Acharya A et al (2020) Chronic morphine administration differentially modulates viral reservoirs in SIVmac251 infected rhesus macaque model. J Virol. 01657–01620. https://doi.org/10.1128/JVI.01657-20

Allers K et al (2020) The colonic mucosa-associated microbiome in SIV infection: shift towards Bacteroidetes coincides with mucosal CD4+ T cell depletion and enterocyte damage. Sci Rep 10:10887. https://doi.org/10.1038/s41598-020-67843-4

Armstrong AJS et al (2018) An exploration of Prevotella-rich microbiomes in HIV and men who have sex with men Microbiome 6:198. https://doi.org/10.1186/s40168-018-0580-7

Article  Google Scholar 

Arumugam M et al (2011) Enterotypes of the human gut microbiome Nature 473:174–180. https://doi.org/10.1038/nature09944

Article  CAS  Google Scholar 

Blum FC et al (2020) Microbial Dysbiosis During Simian Immunodeficiency Virus Infection is Partially Reverted with Combination Anti-retroviral Therapy Scientific Reports 10:6387. https://doi.org/10.1038/s41598-020-63196-0

Article  CAS  Google Scholar 

Brault MA, Spiegelman D, Hargreaves J, Nash D, Vermund SH (2019) Treatment as Prevention: Concepts and Challenges for Reducing HIV Incidence. J Acquir Immune Defic Syndr (1999) 82(2):S104–s112. https://doi.org/10.1097/qai.0000000000002168

CDC Diagnoses of HIV infection in the United States and dependent areas. 2020

Chou R et al (2019) Preexposure Prophylaxis for the Prevention of HIV Infection: Evidence Report and Systematic Review for the US Preventive Services Task Force Jama 321:2214–2230. https://doi.org/10.1001/jama.2019.2591

Article  Google Scholar 

Clifford DB, Ances BM (2013) HIV-associated neurocognitive disorder. Lancet Infect Dis 13:976–986. https://doi.org/10.1016/S1473-3099(13)70269-X

Article  Google Scholar 

Cohen MS et al (2011) Prevention of HIV-1 Infection with early antiretroviral therapy. N Engl J Med 365:493–505. https://doi.org/10.1056/NEJMoa1105243

Costea PI et al (2018) Enterotypes in the landscape of gut microbial community composition. Nat Microbiol 3:8–16. https://doi.org/10.1038/s41564-017-0072-8

Article  CAS  Google Scholar 

Crakes KR, Jiang G (2019) Gut microbiome alterations during HIV/SIV infection: implications for HIV Cure. Front Microbiol 10. https://doi.org/10.3389/fmicb.2019.01104

Del Borgo C, Izzi I, Chiarotti F, Del Forno A, Moscati AM, Cornacchione E, Fantoni M (2001) Multidimensional aspects of pain in HIV-infected individuals. AIDS Patient Care STDS 15:95–102. https://doi.org/10.1089/108729101300003690

Article  Google Scholar 

Dillon SM et al (2017) Low abundance of colonic butyrate-producing bacteria in HIV infection is associated with microbial translocation and immune activation. AIDS (London, England) 31:511–521. https://doi.org/10.1097/qad.0000000000001366

Dillon SM et al (2014) An altered intestinal mucosal microbiome in HIV-1 infection is associated with mucosal and systemic immune activation and endotoxemia. Mucosal Immunol 7:983–994. https://doi.org/10.1038/mi.2013.116

Donohoe DR, Garge N, Zhang X, Sun W, O’Connell TM, Bunger MK, Bultman SJ (2011) The microbiome and butyrate regulate energy metabolism and autophagy in the mammalian colon. Cell Metab 13:517–526. https://doi.org/10.1016/j.cmet.2011.02.018

Article  CAS  Google Scholar 

Dubourg G et al (2016) Gut microbiota associated with HIV infection is significantly enriched in bacteria tolerant to oxygen BMJ Open Gastroenterol 3:e000080–e000080. https://doi.org/10.1136/bmjgast-2016-000080

Article  Google Scholar 

Iljazovic A et al (2020) Perturbation of the gut microbiome by Prevotella spp. enhances host susceptibility to mucosal inflammation Mucosal. Immunol. https://doi.org/10.1038/s41385-020-0296-4

Imamichi H et al (2020) Defective HIV-1 proviruses produce viral proteins. Proc Natl Acad Sci 117:3704. https://doi.org/10.1073/pnas.1917876117

Kang M et al (2017) The effect of gut microbiome on tolerance to morphine mediated antinociception in mice Scientific reports 7:42658. https://doi.org/10.1038/srep42658

Article  CAS  Google Scholar 

Kaur US et al (2018) High Abundance of genus Prevotella in the gut of perinatally HIV-infected children is associated with IP-10 levels despite therapy. Sci Rep 8:17679. https://doi.org/10.1038/s41598-018-35877-4

Kelley CF et al (2017) The rectal mucosa and condomless receptive anal intercourse in HIV-negative MSM: implications for HIV transmission and prevention Mucosal immunology 10:996–1007. https://doi.org/10.1038/mi.2016.97

Article  CAS  Google Scholar 

Kovatcheva-Datchary P et al (2015) Dietary Fiber-Induced Improvement in Glucose Metabolism Is Associated with Increased Abundance of Prevotella. Cell Metab 22:971–982. https://doi.org/10.1016/j.cmet.2015.10.001

Article  CAS  Google Scholar 

Larue F, Fontaine A, Colleau SM (1997) Underestimation and undertreatment of pain in HIV disease: multicentre study BMJ (Clinical research ed) 314:23–28. https://doi.org/10.1136/bmj.314.7073.23

Article  CAS  Google Scholar 

Li SX, Armstrong A, Neff CP, Shaffer M, Lozupone CA, Palmer BE (2016) Complexities of Gut Microbiome Dysbiosis in the Context of HIV Infection and Antiretroviral Therapy. Clin Pharmacol Ther 99:600–611. https://doi.org/10.1002/cpt.363

Article  CAS  Google Scholar 

Li SX et al (2019) Gut microbiota from high-risk men who have sex with men drive immune activation in gnotobiotic mice and in vitro HIV infection. PLoS Pathog 15:e1007611. https://doi.org/10.1371/journal.ppat.1007611

Article  CAS  Google Scholar 

Louis P, Flint HJ (2007) Development of a semiquantitative degenerate real-time PCR-based assay for estimation of numbers of butyryl-coenzyme a (CoA) CoA transferase genes in complex bacterial samples. Appl Environ Microbiol 73:2009. https://doi.org/10.1128/AEM.02561-06

Maeda Y, Takeda K (2019) Host–microbiota interactions in rheumatoid arthritis. Exp Mol Med 51:1–6. https://doi.org/10.1038/s12276-019-0283-6

Makki K, Deehan EC, Walter J, Bäckhed F (2018) The Impact of Dietary Fiber on Gut Microbiota in Host Health and Disease. Cell Host Microbe 23:705–715. https://doi.org/10.1016/j.chom.2018.05.012

Article  CAS  Google Scholar 

Meng J et al (2020) Opioids impair intestinal epithelial repair in HIV-infected humanized mice. Front Immunol 10. https://doi.org/10.3389/fimmu.2019.02999

Miaskowski C, Penko JM, Guzman D, Mattson JE, Bangsberg DR, Kushel MB (2011) Occurrence and characteristics of chronic pain in a community-based cohort of indigent adults living with HIV infection. The Journal of Pain : Official Journal of the American Pain Society 12:1004–1016. https://doi.org/10.1016/j.jpain.2011.04.002

Article  Google Scholar 

Rodger AJ et al (2019) Risk of HIV transmission through condomless sex in serodifferent gay couples with the HIV-positive partner taking suppressive antiretroviral therapy (PARTNER): final results of a multicentre, prospective, observational study. Lancet (London, England) 393:2428–2438. https://doi.org/10.1016/s0140-6736(19)30418-0

Salem M, Ronit A, Gaardbo JC, Lund TT, Ullum H, Gerstoft J, Nielsen SD (2013) Altered balance between IL-17A– and IL-17F–producing Th17 cells in HIV-infected patients. JAIDS J Acquir Immune Defic Syndr 63

Salonen A et al (2010) Comparative analysis of fecal DNA extraction methods with phylogenetic microarray: Effective recovery of bacterial and archaeal DNA using mechanical cell lysis. J Microbiol Methods 81:127–134. https://doi.org/10.1016/j.mimet.2010.02.007

Article  CAS  Google Scholar 

Siddiqui S, Bao D, Doyle-Meyers L, Dufour J, Wu Y, Liu YZ, Ling B (2020) Alterations of the gut bacterial microbiota in rhesus macaques with SIV infection and on short- or long-term antiretroviral therapy Sci Rep 10:19056. https://doi.org/10.1038/s41598-020-76145-8

Article  CAS  Google Scholar 

Sindberg GM et al (2019) Morphine Potentiates Dysbiotic Microbial and Metabolic Shifts in Acute SIV Infection. J Neuroimmune Pharmacol 14:200–214. https://doi.org/10.1007/s11481-018-9805-6

Article  Google Scholar 

Tang C et al (2018) Suppression of IL-17F, but not of IL-17A, provides protection against colitis by inducing Treg cells through modification of the intestinal microbiota. Nat Immunol 19:755–765. https://doi.org/10.1038/s41590-018-0134-y

Thurman M, Johnson S, Acharya A, Pallikkuth S, Mahesh M, Byrareddy SN (2020) Biomarkers of Activation and Inflammation to Track Disparity in Chronological and Physiological Age of People Living With HIV on Combination Antiretroviral Therapy Front Immunol 11:583934. https://doi.org/10.3389/fimmu.2020.583934

Article  CAS  Google Scholar 

UNAIDS (2019) Global HIV & AIDS statistics — 2019 fact sheet. Accessed February 29, 2020 2020

Vanhamel J, Bruggemans A, Debyser Z (2019) Establishment of latent HIV-1 reservoirs: what do we really know? J Virus Erad 5:3–9

Article  Google Scholar 

Wang F, Meng J, Zhang L, Johnson T, Chen C, Roy S (2018) Morphine induces changes in the gut microbiome and metabolome in a morphine dependence model Scientific reports 8:3596. https://doi.org/10.1038/s41598-018-21915-8

Article  CAS  Google Scholar 

Williams AR, Bisaga A (2016) From AIDS to Opioids - How to Combat an Epidemic. N Engl J Med 375:813–815. https://doi.org/10.1056/NEJMp1604223

Article  Google Scholar 

Xu Y et al (2017) Bacterial diversity of intestinal microbiota in patients with substance use disorders revealed by 16S rRNA gene deep sequencing. Sci Rep 7:3628 https://doi.org/10.1038/s41598-017-03706-9

Zhang L et al (2019) Morphine tolerance is attenuated in germfree mice and reversed by probiotics, implicating the role of gut microbiome. Proc Natl Acad Sci 116:13523 https://doi.org/10.1073/pnas.1901182116

Zhou L et al (2018) Faecalibacterium prausnitzii Produces Butyrate to Maintain Th17/Treg Balance and to Ameliorate Colorectal Colitis by Inhibiting Histone Deacetylase 1 Inflammatory bowel diseases 24:1926–1940 https://doi.org/10.1093/ibd/izy182