Analysis of the gut microbiome of patients with HIV infection using 16S rRNA-sequencing

Cover Page


Cite item

Full Text

Open Access Open Access
Restricted Access Access granted
Restricted Access Subscription or Fee Access

Abstract

BACKGROUND: The microbiota of the gastrointestinal tract is one of the important factors that ensure the normal functioning of the human body. Patients with HIV infection are most susceptible to intestinal infections and changes in the composition of the microbiota, both due to exposure to the virus itself and reduced immunity. This study describes changes in the composition of the intestinal microflora of patients with HIV infection at the stage of secondary diseases, with and without antiretroviral therapy.

AIM: To determine the composition of the gut microbiome in patients with HIV infection on and off antiretroviral therapy using DNA sequencing of the hypervariable regions of the 16S rRNA gene.

MATERIALS AND METHODS: The study analyzed a group of 10 patients with a confirmed diagnosis of HIV infection and diarrheal syndrome. To clarify a possible etiological factor and determine the characteristics of the microbiocenosis of the gastrointestinal tract, stool analysis was performed using the 16S rRNA-sequencing method.

RESULTS: The study revealed significant changes in the composition of the microbiome: depletion of the Bacteroidetes type and increased number of the Proteobacteria type. A statistically significant difference was found in the composition of the types of microbiota in healthy people and patients with HIV infection (p <0.05). The normal flora was represented by only two microorganisms: Bifidobacterium breve and Lactobacillus rhamnosus. Conditionally pathogenic microorganisms were identified, namely, Enterococcus faecium, E. faecalis, Escherichia coli, Klebsiella pneumoniae, Citrobacter freundii, Enterococcus durans, Klebsiella sp., Pantoea agglomerans, K. variicola, E. hirae, E. coli TOP550-1, Clostridioides difficile, and Staphylococcus aureus. These bacteria may be the cause of diarrheal syndrome in patients with HIV infection.

CONCLUSION: In patients with HIV infection, bacterial diversity is reduced, normal flora is depleted, and a specific microbial profile is formed. Several conditionally pathogenic microorganisms can cause diarrhea in patients with HIV infection. Analysis of 16S rRNA-sequencing can be a non-invasive method for diagnosing changes in the composition of the intestinal microflora and clarifying the etiological factor of diarrheal syndrome.

Full Text

Restricted Access

About the authors

Darya M. Popova

Peoples’ Friendship University of Russia; Infectious Diseases Clinical Hospital No 2, Moscow

Email: popova-d@rudn.ru
ORCID iD: 0000-0002-4056-9192
Russian Federation, Moscow; Moscow

Sergey L. Voznesenskiy

Peoples’ Friendship University of Russia

Author for correspondence.
Email: voznesenskiy-sl@rudn.ru
ORCID iD: 0000-0001-5669-1910
SPIN-code: 4487-6744

MD, Cand. Sci. (Med.), Associate Professor

Russian Federation, Moscow

Elena V. Petrova

Infectious Diseases Clinical Hospital No 2, Moscow

Email: evi1963@yandex.ru
ORCID iD: 0000-0002-6896-6851
Russian Federation, Moscow

Polina V. Klimkova

Infectious Diseases Clinical Hospital No 2, Moscow

Email: pvk20@mail.ru
ORCID iD: 0000-0001-6046-7815
Russian Federation, Moscow

References

  1. Stoma IO. Microbiome in medicine: a guide for physicians. Moscow: GEOTAR-Media; 2020. 320 p. (In Russ). doi: 10.33029/9704-5844-0-MIM-2020-1-320
  2. Qin J, Li R, Raes J, et al.; MetaHIT Consortium. A human gut microbial gene catalogue established by metagenomic sequencing. Nature. 2010;464(7285):59–65. doi: 10.1038/nature08821
  3. Massanella M, Fromentin R, Chomont N. Residual inflammation and viral reservoirs: alliance against an HIV cure. Curr Opin HIV AIDS. 2016;11(2):234–241. doi: 10.1097/COH.0000000000000230
  4. Chun TW, Nickle DC, Justement JS, et al. Persistence of HIV in gut-associated lymphoid tissue despite long-term antiretroviral therapy. J Infect Dis. 2008;197(5):714–720. doi: 10.1086/527324
  5. Buckheit RW 3rd, Salgado M, Martins KO, Blankson JN. The implications of viral reservoirs on the elite control of HIV-1 infection. Cell Mol Life Sci. 2013;70(6):1009–1019. doi: 10.1007/s00018-012-1101-7
  6. Vesterbacka J, Rivera J, Noyan K, et al. Richer gut microbiota with distinct metabolic profile in HIV infected Elite Controllers. Sci Rep. 2017;7(1):6269. doi: 10.1038/s41598-017-06675-1
  7. Patel JB. 16S rRNA gene sequencing for bacterial pathogen identification in the clinical laboratory. Mol Diagn. 2001;6(4):313–321. doi: 10.1054/modi.2001.29158
  8. Drancourt M, Bollet C, Carlioz A, et al. 16S ribosomal DNA sequence analysis of a large collection of environmental and clinical unidentifiable bacterial isolates. J Clin Microbiol. 2000; 38(10):3623–3630. doi: 10.1128/JCM.38.10.3623-3630.2000
  9. Mignard S, Flandrois JP. 16S rRNA sequencing in routine bacterial identification: a 30-month experiment. J Microbiol Methods. 2006;67(3):574–581. doi: 10.1016/j.mimet.2006.05.009
  10. Kozhevnikov AA, Raskina KV, Martynova EYu, et al. Intestinal microbiota: modern ideas about species composition, functions and research methods. RMJ. 2017;(17):1244–1247. (In Russ).
  11. Khlyustova Ya. Akkermansia bacteria: what is it and how to increase their content in the intestine. Atlas Blog. Available from: https://atlas.ru/blog/baktierii-akkermansia-chto-eto-i-kak-povysit-ikh-sodierzhaniie-v-kishiechnikie/. Accessed: Nov 10, 2022. (In Russ).
  12. Prevotella (prevotella, a genus of bacteria). Istok-System Gastroscan. Available from: https://www.gastroscan.ru/handbook/118/7105. Accessed: Nov 10, 2022. (In Russ).
  13. Roseburia (roseburia, a genus of bacteria). Istok-System Gastroscan. Available from: https://www.gastroscan.ru/handbook/118/7643. Accessed: Nov 10, 2022. (In Russ).
  14. Qiao Y, Zhang Z, Zhai Y, et al. Apigenin Alleviates Obesity-Associated Metabolic Syndrome by Regulating the Composition of the Gut Microbiome. Front Microbiol. 2022;12:805827. doi: 10.3389/fmicb.2021.805827
  15. Eubacterium hallii. Istok-System Gastroscan. Available from: https://www.gastroscan.ru/handbook/118/8843. Accessed: Nov 10, 2022. (In Russ).
  16. Metody i ob”yekty metagenomnykh issledovaniy. metagenomnoye sekvenirovaniye kishechnoy mikrobioty [Methods and objects of metagenomic research. Metagenomic sequencing of the intestinal microbiota]. Available from: http://propionix.ru/metagenomika-i-mikrobiom. Accessed: Nov 10, 2022. (In Russ).
  17. Crakes KR, Jiang G. Gut Microbiome Alterations During HIV/SIV Infection: Implications for HIV Cure. Front Microbiol. 2019;10:1104. doi: 10.3389/fmicb.2019.01104
  18. Dillon SM, Lee EJ, Kotter CV, et al. An altered intestinal mucosal microbiome in HIV-1 infection is associated with mucosal and systemic immune activation and endotoxemia. Mucosal Immunol. 2014;7(4):983–994. doi: 10.1038/mi.2013.116
  19. Imahashi M, Ode H, Kobayashi A, et al. Impact of long-term antiretroviral therapy on gut and oral microbiotas in HIV-1-infected patients. Sci Rep. 2021;11(1):960. doi: 10.1038/s41598-020-80247-8

Supplementary files

Supplementary Files
Action
1. Fig. 1. The main types of gastrointestinal microorganisms of healthy people and patients with HIV infection on and outside ART.

Download (307KB)

Copyright (c) 2022 Eco-vector



СМИ зарегистрировано Федеральной службой по надзору в сфере связи, информационных технологий и массовых коммуникаций (Роскомнадзор).
Регистрационный номер и дата принятия решения о регистрации СМИ: 014448 от 08.02.1996
СМИ зарегистрировано Федеральной службой по надзору в сфере связи, информационных технологий и массовых коммуникаций (Роскомнадзор).
Регистрационный номер и дата принятия решения о регистрации СМИ: серия ЭЛ № ФС 77 - 80652 от 15.03.2021
.


This website uses cookies

You consent to our cookies if you continue to use our website.

About Cookies