1236.

Gill SR, Pop M, Deboy RT, Eckburg PB, Turnbaugh PJ, Samuel BS, et al. Metagenomic analysis of the human distal gut microbiome. Science. 2006;312(5778):1355-1359. Doi: 10.1126/science.1124234.

Glendinning L, Free A. Supra-Organismal Interactions in the Human Intestine Front Cell Infect Microbiol. 2014;4(47):1-4. Doi:10.3389/fcimb.2014.00047.

Goddard AF, Staudinger BJ, Dowd SE, Joshi-Datar A, Wolcott RD, Aitken ML, et al. Direct sampling of cystic fibrosis lungs indicates that DNA-based analyses of upper-airway specimens can misrepresent lung microbiota. Proc Natl Acad Sci USA. 2012;109(34):13769-13774. Doi: 10.1073/pnas.1107435109.

Grice EA, Kong HH, Conlan S, Deming CB, Davis J, Young AC, et al. Topographical and temporal diversity of the human skin microbiome. Science. 2009;324(5931):1190-1192. Doi: 10.1126/science.1171700.

Gross EL, Leys EJ, Gasparovich SR, Firestone ND, Schwartzbaum JA, Janies DA, et al. Bacterial 16S sequence analysis of severe caries in young permanent teeth. J Clin Microbiol. 2010;48(11):4121-4128. Doi: 10.1128/JCM.01232-10.

Group NHW, Peterson J, Garges S, Giovanni M, McInnes P, Wang L, et al. The NIH Human Microbiome Project. Genome Res. 2009;19(12):2317-2323. Doi:10.1101/gr.096651.109.

Guss AM, Roeselers G, Newton IL, Young CR, Klepac-Ceraj V, Lory S, et al. Phylogenetic and metabolic diversity of bacteria associated with cystic fibrosis. ISME J. 2011;5(1):20-29. Doi: 10.1038/ismej.2010.88.

Hamady M, Knight R. Microbial community profiling for human microbiome projects: Tools, techniques, and challenges. Genome Res. 2009;19(7):1141-1152. Doi: 10.1101/gr.085464.108.

Handelsman J. Metagenomics: application of genomics to uncultured microorganisms. Microbiol Mol Biol Rev. 2004;68(4):669-685. Doi: 10.1128/MMBR.68.4.669-685.2004.

Hartman AL, Riddle S, McPhillips T, Ludascher B, Eisen JA. Introducing W.A.T.E.R.S.: a workflow for the alignment, taxonomy, and ecology of ribosomal sequences. BMC bioinformatics. 2010;11:317. Doi: 10.1186/1471-2105-11-317.

Hilty M, Burke C, Pedro H, Cardenas P, Bush A, Bossley C, et al. Disordered microbial communities in asthmatic airways. PLoS One. 2010;5(1):e8578. Doi: 10.1371/journal.pone.0008578.

Huang S, Yang F, Zeng X, Chen J, Li R, Wen T, et al. Preliminary characterization of the oral microbiota of Chinese adults with and without gingivitis. BMC Oral Health. 2011;11:33. Doi: 10.1016/j.jaci.2010.10.048.

Huang YJ, Nelson CE, Brodie EL, Desantis TZ, Baek MS, Liu J, et al. Airway microbiota and bronchial hyperresponsiveness in patients with suboptimally controlled asthma. J Allergy Clin Immunol. 2011;127(2):372-381. Doi: 10.1016/j.jaci.2010.10.048.

Huffnagle GB. The microbiota and allergies/asthma. PLoS Pathog. 2010;6(5):e1000549. Doi: 10.1371/journal.ppat.1000549.

Kim M, Oh HS, Park SC, Chun J. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol. 2014;64(2):346-351. Doi:10.1099/ijs.0.059774-0.

Lee S, Sung J, Lee J, Ko G. Comparison of the gut microbiotas of healthy adult twins living in South Korea and the United States. Appl Environ Microbiol. 2011;77(20):7433-7437. Doi: 10.1128/AEM.05490-11.

Lemon KP, Armitage GC, Relman DA, Fischbach MA. Microbiota-targeted therapies: an ecological perspective. Sci Transl Med. 2012;4(137):137rv5. Doi: 10.1126/scitranslmed.3004183.

Lemon KP, Klepac-Ceraj V, Schiffer HK, Brodie EL, Lynch SV, Kolter R. Comparative analyses of the bacterial microbiota of the human nostril and oropharynx. MBio. 2010;1(3):e00129-10. Doi: 10.1128/mBio.00129-10.

Ley RE, Lozupone CA, Hamady M, Knight R, Gordon JI. Worlds within worlds: evolution of the vertebrate gut microbiota. Nat Rev Microbiol. 2008;6(10):776-788. Doi: 10.1038/nrmicro1978.

Ley RE, Peterson DA, Gordon JI. Ecological and evolutionary forces shaping microbial diversity in the human intestine. Cell. 2006;124(4):837-848. Doi: 10.1016/j.cell.2006.02.017.

Ling Z, Kong J, Liu F, Zhu H, Chen X, Wang Y, et al. Molecular analysis of the diversity of vaginal microbiota associated with bacterial vaginosis. BMC Genomics. 2010;11:488. Doi: 10.1186/1471-2164-11-488.

Ma B, Forney LJ, Ravel J. Vaginal microbiome: rethinking health and disease. Annu Rev Microbiol. 2012;66:371-389. Doi: 10.1146/annurev-micro-092611-150157.

Marri PR, Stern DA, Wright AL, Billheimer D, Martinez FD. Asthma-associated differences in microbial composition of induced sputum. J Allergy Clin Immunol. 2013;131(2):346-352. Doi: 10.1016/j.jaci.2012.11.013.

Mertz D, Frei R, Jaussi B, Tietz A, Stebler C, Fluckiger U, et al. Throat swabs are necessary to reliably detect carriers of Staphylococcus aureus. Clin Infect Dis. 2007;45(4):475-477. Doi: 10.1086/520016.

Morgan XC, Huttenhower C. Chapter 12: Human microbiome analysis. PLoS Comput Biol. 2012;8(12):e1002808. Doi: 10.1371/journal.pcbi.1002808.

Muegge BD, Kuczynski J, Knights D, Clemente JC, Gonzalez A, Fontana L, et al. Diet drives convergence in gut microbiome functions across mammalian phylogeny and within humans. Science. 2011;332(6032):970-974. Doi:10.1126/science.1198719.

Mueller NT, Bakacs E, Combellick J, Grigoryan Z, Dominguez-Bello MG. The infant microbiome development: mom matters. Trends in molecular medicine. 2015;21(2):109-117. Doi:10.1038/ncomms7342.

O'Keefe SJ, Li JV, Lahti L, Ou J, Carbonero F, Mohammed K, et al. Fat, fibre and cancer risk in African Americans and rural Africans. Nature communications. 2015;6:6342. Doi: 10.1038/ncomms7342.

Ocejo-Vinyals JG, Lavin-Alconero L, Sanchez-Velasco P, Guerrero-Alonso MA, Ausin F, Farinas MC, et al. Mannose-binding lectin promoter polymorphisms and gene variants in pulmonary tuberculosis patients from cantabria (northern Spain). Pulm Med. 2012;(2012):1-6. Doi: 10.1155/2012/469128.

Proctor LM. The Human Microbiome Project in 2011 and beyond. Cell Host Microbe. 2011;10(4):287-291. Doi: 10.1016/j.chom.2011.10.001.

Ravel J, Gajer P, Abdo Z, Schneider GM, Koenig SS, McCulle SL, et al. Vaginal microbiome of reproductive-age women. Proc Natl Acad Sci USA. 2011;108(Suppl1):4680-4687. Doi: 10.1073/pnas.1002611107.

Salvucci E. El Agotamiento del bioma y sus consecuencias. Acta biol Colomb. 2013;18(1):31-42.

Sapkota AR, Berger S, Vogel TM. Human pathogens abundant in the bacterial metagenome of cigarettes. Environ Health Perspect. 2010;118(3):351-356. Doi: 10.1128/AEM.01541-09.

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(23):7537-7541. Doi: 10.1128/AEM.01541-09.

Schommer NN, Gallo RL. Structure and function of the human skin microbiome. Trends Microbiol. 2013;21(12):660-668. Doi: 10.1016/j.tim.2013.10.001.

Segal LN, Blaser MJ. A brave new world: the lung microbiota in an era of change. Anna Am Thorac Soc. 2014;11(Suppl1):S21-S27. Doi:10.1513/AnnalsATS.201306-189MG.

Sethi S, Evans N, Grant BJ, Murphy TF. New strains of bacteria and exacerbations of chronic obstructive pulmonary disease. N Engl J Med. 2002;347(7):465-471. Doi: 10.1056/NEJMoa012561.

Sharma R, Young C, Neu J. Molecular modulation of intestinal epithelial barrier: contribution of microbiota. J Biomed Biotechnol. 2010;2010:1-15. Doi: 10.1155/2010/305879.

Sharma SK, Mohan A. Tuberculosis: From an incurable scourge to a curable disease–journey over a millennium. Indian J Med Res. 2013;137(3):455-493. Doi: IndianJMedRes_2013_137_3_455_110999.

Silva MJ, Carneiro MB, dos Anjos Pultz B, Pereira Silva D, Lopes ME, dos Santos LM. The multifaceted role of commensal microbiota in homeostasis and gastrointestinal diseases. J Immunol Res. 2015;2015:1-14. Doi: 10.1155/2015/321241.

Stearns JC, Lynch MD, Senadheera DB, Tenenbaum HC, Goldberg MB, Cvitkovitch DG, et al. Bacterial biogeography of the human digestive tract. Sci Rep. 2011;1:170. Doi: 10.1038/srep00170.

Suez J, Korem T, Zeevi D, Zilberman-Schapira G, Thaiss CA, Maza O, et al. Artificial sweeteners induce glucose intolerance by altering the gut microbiota. Nature. 2014;514(7521):181-186. Doi: 10.1038/nature13793.

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(7228):480-484. Doi:10.1038/nature07540.

Turnbaugh PJ, Ley RE, Hamady M, Fraser-Liggett CM, Knight R, Gordon JI. The human microbiome project. Nature. 2007;449(7164):804-810.Doi:10.1038/nature06244.

Ursell LK, Clemente JC, Rideout JR, Gevers D, Caporaso JG, Knight R. The interpersonal and intrapersonal diversity of human-associated microbiota in key body sites. J Allergy Clin Immunol. 2012;129(5):1204-1208. Doi:10.1016/j.jaci.2012.03.010.

Wang WL, Xu SY, Ren ZG, Tao L, Jiang JW, Zheng SS. Application of metagenomics in the human gut microbiome. World J Gastroenterol. 2015;21(3):803-814. Doi:10.3748/wjg.v21.i3.803.

Willner D, Haynes MR, Furlan M, Schmieder R, Lim YW, Rainey PB, et al. Spatial distribution of microbial communities in the cystic fibrosis lung. ISME J. 2012;6(2):471-474. Doi:10.1038/ismej.2011.104.

Wu GD, Chen J, Hoffmann C, Bittinger K, Chen YY, Keilbaugh SA, et al. Linking long-term dietary patterns with gut microbial enterotypes. Science. 2011;334(6052):105-108. Doi:10.1126/science.1208344.

Zaneveld J, Turnbaugh PJ, Lozupone C, Ley RE, Hamady M, Gordon JI, et al. Host-bacterial coevolution and the search for new drug targets. Curr Opin Chem Biol. 2008;12(1):109-114. Doi: 10.1016/j.cbpa.2008.01.015.

Zhang M, Li Q, Zhang XY, Ding X, Zhu D, Zhou X. Relevance of lower airway bacterial colonization, airway inflammation, and pulmonary function in the stable stage of chronic obstructive pulmonary disease. Eur J Clin Microbiol Infect Dis. 2010;29(12):1487-1493. Doi: 10.1007/s10096-010-1027-7.

Zhou X, Brown CJ, Abdo Z, Davis CC, Hansmann MA, Joyce P, et al. Differences in the composition of vaginal microbial communities found in healthy Caucasian and black women. ISME J. 2007;1(2):121-133. Doi:10.1038/ismej.2007.12.

Zhou Y, Lin P, Li Q, Han L, Zheng H, Wei Y, et al. Analysis of the microbiota of sputum samples from patients with lower respiratory tract infections. Acta Biochim Biophys Sin. 2010;42(10):754-761. Doi:10.1093/abbs/gmq081.