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The Microbiome in HIV-Infected Children

  • Robin J. GreenEmail author
Chapter
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Abstract

Every human being has, within itself, a microbiome, which includes the gastrointestinal tract, the respiratory tract, the genito-urinary tract and the skin. Whilst the most well-known species are bacteria, there is also a microbiome of fungi and viruses in all these regions. Humans and microbes have evolved together over eons of time, and thus, the human immune system and the microbiome demonstrate complex interactions. The presence and functioning of a microbiome is critical to the development of the human immune response, and, in turn, the immune system functions to maintain the microbiome. A number of factors are present in modern lifestyles that actively destroy the ‘normal’ microbiome and result in a process known as dysbiosis.

Over the last few years, the importance of the microbiome in HIV-infected children (and adults) has emerged. It is highly likely that the microbiome is unique in HIV-infected individuals and that specific clusters determine processes and profiles in various organ systems. In HIV-infected individuals dysbiosis has many forms, including reduced diversity or even increased diversity, but with replacement by pathogenic taxa.

It is now becoming clear that susceptibility to, progression of, and co-morbidities in HIV-infected patients (especially children) is also intimately linked to microbial diversity. The presence of a microbiome, and dysbiotic factors, are functional in many organ systems of children who are HIV-infected.

Keywords

Microbiome Human immunodeficiency virus (HIV) Dysbiosis Gastrointestinal tract (GIT) Respiratory tract Oral flora 

References

  1. 1.
    Gill SR, Pop M, Deboy RT, et al. Metagenomic analysis of the human distal gut microbiome. Science. 2006;312(5778):1355–9.PubMedPubMedCentralCrossRefGoogle Scholar
  2. 2.
    Bäckhed F, Ley RE, Sonnenburg JL, Peterson DA, Gordon JI. Host bacterial mutualism in the human intestine. Science. 2005;307(5717):1915–20.PubMedCrossRefPubMedCentralGoogle Scholar
  3. 3.
    Clarridge JE. Impact of 16S rRNA gene sequence analysis for identification of bacteria on clinical microbiology and infectious diseases. Clin Microbiol Rev. 2004;17(4):840–62.PubMedPubMedCentralCrossRefGoogle Scholar
  4. 4.
    Schuster SC. Next-generation sequencing transforms today’s biology. Nat Methods. 2008;5(1):16–8.PubMedCrossRefPubMedCentralGoogle Scholar
  5. 5.
    Turnbaugh PJ, Ley RE, Hamady M, Fraser-Liggett CM, Knight R, Gordon JI. The human microbiome project. Nature. 2007;449(7164):804–10.PubMedPubMedCentralCrossRefGoogle Scholar
  6. 6.
    Peterson J, Garges S, Giovanni M, NIH HMP Working Group, et al. The NIH human microbiome project. Genome Res. 2009;19(12):2317–23.PubMedPubMedCentralCrossRefGoogle Scholar
  7. 7.
    Mackie RI, Sghir A, Gaskins HR. Developmental microbial ecology of the neonatal gastrointestinal tract. Am J Clin Nutr. 1999;69(5):1035S–45S.PubMedCrossRefPubMedCentralGoogle Scholar
  8. 8.
    DiGiulio DB. Diversity of microbes in amniotic fluid. Semin Fetal Neonatal Med. 2012;17(1):2–11.PubMedCrossRefPubMedCentralGoogle Scholar
  9. 9.
    Aagaard K, Ma J, Antony KM, Ganu R, Petrosino J, Versalovic J. The placenta harbors a unique microbiome. Sci Transl Med. 2014;6(237):237ra65.PubMedPubMedCentralCrossRefGoogle Scholar
  10. 10.
    Gollwitzer ES, Saglani S, Trompette A, et al. Lung microbiota promotes tolerance to allergens in neonates via PD-L1. Nat Med. 2014;20(6):642–7.PubMedCrossRefPubMedCentralGoogle Scholar
  11. 11.
    Teo SM, Mok D, Pham K, et al. The infant nasopharyngeal microbiome impacts severity of lower respiratory infection and risk of asthma development. Cell Host Microbe. 2015;17(5):704–15.PubMedPubMedCentralCrossRefGoogle Scholar
  12. 12.
    Biesbroek G, Tsivtsivadze E, Sanders EA, et al. Early respiratory microbiota composition determines bacterial succession patterns and respiratory health in children. Am J Respir Crit Care Med. 2014;190(11):1283–92.PubMedCrossRefPubMedCentralGoogle Scholar
  13. 13.
    Scagnolari C, Antonelli G. Type I interferon and HIV: subtle balance between antiviral activity, immunopathogenesis and the microbiome. Cytokine Growth Factor Rev. 2018;40:19–31.PubMedCrossRefPubMedCentralGoogle Scholar
  14. 14.
    Koay WLA, Siems LV, Persaud D. The microbiome and HIV persistence: implications for viral remission and cure. Curr Opin HIV AIDS. 2018;13(1):61–8.PubMedPubMedCentralCrossRefGoogle Scholar
  15. 15.
    Frank DN, Manigart O, Leroy V. Altered vaginal microbiota are associated with perinatal mother-to-child transmission of HIV in African women from Burkina Faso. J Acquir Immune Defic Syndr. 2012;60(3):299–306.PubMedPubMedCentralCrossRefGoogle Scholar
  16. 16.
    Berard AR, Perner M, Mutch S, Farr Zuend C, McQueen P, Burgener AD. Understanding mucosal and microbial functionality of the female reproductive tract by metaproteomics: implications for HIV transmission. Am J Reprod Immunol. 2018;80(2):e12977.PubMedCrossRefPubMedCentralGoogle Scholar
  17. 17.
    Farcasanu M, Kwon DS. The influence of cervicovaginal microbiota on mucosal immunity and prophylaxis in the battle against HIV. Curr HIV/AIDS Rep. 2018;15(1):30–8.PubMedCrossRefPubMedCentralGoogle Scholar
  18. 18.
    Wessels JM, Lajoie J, Vitali D. Association of high-risk sexual behaviour with diversity of the vaginal microbiota and abundance of Lactobacillus. PLoS One. 2017;12(11):e0187612.PubMedPubMedCentralCrossRefGoogle Scholar
  19. 19.
    Scully EP. Sex differences in HIV infection. Curr HIV/AIDS Rep. 2018;15(2):136–46.PubMedPubMedCentralCrossRefGoogle Scholar
  20. 20.
    Abdool Karim SS, Passmore JS, Baxter C. The microbiome and HIV prevention strategies in women. Curr Opin HIV AIDS. 2018;13(1):81–7.PubMedCrossRefPubMedCentralGoogle Scholar
  21. 21.
    McClelland RS, Lingappa JR, Srinivasan S, et al. Evaluation of the association between the concentrations of key vaginal bacteria and the increased risk of HIV acquisition in African women from five cohorts: a nested case-control study. Lancet Infect Dis. 2018;18(5):554–64.PubMedPubMedCentralCrossRefGoogle Scholar
  22. 22.
    Vázquez-Castellanos JF, Serrano-Villar S, Jiménez-Hernández N, et al. Interplay between gut microbiota metabolism and inflammation in HIV infection. SME J. 2018;12(8):1964–76.Google Scholar
  23. 23.
    Wood LF, Brown BP, Lennard K, et al. Feeding-related gut microbial composition associates with peripheral T cell activation and mucosal gene expression in African infants. Clin Infect Dis. 2018;67(8):1237–46.  https://doi.org/10.1093/cid/ciy265.CrossRefPubMedPubMedCentralGoogle Scholar
  24. 24.
    Neff CP, Krueger O, Xiong K, et al. Fecal microbiota composition drives immune activation in HIV-infected individuals. EBioMedicine. 2018;30:192–202.PubMedPubMedCentralCrossRefGoogle Scholar
  25. 25.
    Reis EC, da Silva LT, da Silva WC, Rios A, Duarte AJ, Oshiro TM, Crovella S, Pontillo A. Host genetics contributes to the effectiveness of dendritic cell-based HIV immunotherapy. Hum Vaccin Immunother. 2018;14(8):1995–2002.  https://doi.org/10.1080/21645515.2018.1463942.CrossRefPubMedPubMedCentralGoogle Scholar
  26. 26.
    Zhou Y, Ou Z, Tang X, et al. Alterations in the gut microbiota of patients with acquired immune deficiency syndrome. J Cell Mol Med. 2018;22(4):2263–71.PubMedPubMedCentralCrossRefGoogle Scholar
  27. 27.
    Powis KM, Souda S, Lockman S, et al. Cotrimoxazole prophylaxis was associated with enteric commensal bacterial resistance among HIV-exposed infants in a randomized controlled trial, Botswana. J Int AIDS Soc. 2017;20:3.CrossRefGoogle Scholar
  28. 28.
    Nel E. Severe acute malnutrition. Curr Opin Clin Nutr Metab Care. 2018;21(3):195–9.PubMedCrossRefPubMedCentralGoogle Scholar
  29. 29.
    Goldberg BE, Mongodin EF, Jones CE, Chung M, Fraser CM, Tate A, Zeichner SL. The oral bacterial communities of children with well-controlled HIV infection and without HIV Infection. PLoS One. 2015;10(7):e0131615.PubMedPubMedCentralCrossRefGoogle Scholar
  30. 30.
    Sharifzadeh A, Khosravi AR, Shokri H, Asadi Jamnani F, Hajiabdolbaghi M, Ashrafi Tamami I. Oral microflora and their relation to risk factors in HIV+ patients with oropharyngeal candidiasis. J Mycol Med. 2013;23(2):105–12.PubMedCrossRefPubMedCentralGoogle Scholar
  31. 31.
    Starr JR, Huang Y, Lee KH, Pediatric HIV/AIDS Cohort Study. Oral microbiota in youth with perinatally acquired HIV infection. Microbiome. 2018;6(1):100.PubMedPubMedCentralCrossRefGoogle Scholar
  32. 32.
    Lewy T, Hong BY, Weiser B, Burger H, Tremain A, Weinstock G, Anastos K, George M. Oral microbiome in HIV-infected women: shifts in the abundance of pathogenic and beneficial bacteria are associated with aging, HIV load, CD4 count, and ART. AIDS Res Hum Retrovir. 2017;35(3):276–86.  https://doi.org/10.1089/AID.2017.0200.CrossRefGoogle Scholar
  33. 33.
    Bhattacharya SD, Niyogi SK, Bhattacharyya S, Arya BK, Chauhan N, Mandal S. Associations between potential bacterial pathogens in the nasopharynx of HIV-infected children. Indian J Pediatr. 2012;79(11):1447–53.PubMedCrossRefPubMedCentralGoogle Scholar
  34. 34.
    Kelly MS, Surette MG, Smieja M, et al. The nasopharyngeal microbiota of children with respiratory infections in Botswana. Pediatr Infect Dis J. 2017;36(9):e211–8.PubMedPubMedCentralCrossRefGoogle Scholar
  35. 35.
    Masekela R, Anderson R, Moodley T, Kitchin OP, Risenga SM, Becker PJ, Green RJ. HIV-related bronchiectasis in children: an emerging spectre in high tuberculosis burden areas. Int J TB Lung Dis. 2012;16:114–9.CrossRefGoogle Scholar
  36. 36.
    Masekela R, Vosloo S, Venter SN, de Beer WZ, Green RJ. The lung microbiome in children with HIV-bronchiectasis: a cross-sectional pilot study. BMC Pulm Med. 2018;18(1):87.PubMedPubMedCentralCrossRefGoogle Scholar
  37. 37.
    Gonzalez-Martinez C, Kranzer K, McHugh G, BREATHE Study Team, et al. Azithromycin versus placebo for the treatment of HIV-associated chronic lung disease in children and adolescents (BREATHE trial): study protocol for a randomised controlled trial. Trials. 2017;18(1):622.PubMedPubMedCentralCrossRefGoogle Scholar
  38. 38.
    Lagathu C, Cossarizza A, Béréziat V, Nasi M, Capeau J, Pinti M. Basic science and pathogenesis of ageing with HIV: potential mechanisms and biomarkers. AIDS. 2017;31(Suppl 2):S105–19.PubMedCrossRefPubMedCentralGoogle Scholar
  39. 39.
    Monachese M, Cunningham-Rundles S, Diaz MA, et al. Probiotics and prebiotics to combat enteric infections and HIV in the developing world: a consensus report. Gut Microbes. 2011;2(3):198–207.PubMedCrossRefPubMedCentralGoogle Scholar
  40. 40.
    Ishizaki A, Bi X, Nguyen LV, Matsuda K, Pham HV, Phan CTT, Khu DTK, Ichimura H. Effects of short-term probiotic ingestion on immune profiles and microbial translocation among HIV-1-infected Vietnamese children. Int J Mol Sci. 2017;18(10):E2185.PubMedCrossRefPubMedCentralGoogle Scholar
  41. 41.
    Arnbjerg CJ, Vestad B, Hov JR, et al. Effect of lactobacillus rhamnosus GG supplementation on intestinal inflammation assessed by Pet/MRI scans and gut microbiota composition in HIV-infected individuals. J Acquir Immune Defic Syndr. 2018;78(4):450–7.  https://doi.org/10.1097/QAI.0000000000001693.CrossRefPubMedPubMedCentralGoogle Scholar
  42. 42.
    Deusch S, Serrano-Villar S, Rojo D, et al. Effects of HIV, antiretroviral therapy and prebiotics on the active fraction of the gut microbiota. AIDS. 2018;32(10):1229–37.PubMedCrossRefPubMedCentralGoogle Scholar
  43. 43.
    Serrano-Villar S, de Lagarde M, Vázquez-Castellanos J, et al. Effects of immunonutrition in advanced HIV disease: a randomized placebo controlled clinical trial (Promaltia Study). Clin Infect Dis. 2018;68(1):120–30.  https://doi.org/10.1093/cid/ciy414.CrossRefGoogle Scholar
  44. 44.
    Presti RM, Handley SA, Droit L, et al. Alterations in the oral microbiome in HIV-infected participants after antiretroviral therapy administration are influenced by immune status. AIDS. 2018;32(10):1279–87.PubMedPubMedCentralCrossRefGoogle Scholar
  45. 45.
    Maloupazoa Siawaya AC, Kuissi Kamgaing E, Minto’o Rogombe S, et al. HIV-exposed uninfected compared with unexposed infants show the presence of leucocytes, lower lactoferrin levels and antimicrobial-resistant micro-organisms in the stool. Paediatr Int Child Health. 2019;39(4):249–58.PubMedCrossRefPubMedCentralGoogle Scholar
  46. 46.
    Machiavelli A, Duarte RTD, Pires MMS, Zárate-Bladés CR, Pinto AR. The impact of in utero HIV exposure on gut microbiota, inflammation, and microbial translocation. Gut Microbes. 2019;10(5):599–614.PubMedPubMedCentralCrossRefGoogle Scholar
  47. 47.
    Dzanibe S, Jaspan HB, Zulu MZ, Kiravu A, Gray CM. Impact of maternal HIV exposure, feeding status, and microbiome on infant cellular immunity. J Leukoc Biol. 2019;105:281–9.PubMedCrossRefPubMedCentralGoogle Scholar
  48. 48.
    Qian Y, Yang X, Xu S, Wu C, Qin N, Chen SD, Xiao Q. Detection of microbial 16S rRNA gene in the blood of patients with Parkinson’s disease. Front Ageing Neurosci. 2018;10:156.CrossRefGoogle Scholar

Copyright information

© Springer Nature Switzerland AG 2020

Authors and Affiliations

  1. 1.Department of Paediatrics and Child HealthUniversity of PretoriaPretoriaSouth Africa

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