Gut microbiota in HIV-pneumonia patients is related to peripheral CD4 counts, lung microbiota, and in vitro macrophage dysfunction.

Pneumonia is common and frequently fatal in HIV-infected patients, due to rampant, systemic inflammation and failure to control microbial infection. While airway microbiota composition is related to local inflammatory response, gut microbiota has been shown to correlate with the degree of peripheral immune activation (IL6 and IP10 expression) in HIV-infected patients. We thus hypothesized that both airway and gut microbiota are perturbed in HIV-infected pneumonia patients, that the gut microbiota is related to peripheral CD4+ cell counts, and that its associated products differentially program immune cell populations necessary for controlling microbial infection in CD4-high and CD4-low patients. To assess these relationships, paired bronchoalveolar lavage and stool microbiota (bacterial and fungal) from a large cohort of Ugandan, HIV-infected patients with pneumonia were examined, and in vitro tests of the effect of gut microbiome products on macrophage effector phenotypes performed. While lower airway microbiota stratified into three compositionally distinct microbiota as previously described, these were not related to peripheral CD4 cell count. In contrast, variation in gut microbiota composition significantly related to CD4 cell count, lung microbiota composition, and patient mortality. Compared with patients with high CD4+ cell counts, those with low counts possessed more compositionally similar airway and gut microbiota, evidence of microbial translocation, and their associated gut microbiome products reduced macrophage activation and IL-10 expression and increased IL-1β expression in vitro. These findings suggest that the gut microbiome is related to CD4 status and plays a key role in modulating macrophage function, critical to microbial control in HIV-infected patients with pneumonia

Distinct lung microbiota associate with HIV-associated chronic lung disease in children.

Chronic lung disease (CLD) is a common co-morbidity for HIV-positive children and adolescents on antiretroviral therapy (ART) in sub-Saharan Africa. In this population, distinct airway microbiota may differentially confer risk of CLD. In a cross-sectional study of 202 HIV-infected children aged 6-16 years in Harare, Zimbabwe, we determined the association of sputum microbiota composition (using 16S ribosomal RNA V4 gene region sequencing) with CLD defined using clinical, spirometric, or radiographic criteria. Forty-two percent of children were determined to have CLD according to our definition. Dirichlet multinomial mixtures identified four compositionally distinct sputum microbiota structures. Patients whose sputum microbiota was dominated by Haemophilus, Moraxella or Neisseria (HMN) were at 1.5 times higher risk of CLD than those with Streptococcus or Prevotella (SP)-dominated microbiota (RR = 1.48, p = 0.035). Cell-free products of HMN sputum microbiota induced features of epithelial disruption and inflammatory gene expression in vitro, indicating enhanced pathogenic potential of these CLD-associated microbiota. Thus, HIV-positive children harbor distinct sputum microbiota, with those dominated by Haemophilus, Moraxella or Neisseria associated with enhanced pathogenesis in vitro and clinical CLD

Investigating the Role of the Lung and Gut Microbiota in HIV-associated Bacterial Pneumonia

In the era of highly active antiretroviral therapy (HAART), human immunodeficiency virus (HIV) infected patients are living longer, healthier lives, yet pulmonary infections still pose a common and frequently fatal co-morbidity in this population. Despite the frequency and severity of this disease, particularly within HIV and TB co-endemic regions of Africa, little is known about factors that determine patient endotypes, disease severity, and outcomes. Advanced HIV infection is known to compromise mucosal barrier defense, lead to macrophage dysfunction, and shift lung and gut microbiota composition. Hence we hypothesized that distinct pathogenic microbiota exist on these mucosal surfaces and relate to patient immune and disease endotypes in HIV infected patients with bacterial pneumonia. We initially profiled 16S rRNA in bronchoalveolar lavage (BAL) from a large cohort (n=182) of Ugandan HIV-pneumonia patients and identified three lower airway community states that repeated across the population and differentially related to microbiological, immunological, and clinical factors. Patients with the lowest mortality rate possessed Gammaproteobacteria-dominated communities, while patients with the highest mortality rate were colonized by Prevotellaceae-dominated communities, expressed more T-helper 2 (Th2) and Th17 cytokines within their lower airways, and were more frequently administered the antibiotic ceftriaxone. Building on these observations, we examined bacterial and fungal microbiota composition in paired BAL and stool samples from an independent cohort (n=120) and validated these airway microbiota states. Additionally, we demonstrated that gut microbiota composition is related to circulating CD4 count, airway microbiota composition, and patient outcomes. Gut microbiota from patients with the lowest CD4 counts were enriched for microbes shared with patient airways (based on identical 16S rRNA sequences) and were depleted of traditional gut-associated microbes. Compared to patients with high CD4 counts, sterile microbial products from patients with low CD4 counts induced fewer activated and CD206+IL-10+ tissue repair macrophages and more IL-1b+ pro-inflammatory macrophages in vitro. Overall, we demonstrate that there are a small number of distinct lower airway and gut microbiota within HIV infected patients with bacterial pneumonia that are differentially related to immune and patient outcomes. Stratifying patients based on lung and gut microbial communities may allow for more effective endotyping, leading to novel, tailored patient treatments

Saturated Fatty Acids Engage an IRE1α-Dependent Pathway to Activate the NLRP3 Inflammasome in Myeloid Cells.

Diets rich in saturated fatty acids (SFAs) produce a form of tissue inflammation driven by "metabolically activated" macrophages. We show that SFAs, when in excess, induce a unique transcriptional signature in both mouse and human macrophages that is enriched by a subset of ER stress markers, particularly IRE1α and many adaptive downstream target genes. SFAs also activate the NLRP3 inflammasome in macrophages, resulting in IL-1β secretion. We found that IRE1α mediates SFA-induced IL-1β secretion by macrophages and that its activation by SFAs does not rely on unfolded protein sensing. We show instead that the ability of SFAs to stimulate either IRE1α activation or IL-1β secretion can be specifically reduced by preventing their flux into phosphatidylcholine (PC) or by increasing unsaturated PC levels. Thus, IRE1α is an unrecognized intracellular PC sensor critical to the process by which SFAs stimulate macrophages to secrete IL-1β, a driver of diet-induced tissue inflammation

Saturated Fatty Acids Engage an IRE1α-Dependent Pathway to Activate the NLRP3 Inflammasome in Myeloid Cells

Diets rich in saturated fatty acids (SFAs) produce a form of tissue inflammation driven by “metabolically activated” macrophages. We show that SFAs, when in excess, induce a unique transcriptional signature in both mouse and human macrophages that is enriched by a subset of ER stress markers, particularly IRE1α and many adaptive downstream target genes. SFAs also activate the NLRP3 inflammasome in macrophages, resulting in IL-1β secretion. We found that IRE1α mediates SFA-induced IL-1β secretion by macrophages and that its activation by SFAs does not rely on unfolded protein sensing. We show instead that the ability of SFAs to stimulate either IRE1α activation or IL-1β secretion can be specifically reduced by preventing their flux into phosphatidylcholine (PC) or by increasing unsaturated PC levels. Thus, IRE1α is an unrecognized intracellular PC sensor critical to the process by which SFAs stimulate macrophages to secrete IL-1β, a driver of diet-induced tissue inflammation