2017 / 02

Следующая статья
DOI: 10.24075/brsmu.2017-02-01

ОБЗОР

Микробиом человека

А. В. Чаплин1, Д. В. Ребриков2,3, М. Н. Болдырева4
Информация об авторах

1 Кафедра микробиологии и вирусологии, педиатрический факультет,
Российский национальный исследовательский медицинский университет имени Н. И. Пирогова, Москва

2 НИИ трансляционной медицины,
Российский национальный исследовательский медицинский университет имени Н. И. Пирогова, Москва

3 Лаборатория клеточных технологий,
Научный центр акушерства, гинекологии и перинатологии имени академика В. И. Кулакова, Москва

4 Отдел научных разработок,
ООО «НПФ ДНК-Технология», Москва

Для корреспонденции: Андрей Викторович Чаплин
ул. Островитянова, д. 1, г. Москва, 117997; moc.liamg@kidemoloko

Информация о статье

Вклад всех авторов в работу равнозначен: подбор и анализ литературы, планирование структуры статьи, интерпретация данных литературы, подготовка черновика рукописи, внесение исправлений.

Статья получена: 16.04.2017 Статья принята к печати: 22.04.2017 Опубликовано online: 27.05.2017
|
  1. Stinson LF, Payne MS, Keelan JA. Planting the seed: Origins, composition, and postnatal health significance of the fetal gastrointestinal microbiota. Crit Rev Microbiol. 2017 May; 43 (3): 352–69.
  2. Fitzstevens JL, Smith KC, Hagadorn JI, Caimano MJ, Matson AP, Brownell EA. Systematic Review of the Human Milk Microbiota. Nutr Clin Pract. 2016 Sep 27. pii: 0884533616670150. PubMed PMID: 27679525.
  3. Jakobsson HE, Abrahamsson TR, Jenmalm MC, Harris K, Quince C, Jernberg C, et al. Decreased gut microbiota diversity, delayed Bacteroidetes colonisation and reduced Th1 responses in infants delivered by Caesarean section. Gut. 2014 Apr; 63 (4): 559-66.
  4. Rutayisire E, Huang K, Liu Y, Tao F. The mode of delivery affects the diversity and colonization pattern of the gut microbiota during the first year of infants’ life: a systematic review. BMC Gastroenterol. 2016 Jul 30; 16 (1): 86.
  5. Falony G, Joossens M, Vieira-Silva S, Wang J, Darzi Y, Faust K, et al. Population-level analysis of gut microbiome variation. Science. 2016 Apr 29; 352 (6285): 560–4.
  6. Kulagina EV, Efimov BA, Maximov PY, Kafarskaia LI, Chaplin AV,
  7. De Filippo C, Cavalieri D, Di Paola M, Ramazzotti M, Poullet JB, Massart S, et al. Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa. Proc Natl Acad Sci U S A. 2010 Aug 17; 107 (33): 14691–6.
  8. Tyakht AV, Kostryukova ES, Popenko AS, Belenikin MS, Pavlenko AV, Larin AK, et al. Human gut microbiota community structures in urban and rural populations in Russia. Nat Commun. 2013; 4: 2469.
  9. Arumugam M, Raes J, Pelletier E, Le Paslier D, Yamada T, Mende DR, et al. Enterotypes of the human gut microbiome. Nature. 2011 May 12; 473 (7346): 174–80.
  10. Evans JM, Morris LS, Marchesi JR. The gut microbiome: the role of a virtual organ in the endocrinology of the host. J Endocrinol. 2013 Aug 28; 218 (3): R37–47.
  11. Clarke G, Stilling RM, Kennedy PJ, Stanton C, Cryan JF, Dinan TG. Minireview: Gut Microbiota: The Neglected Endocrine Organ. Mol Endocrinol. 2014 Aug; 28 (8): 1221–38.
  12. Rooks MG, Garrett WS. Gut microbiota, metabolites and host immunity. Nat Rev Immunol. 2016 May 27; 16 (6): 341–52.
  13. Canfora EE, Jocken JW, Blaak EE. Short-chain fatty acids in control of body weight and insulin sensitivity. Nat Rev Endocrinol. 2015 Oct; 11 (10): 577–91.
  14. Kamada N, Kim Y-G, Sham HP, Vallance BA, Puente JL, Martens EC, et al. Regulated virulence controls the ability of a pathogen to compete with the gut microbiota. Science. 2012 Jun 8; 336 (6086): 1325–9.
  15. Dobson A, Cotter PD, Ross RP, Hill C. Bacteriocin production: a probiotic trait? Appl Environ Microbiol. 2012 Jan; 78 (1): 1–6.
  16. Buffie CG, Bucci V, Stein RR, McKenney PT, Ling L, Gobourne A, et al. Precision microbiome reconstitution restores bile acid mediated resistance to Clostridium difficile. Nature. 2015 Jan 8; 517 (7533): 205–8.
  17. Ивашкин В. Т., Шифрин О. С., Тертычный А. С., Полуэктова Е. А., Лапина Т. Л., Ляшенко О.С. и др. Clostridium difficile-ассоциированная болезнь. Рос. журн. гастроэнтерол. гепатол. колопроктол. 2016; 25 (6): 5–17.
  18. Goldenberg JZ, Ma SS, Saxton JD, Martzen MR, Vandvik PO, Thorlund K, et al. Probiotics for the prevention of Clostridium difficile-associated diarrhea in adults and children. Cochrane Database Syst Rev. 2013 May 31; (5): CD006095.
  19. Cammarota G, Ianiro G, Gasbarrini A. Fecal Microbiota Transplantation for the Treatment of Clostridium difficile Infection: a Systematic Review. J Clin Gastroenterol. 2014 Sep; 48 (8): 693–702.
  20. Olle B. Who Will Figure Out How to Make a Business Out of Fecal Transplants? [Internet]. 2013 May 3 [cited 2017 Apr 3]; [about 7 p.]. Available from: http://www.fiercebiotech.com/r-d/who-will- figure-out-how-to-make-a-business-out-of-fecal-transplants
  21. Hodzic Z, Bolock AM, Good M. The Role of Mucosal Immunity in the Pathogenesis of Necrotizing Enterocolitis. Front Pediatr. 2017 Mar 3; 5: 40.
  22. Pammi M, Cope J, Tarr PI, Warner BB, Morrow AL, Mai V, et al. Intestinal dysbiosis in preterm infants preceding necrotizing enterocolitis: a systematic review and meta-analysis. Microbiome. 2017 Mar 9; 5 (1): 31.
  23. AlFaleh K, Anabrees J. Probiotics for prevention of necrotizing enterocolitis in preterm infants. Cochrane Database Syst Rev. 2014 Apr 10; (4): CD005496.
  24. Leung A, Tsoi H, Yu J. Fusobacterium and Escherichia: models of colorectal cancer driven by microbiota and the utility of microbiota in colorectal cancer screening. Expert Rev Gastroenterol Hepatol. 2015 May; 9 (5): 651–7.
  25. Graillot V, Dormoy I, Dupuy J, Shay JW, Huc L, Mirey G, et al. Genotoxicity of Cytolethal Distending Toxin (CDT) on Isogenic Human Colorectal Cell Lines: Potential Promoting Effects for Colorectal Carcinogenesis. Front Cell Infect Microbiol. 2016 Mar 23; 6: 34.
  26. Needell JC, Zipris D. The Role of the Intestinal Microbiome in Type 1 Diabetes Pathogenesis. Curr Diab Rep. 2016 Oct; 16 (10): 89.
  27. Boulangé CL, Neves AL, Chilloux J, Nicholson JK, Dumas M-E. Impact of the gut microbiota on inflammation, obesity, and metabolic disease. Genome Med. 2016 Apr 20; 8 (1): 42.
  28. Ding HT, Taur Y, Walkup JT. Gut Microbiota and Autism: Key Concepts and Findings. J Autism Dev Disord. 2017 Feb; 47 (2): 480–9.
  29. Jünemann S, Prior K, Szczepanowski R, Harks I, Ehmke B, Goesmann A, et al. Bacterial community shift in treated periodontitis patients revealed by ion torrent 16S rRNA gene amplicon sequencing. PloS One. 2012; 7 (8): e41606.
  30. Зорина О. А., Кулаков А. А., Ребриков Д. В. Количественная оценка соотношения патогенных представителей микробиоценоза полости рта в норме и при пародонтите. Стоматология. 2011; 90 (3): 40–2.
  31. Yanushevich OO, Ayvazova RA, Shibaeva AV, Rebrikov DV, Trubnikova EV, Kudykina YK, et al. Quantitative PCR studies of Aggregatibacter actinomycetemcomitans and Treponema denticola/Tanerella forsythensis Complex as Etiological Factors of Chronic Periodontitis. Bull Exp Biol Med. 2016 Feb; 160 (4): 495–7.
  32. Шибаева А. В., Айвазова Р. А., Ребриков Д. В., Трубнико- ва Е. В., Кудыкина Ю. К., Белякова А. В. и др. Применение метода ПЦР в реальном времени для изучения микробиома пародонта у пациентов с сочетанной патологией гастродуоденальной зоны и хроническим пародонтитом. Мол. ген., микробиол. и вирусол. 2016; 34 (1): 26–30.
  33. Петрухина Н. Б., Зорина О. А., Ших Е. В., Шибаева А. В., Шевелев А. Б. Изучение взаимосвязи состава микробиома пародонта и кишечника в норме и при патологии методами глубокого секвенирования. Стоматология. 2016; 95 (2): 8–13.
  34. Зорина О. А., Аймадинова Н. К., Басова А. А., Шибаева А. В., Ребриков Д. В. Гендерные различия в микробиоме пародонтального кармана у пациентов с хроническим генерализованным пародонтитом. Стоматология. 2016; 95 (3): 10–6.
  35. Зорина О. А., Петрухина Н. Б., Басова А. А., Шибаева А. В., Трубникова Е. В., Шевелев А. Б. Идентификация ключевых элементов нормальной и патогенной микрофлоры, определяющей состояние пародонта, методом NGS-секвенирования банков 16S-рДНК бактериальных консорциумов пародонта. Стоматология. 2014; 93 (6): 25–31.
  36. Franasiak JM, Scott RT Jr. Reproductive tract microbiome in assisted reproductive technologies. Fertil Steril. 2015 Dec; 104 (6): 1364–71.
  37. Болдырева М. Н., Байрамова Г. Р., Бурменская О. В. Диагностические возможности метода ПЦР в режиме реального времени для оценки биоты и локального воспаления в тканях урогенитального тракта. Справ. зав. КДЛ. 2015; (1): 9–17.
  38. Human Microbiome Project Consortium. Structure, function and diversity of the healthy human microbiome. Nature. 2012 Jun 13; 486 (7402): 207–14.
  39. Swidsinski A, Verstraelen H, Loening-Baucke V, Swidsinski S, Mendling W, Halwani Z. Presence of a polymicrobial endometrial biofilm in patients with bacterial vaginosis. PLoS One. 2013; 8 (1): e53997.
  40. Selman H, Mariani M, Barnocchi N, Mencacci A, Bistoni F, Arena S, et al. Examination of bacterial contamination at the time of embryo transfer, and its impact on the IVF/pregnancy outcome. J Assist Reprod Genet. 2007 Sep; 24 (9): 395–9.
  41. Шипицына Е. В., Мартикайнен З. М., Воробьева Н. Е., Ер- мошкина М. С., Степанова О. С., Донников А. Е. и др. Применение теста Фемофлор для оценки микробиоценоза влагалища. Журн. акуш. и женск. бол. 2009; 58 (3): 44–50.
  42. Болдырева М. Н., Липова Е. В., Алексеев Л. П., Витвиц- кая Ю. Г., Гуськова И. А. Характеристика биоты урогенитального тракта у женщин репродуктивного возраста методом ПЦР в реальном времени. Журн. акуш. и женск. бол. 2009; 58 (6): 36–42.
  43. Hyman RW, Herndon CN, Jiang H, Palm C, Fukushima M, Bernstein D, et al. The dynamics of the vaginal microbiome during infertility therapy with in vitro fertilization-embryo transfer. J Assist Reprod Genet. 2012 Feb; 29 (2): 105–15.
  44. Hein M, Petersen AC, Helmig RB, Uldbjerg N, Reinholdt J. Immunoglobulin levels and phagocytes in the cervical mucus plug at term of pregnancy. Acta Obstet Gynecol Scand. 2005 Aug; 84 (8): 734–42.
  45. Ulcova-Gallova Z. Immunological and physicochemical properties of cervical ovulatory mucus. J Reprod Immunol. 2010 Nov; 86 (2): 115–21.
  46. Lieberman JA, Moscicki AB, Sumerel JL, Ma Y, Scott ME. Determination of cytokine protein levels in cervical mucus samples from young women by a multiplex immunoassay method and assessment of correlates. Clin Vaccine Immunol. 2008 Jan; 15 (1): 49–54.
  47. Ming L, Xiaoling P, Yan L, Lili W, Qi W, Xiyong Y, et al. Purification of antimicrobial factors from human cervical mucus. Hum Reprod. 2007 Jul; 22 (7): 1810–5.
  48. Ansbacher R, Boyson WA, Morris JA. Sterility of the uterine cavity. Am J Obstet Gynecol. 1967 Oct 1; 99 (3): 394–6.
  49. Zervomanolakis I, Ott HW, Hadziomerovic D, Mattle V, Seeber BE, Virgolini I, et al. Physiology of upward transport in the human female genital tract. Ann N Y Acad Sci. 2007 Apr; 1101: 1–20.
  50. Mitchell CM, Haick A, Nkwopara E, Garcia R, Rendi M, Agnew K, et al. Colonization of the upper genital tract by vaginal bacterial species in nonpregnant women. Am J Obstet Gynecol. 2015 May; 212 (5): 611. e1–9.
  51. Artley JK, Braude PR, Cooper P. Vaginal squamous cells in follicular aspirates following transvaginal puncture. Hum Reprod. 1993 Aug; 8 (8): 1272–3.
  52. Cottell E, McMorrow J, Lennon B, Fawsy M, Cafferkey M, Harrison RF. Microbial contamination in an in vitro fertilization- embryo transfer system. Fertil Steril. 1996 Nov; 66 (5): 776–80.
  53. Saltes B, Molo MW, Binor Z, Radwanska E. Bacterial contamination after transvaginal aspiration (TVA) of oocytes. J Assist Reprod Genet. 1995 Oct; 12 (9): 657–8.
  54. Pelzer ES, Allan JA, Cunningham K, Mengersen K, Allan JM, Launchbury T, et al. Microbial colonization of follicular fluid: alterations in cytokine expression and adverse assisted reproduction technology outcomes. Hum Reprod. 2011 Jul; 26 (7): 1799–812.
  55. Spence MR, Blanco LJ, Patel J, Brockman MT. A comparative evaluation of vaginal, cervical and peritoneal flora in normal, healthy women: a preliminary report. Sex Transm Dis. 1982 Jan– Mar; 9 (1): 37–40.
  56. Pelzer ES, Allan JA, Waterhouse MA, Ross T, Beagley KW, Knox CL. Microorganisms within Human Follicular Fluid: Effects on IVF. PLoS One. 2013; 8 (3): e59062.
  57. Bowie WR, Pollock HM, Forsyth PS, Floyd JF, Alexander ER, Wang SP, et al. Bacteriology of the urethra in normal men and men with nongonococcal urethritis. J Clin Microbiol. 1977 Nov; 6 (5): 482–8.
  58. Nelson DE, Van Der Pol B, Dong Q, Revanna KV, Fan B, Easwaran S, et al. Characteristic Male Urine Microbiomes Associate with Asymptomatic Sexually Transmitted Infection. PLoS One. 2010 Nov 24; 5 (11): e14116.
  59. Liu CM, Hungate BA, Tobian AA, Ravel J, Prodger JL, Serwadda D, et al. Penile microbiota and female partner bacterial vaginosis in Rakai, Uganda. MBio. 2015 Jun 16; 6 (3): e00589–15.
  60. Ma B, Forney LJ, Ravel J. Vaginal microbiome: rethinking health and disease. Annu Rev Microbiol. 2012; 66: 371–89.
  61. Hou D, Zhou X, Zhong X, Settles ML, Herring J, Wang L, et al. Microbiota of the seminal fluid from healthy and infertile men. Fertil Steril. 2013 Nov; 100 (5): 1261–9.
  62. Weng SL, Chiu CM, Lin FM, Huang WC, Liang C, Yang T, et al. Bacterial communities in semen from men of infertile couples: metagenomic sequencing reveals relationships of seminal microbiota to semen quality. PLoS One. 2014 Oct 23; 9 (10): e110152.