Dysbiosis and its discontents

mBio

Volumn 8, Issue 5, 2017, Pages

  Hooks, Katarzyna B ^a,b   O’Malley, Maureen A ^a  

^a UNIVERSITÉ DE BORDEAUX   (France)

^b CNRS Bordeaux Segalen University   (France)

Author keywords

Dysbiosis; Homeostasis; Microbial diversity; Microbiome; Microbiota

Indexed keywords

ARTICLE; COMMENSALISM; DYSBIOSIS; EUBIOSIS; HISTORICAL PERIOD; HOMEOSTASIS; HUMAN; MICROBIAL DIVERSITY; MICROBIOME; MICROFLORA; MODERN TIMES; NONHUMAN; NORMOBIOSIS; PRIORITY JOURNAL; QUALITATIVE ANALYSIS; QUANTITATIVE ANALYSIS; RESEARCH; SPECIES COMPOSITION; BIODIVERSITY;

BIODIVERSITY; DYSBIOSIS; HOMEOSTASIS; HUMANS; MICROBIOTA;

EID: 85033726499     PISSN: 21612129     EISSN: 21507511     Source Type: Journal    
DOI: 10.1128/mBio.01492-17     Document Type: Article

References (74)

1. Olesen SW, Alm EJ. 2016. Dysbiosis is not an answer. Nat Microbiol 1:16228. https://doi.org/10.1038/nmicrobiol.2016.228.
2. Levy M, Kolodziejczyk AA, Thaiss CA, Elinav E. 2017. Dysbiosis and the immune system. Nat Rev Immunol 17:219–232. https://doi.org/10.1038/nri.2017.7.
3. Stecher B, Maier L, Hardt WD. 2013. ‘Blooming’ in the gut: how dysbiosis might contribute to pathogen evolution. Nat Rev Microbiol 11:277–284. https://doi.org/10.1038/nrmicro2989.
4. Wing MR, Patel SS, Ramezani A, Raj DS. 2016. Gut microbiome in chronic kidney disease. Exp Physiol 101:471–477. https://doi.org/10.1113/EP085283.
5. Metchnikoff É. 1908. Études sur la flore intestinale. Putréfaction intestinale. Ann Inst Pasteur 22:930–955.
6. Metchnikoff É. 1903. The nature of man: studies in optimistic philosophy. G. P. Putnam, New York, NY.
7. Metchnikoff É. 1908. The prolongation of life: optimistic studies. Putnam and Sons, New York, NY.
8. Furney E. 1891. Culture, a modern method. I. H. Brown & Company, New York, NY.
9. Scheunert CA. 1920. Über Knochenweiche bei Pferden und ‘Dysbiose der Darmflora.’ Z Infekt 21:105–121.
10. Joost HG. 2012. Carl Arthur Scheunert’s experiments on human nutrition, 1938-1943: boundary transgressions of a scientist under national socialism. Medizinhist J 47:296–334.
11. Savage DC. 2001. Microbial biota of the human intestine: a tribute to some pioneering scientists. Curr Issues Intest Microbiol 2:1–15.
12. Haenel H. 1961. Some rules in the ecology of the intestinal microflora of man. J Appl Bacteriol 24:242–251. https://doi.org/10.1111/j.1365-2672.1961.tb00260.x.
13. Blasiu AP, Diepold G, Ries J. 1954. Therapeutische Mitteilungen: zur Anwendung mikrobieller Stoffwechsel-produkte während und nach der Strahlenbehandlung Krebskranker. Münch Med Wochenschr 96: 347–349.
14. Florkiewicz H, Szurska G. 1963. Rola preparatu Hylak forte* w zapobie-ganiu dysbakteriozie po doustnym stosowaniu antybiotyków. Pol Tyg Lek 18:1066–1068.
15. Haenel H, Schmidt EF, Feldheim G. 1959. Fäkale Dysbiose im Säugling-salter. Z Kinderheilkd 603:595–603.
16. Haenel H. 1970. Human normal and abnormal gastrointestinal flora. Am J Clin Nutr 23:1433–1439.
17. Haenel H. 1986., Symposium status and perspectives in gastro-intestinal microecology. Food/Nahrung 30:575–583. https://doi.org/10.1002/food.19860300602.
18. Haenel H, Bendig J. 1975. Intestinal flora in health and disease. Prog Food Nutr Sci 1:21–64.
19. Prescott SL. 2017. History of medicine: origin of the term microbiome and why it matters. Hum Microbiome J 4:24–25. https://doi.org/10.1016/j.humic.2017.05.004.
20. Petersen C, Round JL. 2014. Defining dysbiosis and its influence on host immunity and disease. Cell Microbiol 16:1024–1033. https://doi.org/10.1111/cmi.12308.
21. Vangay P, Ward T, Gerber JS, Knights D. 2015. Antibiotics, pediatric dysbiosis, and disease. Cell Host Microbe 17:553–564. https://doi.org/10.1016/j.chom.2015.04.006.
22. Knights D, Lassen KG, Xavier RJ. 2013. Advances in inflammatory bowel disease pathogenesis: linking host genetics and the microbiome. Gut 62:1505–1510. https://doi.org/10.1136/gutjnl-2012-303954.
23. Holzapfel WH, Haberer P, Snel J, Schillinger U, Huisin’t Veld JH. 1998. Overview of gut flora and probiotics. Int J Food Microbiol 41:85–101. https://doi.org/10.1016/S0168-1605(98)00044-0.
24. Antharam VC, Li EC, Ishmael A, Sharma A, Mai V, Rand KH, Wang GP. 2013. Intestinal dysbiosis and depletion of butyrogenic bacteria in Clostridium difficile infection and nosocomial diarrhea. J Clin Microbiol 51: 2884–2892. https://doi.org/10.1128/JCM.00845-13.
25. Chow J, Mazmanian SK. 2010. A pathobiont of the microbiota balances host colonization and intestinal inflammation. Cell Host Microbe 7:265–276. https://doi.org/10.1016/j.chom.2010.03.004.
26. McDonald D, Ackermann G, Khailova L, Baird C, Heyland D, Kozar R, Lemieux M, Derenski K, King J, Vis-Kampen C, Knight R, Wischmeyer PE. 2016. Extreme dysbiosis of the microbiome in critical illness. mSphere 1:e00199-16. https://doi.org/10.1128/mSphere.00199-16.
27. Voigt AY, Costea PI, Kultima JR, Li SS, Zeller G, Sunagawa S, Bork P. 2015. Temporal and technical variability of human gut metagenomes. Genome Biol 16:73. https://doi.org/10.1186/s13059-015-0639-8.
28. Bäckhed F, Fraser CM, Ringel Y, Sanders ME, Sartor RB, Sherman PM, Versalovic J, Young V, Finlay BB. 2012. Defining a healthy human gut microbiome: current concepts, future directions, and clinical applications. Cell Host Microbe 12:611–622. https://doi.org/10.1016/j.chom.2012.10.012.
29. Kim BS, Jeon YS, Chun J. 2013. Current status and future promise of the human microbiome. Pediatr Gastroenterol Hepatol Nutr 16:71–79. https://doi.org/10.5223/pghn.2013.16.2.71.
30. Hooper LV, Littman DR, Macpherson AJ. 2012. Interactions between the microbiota and the immune system. Science 336:1268–1273. https://doi.org/10.1126/science.1223490.
31. Moya A, Ferrer M. 2016. Functional redundancy-induced stability of gut microbiota subjected to disturbance. Trends Microbiol 24:402–413. https://doi.org/10.1016/j.tim.2016.02.002.
32. Lozupone CA, Stombaugh JI, Gordon JI, Jansson JK, Knight R. 2012. Diversity, stability and resilience of the human gut microbiota. Nature 489:220–230. https://doi.org/10.1038/nature11550.
33. Chassard C, Dapoigny M, Scott KP, Crouzet L, Del’homme C, Marquet P, Martin JC, Pickering G, Ardid D, Eschalier A, Dubray C, Flint HJ, Bernalier-Donadille A. 2012. Functional dysbiosis within the gut microbiota of patients with constipated-irritable bowel syndrome. Aliment Pharmacol Ther 35:828–838. https://doi.org/10.1111/j.1365-2036.2012.05007.x.
34. Reid G, Younes JA, Van der Mei HC, Gloor GB, Knight R, Busscher HJ. 2011. Microbiota restoration: natural and supplemented recovery of human microbial communities. Nat Rev Microbiol 9:27–38. https://doi.org/10.1038/nrmicro2473.
35. Eberl G. 2010. A new vision of immunity: homeostasis of the superorganism. Mucosal Immunol 3:450–460. https://doi.org/10.1038/mi.2010.20.
36. Neish AS. 2009. Microbes in gastrointestinal health and disease. Gastro-enterology 136:65–80. https://doi.org/10.1053/j.gastro.2008.10.080.
37. Relman DA. 2015. The human microbiome and the future practice of medicine. JAMA 314:1127–1128. https://doi.org/10.1001/jama.2015.10700.
38. Mondot S, de Wouters T, Doré J, Lepage P. 2013. The human gut microbiome and its dysfunctions. Dig Dis 31:278–285. https://doi.org/10.1159/000354678.
39. Iebba V, Totino V, Gagliardi A, Santangelo F, Cacciotti F, Trancassini M, Mancini C, Cicerone C, Corazziari E, Pantanella F, Schippa S. 2016. Eubiosis and dysbiosis: the two sides of the microbiota. New Microbiol 39:1–12.
40. Shin NR, Whon TW, Bae JW. 2015. Proteobacteria: microbial signature of dysbiosis in gut microbiota. Trends Biotechnol 33:496–503. https://doi.org/10.1016/j.tibtech.2015.06.011.
41. Jeffery IB, Lynch DB, O’Toole PW. 2016. Composition and temporal stability of the gut microbiota in older persons. ISME J 10:170–182. https://doi.org/10.1038/ismej.2015.88.
42. Shade A. 2017. Diversity is the question, not the answer. ISME J 11:1–6. https://doi.org/10.1038/ismej.2016.118.
43. Johnson KVA, Burnet PWJ. 2016. Microbiome: should we diversify from diversity? Gut Microbes 7:455–458. https://doi.org/10.1080/19490976.2016.1241933.
44. Buffie CG, Bucci V, Stein RR, McKenney PT, Ling L, Gobourne A, No D, Liu H, Kinnebrew M, Viale A, Littmann E, van den Brink MRM, Jenq RR, Taur Y, Sander C, Cross JR, Toussaint NC, Xavier JB, Pamer EG. 2015. Precision microbiome reconstitution restores bile acid mediated resistance to Clostridium difficile. Nature 517:205–208. https://doi.org/10.1038/nature13828.
45. Stein RR, Bucci V, Toussaint NC, Buffie CG, Rätsch G, Pamer EG, Sander C, Xavier JB. 2013. Ecological modeling from time-series inference: insight into dynamics and stability of intestinal microbiota. PLoS Comput Biol 9:e1003388. https://doi.org/10.1371/journal.pcbi.1003388.
46. Rojo D, Méndez-García C, Raczkowska BA, Bargiela R, Moya A, Ferrer M, Barbas C. 2017. Exploring the human microbiome from multiple perspectives: factors altering its composition and function. FEMS Microbiol Rev 41:453–478. https://doi.org/10.1093/femsre/fuw046.
47. Blumstein DT, Levy K, Mayer E, Harte J. 2014. Gastrointestinal dysbiosis. Evol Med Publ Health 2014:163. https://doi.org/10.1093/emph/eou029.
48. Sonnenburg ED, Sonnenburg JL. 2014. Starving our microbial self: the deleterious consequences of a diet deficient in microbiota-accessible carbohydrates. Cell Metab 20:779–786. https://doi.org/10.1016/j.cmet.2014.07.003.
49. Oh J, Byrd AL, Park M, NISC Comparative Sequencing Program, Kong HH, Segre JA. 2016. Temporal stability of the human skin microbiome. Cell 165:854–866. https://doi.org/10.1016/j.cell.2016.04.008.
50. Martínez I, Muller CE, Walter J. 2013. Long-term temporal analysis of the human fecal microbiota revealed a stable core of dominant bacterial species. PLoS One 8:e69621. https://doi.org/10.1371/journal.pone.0069621.
51. Faith JJ, Guruge JL, Charbonneau M, Subramanian S, Seedorf H, Goodman AL, Clemente JC, Knight R, Heath AC, Leibel RL, Rosenbaum M, Gordon JI. 2013. The long-term stability of the human gut microbiota. Science 341:1237439. https://doi.org/10.1126/science.1237439.
52. Coyte KZ, Schluter J, Foster KR. 2015. The ecology of the microbiome: networks, competition, and stability. Science 350:663–666. https://doi.org/10.1126/science.aad2602.
53. Foster KR, Schluter J, Coyte KZ, Rakoff-Nahoum S. 2017. The evolution of the host microbiome as an ecosystem on a leash. Nature 548:43–51. https://doi.org/10.1038/nature23292.
54. Aldunate M, Srbinovski D, Hearps AC, Latham CF, Ramsland PA, Gu-gasyan R, Cone RA, Tachedjian G. 2015. Antimicrobial and immune modulatory effects of lactic acid and short chain fatty acids produced by vaginal microbiota associated with eubiosis and bacterial vaginosis. Front Physiol 6:164. https://doi.org/10.3389/fphys.2015.00164.
55. Lepage P, Leclerc MC, Joossens M, Mondot S, Blottière HM, Raes J, Ehrlich D, Doré J. 2013. A metagenomic insight into our gut’s microbiome. Gut 62:146–158. https://doi.org/10.1136/gutjnl-2011-301805.
56. Casén C, Vebø HC, Sekelja M, Hegge FT, Karlsson MK, Ciemniejewska E, Dzankovic S, Frøyland C, Nestestog R, Engstrand L, Munkholm P, Nielsen OH, Rogler G, Simrén M, Öhman L, Vatn MH, Rudi K. 2015. Deviations in human gut microbiota: a novel diagnostic test for determining dysbiosis in patients with IBS or IBD. Aliment Pharmacol Ther 42:71–83. https://doi.org/10.1111/apt.13236.
57. Schulberg J, De Cruz P. 2016. Characterisation and therapeutic manipulation of the gut microbiome in inflammatory bowel disease. Intern Med J 46:266–273. https://doi.org/10.1111/imj.13003.
58. Doré J, Corthier G. 2010. The human intestinal microbiota. Gastroenterol Clin Biol 34(Suppl 1):S7–S15. https://doi.org/10.1016/S0399-8320(10) 70015-4.
59. Rosebury T. 1962. Microorganisms indigenous to man. McGraw-Hill, New York, NY.
60. Gevers D, Kugathasan S, Denson LA, Vázquez-Baeza Y, Van Treuren W, Ren B, Schwager E, Knights D, Song SJ, Yassour M, Morgan XC, Kostic AD, Luo C, González A, McDonald D, Haberman Y, Walters T, Baker S, Rosh J, Stephens M, Heyman M, Markowitz J, Baldassano R, Griffiths A, Sylvester F, Mack D, Kim S, Crandall W, Hyams J, Huttenhower C, Knight R, Xavier RJ. 2014. The treatment-naive microbiome in new-onset Crohn’s disease. Cell Host Microbe 15:382–392. https://doi.org/10.1016/j.chom.2014.02.005.
61. Falony G, Joossens M, Vieira-Silva S, Wang J, Darzi Y, Faust K, Kurilshikov A, Bonder MJ, Valles-Colomer M, Vandeputte D, Tito RY, Chaffron S, Rymenans L, Verspecht C, De Sutter L, Lima-Mendez G, D’hoe K, Jonck-heere K, Homola D, Garcia R, Tigchelaar EF, Eeckhaudt L, Fu J, Henckaerts L, Zhernakova A, Wijmenga C, Raes J. 2016. Population-level analysis of gut microbiome variation. Science 352:560–564. https://doi.org/10.1126/science.aad3503.
62. Nicolas S, Blasco-Baque V, Fournel A, Gilleron J, Klopp P, Waget A, Ceppo F, Marlin A, Padmanabhan R, Iacovoni JS, Tercé F, Cani PD, Tanti JF, Burcelin R, Knauf C, Cormont M, Serino M. 2017. Transfer of dysbiotic gut microbiota has beneficial effects on host liver metabolism. Mol Syst Biol 13:921. https://doi.org/10.15252/msb.20167356.
63. Buttó LF, Haller D. 2016. Dysbiosis in intestinal inflammation: cause or consequence. Int J Med Microbiol 306:302–309. https://doi.org/10.1016/j.ijmm.2016.02.010.
64. Wu GD, Lewis JD. 2013. Analysis of the human gut microbiome and association with disease. Clin Gastroenterol Hepatol 11:774–777. https://doi.org/10.1016/j.cgh.2013.03.038.
65. Maynard CL, Elson CO, Hatton RD, Weaver CT. 2012. Reciprocal interactions of the intestinal microbiota and immune system. Nature 489: 231–241. https://doi.org/10.1038/nature11551.
66. Arrieta MC, Walter J, Finlay BB. 2016. Human microbiota-associated mice: a model with challenges. Cell Host Microbe 19:575–578. https://doi.org/10.1016/j.chom.2016.04.014.
67. Nibali L, Henderson B, Sadiq ST, Donos N. 2014. Genetic dysbiosis: the role of microbial insults in chronic inflammatory diseases. J Oral Microbiol 6. https://doi.org/10.3402/jom.v6.22962.
68. Williams MR, Gallo RL. 2015. The role of the skin microbiome in atopic dermatitis. Curr Allergy Asthma Rep 15:65. https://doi.org/10.1007/s11882-015-0567-4.
69. Lewis JD, Chen EZ, Baldassano RN, Otley AR, Griffiths AM, Lee D, Bittinger K, Bailey A, Friedman ES, Hoffmann C, Albenberg L, Sinha R, Compher C, Gilroy E, Nessel L, Grant A, Chehoud C, Li H, Wu GD, Bushman FD. 2015. Inflammation, antibiotics, and diet as environmental stressors of the gut microbiome in pediatric Crohn’s disease. Cell Host Microbe 18:489–500. https://doi.org/10.1016/j.chom.2015.09.008.
70. Youmans BP, Ajami NJ, Jiang ZD, Campbell F, Wadsworth WD, Petrosino JF, DuPont HL, Highlander SK. 2015. Characterization of the human gut microbiome during travelers’ diarrhea. Gut Microbes 6:110–119. https://doi.org/10.1080/19490976.2015.1019693.
71. Lawley TD, Clare S, Walker AW, Stares MD, Connor TR, Raisen C, Goulding D, Rad R, Schreiber F, Brandt C, Deakin LJ, Pickard DJ, Duncan SH, Flint HJ, Clark TG, Parkhill J, Dougan G. 2012. Targeted restoration of the intestinal microbiota with a simple, defined bacteriotherapy resolves relapsing Clostridium difficile disease in mice. PLoS Pathog 8:e1002995. https://doi.org/10.1371/journal.ppat.1002995.
72. Jones ML, Ganopolsky JG, Martoni CJ, Labbé A, Prakash S. 2014. Emerging science of the human microbiome. Gut Microbes 5:446–457. https://doi.org/10.4161/gmic.29810.
73. Bested AC, Logan AC, Selhub EM. 2013. Intestinal microbiota, probiotics and mental health: from Metchnikoff to modern advances: part III— convergence toward clinical trials. Gut Pathog 5:4. https://doi.org/10.1186/1757-4749-5-4.
74. Sommer F, Bäckhed F. 2013. The gut microbiota—masters of host development and physiology. Nat Rev Microbiol 11:227–238. https://doi.org/10.1038/nrmicro2974.