Interplay between gut microbiota metabolism and inflammation in HIV infection

HIV infection causes a disruption of gut-associated lymphoid tissue, driving a shift in the composition of gut microbiota. A deeper understanding of the metabolic changes and how they affect the interplay with the host is needed. Here, we assessed functional modifications of HIV-associated microbiota by combining metagenomic and metatranscriptomic analyses. The transcriptionally active microbiota was well-adapted to the inflamed environment, overexpressing pathways related to resistance to oxidative stress. Furthermore, gut inflammation was maintained by the Gram-negative nature of the HIV-associated microbiota and underexpression of anti-inflammatory processes, such as short chain fatty acid biosynthesis or indole production. We performed co-occurrence and metabolic network analyses that showed relevance in the microbiota structure of both taxonomic and metabolic HIV-associated biomarkers. The Bayesian network revealed the most determinant pathways for maintaining the structure stability of the bacterial community. In addition, we identified the taxa's contribution to metabolic activities and their interactions with host health.This work was supported by grants to AM from the Spanish Ministry of Economy and Competitiveness (projects SAF 2012-31187, SAF2013-49788-EXP, and SAF2015-65878-R), the Carlos III Institute of Health (projects PIE14/00045 and AC15/00022), and the Generalitat Valenciana (project PrometeoII/2014/065) and was co-financed by FEDER. This work was supported by the Instituto de Salud Carlos III (Plan Estatal de IþDþi 2013–2016, project PI15/00345 and the Spanish AIDS Research Network (RD16/0025/0001 project) and co-financed by the European Development Regional Fund “A way to achieve Europe” (ERDF). JFV-C was supported by a CONACYT-SECITI fellowship, México. C.B.; DR and MF were funded by the Spanish Ministry of Economy and Competitiveness (CTQ2014-55279-R and BIO2014- 54494-R). SSV was supported by a grant from the Spanish Ministry of Science and Innovation (Contratos Juan Rodés, ECC/1051/2013). SM was funded by the Hospital Universitario Ramón y Cajal. VE was funded by the Hospital Clínico San Carlos. MJG was supported by a grant from the Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO) (UGP-14-116).Peer reviewe