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Guo Y, Tang G, Wang Z, Chu Q, Zhang X, Xu X, Fan Y. Characterization of the gut microbiota in different immunological responses among PLWH. Sci Rep 2025; 15:14311. [PMID: 40275044 PMCID: PMC12022085 DOI: 10.1038/s41598-025-98379-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2024] [Accepted: 04/10/2025] [Indexed: 04/26/2025] Open
Abstract
Despite gut microbial dysbiosis has been demonstrated in people living with HIV (PLWH), the association between gut microbial and inflammatory cytokines in PLWH with different immunoreaction to antiretroviral therapy (ART) is poorly understood. The purpose of this study is to explore between gut microbial and inflammatory cytokines in PLWH with different immunoreaction. 68 PLWH and 27 healthy controls(HCs) in Anhui Province were recruited from December 2021 to March 2022, including 35 immunological responders (IRs) (CD4+T-cell count ≥ 350 cells/µL) and 33 immunological non-responders (INRs) (CD4+T-cell count < 350 cells/µL) without comorbidities. Blood and stool samples were collected from all participants. Blood was used to detect microbial translocation biomarkers and inflammatory cytokines. Luminex Multifactor Detection Technology was performed to quantify plasma microbial translocation biomarkers and inflammation cytokines. Bacterial 16S rDNA sequencing was performed on stool samples. Microbiome sequencing revealed that the relative abundances of Fusobacteria, Actinobacteria, Verrucomicrobiaceae Acidaminococcaceae, Fusobacteriaceae and Megasphaera were greater, whereas Verrucomicrobia, Ruminococcaceae, Megamonas, Faecalibacterium, Roseburia and Dialister were more depleted in the HIV groups than those in the HCs (all P < 0.05). In the INRs group, the relative abundances of Actinomycetales, Micrococcaceae, Actinomyces, Intestinibacter, Rothia were greater (all P < 0.05), whereas Sutterellaceae, Parabacteroides, Veillonella, Butyricimonas resulted less abundant than in the IRs (all P < 0.05). TNF-ɑ are negatively correlated with the abundances of Dialiste (P = 0.022). CD54 are negatively correlated with Dialister and Subdoligranulum (P = 0.011). Recent and baseline CD4+T cells counts are directly proportional to Butyricimonas and Parabacteroides, while are inversely proportional with Veillonella and Rothia (all P < 0.05). Dysbiosis of the gut microbial might be one of the factors leading to the different immunoreaction and therapeutic effects of ART.
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Affiliation(s)
- Yanyan Guo
- Chuzhou Center for Disease Control and Prevention, Chuzhou, 239000, Anhui, China
| | - Gan Tang
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, China
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, Anhui, China
| | - Ziwei Wang
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, China
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, Anhui, China
| | - Qinshu Chu
- Anhui Provincial Center for Disease Control and Prevention, Hefei, 230601, Anhui, China
| | - Xinhong Zhang
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, China
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, Anhui, China
| | - Xuewei Xu
- Chuzhou Center for Disease Control and Prevention, Chuzhou, 239000, Anhui, China.
| | - Yinguang Fan
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, China.
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, Anhui, China.
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Català-Moll F, Paredes R. The rectal microbiome: understanding its role in HIV transmission. Curr Opin HIV AIDS 2025; 20:159-164. [PMID: 39773907 DOI: 10.1097/coh.0000000000000906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2025]
Abstract
PURPOSE OF REVIEW Condomless receptive anal intercourse stands out as the sexual practice with highest risk of HIV-1 infection. Recent studies have suggested that the gut microbiome influences susceptibility to HIV transmission. This review explores recent research on host risk factors, the rectal microbiome composition, local inflammation, and bacteria-derived mediators that may affect HIV transmission. RECENT FINDINGS Constitutive host factors such as rectal mucosal structure and immune cell populations in the rectum contribute to increased susceptibility. Changes in the composition of the rectal microbiota, influenced by sexual practices and HIV infection modulate immune activation and inflammation, impacting HIV susceptibility. Bacteria-derived mediators may further influence immune responses and HIV replication in the rectal mucosa. SUMMARY Understanding the role of the rectal microbiome in HIV transmission has important clinical implications. Targeted interventions that modulate the microbiome may reduce susceptibility to HIV transmission by regulating immune responses and inflammation. Further research into the host-microbiome interactions could lead to novel preventive and therapeutic strategies to mitigate HIV transmission.
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Affiliation(s)
- Francesc Català-Moll
- IrsiCaixa, Badalona
- CIBER of Precision Medicine against Antimicrobial Resistance MePRAM, ISCIII
| | - Roger Paredes
- IrsiCaixa, Badalona
- CIBER of Precision Medicine against Antimicrobial Resistance MePRAM, ISCIII
- CIBER of Persistent COVID REiCOP
- CIBER of Infectious Diseases CIBERINFEC, ISCIII, Madrid
- Universitat Autònoma de Barcelona (UAB), Barcelona
- Universitat de Vic-Universitat Central de Catalunya (UVic-UCC), Vic, Spain
- Center for Global Health and Diseases, Department of Pathology, Case Western. Reserve University, Cleveland, Ohio, USA
- Fundació Lluita contra les Infeccions
- Department of Infectious Diseases, Hospital Universitari Germans Trias i Pujol, Badalona, Spain
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3
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Marín-Sánchez N, Paredes R, Borgognone A. Exploring potential associations between the human microbiota and reservoir of latent HIV. Retrovirology 2024; 21:21. [PMID: 39614246 PMCID: PMC11605983 DOI: 10.1186/s12977-024-00655-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2024] [Accepted: 11/20/2024] [Indexed: 12/01/2024] Open
Abstract
BACKGROUND The rapid establishment and persistence of latent HIV-1 reservoirs is one of the main obstacles towards an HIV cure. While antiretroviral therapy supresses viral replication, it does not eradicate the latent reservoir of HIV-1-infected cells. Recent evidence suggests that the human microbiome, particularly the gut microbiome, may have the potential to modulate the HIV-1 reservoir. However, literature is limited and the exact mechanisms underlying the role of the microbiome in HIV immunity and potential regulation of the viral reservoir remain poorly understood. RESULTS Here, we review updated knowledge on the associations between the human microbiome and HIV reservoir across different anatomical sites, including the gut, the lungs and blood. We provide an overview of the predominant taxa associated with prominent microbiome changes in the context of HIV infection. Based on the current evidence, we summarize the main study findings, with specific focus on consistent bacterial and related byproduct associations. Specifically, we address the contribution of immune activation and inflammatory signatures on HIV-1 persistence. Furthermore, we discuss possible scenarios by which bacterial-associated inflammatory mediators, related metabolites and host immune signatures may modulate the HIV reservoir size. Finally, we speculate on potential implications of microbiome-based therapeutics for future HIV-1 cure strategies, highlighting challenges and limitations inherent in this research field. CONCLUSIONS Despite recent advances, this review underscores the need for further research to deepen the understanding of the complex interplay between the human microbiome and HIV reservoir. Further integrative multi-omics assessments and functional studies are crucial to test the outlined hypothesis and to identify potential therapeutic targets ultimately able to achieve an effective cure for HIV.
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Affiliation(s)
- Nel Marín-Sánchez
- IrsiCaixa, Badalona, Catalonia, Spain
- Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Roger Paredes
- IrsiCaixa, Badalona, Catalonia, Spain.
- Department of Infectious Diseases, Hospital Germans Trias i Pujol, Badalona, Catalonia, Spain.
- Department of Pathology, Center for Global Health and Diseases, Case Western Reserve University School of Medicine, Cleveland, OH, USA.
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Boukadida C, Peralta-Prado A, Chávez-Torres M, Romero-Mora K, Rincon-Rubio A, Ávila-Ríos S, Garrido-Rodríguez D, Reyes-Terán G, Pinto-Cardoso S. Alterations of the gut microbiome in HIV infection highlight human anelloviruses as potential predictors of immune recovery. MICROBIOME 2024; 12:204. [PMID: 39420423 PMCID: PMC11483978 DOI: 10.1186/s40168-024-01925-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2024] [Accepted: 09/03/2024] [Indexed: 10/19/2024]
Abstract
BACKGROUND HIV-1 infection is characterized by a massive depletion of mucosal CD4 T cells that triggers a cascade of events ultimately linking gut microbial dysbiosis to HIV-1 disease progression and pathogenesis. The association between HIV infection and the enteric virome composition is less characterized, although viruses are an essential component of the gut ecosystem. Here, we performed a cross-sectional analysis of the fecal viral (eukaryotic viruses and bacteriophages) and bacterial microbiome in people with HIV (PWH) and in HIV-negative individuals. To gain further insight into the association between the gut microbiome composition, HIV-associated immunodeficiency, and immune recovery, we carried out a longitudinal study including 14 PWH who initiated antiretroviral therapy (ART) and were followed for 24 months with samplings performed at baseline (before ART) and at 2, 6, 12, and 24 months post-ART initiation. RESULTS Our data revealed a striking expansion in the abundance and prevalence of several human virus genomic sequences (Anelloviridae, Adenoviridae, and Papillomaviridae) in stool samples of PWH with severe immunodeficiency (CD4 < 200). We also noted a decreased abundance of sequences belonging to two plant viruses from the Tobamovirus genus, a reduction in bacterial alpha diversity, and a decrease in Inoviridae bacteriophage sequences. Short-term ART (24 months) was linked to a significant decrease in human Anelloviridae sequences. Remarkably, the detection of Anellovirus sequences at baseline independently predicted poor immune recovery, as did low CD4 T cell counts. The bacterial and bacteriophage populations were unique to each PWH with individualized trajectories; we found no discernable pattern of clustering after 24 months on ART. CONCLUSION Advanced HIV-1 infection was associated with marked alterations in the virome composition, in particular a remarkable expansion of human anelloviruses, with a gradual restoration after ART initiation. In addition to CD4 T cell counts, anellovirus sequence detection might be useful to predict and monitor immune recovery. This study confirms data on the bacteriome and expands our knowledge on the viral component of the gut microbiome in HIV-1 infection. Video Abstract.
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Affiliation(s)
- Celia Boukadida
- Departamento del Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Ciudad de México, México
| | - Amy Peralta-Prado
- Departamento del Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Ciudad de México, México
| | - Monserrat Chávez-Torres
- Departamento del Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Ciudad de México, México
| | - Karla Romero-Mora
- Departamento del Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Ciudad de México, México
| | - Alma Rincon-Rubio
- Departamento del Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Ciudad de México, México
| | - Santiago Ávila-Ríos
- Departamento del Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Ciudad de México, México
| | - Daniela Garrido-Rodríguez
- Departamento del Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Ciudad de México, México
| | - Gustavo Reyes-Terán
- Departamento del Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Ciudad de México, México
- Comisión Coordinadora de Institutos Nacionales de Salud y Hospitales de Alta Especialidad, Ciudad de México, México
| | - Sandra Pinto-Cardoso
- Departamento del Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Ciudad de México, México.
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Flynn JK, Ortiz AM, Vujkovic-Cvijin I, Welles HC, Simpson J, Castello Casta FM, Yee DS, Rahmberg AR, Brooks KL, De Leon M, Knodel S, Birse K, Noel-Romas L, Deewan A, Belkaid Y, Burgener A, Brenchley JM. Translocating bacteria in SIV infection are not stochastic and preferentially express cytosine methyltransferases. Mucosal Immunol 2024; 17:1089-1101. [PMID: 39089468 PMCID: PMC11471372 DOI: 10.1016/j.mucimm.2024.07.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 07/17/2024] [Accepted: 07/24/2024] [Indexed: 08/04/2024]
Abstract
Microbial translocation is a significant contributor to chronic inflammation in people living with HIV (PLWH) and is associated with increased mortality and morbidity in individuals treated for long periods with antiretrovirals. The use of therapeutics to treat microbial translocation has yielded mixed effects, in part, because the species and mechanisms contributing to translocation in HIV remain incompletely characterized. To characterize translocating bacteria, we cultured translocators from chronically SIV-infected rhesus macaques. Proteomic profiling of these bacteria identified cytosine-specific methyltransferases as a common feature and therefore, a potential driver of translocation. Treatment of translocating bacteria with the cytosine methyltransferase inhibitor decitabine significantly impaired growth for several species in vitro. In rhesus macaques, oral treatment with decitabine led to some transient decreases in translocator taxa in the gut microbiome. These data provide mechanistic insight into bacterial translocation in lentiviral infection and explore a novel therapeutic intervention that may improve the prognosis of PLWH.
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Affiliation(s)
- Jacob K Flynn
- Barrier Immunity Section, Laboratory of Viral Diseases, NIAID, NIH, Bethesda, MD, USA
| | - Alexandra M Ortiz
- Barrier Immunity Section, Laboratory of Viral Diseases, NIAID, NIH, Bethesda, MD, USA
| | - Ivan Vujkovic-Cvijin
- Metaorganism Immunity Section, Laboratory of Host Immunity and Microbiome, NIAID, NIH, Bethesda, MD, USA
| | - Hugh C Welles
- Metaorganism Immunity Section, Laboratory of Host Immunity and Microbiome, NIAID, NIH, Bethesda, MD, USA
| | - Jennifer Simpson
- Barrier Immunity Section, Laboratory of Viral Diseases, NIAID, NIH, Bethesda, MD, USA
| | | | - Debra S Yee
- Barrier Immunity Section, Laboratory of Viral Diseases, NIAID, NIH, Bethesda, MD, USA
| | - Andrew R Rahmberg
- Barrier Immunity Section, Laboratory of Viral Diseases, NIAID, NIH, Bethesda, MD, USA
| | - Kelsie L Brooks
- Barrier Immunity Section, Laboratory of Viral Diseases, NIAID, NIH, Bethesda, MD, USA
| | - Marlon De Leon
- Center for Global Health and Diseases, Case Western Reserve University, Cleveland, OH, USA; Department of Obstetrics & Gynecology, University of Manitoba, Winnipeg, MB, Canada
| | - Samantha Knodel
- Center for Global Health and Diseases, Case Western Reserve University, Cleveland, OH, USA; Department of Obstetrics & Gynecology, University of Manitoba, Winnipeg, MB, Canada
| | - Kenzie Birse
- Center for Global Health and Diseases, Case Western Reserve University, Cleveland, OH, USA; Department of Obstetrics & Gynecology, University of Manitoba, Winnipeg, MB, Canada
| | - Laura Noel-Romas
- Center for Global Health and Diseases, Case Western Reserve University, Cleveland, OH, USA; Department of Obstetrics & Gynecology, University of Manitoba, Winnipeg, MB, Canada
| | - Anshu Deewan
- Integrated Data Sciences Section, Research Technologies Branch, NIAID, NIH, Bethesda, MD, USA
| | - Yasmine Belkaid
- Metaorganism Immunity Section, Laboratory of Host Immunity and Microbiome, NIAID, NIH, Bethesda, MD, USA; Metaorganism Unit, Immunology Department, Institut Pasteur, 75724 Paris, France
| | - Adam Burgener
- Center for Global Health and Diseases, Case Western Reserve University, Cleveland, OH, USA; Department of Obstetrics & Gynecology, University of Manitoba, Winnipeg, MB, Canada; Department of Medicine Solna, Karolinksa Institutet, Stockholm, Sweden
| | - Jason M Brenchley
- Barrier Immunity Section, Laboratory of Viral Diseases, NIAID, NIH, Bethesda, MD, USA.
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6
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Hu J, Hu J, Han D. Causal relationships between gut microbiota, plasma metabolites, and HIV infection: insights from Mendelian randomization and mediation analysis. Virol J 2024; 21:204. [PMID: 39215321 PMCID: PMC11365174 DOI: 10.1186/s12985-024-02480-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Accepted: 08/21/2024] [Indexed: 09/04/2024] Open
Abstract
OBJECTIVE Gut dysbiosis and metabolic abnormalities have been implicated in HIV infection. However, the exact causal relationships among the gut microbiota, metabolites, and HIV infection remain poorly understood. Our study involving Mendelian randomization (MR) and mediation analysis aims to unveil these causalities. METHODS Genetic instrumental variables for the gut microbiota were retrieved from MiBioGen consortium (n = 18,340). Metabolism-related genetic variants were sourced from the CLSA cohort (n = 8299). GWAS summary statistics for symptomatic HIV infection were derived from the FinnGen study (n = 309,154), and the UK Biobank (n = 208,808). We performed the bidirectional two-sample MR to assess causalities with the inverse-variance weighted (IVW) method as the primary analysis. Moreover, we executed a mediation analysis using two-step MR methods. RESULTS Compared to the causal effects of HIV infection on gut microbiota (or metabolites), those of gut microbiota (or plasma metabolites) on the risk of HIV infection were more substantial. Phylum Proteobacteria (OR: 2.114, 95% CI 1.042-4.288, P = 0.038), and genus Ruminococcaceae UCG013 (OR: 2.127, 95% CI 1.080-4.191, P = 0.029) exhibited an adverse causal effect on HIV infection, whereas genus Clostridium sensu stricto 1(OR: 0.491, 95% CI 0.252-0.956, P = 0.036) and family Erysipelotrichaceae (OR: 0.399, 95% CI 0.193-0.827, P = 0.013) acted as significant protective factors for HIV. The salicyluric glucuronide level (OR = 2.233, 95% CI 1.120-4.453, P = 0.023) exhibited a considerably adverse causal effect on HIV infection. Conversely, the salicylate-to-citrate ratio (OR: 0.417, 95% CI 0.253-0.688, P = 0.001) was identified as a protective factor for HIV. We identified only one bidirectional causality between 1-palmitoyl-GPI and HIV infection. Mechanistically, genus Haemophilus mediated the causal effects of three phospholipids on HIV infection risk: 1-palmitoyl-GPI (mediation proportion = 33.7%, P = 0.018), 1-palmitoyl-2-arachidonoyl-GPI (mediation proportion = 18.3%, P = 0.019), and 1-linoleoyl-2-linolenoyl-GPC (mediation proportion = 20.3%, P = 0.0216). Additionally, 5-Dodecenoylcarnitine (C12:1) mediated the causal effect of genus Sellimonas on the risk of HIV infection (mediation proportion = 13.7%, P = 0.0348). CONCLUSION Our study revealed that gut microbiota and metabolites causally influence HIV infection risk more substantially than the reverse. We identified the bidirectional causality between 1-palmitoyl-GPI (16:0) and HIV infection, and elucidated four mediation relationships. These findings provide genetic insights into prediction, prevention, and personalized medicine of HIV infection.
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Affiliation(s)
- Jiapeng Hu
- Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang, China
| | - Jinxin Hu
- Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang, China
- Medical Research Center, Liaoning Key Laboratory of Research and Application of Animal Models for Environmental and Metabolic Diseases, Shengjing Hospital of China Medical University, Shenyang, China
| | - Dan Han
- Department of Neonatology, The First Hospital of China Medical University, Shenyang, China.
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Bar Ziv O, Cahn A, Jansen T, Istomin V, Kedem E, Olshtain-Pops K, Israel S, Oster Y, Orenbuch-Harroch E, Korem M, Strahilevitz J, Levy I, Valdés-Mas R, Ivanova V, Elinav E, Shahar E, Elinav H. Diagnosis and Risk Factors of Prediabetes and Diabetes in People Living With Human Immunodeficiency Virus: Evaluation of Clinical and Microbiome Parameters. J Infect Dis 2024; 230:411-420. [PMID: 38557867 DOI: 10.1093/infdis/jiae167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 03/08/2024] [Accepted: 03/28/2024] [Indexed: 04/04/2024] Open
Abstract
Diabetes mellitus (DM) is more common among people living with human immunodeficiency virus (PLWH) compared with healthy individuals. In a prospective multicenter study (N = 248), we identified normoglycemic (48.7%), prediabetic (44.4%), and diabetic (6.9%) PLWH. Glycosylated hemoglobin (HbA1c) and fasting blood glucose (FBG) sensitivity in defining dysglycemia was 96.8%, while addition of oral glucose tolerance test led to reclassification of only 4 patients. Inclusion of 93 additional PLWH with known DM enabled identification of multiple independent predictors of dysglycemia or diabetes: older age, higher body mass index, Ethiopian origin, HIV duration, lower integrase inhibitor exposure, and advanced disease at diagnosis. Shotgun metagenomic microbiome analysis revealed 4 species that were significantly expanded with hyperglycemia/hyperinsulinemia, and 2 species that were differentially more prevalent in prediabetic/diabetic PLWH. Collectively, we uncover multiple potential host and microbiome predictors of altered glycemic status in PLWH, while demonstrating that FBG and HbA1c likely suffice for diabetes screening. These potential diabetic predictors merit future prospective validation.
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Affiliation(s)
- Omer Bar Ziv
- Department of Military Medicine and "Zameret," Faculty of Medicine, Hebrew University, and Israel and Medical Corps, Israel Defense Forces
| | - Avivit Cahn
- Diabetes Unit, Department of Endocrinology and Metabolism, Hadassah Medical Center
- Faculty of Medicine, Hebrew University, Jerusalem
| | - Tallulah Jansen
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot
| | | | - Eynat Kedem
- Allergy, Immunology and AIDS Unit, Rambam Medical Center, Haifa
| | - Karen Olshtain-Pops
- Faculty of Medicine, Hebrew University, Jerusalem
- Hadassah AIDS Center, Department of Clinical Microbiology and Infectious Diseases, Hadassah Medical Center, Jerusalem
| | - Sarah Israel
- Faculty of Medicine, Hebrew University, Jerusalem
- Hadassah AIDS Center, Department of Clinical Microbiology and Infectious Diseases, Hadassah Medical Center, Jerusalem
| | - Yonatan Oster
- Faculty of Medicine, Hebrew University, Jerusalem
- Hadassah AIDS Center, Department of Clinical Microbiology and Infectious Diseases, Hadassah Medical Center, Jerusalem
| | - Efrat Orenbuch-Harroch
- Faculty of Medicine, Hebrew University, Jerusalem
- Hadassah AIDS Center, Department of Clinical Microbiology and Infectious Diseases, Hadassah Medical Center, Jerusalem
| | - Maya Korem
- Faculty of Medicine, Hebrew University, Jerusalem
- Hadassah AIDS Center, Department of Clinical Microbiology and Infectious Diseases, Hadassah Medical Center, Jerusalem
| | - Jacob Strahilevitz
- Faculty of Medicine, Hebrew University, Jerusalem
- Hadassah AIDS Center, Department of Clinical Microbiology and Infectious Diseases, Hadassah Medical Center, Jerusalem
| | - Itzchak Levy
- Infectious Diseases Unit, Sheba Medical Center, Tel Hashomer, Israel
| | - Rafael Valdés-Mas
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot
| | - Valeria Ivanova
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot
| | - Eran Elinav
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot
- Division of Microbiome and Cancer, German Cancer Research Center, Heidelberg, Germany
| | - Eduardo Shahar
- Allergy, Immunology and AIDS Unit, Rambam Medical Center, Haifa
| | - Hila Elinav
- Faculty of Medicine, Hebrew University, Jerusalem
- Hadassah AIDS Center, Department of Clinical Microbiology and Infectious Diseases, Hadassah Medical Center, Jerusalem
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8
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Brenchley JM, Serrano-Villar S. From dysbiosis to defense: harnessing the gut microbiome in HIV/SIV therapy. MICROBIOME 2024; 12:113. [PMID: 38907315 PMCID: PMC11193286 DOI: 10.1186/s40168-024-01825-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Accepted: 04/26/2024] [Indexed: 06/23/2024]
Abstract
BACKGROUND Although the microbiota has been extensively associated with HIV pathogenesis, the majority of studies, particularly those using omics techniques, are largely correlative and serve primarily as a basis for hypothesis generation. Furthermore, most have focused on characterizing the taxonomic composition of the bacterial component, often overlooking other levels of the microbiome. The intricate mechanisms by which the microbiota influences immune responses to HIV are still poorly understood. Interventional studies on gut microbiota provide a powerful tool to test the hypothesis of whether we can harness the microbiota to improve health outcomes in people with HIV. RESULTS Here, we review the multifaceted role of the gut microbiome in HIV/SIV disease progression and its potential as a therapeutic target. We explore the complex interplay between gut microbial dysbiosis and systemic inflammation, highlighting the potential for microbiome-based therapeutics to open new avenues in HIV management. These include exploring the efficacy of probiotics, prebiotics, fecal microbiota transplantation, and targeted dietary modifications. We also address the challenges inherent in this research area, such as the difficulty in inducing long-lasting microbiome alterations and the complexities of study designs, including variations in probiotic strains, donor selection for FMT, antibiotic conditioning regimens, and the hurdles in translating findings into clinical practice. Finally, we speculate on future directions for this rapidly evolving field, emphasizing the need for a more granular understanding of microbiome-immune interactions, the development of personalized microbiome-based therapies, and the application of novel technologies to identify potential therapeutic agents. CONCLUSIONS Our review underscores the importance of the gut microbiome in HIV/SIV disease and its potential as a target for innovative therapeutic strategies.
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Affiliation(s)
- Jason M Brenchley
- Barrier Immunity Section, Lab of Viral Diseases, NIAID, NIH, Bethesda, MA, USA.
| | - Sergio Serrano-Villar
- Department of Infectious Diseases, Hospital Universitario Ramon y Cajal, IRYCIS and CIBERInfec, Madrid, Spain.
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9
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Trøseid M, Nielsen SD, Vujkovic-Cvijin I. Gut microbiome and cardiometabolic comorbidities in people living with HIV. MICROBIOME 2024; 12:106. [PMID: 38877521 PMCID: PMC11177534 DOI: 10.1186/s40168-024-01815-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 04/12/2024] [Indexed: 06/16/2024]
Abstract
BACKGROUND Despite modern antiretroviral therapy (ART), people living with HIV (PLWH) have increased relative risk of inflammatory-driven comorbidities, including cardiovascular disease (CVD). The gut microbiome could be one of several driving factors, along with traditional risk factors and HIV-related risk factors such as coinfections, ART toxicity, and past immunodeficiency. RESULTS PLWH have an altered gut microbiome, even after adjustment for known confounding factors including sexual preference. The HIV-related microbiome has been associated with cardiometabolic comorbidities, and shares features with CVD-related microbiota profiles, in particular reduced capacity for short-chain fatty acid (SCFA) generation. Substantial inter-individual variation has so far been an obstacle for applying microbiota profiles for risk stratification. This review covers updated knowledge and recent advances in our understanding of the gut microbiome and comorbidities in PLWH, with specific focus on cardiometabolic comorbidities and inflammation. It covers a comprehensive overview of HIV-related and comorbidity-related dysbiosis, microbial translocation, and microbiota-derived metabolites. It also contains recent data from studies in PLWH on circulating metabolites related to comorbidities and underlying gut microbiota alterations, including circulating levels of the SCFA propionate, the histidine-analogue imidazole propionate, and the protective metabolite indole-3-propionic acid. CONCLUSIONS Despite recent advances, the gut microbiome and related metabolites are not yet established as biomarkers or therapeutic targets. The review gives directions for future research needed to advance the field into clinical practice, including promises and pitfalls for precision medicine. Video Abstract.
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Affiliation(s)
- Marius Trøseid
- Research Institute of Internal Medicine, Oslo University Hospital Rikshospitalet, Oslo, Norway.
- Section for Clinical Immunology and Infectious Diseases, Oslo University Hospital Rikshospitalet, Oslo, Norway.
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway.
| | - Susanne Dam Nielsen
- Department of Infectious Diseases, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, Blegdamsvej 3B, Copenhagen, 2200, Denmark
- Department of Surgical Gastroenterology and Transplantation, Rigshospitalet, University of Copenhagen, Blegdamsvej 9, Copenhagen Oe, 2100, Denmark
| | - Ivan Vujkovic-Cvijin
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Karsh Division of Gastroenterology & Hepatology, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- F. Widjaja Inflammatory Bowel Disease Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
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10
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Rubio Garcia E, Casadellà M, Parera M, Vila J, Paredes R, Noguera-Julian M. Gut resistome linked to sexual preference and HIV infection. BMC Microbiol 2024; 24:201. [PMID: 38851693 PMCID: PMC11162057 DOI: 10.1186/s12866-024-03335-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 05/16/2024] [Indexed: 06/10/2024] Open
Abstract
BACKGROUND People living with HIV (PLWH) are at increased risk of acquisition of multidrug resistant organisms due to higher rates of predisposing factors. The gut microbiome is the main reservoir of the collection of antimicrobial resistance determinants known as the gut resistome. In PLWH, changes in gut microbiome have been linked to immune activation and HIV-1 associated complications. Specifically, gut dysbiosis defined by low microbial gene richness has been linked to low Nadir CD4 + T-cell counts. Additionally, sexual preference has been shown to strongly influence gut microbiome composition in PLWH resulting in different Prevotella or Bacteroides enriched enterotypes, in MSM (men-who-have-sex-with-men) or no-MSM, respectively. To date, little is known about gut resistome composition in PLWH due to the scarcity of studies using shotgun metagenomics. The present study aimed to detect associations between different microbiome features linked to HIV-1 infection and gut resistome composition. RESULTS Using shotgun metagenomics we characterized the gut resistome composition of 129 HIV-1 infected subjects showing different HIV clinical profiles and 27 HIV-1 negative controls from a cross-sectional observational study conducted in Barcelona, Spain. Most no-MSM showed a Bacteroides-enriched enterotype and low microbial gene richness microbiomes. We did not identify differences in resistome diversity and composition according to HIV-1 infection or immune status. However, gut resistome was more diverse in MSM group, Prevotella-enriched enterotype and gut micorbiomes with high microbial gene richness compared to no-MSM group, Bacteroides-enriched enterotype and gut microbiomes with low microbial gene richness. Additionally, gut resistome beta-diversity was different according to the defined groups and we identified a set of differentially abundant antimicrobial resistance determinants based on the established categories. CONCLUSIONS Our findings reveal a significant correlation between gut resistome composition and various host variables commonly associated with gut microbiome, including microbiome enterotype, microbial gene richness, and sexual preference. These host variables have been previously linked to immune activation and lower Nadir CD4 + T-Cell counts, which are prognostic factors of HIV-related comorbidities. This study provides new insights into the relationship between antibiotic resistance and clinical characteristics of PLWH.
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Affiliation(s)
- Elisa Rubio Garcia
- Department of Microbiology, CDB, Hospital Clinic, University of Barcelona, Barcelona, Spain.
- Molecuar Core Facilty, Hospital Clínic de Barcelona, Barcelona, Spain.
- ISGlobal Barcelona Institute for Global Health, Barcelona, Spain.
| | | | | | - Jordi Vila
- Department of Microbiology, CDB, Hospital Clinic, University of Barcelona, Barcelona, Spain
- ISGlobal Barcelona Institute for Global Health, Barcelona, Spain
- Infectious Disease Networking Biomedical Research Center (CIBERINFEC), Carlos III Health Institute, Madrid, Spain
| | - Roger Paredes
- IrsiCaixa, Ctra de Canyet S/N, 08916, Badalona, Spain
- Universitat de Vic-Universitat Central de Catalunya, Vic, Spain
- Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
- Department of Infectious Diseasest &, Lluita Contra La SIDA Foundation, Hospital Universitari Germans Trias I Pujol, Badalona, Spain
- Infectious Disease Networking Biomedical Research Center (CIBERINFEC), Carlos III Health Institute, Madrid, Spain
| | - Marc Noguera-Julian
- IrsiCaixa, Ctra de Canyet S/N, 08916, Badalona, Spain
- Universitat de Vic-Universitat Central de Catalunya, Vic, Spain
- Infectious Disease Networking Biomedical Research Center (CIBERINFEC), Carlos III Health Institute, Madrid, Spain
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11
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Runtuwene LR, Parbie PK, Mizutani T, Ishizaka A, Matsuoka S, Abana CZY, Kushitor D, Bonney EY, Ofori SB, Kiyono H, Ishikawa K, Ampofo WK, Matano T. Longitudinal analysis of microbiome composition in Ghanaians living with HIV-1. Front Microbiol 2024; 15:1359402. [PMID: 38426062 PMCID: PMC10902004 DOI: 10.3389/fmicb.2024.1359402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 01/18/2024] [Indexed: 03/02/2024] Open
Abstract
Human immunodeficiency virus (HIV) 1 infection is known to cause gut microbiota dysbiosis. Among the causes is the direct infection of HIV-1 in gut-resident CD4+ T cells, causing a cascade of phenomena resulting in the instability of the gut mucosa. The effect of HIV infection on gut microbiome dysbiosis remains unresolved despite antiretroviral therapy. Here, we show the results of a longitudinal study of microbiome analysis of people living with HIV (PLWH). We contrasted the diversity and composition of the microbiome of patients with HIV at the first and second time points (baseline_case and six months later follow-up_case, respectively) with those of healthy individuals (baseline_control). We found that despite low diversity indices in the follow-up_case, the abundance of some genera was recovered but not completely, similar to baseline_control. Some genera were consistently in high abundance in PLWH. Furthermore, we found that the CD4+ T-cell count and soluble CD14 level were significantly related to high and low diversity indices, respectively. We also found that the abundance of some genera was highly correlated with clinical features, especially with antiretroviral duration. This includes genera known to be correlated with worse HIV-1 progression (Achromobacter and Stenotrophomonas) and a genus associated with gut protection (Akkermansia). The fact that a protector of the gut and genera linked to a worse progression of HIV-1 are both enriched may signify that despite the improvement of clinical features, the gut mucosa remains compromised.
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Affiliation(s)
- Lucky Ronald Runtuwene
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
| | - Prince Kofi Parbie
- Department of Virology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
- Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO, United States
| | - Taketoshi Mizutani
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
- The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Aya Ishizaka
- The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Saori Matsuoka
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Christopher Zaab-Yen Abana
- Department of Virology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Dennis Kushitor
- Department of Virology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Evelyn Yayra Bonney
- Department of Virology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Sampson Badu Ofori
- Department of Internal Medicine, Eastern Regional Hospital Koforidua, Ghana Health Service, Koforidua, Ghana
| | - Hiroshi Kiyono
- The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Institute for Global Prominent Research, Graduate School of Medicine, Chiba University, Chiba, Japan
- Department of Medicine, Chiba University-University of California San Diego Center for Mucosal Immunology, Allergy and Vaccines (cMAV), University of California San Diego, San Diego, CA, United States
| | - Koichi Ishikawa
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - William Kwabena Ampofo
- Department of Virology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Tetsuro Matano
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan
- The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
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12
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Rubio-Garcia E, Ferrando N, Martin N, Ballesté-Delpierre C, Miró JM, Paredes R, Casals-Pascual C, Vila J. In vitro antibacterial activity of antiretroviral drugs on key commensal bacteria from the human microbiota. Front Cell Infect Microbiol 2024; 13:1306430. [PMID: 38259963 PMCID: PMC10801051 DOI: 10.3389/fcimb.2023.1306430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 12/11/2023] [Indexed: 01/24/2024] Open
Abstract
Introduction Antiretroviral therapy has improved life expectancy in HIV-infected patients. However, people living with HIV under antiretroviral therapy are at higher risks of developing chronic complications and acquiring multidrug resistant bacteria than healthy population. These factors have been associated with shifts in gut microbiome composition and immune activation. It is unclear how antiretroviral drugs affect gut microbiota composition, but it has been observed that antiretroviral treatment is not able to fully restore gut health after HIV infection. Additionally, some antiretroviral drugs have shown antibacterial activity suggesting that these drugs could have a direct impact on the human microbiome composition. Methods We determined the in vitro antibacterial activity of 16 antiretroviral drugs against a set of key clinically relevant and human commensal bacterial strains. Results Our results demonstrate that 5 antiretroviral drugs have in vitro antibacterial activity against gut and vaginal human commensal bacteria. Zidovudine has antibacterial activity against Escherichia coli, Klebsiella pneumoniae and Prevotella bivia, abacavir against Gardnerella vaginalis, efavirenz against G. vaginalis and P. bivia and bictegravir against Enterococcus spp. and G. vaginalis. Moreover, we describe for the first time that elvitegravir has antibacterial activity against G. vaginalis and P. bivia and, most importantly, against vancomycin-resistant Enterococcus spp. and methicillin-resistant Staphylococcus aureus strains with MIC values of 4-16 and 4 µg/mL, respectively showing high level of effectiveness against the tested multidrug-resistant bacteria. Discussion Our results underscore that some antiretroviral drugs may influence the human microbiota composition. In addition, we report the potential use of elvitegravir to treat multidrug-resistant Gram-positive bacteria warranting the need of clinical studies to repurpose this antiretroviral drug.
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Affiliation(s)
- Elisa Rubio-Garcia
- Department of Clinical Microbiology, Centre de Diagnòstic Biomèdic (CDB), Hospital Clínic of Barcelona, Barcelona, Spain
- Molecular Core Facility, Centre de Diagnòstic Biomèdic (CDB), Hospital Clínic of Barcelona, Barcelona, Spain
- Departament de Fonaments Clínics, Facultat de Medicina i Ciències de la Salut, Universitat de Barcelona, Barcelona, Spain
- Barcelona Institute for Global Health (ISGlobal), Barcelona, Spain
| | - Núria Ferrando
- Barcelona Institute for Global Health (ISGlobal), Barcelona, Spain
| | - Núria Martin
- Barcelona Institute for Global Health (ISGlobal), Barcelona, Spain
| | - Clara Ballesté-Delpierre
- Barcelona Institute for Global Health (ISGlobal), Barcelona, Spain
- Infectious Disease Networking Biomedical Research Center, Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Jose M. Miró
- Infectious Disease Networking Biomedical Research Center, Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
- Infectious diseases Service. Hospital Clínic-IDIBAPS. University of Barcelona, Barcelona, Spain
| | - Roger Paredes
- Infectious Disease Networking Biomedical Research Center, Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
- Fundació Lluita Contra les Infeccions, Department of Infectious Diseases, Hospital Germans Trias i Pujol, Badalona, Barcelona, Spain
- IrsiCaixa AIDS Research Institute, Badalona, Catalonia, Spain
- Center for Global Health and Diseases, Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH, United States
| | - Climent Casals-Pascual
- Department of Clinical Microbiology, Centre de Diagnòstic Biomèdic (CDB), Hospital Clínic of Barcelona, Barcelona, Spain
- Departament de Fonaments Clínics, Facultat de Medicina i Ciències de la Salut, Universitat de Barcelona, Barcelona, Spain
- Barcelona Institute for Global Health (ISGlobal), Barcelona, Spain
- Infectious Disease Networking Biomedical Research Center, Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Jordi Vila
- Department of Clinical Microbiology, Centre de Diagnòstic Biomèdic (CDB), Hospital Clínic of Barcelona, Barcelona, Spain
- Departament de Fonaments Clínics, Facultat de Medicina i Ciències de la Salut, Universitat de Barcelona, Barcelona, Spain
- Barcelona Institute for Global Health (ISGlobal), Barcelona, Spain
- Infectious Disease Networking Biomedical Research Center, Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
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Hishiya N, Uno K, Nakano A, Konishi M, Higashi S, Eguchi S, Ariyoshi T, Matsumoto A, Oka K, Takahashi M, Suzuki Y, Horiuchi S, Hirai N, Ogawa Y, Ogawa T, Nakano R, Mikasa K, Kasahara K, Yano H. Association between the gut microbiome and organic acid profiles in a Japanese population with HIV infection. J Infect Chemother 2024; 30:58-66. [PMID: 37708940 DOI: 10.1016/j.jiac.2023.09.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 09/04/2023] [Accepted: 09/12/2023] [Indexed: 09/16/2023]
Abstract
INTRODUCTION An increased incidence of metabolic syndrome has been observed in human immunodeficiency virus (HIV)-infected individuals. In contrast, gut dysbiosis is involved in various pathogeneses, including vascular endothelial disorders. Organic acids, including short-chain fatty acids (SCFAs), are essential for maintaining gut homeostasis. Therefore, this study aimed to explore the gut microbiome profile and organic acids in a Japanese population infected with HIV. METHODS Forty-nine patients with HIV infection on combination antiretroviral therapy (cART) were enrolled and divided into the high and low CD4 groups based on a CD4 cutoff of 350 cells/μL. Stool samples were analyzed by 16S ribosomal RNA next-generation sequencing and high-performance liquid chromatography. The association between the gut microbiome, including bacterial taxa and organic acids, was statistically analyzed. RESULTS The fecal microbial community composition was significantly different between HIV patients with CD4 counts above and below 350 cells/μL. The relative abundance of Roseburia, Prevotella, Prevotella_9, and [Clostridium]_methylpentosum_group were significantly enriched in the high CD4 group. Fecal succinic acid tended to be more abundant in the low CD4 group, and acetic, propionic, and butyric acids tended to be more abundant in the high CD4 group. Roseburia was positively correlated with butyric acid levels. Prevotella_9 and Prevotella were negatively correlated with succinic acid levels and positively correlated with acetic and propionic acid levels. CONCLUSIONS This study showed intestinal dysbiosis bordering on a CD4 count of 350 in patients with HIV infection undergoing cART. These findings might help in understanding intestinal damage and systemic inflammation in HIV infection.
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Affiliation(s)
- Naokuni Hishiya
- Department of Microbiology and Infectious Diseases, Nara Medical University, 840 Shijo-cho, Kashihara, Nara, 634-8521, Japan; Department of Infectious Diseases, Nara City Hospital, 1-50-1 Higashikidera-cho, Nara-Shi, Nara, 630-8305, Japan
| | - Kenji Uno
- Department of Infectious Diseases, Minami-Nara General Medical Center, 8-1 Fukugami, Oyodo-Cho, Yoshino-Gun, Nara, 638-8551, Japan
| | - Akiyo Nakano
- Department of Microbiology and Infectious Diseases, Nara Medical University, 840 Shijo-cho, Kashihara, Nara, 634-8521, Japan.
| | - Mitsuru Konishi
- Center for Health Control, Nara Medical University, 840 Shijo-cho, Kashihara, Nara, 634-8521, Japan; Center for Infectious Diseases, Nara Medical University, 840 Shijo-cho, Kashihara, Nara, 634-8521, Japan
| | - Seiya Higashi
- R&D Division, Miyarisan Pharmaceutical Co., Ltd., 2-22-9 Toro-Cho, Kita-Ku, Saitama-Shi, Saitama, 331-0804, Japan
| | - Shuhei Eguchi
- R&D Division, Miyarisan Pharmaceutical Co., Ltd., 2-22-9 Toro-Cho, Kita-Ku, Saitama-Shi, Saitama, 331-0804, Japan
| | - Tadashi Ariyoshi
- R&D Division, Miyarisan Pharmaceutical Co., Ltd., 2-22-9 Toro-Cho, Kita-Ku, Saitama-Shi, Saitama, 331-0804, Japan
| | - Asami Matsumoto
- R&D Division, Miyarisan Pharmaceutical Co., Ltd., 2-22-9 Toro-Cho, Kita-Ku, Saitama-Shi, Saitama, 331-0804, Japan
| | - Kentaro Oka
- R&D Division, Miyarisan Pharmaceutical Co., Ltd., 2-22-9 Toro-Cho, Kita-Ku, Saitama-Shi, Saitama, 331-0804, Japan
| | - Motomichi Takahashi
- R&D Division, Miyarisan Pharmaceutical Co., Ltd., 2-22-9 Toro-Cho, Kita-Ku, Saitama-Shi, Saitama, 331-0804, Japan
| | - Yuki Suzuki
- Department of Microbiology and Infectious Diseases, Nara Medical University, 840 Shijo-cho, Kashihara, Nara, 634-8521, Japan
| | - Saori Horiuchi
- Department of Microbiology and Infectious Diseases, Nara Medical University, 840 Shijo-cho, Kashihara, Nara, 634-8521, Japan
| | - Nobuyasu Hirai
- Department of Microbiology and Infectious Diseases, Nara Medical University, 840 Shijo-cho, Kashihara, Nara, 634-8521, Japan; Department of Gastroenterology, Seichokai Fuchu Hospital, 1-10-17 Hiko-Cho, Izumi, Osaka, 594-0076, Japan
| | - Yoshihiko Ogawa
- Department of Infectious Diseases, Sakai City Medical Center, 1-1-1 Ebaraji-Cho, Nishi-Ku, Sakai, Osaka, 593-8304, Japan
| | - Taku Ogawa
- Department of Microbiology and Infection Control, Osaka Medical and Pharmaceutical University, 2-7 Daigaku-machi, Takatsuki, Osaka, 569-8686, Japan
| | - Ryuichi Nakano
- Department of Microbiology and Infectious Diseases, Nara Medical University, 840 Shijo-cho, Kashihara, Nara, 634-8521, Japan
| | - Keiichi Mikasa
- Center for Infectious Diseases, Nara Medical University, 840 Shijo-cho, Kashihara, Nara, 634-8521, Japan; Department of Internal Medicine, Nara Koseikai Hospital, 769-3 Shigi-cho, Yamatokoriyama, Nara, 639-1039, Japan
| | - Kei Kasahara
- Center for Infectious Diseases, Nara Medical University, 840 Shijo-cho, Kashihara, Nara, 634-8521, Japan
| | - Hisakazu Yano
- Department of Microbiology and Infectious Diseases, Nara Medical University, 840 Shijo-cho, Kashihara, Nara, 634-8521, Japan
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Anzà S, Schneider D, Daniel R, Heistermann M, Sangmaneedet S, Ostner J, Schülke O. The long-term gut bacterial signature of a wild primate is associated with a timing effect of pre- and postnatal maternal glucocorticoid levels. MICROBIOME 2023; 11:165. [PMID: 37501202 PMCID: PMC10373267 DOI: 10.1186/s40168-023-01596-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 06/11/2023] [Indexed: 07/29/2023]
Abstract
BACKGROUND During development, elevated levels of maternal glucocorticoids (GCs) can have detrimental effects on offspring morphology, cognition, and behavior as well as physiology and metabolism. Depending on the timing of exposure, such effects may vary in strength or even reverse in direction, may alleviate with age, or may concern more stable and long-term programming of phenotypic traits. Maternal effects on gut bacterial diversity, composition, and function, and the persistence of such effects into adulthood of long-lived model species in the natural habitats remain underexplored. RESULTS In a cross-sectional sample of infant, juvenile, and adult Assamese macaques, the timing of exposure to elevated maternal GCs during ontogeny was associated with the gut bacterial community of the offspring. Specifically, naturally varying maternal GC levels during early but not late gestation or lactation were associated with reduced bacterial richness. The overall effect of maternal GCs during early gestation on the gut bacterial composition and function exacerbated with offspring age and was 10 times stronger than the effect associated with exposure during late prenatal or postnatal periods. Instead, variation in maternal GCs during the late prenatal or postnatal period had less pronounced or less stable statistical effects and therefore a weaker effect on the entire bacterial community composition, particularly in adult individuals. Finally, higher early prenatal GCs were associated with an increase in the relative abundance of several potential pro-inflammatory bacteria and a decrease in the abundance of Bifidobacterium and other anti-inflammatory taxa, an effect that exacerbated with age. CONCLUSIONS In primates, the gut microbiota can be shaped by developmental effects with strong timing effects on plasticity and potentially detrimental consequences for adult health. Together with results on other macaque species, this study suggests potential detrimental developmental effects similar to rapid inflammaging, suggesting that prenatal exposure to high maternal GC concentrations is a common cause underlying both phenomena. Our findings await confirmation by metagenomic functional and causal analyses and by longitudinal studies of long-lived, ecologically flexible primates in their natural habitat, including developmental effects that originate before birth. Video Abstract.
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Affiliation(s)
- Simone Anzà
- Behavioral Ecology Department, University of Goettingen, Goettingen, Germany.
- Primate Social Evolution Group, German Primate Center, Leibniz Institute for Primate Research, Goettingen, Germany.
- Leibniz ScienceCampus Primate Cognition, German Primate Center, Leibniz Institute for Primate Research, Goettingen, Germany.
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Göttingen, Göttingen, Germany.
| | - Dominik Schneider
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Göttingen, Göttingen, Germany
| | - Rolf Daniel
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Göttingen, Göttingen, Germany
| | - Michael Heistermann
- Endocrinology Laboratory, German Primate Center, Leibniz Institute for Primate Research, Goettingen, Germany
| | - Somboon Sangmaneedet
- Department of Pathobiology, Faculty of Veterinary Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Julia Ostner
- Behavioral Ecology Department, University of Goettingen, Goettingen, Germany
- Primate Social Evolution Group, German Primate Center, Leibniz Institute for Primate Research, Goettingen, Germany
- Leibniz ScienceCampus Primate Cognition, German Primate Center, Leibniz Institute for Primate Research, Goettingen, Germany
| | - Oliver Schülke
- Behavioral Ecology Department, University of Goettingen, Goettingen, Germany
- Primate Social Evolution Group, German Primate Center, Leibniz Institute for Primate Research, Goettingen, Germany
- Leibniz ScienceCampus Primate Cognition, German Primate Center, Leibniz Institute for Primate Research, Goettingen, Germany
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15
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Lacunza E, Fink V, Salas ME, Canzoneri R, Naipauer J, Williams S, Coso O, Sued O, Cahn P, Mesri EA, Abba MC. Oral and anal microbiome from HIV-exposed individuals: role of host-associated factors in taxa composition and metabolic pathways. NPJ Biofilms Microbiomes 2023; 9:48. [PMID: 37438354 DOI: 10.1038/s41522-023-00413-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 06/20/2023] [Indexed: 07/14/2023] Open
Abstract
Evidence indicates that the microbiome plays a significant role in HIV immunopathogenesis and associated complications. This study aimed to characterize the oral and anal microbiome of Men who have Sex with Men (MSM) and Transgender Women (TGW), with and without HIV. One hundred and thirty oral and anal DNA-derived samples were obtained from 78 participants and subjected to shotgun metagenomics sequencing for further microbiome analysis. Significant differences in the microbiome composition were found among subjects associated with HIV infection, gender, sex behavior, CD4+ T-cell counts, antiretroviral therapy (ART), and the presence of HPV-associated precancerous anal lesions. Results confirm the occurrence of oncogenic viromes in this high HIV-risk population. The oral microbiome in HIV-associated cases exhibited an enrichment of bacteria associated with periodontal disease pathogenesis. Conversely, anal bacteria showed a significant decrease in HIV-infected subjects (Coprococcus comes, Finegoldia magna, Blautia obeum, Catenibacterium mitsuokai). TGW showed enrichment in species related to sexual transmission, which concurs that most recruited TGW are or have been sex workers. Prevotella bivia and Fusobacterium gonidiaformans were positively associated with anal precancerous lesions among HIV-infected subjects. The enrichment of Holdemanella biformis and C. comes was associated with detectable viral load and ART-untreated patients. Metabolic pathways were distinctly affected by predominant factors linked to sexual behavior or HIV pathogenesis. Gene family analysis identified bacterial gene signatures as potential prognostic and predictive biomarkers for HIV/AIDS-associated malignancies. Conclusions: Identified microbial features at accessible sites are potential biomarkers for predicting precancerous anal lesions and therapeutic targets for HIV immunopathogenesis.
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Affiliation(s)
- Ezequiel Lacunza
- Centro de Investigaciones Inmunológicas Básicas y Aplicadas (CINIBA), Facultad de Ciencias Médicas, Universidad Nacional de La Plata, La Plata, Argentina.
| | - Valeria Fink
- Dirección de Investigaciones, Fundación Huésped, Buenos Aires, Argentina
| | - María E Salas
- Centro de Investigaciones Inmunológicas Básicas y Aplicadas (CINIBA), Facultad de Ciencias Médicas, Universidad Nacional de La Plata, La Plata, Argentina
| | - Romina Canzoneri
- Centro de Investigaciones Inmunológicas Básicas y Aplicadas (CINIBA), Facultad de Ciencias Médicas, Universidad Nacional de La Plata, La Plata, Argentina
| | - Julián Naipauer
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), CONICET - Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Sion Williams
- University of Miami - Center for AIDS Research (UM-CFAR) / Sylvester Comprehensive Cancer Center (CCC), University of Miami Miller School of Medicine, Miami, FL, USA
| | - Omar Coso
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), CONICET - Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Omar Sued
- Pan American Health Organization, Washington, USA
| | - Pedro Cahn
- Dirección de Investigaciones, Fundación Huésped, Buenos Aires, Argentina
| | - Enrique A Mesri
- University of Miami - Center for AIDS Research (UM-CFAR) / Sylvester Comprehensive Cancer Center (CCC), University of Miami Miller School of Medicine, Miami, FL, USA
| | - Martín C Abba
- Centro de Investigaciones Inmunológicas Básicas y Aplicadas (CINIBA), Facultad de Ciencias Médicas, Universidad Nacional de La Plata, La Plata, Argentina.
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16
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The Gut Microbiome, Microbial Metabolites, and Cardiovascular Disease in People Living with HIV. Curr HIV/AIDS Rep 2023; 20:86-99. [PMID: 36708497 DOI: 10.1007/s11904-023-00648-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/19/2022] [Indexed: 01/29/2023]
Abstract
PURPOSE OF REVIEW To synthesize recent evidence relating the gut microbiome and microbial metabolites to cardiovascular disease (CVD) in people living with HIV (PLWH). RECENT FINDINGS A few cross-sectional studies have reported on the gut microbiome and cardiovascular outcomes in the context of HIV, with no consistent patterns emerging. The largest such study found that gut Fusobacterium was associated with carotid artery plaque. More studies have evaluated microbial metabolite trimethylamine N-oxide with CVD risk in PLWH, but results were inconsistent, with recent prospective analyses showing null effects. Studies of other microbial metabolites are scarce. Microbial translocation biomarkers (e.g., lipopolysaccharide binding protein) have been related to incident CVD in PLWH. Microbial translocation may increase CVD risk in PLWH, but there is insufficient and/or inconsistent evidence regarding specific microbial species and microbial metabolites associated with cardiovascular outcomes in PLWH. Further research is needed in large prospective studies integrating the gut microbiome, microbial translocation, and microbial metabolites with cardiovascular outcomes in PLWH.
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Littlefield KM, Schneider JM, Neff CP, Soesanto V, Siebert JC, Nusbacher NM, Moreno-Huizar N, Cartwright IM, Armstrong AJS, Colgen SP, Lozupone CA, Palmer BE. Elevated inflammatory fecal immune factors in men who have sex with men with HIV associate with microbiome composition and gut barrier function. Front Immunol 2022; 13:1072720. [PMID: 36605218 PMCID: PMC9808389 DOI: 10.3389/fimmu.2022.1072720] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 11/30/2022] [Indexed: 12/24/2022] Open
Abstract
Introduction People living with HIV infection (PLWH) exhibit elevated levels of gastrointestinal inflammation. Potential causes of this inflammation include HIV infection and associated immune dysfunction, sexual behaviors among men who have sex with men (MSM) and gut microbiome composition. Methods To better understand the etiology of gastrointestinal inflammation we examined levels of 28 fecal soluble immune factors (sIFs) and the fecal microbiome in well-defined cohorts of HIV seronegative MSM (MSM-SN), MSM with untreated HIV infection (MSM-HIV) and MSM with HIV on anti-retroviral treatment (MSMART). Additionally, fecal solutes from these participants were used to stimulate T-84 colonic epithelial cells to assess barrier function. Results Both MSM cohorts with HIV had elevated levels of fecal calprotectin, a clinically relevant marker of GI inflammation, and nine inflammatory fecal sIFs (GM-CSF, ICAM-1, IL-1β, IL-12/23, IL-15, IL-16, TNF-β, VCAM-1, and VEGF). Interestingly, four sIFs (GM-CSF, ICAM-1, IL-7 and IL-12/23) were significantly elevated in MSM-SN compared to seronegative male non-MSM. Conversely, IL-22 and IL-13, cytokines beneficial to gut health, were decreased in all MSM with HIV and MSM-SN respectively. Importantly, all of these sIFs significantly correlated with calprotectin, suggesting they play a role in GI inflammation. Principal coordinate analysis revealed clustering of fecal sIFs by MSM status and significant associations with microbiome composition. Additionally, fecal solutes from participants in the MSM-HIV cohort significantly decreased colonic transcellular fluid transport in vitro, compared to non-MSM-SN, and this decrease associated with overall sIF composition and increased concentrations of eight inflammatory sIFs in participants with HIV. Lastly, elevated levels of plasma, sCD14 and sCD163, directly correlated with decreased transcellular transport and microbiome composition respectively, indicating that sIFs and the gut microbiome are associated with, and potentially contribute to, bacterial translocation. Conclusion Taken together, these data demonstrate that inflammatory sIFs are elevated in MSM, regardless of HIV infection status, and are associated with the gut microbiome and intestinal barrier function.
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Affiliation(s)
| | | | - Charles P. Neff
- Department of Medicine, University of Colorado, Aurora, CO, United States
| | - Victoria Soesanto
- Department of Medicine, University of Colorado, Aurora, CO, United States
| | - Janet C. Siebert
- Department of Medicine, University of Colorado, Aurora, CO, United States
- CytoAnalytics, Denver, CO, United States
| | - Nichole M. Nusbacher
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Nancy Moreno-Huizar
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Ian M. Cartwright
- Department of Medicine, University of Colorado, Aurora, CO, United States
| | - Abigail J. S. Armstrong
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Sean P. Colgen
- Department of Medicine, University of Colorado, Aurora, CO, United States
| | - Catherine A. Lozupone
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Brent E. Palmer
- Department of Medicine, University of Colorado, Aurora, CO, United States
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Wang H, Shi X, Yang H, Du Y, Xue J. Metagenomic next-generation sequencing shotgun for the diagnosis of infection in connective tissue diseases: A retrospective study. Front Cell Infect Microbiol 2022; 12:865637. [PMID: 36569204 PMCID: PMC9772835 DOI: 10.3389/fcimb.2022.865637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 11/16/2022] [Indexed: 12/13/2022] Open
Abstract
Objective Patients with connective tissue diseases (CTDs) are at high risk of infection due to various reasons. The purpose of the study was to investigate the infection diagnosis value of metagenomic next-generation sequencing (mNGS) shotgun in CTDs to guide the use of anti-infective therapy more quickly and accurately. Methods In this retrospective study, a total of 103 patients with CTDs admitted with suspected infection between December 2018 and September 2021 were assessed using mNGS as well as conventional microbiological tests (CMT). Results Among these 103 patients, 65 were confirmed to have an infection (Group I) and 38 had no infection (Group II). mNGS reached a sensitivity of 92.31% in diagnosing pathogens in Group I. Moreover, mNGS showed good performance in identifying mixed infection. In all infection types, lung infection was the most common. mNGS also played an important role in detecting Pneumocystis jirovecii, which was associated with low CD4+ T-cell counts inextricably. Conclusion mNGS is a useful tool with outstanding diagnostic potential in identifying pathogens in patients with CTDs and conduce to provide guidance in clinical practice.
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Affiliation(s)
- Huyan Wang
- Department of Rheumatology, the Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Xiaowei Shi
- Department of Rheumatology, the Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China,Department of Rheumatology and Immunology, Jinhua Hospital of Zhejiang University, Jinhua, China
| | - Huanhuan Yang
- Department of Rheumatology, the Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China,Department of Nephrology, Affiliated Hangzhou Xixi Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Yan Du
- Department of Rheumatology, the Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China,*Correspondence: Yan Du, ; Jing Xue,
| | - Jing Xue
- Department of Rheumatology, the Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China,*Correspondence: Yan Du, ; Jing Xue,
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Immune-Related Gene Profile in HIV-Infected Patients with Discordant Immune Response. IRANIAN BIOMEDICAL JOURNAL 2022; 26:485-91. [PMID: 36380676 PMCID: PMC9841224 DOI: 10.52547/ibj.3750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Background Background: In spite of many reports on persistent low CD4 T cell counts and change in immune-related gene expression level in patients with HIV infection, there is still uncertainty about significant association between gene expression level and HIV infection in patients with and without discordant immune response (DIR). The aim of this study was to compare the expression level of CD4, CCL5, IFN-γ, STAT1, APOBEC3G, CD45, and ICAM-1 genes in HIV-1-positive patients with and without DIR. Methods Methods: In this study, 30 HIV-1-positive patients (15 patients with and 15 patients without DIR [control group]) were included. PBMCs of the patients were collected through density radient centrifugation with Ficoll-Hypaque. RNeasy Plus Mini kit was used to extract RNA. Relative expression levels of CD4, CCL5, IFN-γ, STAT1, APOBEC3G, CD45, and ICAM-1 genes were evaluated by real-time PCR. The data were analyzed using one-way ANOVA. Results Results: CD4 T cell counts were significantly lower in DIR patients than the control group (p < 0.01). While there was no significant difference in the relative expression levels of CD4, CCL5, IFN-γ, STAT1, CD45, and ICAM-1 between patients with DIR and control group, APOBEC3G expression level was significantly higher in the patients with DIR as compare to the control group (p < 0.01). Conclusion Conclusion: Our findings suggest a significantly higher APOBEC3G expression level in patients with DIR, suggesting the potential role of APOBEC3G in patients with immunological discordance besides its suppressing role in HIV-1 infection. Confirmation of this hypothesis requires further research.
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Hove-Skovsgaard M, Møller DL, Hald A, Gerstoft J, Lundgren J, Ostrowski SR, Nielsen SD. Improved induced innate immune response after cART initiation in people with HIV. Front Immunol 2022; 13:974767. [PMID: 36059528 PMCID: PMC9428745 DOI: 10.3389/fimmu.2022.974767] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 07/25/2022] [Indexed: 11/30/2022] Open
Abstract
Introduction Impairment of the innate immune function may contribute to the increased risk of bacterial and viral infections in people with HIV (PWH). In this study we aimed to investigate the induced innate immune responses in PWH prior to and after initiation of combinational antiretroviral therapy (cART). Furthermore, we aimed to investigate if the induced innate immune responses before initiation of cART were associated with CD4+ T-cell recovery one year after initiating cART. Material and method The induced innate immune response was assessed by the TruCulture® whole blood technique in 32 PWH before cART initiation and after 1, 6 and 12 months. To mimic bacterial and viral infections we used a panel of three stimuli (lipopolysaccharide (LPS), resiquimod (R848), and polyinosinic:polycytidylic acid (Poly I:C)) to stimulate the extracellular Toll-like receptor (TLR) 4 and the intracellular TLR7/8 and TLR3, respectively. The following cytokine responses were analyzed by Luminex 200: Tumor Necrosis Factor (TNF)-α, Interleukin (IL)-1b, IL-6, IL-8, IL-10, IL-12p40, IL17A, Interferon (IFN)-α, and IFN-γ. Results At baseline PWH with nadir CD4+ T-cell count <350 cell/µL had lower levels of LPS-, R848-, and Poly I:C-induced IL-6 and IFN-γ, LPS- and R848-induced TNF-α and IL-12, LPS induced IL-1b, and R848-induced IL-10 than PWH with nadir CD4+ T-cell count >350 cells/µL. The majority (>50%) had induced cytokine concentrations below the reference intervals at baseline which was most pronounced for the LPS- and Poly I:C-induced responses. The induced responses in the whole population improved after 12 months of cART, and more PWH had induced cytokine concentrations within the reference intervals after 12 months. However, the majority of PWH still had LPS-induced INF-α, INF-γ and Poly I:C-induced TNF-α and IL-6 below the reference interval. The induced innate immune responses before cART initiation were not associated with the CD4+ T-cell recovery after 12 months of cART. Conclusion The innate immune response was impaired in PWH, with a more pronounced impairment in PWH with low nadir CD4+ T-cell count. Initiation of cART improved the innate immune response, but compared to the reference intervals, some impairment remained in PWH without viral replication.
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Affiliation(s)
- Malene Hove-Skovsgaard
- Department of Infectious Diseases, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Dina Leth Møller
- Department of Infectious Diseases, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Annemette Hald
- Department of Infectious Diseases, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Jan Gerstoft
- Department of Infectious Diseases, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Jens Lundgren
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
- Centre of Excellence for Health, Immunity, and Infections, Department of Infectious Diseases, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Sisse Rye Ostrowski
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Immunology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Susanne Dam Nielsen
- Department of Infectious Diseases, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
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Pandrea I, Brooks K, Desai RP, Tare M, Brenchley JM, Apetrei C. I've looked at gut from both sides now: Gastrointestinal tract involvement in the pathogenesis of SARS-CoV-2 and HIV/SIV infections. Front Immunol 2022; 13:899559. [PMID: 36032119 PMCID: PMC9411647 DOI: 10.3389/fimmu.2022.899559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 07/25/2022] [Indexed: 01/08/2023] Open
Abstract
The lumen of the gastrointestinal (GI) tract contains an incredibly diverse and extensive collection of microorganisms that can directly stimulate the immune system. There are significant data to demonstrate that the spatial localization of the microbiome can impact viral disease pathogenesis. Here we discuss recent studies that have investigated causes and consequences of GI tract pathologies in HIV, SIV, and SARS-CoV-2 infections with HIV and SIV initiating GI pathology from the basal side and SARS-CoV-2 from the luminal side. Both these infections result in alterations of the intestinal barrier, leading to microbial translocation, persistent inflammation, and T-cell immune activation. GI tract damage is one of the major contributors to multisystem inflammatory syndrome in SARS-CoV-2-infected individuals and to the incomplete immune restoration in HIV-infected subjects, even in those with robust viral control with antiretroviral therapy. While the causes of GI tract pathologies differ between these virus families, therapeutic interventions to reduce microbial translocation-induced inflammation and improve the integrity of the GI tract may improve the prognoses of infected individuals.
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Affiliation(s)
- Ivona Pandrea
- Department of Pathology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
- Department of Infectious Diseases and Microbiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, United States
| | - Kelsie Brooks
- Barrier Immunity Section, Laboratory of Viral Diseases, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Rahul P. Desai
- Department of Pathology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
- Division of Infectious Diseases, Department of Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - Minali Tare
- Department of Pathology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
- Division of Infectious Diseases, Department of Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - Jason M. Brenchley
- Barrier Immunity Section, Laboratory of Viral Diseases, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Cristian Apetrei
- Department of Infectious Diseases and Microbiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, United States
- Division of Infectious Diseases, Department of Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
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22
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Ashuro AA, Zhang SC, Wang T, Chu QS, Fu YS, Fan YG, Ye DQ. The Effect of protease inhibitors-based antiretroviral therapy on serum/plasma interleukin-6 levels among PLHIV: a systematic review and meta-analysis. J Med Virol 2022; 94:4669-4676. [PMID: 35665943 DOI: 10.1002/jmv.27912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 05/15/2022] [Accepted: 05/31/2022] [Indexed: 11/07/2022]
Abstract
INTRODUCTION Recommended treatment regimen for HIV infection includes protease inhibitors/ritonavir (PIs/r) combined with two nucleoside reverse transcriptase inhibitors (2NRTIs), that enable to achieve and maintain viral suppression, restore and preserve immune function. However, there were inconsistent findings on the levels of interleukin-6 levels (IL-6). METHODOLOGY Systematic review and meta-analysis were performed to quantify the pooled effects of PIs/r-based ART on serum/plasma IL-6 levels in PLHIV. PubMed, Web of Science, and Embase were searched from the earliest record to November 4, 2020. Data analysis was conducted on Stata version 16 and Review Manager 5.3. A random-effect model was used to compute a pooled effect size and weighted mean difference (WMD) was considered the summary effect size. Heterogeneity between studies was estimated by Cochrane's Q test (chi-square test) and I-square statistic and subgroup analysis were performed to explore the source of heterogeneity. RESULT Initial search identified 3098 records and five studies (seven trials) met inclusion criteria. The pooled mean difference in serum/plasma IL-6 levels from baseline to follow-up was 0.534 pg/ml (95% CI: -0.012, 1.08, P=0.05, I2 =76.4%). In subgroup analysis, there was a significant association between increased serum/plasma IL-6 levels, and age group ≥35 years old, baseline CD4+ counts <350 cell/mm3 , and mean viral load ≥ 4.5 log10 copies/ml. CONCLUSION We found that serum/plasma IL-6 levels increased after combined anti-retroviral therapy (cART) among treatment-naïve individuals who initiated a successful combination of PIs/r with 2NRTIs. This result also highlights the need to monitor serum/plasma IL-6 levels during antiviral therapy, which may aid in the effective future treatment of systemic inflammation and related disorders following elevated IL-6 levels. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Akililu Alemu Ashuro
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, 81 Meishan Road, Hefei, Anhui, 230032, PR China.,Anhui Province Key Laboratory of Major Autoimmune Diseases, Anhui Medical University, China, 81 Meishan Road, Hefei, Anhui, 230032, PR China
| | - Si-Chen Zhang
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, 81 Meishan Road, Hefei, Anhui, 230032, PR China.,Anhui Province Key Laboratory of Major Autoimmune Diseases, Anhui Medical University, China, 81 Meishan Road, Hefei, Anhui, 230032, PR China
| | - Ting Wang
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, 81 Meishan Road, Hefei, Anhui, 230032, PR China.,Anhui Province Key Laboratory of Major Autoimmune Diseases, Anhui Medical University, China, 81 Meishan Road, Hefei, Anhui, 230032, PR China
| | - Qin-Shu Chu
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, 81 Meishan Road, Hefei, Anhui, 230032, PR China.,Anhui Province Key Laboratory of Major Autoimmune Diseases, Anhui Medical University, China, 81 Meishan Road, Hefei, Anhui, 230032, PR China
| | - Yuan-Sheng Fu
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, 81 Meishan Road, Hefei, Anhui, 230032, PR China.,Anhui Province Key Laboratory of Major Autoimmune Diseases, Anhui Medical University, China, 81 Meishan Road, Hefei, Anhui, 230032, PR China
| | - Yin-Guang Fan
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, 81 Meishan Road, Hefei, Anhui, 230032, PR China.,Anhui Province Key Laboratory of Major Autoimmune Diseases, Anhui Medical University, China, 81 Meishan Road, Hefei, Anhui, 230032, PR China
| | - Dong-Qing Ye
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, 81 Meishan Road, Hefei, Anhui, 230032, PR China.,Anhui Province Key Laboratory of Major Autoimmune Diseases, Anhui Medical University, China, 81 Meishan Road, Hefei, Anhui, 230032, PR China
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23
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Borgognone A, Noguera-Julian M, Oriol B, Noël-Romas L, Ruiz-Riol M, Guillén Y, Parera M, Casadellà M, Duran C, Puertas MC, Català-Moll F, De Leon M, Knodel S, Birse K, Manzardo C, Miró JM, Clotet B, Martinez-Picado J, Moltó J, Mothe B, Burgener A, Brander C, Paredes R. Gut microbiome signatures linked to HIV-1 reservoir size and viremia control. MICROBIOME 2022; 10:59. [PMID: 35410461 PMCID: PMC9004083 DOI: 10.1186/s40168-022-01247-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 02/16/2022] [Indexed: 05/28/2023]
Abstract
BACKGROUND The potential role of the gut microbiome as a predictor of immune-mediated HIV-1 control in the absence of antiretroviral therapy (ART) is still unknown. In the BCN02 clinical trial, which combined the MVA.HIVconsv immunogen with the latency-reversing agent romidepsin in early-ART treated HIV-1 infected individuals, 23% (3/13) of participants showed sustained low-levels of plasma viremia during 32 weeks of a monitored ART pause (MAP). Here, we present a multi-omics analysis to identify compositional and functional gut microbiome patterns associated with HIV-1 control in the BCN02 trial. RESULTS Viremic controllers during the MAP (controllers) exhibited higher Bacteroidales/Clostridiales ratio and lower microbial gene richness before vaccination and throughout the study intervention when compared to non-controllers. Longitudinal assessment indicated that the gut microbiome of controllers was enriched in pro-inflammatory bacteria and depleted in butyrate-producing bacteria and methanogenic archaea. Functional profiling also showed that metabolic pathways related to fatty acid and lipid biosynthesis were significantly increased in controllers. Fecal metaproteome analyses confirmed that baseline functional differences were mainly driven by Clostridiales. Participants with high baseline Bacteroidales/Clostridiales ratio had increased pre-existing immune activation-related transcripts. The Bacteroidales/Clostridiales ratio as well as host immune-activation signatures inversely correlated with HIV-1 reservoir size. CONCLUSIONS The present proof-of-concept study suggests the Bacteroidales/Clostridiales ratio as a novel gut microbiome signature associated with HIV-1 reservoir size and immune-mediated viral control after ART interruption. Video abstract.
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Affiliation(s)
- Alessandra Borgognone
- IrsiCaixa AIDS Research Institute, Hospital Universitari Germans Trias i Pujol, Barcelona, Catalonia, Spain.
| | - Marc Noguera-Julian
- IrsiCaixa AIDS Research Institute, Hospital Universitari Germans Trias i Pujol, Barcelona, Catalonia, Spain
- CIBERINFEC, Madrid, Spain
- University of Vic-Central University of Catalonia (UVic-UCC), Vic, Catalonia, Spain
| | - Bruna Oriol
- IrsiCaixa AIDS Research Institute, Hospital Universitari Germans Trias i Pujol, Barcelona, Catalonia, Spain
- Universitat Autonoma de Barcelona (UAB), Barcelona, Catalonia, Spain
| | - Laura Noël-Romas
- Center for Global Health and Diseases, Department of Pathology, Case Western Reserve University, Cleveland, OH, USA
- Department of Obstetrics & Gynecology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Marta Ruiz-Riol
- IrsiCaixa AIDS Research Institute, Hospital Universitari Germans Trias i Pujol, Barcelona, Catalonia, Spain
- CIBERINFEC, Madrid, Spain
| | - Yolanda Guillén
- Institut Mar d'Investigacions mediques (IMIM), CIBERONC, Barcelona, Catalonia, Spain
| | - Mariona Parera
- IrsiCaixa AIDS Research Institute, Hospital Universitari Germans Trias i Pujol, Barcelona, Catalonia, Spain
| | - Maria Casadellà
- IrsiCaixa AIDS Research Institute, Hospital Universitari Germans Trias i Pujol, Barcelona, Catalonia, Spain
| | - Clara Duran
- IrsiCaixa AIDS Research Institute, Hospital Universitari Germans Trias i Pujol, Barcelona, Catalonia, Spain
- Universitat Autonoma de Barcelona (UAB), Barcelona, Catalonia, Spain
| | - Maria C Puertas
- IrsiCaixa AIDS Research Institute, Hospital Universitari Germans Trias i Pujol, Barcelona, Catalonia, Spain
- CIBERINFEC, Madrid, Spain
| | - Francesc Català-Moll
- IrsiCaixa AIDS Research Institute, Hospital Universitari Germans Trias i Pujol, Barcelona, Catalonia, Spain
| | - Marlon De Leon
- Center for Global Health and Diseases, Department of Pathology, Case Western Reserve University, Cleveland, OH, USA
| | - Samantha Knodel
- Center for Global Health and Diseases, Department of Pathology, Case Western Reserve University, Cleveland, OH, USA
- Department of Obstetrics & Gynecology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Kenzie Birse
- Center for Global Health and Diseases, Department of Pathology, Case Western Reserve University, Cleveland, OH, USA
- Department of Obstetrics & Gynecology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Christian Manzardo
- Infectious Diseases Service, Hospital Clinic-Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona, Barcelona, Catalonia, Spain
| | - José M Miró
- CIBERINFEC, Madrid, Spain
- Infectious Diseases Service, Hospital Clinic-Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona, Barcelona, Catalonia, Spain
| | - Bonaventura Clotet
- IrsiCaixa AIDS Research Institute, Hospital Universitari Germans Trias i Pujol, Barcelona, Catalonia, Spain
- CIBERINFEC, Madrid, Spain
- University of Vic-Central University of Catalonia (UVic-UCC), Vic, Catalonia, Spain
- Universitat Autonoma de Barcelona (UAB), Barcelona, Catalonia, Spain
- Fight AIDS Foundation, Infectious Diseases Department, Germans Trias i Pujol University Hospital, Barcelona, Catalonia, Spain
- Department of Infectious Diseases Service, Germans Trias i Pujol University Hospital, Barcelona, Catalonia, Spain
| | - Javier Martinez-Picado
- IrsiCaixa AIDS Research Institute, Hospital Universitari Germans Trias i Pujol, Barcelona, Catalonia, Spain
- CIBERINFEC, Madrid, Spain
- University of Vic-Central University of Catalonia (UVic-UCC), Vic, Catalonia, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Catalonia, Spain
| | - José Moltó
- CIBERINFEC, Madrid, Spain
- Fight AIDS Foundation, Infectious Diseases Department, Germans Trias i Pujol University Hospital, Barcelona, Catalonia, Spain
- Department of Infectious Diseases Service, Germans Trias i Pujol University Hospital, Barcelona, Catalonia, Spain
| | - Beatriz Mothe
- IrsiCaixa AIDS Research Institute, Hospital Universitari Germans Trias i Pujol, Barcelona, Catalonia, Spain
- CIBERINFEC, Madrid, Spain
- University of Vic-Central University of Catalonia (UVic-UCC), Vic, Catalonia, Spain
- Fight AIDS Foundation, Infectious Diseases Department, Germans Trias i Pujol University Hospital, Barcelona, Catalonia, Spain
- Department of Infectious Diseases Service, Germans Trias i Pujol University Hospital, Barcelona, Catalonia, Spain
| | - Adam Burgener
- Center for Global Health and Diseases, Department of Pathology, Case Western Reserve University, Cleveland, OH, USA
- Department of Obstetrics & Gynecology, University of Manitoba, Winnipeg, Manitoba, Canada
- Department of Medicine Solna, Center for Molecular Medicine, Karolinska Institute, Karolinska University Hospital, Stockholm, Sweden
| | - Christian Brander
- IrsiCaixa AIDS Research Institute, Hospital Universitari Germans Trias i Pujol, Barcelona, Catalonia, Spain
- CIBERINFEC, Madrid, Spain
- University of Vic-Central University of Catalonia (UVic-UCC), Vic, Catalonia, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Catalonia, Spain
| | - Roger Paredes
- IrsiCaixa AIDS Research Institute, Hospital Universitari Germans Trias i Pujol, Barcelona, Catalonia, Spain.
- CIBERINFEC, Madrid, Spain.
- University of Vic-Central University of Catalonia (UVic-UCC), Vic, Catalonia, Spain.
- Universitat Autonoma de Barcelona (UAB), Barcelona, Catalonia, Spain.
- Center for Global Health and Diseases, Department of Pathology, Case Western Reserve University, Cleveland, OH, USA.
- Fight AIDS Foundation, Infectious Diseases Department, Germans Trias i Pujol University Hospital, Barcelona, Catalonia, Spain.
- Department of Infectious Diseases Service, Germans Trias i Pujol University Hospital, Barcelona, Catalonia, Spain.
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Sherrill-Mix S, Yang M, Aldrovandi GM, Brenchley JM, Bushman FD, Collman RG, Dandekar S, Klatt NR, Lagenaur LA, Landay AL, Paredes R, Tachedjian G, Turpin JA, Serrano-Villar S, Lozupone CA, Ghosh M. A Summary of the Sixth International Workshop on Microbiome in HIV Pathogenesis, Prevention, and Treatment. AIDS Res Hum Retroviruses 2022; 38:173-180. [PMID: 34969255 PMCID: PMC9009592 DOI: 10.1089/aid.2021.0173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
In October of 2020, researchers from around the world met online for the sixth annual International Workshop on Microbiome in HIV Pathogenesis, Prevention, and Treatment. New research was presented on the roles of the microbiome on immune response and HIV transmission and pathogenesis and the potential for alterations in the microbiome to decrease transmission and affect comorbidities. This article presents a summary of the findings reported.
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Affiliation(s)
- Scott Sherrill-Mix
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Address correspondence to: Scott Sherrill-Mix, Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, 424 Johnson Pavilion, 3610 Hamilton Walk, Philadelphia, PA 19104, USA
| | - Michelle Yang
- Department of Epidemiology, The George Washington University, Washington, District of Columbia, USA
| | - Grace M. Aldrovandi
- Department of Pediatrics, University of California, Los Angeles, California, USA
| | | | - Frederic D. Bushman
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Ronald G. Collman
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Satya Dandekar
- Department of Medical Microbiology and Immunology, University of California, Davis, Davis, California, USA
| | - Nichole R. Klatt
- Department of Medicine, University of Minnesota, Minneapolis, Minnesota, USA
| | | | - Alan L. Landay
- Division of Gerontology, Department of Internal Medicine, Rush University Medical Center, Chicago, Illinois, USA
| | - Roger Paredes
- Institut de Recerca de la SIDA IrsiCaixa i Unitat VIH, Universitat Autònoma de Barcelona, Universitat de Vic, Catalonia, Spain
| | | | - Jim A. Turpin
- Divison of AIDS, NIAID, NIH, Bethesda, Maryland, USA
| | - Sergio Serrano-Villar
- Department of Infectious Diseases, Hospital Universitario Ramon y Cajal, Madrid, Spain
| | | | - Mimi Ghosh
- Department of Epidemiology, The George Washington University, Washington, District of Columbia, USA
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25
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Mingjun Z, Fei M, Zhousong X, Wei X, Jian X, Yuanxue Y, Youfeng S, Zhongping C, Yiqin L, Xiaohong Z, Ying C, Zhenbing W, Zehu D, Lanjuan L. 16S rDNA sequencing analyzes differences in intestinal flora of human immunodeficiency virus (HIV) patients and association with immune activation. Bioengineered 2022; 13:4085-4099. [PMID: 35129067 PMCID: PMC8974104 DOI: 10.1080/21655979.2021.2019174] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
To clarify the influence of HIV on the intestinal flora and the interrelationship with CD4 T cells, the present study collected stool specimens from 33 HIV patients and 28 healthy subjects to compare the differences in the intestinal flora and CD4 T cells in a 16S rDNA-sequencing approach. ELISA was used to detect the expressions of interleukin 2 (IL-2), IL-8, and tumor necrosis factor-α (TNF-α). Meanwhile, correlation analysis with the different bacterial populations in each group was carried out. The results revealed that Alpha diversity indices of the intestinal flora of HIV patients were markedly lower than that of the healthy group (p < 0.05). The top five bacterial species in the HIV group were Bacteroides (23.453%), Prevotella (19.237%), Fusobacterium (12.408%), Lachnospira (3.811%), and Escherichia-Shigella (3.126%). Spearman correlation analysis results indicated that Fusobacterium_mortiferum, Fusobacterium, and Gammaproteobacteria were positively correlated with TNF-α (p < 0.05), whereas Ruminococcaceae, Bacteroidales was negatively correlated with TNF-α (p < 0.05). Additionally, Agathobacter was positively correlated with contents of IL-2 and IL-8 (p < 0.05), whereas Prevotellaceae, and Prevotella were negatively correlated with IL-8 content (p < 0.05). Furthermore, the top five strains in the CD4 high group (≥350/mm3) included Bacteroides (23.286%), Prevotella (21.943%), Fusobacterium (10.479%), Lachnospira (4.465%), and un_f_Lachnospiraceae (2.786%). Taken together, the present study identified that Fusobacterium and Escherichia-Shigella were specific and highly abundant in the HIV group and a correlation between the different bacterial flora and the contents of IL-2, IL-8, and TNF-α was revealed.
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Affiliation(s)
- Zhang Mingjun
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Department of Laboratory Medicine, People's Hospital of Jiulongpo District, Chongqing, China
| | - Mo Fei
- Department of Laboratory Medicine, People's Hospital of Jiulongpo District, Chongqing, China
| | - Xu Zhousong
- Department of Laboratory Medicine, People's Hospital of Jiulongpo District, Chongqing, China
| | - Xu Wei
- Department of Laboratory Medicine, Hangzhou Shulan Hospital, Zhejiang University, Hangzhou, China.,Department of Laboratory Medicine, Hangzhou Tongchuang Medical Laboratory Co. LTD, Hangzhou, China
| | - Xu Jian
- Department of Laboratory Medicine, Chongqing Precision Medical Industry Technology Research Institute, Chongqing, China
| | - Yi Yuanxue
- Department of Laboratory Medicine, Chongqing Precision Medical Industry Technology Research Institute, Chongqing, China.,Department of Laboratory Medicine, Chongqing D.A. Medical Laboratory, Chongqing, China
| | - Shen Youfeng
- Department of Laboratory Medicine, Chongqing Precision Medical Industry Technology Research Institute, Chongqing, China.,Department of Laboratory Medicine, Chongqing D.A. Medical Laboratory, Chongqing, China
| | - Chen Zhongping
- Department of Laboratory Medicine, People's Hospital of Jiulongpo District, Chongqing, China
| | - Long Yiqin
- Department of Laboratory Medicine, People's Hospital of Jiulongpo District, Chongqing, China
| | - Zhao Xiaohong
- Department of Laboratory Medicine, People's Hospital of Jiulongpo District, Chongqing, China
| | - Cheng Ying
- Department of Laboratory Medicine, Hangzhou Shulan Hospital, Zhejiang University, Hangzhou, China
| | - Wang Zhenbing
- Department of Laboratory Medicine, Chongqing Precision Medical Industry Technology Research Institute, Chongqing, China.,Department of Laboratory Medicine, Chongqing D.A. Medical Laboratory, Chongqing, China
| | - Deng Zehu
- Department of Laboratory Medicine, People's Hospital of Jiulongpo District, Chongqing, China
| | - Li Lanjuan
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
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26
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Nie K, Ma K, Luo W, Shen Z, Yang Z, Xiao M, Tong T, Yang Y, Wang X. Roseburia intestinalis: A Beneficial Gut Organism From the Discoveries in Genus and Species. Front Cell Infect Microbiol 2021; 11:757718. [PMID: 34881193 PMCID: PMC8647967 DOI: 10.3389/fcimb.2021.757718] [Citation(s) in RCA: 246] [Impact Index Per Article: 61.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 10/29/2021] [Indexed: 12/12/2022] Open
Abstract
Roseburia intestinalis is an anaerobic, Gram-positive, slightly curved rod-shaped flagellated bacterium that produces butyrate in the colon. R. intestinalis has been shown to prevent intestinal inflammation and maintain energy homeostasis by producing metabolites. Evidence shows that this bacterium contributes to various diseases, such as inflammatory bowel disease, type 2 diabetes mellitus, antiphospholipid syndrome, and atherosclerosis. This review reveals the potential therapeutic role of R. intestinalis in human diseases. Patients with inflammatory bowel disease exhibit significant changes in R. intestinalis abundance, and they may benefit a lot from modulations targeting R. intestinalis. The data reviewed here demonstrate that R. intestinalis plays its role in regulating barrier homeostasis, immune cells, and cytokine release through its metabolite butyrate, flagellin and other. Recent advancements in the application of primary culture technology, culture omics, single-cell sequencing, and metabonomics technology have improved research on Roseburia and revealed the benefits of this bacterium in human health and disease treatment.
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Affiliation(s)
- Kai Nie
- Department of Gastroenterology, The Third Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Cancer Research Institute, Central South University, Changsha, China
| | - Kejia Ma
- Department of Gastroenterology, The Third Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Cancer Research Institute, Central South University, Changsha, China
| | - Weiwei Luo
- Department of Gastroenterology, The Third Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Cancer Research Institute, Central South University, Changsha, China
| | - Zhaohua Shen
- Department of Gastroenterology, The Third Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Cancer Research Institute, Central South University, Changsha, China
| | - Zhenyu Yang
- Department of Gastroenterology, The Third Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Cancer Research Institute, Central South University, Changsha, China
| | - Mengwei Xiao
- Department of Gastroenterology, The Third Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Cancer Research Institute, Central South University, Changsha, China
| | - Ting Tong
- Department of Gastroenterology, The Third Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Cancer Research Institute, Central South University, Changsha, China
| | - Yuanyuan Yang
- Department of Gastroenterology, The Third Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Cancer Research Institute, Central South University, Changsha, China
| | - Xiaoyan Wang
- Department of Gastroenterology, The Third Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Cancer Research Institute, Central South University, Changsha, China
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27
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Presti RM, Yeh E, Williams B, Landay A, Jacobson JM, Wilson C, Fichtenbaum CJ, Utay NS, Dube MP, Klingman KL, Estes JD, Flynn JK, Loftin A, Brenchley JM, Andrade A, Kitch DW, Overton ET. A Randomized, Placebo-Controlled Trial Assessing the Effect of VISBIOME ES Probiotic in People With HIV on Antiretroviral Therapy. Open Forum Infect Dis 2021; 8:ofab550. [PMID: 34888397 PMCID: PMC8651169 DOI: 10.1093/ofid/ofab550] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 11/02/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND A5350, a phase II, randomized, double-blind study, evaluated the safety and tolerability of the probiotic Visbiome Extra Strength (ES) over 24 weeks and measured effects on inflammation and intestinal barrier function. METHODS The primary outcome was change in soluble CD14 (sCD14) levels; secondary outcomes included safety and tolerability, markers of inflammation and cellular activation, and microbiome. In a substudy, gut permeability was assessed by paired colonic biopsies measuring the area of lamina propria occupied by CD4+ cells, interleukin (IL)-17+ cells, and myeloperoxidase (MPO). Changes between arms were compared with the 2-sample t test with equal variance or the Wilcoxon rank-sum test. For safety, the highest graded adverse events (AEs) were compared between arms using the Fisher exact test. RESULTS Overall, 93 participants enrolled: 86% male, median age 51 years, median CD4 count 712 cells/mm3. Visbiome ES was safe and well tolerated. There was no difference in mean change in sCD14 from baseline to week 25/26 between placebo (mean change, 92.3 µg/L; 95% CI, -48.5 to 233 µg/L) and Visbiome ES (mean change, 41.0 µg/L; 95% CI, -94.1 to 176.2 µg/L; P=.60). Similarly, no statistically significant differences between arms in inflammatory marker changes were identified. In substudy participants, no statistical differences between arms for change in cellular marker expression or gut permeability were observed (P>.05 for all). The microbiome demonstrated increased probiotic species and a significant decrease in Gammaproteobacteria (P=.044) in the Visbiome ES arm. CONCLUSIONS Visbiome ES was safe and altered the microbiome but demonstrated no effect on systemic inflammatory markers, pathology, or gut permeability in antiretroviral therapy-treated people with HIV.
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Affiliation(s)
- Rachel M Presti
- Washington University School of Medicine, St. Louis, Missouri, USA
| | - Eunice Yeh
- Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | | | - Alan Landay
- Rush University Medical Center, Chicago, Illinois, USA
| | - Jeffrey M Jacobson
- Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Cara Wilson
- University of Colorado, Anschutz Medical Center, Aurora, Colorado, USA
| | | | - Netanya S Utay
- University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Michael P Dube
- University of Southern California, Keck School of Medicine, Los Angeles, California, USA
| | | | - Jacob D Estes
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Portland, Oregon, USA
| | - Jacob K Flynn
- Barrier Immunity Section, Lab of Viral Diseases, NIAID, NIH, Bethesda, Maryland, USA
| | - Amanda Loftin
- Barrier Immunity Section, Lab of Viral Diseases, NIAID, NIH, Bethesda, Maryland, USA
| | - Jason M Brenchley
- Barrier Immunity Section, Lab of Viral Diseases, NIAID, NIH, Bethesda, Maryland, USA
| | | | - Douglas W Kitch
- Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Edgar T Overton
- University of Alabama at Birmingham, Birmingham, Alabama, USA
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Abstract
Purpose of Review Observations of differing bacterial, intestinal microbiomes in people living with HIV have propelled interest in contributions of the microbiome to HIV disease. Non-human primate (NHP) models of HIV infection provide a controlled setting for assessing contributions of the microbiome by standardizing environmental confounders. We provide an overview of the findings of microbiome contributions to aspects of HIV disease derived from these animal models. Recent Findings Observations of differing bacterial, intestinal microbiomes are inconsistently observed in the NHP model following SIV infection. Differences in lentiviral susceptibility and vaccine efficacy have been attributed to variations in the intestinal microbiome; however, by-and-large, these differences have not been experimentally assessed. Summary Although compelling associations exist, clearly defined contributions of the microbiome to HIV and SIV disease are lacking. The empirical use of comprehensive multi-omics assessments and longitudinal and interventional study designs in NHP models is necessary to define this contribution more clearly.
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Affiliation(s)
- Jason M Brenchley
- Barrier Immunity Section, Laboratory of Viral Diseases, National Institutes of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, USA
| | - Alexandra M Ortiz
- Barrier Immunity Section, Laboratory of Viral Diseases, National Institutes of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, USA.
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29
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Rousseau RK, Walmsley SL, Lee T, Rosenes R, Reinhard RJ, Malazogu F, Benko E, Huibner S, Kovacs CM, Singer J, Kim CJ, Kaul R. A randomized, blinded, placebo-controlled trial of De Simone formulation probiotic during HIV-associated suboptimal CD4+ T cell recovery. J Acquir Immune Defic Syndr 2021; 89:199-207. [PMID: 34693932 DOI: 10.1097/qai.0000000000002840] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 10/04/2021] [Indexed: 11/25/2022]
Abstract
OBJECTIVE To assess whether probiotic supplementation may reduce disease-linked systemic immune activation in people living with HIV with the immunologic non-responder (INR) phenotype. DESIGN Phase 2b, randomized, double-blind, placebo-controlled pilot trial. METHODS HIV-positive individuals with blood CD4+ T cell counts <350/mm3 despite viral suppression were randomized 2:1 to receive De Simone Formulation Probiotic (DSFP; "Visbiome" commercially) or placebo for 48 weeks; target enrolment was 36 patients. The primary endpoint was change in blood CD8+ T cell co-expression of HLA-DR and CD38 ("CD8 activation"). Secondary endpoints included biomarkers of inflammation, immune reconstitution, bacterial translocation, and gut permeability. Adjusted linear regression and linear mixed methods regression evaluated the differences between study arms from baseline to week 48. Study monitoring was done by the CIHR Canadian HIV Trials Network Data Safety Monitoring Committee. RESULTS Nineteen patients received DSFP, while 10 received placebo. One probiotic-arm patient withdrew early. Blood CD8 activation increased 0.82 percentage points (pp) in the probiotic arm (95% confidence interval [CI];-1.23,2.87;) and decreased by 2.06pp in the placebo arm (-4.81,0.70; between arms p=0.097). CD4+ T cell activation (%HLA-DR+) decreased in the placebo arm (-3.79pp [-7.32,-0.26]) but increased in the probiotic arm (1.64 [-0.98,4.26]; between arms p=0.018). No differences were observed in plasma or urine biomarkers of inflammation or microbial translocation. CONCLUSIONS Blood immune activation markers in INR individuals on effective ART were not reduced by supplementation with DSFP; CD4+ T cell activation may have been increased.
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Affiliation(s)
- Rodney K Rousseau
- University of Toronto, Departments of Immunology, Medicine, and Internal Medicine, Toronto, Canada University Health Network, Toronto General Hospital Immunodeficiency Clinic, Toronto, Canada Toronto General Hospital Research Institute, Toronto, Canada CIHR Canadian HIV Trials Network, Vancouver, Canada Centre for Health Evaluation & Outcomes Sciences, Vancouver, Canada Community Health Advocate and Consultant (Independent), Toronto, Canada Public/Global Health Consultant (Independent), San Francisco, USA Maple Leaf Medical Clinic, Toronto, Canada
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30
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Nganou-Makamdop K, Talla A, Sharma AA, Darko S, Ransier A, Laboune F, Chipman JG, Beilman GJ, Hoskuldsson T, Fourati S, Schmidt TE, Arumugam S, Lima NS, Moon D, Callisto S, Schoephoerster J, Tomalka J, Mugyenyi P, Ssali F, Muloma P, Ssengendo P, Leda AR, Cheu RK, Flynn JK, Morou A, Brunet-Ratnasingham E, Rodriguez B, Lederman MM, Kaufmann DE, Klatt NR, Kityo C, Brenchley JM, Schacker TW, Sekaly RP, Douek DC. Translocated microbiome composition determines immunological outcome in treated HIV infection. Cell 2021; 184:3899-3914.e16. [PMID: 34237254 DOI: 10.1016/j.cell.2021.05.023] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 02/03/2021] [Accepted: 05/17/2021] [Indexed: 12/13/2022]
Abstract
The impact of the microbiome on HIV disease is widely acknowledged although the mechanisms downstream of fluctuations in microbial composition remain speculative. We detected rapid, dynamic changes in translocated microbial constituents during two years after cART initiation. An unbiased systems biology approach revealed two distinct pathways driven by changes in the abundance ratio of Serratia to other bacterial genera. Increased CD4 T cell numbers over the first year were associated with high Serratia abundance, pro-inflammatory innate cytokines, and metabolites that drive Th17 gene expression signatures and restoration of mucosal integrity. Subsequently, decreased Serratia abundance and downregulation of innate cytokines allowed re-establishment of systemic T cell homeostasis promoting restoration of Th1 and Th2 gene expression signatures. Analyses of three other geographically distinct cohorts of treated HIV infection established a more generalized principle that changes in diversity and composition of translocated microbial species influence systemic inflammation and consequently CD4 T cell recovery.
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Affiliation(s)
- Krystelle Nganou-Makamdop
- Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Institute of Clinical and Molecular Virology, University Hospital Erlangen, 91054 Erlangen, Germany
| | - Aarthi Talla
- Department of Pathology, Case Western Reserve University, Cleveland, OH 10900, USA; Allen Institute for Immunology, Seattle, WA 98109, USA
| | - Ashish Arunkumar Sharma
- Department of Pathology, Case Western Reserve University, Cleveland, OH 10900, USA; Pathology Advanced Translational Research Unit, Department of Pathology and Laboratory Medicine, School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Sam Darko
- Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Amy Ransier
- Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Farida Laboune
- Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jeffrey G Chipman
- Department of Surgery, University of Minnesota, Minneapolis, MN 55455, USA
| | - Gregory J Beilman
- Department of Surgery, University of Minnesota, Minneapolis, MN 55455, USA
| | - Torfi Hoskuldsson
- Department of Surgery, University of Minnesota, Minneapolis, MN 55455, USA
| | - Slim Fourati
- Department of Pathology, Case Western Reserve University, Cleveland, OH 10900, USA; Pathology Advanced Translational Research Unit, Department of Pathology and Laboratory Medicine, School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Thomas E Schmidt
- Department of Medicine, University of Minnesota, Minneapolis, MN 55455, USA
| | - Sahaana Arumugam
- Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Noemia S Lima
- Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Damee Moon
- Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Samuel Callisto
- Department of Medicine, University of Minnesota, Minneapolis, MN 55455, USA
| | | | - Jeffery Tomalka
- Department of Pathology, Case Western Reserve University, Cleveland, OH 10900, USA; Pathology Advanced Translational Research Unit, Department of Pathology and Laboratory Medicine, School of Medicine, Emory University, Atlanta, GA 30322, USA
| | | | | | | | | | - Ana R Leda
- Department of Pediatrics, Miller School of Medicine, University of Miami, Miami, FL 33124, USA
| | - Ryan K Cheu
- Department of Pediatrics, Miller School of Medicine, University of Miami, Miami, FL 33124, USA
| | - Jacob K Flynn
- Barrier Immunity Section, Laboratory of Viral Diseases, NIAID/NIH, Bethesda, MD 20892, USA
| | - Antigoni Morou
- Research Centre of the Centre Hospitalier de l'Université de Montréal, Montreal, QC H3C 3J7, Canada; Université de Montréal, Montreal, QC H3C 3J7, Canada; Roche Diagnostics GmbH, 82377 Penzberg, Germany
| | - Elsa Brunet-Ratnasingham
- Research Centre of the Centre Hospitalier de l'Université de Montréal, Montreal, QC H3C 3J7, Canada; Université de Montréal, Montreal, QC H3C 3J7, Canada
| | - Benigno Rodriguez
- Case Western Reserve University School of Medicine, Cleveland, OH 10900, USA
| | - Michael M Lederman
- Case Western Reserve University School of Medicine, Cleveland, OH 10900, USA
| | - Daniel E Kaufmann
- Research Centre of the Centre Hospitalier de l'Université de Montréal, Montreal, QC H3C 3J7, Canada; Université de Montréal, Montreal, QC H3C 3J7, Canada
| | - Nichole R Klatt
- Department of Pediatrics, Miller School of Medicine, University of Miami, Miami, FL 33124, USA
| | - Cissy Kityo
- Joint Clinical Research Center, Kampala, Uganda
| | - Jason M Brenchley
- Barrier Immunity Section, Laboratory of Viral Diseases, NIAID/NIH, Bethesda, MD 20892, USA
| | - Timothy W Schacker
- Department of Medicine, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Rafick P Sekaly
- Department of Pathology, Case Western Reserve University, Cleveland, OH 10900, USA; Pathology Advanced Translational Research Unit, Department of Pathology and Laboratory Medicine, School of Medicine, Emory University, Atlanta, GA 30322, USA.
| | - Daniel C Douek
- Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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31
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Flynn JK, Langner CA, Karmele EP, Baker PJ, Pei L, Gorfu EG, Bochart RM, Santiana M, Smelkinson MG, Nutman TB, Altan-Bonnet N, Bosinger SE, Kelsall BL, Brenchley JM, Ortiz AM. Luminal microvesicles uniquely influence translocating bacteria after SIV infection. Mucosal Immunol 2021; 14:937-948. [PMID: 33731830 PMCID: PMC8225551 DOI: 10.1038/s41385-021-00393-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 12/23/2020] [Accepted: 02/16/2021] [Indexed: 02/04/2023]
Abstract
Microbial translocation contributes to persistent inflammation in both treated and untreated HIV infection. Although translocation is due in part to a disintegration of the intestinal epithelial barrier, there is a bias towards the translocation of Proteobacteria. We hypothesized that intestinal epithelial microvesicle cargo differs after HIV infection and contributes to biased translocation. We isolated gastrointestinal luminal microvesicles before and after progressive simian immunodeficiency virus (SIV) infection in rhesus macaques and measured miRNA and antimicrobial peptide content. We demonstrate that these microvesicles display decreased miR-28-5p, -484, -584-3p, and -584-5p, and let-7b-3p, as well as increased beta-defensin 1 after SIV infection. We further observed dose-dependent growth sensitivity of commensal Lactobacillus salivarius upon co-culture with isolated microvesicles. Infection-associated microvesicle differences were not mirrored in non-progressively SIV-infected sooty mangabeys. Our findings describe novel alterations of antimicrobial control after progressive SIV infection that influence the growth of translocating bacterial taxa. These studies may lead to the development of novel therapeutics for treating chronic HIV infection, microbial translocation, and inflammation.
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Affiliation(s)
- Jacob K. Flynn
- Barrier Immunity Section, Laboratory of Viral Diseases, Division of Intramural Research, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD 20892
| | - Charlotte A. Langner
- Barrier Immunity Section, Laboratory of Viral Diseases, Division of Intramural Research, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD 20892
| | - Erik P. Karmele
- Mucosal Immunobiology Section, Laboratory of Molecular Immunology, NIAID, NIH, Bethesda, MD 20892
| | - Phillip J. Baker
- Barrier Immunity Section, Laboratory of Viral Diseases, Division of Intramural Research, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD 20892
| | - Luxin Pei
- Barrier Immunity Section, Laboratory of Viral Diseases, Division of Intramural Research, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD 20892
| | - Edlawit G. Gorfu
- Barrier Immunity Section, Laboratory of Viral Diseases, Division of Intramural Research, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD 20892
| | - Rachele M. Bochart
- Division of Animal Resources, Yerkes National Primate Research Center (YNPRC), Atlanta, GA 30329
| | - Marianita Santiana
- Laboratory of Host-Pathogen Dynamics, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892
| | | | - Thomas B. Nutman
- Helminth Immunology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Nihal Altan-Bonnet
- Laboratory of Host-Pathogen Dynamics, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892
| | - Steven E. Bosinger
- Yerkes Nonhuman Primate Genomics Core Laboratory, YNPRC, Atlanta, GA 30329,Division of Microbiology & Immunology, YNPRC, Atlanta, GA 30329,Department of Pathology & Laboratory Medicine, School of Medicine, Emory University, Atlanta, GA 30329
| | - Brian L. Kelsall
- Mucosal Immunobiology Section, Laboratory of Molecular Immunology, NIAID, NIH, Bethesda, MD 20892
| | - Jason M. Brenchley
- Barrier Immunity Section, Laboratory of Viral Diseases, Division of Intramural Research, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD 20892,Corresponding author: Jason Brenchley, 4 Memorial Drive, 9000 Rockville Pike, Bethesda MD 20892, Phone: 301-496-1498, Fax: 301-480-1535,
| | - Alexandra M. Ortiz
- Barrier Immunity Section, Laboratory of Viral Diseases, Division of Intramural Research, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD 20892
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Bai X, Narayanan A, Nowak P, Ray S, Neogi U, Sönnerborg A. Whole-Genome Metagenomic Analysis of the Gut Microbiome in HIV-1-Infected Individuals on Antiretroviral Therapy. Front Microbiol 2021; 12:667718. [PMID: 34248876 PMCID: PMC8267369 DOI: 10.3389/fmicb.2021.667718] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Accepted: 05/31/2021] [Indexed: 01/14/2023] Open
Abstract
Gut microbiome plays a significant role in HIV-1 immunopathogenesis and HIV-1-associated complications. Previous studies have mostly been based on 16S rRNA gene sequencing, which is limited in taxonomic resolution at the genus level and inferred functionality. Herein, we performed a deep shotgun metagenomics study with the aim to obtain a more precise landscape of gut microbiome dysbiosis in HIV-1 infection. A reduced tendency of alpha diversity and significantly higher beta diversity were found in HIV-1-infected individuals on antiretroviral therapy (ART) compared to HIV-1-negative controls. Several species, such as Streptococcus anginosus, Actinomyces odontolyticus, and Rothia mucilaginosa, were significantly enriched in the HIV-1-ART group. Correlations were observed between the degree of immunodeficiency and gut microbiome in terms of microbiota composition and metabolic pathways. Furthermore, microbial shift in HIV-1-infected individuals was found to be associated with changes in microbial virulome and resistome. From the perspective of methodological evaluations, our study showed that different DNA extraction protocols significantly affect the genomic DNA quantity and quality. Moreover, whole metagenome sequencing depth affects critically the recovery of microbial genes, including virulome and resistome, while less than 5 million reads per sample is sufficient for taxonomy profiling in human fecal metagenomic samples. These findings advance our understanding of human gut microbiome and their potential associations with HIV-1 infection. The methodological assessment assists in future study design to accurately assess human gut microbiome.
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Affiliation(s)
- Xiangning Bai
- Division of Clinical Microbiology, Department of Laboratory Medicine, ANA Futura, Karolinska Institutet, Stockholm, Sweden.,Division of Infectious Diseases, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden.,State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.,Division of Laboratory Medicine, Oslo University Hospital, Oslo, Norway
| | - Aswathy Narayanan
- Division of Infectious Diseases, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Piotr Nowak
- Division of Infectious Diseases, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden.,Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden.,The Laboratory for Molecular Infection Medicine Sweden MIMS, Umeå University, Umeå, Sweden
| | - Shilpa Ray
- Division of Clinical Microbiology, Department of Laboratory Medicine, ANA Futura, Karolinska Institutet, Stockholm, Sweden.,The Laboratory for Molecular Infection Medicine Sweden MIMS, Umeå University, Umeå, Sweden
| | - Ujjwal Neogi
- Division of Clinical Microbiology, Department of Laboratory Medicine, ANA Futura, Karolinska Institutet, Stockholm, Sweden
| | - Anders Sönnerborg
- Division of Clinical Microbiology, Department of Laboratory Medicine, ANA Futura, Karolinska Institutet, Stockholm, Sweden.,Division of Infectious Diseases, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden.,Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
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Rectal microbiota diversity in Kenyan MSM is inversely associated with frequency of receptive anal sex, independent of HIV status. AIDS 2021; 35:1091-1101. [PMID: 33534201 DOI: 10.1097/qad.0000000000002829] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
OBJECTIVE Both HIV infection and identifying as MSM have been linked to altered rectal microbiota composition, but few studies have studied sexual behavioural associations with rectal microbiota within MSM. In addition, most rectal microbiota studies in MSM have been limited geographically to Europe and North America, and replication of findings in lower and middle-income countries is lacking. DESIGN A cross-sectional study. METHODS We enrolled MSM from Nairobi, Kenya, and determined their HIV/sexually transmitted infection status. Rectal specimens were obtained for 16s rRNA sequencing of the rectal microbiota, and sexual behaviour was characterized using a standardized questionnaire. Microbiome differences were modelled using nonparametric statistics, Bray-Curtis ecological distance metrics and analyses of differential taxa abundance. Multivariable linear regression was used to model HIV status and recent sexual activity as predictors of alpha diversity, controlling for a range of covariates. RESULTS Alpha diversity was consistently lower in Kenyan HIV-infected MSM (n = 80), including those on antiretroviral therapy (ART) compared with HIV-uninfected MSM. A statistical trend was observed for clustering of HIV status by Prevotella or Bacteroides dominance (P = 0.13). Several taxa were enriched in HIV-positive men, including Roseburia, Lachnospira, Streptococcus and Granulicatella. Receptive anal sex with several types of sexual partners (paying, regular, casual) was associated with lower Chao1 and Simpson diversity, independent of HIV status, while HIV infection was associated lower Chao1 (P = 0.030) but not Simpson diversity (P = 0.49). CONCLUSION Both HIV infection and sexual behaviour were associated with rectal microflora alpha diversity, in particular richness, but not Prevotella spp. dominance, in Kenyan MSM. Associations were more robust for sexual behaviour.
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Armstrong AJS, Quinn K, Fouquier J, Li SX, Schneider JM, Nusbacher NM, Doenges KA, Fiorillo S, Marden TJ, Higgins J, Reisdorph N, Campbell TB, Palmer BE, Lozupone CA. Systems Analysis of Gut Microbiome Influence on Metabolic Disease in HIV-Positive and High-Risk Populations. mSystems 2021; 6:e01178-20. [PMID: 34006628 PMCID: PMC8269254 DOI: 10.1128/msystems.01178-20] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 04/15/2021] [Indexed: 12/20/2022] Open
Abstract
Poor metabolic health, characterized by insulin resistance and dyslipidemia, is higher in people living with HIV and has been linked with inflammation, antiretroviral therapy (ART) drugs, and ART-associated lipodystrophy (LD). Metabolic disease is associated with gut microbiome composition outside the context of HIV but has not been deeply explored in HIV infection or in high-risk men who have sex with men (HR-MSM), who have a highly altered gut microbiome composition. Furthermore, the contribution of increased bacterial translocation and associated systemic inflammation that has been described in HIV-positive and HR-MSM individuals has not been explored. We used a multiomic approach to explore relationships between impaired metabolic health, defined using fasting blood markers, gut microbes, immune phenotypes, and diet. Our cohort included ART-treated HIV-positive MSM with or without LD, untreated HIV-positive MSM, and HR-MSM. For HIV-positive MSM on ART, we further explored associations with the plasma metabolome. We found that elevated plasma lipopolysaccharide binding protein (LBP) was the most important predictor of impaired metabolic health and network analysis showed that LBP formed a hub joining correlated microbial and immune predictors of metabolic disease. Taken together, our results suggest the role of inflammatory processes linked with bacterial translocation and interaction with the gut microbiome in metabolic disease among HIV-positive and -negative MSM.IMPORTANCE The gut microbiome in people living with HIV (PLWH) is of interest since chronic infection often results in long-term comorbidities. Metabolic disease is prevalent in PLWH even in well-controlled infection and has been linked with the gut microbiome in previous studies, but little attention has been given to PLWH. Furthermore, integrated analyses that consider gut microbiome, together with diet, systemic immune activation, metabolites, and demographics, have been lacking. In a systems-level analysis of predictors of metabolic disease in PLWH and men who are at high risk of acquiring HIV, we found that increased lipopolysaccharide-binding protein, an inflammatory marker indicative of compromised intestinal barrier function, was associated with worse metabolic health. We also found impaired metabolic health associated with specific dietary components, gut microbes, and host and microbial metabolites. This study lays the framework for mechanistic studies aimed at targeting the microbiome to prevent or treat metabolic endotoxemia in HIV-infected individuals.
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Affiliation(s)
- Abigail J S Armstrong
- Department of Medicine, University of Colorado Denver, Aurora, Colorado, USA
- Department of Immunology and Microbiology, University of Colorado Denver, Aurora, Colorado, USA
- Center for Advanced Biotechnology and Medicine, Rutgers the State University, Piscataway, New Jersey, USA
| | - Kevin Quinn
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado, Aurora, Colorado, USA
| | - Jennifer Fouquier
- Department of Medicine, University of Colorado Denver, Aurora, Colorado, USA
| | - Sam X Li
- Department of Medicine, University of Colorado Denver, Aurora, Colorado, USA
| | | | - Nichole M Nusbacher
- Department of Medicine, University of Colorado Denver, Aurora, Colorado, USA
| | - Katrina A Doenges
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado, Aurora, Colorado, USA
| | - Suzanne Fiorillo
- Department of Medicine, University of Colorado Denver, Aurora, Colorado, USA
| | - Tyson J Marden
- Colorado Clinical and Translational Sciences Institute, Aurora, Colorado, USA
| | - Janine Higgins
- Department of Pediatrics, Section of Endocrinology, University of Colorado, Aurora, Colorado, USA
| | - Nichole Reisdorph
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado, Aurora, Colorado, USA
| | - Thomas B Campbell
- Department of Medicine, University of Colorado Denver, Aurora, Colorado, USA
| | - Brent E Palmer
- Department of Medicine, University of Colorado Denver, Aurora, Colorado, USA
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Gut Microbiota Diversity in HIV-Infected Patients on Successful Antiretroviral Treatment is Linked to Sexual Preferences but not CD4 Nadir. Arch Immunol Ther Exp (Warsz) 2021; 69:14. [PMID: 33983543 DOI: 10.1007/s00005-021-00616-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Accepted: 04/23/2021] [Indexed: 12/20/2022]
Abstract
The effects of HIV infection and antiretroviral therapy (ART) on the gut microbiome are poorly understood and the literature data are inconsistent. The aim of this study was to assess the alpha and beta diversity of the fecal microbiota in HIV-infected patients on successful antiretroviral therapy with regard to sexual preferences and CD4 nadir. Thirty-six HIV-infected ART-treated patients with HIV viremia below 20 copies/ml and CD4 > 500 cells/μl were divided into two subgroups based on CD4 nadir. The composition of the intestinal microbiota was assessed by 16SrRNA sequencing (MiSeq Illumina). The alpha and beta diversity were analyzed according to CD4 nadir count and sexual preference. Several alpha diversity indexes were significantly higher in the MSM group than in heterosexual patients. The alpha diversity did not differ significantly between patients with CD4 nadir > 500 cells/μl and CD4 nadir < 200 cells/μl. Beta diversity was also associated with sexual preference. A significant difference in Weighted Unifrac was observed between all MSM and all non-MSM participants (p = 0.001). The MSM group was more diverse and demonstrated greater distances in Weighted Unifrac than the non-MSM group. The relative abundance of the Prevotella enterotype was higher in the MSM than the non-MSM group. Sexual preferences demonstrated a stronger influence on alpha and beta diversity in HIV-infected patients following successful antiretroviral treatment than HIV infection itself. The observed lack of association between CD4 nadir and alpha and beta diversity may be caused by the restoration of the faecal microbiota following antiretroviral treatment.
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DeJong EN, Surette MG, Bowdish DME. The Gut Microbiota and Unhealthy Aging: Disentangling Cause from Consequence. Cell Host Microbe 2021; 28:180-189. [PMID: 32791111 DOI: 10.1016/j.chom.2020.07.013] [Citation(s) in RCA: 224] [Impact Index Per Article: 56.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 07/03/2020] [Accepted: 07/21/2020] [Indexed: 12/20/2022]
Abstract
The gut microbiota changes with age, but it is not clear to what degree these changes are due to physiologic changes, age-associated inflammation or immunosenescence, diet, medications, or chronic health conditions. Observational studies in humans find that there are profound differences between the microbiomes of long-lived and frail individuals, but the degree to which these differences promote or prevent late-life health is unclear. Studies in model organisms demonstrate that age-related microbial dysbiosis causes intestinal permeability, systemic inflammation, and premature mortality, but identifying causal relationships have been challenging. Herein, we review how physiological and immune changes contribute to microbial dysbiosis and the degree to which microbial dysbiosis contributes to late-life health conditions. We discuss the features of the aging microbiota that make it more amenable to diet and pre- and probiotic interventions. Health interventions that promote a diverse microbiome could influence the health of older adults.
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Affiliation(s)
- Erica N DeJong
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON L8N 3Z5, Canada; McMaster Immunology Research Centre, McMaster University, Hamilton, ON L8N 3Z5, Canada; Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8N 3Z5, Canada
| | - Michael G Surette
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8N 3Z5, Canada; Department of Biochemistry & Biomedical Sciences, McMaster University, Hamilton, ON L8N 3Z5, Canada; Department of Medicine, McMaster University, Hamilton, ON L8N 3Z5, Canada; Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, ON L8N 3Z5, Canada
| | - Dawn M E Bowdish
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON L8N 3Z5, Canada; McMaster Immunology Research Centre, McMaster University, Hamilton, ON L8N 3Z5, Canada; Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8N 3Z5, Canada.
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Abstract
PURPOSE OF REVIEW To evaluate the current scientific basis for administering probiotics to people living with HIV (PLHIV) to alleviate chronic inflammation and subsequently improve their prognosis. RECENT FINDINGS The gut microbiome is a potential contributing factor to low-grade inflammation in HIV infection, and there is a scientific rationale for attempting to attenuate inflammation by administering probiotics. Sixteen reports from clinical studies in antiretroviral therapy (ART)-treated PLHIV assessing inflammation after probiotic intervention have been identified; half of them randomized control trials (RCT). Some of the studies report improvement in some parameters of inflammation, but results are inconsistent. No studies report improvement of CD4 counts. None of the RCTs report improvements in any markers of inflammation when analyzed according to protocol. SUMMARY Current scientific evidence does not support the use of probiotics to alleviate inflammation in HIV infection. The potential effect of probiotic intervention in ART-treated PLHIV with high risk for inflammation remains to be investigated.
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Ancona G, Merlini E, Tincati C, Barassi A, Calcagno A, Augello M, Bono V, Bai F, Cannizzo ES, d'Arminio Monforte A, Marchetti G. Long-Term Suppressive cART Is Not Sufficient to Restore Intestinal Permeability and Gut Microbiota Compositional Changes. Front Immunol 2021; 12:639291. [PMID: 33717191 PMCID: PMC7952451 DOI: 10.3389/fimmu.2021.639291] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 02/04/2021] [Indexed: 12/22/2022] Open
Abstract
Background: We explored the long-term effects of cART on markers of gut damage, microbial translocation, and paired gut/blood microbiota composition, with a focus on the role exerted by different drug classes. Methods: We enrolled 41 cART naïve HIV-infected subjects, undergoing blood and fecal sampling prior to cART (T0) and after 12 (T12) and 24 (T24) months of therapy. Fifteen HIV-uninfected individuals were enrolled as controls. We analyzed: (i) T-cell homeostasis (flow cytometry); (ii) microbial translocation (sCD14, EndoCab, 16S rDNA); (iii) intestinal permeability and damage markers (LAC/MAN, I-FABP, fecal calprotectin); (iv) plasma and fecal microbiota composition (alpha- and beta-diversity, relative abundance); (v) functional metagenome predictions (PICRUSt). Results: Twelve and twenty four-month successful cART resulted in a rise in EndoCAb (p = 0.0001) and I-FABP (p = 0.039) vis-à-vis stable 16S rDNA, sCD14, calprotectin and LAC/MAN, along with reduced immune activation in the periphery. Furthermore, cART did not lead to substantial modifications of microbial composition in both plasma and feces and metabolic metagenome predictions. The stratification according to cART regimens revealed a feeble effect on microbiota composition in patients on NNRTI-based or INSTI-based regimens, but not PI-based regimens. Conclusions: We hereby show that 24 months of viro-immunological effective cART, while containing peripheral hyperactivation, exerts only minor effects on the gastrointestinal tract. Persistent alteration of plasma markers indicative of gut structural and functional impairment seemingly parallels enduring fecal dysbiosis, irrespective of drug classes, with no effect on metabolic metagenome predictions.
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Affiliation(s)
- Giuseppe Ancona
- Clinic of Infectious Diseases, Department of Health Sciences, University of Milan, Azienda Socio Sanitaria Territoriale Santi Paolo e Carlo, Milan, Italy
| | - Esther Merlini
- Clinic of Infectious Diseases, Department of Health Sciences, University of Milan, Azienda Socio Sanitaria Territoriale Santi Paolo e Carlo, Milan, Italy
| | - Camilla Tincati
- Clinic of Infectious Diseases, Department of Health Sciences, University of Milan, Azienda Socio Sanitaria Territoriale Santi Paolo e Carlo, Milan, Italy
| | - Alessandra Barassi
- Biochemistry Laboratory, Department of Health Sciences, University of Milan, Azienda Socio Sanitaria Territoriale Santi Paolo e Carlo, Milan, Italy
| | - Andrea Calcagno
- Unit of Infectious Diseases, Department of Medical Sciences, University of Turin, Turin, Italy
| | - Matteo Augello
- Clinic of Infectious Diseases, Department of Health Sciences, University of Milan, Azienda Socio Sanitaria Territoriale Santi Paolo e Carlo, Milan, Italy
| | - Valeria Bono
- Clinic of Infectious Diseases, Department of Health Sciences, University of Milan, Azienda Socio Sanitaria Territoriale Santi Paolo e Carlo, Milan, Italy
| | - Francesca Bai
- Clinic of Infectious Diseases, Department of Health Sciences, University of Milan, Azienda Socio Sanitaria Territoriale Santi Paolo e Carlo, Milan, Italy
| | - Elvira S Cannizzo
- Clinic of Infectious Diseases, Department of Health Sciences, University of Milan, Azienda Socio Sanitaria Territoriale Santi Paolo e Carlo, Milan, Italy
| | - Antonella d'Arminio Monforte
- Clinic of Infectious Diseases, Department of Health Sciences, University of Milan, Azienda Socio Sanitaria Territoriale Santi Paolo e Carlo, Milan, Italy
| | - Giulia Marchetti
- Clinic of Infectious Diseases, Department of Health Sciences, University of Milan, Azienda Socio Sanitaria Territoriale Santi Paolo e Carlo, Milan, Italy
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Abstract
The usage of combination antiretroviral therapy in people with HIV (PWH) has incited profound improvement in morbidity and mortality. Yet, PWH may not experience full restoration of immune function which can manifest with non-AIDS comorbidities that frequently associate with residual inflammation and can imperil quality of life or longevity. In this review, we discuss the pathogenesis underlying chronic inflammation and residual immune dysfunction in PWH, as well as potential therapeutic interventions to ameliorate them and prevent incidence or progression of non-AIDS comorbidities. Current evidence advocates that early diagnosis and prompt initiation of therapy at high CD4 counts may represent the best available approach for an improved immune recovery in PWH.
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Affiliation(s)
- Catherine W Cai
- HIV Pathogenesis Section, Laboratory of Immunoregulation, NIAID, NIH, United States
| | - Irini Sereti
- HIV Pathogenesis Section, Laboratory of Immunoregulation, NIAID, NIH, United States.
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Rosel-Pech C, Chávez-Torres M, Bekker-Méndez VC, Pinto-Cardoso S. Therapeutic avenues for restoring the gut microbiome in HIV infection. Curr Opin Pharmacol 2020; 54:188-201. [PMID: 33271427 DOI: 10.1016/j.coph.2020.09.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 09/11/2020] [Accepted: 09/24/2020] [Indexed: 02/07/2023]
Abstract
The interplay between the gut microbiota, the intestinal barrier and the mucosal immune system is profoundly altered in Human Immunodeficiency Virus (HIV) infection. An HIV-associated microbial dysbiotic signature has been difficult to define due to the strong impact of confounders that are intimately linked with HIV infection, namely HIV risk behaviors. When controlling for sexual preference and gender, HIV-associated microbial dysbiotic signatures are characterized by an increase in deleterious taxa and a decrease in beneficial bacteria and their respective metabolic end-products. First attempts to restore the gut microbiota of HIV subjects on Antiretroviral Therapy using Fecal Microbiota Transplantation proved to be safe and reported mild transient engraftment of donor microbiota and no effect on markers of HIV disease progression. This review focuses on the current evidence supporting a role for microbial dysbiosis in HIV pathogenesis, and reviews current microbiome-based therapeutics for restoring the gut microbiota in HIV infection.
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Affiliation(s)
- Cecilia Rosel-Pech
- Unidad de Investigación Médica en Inmunología e Infectología, Hospital de Infectología "Dr. Daniel Méndez Hernández", Centro Médico Nacional "La Raza", IMSS, Ciudad de México, Mexico; Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Monserrat Chávez-Torres
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Ciudad de México, Mexico; Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Ciudad de México, Mexico
| | - Vilma Carolina Bekker-Méndez
- Unidad de Investigación Médica en Inmunología e Infectología, Hospital de Infectología "Dr. Daniel Méndez Hernández", Centro Médico Nacional "La Raza", IMSS, Ciudad de México, Mexico
| | - Sandra Pinto-Cardoso
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Ciudad de México, Mexico.
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Jasinska AJ, Dong TS, Lagishetty V, Katzka W, Jacobs JP, Schmitt CA, Cramer JD, Ma D, Coetzer WG, Grobler JP, Turner TR, Freimer N, Pandrea I, Apetrei C. Shifts in microbial diversity, composition, and functionality in the gut and genital microbiome during a natural SIV infection in vervet monkeys. MICROBIOME 2020; 8:154. [PMID: 33158452 PMCID: PMC7648414 DOI: 10.1186/s40168-020-00928-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 10/06/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND The microbiota plays an important role in HIV pathogenesis in humans. Microbiota can impact health through several pathways such as increasing inflammation in the gut, metabolites of bacterial origin, and microbial translocation from the gut to the periphery which contributes to systemic chronic inflammation and immune activation and the development of AIDS. Unlike HIV-infected humans, SIV-infected vervet monkeys do not experience gut dysfunction, microbial translocation, and chronic immune activation and do not progress to immunodeficiency. Here, we provide the first reported characterization of the microbial ecosystems of the gut and genital tract in a natural nonprogressing host of SIV, wild vervet monkeys from South Africa. RESULTS We characterized fecal, rectal, vaginal, and penile microbiomes in vervets from populations heavily infected with SIV from diverse locations across South Africa. Geographic site, age, and sex affected the vervet microbiome across different body sites. Fecal and vaginal microbiome showed marked stratification with three enterotypes in fecal samples and two vagitypes, which were predicted functionally distinct within each body site. External bioclimatic factors, biome type, and environmental temperature influenced microbiomes locally associated with vaginal and rectal mucosa. Several fecal microbial taxa were linked to plasma levels of immune molecules, for example, MIG was positively correlated with Lactobacillus and Escherichia/Shigella and Helicobacter, and IL-10 was negatively associated with Erysipelotrichaceae, Anaerostipes, Prevotella, and Anaerovibrio, and positively correlated with Bacteroidetes and Succinivibrio. During the chronic phase of infection, we observed a significant increase in gut microbial diversity, alterations in community composition (including a decrease in Proteobacteria/Succinivibrio in the gut) and functionality (including a decrease in genes involved in bacterial invasion of epithelial cells in the gut), and partial reversibility of acute infection-related shifts in microbial abundance observed in the fecal microbiome. As part of our study, we also developed an accurate predictor of SIV infection using fecal samples. CONCLUSIONS The vervets infected with SIV and humans infected with HIV differ in microbial responses to infection. These responses to SIV infection may aid in preventing microbial translocation and subsequent disease progression in vervets, and may represent host microbiome adaptations to the virus. Video Abstract.
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Affiliation(s)
- Anna J Jasinska
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA, USA.
- Department of Molecular Genetics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland.
- Eye on Primates, Los Angeles, CA, USA.
| | - Tien S Dong
- The Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Venu Lagishetty
- The Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - William Katzka
- The Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Jonathan P Jacobs
- The Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
- Division of Gastroenterology, Hepatology and Parenteral Nutrition, VA Greater Los Angeles Healthcare System, Los Angeles, CA, USA
- UCLA Microbiome Center, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | | | - Jennifer Danzy Cramer
- Department of Sociology, Anthropology, and General Studies, American Public University System, Charles Town, WV, USA
| | - Dongzhu Ma
- Department of Orthopedic Surgery, University of Pittsburgh, Pittsburgh, PA, USA
| | - Willem G Coetzer
- Department of Genetics, University of the Free State, Bloemfontein, South Africa
| | - J Paul Grobler
- Department of Genetics, University of the Free State, Bloemfontein, South Africa
| | - Trudy R Turner
- Department of Genetics, University of the Free State, Bloemfontein, South Africa
- Department of Anthropology, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Nelson Freimer
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA, USA
| | - Ivona Pandrea
- Department of Pathology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Cristian Apetrei
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
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Gelpi M, Vestad B, Hansen SH, Holm K, Drivsholm N, Goetz A, Kirkby NS, Lindegaard B, Lebech AM, Hoel H, Michelsen AE, Ueland T, Gerstoft J, Lundgren J, Hov JR, Nielsen SD, Trøseid M. Impact of Human Immunodeficiency Virus-Related Gut Microbiota Alterations on Metabolic Comorbid Conditions. Clin Infect Dis 2020; 71:e359-e367. [PMID: 31894240 DOI: 10.1093/cid/ciz1235] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 12/30/2019] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND We aimed to identify a human immunodeficiency virus (HIV)-related microbiota signature, independent of sexual preferences and demographic confounders, in order to assess a possible impact of the microbiome on metabolic comorbid conditions. METHODS Bacterial 16S ribosomal RNA analyses were performed on stool samples from 405 HIV-infected and 111 uninfected participants of the Copenhagen Comorbidity in HIV Infection (COCOMO) study. Individuals were stratified according to sexual behavior (men who have sex with men [MSM] vs non-MSM). RESULTS After excluding MSM-associated microbiota traits and adjusting for confounders, we identified an HIV-related microbiota signature, consisting of lower biodiversity, increased relative abundance of the bacterial clades Gammaproteobacteria and Desulfovibrionaceae and decrease in several Clostridia. This microbiota profile was associated with a 2-fold excess risk of metabolic syndrome, driven by increase in Desulfovibrionaceae and decrease in Clostridia (Butyrivibrio, Coprococcus 2, Lachnospiraceae UCG-001 and CAG-56). This association was accentuated (5-fold excess risk) in individuals with previous severe immunodeficiency, which also modified the association between HIV-related microbiota signature and visceral adipose tissue (VAT) area (P for interaction = .01). Accordingly, HIV-related microbiota was associated with 30-cm2 larger VAT in individuals with history of severe immunodeficiency, but not in those without. CONCLUSION The HIV-related microbiota was associated with increased risk of metabolic syndrome and VAT accumulation, particularly in individuals with previous severe immunodeficiency, driven by increased Desulfovibrionaceae and lower abundance of several Clostridia. Our findings suggest a potential interplay between HIV-related microbiota, immune dysfunction and metabolic comorbid conditions. Interventions targeting the gut microbiome may be warranted to reduce cardiovascular risk, particularly in individuals with previous immunodeficiency.
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Affiliation(s)
- Marco Gelpi
- Viro-immunology Research Unit, Department of Infectious Diseases 8632, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Beate Vestad
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Research Institute of Internal Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital Rikshospitalet, Oslo, Norway
| | - Simen Hyll Hansen
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Research Institute of Internal Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital Rikshospitalet, Oslo, Norway
- Norwegian PSC Research Center, Department of Transplantation Medicine, Oslo University Hospital Rikshospitalet, Oslo, Norway
| | - Kristian Holm
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Research Institute of Internal Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital Rikshospitalet, Oslo, Norway
- Norwegian PSC Research Center, Department of Transplantation Medicine, Oslo University Hospital Rikshospitalet, Oslo, Norway
| | - Ninna Drivsholm
- Viro-immunology Research Unit, Department of Infectious Diseases 8632, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Alexandra Goetz
- Research Institute of Internal Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital Rikshospitalet, Oslo, Norway
- Norwegian PSC Research Center, Department of Transplantation Medicine, Oslo University Hospital Rikshospitalet, Oslo, Norway
| | - Nicolai Søren Kirkby
- Department of Microbiology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Birgitte Lindegaard
- Center for inflammation and Metabolism, Rigshospitalet, København, Denmark
- Department of Pulmonary and Infectious Diseases, Nordsjællands Hospital, Hillerød, Denmark
| | - Anne-Mette Lebech
- Department of Infectious Diseases, Hvidovre Hospital, Copenhagen University Hospital, Copenhagen, Denmark
| | - Hedda Hoel
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Research Institute of Internal Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital Rikshospitalet, Oslo, Norway
- Medical Department, Lovisenberg Hospital, Oslo, Norway
| | - Annika E Michelsen
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Research Institute of Internal Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital Rikshospitalet, Oslo, Norway
| | - Thor Ueland
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Research Institute of Internal Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital Rikshospitalet, Oslo, Norway
| | - Jan Gerstoft
- Viro-immunology Research Unit, Department of Infectious Diseases 8632, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Jens Lundgren
- Viro-immunology Research Unit, Department of Infectious Diseases 8632, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
- Centre of Excellence for Health, Immunity and Infections, Department of Infectious Diseases 8632, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Johannes Roksund Hov
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Research Institute of Internal Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital Rikshospitalet, Oslo, Norway
- Norwegian PSC Research Center, Department of Transplantation Medicine, Oslo University Hospital Rikshospitalet, Oslo, Norway
- Section of Gastroenterology, Department of Transplantation Medicine, Oslo University Hospital Rikshospitalet, Oslo, Norway
| | - Susanne Dam Nielsen
- Viro-immunology Research Unit, Department of Infectious Diseases 8632, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Marius Trøseid
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Research Institute of Internal Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital Rikshospitalet, Oslo, Norway
- Section of Clinical Immunology and Infectious Diseases, Department of Rheumatology, Dermatology and Infectious Diseases, Oslo, Norway
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Ruiz-Briseño MDR, De Arcos-Jiménez JC, Ratkovich-González S, Sánchez-Reyes K, González-Hernández LA, Andrade-Villanueva JF, Alvarez-Zavala M. Association of intestinal and systemic inflammatory biomarkers with immune reconstitution in HIV+ patients on ART. JOURNAL OF INFLAMMATION-LONDON 2020; 17:32. [PMID: 33071649 PMCID: PMC7558748 DOI: 10.1186/s12950-020-00262-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 09/30/2020] [Indexed: 12/31/2022]
Abstract
Background HIV infection is characterized by CD4+ T-cells depletion related to gut damage, microbial translocation, immune activation and intestinal and systemic low-grade inflammation. With the use of antiretroviral treatment, these alterations in HIV+ patients reach similar levels to HIV- controls. However, almost 20% patients have deficient immune reconstitution of CD4+ T-cells, which make them more susceptible to develop non-AIDS and AIDS comorbidities. Methods HIV+ patients on ART, with sustained virologic control were grouped according to their immune reconstitution as: immunological responders (n = 18) and immunological non-responders (n = 18); also, HIV- controls were enrolled (n = 14). CD4+ and CD8+ T-cell activation (HLA-DR+ and CD38+ single and co-expression) were measured by flow cytometry. Serum levels of sCD14, sCD163, lipopolysaccharide, I-FABP, sST2, as well as fecal levels of calprotectin, lactoferrin and secretory IgA were evaluated by ELISA. Levels of C-reactive protein were determined by a high sensibility singleplex bead-based immunoassay. Serum and fecal concentrations of proinflammatory cytokines were quantified by multiplex bead-based immunoassay. Results HLA-DR+ and CD38+ co-expression, as well as median fluorescence intensity in CD4+ and CD8+ T-cells subpopulations was greater in immunological non-responders group, after normalization and fold change calculation. Similarly, this group presented higher levels of sCD14, C-reactive protein, as well as fecal calprotectin and lactoferrin. Furthermore, both HIV+ groups showed elevated levels of proinflammatory cytokines in stool. Conclusions Our data suggests that despite the virologic control, HIV+ patients under treatment with deficient immune reconstitution showed elevation of both innate and T-cells immune activation, as well as intestinal and systemic inflammation. However, some patients with CD4+ T-cells count above 350 cells/μL also presented these alterations. Future studies are necessary to evaluate the dynamics of multiple systemic and intestinal biomarkers in diverse types of HIV+ patients, as such as their clinical impact.
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Affiliation(s)
- Mariana Del Rocio Ruiz-Briseño
- Molecular Biology in Medicine PhD Program, Universidad de Guadalajara, Guadalajara, Jalisco Mexico.,HIV and Immunodeficiencies Research Institute (InIVIH), Universidad de Guadalajara, Guadalajara, Jalisco Mexico
| | - Judith Carolina De Arcos-Jiménez
- Molecular Biology in Medicine PhD Program, Universidad de Guadalajara, Guadalajara, Jalisco Mexico.,HIV and Immunodeficiencies Research Institute (InIVIH), Universidad de Guadalajara, Guadalajara, Jalisco Mexico
| | - Sarah Ratkovich-González
- Molecular Biology in Medicine PhD Program, Universidad de Guadalajara, Guadalajara, Jalisco Mexico.,HIV and Immunodeficiencies Research Institute (InIVIH), Universidad de Guadalajara, Guadalajara, Jalisco Mexico
| | - Karina Sánchez-Reyes
- HIV and Immunodeficiencies Research Institute (InIVIH), Universidad de Guadalajara, Guadalajara, Jalisco Mexico
| | - Luz A González-Hernández
- HIV and Immunodeficiencies Research Institute (InIVIH), Universidad de Guadalajara, Guadalajara, Jalisco Mexico.,HIV Unit Department, Antiguo Hospital Civil de Guadalajara "Fray Antonio Alcalde", Guadalajara, Jalisco Mexico
| | - Jaime F Andrade-Villanueva
- HIV and Immunodeficiencies Research Institute (InIVIH), Universidad de Guadalajara, Guadalajara, Jalisco Mexico.,HIV Unit Department, Antiguo Hospital Civil de Guadalajara "Fray Antonio Alcalde", Guadalajara, Jalisco Mexico
| | - Monserrat Alvarez-Zavala
- HIV and Immunodeficiencies Research Institute (InIVIH), Universidad de Guadalajara, Guadalajara, Jalisco Mexico
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Zhou J, Zhang Y, Cui P, Luo L, Chen H, Liang B, Jiang J, Ning C, Tian L, Zhong X, Ye L, Liang H, Huang J. Gut Microbiome Changes Associated With HIV Infection and Sexual Orientation. Front Cell Infect Microbiol 2020; 10:434. [PMID: 33102244 PMCID: PMC7546801 DOI: 10.3389/fcimb.2020.00434] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 07/15/2020] [Indexed: 12/20/2022] Open
Abstract
Background: Many studies have explored changes in the gut microbiome associated with HIV infection, but the consistent pattern of changes has not been clarified. Men who have sex with men (MSM) are very likely to be an independent influencing factor of the gut microbiome, but relevant research is still lacking. Methods: We conducted a meta-analysis by screening 12 published studies of 16S rRNA gene amplicon sequencing of gut microbiomes related to HIV/AIDS (six of these studies contain data that is relevant and available to MSM) from NCBI and EBI databases. The analysis of gut microbiomes related to HIV infection status and MSM status included 1,288 samples (HIV-positive (HIV+) individuals, n = 744; HIV-negative (HIV–) individuals, n = 544) and 632 samples (MSM, n = 328; non-MSM, n = 304), respectively. The alpha diversity indexes, beta diversity indexes, differentially enriched genera, differentially enriched species, and differentially enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) functional pathways related to gut microbiomes were calculated. Finally, the overall trend of the above indicators was evaluated. Results: Our results indicate that HIV+ status is associated with decreased alpha diversity of the gut microbiome. MSM status is an important factor that affects the study of HIV-related gut microbiomes; that is, MSM are associated with alpha diversity changes in the gut microbiome regardless of HIV infection, and the changes in the gut microbiome composition of MSM are more significant than those of HIV+ individuals. A consistent change in Bacteroides caccae, Bacteroides ovatus, Bacteroides uniformis, and Prevotella stercorea was found in HIV+ individuals and MSM. The differential expression of the gut microbiome may be accompanied by changes in functional pathways of carbohydrate metabolism, amino acid metabolism, and lipid Metabolism. Conclusions: This study shows that the changes in the gut microbiome are related to HIV and MSM status. Importantly, MSM status may have a far greater impact on the gut microbiome than HIV status.
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Affiliation(s)
- Jie Zhou
- Guangxi Key Laboratory of AIDS Prevention and Treatment, Guangxi Universities Key Laboratory of Prevention and Control of Highly Prevalent Disease, Guangxi Medical University, Nanning, China.,School of Public Health, Guangxi Medical University, Nanning, China
| | - Yu Zhang
- Guangxi Key Laboratory of AIDS Prevention and Treatment, Guangxi Universities Key Laboratory of Prevention and Control of Highly Prevalent Disease, Guangxi Medical University, Nanning, China.,School of Public Health, Guangxi Medical University, Nanning, China
| | - Ping Cui
- Guangxi Key Laboratory of AIDS Prevention and Treatment, Guangxi Universities Key Laboratory of Prevention and Control of Highly Prevalent Disease, Guangxi Medical University, Nanning, China.,Guangxi Collaborative Innovation Center for Biomedicine, Life Science Institute, Guangxi Medical University, Nanning, China
| | - Lijia Luo
- Guangxi Key Laboratory of AIDS Prevention and Treatment, Guangxi Universities Key Laboratory of Prevention and Control of Highly Prevalent Disease, Guangxi Medical University, Nanning, China.,School of Public Health, Guangxi Medical University, Nanning, China
| | - Hui Chen
- Guangxi Key Laboratory of AIDS Prevention and Treatment, Guangxi Universities Key Laboratory of Prevention and Control of Highly Prevalent Disease, Guangxi Medical University, Nanning, China.,The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Bingyu Liang
- Guangxi Key Laboratory of AIDS Prevention and Treatment, Guangxi Universities Key Laboratory of Prevention and Control of Highly Prevalent Disease, Guangxi Medical University, Nanning, China.,School of Public Health, Guangxi Medical University, Nanning, China
| | - Junjun Jiang
- Guangxi Key Laboratory of AIDS Prevention and Treatment, Guangxi Universities Key Laboratory of Prevention and Control of Highly Prevalent Disease, Guangxi Medical University, Nanning, China.,School of Public Health, Guangxi Medical University, Nanning, China
| | - Chuanyi Ning
- Guangxi Key Laboratory of AIDS Prevention and Treatment, Guangxi Universities Key Laboratory of Prevention and Control of Highly Prevalent Disease, Guangxi Medical University, Nanning, China.,Guangxi Collaborative Innovation Center for Biomedicine, Life Science Institute, Guangxi Medical University, Nanning, China
| | - Li Tian
- Guangxi Key Laboratory of AIDS Prevention and Treatment, Guangxi Universities Key Laboratory of Prevention and Control of Highly Prevalent Disease, Guangxi Medical University, Nanning, China.,The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Xiaodan Zhong
- Guangxi Key Laboratory of AIDS Prevention and Treatment, Guangxi Universities Key Laboratory of Prevention and Control of Highly Prevalent Disease, Guangxi Medical University, Nanning, China.,The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Li Ye
- Guangxi Key Laboratory of AIDS Prevention and Treatment, Guangxi Universities Key Laboratory of Prevention and Control of Highly Prevalent Disease, Guangxi Medical University, Nanning, China.,School of Public Health, Guangxi Medical University, Nanning, China.,Guangxi Collaborative Innovation Center for Biomedicine, Life Science Institute, Guangxi Medical University, Nanning, China
| | - Hao Liang
- Guangxi Key Laboratory of AIDS Prevention and Treatment, Guangxi Universities Key Laboratory of Prevention and Control of Highly Prevalent Disease, Guangxi Medical University, Nanning, China.,School of Public Health, Guangxi Medical University, Nanning, China.,Guangxi Collaborative Innovation Center for Biomedicine, Life Science Institute, Guangxi Medical University, Nanning, China
| | - Jiegang Huang
- Guangxi Key Laboratory of AIDS Prevention and Treatment, Guangxi Universities Key Laboratory of Prevention and Control of Highly Prevalent Disease, Guangxi Medical University, Nanning, China.,School of Public Health, Guangxi Medical University, Nanning, China
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45
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Gojanovich GS, Jacobson DL, Jao J, Russell JS, Van Dyke RB, Libutti DE, Sharma TS, Geffner ME, Gerschenson M. Mitochondrial Dysfunction and Insulin Resistance in Pubertal Youth Living with Perinatally Acquired HIV. AIDS Res Hum Retroviruses 2020; 36:703-711. [PMID: 32586116 DOI: 10.1089/aid.2020.0067] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Mitochondrial dysfunction (MD) is linked to cardiometabolic complications, such as obesity and insulin resistance (IR), the frequencies of which are higher in adults living with HIV infection and receiving combination antiretroviral therapies (ARV). ARV-treated youth living with perinatally acquired HIV infection (YLPHIV) may be especially susceptible to IR due to long-term exposure to both factors. Medical histories, fasting blood chemistry panels, and mitochondrial function in banked peripheral blood mononuclear cells (PBMCs) were assessed in eligible YLPHIV from the Pediatric HIV/AIDS Cohort Study (PHACS)/Adolescent Master Protocol (AMP) Mitochondrial Determinants Component cohort, stratified by Homeostatic Model Assessment of IR (HOMA-IR) score: case (score ≥4, n = 39) or control (score <4, n = 105). PBMCs were sources for mitochondrial (mt) DNA copies/cell; mtRNA transcript levels of oxidative phosphorylation (OXPHOS) subunits NADH dehydrogenases 1 and 6, and cytochrome B; and enzymatic activities of OXPHOS Complexes I (CI) and IV (CIV). Logistic regression models were fit to estimate the odds of IR case diagnosis, adjusted for sex, race/ethnicity, body mass index (BMI) z-score, and Tanner stage. IR cases were similar to controls by age, sex, and race/ethnicity. Cases had higher median levels of peak HIV viral load, lactate, pyruvate, triglycerides, and BMI z-scores. OXPHOS CI enzymatic activity was lower in cases (log10 1.62 vs. 1.70) and inversely correlated with HOMA-IR score (r = -0.157, p = .061), but did not associate with IR in adjusted models. Fully adjusted models indicated associations of nadir CD4% [odds ratio (OR) = 0.95, 95% confidence intervals (CIs) = 0.90-1.00] or peak HIV load (OR = 3.48, 95% CIs = 1.70-10.79) with IR. IR in YLPHIV was strongly associated with morphometrics, but early virologic and immunologic factors may also influence MD.
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Affiliation(s)
- Greg S. Gojanovich
- Department of Cell and Molecular Biology, John A. Burns School of Medicine, University of Hawaii, Honolulu, Hawaii, USA
| | - Denise L. Jacobson
- Center for Biostatistics in AIDS Research, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Jennifer Jao
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Jonathan S. Russell
- Center for Biostatistics in AIDS Research, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Russell B. Van Dyke
- Department of Pediatrics, Tulane University School of Medicine, New Orleans, Louisiana, USA
| | - Daniel E. Libutti
- Department of Cell and Molecular Biology, John A. Burns School of Medicine, University of Hawaii, Honolulu, Hawaii, USA
| | - Tanvi S. Sharma
- Division of Infectious Diseases, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Mitchell E. Geffner
- Saban Research Institute, Children's Hospital Los Angeles, Los Angeles, California, USA
| | - Mariana Gerschenson
- Department of Cell and Molecular Biology, John A. Burns School of Medicine, University of Hawaii, Honolulu, Hawaii, USA
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Abstract
Antiretroviral therapies efficiently block HIV-1 replication but need to be maintained for life. Moreover, chronic inflammation is a hallmark of HIV-1 infection that persists despite treatment. There is, therefore, an urgent need to better understand the mechanisms driving HIV-1 pathogenesis and to identify new targets for therapeutic intervention. In the past few years, the decisive role of cellular metabolism in the fate and activity of immune cells has been uncovered, as well as its impact on the outcome of infectious diseases. Emerging evidence suggests that immunometabolism has a key role in HIV-1 pathogenesis. The metabolic pathways of CD4+ T cells and macrophages determine their susceptibility to infection, the persistence of infected cells and the establishment of latency. Immunometabolism also shapes immune responses against HIV-1, and cell metabolic products are key drivers of inflammation during infection. In this Review, we summarize current knowledge of the links between HIV-1 infection and immunometabolism, and we discuss the potential opportunities and challenges for therapeutic interventions.
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47
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Sainz T, Gosalbes MJ, Talavera A, Jimenez-Hernandez N, Prieto L, Escosa L, Guillén S, Ramos JT, Muñoz-Fernández MÁ, Moya A, Navarro ML, Mellado MJ, Serrano-Villar S. Effect of a Nutritional Intervention on the Intestinal Microbiota of Vertically HIV-Infected Children: The Pediabiota Study. Nutrients 2020; 12:2112. [PMID: 32708743 PMCID: PMC7400861 DOI: 10.3390/nu12072112] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 07/08/2020] [Accepted: 07/10/2020] [Indexed: 02/07/2023] Open
Abstract
AIMS The gut microbiota exerts a critical influence in the immune system. The gut microbiota of human virus immunodeficiency (HIV)-infected children remains barely explored. We aimed to characterize the fecal microbiota in vertically HIV-infected children and to explore the effects of its modulation with a symbiotic nutritional intervention. METHODS a pilot, double blind, randomized placebo-controlled study including HIV-infected children who were randomized to receive a nutritional supplementation including prebiotics and probiotics or placebo for four weeks. HIV-uninfected siblings were recruited as controls. The V3-V4 region of the 16S rRNA gene was sequenced in fecal samples. RESULTS 22 HIV-infected children on antiretroviral therapy (ART) and with viral load (VL) <50/mL completed the follow-up period. Mean age was 11.4 ± 3.4 years, eight (32%) were male. Their microbiota showed reduced alpha diversity compared to controls and distinct beta diversity at the genus level (Adonis p = 0.042). Patients showed decreased abundance of commensals Faecalibacterium and an increase in Prevotella, Akkermansia and Escherichia. The nutritional intervention shaped the microbiota towards the control group, without a clear directionality. CONCLUSIONS Vertical HIV infection is characterized by changes in gut microbiota structure, distinct at the compositional level from the findings reported in adults. A short nutritional intervention attenuated bacterial dysbiosis, without clear changes at the community level. SUMMARY In a group of 24 vertically HIV-infected children, in comparison to 11 uninfected controls, intestinal dysbiosis was observed despite effective ART. Although not fully effective to restore the microbiota, a short intervention with pre/probiotics attenuated bacterial dysbiosis.
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Affiliation(s)
- Talía Sainz
- Servicio de Pediatría, Hospital Universitario La Paz and IdiPAZ, 28046 Madrid, Spain; (L.E.); (M.J.M.)
- Red de Investigación CoRISpe integrada en la Red en Infectología Pediátrica (RITIP), 28046 Madrid, Spain; (L.P.); (S.G.); (J.T.R.); (M.L.N.)
| | - María José Gosalbes
- Área Genómica y Salud, Fundación para el Fomento de la Investigación Sanitaria y Biomédica (FISABIO), 46010 Valencia, Spain; (M.J.G.); (N.J.-H.); (A.M.)
- CIBER en Epidemiología y Salud Pública, 28029 Madrid, Spain
| | - Alba Talavera
- Bioinformatics Unit, Hospital Universitario Ramón y Cajal and IRYCIS, 28034 Madrid, Spain;
| | - Nuria Jimenez-Hernandez
- Área Genómica y Salud, Fundación para el Fomento de la Investigación Sanitaria y Biomédica (FISABIO), 46010 Valencia, Spain; (M.J.G.); (N.J.-H.); (A.M.)
- CIBER en Epidemiología y Salud Pública, 28029 Madrid, Spain
| | - Luis Prieto
- Red de Investigación CoRISpe integrada en la Red en Infectología Pediátrica (RITIP), 28046 Madrid, Spain; (L.P.); (S.G.); (J.T.R.); (M.L.N.)
- Servicio de Pediatría, Hospital 12 de Octubre and I+12, 28041 Madrid, Spain
| | - Luis Escosa
- Servicio de Pediatría, Hospital Universitario La Paz and IdiPAZ, 28046 Madrid, Spain; (L.E.); (M.J.M.)
- Red de Investigación CoRISpe integrada en la Red en Infectología Pediátrica (RITIP), 28046 Madrid, Spain; (L.P.); (S.G.); (J.T.R.); (M.L.N.)
| | - Sara Guillén
- Red de Investigación CoRISpe integrada en la Red en Infectología Pediátrica (RITIP), 28046 Madrid, Spain; (L.P.); (S.G.); (J.T.R.); (M.L.N.)
- Servicio de Pediatría, Hospital de Getafe, 28901 Madrid, Spain
| | - José Tomás Ramos
- Red de Investigación CoRISpe integrada en la Red en Infectología Pediátrica (RITIP), 28046 Madrid, Spain; (L.P.); (S.G.); (J.T.R.); (M.L.N.)
- Spain Servicio de Pediatría, Hospital Clinico San Carlos and UCM, 28040 Madrid, Spain
| | - María Ángeles Muñoz-Fernández
- Laboratorio InmunoBiología Molecular, Sección Inmunología, Hospital General Universitario Gregorio Marañón and Spanish HIV HGM BioBank, Madrid Spain, Networking Research Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), 28007 Madrid, Spain;
| | - Andrés Moya
- Área Genómica y Salud, Fundación para el Fomento de la Investigación Sanitaria y Biomédica (FISABIO), 46010 Valencia, Spain; (M.J.G.); (N.J.-H.); (A.M.)
- CIBER en Epidemiología y Salud Pública, 28029 Madrid, Spain
- Instituto de Biología Integrativa de Sistemas, Universidad de Valencia, 46003 Valencia, Spain
| | - Maria Luisa Navarro
- Red de Investigación CoRISpe integrada en la Red en Infectología Pediátrica (RITIP), 28046 Madrid, Spain; (L.P.); (S.G.); (J.T.R.); (M.L.N.)
- Servicio de Pediatría, Hospital General Universitario Gregorio Marañón, 28007 Madrid, Spain
| | - María José Mellado
- Servicio de Pediatría, Hospital Universitario La Paz and IdiPAZ, 28046 Madrid, Spain; (L.E.); (M.J.M.)
- Red de Investigación CoRISpe integrada en la Red en Infectología Pediátrica (RITIP), 28046 Madrid, Spain; (L.P.); (S.G.); (J.T.R.); (M.L.N.)
| | - Sergio Serrano-Villar
- Servicio de Enfermedades Infecciosas, Hospital Universitario Ramón y Cajal and IRYCIS, 28034 Madrid, Spain;
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Piggott DA, Tuddenham S. The gut microbiome and frailty. Transl Res 2020; 221:23-43. [PMID: 32360945 PMCID: PMC8487348 DOI: 10.1016/j.trsl.2020.03.012] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Revised: 03/26/2020] [Accepted: 03/27/2020] [Indexed: 12/12/2022]
Abstract
The human microbiome is constituted by an extensive network of organisms that lie at the host/environment interface and transduce signals that play vital roles in human health and disease across the lifespan. Frailty is a critical aging-related syndrome marked by diminished physiological reserve and heightened vulnerability to stress, predictive of major adverse clinical outcomes including death. While recent studies suggest the microbiome may impact key pathways critical to frailty pathophysiology, direct evaluation of the microbiome-frailty relationship remains limited. In this article, we review the complex interplay of biological, behavioral, and environmental factors that may influence shifts in gut microbiome composition and function in aging populations and the putative implications of such shifts for progression to frailty. We discuss HIV infection as a key prototype for elucidating the complex pathways via which the microbiome may precipitate frailty. Finally, we review considerations for future research efforts.
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Affiliation(s)
- Damani A Piggott
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Epidemiology, Johns Hopkins University School of Public Health, Baltimore, Maryland.
| | - Susan Tuddenham
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
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49
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HIV-associated gut dysbiosis is independent of sexual practice and correlates with noncommunicable diseases. Nat Commun 2020; 11:2448. [PMID: 32415070 PMCID: PMC7228978 DOI: 10.1038/s41467-020-16222-8] [Citation(s) in RCA: 121] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Accepted: 04/15/2020] [Indexed: 02/08/2023] Open
Abstract
Loss of gut mucosal integrity and an aberrant gut microbiota are proposed mechanisms contributing to chronic inflammation and increased morbidity and mortality during antiretroviral-treated HIV disease. Sexual practice has recently been uncovered as a major source of microbiota variation, potentially confounding prior observations of gut microbiota alterations among persons with HIV (PWH). To overcome this and other confounding factors, we examine a well-powered subset of AGEhIV Cohort participants comprising antiretroviral-treated PWH and seronegative controls matched for age, body-mass index, sex, and sexual practice. We report significant gut microbiota differences in PWH regardless of sex and sexual practice including Gammaproteobacteria enrichment, Lachnospiraceae and Ruminococcaceae depletion, and decreased alpha diversity. Men who have sex with men (MSM) exhibit a distinct microbiota signature characterized by Prevotella enrichment and increased alpha diversity, which is linked with receptive anal intercourse in both males and females. Finally, the HIV-associated microbiota signature correlates with inflammatory markers including suPAR, nadir CD4 count, and prevalence of age-associated noncommunicable comorbidities.
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Coleman SL, Neff CP, Li SX, Armstrong AJ, Schneider JM, Sen S, Fennimore B, Campbell TB, Lozupone CA, Palmer BE. Can gut microbiota of men who have sex with men influence HIV transmission? Gut Microbes 2020; 11:610-619. [PMID: 32036739 PMCID: PMC7524317 DOI: 10.1080/19490976.2019.1700756] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Gaining a complete understanding of transmission risk factors will assist in efforts to reduce new HIV infections, especially within the disproportionally affected population of men who have sex with men (MSM). We recently reported that the fecal microbiota of MSM elevates immune activation in gnotobiotic mice and enhances HIV infection in vitro over that of fecal microbiota from men who have sex with women. We also demonstrated elevation of the gut homing marker CD103 (integrin αE) on CD4+ T cells by MSM-microbiota. Here we provide additional evidence that the gut microbiota is a risk factor for HIV transmission in MSM by showing elevated frequencies of the HIV co-receptor CCR5 on CD4+ T cells in human rectosigmoid colon biopsies. We discuss our interest in specific MSM-associated bacteria and propose the influx of CD103+ and CCR5+ CD4+ T cells into the colon as a potential link between the MSM microbiota and HIV transmission.
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Affiliation(s)
- Sara L. Coleman
- Division of Allergy and Clinical Immunology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - C. Preston Neff
- Division of Allergy and Clinical Immunology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Sam X. Li
- Division of Allergy and Clinical Immunology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Abigail J.S. Armstrong
- Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Jennifer M. Schneider
- Division of Allergy and Clinical Immunology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Sharon Sen
- Division of Allergy and Clinical Immunology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Blair Fennimore
- Division of Gastroenterology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Thomas B. Campbell
- Division of Infectious Diseases, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Catherine A. Lozupone
- Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Brent E. Palmer
- Division of Allergy and Clinical Immunology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA,CONTACT Brent E. Palmer Division of Allergy and Clinical Immunology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
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