Gut microbiota: its development and relation to certain diseases

1. Bäckhed F., Frase C. M., Rigel Y., Sanders M. E., Sartor R. B., Sherman P. M., Versalovic J., Young V., Finlay B. B. Defining a healthy human gut microbiome: current concepts, future directions, and clinical applications. Cell Host Microbe 2012; 12, 611–622.

2. NIH Human Microbiome Project. https://hmpdacc.org/hmp/overview/ (6. 11. 2017).

3. Jandhyala S. M., Talukdar, R., Subramanyam, C., Vuyyuru H., Sasikala M., Nageshwar Reddy D. Role of the normal gut microbiota. World J. Gastroenterol. 2015; 21, 8787–8803.

4. Mayer E. A., Tillisch K., Gupta A. Gut/brain axis and the microbiota. J. Clin. Invest. 2015; 125, 926–938.

5. Human Microbiome Project Consortium. A framework for human microbiome research. Nature 2012; 486, 215–221.

6. Belizário J. E., Napolitano M. Human microbiomes and their roles in dysbiosis, common disease, and novel therapeutic approaches. Front. Microbiol. 2015; 6: 1050.

7. Turnbaugh P. J., Hamady M., Yatsunenko T., Cantarel B. L., Duncan A., Ley R. E., Sogin M. L., Jones W. J., Roe B. A., Affourtit J. P., Egholm M., Henrissat B., Heath A. C., Knight R., Gordon J. I. A core gut microbiome in obese and lean twins. Nature 2009; 457, 480–484.

8. Turnbaugh P. J., Gordon J. I. The core gut microbiome, energy balance and obesity. J. Physiol. 2009; 587, 4153–4158.

9. Human Microbiome Project Consortium. Structure, function and diversity of the healthy human. Nature 2013; 486: 207–2014.

10. Zoetendal E. G., Rajilic-Stojanovic M., de Vos W. M. High-throughput diversity and functionality analysis of the gastrointestinal tract microbiota. Gut 2008; 57, 1605–1615.

11. Arumugam M., Raes J., Pelletier E., Le Paslier D., Yamada T., Mende D. R., Fernandes G. R., Tap J., Bruls T., Batto J. M., Bertalan M., Borruel N., Casellas F., Fernandez L., Gautier L., Hansen T., Hattori M., Hayashi T., Kleerebezem M., Kurokawa K., Leclerc M., Levenez F., Manichanh C., Nielsen H. B., Nielsen T., Pons N., Poulain J., Qin J., Sicheritz-Ponten T., Tims S., Torrents D., Ugarte E., Zoetendal E. G., Wang J., Guarner F., Pedersen O., de Vos W. M., Brunak S., Doré J., MetaHIT Consortium, Antolín M., Artiguenave F., Blottiere H. M., Almeida M., Brechot C., Cara C., Chervaux C., Cultrone A., Delorme C., Denariaz G., Dervyn R., Foerstner K. U., Friss C., van de Guchte M., Guedon E., Haimet F., Huber W., van Hylckama-Vlieg J., Jamet A., Juste C., Kaci G., Knol J., Lakhdari O., Layec S., Le Roux K., Maguin E., Mérieux A., Melo Minardi R., M‘rini C., Muller J., Oozeer R., Parkhill J., Renault P., Rescigno M., Sanchez N., Sunagawa S., Torrejon A., Turner K., Vandemeulebrouck G., Varela E., Winogradsky Y., Zeller G., Weissenbach J., Ehrlich S. D., Bork P. Enterotypes of the human gut microbiome. Nature 2011; 473, 174–180.

12. Segata N., Haake S. K., Mannon P., Lemon K. P., Waldron L., Gevers D., Huttenhower C., Izard J. Composition of the adult digestive tract bacterial microbiome based on seven mouth surfaces, tonsils, throat and stool samples. Genome Biol. 2012; 13, R42.

13. Dave M., Higgins P. D., Middha S., Rioux K. P. The human gut microbiome: current knowledge, challenges, and future directions. Trans. Res. 2012; 160, 246–257.

14. Wu G. D., Chen J., Hoffman Ch., Bittinger K., Chen Y. Y., Keilbaugh S. A., Bewtra M., Knights D., Walters W. A., Knight R., Sinha R., Gilroy E., Gupta K., Baldassano R., Nessel L., Li H., Bushman F. D., Lewis J. D. Linking tong-term dietary patterns with gut microbial enterotypes. Science 2011; 334, 105–108.

15. Faith J. J., Guruge J. L., Charbonneau M., Subramanian S., Seedorf H., Goodman A. L., Clemente J. C., Knight R., Heath A. C., Leibel R. L., Rosenbaum M., Gordon J. I. The long-term stability of the human gut microbiota. Science 2013; 341, 12377439.

16. Jiménez E., Marín M. L., Martín R., Odriozola J. M., Olivares M., Xaus J., Fernández L., Rodríguez J. M. Is meconium from healthy newborns actually sterile? Res. Microbiol. 2008; 159, 187–193.

17. Satokari R., Grönroos T., Laitinen K., Salminen S., Isolauri E. Bifidobacterium and Lactobacillus DNA in the human placenta. Lett. Appl. Microbiol. 2009; 48, 8–12.

18. Aagaard K., Ma J., Antony J. M., Ganu R., Petrosino J., Versalovic J. The placenta harbors a unique microbiome. Sci. Transl. Med. 2014; 6, 237ra265.

19. Huure A., Kalliomäki M., Rautava S., Rinne M., Salminen S., Isolauri E. Mode of delivery – effects on gut microbiota and humoral immunity. Neonatology 2008; 93, 236–240.

20. DiGiulio D. B., Romero R., Amogan H. P., Kusanovic J. P., Bik E. M., Gotsch F., Kim C. J., Erez O., Edwin S., Relman D. A. Microbial prevalence, diversity and abundance in amniotic fluid during preterm labor: a molecular and culture-based investigation. PLoS One 2008; 3, e3056.

21. Dominguez-Bella M. G., Costello E. K., Contreras M., Magris M., Hidalgo G., Fierer N., Knight R. Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns. Proc. Natl. Acad. Sci. USA 2010; 107, 11971–11975.

22. Bäckhed, F., Roswall, J., Peng, Y., Feng, Q., Jia, H., Kovatcheva-Datchary, P., Li Y., Xia Y., Xie H., Zhong H., Khan M. T., Zhang J., Li J., Xiao L., Al-Aama J., Zhang D., Lee Y. S., Kotowska D., Colding C., Tremaroli V., Yin Y., Bergman S., Xu X., Madsen L., Kristiansen K., Dahlgren J., Wang J. Dynamics and stabilization of the human gut microbiome during the first year of life. Cell Host Microbe 2015; 17, 690–703.

23. Lloyd-Price J., Abu-Ali G., Huttenhower C. The healthy human microbiome. Genome Med. 2016; 8, 51.

24. Zivkovic A. M., German J. B., Lebrilla C. B., Mills D. A. Human milk glycobiome and its impact on the infant gastrointestinal microbiota. Proc. Natl. Acad. Sci. USA 2011; 108, 4653–4658.

25. Charbonneau M. R., O´Donnell D., BLaton L. V., Totten S. M., Davis J. C., Barratt M. J., Cheng J., Guruge J., Talcott M., Bain J. R., Muehlbauer M. J., Ilkayeva O., Wu C., Struckmeyer T., Barile D., Mangani C., Jorgensen J., Fan Y. M., Maleta K., Dewey K. G., Ashorn P., Newgard C. B., Lebrilla C., Mills D. A., Gordon J. I. Salylated milk oligosaccharides promote microbiota-dependent growth models of infant undernutrition. Cell 2016; 164, 859–871.

26. Koenig J. E., Spor A., Scalfone N., Fricker A. D., Stombaugh J., Knight R., Angenent L. T., Ley R. E. Succession of microbial consortia in the developing infant gut microbiome. Proc. Natl. Acad. Sci. USA 2011; 108(Suppl 1), 4578–4585.

27. Yatsunenko T., Rey F. E., Manary M. J., Trehan I., Dominguez-Bello M. G., Contreras M., Magris M., Hidalgo G., Baldassano R. N., Anokhin A. P., Heath A. C., Warner B., Reeder J., Kuczynski J., Caporaso J. G., Lozupone C. A., Lauber C., Clemente J. C., Knights D., Knight R., Gordon J. I. Human gut microbiome viewed across age and geography. Nature 2012; 486, 222–227.

28. Monsen A. L., Refsum H., Markestad T., Ueland P. M. Cobalamin status and its biochemical merkers methylmalonic acid and homocysteine in different age groups from 4 days to 19 years. Clin. Chem. 2003; 49, 2067–2075.

29. Andersson A. F., Lindberg M., Jakobsson H., Bäckhed F., Nyrén P., Engstrand L. Comparative analysis of human gut microbiota by barcoded pyrosequencing. PLoS One 2008; 3, e2836.

30. Zwielehner J., Liszt K., Handschur M., Lassl C., Lapin A., Haslberger A. G. Combined PCR-DGGE fingerprinting and quantitative-PCR indicates shift in fecal population sizes and Clostridium cluster IV in institutionalized elderly. Exp. Gerontol. 2009; 44, 440–446.

31. Claesson M. J., Cusack S., O´Sullivan O., Greene-Diniz R., de Weerd H., Flannery E., Marchesi J. R., Falush D., Dinan T., Fitzgerald G., Stanton C., van Sinderen D., O‘Connor M., Harnedy N., O‘Connor K., Henry C., O‘Mahony D., Fitzgerald A. P., Shanahan F., Twomey C., Hill C., Ross R. P., O‘Toole P. W. Composition, variability, and temporal stability of the intestinal microbiota in elderly. Proc. Natl. Acad. Sci. USA 2011; 108 Suppl. 1, 4586–4591.

32. Petersen C., Round J. L. Defining dysbiosis and its influence on host immunity and disease. Cell Microbiol. 2014; 16, 1024–1033.

33. Round J. L., Lee S. M., Li J., Tran G., Jabri B., Chatila T. A., Mazmanian S. K. The Toll-like receptor 2 pathway establishes colonization by a commensal of the human microbiota. Science 2011; 332, 974–977.

34. Atarashi K., Tanoue T., Oshima K., Suda W., Nagano Y., Nishikawa H., Fukuda S., Saito T., Narushima S., Hase K., Kim S., Fritz J. V., Wilmes P., Ueha S., Matsushima K., Ohno H., Olle B., Sakaguchi S., Taniguchi T., Morita H., Hattori M., Honda K. Treg induction by a rationally selected mixture of Clostridia strains from the human microbiota. Nature 2013; 500, 232–236.

35. Ospelt C, Gay S. TLRs and chronic inflammation. Int. J. Biochem. Cell Biol. 2010; 42, 495–505.

36. Frantz A. L., Rogier E. W., Weber C. R., Shen L., Cohen D. A., Fenton L. A., Bruno M. E., Kaetzel C. S. Targeted deletion of MyD88 in intestinal epithelial cells results in compromised antibacterial immunity associated with downregulation of polymeric immunoglobulin receptor, mucin-2, and antibacterial peptides. Mucosal Immunol. 2012; 5, 501–512.

37. Demeria D., Ewaschuk J., Madsen K. Interactions of Lactobacillus with immune system. Ljungh Å., Wadström T. eds. Lactobacillus molecular biology: from genomics to probiotics, 1st ed. Norfolk: Caister Academic Press 2009.

38. O’Hara A. M., Shanahan F. The gut flora as a forgotten organ. EMBO Rep. 2006; 7, 688–693.

39. Lebeer S., Vanderleyden J., De Keersmaecke, S. C. J. Host interactions of probiotic bacterial surface molecules: comparison with commensals and pathogens. Nat. Rev. 2010; 8, 171–184.

40. Erridge C., Pridmore A., Eley A., Stewart J., Poxton I. R. Lipopolysaccharides of Bacteroides fragilis, Chlamydia trachomatis and Pseudomonas aeruginosa signal through Toll-like receptor 2. J. Med. Microbiol. 2004; 53, 735–740.

41. Guani-Guerra E., Santoz-Mendoza T., Lugo-Reyes S. O., Terán L. M. Antimicrobial peptides: general overview and clinical implications in human health and disease. Clin. Immunol. 2010; 135, 1–11.

42. Ostaff M. J., Stange E. F., Wehkamp J. Antimicrobial peptides ad gut microbiota in homeostasis and pathology. EMBO Mol. Med. 2013; 5, 1465–1483.

43. Round J. L., Mazmanian S. K. The gut microbiota shapes intestinal immune responses during health and disease. Nat. Rev. Immunol. 2009; 9, 313–323.

44. Clemente J. C., Ursell L.K., Wegener Perfrey W., Knight R. The impact of the gut microbiota on human health: an integrative view. Cell 2012; 148, 1258–1270.

45. Sartor R. B., Mazmanian S. K. Intestinal microbes in inflammatory bowel diseases. Am. J. Gastroenterol. Suppl. 2012; 1, 15–21.

46. Brown C. T., Sharon I., Thomas B. C., Castelle C. J., Morowitz M. J., Banfield J. F. Genome resolved analysis of a premature infant gut microbial community reveals a Varibaculum cambriese genome and a shift towards fermentation-based metabolism during the third week of life. Microbiome 2013; 1, 30.

47. Lemon K. P., Armitage G. C., Relman D. A., Fischbach M. A. Microbiota-targeted therapies: an ecological perspective. Sci. Transl. Med. 2012; 4, 137–135.

48. Costello E. K., Stagaman K., Dethlefsen L., Bohannan B. J., Relman D. A. The application of ecological theory toward an understanding of the human microbiome. Science 2012; 336, 1255–1262.

49. Burke C., Steinberg P., Rusch D., Kjelleberg S., Thomas T. Bacterial community assembly based on functional genes rather than species. Proc. Natl. Acad. Sci. USA 2011; 108, 14288–14293.

50. Turnbaugh P. J., Ley R. E., Hamady M., Fraser-Liggett C., Knight R., Gordon J. I. The human microbiome project. Nature 2007; 449, 804–810.

51. Flores G. E., Caporaso J. G., Henley J. B., Rideout J. R., Domogala D., Chase J., Leff J. W., Vázquez-Baeza Y., Gonzalez A., Knight R., Dunn R. R., Fierer N. Temporal variability is a personalized feature of the human microbiome. Genome Biol. 2014; 15, 531.

52. Blaser M. Who are we? EMBO Rep. 2006; 7, 956–960.

53. Strachan D. P. Hay fever, hygiene, and household size. BMJ 1989; 299, 1259–1260.

54. Cookson W. O., Moffatt M. F. Asthma: an epidemic in the absence of infection? Science 1997; 275, 41–42.

55. Swanson H. I. Drug metabolism by the host and gut microbiota: a partnership or rivalry? Drug Metab. Dispos. 2015; 43, 1499–1504.

56. McDermott A. J., Huffnagel G. B. The microbiome and regulation of mucosal immunity. Immunology 2014; 142, 24–31.

57. Maranduba C. M., De Castro S. B, de Souza G. T., Rossato C., da Guia F. C:, Valente M. A. S., Rettore J. V. P, Maranduba C. P., de Souza C. M., do Carmo A. M. R., Macedo G. C., de Sá Silva F. Intestinal microbiota modulators of the immune system and neuroimmune system: impact on the host health and homeostasis. J. Immunol. Res. 2015; 2015, 931574.

58. Blaser M., Falkow S. What are the consequences of the disappearing human microbiota? Nat. Rev. Microbiol. 2009; 7, 887–894.

59. Dethlefsen L., Huse S., Sogin M. L., Relman D. A. The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rDNA sequencing. PLoS Biol. 2008; 6, e280.

60. Sokol H., Pigneur B., Watterlot L., Lakhdari O., Bermúdez-Humarán L. G., Gratadoux J. J., Blugeon S., Bridonneau C., Furet J. P., Corthier G., Grangette C., Vasquez N., Pochart P., Trugnan G., Thomas G., Blottière H. M., Doré J., Marteau P., Seksik P., Langella P. Faecalibacterium prausnitzii is an anti-inflammatory commensal bacterium identified by gut microbiota analysis o Crohn disease patients. Proc. Natl. Acad. Sci. USA 2008; 105, 16731–16736.

61. Rutter M., Saunders B., Wilkinson K., Rumbles S., Schofield G., Kamm M., Williams C., Price A., Talbot I., Forbes A. Severity of inflammation is a risk factor for colorectal neoplasia in ulcerative colitis. Gastroenterology 2004; 126, 451–459.

62. Knights D., Lassen K. G., Xavier R. J. Advances in inflammatory bowel disease pathogenesis: linking host genetics and the microbiome. Gut 2013; 62, 1505–1510.

63. Collins S. M. A role for the gut microbiota in IBS. Nat. Rev. Gastroenterol. Hepatol. 2014; 11, 497–505.

64. Borges-Canha M., Portela-Cidade J. P., Dinis-Ribeiro M., Leite-Moreira A. F., Pimentel-Nunes P. Role of colonic microbiota in colorectal carcinogenesis: A systematic review. Rev. Esp. Enferm. Dig. 2015; 107, 659–671.

65. Hur K. Y., Lee MS. Gut microbiota and metabolic disorders. Diabetes Metab. J. 2015; 39, 198–203.

66. Aarslan N. Obesity, fatty liver disease and intestinal microbiota. World J. Gastroenterol. 2014; 20, 16452.

67. Horning M. The role of microbes and autoimmunity in the pathogenesis of neuropsychiatric illness. Cur. Opin Rheumatol 2013; 25, 488–795.

68. Fujimura K. E., Lynch S.V. Microbiota in allergy and asthma and the emerging relationship with the gut microbiome. Cell Host Microbe 2015; 17, 592–602.

69. Seekatz A. M., Young V. B. Clostridium difficile and the microbiota. J. Clin. Invest. 2014; 124, 4182.

70. Clarke G., Stilling R. M., Kennedy P. J., Stanton C., Cryan J. F., Dinan T. G. Minireview. Gut microbiota: the neglected endocrine organ. Mol. Endocrinol. 2014; 28, 1221–1238.

71. Ridaura V., Belkaid Y. Gut microbiota: the link to your second brain. Cell 2015; 161, 193–194.

72. Rhee S. H, Pothoulakis C., Mayer E. A. Principles and clinical implications of the brain-gut enteric microbiota axis. Nat. Rev. Gastroenterol. Hepatol. 2009; 6, 306–314.

73. Collins S. M., Surette M., Bercik P. The interplay between the intestinal microbiota and the brain. Na. Rev. Microbiol. 2012; 10, 735–742.

74. Rosenfeld C. S. Microbiome disturbances and autism spectrum disorders. Drug Metab. Dispos. 2015; 43, 1557–1571.

75. Marque A. H, O‘Connor T. G., Roth C., Susser E., Bjørke-Monsen A. L. The influence of maternal prenatal and early childhood nutrition and maternal prenatal stress on offspring immune system development and neurodevelopmental disorders. Front. Neurosci. 2013; 7, 120.

76. Bale T. L., Baram T. Z., Brown A. S., Goldstein J. M., Insel T. R., McCarthy M. M., Nemeroff C. B., Reyes T. M., Simerly R. B., Susser E. S., Nestler E. J. Early life programming and neurodevelopmental disorders. Biol. Psychiatry. 2010; 68, 314–319.

77. Mittal V. A., Ellman L. M., Cannon T. D. Gene-environmental interaction and covariation in schizophrenia: the role of obstetric complications. Schizophr. Bull. 2008; 34, 1083–1094.

78. Finegold S. M. State of art; microbiology in health and disease. Intestinal bacterial flora in autism. Anaerobe 2011; 17, 367–368.

79. Donnet-Hughes A., Perez P. F., Doré J., Leclerc M., Levenez F., Benyacoub J., Serrant P., Segura-Roggero I., Schiffrin E. J. Potential role of intestinal microbiota of the mother in neonatal immune education. Proc. Nutr. Soc. 2010; 69, 407–415.

80. Borre Y. E, O´Keeffe, G. W, Clarke G., Stanton C., Dinan T. G., Cryan J. F. Microbiota and neurodevelopmental windows: implications for brain disorders. Trends Mol. Med. 2014; 20, 509–518.

81. Marchesi J. R., Adams D. H., Fava F., Hermes G. D., Hirschfield G. M., Hold G., Quraishi M. N., Kinross J., Smidt H., Tuohy K. M., Thomas L. V., Zoetendal E. G., Hart A. The gut microbiota and host health: a new clinical frontier. Gut 2015; 65, 330–339.