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Luján 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 2020; 17:13-25. [PMID: 30854974 DOI: 10.2174/1570162x17666190311114808] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 02/25/2019] [Accepted: 03/06/2019] [Indexed: 12/18/2022]
Abstract
During HIV infection, massive destruction of CD4+ T cells ensues, preferentially depleting the Th17 subset at the gut-associated lymphoid tissue (GALT), leading to a loss of mucosal integrity and an increase in cell permeability. This process favors microbial translocation between the intestinal lumen and the circulatory system, contributing to persistent immune activation and chronic inflammation characteristic of HIV infection. Thus, the gut microbiota plays an integral role in maintaining the structure and function of the mucosal barrier, a critical factor for immune homeostasis. However, in the context of HIV infection, changes in the gut microbiota have been reported and have been linked to disease progression. Here, we review evidence for the role of the gut microbiota in intestinal homeostasis, its contribution to HIV pathogenesis, as well as its use in the development of therapeutic strategies.
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Affiliation(s)
- Jorge A Luján
- Grupo Inmunovirologia, Facultad de Medicina. Universidad de Antioquia, Medellin, Colombia
| | - Maria T Rugeles
- Grupo Inmunovirologia, Facultad de Medicina. Universidad de Antioquia, Medellin, Colombia
| | - Natalia A Taborda
- Grupo Inmunovirologia, Facultad de Medicina. Universidad de Antioquia, Medellin, Colombia.,Grupo de Investigaciones Biomédicas, Facultad de Ciencias de la Salud, Corporación Universitaria Remington, Medellín, Colombia
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Tuddenham SA, Koay WLA, Zhao N, White JR, Ghanem KG, Sears CL. The Impact of Human Immunodeficiency Virus Infection on Gut Microbiota α-Diversity: An Individual-level Meta-analysis. Clin Infect Dis 2020; 70:615-627. [PMID: 30921452 PMCID: PMC7319268 DOI: 10.1093/cid/ciz258] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Accepted: 03/22/2019] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Whether human immunodeficiency virus (HIV) infection impacts gut microbial α-diversity is controversial. We reanalyzed raw 16S ribosomal RNA (rRNA) gene sequences and metadata from published studies to examine α-diversity measures between HIV-uninfected (HIV-) and HIV-infected (HIV+) individuals. METHODS We conducted a systematic review and individual level meta-analysis by searching Embase, Medline, and Scopus for original research studies (inception to 31 December 2017). Included studies reported 16S rRNA gene sequences of fecal samples from HIV+ patients. Raw sequence reads and metadata were obtained from public databases or from study authors. Raw reads were processed through standardized pipelines with use of a high-resolution taxonomic classifier. The χ2 test, paired t tests, and generalized linear mixed models were used to relate α-diversity measures and clinical metadata. RESULTS Twenty-two studies were identified with 17 datasets available for analysis, yielding 1032 samples (311 HIV-, 721 HIV+). HIV status was associated with a decrease in measures of α-diversity (P < .001). However, in stratified analysis, HIV status was associated with decreased α-diversity only in women and in men who have sex with women (MSW) but not in men who have sex with men (MSM). In analyses limited to women and MSW, controlling for HIV status, women displayed increased α-diversity compared with MSW. CONCLUSIONS Our study suggests that HIV status, sexual risk category, and gender impact gut microbial community α-diversity. Future studies should consider MSM status in gut microbiome analyses.
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Affiliation(s)
| | - Wei Li A Koay
- Children’s National Medical Center, Baltimore, Maryland
- George Washington University, Washington, District of Columbia, Baltimore, Maryland
| | - Ni Zhao
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | | | - Khalil G Ghanem
- Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Cynthia L Sears
- Johns Hopkins University School of Medicine, Baltimore, Maryland
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Gabrielli S, Furzi F, Fontanelli Sulekova L, Taliani G, Mattiucci S. Occurrence of Blastocystis-subtypes in patients from Italy revealed association of ST3 with a healthy gut microbiota. Parasite Epidemiol Control 2020; 9:e00134. [PMID: 32258445 PMCID: PMC7096745 DOI: 10.1016/j.parepi.2020.e00134] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 12/27/2019] [Accepted: 12/30/2019] [Indexed: 12/18/2022] Open
Abstract
An epidemiological survey on Blastocystis was carried out enrolling a total of 2524 subjects referred to the Umberto I Academic Hospital in Rome, for the routine parasitological exams, during 2017–2018. The studied population included a sample of immunocompromised individuals (N = 130) followed at the same hospital. DNA sequencing of the small subunit rRNA gene (SSU rDNA) locus was performed on samples positive to the coproparasitological analysis to molecular characterize the Blastocystis-subtypes. Microscopical analysis detected Blastocystis in 192/2524 (7.6%) of the enrolled subjects. It was the organism most frequently identified in the analysed faecal samples diagnosed in single infection (5.6%) or in co-infection with other enteric protozoa (2%). Furthermore, it was found mainly in immunocompromised patients (22.3%) compared to immunocompetent ones (6.8%). As expected, ST3 was the most occurring subtype identified in 40% of the subjects, followed by ST1 (29%), ST2 (16%), ST4 (12%), and ST7 (3%). Next-generation sequencing (NGS) of the 16S rDNA was performed on a sub-sample of Blastocystis-ST3-carriers, homogenous by age and gender, as well as on Blastocystis-free subjects, to profile and compare their gut bacterial composition. A higher bacterial diversity was found in ST3-Blastocystis-carriers, which exhibited a high abundance of Prevotella, Methanobrevibacter and Ruminococcus while, a high percentage of Bacteroides was found in Blastocystis-free subjects. This study evidenced the presence of Blastocystis in 7.6% of faecal samples in Italy and a high circulation of the protist among immunocompromised patients (22.3%). Molecular characterization of positive samples evidenced the occurrence of five different subtypes, including zoonotic ST such as the ST7, highlighting the risk of transmission from animals. Study of the gut microbiota composition confirms previous evidences according to which, the colonisation by Blastocystis would be linked with an eubiotic gut characterized by potentially beneficial species such as Prevotella and Ruminococcus, rather than with a dysbiotic state, with a high abundance of Enterobacteriaceae, and corroborated the role of the protist as “an old friend” of the human gut. Microscopical analysis detected Blastocystis in 7.6% subjects in Italy. Molecular methods allowed the identification of 5 STs (ST1, ST2, ST3, ST4, ST7). ST3 resulted the most frequent subtype. NGS of the 16S rDNA gene was performed in Blastocystis-ST3-carriers. Blastocystis-ST3 resulted correlated to an eubiotic gut characterized by potentially beneficial species.
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Affiliation(s)
- Simona Gabrielli
- Department of Public Health and Infectious Diseases, "Sapienza-University of Rome", Piazzale Aldo Moro 5, 00185 Rome, Italy
- Diagnostic Parasitology laboratory, Academic Hospital "Policlinico Umberto I", Rome, Viale del Policlinico 155, 00185 Rome, Italy
| | - Federica Furzi
- Department of Public Health and Infectious Diseases, "Sapienza-University of Rome", Piazzale Aldo Moro 5, 00185 Rome, Italy
| | | | - Gloria Taliani
- Department of Translation and Precision Medicine, "Sapienza University of Rome", 00185 Rome, Italy
| | - Simonetta Mattiucci
- Department of Public Health and Infectious Diseases, "Sapienza-University of Rome", Piazzale Aldo Moro 5, 00185 Rome, Italy
- Diagnostic Parasitology laboratory, Academic Hospital "Policlinico Umberto I", Rome, Viale del Policlinico 155, 00185 Rome, Italy
- Corresponding author at: Department of Public Health and Infectious Diseases, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy.
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Fontanelli Sulekova L, Gabrielli S, Furzi F, Milardi GL, Biliotti E, De Angelis M, Iaiani G, Fimiani C, Maiorano M, Mattiucci S, Taliani G. Molecular characterization of Blastocystis subtypes in HIV-positive patients and evaluation of risk factors for colonization. BMC Infect Dis 2019; 19:876. [PMID: 31640585 PMCID: PMC6805496 DOI: 10.1186/s12879-019-4537-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 10/09/2019] [Indexed: 01/11/2023] Open
Abstract
Background Blastocystis is one of the most common intestinal protozoa in human faecal samples with uncertain impact on public health. Studies on the prevalence of Blastocystis in HIV-positive patients are limited and dated. Methods A cross-sectional study was carried out involving 156 HIV-positive patients to evaluate the prevalence of Blastocystis-subtypes by molecular amplification and sequencing the small subunit rRNA gene (SSU rDNA), to identify the risk factors for its transmission, to examine the relationship between the presence of the protist and gastrointestinal disorders. Furthermore, the evaluation of the faecal calprotectin by immunoassay from a sample of subjects was performed to evaluate the gut inflammation in Blastocystis-carriers. Results Blastocystis-subtypes ST1, ST2, ST3, ST4 were identified in 39 HIV-positive patients (25%). No correlation was found between the presence of the protist and virological or epidemiological risk factors. Blastocystis was more frequently detected in homosexual subjects (p = 0.037) infected by other enteric protozoa (p = 0.0001) and with flatulence (p = 0.024). No significant differences in calprotectin level was found between Blastocystis-carriers and free ones. Conclusions Blastocystis is quite common in HIV-positive patients on ART showing in examined patients 25% prevalence. Homosexual behaviour may represent a risk factor for its transmission, while CD4 count and viremia didn’t correlate with the presence of the protist. The pathogenetic role of Blastocystis remains unclear and no gut inflammation status was detected in Blastocystis-carriers. The only symptom associated with Blastocystis was the flatulence, evidencing a link between the presence of the protist and the composition and stability of gut microbiota.
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Affiliation(s)
| | - Simona Gabrielli
- Clinical Diagnostic Parasitology laboratory, Umberto I Academic Hospital, 00185, Rome, Italy. .,Department of Public Health and Infectious Diseases, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185, Rome, Italy.
| | - Federica Furzi
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Giovanni Luigi Milardi
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Elisa Biliotti
- Department of Translation and Precision Medicine, Sapienza University of Rome, 00185, Rome, Italy
| | - Maurizio De Angelis
- Department of Translation and Precision Medicine, Sapienza University of Rome, 00185, Rome, Italy
| | - Giancarlo Iaiani
- Department of Translation and Precision Medicine, Sapienza University of Rome, 00185, Rome, Italy
| | - Caterina Fimiani
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Myriam Maiorano
- Department of Translation and Precision Medicine, Sapienza University of Rome, 00185, Rome, Italy
| | - Simonetta Mattiucci
- Clinical Diagnostic Parasitology laboratory, Umberto I Academic Hospital, 00185, Rome, Italy.,Department of Public Health and Infectious Diseases, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Gloria Taliani
- Department of Translation and Precision Medicine, Sapienza University of Rome, 00185, Rome, Italy
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Loiseau C, Cooper MM, Doolan DL. Deciphering host immunity to malaria using systems immunology. Immunol Rev 2019; 293:115-143. [PMID: 31608461 DOI: 10.1111/imr.12814] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Revised: 09/18/2019] [Accepted: 09/20/2019] [Indexed: 12/11/2022]
Abstract
A century of conceptual and technological advances in infectious disease research has changed the face of medicine. However, there remains a lack of effective interventions and a poor understanding of host immunity to the most significant and complex pathogens, including malaria. The development of successful interventions against such intractable diseases requires a comprehensive understanding of host-pathogen immune responses. A major advance of the past decade has been a paradigm switch in thinking from the contemporary reductionist (gene-by-gene or protein-by-protein) view to a more holistic (whole organism) view. Also, a recognition that host-pathogen immunity is composed of complex, dynamic interactions of cellular and molecular components and networks that cannot be represented by any individual component in isolation. Systems immunology integrates the field of immunology with omics technologies and computational sciences to comprehensively interrogate the immune response at a systems level. Herein, we describe the system immunology toolkit and report recent studies deploying systems-level approaches in the context of natural exposure to malaria or controlled human malaria infection. We contribute our perspective on the potential of systems immunity for the rational design and development of effective interventions to improve global public health.
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Affiliation(s)
- Claire Loiseau
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, Qld, Australia
| | - Martha M Cooper
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, Qld, Australia
| | - Denise L Doolan
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, Qld, Australia
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γδ T-cell subsets in HIV controllers: potential role of Tγδ17 cells in the regulation of chronic immune activation. AIDS 2019; 33:1283-1292. [PMID: 30870199 DOI: 10.1097/qad.0000000000002196] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
OBJECTIVES HIV controllers (HICs) are rare HIV-infected individuals able to maintain undetectable viremia in the absence of antiretroviral treatment. Although HIV-specific cytotoxic T cells have been well deciphered in HIC, γδ T lymphocytes remain largely uncharacterized. The aim of this study was to analyse phenotypic and functional characteristics of γδ T cells and their relationship with immune activation, which remains abnormally elevated and associated with comorbidities in HICs. METHODS Peripheral blood mononuclear cells (PBMCs) were isolated from 16 HICs, 16 patients with untreated chronic HIV infection (UT-CHI) and 20 healthy donors. Surface marker expression and cytokine production by γδ T cells were analysed by flow cytometry. RESULTS Despite normal frequencies of total γδ T cells, the Vδ2/Vδ2 ratio was significantly reduced in HIC, albeit to a lesser extent than UT-CHI patients. Of note, nine HICs showed elevated Vδ2 γδ T cells, as patients with UT-CHI, which was associated with higher CD8 T-cell activation. Interleukin (IL)-17-production by γδ T cells (Tγδ17) was better preserved in HIC than in UT-CHI patients. Proportion of total γδ T cells positively correlated with CD8 T-cell activation and HIV-DNA, IP-10 and sCD14 levels. Conversely, Tγδ17 cells negatively correlated with CD8 T-cell activation and plasma sCD14 levels. Moreover, transforming growth factor (TGF)-β producing Vδ2 T cells were as dramatically depleted in HIC as in UT-CHI patients. CONCLUSION The relative preservation of IL-17-producing γδ T cells in HIC and their negative association with immune activation raise the hypothesis that Tγδ17 cells - potentially through prevention of microbial translocation - may participate in the control of chronic systemic immune activation.
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Abstract
PURPOSE OF REVIEW We aim to provide an in-depth review of recent literature highlighting the role of inflammation involving the adipose tissue, liver, skeletal muscles, and gastrointestinal tract in the development of metabolic complications among persons living with HIV (PLWH). RECENT FINDINGS Recent studies in PLWH have demonstrated a significant association between circulating inflammatory markers and development of insulin resistance and metabolic complications. In adipose tissue, pro-inflammatory cytokine expression inhibits adipocyte insulin signaling, which alters lipid and glucose homeostasis. Increased lipolysis and lipogenesis elevate levels of circulating free fatty acids and promote ectopic fat deposition in liver and skeletal muscles. This leads to lipotoxicity characterized by a pro-inflammatory response with worsening insulin resistance. Finally, HIV is associated with gastrointestinal tract inflammation and changes in the gut microbiome resulting in reduced diversity, which is an additional risk factor for diabetes. Metabolic complications in PLWH are in part due to chronic, multisite tissue inflammation resulting in dysregulation of glucose and lipid trafficking, utilization, and storage.
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Distinct gut microbiota profile in antiretroviral therapy-treated perinatally HIV-infected patients associated with cardiac and inflammatory biomarkers. AIDS 2019; 33:1001-1011. [PMID: 30946154 DOI: 10.1097/qad.0000000000002131] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
OBJECTIVE Persistent inflammation and higher risk to develop cardiovascular diseases still represent a major complication for HIV-infected patients despite effective antiretroviral therapy (ART). We investigated the correlation between the gut microbiota profile, markers of inflammation, vascular endothelial activation (VEA) and microbial translocation (MT) in perinatally HIV-infected patients (PHIV) under ART. DESIGN Cross-sectional study including 61 ART-treated PHIV (age range 3-30 years old) and 71 age-matched healthy controls. Blood and stool sample were collected at the same time and analyzed for gut microbiota composition and plasma biomarkers. METHODS Gut microbiota composition was determined by 16S rRNA targeted-metagenomics. Soluble markers of MT, inflammation and VEA were quantified by ELISA or Luminex assay. Markers of immune activation were analyzed by flow cytometry on CD4 and CD8T cells. RESULTS We identified two distinct gut microbiota profiles (groups A and B) among PHIV. No different clinical parameters (age, sex, ethnicity, clinical class), dietary and sexual habits were found between the groups. The group A showed a relative dominance of Akkermansia muciniphila, whereas gut microbiota of group B was characterized by a higher biodiversity. The analysis of soluble markers revealed a significantly higher level of soluble E-selectine (P = 0.0296), intercellular adhesion molecule-1 (P = 0.0028), vascular adhesion molecule-1 (P = 0.0230), IL-6 (P = 0.0247) and soluble CD14 (P = 0.0142) in group A compared with group B. CONCLUSION Distinctive gut microbiota profiles are differently associated with inflammation, microbial translocation and VEA. Future studies are needed to understand the role of A. muciniphila and risk to develop cardiovascular diseases in PHIV.
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Wang Z, Qi Q. Gut microbial metabolites associated with HIV infection. Future Virol 2019; 14:335-347. [PMID: 31263508 PMCID: PMC6595475 DOI: 10.2217/fvl-2019-0002] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 04/25/2019] [Indexed: 02/06/2023]
Abstract
HIV infection has been associated with alterations in gut microbiota and related microbial metabolite production. However, the mechanisms of how these functional microbial metabolites may affect HIV immunopathogenesis and comorbidities, such as cardiovascular disease and other metabolic diseases, remain largely unknown. Here we review the current understanding of gut microbiota and related metabolites in the context of HIV infection. We focus on several bacteria-produced metabolites, including tryptophan catabolites, short-chain fatty acids and trimethylamine-N-oxide (TMAO), and discuss their implications in HIV infection and comorbidities. We also prospect future studies using integrative multiomics approaches to better understand host-microbiota-metabolites interactions in HIV infection, and facilitate integrative medicine utilizing the microbiota in HIV infection.
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Affiliation(s)
- Zheng Wang
- Department of Epidemiology & Population Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Qibin Qi
- Department of Epidemiology & Population Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA
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Abstract
OBJECTIVE We employed a high-dimensional covariate adjustment method in microbiome analysis to better control for behavioural and clinical confounders, and in doing so examine the effects of HIV on the rectal microbiome. DESIGN Three hundred and eighty-three MSM were grouped into four HIV viremia categories: HIV negative (n = 200), HIV-positive undetectable (HIV RNA < 20 copies/ml; n = 66), HIV-positive suppressed (RNA 20-200 copies/ml; n = 72) and HIV-positive viremic (RNA > 200 copies/ml; n = 45). METHODS We performed 16S rRNA gene sequencing on rectal swab samples and used inverse probability of treatment-weighted marginal structural models to examine differences in microbial composition by HIV viremia category. RESULTS HIV viremia explained a significant amount of variability in microbial composition in both unadjusted and covariate-adjusted analyses (R = 0.011, P = 0.02). Alterations in bacterial taxa were more apparent with increasing viremia. Relative to the HIV-negative group, HIV-positive undetectable participants showed depletions in Brachyspira, Campylobacter and Parasutterella, while suppressed participants demonstrated depletions in Barnesiella, Brachyspira and Helicobacter. The microbial signature of viremic men was most distinct, showing enrichment in inflammatory genera Peptoniphilus, Porphyromonas and Prevotella and depletion of Bacteroides, Brachyspira and Faecalibacterium, among others. CONCLUSION Our study shows that, after accounting for the influence of multiple confounding factors, HIV is associated with dysbiosis in the gastrointestinal microbiome in a dose-dependent manner. This analytic approach may allow for better identification of true microbial associations by limiting the effects of confounding, and thus improve comparability across future studies.
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Armstrong AJS, Shaffer M, Nusbacher NM, Griesmer C, Fiorillo S, Schneider JM, Preston Neff C, Li SX, Fontenot AP, Campbell T, Palmer BE, Lozupone CA. An exploration of Prevotella-rich microbiomes in HIV and men who have sex with men. MICROBIOME 2018; 6:198. [PMID: 30396369 PMCID: PMC6219090 DOI: 10.1186/s40168-018-0580-7] [Citation(s) in RCA: 110] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 10/17/2018] [Indexed: 05/12/2023]
Abstract
BACKGROUND Gut microbiome characteristics associated with HIV infection are of intense research interest but a deep understanding has been challenged by confounding factors across studied populations. Notably, a Prevotella-rich microbiome described in HIV-infected populations is now understood to be common in men who have sex with men (MSM) regardless of HIV status, but driving factors and potential health implications are unknown. RESULTS Here, we further define the MSM-associated gut microbiome and describe compositional differences between the fecal microbiomes of Prevotella-rich MSM and non-MSM that may underlie observed pro-inflammatory properties. Furthermore, we show relatively subtle gut microbiome changes in HIV infection in MSM and women that include an increase in potential pathogens that is ameliorated with antiretroviral therapy (ART). Lastly, using a longitudinal cohort, we describe microbiome changes that happen after ART initiation. CONCLUSIONS This study provides an in-depth characterization of microbiome differences that occur in a US population infected with HIV and demonstrates the degree to which these differences may be driven by lifestyle factors, ART, and HIV infection itself. Understanding microbiome compositions that occur with sexual behaviors that are high risk for acquiring HIV and untreated and ART-treated HIV infection will guide the investigation of immune and metabolic functional implications to ultimately target the microbiome therapeutically.
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Affiliation(s)
- Abigail J. S. Armstrong
- Department of Medicine, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO USA
- Department of Immunology and Microbiology, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO USA
| | - Michael Shaffer
- Department of Medicine, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO USA
- Computational Bioscience Program, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO USA
| | - Nichole M. Nusbacher
- Department of Medicine, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO USA
| | - Christine Griesmer
- Department of Surgery, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO USA
| | - Suzanne Fiorillo
- Department of Surgery, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO USA
| | - Jennifer M. Schneider
- Department of Medicine, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO USA
| | - C. Preston Neff
- Department of Medicine, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO USA
| | - Sam X. Li
- Department of Medicine, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO USA
| | - Andrew P. Fontenot
- Department of Medicine, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO USA
| | - Thomas Campbell
- Department of Surgery, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO USA
| | - Brent E. Palmer
- Department of Medicine, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO USA
| | - Catherine A. Lozupone
- Department of Medicine, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO USA
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Gut microbiota and plasma metabolites associated with diabetes in women with, or at high risk for, HIV infection. EBioMedicine 2018; 37:392-400. [PMID: 30366816 PMCID: PMC6286648 DOI: 10.1016/j.ebiom.2018.10.037] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 10/11/2018] [Accepted: 10/12/2018] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Gut microbiota alteration has been implicated in HIV infection and metabolic disorders. The relationship between gut microbiota and diabetes has rarely been studied in HIV-infected individuals, who have excess risk of metabolic disorders. METHODS Our study during 2015-2016 enrolled predominantly African Americans and Hispanics in the Women's Interagency HIV Study. We studied 28 women with long-standing HIV infection under antiretroviral therapy and 20 HIV-uninfected, but at high risk of infection, women (16 HIV+ and 6 HIV- with diabetes). Fecal samples were analyzed by sequencing prokaryotic16S rRNA gene. Plasma metabolomics profiling was performed by liquid chromatography-tandem mass spectrometry. FINDINGS No significant differences in bacterial α- or β-diversity were observed by diabetes or HIV serostatus (all P > .1). Relative abundances of four genera (Finegoldia, Anaerococcus, Sneathia, and Adlercreutzia) were lower in women with diabetes compared to those without diabetes (all P < .01). In women with diabetes, plasma levels of several metabolites in tryptophan catabolism (e,g., kynurenine/tryptophan ratio), branched-chain amino acid and proline metabolism pathways were higher, while glycerophospholipids were lower (all P < .05). Results were generally consistent between HIV-infected and HIV-uninfected women, and no significant modification effects by HIV serostatus were observed (all Pinteraction > 0.05). Anaerococcus, known to produce butyrate which is involved in anti-inflammation and glucose metabolism, showed an inverse correlation with kynurenine/tryptophan ratio (r = -0.38, P < .01). INTERPRETATION Among women with or at high risk for HIV infection, diabetes is associated with gut microbiota and plasma metabolite alteration, including depletion of butyrate-producing bacterial population along with higher tryptophan catabolism. FUND: NHLBI (K01HL129892, R01HL140976) and FMF.
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Gut microbial diversity in HIV infection post combined antiretroviral therapy: a key target for prevention of cardiovascular disease. Curr Opin HIV AIDS 2018; 13:38-44. [PMID: 29045253 PMCID: PMC5718258 DOI: 10.1097/coh.0000000000000426] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
PURPOSE OF REVIEW Although the HIV-infected population is living longer and getting older under current treatment regimens, significant challenges arise for health management as the infection is associated with various premature aging phenotypes, particularly increased incidence of cardiovascular diseases (CVDs). Here we review the current understanding of HIV-related gut dysbiosis in association with CVD and advances in clinical trials aiming to restore gut microbial diversity. RECENT FINDING Identification of a unique signature for gut dysbiosis in HIV infection between different cohorts remains challenging. However, low diversity of microbiota combined with the outgrowth of pathogenic bacterial species together with dysregulated metabolic pathways have been linked to compromised gut immunity, bacterial translocation and systemic inflammation, hence higher CVD risk among different cohorts. Data from recent clinical trials aiming to evaluate the tolerability and efficacy of probiotics in treated HIV+ patients are promising and support a significant increase in microbiota diversity and reduction of systemic inflammation. However, the impact of these microbial and immunological corrections on the prevalence of CVD in HIV+ patients remains unclear. SUMMARY Positive immunological outcomes following enrichment of the gut microbial diversity have been documented, and further trials are in progress to evaluate the range of patients, with different immunological backgrounds, who might benefit from these treatments.
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Abstract
PURPOSE OF REVIEW This article discusses the interaction between HIV infection, the gut microbiome, inflammation and immune activation, and HIV reservoirs, along with interventions to target the microbiome and their implications for HIV remission and cure. RECENT FINDINGS Most studies show that HIV-infected adults have a gut microbiome associated with decreased bacterial richness and diversity, and associated systemic inflammation and immune activation. A unique set of individuals, elite controllers, who spontaneously control HIV replication, have a similar microbiome to HIV-uninfected individuals. Conversely, exposure to maternal HIV in infants was shown to alter the gut microbiome, even in infants who escaped perinatal infection. Emerging research highlights the importance of the metabolomics and metaproteomics of the gut microbiome, which may have relevance for HIV remission and cure. Together, these studies illustrate the complexity of the relationship between HIV infection, the gut microbiome, and its systemic effects. SUMMARY Understanding the association of HIV with the microbiome, metabolome, and metaproteome may lead to novel therapies to decrease inflammation and immune activation, and impact HIV reservoir size and vaccine responses. Further research in this area is important to inform HIV remission and cure treatments.
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The functional consequences of the microbiome in HIV: insights from metabolomic studies. Curr Opin HIV AIDS 2018; 13:88-94. [PMID: 29035945 DOI: 10.1097/coh.0000000000000430] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
PURPOSE OF REVIEW It is critical to gain insight into the metabolic pathways by which the microbiota might influence HIV immunopathogenesis to exploit host-microbiota interactions. The aim of this review is to sketch a very broad picture of recent advances in our knowledge of how HIV might affect the microbiota, with a focus on specific gene products, particularly, metabolites produced by the microbiota that may affect HIV immunopathogenesis. RECENT FINDINGS First, we describe the different approaches used to explore imbalances in effector microbial products during HIV infection. Then, we review the mechanisms by which the microbiota might affect HIV immunopathogenesis. We cover several aspects of HIV immunopathogenesis, including systemic inflammation, mucosal immunity, enterocyte barrier integrity, HIV persistence and effects on HIV-specific humoral and cytotoxic responses. The altered interplay between mucosal immunity and dysbiotic bacteria helps to explain poorly understood observations in HIV infection, including susceptibility to HIV acquisition or the risk of HPV-related cancers, lung infections and cardiovascular disease. SUMMARY Although there is an urgent need to standardize the methods used for assessing the functional level of the microbiota, it is recognized that functional modulation of the microbiota for therapeutic purposes should be evaluated to improve HIV care.
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Malaria, tuberculosis and HIV: what's new? Contribution of the Institut Hospitalo-Universitaire Méditerranée Infection in updated data. New Microbes New Infect 2018; 26:S23-S30. [PMID: 30402240 PMCID: PMC6205578 DOI: 10.1016/j.nmni.2018.06.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2018] [Revised: 06/01/2018] [Accepted: 06/05/2018] [Indexed: 11/22/2022] Open
Abstract
The Institut Hospitalo-Universitaire Méditerranée Infection is positioned for the diagnosis, prevention and treatment of the ‘big three’ killer diseases: malaria, tuberculosis and HIV. We implemented the use of new diagnostic samples such as stools and new diagnostic tests such as mass spectrometry for the dual identification of vectors and pathogens. Furthermore, advances in the prevention and treatment of malaria and tuberculosis are reviewed, along with advances in the understanding of the role of microbiota in the resistance to HIV infection. These achievements represent a major step towards a better management of the ‘big three’ diseases worldwide.
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Sui Y, Dzutsev A, Venzon D, Frey B, Thovarai V, Trinchieri G, Berzofsky JA. Influence of gut microbiome on mucosal immune activation and SHIV viral transmission in naive macaques. Mucosal Immunol 2018; 11:1219-1229. [PMID: 29858581 PMCID: PMC6030500 DOI: 10.1038/s41385-018-0029-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 03/23/2018] [Accepted: 04/02/2018] [Indexed: 02/04/2023]
Abstract
It is unknown whether the gut microbiome affects HIV transmission. In our recent SHIV vaccine study, we found that the naive rhesus macaques from two different sources had significantly different rates of infection against repeated low-dose intrarectal challenge with SHIVSF162P4 virus. Exploring causes, we found that the more susceptible group of seven macaques had significantly more activated CD4+CCR5+Ki67+ T cells in the rectal mucosa than the more resistant group of 11 macaques from a different source. The prevalence of pre-challenge activated rectal CD4 T cells in the naive macaques correlated inversely with the number of challenges required to infect. Because the two naive groups came from different sources, we hypothesized that their microbiomes may differ and might explain the activation difference. Indeed, after sequencing 16s rRNA, we found differences between the two naive groups that correlated with immune activation status. Distinct gut microbiota induced different levels of immune activation ex vivo. Significantly lower ratios of Bacteroides to Prevotella, and significantly lower levels of Firmicutes were found in the susceptible cohort, which were also inversely correlated with high levels of immune activation in the rectal mucosa. Thus, host-microbiome interactions might influence HIV/SIV mucosal transmission through effects on mucosal immune activation.
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Affiliation(s)
- Yongjun Sui
- Vaccine Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892,Corresponding authors: Yongjun Sui, Vaccine Branch, National Cancer Institute, National Institutes of Health, 41 Medlars Drive, Bethesda, MD 20892 USA, Ph: 240-760-6716, Fx: 240-541-4453, ; Jay A. Berzofsky, Vaccine Branch, National Cancer Institute, National Institutes of Health, 41 Medlars Drive, Bethesda, MD 20892 USA, Ph: 240-760-6148, Fx: 240-541-4452,
| | - Amiran Dzutsev
- Cancer and Inflammation Program, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - David Venzon
- Biostatistics and Data Management Section, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Blake Frey
- Vaccine Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Vishal Thovarai
- Cancer and Inflammation Program, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Giorgio Trinchieri
- Cancer and Inflammation Program, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Jay A. Berzofsky
- Vaccine Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892,Corresponding authors: Yongjun Sui, Vaccine Branch, National Cancer Institute, National Institutes of Health, 41 Medlars Drive, Bethesda, MD 20892 USA, Ph: 240-760-6716, Fx: 240-541-4453, ; Jay A. Berzofsky, Vaccine Branch, National Cancer Institute, National Institutes of Health, 41 Medlars Drive, Bethesda, MD 20892 USA, Ph: 240-760-6148, Fx: 240-541-4452,
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Impact of HIV and Type 2 diabetes on Gut Microbiota Diversity, Tryptophan Catabolism and Endothelial Dysfunction. Sci Rep 2018; 8:6725. [PMID: 29712976 PMCID: PMC5928109 DOI: 10.1038/s41598-018-25168-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 04/10/2018] [Indexed: 01/04/2023] Open
Abstract
HIV infection and type 2 diabetes are associated with altered gut microbiota, chronic inflammation, and increased cardiovascular risk. We aimed to investigate the combined effect of these diseases on gut microbiota composition and related metabolites, and a potential relation to endothelial dysfunction in individuals with HIV-infection only (n = 23), diabetes only (n = 16) or both conditions (n = 21), as well as controls (n = 24). Fecal microbiota was analyzed by Illumina sequencing of the 16 S rRNA gene. Markers of endothelial dysfunction (asymmetric dimethylarginine [ADMA]), tryptophan catabolism (kynurenine/tryptophan [KT]-ratio), and inflammation (neopterin) were measured by liquid chromatography-tandem mass spectrometry. The combination of HIV and type 2 diabetes was associated with reduced gut microbiota diversity, increased plasma KT-ratio and neopterin. Microbial genes related to tryptophan metabolism correlated with KT-ratio and low alpha diversity, in particular in HIV-infected with T2D. In multivariate analyses, KT-ratio associated with ADMA (β = 4.58 [95% CI 2.53–6.63], p < 0.001), whereas microbiota composition per se was not associated with endothelial dysfunction. Our results indicate that tryptophan catabolism may be related to endothelial dysfunction, with a potentially detrimental interaction between HIV and diabetes. The potential contribution of gut microbiota and the impact for cardiovascular risk should be further explored in prospective studies powered for clinical end points.
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Loucif H, Gouard S, Dagenais-Lussier X, Murira A, Stäger S, Tremblay C, Van Grevenynghe J. Deciphering natural control of HIV-1: A valuable strategy to achieve antiretroviral therapy termination. Cytokine Growth Factor Rev 2018; 40:90-98. [PMID: 29778137 DOI: 10.1016/j.cytogfr.2018.03.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 03/27/2018] [Indexed: 02/06/2023]
Abstract
Antiretroviral therapy (ART) has dramatically reduced HIV-1-associated morbidity and mortality, and has transformed HIV-1 infection into a manageable chronic condition by suppressing viral replication. However, despite recent patient care improvements, ART still fails to cure HIV-1 infection due to the inability to counteract immune defects and metabolic disturbances that are associated with residual inflammation alongside viral persistence. Life-long drug administration also results in multiple side-effects in patients including lipodystrophy and insulin resistance. Thus, it is critical to find new ways to reduce the length of treatment and facilitate the termination of ART, for example by boosting protective immunity. The rare ability of some individuals to naturally control HIV-1 infection despite residual inflammation could be exploited to identify molecular mechanisms involved in host protection that may function as potential therapeutic targets. In this review, we highlight evidence illustrating the molecular and metabolic advantages of HIV-1 controllers over ART treated patients that contribute to the maintenance of effective antiviral immunity.
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Affiliation(s)
- Hamza Loucif
- Institut National de la Recherche Scientifique (INRS)-Institut Armand-Frappier, 531 Boulevard des Prairies, Laval, H7V 1B7, QC, Canada
| | - Steven Gouard
- Institut National de la Recherche Scientifique (INRS)-Institut Armand-Frappier, 531 Boulevard des Prairies, Laval, H7V 1B7, QC, Canada
| | - Xavier Dagenais-Lussier
- Institut National de la Recherche Scientifique (INRS)-Institut Armand-Frappier, 531 Boulevard des Prairies, Laval, H7V 1B7, QC, Canada
| | - Armstrong Murira
- Institut National de la Recherche Scientifique (INRS)-Institut Armand-Frappier, 531 Boulevard des Prairies, Laval, H7V 1B7, QC, Canada
| | - Simona Stäger
- Institut National de la Recherche Scientifique (INRS)-Institut Armand-Frappier, 531 Boulevard des Prairies, Laval, H7V 1B7, QC, Canada
| | - Cécile Tremblay
- Centre de Recherche de l'Université de Montréal, Montréal, QC, Canada
| | - Julien Van Grevenynghe
- Institut National de la Recherche Scientifique (INRS)-Institut Armand-Frappier, 531 Boulevard des Prairies, Laval, H7V 1B7, QC, Canada.
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Sokoya T, Steel HC, Nieuwoudt M, Rossouw TM. HIV as a Cause of Immune Activation and Immunosenescence. Mediators Inflamm 2017; 2017:6825493. [PMID: 29209103 PMCID: PMC5676471 DOI: 10.1155/2017/6825493] [Citation(s) in RCA: 105] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 10/09/2017] [Accepted: 10/11/2017] [Indexed: 12/20/2022] Open
Abstract
Systemic immune activation has emerged as an essential component of the immunopathogenesis of HIV. It not only leads to faster disease progression, but also to accelerated decline of overall immune competence. HIV-associated immune activation is characterized by an increase in proinflammatory mediators, dysfunctional T regulatory cells, and a pattern of T-cell-senescent phenotypes similar to those seen in the elderly. These changes predispose HIV-infected persons to comorbid conditions that have been linked to immunosenescence and inflamm-ageing, such as atherosclerosis and cardiovascular disease, neurodegeneration, and cancer. In the antiretroviral treatment era, development of such non-AIDS-defining, age-related comorbidities is a major cause of morbidity and mortality. Treatment strategies aimed at curtailing persistent immune activation and inflammation may help prevent the development of these conditions. At present, the most effective strategy appears to be early antiretroviral treatment initiation. No other treatment interventions have been found effective in large-scale clinical trials, and no adjunctive treatment is currently recommended in international HIV treatment guidelines. This article reviews the role of systemic immune activation in the immunopathogenesis of HIV infection, its causes and the clinical implications linked to immunosenescence in adults, and the therapeutic interventions that have been investigated.
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Affiliation(s)
- T. Sokoya
- Department of Immunology, Faculty of Health Sciences, Institute for Cellular and Molecular Medicine, University of Pretoria, Pretoria 0001, South Africa
| | - H. C. Steel
- Department of Immunology, Faculty of Health Sciences, Institute for Cellular and Molecular Medicine, University of Pretoria, Pretoria 0001, South Africa
| | - M. Nieuwoudt
- South African Department of Science and Technology (DST)/National Research Foundation (NRF) Centre of Excellence in Epidemiological Modelling and Analysis (SACEMA), Stellenbosch University, Stellenbosch 7600, South Africa
| | - T. M. Rossouw
- Department of Immunology, Faculty of Health Sciences, Institute for Cellular and Molecular Medicine, University of Pretoria, Pretoria 0001, South Africa
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