1 Goulder, P. J. & Walker, B. D. HIV and HLA class I: an evolving relationship. Immunity 37, 426-440, doi:10.1016/j.immuni.2012.09.005 (2012).
2 O'Brien, S. J. & Nelson, G. W. Human genes that limit AIDS. Nature genetics 36, 565-574, doi:10.1038/ng1369 (2004).
3 Paolucci, S., Gulminetti, R., Maserati, R., Dossena, L. & Baldanti, F. Accumulation of defective HIV-1 variants in a patient with slow disease progression. Current HIV research 9, 17-22, doi:10.2174/157016211794582641 (2011).
4 Pancino, G., Saez-Cirion, A., Scott-Algara, D. & Paul, P. Natural Resistance to HIV Infection: Lessons Learned from HIV-Exposed Uninfected Individuals. The Journal of Infectious Diseases 202, S345-S350, doi:10.1086/655973 (2010).
5 Zhang, W. et al. Transcriptomics and Targeted Proteomics Analysis to Gain Insights Into the Immune-control Mechanisms of HIV-1 Infected Elite Controllers. EBioMedicine 27, 40-50, doi:10.1016/j.ebiom.2017.11.031 (2018).
6 Koay, W. L. A., Siems, L. V. & Persaud, D. The microbiome and HIV persistence: implications for viral remission and cure. Curr Opin HIV AIDS 13, 61-68, doi:10.1097/coh.0000000000000434 (2018).
7 Lozupone, C. A. et al. Alterations in the gut microbiota associated with HIV-1 infection. Cell Host Microbe 14, 329-339, doi:10.1016/j.chom.2013.08.006 (2013).
8 Gootenberg, D. B., Paer, J. M., Luevano, J. M. & Kwon, D. S. HIV-associated changes in the enteric microbial community: potential role in loss of homeostasis and development of systemic inflammation. Current opinion in infectious diseases 30, 31-43, doi:10.1097/qco.0000000000000341 (2017).
9 Noguera-Julian, M. et al. Gut Microbiota Linked to Sexual Preference and HIV Infection. EBioMedicine 5, 135-146, doi:10.1016/j.ebiom.2016.01.032 (2016).
10 Villanueva-Millán, M. J., Pérez-Matute, P., Recio-Fernández, E., Lezana Rosales, J. M. & Oteo, J. A. Differential effects of antiretrovirals on microbial translocation and gut microbiota composition of HIV-infected patients. Journal of the International AIDS Society 20, 21526, doi:10.7448/ias.20.1.21526 (2017).
11 Pinto-Cardoso, S. et al. Fecal Bacterial Communities in treated HIV infected individuals on two antiretroviral regimens. Sci Rep 7, 43741, doi:10.1038/srep43741 (2017).
12 Vesterbacka, J. et al. Richer gut microbiota with distinct metabolic profile in HIV infected Elite Controllers. Sci Rep 7, 6269, doi:10.1038/s41598-017-06675-1 (2017).
13 Vernocchi, P., Del Chierico, F. & Putignani, L. Gut Microbiota Profiling: Metabolomics Based Approach to Unravel Compounds Affecting Human Health. Frontiers in microbiology 7, 1144, doi:10.3389/fmicb.2016.01144 (2016).
14 Tarancon-Diez, L. et al. Immunometabolism is a key factor for the persistent spontaneous elite control of HIV-1 infection. EBioMedicine 42, 86-96, doi:10.1016/j.ebiom.2019.03.004 (2019).
15 Sperk, M. et al. Distinct lipid profile, low-level inflammation and increased antioxidant defense as a signature in HIV-1 elite control status. bioRxiv, 2020.2007.2002.183756, doi:10.1101/2020.07.02.183756 (2020).
16 Yoshimura, K. et al. JE-2147: a dipeptide protease inhibitor (PI) that potently inhibits multi-PI-resistant HIV-1. Proc Natl Acad Sci U S A 96, 8675-8680, doi:10.1073/pnas.96.15.8675 (1999).
17 Wang, H. & Kotler, D. P. HIV enteropathy and aging: gastrointestinal immunity, mucosal epithelial barrier, and microbial translocation. Curr Opin HIV AIDS 9, 309-316, doi:10.1097/coh.0000000000000066 (2014).
18 Ehrenpreis, E. D., Carlson, S. J., Boorstein, H. L. & Craig, R. M. Malabsorption and deficiency of vitamin B12 in HIV-infected patients with chronic diarrhea. Digestive diseases and sciences 39, 2159-2162, doi:10.1007/bf02090365 (1994).
19 Castaldo, A. et al. Iron deficiency and intestinal malabsorption in HIV disease. Journal of pediatric gastroenterology and nutrition 22, 359-363, doi:10.1097/00005176-199605000-00004 (1996).
20 Jiménez-Expósito, M. J. et al. Effect of malabsorption on nutritional status and resting energy expenditure in HIV-infected patients. Aids 12, 1965-1972, doi:10.1097/00002030-199815000-00007 (1998).
21 Williams, B., Landay, A. & Presti, R. M. Microbiome alterations in HIV infection a review. Cellular microbiology 18, 645-651, doi:10.1111/cmi.12588 (2016).
22 Nowak, P. et al. Gut microbiota diversity predicts immune status in HIV-1 infection. AIDS 29, 2409-2418, doi:10.1097/QAD.0000000000000869 (2015).
23 Tuddenham, S. A. et al. The Impact of Human Immunodeficiency Virus Infection on Gut Microbiota α-Diversity: An Individual-level Meta-analysis. Clin Infect Dis 70, 615-627, doi:10.1093/cid/ciz258 (2020).
24 Ley, R. E. J. N. r. G. & hepatology. Prevotella in the gut: choose carefully. 13, 69-70 (2016).
25 Costello, E. K. et al. Bacterial community variation in human body habitats across space and time. 326, 1694-1697 (2009).
26 Huttenhower, C. et al. Structure, function and diversity of the healthy human microbiome. Nature 486, 207-214, doi:10.1038/nature11234 (2012).
27 Ley, R. E. Prevotella in the gut: choose carefully. Nature Reviews Gastroenterology & Hepatology 13, 69-70, doi:10.1038/nrgastro.2016.4 (2016).
28 La Reau, A. J. & Suen, G. The Ruminococci: key symbionts of the gut ecosystem. Journal of microbiology (Seoul, Korea) 56, 199-208, doi:10.1007/s12275-018-8024-4 (2018).
29 Daniel, H. & Zietek, T. Taste and move: glucose and peptide transporters in the gastrointestinal tract. Experimental Physiology 100, 1441-1450, doi:10.1113/ep085029 (2015).
30 Inui, K.-i. & Terada, T. in Membrane transporters as drug targets 269-288 (Springer, 2002).
31 Kovatcheva-Datchary, P. et al. Dietary fiber-induced improvement in glucose metabolism is associated with increased abundance of Prevotella. 22, 971-982 (2015).
32 Hendrikx, T. & Schnabl, B. Indoles: metabolites produced by intestinal bacteria capable of controlling liver disease manifestation. Journal of Internal Medicine 286, 32-40, doi:10.1111/joim.12892 (2019).
33 Roager, H. M. & Licht, T. R. Microbial tryptophan catabolites in health and disease. Nature Communications 9, 3294, doi:10.1038/s41467-018-05470-4 (2018).
34 Kaur, H., Bose, C. & Mande, S. S. Tryptophan Metabolism by Gut Microbiome and Gut-Brain-Axis: An in silico Analysis. 13, doi:10.3389/fnins.2019.01365 (2019).
35 Sasaki-Imamura, T., Yoshida, Y., Suwabe, K., Yoshimura, F. & Kato, H. Molecular basis of indole production catalyzed by tryptophanase in the genus Prevotella. FEMS Microbiology Letters 322, 51-59, doi:10.1111/j.1574-6968.2011.02329.x %J FEMS Microbiology Letters (2011).
36 Duerden, B., Collee, J., Brown, R., Deacon, A. & Holbrook, W. J. J. o. M. M. A scheme for the identification of clinical isolates of Gram-negative anaerobic bacilli by conventional bacteriological tests. 13, 231-246 (1980).
37 Lee, J.-H. & Lee, J. Indole as an intercellular signal in microbial communities. FEMS Microbiology Reviews 34, 426-444, doi:10.1111/j.1574-6976.2009.00204.x (2010).
38 Patel, P. A. et al. Indole-based allosteric inhibitors of HIV-1 integrase. Bioorg Med Chem Lett 26, 4748-4752, doi:10.1016/j.bmcl.2016.08.037 (2016).
39 Sahin, K. Investigation of novel indole-based HIV-1 protease inhibitors using virtual screening and text mining. Journal of Biomolecular Structure and Dynamics, 1-11, doi:10.1080/07391102.2020.1775121 (2020).
40 Brigg, S. et al. Novel indole sulfides as potent HIV-1 NNRTIs. Bioorg Med Chem Lett 26, 1580-1584, doi:https://doi.org/10.1016/j.bmcl.2016.02.006 (2016).
41 Zhang, M.-Z., Chen, Q. & Yang, G.-F. A review on recent developments of indole-containing antiviral agents. Eur J Med Chem 89, 421-441, doi:10.1016/j.ejmech.2014.10.065 (2015).
42 WHO. Guideline on when to start antiretroviral therapy and on pre-exposure prophylaxis for HIV. 78 (2015). <https://apps.who.int/iris/bitstream/handle/10665/186275/9789241509565_eng.pdf;jsessionid=B943214C9D13EC015D1948982E062FEC?sequence=1>.
43 Babu, H. et al. Plasma Metabolic Signature and Abnormalities in HIV-Infected Individuals on Long-Term Successful Antiretroviral Therapy. Metabolites 9, doi:10.3390/metabo9100210 (2019).
44 Thévenot, E. A., Roux, A., Xu, Y., Ezan, E. & Junot, C. Analysis of the Human Adult Urinary Metabolome Variations with Age, Body Mass Index, and Gender by Implementing a Comprehensive Workflow for Univariate and OPLS Statistical Analyses. Journal of Proteome Research 14, 3322-3335, doi:10.1021/acs.jproteome.5b00354 (2015).
45 van Domselaar, R. et al. HIV-1 Subtype C with PYxE Insertion Has Enhanced Binding of Gag-p6 to Host Cell Protein ALIX and Increased Replication Fitness. J Virol 93, doi:10.1128/jvi.00077-19 (2019).
46 Shaik, M. M. et al. Structural basis of coreceptor recognition by HIV-1 envelope spike. Nature 565, 318-323, doi:10.1038/s41586-018-0804-9 (2019).
47 Wickham, H. ggplot2. Elegant Graphics for Data Analysis. (Springer International Publishing, 2016).
48 in Wiley StatsRef: Statistics Reference Online 1-15.