Intestinal microbial dysbiosis has been described in individuals with an HIV-1 infection and may underlie persistent inflammation in chronic infection, thereby contributing to disease progression. Herein, we induced an HIV-1-like intestinal dysbiosis in rhesus macaques (Macaca mulatta) with vancomycin treatment and assessed the contribution of dysbiosis to SIV disease progression. Dysbiotic and control animals had similar disease progression, indicating that intestinal microbial dysbiosis similar to that observed in individuals with HIV is not sufficient to accelerate untreated lentiviral disease progression.

Access optionsAccess options

Rent or Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.

Additional information

Publisher’s note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.


  1. 1.

    Ortiz, A. M. & Brenchley, J. M. Curr. Opin. HIV AIDS 13, 15–21 (2018).

  2. 2.

    Brenchley, J. M., Silvestri, G. & Douek, D. C. Immunity 32, 737–742 (2010).

  3. 3.

    Noguera-Julian, M. et al. EBioMedicine 5, 135–146 (2016).

  4. 4.

    Policicchio, B. B., Pandrea, I. & Apetrei, C. Front. Immunol. 7, 12 (2016).

  5. 5.

    Mudd, J. C. & Brenchley, J. M. J. Infect. Dis. 214 Suppl 2, S58–S66 (2016).

  6. 6.

    Ivanov, I. I. et al. Cell 139, 485–498 (2009).

  7. 7.

    Kelly, C. J. et al. Cell Host Microbe 17, 662–671 (2015).

  8. 8.

    Day, C. L. et al. Nature 443, 350–354 (2006).

  9. 9.

    Betts, M. R. et al. Blood 107, 4781–4789 (2006).

  10. 10.

    McKenna, P. et al. PLoS Pathog. 4, e20 (2008).

  11. 11.

    Gosmann, C. et al. Immunity 46, 29–37 (2017).

  12. 12.

    d’Ettorre, G. et al. Immun. Inflamm. Dis. 5, 244–260 (2017).

  13. 13.

    Vujkovic-Cvijin, I. et al. Gut Microbes 8, 440–450 (2017).

  14. 14.

    Hager, C. L. & Ghannoum, M. A. Curr. Opin. HIV AIDS 13, 69–72 (2018).

  15. 15.

    Ortiz, A. M. et al. Mucosal Immunol. 9, 458–467 (2016).

  16. 16.

    Caporaso, J. G. et al. Nat. Methods 7, 335–336 (2010).

  17. 17.

    Langille, M. G. et al. Nat. Biotechnol. 31, 814–821 (2013).

  18. 18.

    Estes, J. D. et al. PLoS Pathog. 6, e1001052 (2010).

  19. 19.

    Hao, X. P. et al. Nat. Commun. 6, 8020 (2015).

  20. 20.

    Brenchley, J. M. et al. Blood 120, 4172–4181 (2012).

  21. 21.

    Segata, N. et al. Genome Biol. 12, R60 (2011).

  22. 22.

    Parks, D. H., Tyson, G. W., Hugenholtz, P. & Beiko, R. G. Bioinformatics 30, 3123–3124 (2014).

Download references


We would like to acknowledge H. Kendall, J. Swerczek, R. Herbert, and all the veterinary staff at the NIH animal center. We would like to thank M. Quiñones, J. Davis, S. Sen and G. Trinchieri, and the NIAID Microbiome Program for technical and analytical assistance. Funding for this study was provided in part by the Division of Intramural Research/NIAID/NIH, by the Oregon National Primate Research Center NIH grant award P51OD011092, and with federal funds from the National Cancer Institute, NIH, under Contract No. HHSN261200800001E. The content of this publication does not necessarily reflect the views or policies of the Department of Health and Human Services (DHHS), nor does the mention of trade names, commercial products, or organizations imply endorsement by the U.S. Government.

Author information


  1. Barrier Immunity Section, Laboratory of Viral Diseases, National Institutes of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA

    • Alexandra M. Ortiz
    • , Jacob K. Flynn
    • , Sarah R. DiNapoli
    • , Carly E. Starke
    • , Stephen H. Lai
    • , MacKenzie E. Long
    • , Ornella Sortino
    • , Carol L. Vinton
    • , Joseph C. Mudd
    •  & Jason M. Brenchley
  2. Mucosal Immunology Section, Laboratory of Parasitic Diseases, NIAID, NIH, Bethesda, MD, USA

    • Ivan Vujkovic-Cvijin
    •  & Yasmine Belkaid
  3. AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, USA

    • Leslie Johnston
    • , Kathleen Busman-Sahay
    •  & Jacob D. Estes
  4. Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, OR, USA

    • Kathleen Busman-Sahay
    •  & Jacob D. Estes
  5. NIAID Microbiome Program, NIH, Bethesda, MD, USA

    • Yasmine Belkaid
  6. Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, USA

    • Jacob D. Estes


  1. Search for Alexandra M. Ortiz in:

  2. Search for Jacob K. Flynn in:

  3. Search for Sarah R. DiNapoli in:

  4. Search for Ivan Vujkovic-Cvijin in:

  5. Search for Carly E. Starke in:

  6. Search for Stephen H. Lai in:

  7. Search for MacKenzie E. Long in:

  8. Search for Ornella Sortino in:

  9. Search for Carol L. Vinton in:

  10. Search for Joseph C. Mudd in:

  11. Search for Leslie Johnston in:

  12. Search for Kathleen Busman-Sahay in:

  13. Search for Yasmine Belkaid in:

  14. Search for Jacob D. Estes in:

  15. Search for Jason M. Brenchley in:


J.M.B. conceived the project. A.M.O. and J.M.B. designed the project and wrote the manuscript. A.M.O., J.K.F., S.R.D., C.E.C.S., S.H.L., M.E.L., O.S., C.L.V., J.C.M., L.J., K.B.-S., J.D.E. and J.M.B. performed experiments. A.M.O., J.K.F., S.R.D., I.V.-C., S.H.L., Y.B., J.D.E. and J.M.B. analyzed data.

Competing interests

The authors declare no competing interests.

Corresponding author

Correspondence to Jason M. Brenchley.

Supplementary information

  1. Supplementary Text and Figures

    Supplementary Figures 1–8 and Supplementary Table 1

  2. Reporting Summary

  3. Supplementary Dataset 1

    LEFSE returned results

About this article

Publication history