Ahluwalia B, Magnusson MK, Ohman L. Mucosal immune system of the gastrointestinal tract: maintaining balance between the good and the bad. Scand J Gastroenterol. 2017;52(11):1185–93.
CAS
PubMed
Google Scholar
Kurashima Y, Kiyono H. Mucosal ecological network of epithelium and immune cells for gut homeostasis and tissue healing. Annu Rev Immunol. 2017;35:119–47.
CAS
PubMed
Google Scholar
Sanz Y, De Palma G. Gut microbiota and probiotics in modulation of epithelium and gut-associated lymphoid tissue function. Int Rev Immunol. 2009;28(6):397–413.
CAS
PubMed
Google Scholar
Lujan JA, Rugeles MT, Taborda NA. Contribution of the microbiota to intestinal homeostasis and its role in the pathogenesis of HIV-1 infection. Curr HIV Res. 2019;17(1):13–25.
CAS
PubMed
Google Scholar
Dillon SM, Frank DN, Wilson CC. The gut microbiome and HIV-1 pathogenesis: a two-way street. AIDS. 2016;30(18):2737–51.
CAS
PubMed
Google Scholar
Bandera A, De Benedetto I, Bozzi G, Gori A. Altered gut microbiome composition in HIV infection: causes, effects and potential intervention. Curr Opin HIV AIDS. 2018;13(1):73–80.
CAS
PubMed
Google Scholar
Wang C, Li Q, Ren J. Microbiota-immune interaction in the pathogenesis of gut-derived infection. Front Immunol. 2019;10:1873.
CAS
PubMed
PubMed Central
Google Scholar
Liu J, Williams B, Frank D, Dillon SM, Wilson CC, Landay AL. Inside out: HIV, the gut microbiome, and the mucosal immune system. J Immunol. 2017;198(2):605–14.
CAS
PubMed
Google Scholar
McDermott AJ, Huffnagle GB. The microbiome and regulation of mucosal immunity. Immunology. 2014;142(1):24–31.
CAS
PubMed
PubMed Central
Google Scholar
Tincati C, Douek DC, Marchetti G. Gut barrier structure, mucosal immunity and intestinal microbiota in the pathogenesis and treatment of HIV infection. AIDS Res Ther. 2016;13:19.
PubMed
PubMed Central
Google Scholar
Zevin AS, McKinnon L, Burgener A, Klatt NR. Microbial translocation and microbiome dysbiosis in HIV-associated immune activation. Curr Opin HIV AIDS. 2016;11(2):182–90.
CAS
PubMed
PubMed Central
Google Scholar
Monaco CL, Gootenberg DB, Zhao G, Handley SA, Ghebremichael MS, Lim ES, et al. Altered virome and bacterial microbiome in human immunodeficiency virus-associated acquired immunodeficiency syndrome. Cell Host Microbe. 2016;19(3):311–22.
CAS
PubMed
PubMed Central
Google Scholar
Lozupone CA, Li M, Campbell TB, Flores SC, Linderman D, Gebert MJ, et al. Alterations in the gut microbiota associated with HIV-1 infection. Cell Host Microbe. 2013;14(3):329–39.
CAS
PubMed
Google Scholar
Shukla S, Kumari S, Bal SK, Monaco DC, Ribeiro SP, Sekaly RP, et al. "Go", "No Go," or "Where to Go"; does microbiota dictate T cell exhaustion, programming, and HIV persistence? Curr Opin HIV AIDS. 2021.
Gori A, Tincati C, Rizzardini G, Torti C, Quirino T, Haarman M, et al. Early impairment of gut function and gut flora supporting a role for alteration of gastrointestinal mucosa in human immunodeficiency virus pathogenesis. J Clin Microbiol. 2008;46(2):757–8.
PubMed
Google Scholar
Rocafort M, Noguera-Julian M, Rivera J, Pastor L, Guillen Y, Langhorst J, et al. Evolution of the gut microbiome following acute HIV-1 infection. Microbiome. 2019;7(1):73.
PubMed
PubMed Central
Google Scholar
Moore RD. Epidemiology of HIV infection in the United States: implications for linkage to care. Clin Infect Dis. 2011;52(Suppl 2):S208–13.
PubMed
PubMed Central
Google Scholar
Li SX, Sen S, Schneider JM, Xiong KN, Nusbacher NM, Moreno-Huizar N, et al. Gut microbiota from high-risk men who have sex with men drive immune activation in gnotobiotic mice and in vitro HIV infection. PLoS Pathog. 2019;15(4):e1007611.
CAS
PubMed
PubMed Central
Google Scholar
Noguera-Julian M, Rocafort M, Guillen Y, Rivera J, Casadella M, Nowak P, et al. Gut microbiota linked to sexual preference and hiv infection. EBioMedicine. 2016;5:135–46.
PubMed
PubMed Central
Google Scholar
Tuddenham S, Koay WL, Sears C. HIV, sexual orientation, and gut microbiome interactions. Dig Dis Sci. 2020;65(3):800–17.
CAS
PubMed
PubMed Central
Google Scholar
Kingsley LA, Detels R, Kaslow R, Polk BF, Rinaldo CR Jr, Chmiel J, et al. Risk factors for seroconversion to human immunodeficiency virus among male homosexuals. Results from the Multicenter AIDS Cohort Study. Lancet. 1987;1(8529):345–9.
CAS
PubMed
Google Scholar
Baggaley RF, White RG, Boily MC. HIV transmission risk through anal intercourse: systematic review, meta-analysis and implications for HIV prevention. Int J Epidemiol. 2010;39(4):1048–63.
PubMed
PubMed Central
Google Scholar
Kaslow RA, Ostrow DG, Detels R, Phair JP, Polk BF, Rinaldo CR Jr. The Multicenter AIDS Cohort Study: rationale, organization, and selected characteristics of the participants. Am J Epidemiol. 1987;126(2):310–8.
CAS
PubMed
Google Scholar
Lyles RH, Munoz A, Yamashita TE, Bazmi H, Detels R, Rinaldo CR, et al. Natural history of human immunodeficiency virus type 1 viremia after seroconversion and proximal to AIDS in a large cohort of homosexual men. Multicenter AIDS Cohort Study. J Infect Dis. 2000;181(3):872–80.
CAS
PubMed
Google Scholar
Jacobson LP, Kirby AJ, Polk S, Phair JP, Besley DR, Saah AJ, et al. Changes in survival after acquired immunodeficiency syndrome (AIDS): 1984-1991. Am J Epidemiol. 1993;138(11):952–64.
CAS
PubMed
Google Scholar
1993 revised classification system for HIV infection and expanded surveillance case definition for AIDS among adolescents and adults. MMWR Recomm Rep. 1992;41(RR-17):1–19.
Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Lozupone CA, Turnbaugh PJ, et al. Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. Proc Natl Acad Sci U S A. 2011;108(Suppl 1):4516–22.
CAS
PubMed
Google Scholar
Han J, Lin K, Sequeira C, Borchers CH. An isotope-labeled chemical derivatization method for the quantitation of short-chain fatty acids in human feces by liquid chromatography-tandem mass spectrometry. Anal Chim Acta. 2015;854:86–94.
CAS
Google Scholar
Lin H, Peddada SD. Analysis of compositions of microbiomes with bias correction. Nat Commun. 2020;11(1):3514.
CAS
PubMed
PubMed Central
Google Scholar
Kaul A, Mandal S, Davidov O, Peddada SD. Analysis of microbiome data in the presence of excess zeros. Front Microbiol. 2017;8:2114.
PubMed
PubMed Central
Google Scholar
Benjamini Y, Hochberg Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc Ser B Methodol. 57:289–300.
Shetty SA, Hugenholtz F, Lahti L, Smidt H, de Vos WM. Intestinal microbiome landscaping: insight in community assemblage and implications for microbial modulation strategies. FEMS Microbiol Rev. 2017;41(2):182–99.
CAS
PubMed
PubMed Central
Google Scholar
Weiss S, Xu ZZ, Peddada S, Amir A, Bittinger K, Gonzalez A, et al. Normalization and microbial differential abundance strategies depend upon data characteristics. Microbiome. 2017;5(1):27.
PubMed
PubMed Central
Google Scholar
Mandal S, Van Treuren W, White RA, Eggesbo M, Knight R, Peddada SD. Analysis of composition of microbiomes: a novel method for studying microbial composition. Microb Ecol Health Dis. 2015;26:27663.
PubMed
Google Scholar
McBride JA, Striker R. Imbalance in the game of T cells: what can the CD4/CD8 T-cell ratio tell us about HIV and health? PLoS Pathog. 2017;13(11):e1006624.
PubMed
PubMed Central
Google Scholar
Brenchley JM, Douek DC. HIV infection and the gastrointestinal immune system. Mucosal Immunol. 2008;1(1):23–30.
CAS
PubMed
PubMed Central
Google Scholar
Dillon SM, Kibbie J, Lee EJ, Guo K, Santiago ML, Austin GL, et al. Low abundance of colonic butyrate-producing bacteria in HIV infection is associated with microbial translocation and immune activation. AIDS. 2017;31(4):511–21.
CAS
PubMed
Google Scholar
Serrano-Villar S, Vazquez-Castellanos JF, Vallejo A, Latorre A, Sainz T, Ferrando-Martinez S, et al. The effects of prebiotics on microbial dysbiosis, butyrate production and immunity in HIV-infected subjects. Mucosal Immunol. 2017;10(5):1279–93.
CAS
PubMed
Google Scholar
Gonzalez-Hernandez LA, Del Rocio Ruiz-Briseno M, Sanchez-Reyes K, Alvarez-Zavala M, Vega-Magana N, Lopez-Iniguez A, et al. Correction to: Alterations in bacterial communities, SCFA and biomarkers in an elderly HIV-positive and HIV-negative population in western Mexico. BMC Infect Dis. 2020;20(1):764.
PubMed
PubMed Central
Google Scholar
Breen EC. Pro- and anti-inflammatory cytokines in human immunodeficiency virus infection and acquired immunodeficiency syndrome. Pharmacol Ther. 2002;95(3):295–304.
CAS
PubMed
Google Scholar
Kelley CF, Kraft CS, de Man TJ, Duphare C, Lee HW, Yang J, et al. The rectal mucosa and condomless receptive anal intercourse in HIV-negative MSM: implications for HIV transmission and prevention. Mucosal Immunol. 2017;10(4):996–1007.
CAS
PubMed
Google Scholar
Dillon SM, Lee EJ, Kotter CV, Austin GL, Dong Z, Hecht DK, 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):983–94.
CAS
PubMed
PubMed Central
Google Scholar
Mutlu EA, Keshavarzian A, Losurdo J, Swanson G, Siewe B, Forsyth C, et al. A compositional look at the human gastrointestinal microbiome and immune activation parameters in HIV infected subjects. PLoS Pathog. 2014;10(2):e1003829.
PubMed
PubMed Central
Google Scholar
Vazquez-Castellanos JF, Serrano-Villar S, Latorre A, Artacho A, Ferrus ML, Madrid N, et al. Altered metabolism of gut microbiota contributes to chronic immune activation in HIV-infected individuals. Mucosal Immunol. 2015;8(4):760–72.
CAS
PubMed
Google Scholar
Lu W, Feng Y, Jing F, Han Y, Lyu N, Liu F, et al. Association between gut microbiota and CD4 recovery in HIV-1 infected patients. Front Microbiol. 2018;9:1451.
PubMed
PubMed Central
Google Scholar
Armstrong AJS, Shaffer M, Nusbacher NM, Griesmer C, Fiorillo S, Schneider JM, et al. An exploration of Prevotella-rich microbiomes in HIV and men who have sex with men. Microbiome. 2018;6(1):198.
PubMed
PubMed Central
Google Scholar
Vujkovic-Cvijin I, Sortino O, Verheij E, Sklar J, Wit FW, Kootstra NA, et al. HIV-associated gut dysbiosis is independent of sexual practice and correlates with noncommunicable diseases. Nat Commun. 2020;11(1):2448.
CAS
PubMed
PubMed Central
Google Scholar
Coleman SL, Neff CP, Li SX, Armstrong AJS, Schneider JM, Sen S, et al. Can gut microbiota of men who have sex with men influence HIV transmission? Gut Microbes. 2020;11(3):610–9.
PubMed
PubMed Central
Google Scholar
Perler BK, Reinhart EM, Montgomery M, Maynard M, Shapiro JM, Belenky P, et al. Evaluation of the microbiome in men taking pre-exposure prophylaxis for HIV prevention. AIDS Behav. 2021;25(7):2005–13.
PubMed
Google Scholar
Nganou-Makamdop K, Talla A, Sharma AA, Darko S, Ransier A, Laboune F, et al. Translocated microbiome composition determines immunological outcome in treated HIV infection. Cell. 2021;184(15):3899–3914 e3816.
CAS
PubMed
Google Scholar
Bai X, Narayanan A, Nowak P, Ray S, Neogi U, Sonnerborg A. Whole-genome metagenomic analysis of the gut microbiome in hiv-1-infected individuals on antiretroviral therapy. Front Microbiol. 2021;12:667718.
PubMed
PubMed Central
Google Scholar
Ancona G, Merlini E, Tincati C, Barassi A, Calcagno A, Augello M, et al. Long-term suppressive cART is not sufficient to restore intestinal permeability and gut microbiota compositional changes. Front Immunol. 2021;12:639291.
CAS
PubMed
PubMed Central
Google Scholar
Dillon SM, Abdo MH, Wilson MP, Liu J, Jankowski CM, Robertson CE, et al. A unique gut microbiome-physical function axis exists in older people with HIV: an exploratory study. AIDS Res Hum Retrovir. 2021;37(7):542–50.
CAS
PubMed
Google Scholar
Armstrong AJS, Quinn K, Fouquier J, Li SX, Schneider JM, Nusbacher NM, et al. Systems analysis of gut microbiome influence on metabolic disease in HIV-positive and high-risk populations. mSystems. 2021;6(3).
do Nascimento WM, Machiavelli A, Ferreira LGE, Cruz Silveira L, de Azevedo SSD, Bello G, et al. Gut microbiome profiles and associated metabolic pathways in HIV-infected treatment-naive patients. Cells. 2021;10(2).
Sui Y, Dzutsev A, Venzon D, Frey B, Thovarai V, Trinchieri G, et al. Influence of gut microbiome on mucosal immune activation and SHIV viral transmission in naive macaques. Mucosal Immunol. 2018;11(4):1219–29.
CAS
PubMed
PubMed Central
Google Scholar
Cook RR, Fulcher JA, Tobin NH, Li F, Lee D, Javanbakht M, et al. Effects of HIV viremia on the gastrointestinal microbiome of young MSM. AIDS. 2019;33(5):793–804.
CAS
PubMed
Google Scholar
Neff CP, Krueger O, Xiong K, Arif S, Nusbacher N, Schneider JM, et al. Fecal microbiota composition drives immune activation in hiv-infected individuals. EBioMedicine. 2018;30:192–202.
PubMed
PubMed Central
Google Scholar
Dubourg G, Lagier JC, Hue S, Surenaud M, Bachar D, Robert C, et al. Gut microbiota associated with HIV infection is significantly enriched in bacteria tolerant to oxygen. BMJ Open Gastroenterol. 2016;3(1):e000080.
PubMed
PubMed Central
Google Scholar
Schnorr SL, Candela M, Rampelli S, Centanni M, Consolandi C, Basaglia G, et al. Gut microbiome of the Hadza hunter-gatherers. Nat Commun. 2014;5:3654.
CAS
PubMed
Google Scholar
Mohr AE, Jager R, Carpenter KC, Kerksick CM, Purpura M, Townsend JR, et al. The athletic gut microbiota. J Int Soc Sports Nutr. 2020;17(1):24.
PubMed
PubMed Central
Google Scholar
Larsen JM. The immune response to Prevotella bacteria in chronic inflammatory disease. Immunology. 2017;151(4):363–74.
CAS
PubMed
PubMed Central
Google Scholar
Pascal V, Pozuelo M, Borruel N, Casellas F, Campos D, Santiago A, et al. A microbial signature for Crohn's disease. Gut. 2017;66(5):813–22.
CAS
PubMed
Google Scholar
Dinh DM, Volpe GE, Duffalo C, Bhalchandra S, Tai AK, Kane AV, et al. Intestinal microbiota, microbial translocation, and systemic inflammation in chronic HIV infection. J Infect Dis. 2015;211(1):19–27.
CAS
PubMed
Google Scholar
Jiang F, Meng D, Weng M, Zhu W, Wu W, Kasper D, et al. The symbiotic bacterial surface factor polysaccharide A on Bacteroides fragilis inhibits IL-1beta-induced inflammation in human fetal enterocytes via toll receptors 2 and 4. PLoS One. 2017;12(3):e0172738.
PubMed
PubMed Central
Google Scholar
Lozupone CA, Rhodes ME, Neff CP, Fontenot AP, Campbell TB, Palmer BE. HIV-induced alteration in gut microbiota: driving factors, consequences, and effects of antiretroviral therapy. Gut Microbes. 2014;5(4):562–70.
PubMed
Google Scholar
Chen W, Liu F, Ling Z, Tong X, Xiang C. Human intestinal lumen and mucosa-associated microbiota in patients with colorectal cancer. PLoS One. 2012;7(6):e39743.
CAS
PubMed
PubMed Central
Google Scholar
Kaakoush NO. Insights into the role of Erysipelotrichaceae in the human host. Front Cell Infect Microbiol. 2015;5:84.
PubMed
PubMed Central
Google Scholar
Mazmanian SK, Round JL, Kasper DL. A microbial symbiosis factor prevents intestinal inflammatory disease. Nature. 2008;453(7195):620–5.
CAS
PubMed
Google Scholar
Round JL, Mazmanian SK. Inducible Foxp3+ regulatory T-cell development by a commensal bacterium of the intestinal microbiota. Proc Natl Acad Sci U S A. 2010;107(27):12204–9.
CAS
PubMed
PubMed Central
Google Scholar
Vatanen T, Kostic AD, d'Hennezel E, Siljander H, Franzosa EA, Yassour M, et al. Variation in microbiome LPS immunogenicity contributes to autoimmunity in humans. Cell. 2016;165(4):842–53.
CAS
PubMed
PubMed Central
Google Scholar
Tan J, McKenzie C, Potamitis M, Thorburn AN, Mackay CR, Macia L. The role of short-chain fatty acids in health and disease. Adv Immunol. 2014;121:91–119.
CAS
PubMed
Google Scholar
Li M, van Esch B, Wagenaar GTM, Garssen J, Folkerts G, Henricks PAJ. Pro- and anti-inflammatory effects of short chain fatty acids on immune and endothelial cells. Eur J Pharmacol. 2018;831:52–9.
CAS
PubMed
Google Scholar
Rau M, Rehman A, Dittrich M, Groen AK, Hermanns HM, Seyfried F, et al. Fecal SCFAs and SCFA-producing bacteria in gut microbiome of human NAFLD as a putative link to systemic T-cell activation and advanced disease. United European Gastroenterol J. 2018;6(10):1496–507.
CAS
PubMed
PubMed Central
Google Scholar
Gonzalez-Hernandez LA, Ruiz-Briseno MDR, Sanchez-Reyes K, Alvarez-Zavala M, Vega-Magana N, Lopez-Iniguez A, et al. Alterations in bacterial communities, SCFA and biomarkers in an elderly HIV-positive and HIV-negative population in western Mexico. BMC Infect Dis. 2019;19(1):234.
PubMed
PubMed Central
Google Scholar
Bindels LB, Porporato P, Dewulf EM, Verrax J, Neyrinck AM, Martin JC, et al. Gut microbiota-derived propionate reduces cancer cell proliferation in the liver. Br J Cancer. 2012;107(8):1337–44.
CAS
PubMed
PubMed Central
Google Scholar
Wada NI, Bream JH, Martinez-Maza O, Macatangay B, Galvin SR, Margolick JB, et al. Inflammatory biomarkers and mortality risk among hiv-suppressed men: a multisite prospective cohort study. Clin Infect Dis. 2016;63(7):984–90.
CAS
PubMed
PubMed Central
Google Scholar
Connolly NC, Riddler SA, Rinaldo CR. Proinflammatory cytokines in HIV disease-a review and rationale for new therapeutic approaches. AIDS Rev. 2005;7(3):168–80.
PubMed
Google Scholar
Brenchley JM, Price DA, Schacker TW, Asher TE, Silvestri G, Rao S, et al. Microbial translocation is a cause of systemic immune activation in chronic HIV infection. Nat Med. 2006;12(12):1365–71.
CAS
PubMed
Google Scholar
Breen EC, Reynolds SM, Cox C, Jacobson LP, Magpantay L, Mulder CB, et al. Multisite comparison of high-sensitivity multiplex cytokine assays. Clin Vaccine Immunol. 2011;18(8):1229–42.
CAS
PubMed
PubMed Central
Google Scholar
Serrano-Villar S, de Lagarde M, Vazquez-Castellanos J, Vallejo A, Bernadino JI, Madrid N, et al. Effects of immunonutrition in advanced human immunodeficiency virus disease: a randomized placebo-controlled clinical trial (promaltia study). Clin Infect Dis. 2019;68(1):120–30.
CAS
PubMed
Google Scholar
Patel P, Borkowf CB, Brooks JT, Lasry A, Lansky A, Mermin J. Estimating per-act HIV transmission risk: a systematic review. AIDS. 2014;28(10):1509–19.
PubMed
Google Scholar