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Fu Y, Ke S, Tang G, Guo Q, Guo Q, Wang Z, Leng R, Fan Y. Characterization of the intestinal microbiota in MSM with HIV infection. BMC Microbiol 2024; 24:192. [PMID: 38831399 PMCID: PMC11145808 DOI: 10.1186/s12866-024-03351-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: 11/24/2023] [Accepted: 05/26/2024] [Indexed: 06/05/2024] Open
Abstract
BACKGROUND HIV-infected persons demonstrate notable disturbances in their intestinal microbiota; however, the impact of intestinal microbiota on HIV susceptibility in men who have sex with men (MSM), as well as the effects of HIV and antiretroviral therapy (ART) on their gut microbiota, remains under active study. Thus, our research focuses on clarifying the distinctions in intestinal microbiota composition among uninfected MSM and non-MSM healthy controls, investigating the alterations in early-stage intestinal microbial communities following HIV infection, and assessing how ART affects the intestinal microbiota. METHODS This study enrolled four participant groups: uninfected MSM, Recent HIV-1 infection (RHI) MSM, MSM on ART, and non-MSM healthy controls, with 30 individuals in each group. We utilized 16S ribosomal DNA (16S rDNA) amplicon sequencing to analyze fecal microbiota and employed Luminex multiplex assays to measure plasma markers for microbial translocation (LBP, sCD14) and the inflammatory marker CRP. FINDINGS Comparing uninfected MSM to non-MSM healthy controls, no substantial variances were observed in α and β diversity. Uninfected MSM had higher average relative abundances of Bacteroidetes, Prevotella, and Alloprevotella, while Bacteroides, Firmicutes, and Faecalibacterium had lower average relative abundances. MSM on ART had lower intestinal microbiota diversity than RHI MSM and uninfected MSM. In MSM on ART, Megasphaera and Fusobacterium increased, while Faecalibacterium and Roseburia decreased at genus level. Additionally, treatment with a non-nucleoside reverse transcriptase inhibitor (NNRTI) led to significant alterations in intestinal microbiota diversity and composition compared to RHI MSM. The random forest model showed that HIV infection biomarkers effectively distinguished between newly diagnosed HIV-infected MSM and HIV-negative MSM, with an ROC AUC of 76.24% (95% CI: 61.17-91.31%). CONCLUSIONS MSM showed early intestinal microbiota imbalances after new HIV infection. MSM on ART experienced worsened dysbiosis, indicating a combined effect of HIV and ART. NNRTI-based treatment notably changed intestinal microbiota, suggesting a potential direct impact of NNRTI drugs on intestinal microbiota.
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Affiliation(s)
- Yuansheng Fu
- Anhui Provincial Center for Disease Control and Prevention, Hefei, Anhui, 230601, China
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, China
| | - Susu Ke
- 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
| | - 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
| | - Qisheng Guo
- 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
| | - Qian Guo
- 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
| | - Ruixue Leng
- 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.
| | - 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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Baltazar-Díaz TA, Andrade-Villanueva JF, Sánchez-Álvarez P, Amador-Lara F, Holguín-Aguirre T, Sánchez-Reyes K, Álvarez-Zavala M, López-Roa RI, Bueno-Topete MR, González-Hernández LA. A Two-Faced Gut Microbiome: Butyrogenic and Proinflammatory Bacteria Predominate in the Intestinal Milieu of People Living with HIV from Western Mexico. Int J Mol Sci 2024; 25:4830. [PMID: 38732048 PMCID: PMC11084381 DOI: 10.3390/ijms25094830] [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: 02/29/2024] [Revised: 04/12/2024] [Accepted: 04/15/2024] [Indexed: 05/13/2024] Open
Abstract
HIV infection results in marked alterations in the gut microbiota (GM), such as the loss of microbial diversity and different taxonomic and metabolic profiles. Despite antiretroviral therapy (ART) partially ablating gastrointestinal alterations, the taxonomic profile after successful new ART has shown wide variations. Our objective was to determine the GM composition and functions in people living with HIV (PLWHIV) under ART in comparison to seronegative controls (SC). Fecal samples from 21 subjects (treated with integrase strand-transfer inhibitors, INSTIs) and 18 SC were included. We employed 16S rRNA amplicon sequencing, coupled with PICRUSt2 and fecal short-chain fatty acid (SCFA) quantification by gas chromatography. The INSTI group showed a decreased α-diversity (p < 0.001) compared to the SC group, at the expense of increased amounts of Pseudomonadota (Proteobacteria), Segatella copri, Lactobacillus, and Gram-negative bacteria. Concurrently, we observed an enrichment in Megasphaera and Butyricicoccus, both SCFA-producing bacteria, and significant elevations in fecal butyrate in this group (p < 0.001). Interestingly, gut dysbiosis in PLWHIV was characterized by a proinflammatory environment orchestrated by Pseudomonadota and elevated levels of butyrate associated with bacterial metabolic pathways, as well as the evident presence of butyrogenic bacteria. The role of this unique GM in PLWHIV should be evaluated, as well as the use of butyrate-based supplements and ART regimens that contain succinate, such as tenofovir disoproxil succinate. This mixed profile is described for the first time in PLWHIV from Mexico.
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Affiliation(s)
- Tonatiuh Abimael Baltazar-Díaz
- Instituto de Investigación en Enfermedades Crónico-Degenerativas, Departamento de Biología Molecular y Genómica, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Sierra Mojada 950, Guadalajara 44340, Mexico;
- Instituto de Investigación en Inmunodeficiencias y VIH, Departamento de Clínicas Médicas, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Hospital 278, Guadalajara 44280, Mexico; (J.F.A.-V.); (K.S.-R.); (M.Á.-Z.)
| | - Jaime F. Andrade-Villanueva
- Instituto de Investigación en Inmunodeficiencias y VIH, Departamento de Clínicas Médicas, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Hospital 278, Guadalajara 44280, Mexico; (J.F.A.-V.); (K.S.-R.); (M.Á.-Z.)
- Unidad de VIH, Hospital Civil de Guadalajara Fray Antonio Alcalde, Hospital 278, Guadalajara 44280, Mexico; (P.S.-Á.); (F.A.-L.); (T.H.-A.)
| | - Paulina Sánchez-Álvarez
- Unidad de VIH, Hospital Civil de Guadalajara Fray Antonio Alcalde, Hospital 278, Guadalajara 44280, Mexico; (P.S.-Á.); (F.A.-L.); (T.H.-A.)
| | - Fernando Amador-Lara
- Unidad de VIH, Hospital Civil de Guadalajara Fray Antonio Alcalde, Hospital 278, Guadalajara 44280, Mexico; (P.S.-Á.); (F.A.-L.); (T.H.-A.)
| | - Tania Holguín-Aguirre
- Unidad de VIH, Hospital Civil de Guadalajara Fray Antonio Alcalde, Hospital 278, Guadalajara 44280, Mexico; (P.S.-Á.); (F.A.-L.); (T.H.-A.)
| | - Karina Sánchez-Reyes
- Instituto de Investigación en Inmunodeficiencias y VIH, Departamento de Clínicas Médicas, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Hospital 278, Guadalajara 44280, Mexico; (J.F.A.-V.); (K.S.-R.); (M.Á.-Z.)
| | - Monserrat Álvarez-Zavala
- Instituto de Investigación en Inmunodeficiencias y VIH, Departamento de Clínicas Médicas, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Hospital 278, Guadalajara 44280, Mexico; (J.F.A.-V.); (K.S.-R.); (M.Á.-Z.)
| | - Rocío Ivette López-Roa
- Laboratorio de Investigación y Desarrollo Farmacéutico, Centro Universitario de Ciencias Exactas e Ingenierías, Universidad de Guadalajara, Marcelino García Barragán 1421, Guadalajara 44430, Mexico;
| | - Miriam Ruth Bueno-Topete
- Instituto de Investigación en Enfermedades Crónico-Degenerativas, Departamento de Biología Molecular y Genómica, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Sierra Mojada 950, Guadalajara 44340, Mexico;
| | - Luz Alicia González-Hernández
- Instituto de Investigación en Inmunodeficiencias y VIH, Departamento de Clínicas Médicas, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Hospital 278, Guadalajara 44280, Mexico; (J.F.A.-V.); (K.S.-R.); (M.Á.-Z.)
- Unidad de VIH, Hospital Civil de Guadalajara Fray Antonio Alcalde, Hospital 278, Guadalajara 44280, Mexico; (P.S.-Á.); (F.A.-L.); (T.H.-A.)
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He M, Zhao N. A Mixed Effect Similarity Matrix Regression Model (SMRmix) for Integrating Multiple Microbiome Datasets at Community Level and its Application in HIV. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.10.584315. [PMID: 38559012 PMCID: PMC10979838 DOI: 10.1101/2024.03.10.584315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Recent studies have highlighted the importance of human microbiota in our health and diseases. However, in many areas of research, individual microbiome studies often offer inconsistent results due to the limited sample sizes and the heterogeneity in study populations and experimental procedures. Integrative analysis of multiple microbiome datasets is necessary. However, statistical methods that incorporate multiple microbiome datasets and account for the study heterogeneity are not available in the literature. In this paper, we develop a mixed effect similarity matrix regression (SMRmix) approach for identifying community level microbiome shifts between outcomes. SMRmix has a close connection with the microbiome kernel association test, one of the most popular approaches for such a task but is only applicable when we have a single study. Via extensive simulations, we show that SMRmix has well-controlled type I error and higher power than some potential competitors. We also applied SMRmix to data from the HIV-reanalysis consortium, a collective effort that obtained all publicly available data on gut microbiome and HIV at December 2017, and obtained consistent associations of gut microbiome with HIV infection, and with MSM status (i.e. men who have sex with men).
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Yang Q, Zaongo SD, Zhu L, Yan J, Yang J, Ouyang J. The Potential of Clostridium butyricum to Preserve Gut Health, and to Mitigate Non-AIDS Comorbidities in People Living with HIV. Probiotics Antimicrob Proteins 2024:10.1007/s12602-024-10227-1. [PMID: 38336953 DOI: 10.1007/s12602-024-10227-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/02/2024] [Indexed: 02/12/2024]
Abstract
A dramatic reduction in mortality among people living with HIV (PLWH) has been achieved during the modern antiretroviral therapy (ART) era. However, ART does not restore gut barrier function even after long-term viral suppression, allowing microbial products to enter the systemic blood circulation and induce chronic immune activation. In PLWH, a chronic state of systemic inflammation exists and persists, which increases the risk of development of inflammation-associated non-AIDS comorbidities such as metabolic disorders, cardiovascular diseases, and cancer. Clostridium butyricum is a human butyrate-producing symbiont present in the gut microbiome. Convergent evidence has demonstrated favorable effects of C. butyricum for gastrointestinal health, including maintenance of the structural and functional integrity of the gut barrier, inhibition of pathogenic bacteria within the intestine, and reduction of microbial translocation. Moreover, C. butyricum supplementation has been observed to have a positive effect on various inflammation-related diseases such as diabetes, ulcerative colitis, and cancer, which are also recognized as non-AIDS comorbidities associated with epithelial gut damage. There is currently scant published research in the literature, focusing on the influence of C. butyricum in the gut of PLWH. In this hypothesis review, we speculate the use of C. butyricum as a probiotic oral supplementation may well emerge as a potential future synergistic adjunctive strategy in PLWH, in tandem with ART, to restore and consolidate intestinal barrier integrity, repair the leaky gut, prevent microbial translocation from the gut, and reduce both gut and systemic inflammation, with the ultimate objective of decreasing the risk for development of non-AIDS comorbidities in PLWH.
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Affiliation(s)
- Qiyu Yang
- Department of Radiation Oncology, Chongqing University Cancer Hospital & Chongqing Cancer Institute & Chongqing Cancer Hospital, Chongqing, China
| | - Silvere D Zaongo
- Department of Infectious Diseases, Chongqing Public Health Medical Center, Chongqing, China
- Clinical Research Center, Chongqing Public Health Medical Center, Chongqing, China
| | - Lijiao Zhu
- Clinical Research Center, Chongqing Public Health Medical Center, Chongqing, China
| | - Jiangyu Yan
- Clinical Research Center, Chongqing Public Health Medical Center, Chongqing, China
| | - Jiadan Yang
- Department of Pharmacy, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China.
| | - Jing Ouyang
- Clinical Research Center, Chongqing Public Health Medical Center, Chongqing, China.
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Borjabad B, Inciarte A, Chivite I, Gonzalez-Cordon A, Mosquera M, Hurtado C, Rovira C, Gonzalez T, Sempere A, Torres B, Calvo J, De La Mora L, Martinez-Rebollar M, Laguno M, Foncillas A, Ambrosioni J, Blanch J, Rodriguez A, Solbes E, Llobet R, Berrocal L, Mallolas J, Miro JM, Alcami J, Blanco JL, Sanchez-Palomino S, De Lazzari E, Martinez E. Efficacy and safety of raltegravir plus lamivudine maintenance therapy. J Antimicrob Chemother 2024; 79:255-261. [PMID: 38039097 DOI: 10.1093/jac/dkad364] [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: 08/21/2023] [Accepted: 11/14/2023] [Indexed: 12/03/2023] Open
Abstract
BACKGROUND Decreasing medication burden with raltegravir plus lamivudine in virologically suppressed persons with HIV (PWH) maintained efficacy and was well tolerated at 24 weeks, but more comprehensive data over longer follow-up are required. METHODS Prospective 48 week extension phase of the raltegravir plus lamivudine arm from a previous 24 week pilot randomized clinical trial in which virologically suppressed PWH were randomized 2:1 to switch to fixed-dose combination 150 mg lamivudine/300 mg raltegravir twice daily or to continue therapy. In this 48 week extension phase, raltegravir was dosed at 1200 mg/day and lamivudine 300 mg/day. Primary outcome was the proportion of PWH with treatment failure at Week 48. Secondary outcomes were changes in ultrasensitive plasma HIV RNA, HIV DNA in CD4 cells, serum IL-6, ultrasensitive C-reactive protein and sCD14, body composition, sleep quality, quality of life and adverse effects. RESULTS Between May 2018 and June 2019, 33 PWH were enrolled. One participant experienced virological failure without resistance mutations and re-achieved sustained virological suppression without therapy discontinuation, and two others discontinued therapy due to adverse effects. Treatment failure was 9% (95% CI 2%-24%) and 3% (95% CI 0%-17%) in the ITT and on-treatment populations. There were significant changes between baseline and Week 48 in serum cytokines but not in other secondary outcomes. CONCLUSIONS Switching to raltegravir and lamivudine in PWH with virological suppression maintains efficacy and is well tolerated. This maintenance regimen might be a cost-effective option for PWH at risk of drug-drug interactions or needing to avoid specific toxicities of certain antiretroviral drugs or their negative impact on comorbidities.
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Affiliation(s)
- Beatriz Borjabad
- Internal Medicine Service, Hospital Moises Broggi, Sant Joan Despí, Spain
| | - Alexy Inciarte
- Infectious Diseases Unit, Hospital Clínic, University of Barcelona 08036, Barcelona, Spain
| | - Ivan Chivite
- Infectious Diseases Unit, Hospital Clínic, University of Barcelona 08036, Barcelona, Spain
| | - Ana Gonzalez-Cordon
- Infectious Diseases Unit, Hospital Clínic, University of Barcelona 08036, Barcelona, Spain
- CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Mar Mosquera
- Infectious Diseases Unit, Hospital Clínic, University of Barcelona 08036, Barcelona, Spain
- CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Carmen Hurtado
- Infectious Diseases Unit, Hospital Clínic, University of Barcelona 08036, Barcelona, Spain
| | - Cristina Rovira
- Infectious Diseases Unit, Hospital Clínic, University of Barcelona 08036, Barcelona, Spain
| | - Tania Gonzalez
- Infectious Diseases Unit, Hospital Clínic, University of Barcelona 08036, Barcelona, Spain
| | - Abiu Sempere
- Infectious Diseases Unit, Hospital Clínic, University of Barcelona 08036, Barcelona, Spain
| | - Berta Torres
- Infectious Diseases Unit, Hospital Clínic, University of Barcelona 08036, Barcelona, Spain
- CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Julia Calvo
- Infectious Diseases Unit, Hospital Clínic, University of Barcelona 08036, Barcelona, Spain
| | - Lorena De La Mora
- Infectious Diseases Unit, Hospital Clínic, University of Barcelona 08036, Barcelona, Spain
- CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Maria Martinez-Rebollar
- Infectious Diseases Unit, Hospital Clínic, University of Barcelona 08036, Barcelona, Spain
- CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Montserrat Laguno
- Infectious Diseases Unit, Hospital Clínic, University of Barcelona 08036, Barcelona, Spain
- CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Alberto Foncillas
- Infectious Diseases Unit, Hospital Clínic, University of Barcelona 08036, Barcelona, Spain
| | - Juan Ambrosioni
- Infectious Diseases Unit, Hospital Clínic, University of Barcelona 08036, Barcelona, Spain
- CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Jordi Blanch
- Infectious Diseases Unit, Hospital Clínic, University of Barcelona 08036, Barcelona, Spain
- Internal Medicine Service, Hospital Universitari de Santa Maria, Lleida, Spain
- CIBER de Salud Mental (CIBERSAM), Instituto de Salud Carlos III, Madrid, Spain
| | - Ana Rodriguez
- Infectious Diseases Unit, Hospital Clínic, University of Barcelona 08036, Barcelona, Spain
| | - Estela Solbes
- Infectious Diseases Unit, Hospital Clínic, University of Barcelona 08036, Barcelona, Spain
| | - Roger Llobet
- Infectious Diseases Unit, Hospital Clínic, University of Barcelona 08036, Barcelona, Spain
| | - Leire Berrocal
- Infectious Diseases Unit, Hospital Clínic, University of Barcelona 08036, Barcelona, Spain
| | - Josep Mallolas
- Infectious Diseases Unit, Hospital Clínic, University of Barcelona 08036, Barcelona, Spain
- CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Jose M Miro
- Infectious Diseases Unit, Hospital Clínic, University of Barcelona 08036, Barcelona, Spain
- CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Jose Alcami
- Infectious Diseases Unit, Hospital Clínic, University of Barcelona 08036, Barcelona, Spain
- CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
- Acquired Immunodeficiency Syndrome (AIDS) Immunopathology Unit, National Center for Microbiology, Institute of Health Carlos III, Majadahonda, Spain
| | - Jose L Blanco
- Infectious Diseases Unit, Hospital Clínic, University of Barcelona 08036, Barcelona, Spain
- CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Sonsoles Sanchez-Palomino
- Infectious Diseases Unit, Hospital Clínic, University of Barcelona 08036, Barcelona, Spain
- CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Elisa De Lazzari
- Infectious Diseases Unit, Hospital Clínic, University of Barcelona 08036, Barcelona, Spain
- CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Esteban Martinez
- Infectious Diseases Unit, Hospital Clínic, University of Barcelona 08036, Barcelona, Spain
- CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
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Ishizaka A, Koga M, Mizutani T, Yamayoshi S, Iwatsuki-Horimoto K, Adachi E, Suzuki Y, Kawaoka Y, Yotsuyanagi H. Association of gut microbiota with the pathogenesis of SARS-CoV-2 Infection in people living with HIV. BMC Microbiol 2024; 24:6. [PMID: 38172680 PMCID: PMC10763188 DOI: 10.1186/s12866-023-03157-5] [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: 10/16/2023] [Accepted: 12/12/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND People living with HIV (PLWH) with chronic inflammation may have an increasing risk for coronavirus disease 2019 (COVID-19) severity; however, the impact of their gut microbiota on COVID-19 is not fully elucidated. Here, we analyzed the temporal changes in the gut microbiota composition of hospitalized severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-infected PLWH (PLWH-CoV) and their correlation with COVID-19 severity. RESULT The 16S rRNA analysis results using stool samples (along the timeline from disease onset) from 12 hospitalized PLWH-CoV, whose median CD4 + T cell count was 671 cells/µl, were compared to those of 19 healthy people and 25 PLWH. Bacterial diversity in PLWH-CoV is not significantly different from that of healthy people and SARS-CoV-2 non-infected PLWH, but a significant difference in the microbiota diversity was observed in the classification according to the disease severity. Immediately after the disease onset, remarkable changes were observed in the gut microbiota of PLWH-CoV, and the changing with a decrease in some short-chain fatty acid-producing bacteria and an increase in colitis-related pathobiont. In the second week after disease onset, relative amounts of specific bacteria distinguished between disease severity. One month after the disease onset, dysbiosis of the gut microbiota persisted, and the number of Enterobacteriaceae, mainly Escherichia-Shigella, which is potentially pathogenic, increased and were enriched in patients who developed post-acute sequelae of COVID-19 (PASC). CONCLUSION The changes in the gut microbiota associated with SARS-CoV-2 infection observed in PLWH in this study indicated a persistent decrease in SCFA-producing bacteria and an intestinal environment with an increase in opportunistic pathogens associated with enteritis. This report demonstrates that the intestinal environment in PLWH tends to show delayed improvement even after COVID-19 recovery, and highlights the importance of the dysbiosis associated with SARS-CoV-2 infection as a potential factor in the COVID-19 severity and the PASC in PLWH.
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Affiliation(s)
- Aya Ishizaka
- Division of Infectious Diseases, Advanced Clinical Research Center, the Institute of Medical Science, the University of Tokyo, Tokyo, Japan
| | - Michiko Koga
- Division of Infectious Diseases, Advanced Clinical Research Center, the Institute of Medical Science, the University of Tokyo, Tokyo, Japan
| | - Taketoshi Mizutani
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, the University of Tokyo, Chiba, Japan.
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, the University of Tokyo, 6-2-3 Kashiwanoha, 277-0882, Kashiwa-shi, Chiba, Japan.
| | - Seiya Yamayoshi
- Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- The Research Center for Global Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo, Japan
| | - Kiyoko Iwatsuki-Horimoto
- Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Eisuke Adachi
- Department of Infectious Diseases and Applied Immunology, IMSUT Hospital of Institute of Medical Science, the University of Tokyo, Tokyo, Japan
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, the University of Tokyo, Chiba, Japan
| | - Yoshihiro Kawaoka
- Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- The Research Center for Global Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo, Japan
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA
- Pandemic Preparedness, Infection and Advanced Research Center, The University of Tokyo, Tokyo, Japan
| | - Hiroshi Yotsuyanagi
- Division of Infectious Diseases, Advanced Clinical Research Center, the Institute of Medical Science, the University of Tokyo, Tokyo, Japan.
- Department of Infectious Diseases and Applied Immunology, IMSUT Hospital of Institute of Medical Science, the University of Tokyo, Tokyo, Japan.
- Division of Infectious Diseases, Advanced Clinical Research Center, Institute of Medical Science, the University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, 108-8639, Tokyo, Japan.
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Li S, Su B, Wu H, He Q, Zhang T. Integrated analysis of gut and oral microbiome in men who have sex with men with HIV Infection. Microbiol Spectr 2023; 11:e0106423. [PMID: 37850756 PMCID: PMC10714972 DOI: 10.1128/spectrum.01064-23] [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: 03/10/2023] [Accepted: 09/11/2023] [Indexed: 10/19/2023] Open
Abstract
IMPORTANCE Our longitudinal integrated study has shown the marked alterations in the gut and oral microbiome resulting from acute and chronic HIV infection and from antiretroviral therapy. Importantly, the relationship between oral and gut microbiomes in people living with acute and chronic HIV infection and "healthy" controls has also been explored. These findings might contribute to a better understanding of the interactions between the oral and gut microbiomes and its potential role in HIV disease progression.
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Affiliation(s)
- Shuang Li
- Beijing Key Laboratory for HIV/AIDS Research, Clinical and Research Center for Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Bin Su
- Beijing Key Laboratory for HIV/AIDS Research, Clinical and Research Center for Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Hao Wu
- Beijing Key Laboratory for HIV/AIDS Research, Clinical and Research Center for Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Qiushui He
- Institute of Biomedicine, Research Center for Infections and Immunity, University of Turku, Turku, Finland
- Department of Medical Microbiology, Capital Medical University, Beijing, China
| | - Tong Zhang
- Beijing Key Laboratory for HIV/AIDS Research, Clinical and Research Center for Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing, China
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Loaiza JD, Chvatal-Medina M, Hernandez JC, Rugeles MT. Integrase inhibitors: current protagonists in antiretroviral therapy. Immunotherapy 2023; 15:1477-1495. [PMID: 37822251 DOI: 10.2217/imt-2023-0011] [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] [Indexed: 10/13/2023] Open
Abstract
Since HIV was identified as the etiological agent of AIDS, there have been significant advances in antiretroviral therapy (ART) that has reduced morbidity/mortality. Still, the viral genome's high mutation rate, suboptimal ART regimens, incomplete adherence to therapy and poor control of the viral load generate variants resistant to multiple drugs. Licensing over 30 anti-HIV drugs worldwide, including integrase inhibitors, has marked a milestone since they are potent and well-tolerated drugs. In addition, they favor a faster recovery of CD4+ T cells. They also increase the diversity profile of the gut microbiota and reduce inflammatory markers. All of these highlight the importance of including them in different ART regimens.
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Affiliation(s)
- John D Loaiza
- Grupo Inmunovirología, Facultad de medicina, Universidad de Antioquia, Medellín, 050010, Colombia
| | - Mateo Chvatal-Medina
- Grupo Inmunovirología, Facultad de medicina, Universidad de Antioquia, Medellín, 050010, Colombia
| | - Juan C Hernandez
- Infettare, Facultad de medicina, Universidad Cooperativa de Colombia, Medellín, 050012, Colombia
| | - Maria T Rugeles
- Grupo Inmunovirología, Facultad de medicina, Universidad de Antioquia, Medellín, 050010, Colombia
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9
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Planchais C, Molinos-Albert LM, Rosenbaum P, Hieu T, Kanyavuz A, Clermont D, Prazuck T, Lefrou L, Dimitrov JD, Hüe S, Hocqueloux L, Mouquet H. HIV-1 treatment timing shapes the human intestinal memory B-cell repertoire to commensal bacteria. Nat Commun 2023; 14:6326. [PMID: 37816704 PMCID: PMC10564866 DOI: 10.1038/s41467-023-42027-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 09/28/2023] [Indexed: 10/12/2023] Open
Abstract
HIV-1 infection causes severe alterations of gut mucosa, microbiota and immune system, which can be curbed by early antiretroviral therapy. Here, we investigate how treatment timing affects intestinal memory B-cell and plasmablast repertoires of HIV-1-infected humans. We show that only class-switched memory B cells markedly differ between subjects treated during the acute and chronic phases of infection. Intestinal memory B-cell monoclonal antibodies show more prevalent polyreactive and commensal bacteria-reactive clones in late- compared to early-treated individuals. Mirroring this, serum IgA polyreactivity and commensal-reactivity are strongly increased in late-treated individuals and correlate with intestinal permeability and systemic inflammatory markers. Polyreactive blood IgA memory B cells, many of which egressed from the gut, are also substantially enriched in late-treated individuals. Our data establish gut and systemic B-cell polyreactivity to commensal bacteria as hallmarks of chronic HIV-1 infection and suggest that initiating treatment early may limit intestinal B-cell abnormalities compromising HIV-1 humoral response.
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Affiliation(s)
- Cyril Planchais
- Humoral Immunology Unit, Institut Pasteur, Université Paris Cité, INSERM U1222, F-75015, Paris, France
| | - Luis M Molinos-Albert
- Humoral Immunology Unit, Institut Pasteur, Université Paris Cité, INSERM U1222, F-75015, Paris, France
- ISGlobal, Hospital Clínic-Universitat de Barcelona, 08036, Barcelona, Spain
| | - Pierre Rosenbaum
- Humoral Immunology Unit, Institut Pasteur, Université Paris Cité, INSERM U1222, F-75015, Paris, France
| | - Thierry Hieu
- Humoral Immunology Unit, Institut Pasteur, Université Paris Cité, INSERM U1222, F-75015, Paris, France
| | - Alexia Kanyavuz
- Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, Université de Paris, 75006, Paris, France
| | - Dominique Clermont
- Collection of the Institut Pasteur, Institut Pasteur, Université Paris Cité, 75015, Paris, France
| | - Thierry Prazuck
- Service des Maladies Infectieuses et Tropicales, CHR d'Orléans-La Source, 45067, Orléans, France
| | - Laurent Lefrou
- Service d'Hépato-Gastro-Entérologie, CHR d'Orléans-La Source, 45067, Orléans, France
| | - Jordan D Dimitrov
- Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, Université de Paris, 75006, Paris, France
| | - Sophie Hüe
- INSERM U955-Équipe 16, Université Paris-Est Créteil, Faculté de Médecine, 94000, Créteil, France
| | - Laurent Hocqueloux
- Service des Maladies Infectieuses et Tropicales, CHR d'Orléans-La Source, 45067, Orléans, France
| | - Hugo Mouquet
- Humoral Immunology Unit, Institut Pasteur, Université Paris Cité, INSERM U1222, F-75015, Paris, France.
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10
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Hussain MA, Watson CWM, Morgan EE, Heaton RK, Letendre SL, Jeste DV, Moore DJ, Iudicello JE. Combined effects of loneliness and inflammation on depression in people with HIV. J Neurovirol 2023; 29:538-554. [PMID: 37651083 PMCID: PMC10645641 DOI: 10.1007/s13365-023-01145-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: 06/17/2022] [Revised: 04/17/2023] [Accepted: 04/24/2023] [Indexed: 09/01/2023]
Abstract
OBJECTIVE Loneliness is prevalent in people with HIV (PWH) and associated with adverse health-related consequences, including depression. Chronic inflammation has been linked to depression in PWH, though its association with loneliness is less well established. Simultaneous examination of inflammation, loneliness and depression is needed to clarify these relationships. This study investigated the relationship between loneliness and inflammation, and the effects of loneliness and inflammation on depression in PWH. METHODS 82 PWH who were on suppressive ART (mean age [SD] = 53.2 [9.0]) completed the UCLA Loneliness Scale-Version 3 and the Center for Epidemiologic Studies Depression Scale as part of a comprehensive evaluation. Biomarkers of systemic inflammation (CRP, IL-6, CCL2/MCP-1, sCD14) and coagulation (D-dimer) were measured in blood using commercial immunoassays. RESULTS Multivariable linear regression analyses revealed that higher D-dimer, CCL2/MCP-1, and sCD14 were significant predictors of loneliness (ps < .05) while accounting for relevant covariates. Stepwise multiple linear regression models that included loneliness, biomarkers, and their interactions as predictors of depressive symptoms revealed significant main effects of loneliness and CCL2/MCP-1 levels (ps < .05), and a significant loneliness by D-dimer interaction (p < .05) whereby higher D-dimer was associated with increased depressive symptoms only at higher levels of loneliness. CONCLUSIONS Increased coagulation activity is associated with loneliness, and in the context of loneliness, may increase risk for depression. Increased inflammation was associated with depression suggesting potentially dissociable underlying biological processes. To the extent that these processes are modifiable, such findings could have important implications in the treatment of loneliness and depression in PWH.
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Affiliation(s)
- Mariam A Hussain
- San Diego State University, University of California San Diego Joint Doctoral Program in Clinical Psychology, San Diego, USA.
- Department of Psychiatry, University of California San Diego, La Jolla, USA.
- HIV Neurobehavioral Research Program, University of California San Diego, San Diego, USA.
| | - C Wei-Ming Watson
- San Diego State University, University of California San Diego Joint Doctoral Program in Clinical Psychology, San Diego, USA
- Department of Psychiatry, University of California San Diego, La Jolla, USA
- HIV Neurobehavioral Research Program, University of California San Diego, San Diego, USA
| | - Erin E Morgan
- Department of Psychiatry, University of California San Diego, La Jolla, USA
- HIV Neurobehavioral Research Program, University of California San Diego, San Diego, USA
| | - Robert K Heaton
- Department of Psychiatry, University of California San Diego, La Jolla, USA
- HIV Neurobehavioral Research Program, University of California San Diego, San Diego, USA
| | - Scott L Letendre
- Department of Psychiatry, University of California San Diego, La Jolla, USA
- HIV Neurobehavioral Research Program, University of California San Diego, San Diego, USA
| | - Dilip V Jeste
- Department of Psychiatry, University of California San Diego, La Jolla, USA
- Department of Neurosciences, University of California San Diego, La Jolla, USA
- Sam and Rose Stein Institute for Research On Aging, University of California San Diego, La Jolla, USA
| | - David J Moore
- Department of Psychiatry, University of California San Diego, La Jolla, USA
- HIV Neurobehavioral Research Program, University of California San Diego, San Diego, USA
| | - Jennifer E Iudicello
- Department of Psychiatry, University of California San Diego, La Jolla, USA
- HIV Neurobehavioral Research Program, University of California San Diego, San Diego, USA
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11
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Villoslada-Blanco P, Pérez-Matute P, Recio-Fernández E, Íñiguez M, Blanco-Navarrete P, Metola L, Ibarra V, Alba J, de Toro M, Oteo JA. Beyond the effects of HIV infection and integrase inhibitors-based therapies on oral bacteriome. Sci Rep 2023; 13:14327. [PMID: 37653055 PMCID: PMC10471600 DOI: 10.1038/s41598-023-41434-5] [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: 03/20/2023] [Accepted: 08/26/2023] [Indexed: 09/02/2023] Open
Abstract
Oral microbiome is the second largest microbial community in humans after gut. Human immunodeficiency virus (HIV) infection triggers an impairment of the immune system which could favour the growth and the colonization of pathogens in the oral cavity, and this dysbiosis has been associated with oral manifestations that worsen the quality of life of these patients. Antiretroviral therapy (ART) could also drive changes in specific oral bacterial taxa associated with such periodontal diseases. Integrase strand transfer inhibitors (INSTIs), therapy of choice in the treatment of naive HIV-patients, are able to reverse the impact of HIV infection on systemic inflammation, gut permeability, and gut bacterial diversity/richness. The objective of this study was to analyse the effects of HIV infection per se and INSTIs on salivary bacteriome composition, taking into consideration other factors such as smoking, that could also have a significant impact on oral microbiome. To accomplish this objective, 26 non-HIV-infected volunteers and 30 HIV-infected patients (15 naive and 15 under INSTIs-regimen) were recruited. Salivary samples were collected to measure lysozyme levels. Oral bacteriome composition was analysed using 16S rRNA gene sequencing. Naive HIV-infected patients showed statistically higher levels of lysozyme compared to controls (p < 0.001) and INSTIs-treated patients (p < 0.05). Our study was unable to detect differences in α nor β-diversity among the three groups analysed, although significant differences in the abundance of some bacterial taxonomical orders were detected (higher abundance in the phylum Pseudomonadota, in the order Acholeplasmatales, and in the genera Ezakiella and Acholeplasma in the naive group compared to controls; and higher abundance in the phylum Mycoplasmatota, in the order Acholeplasmatales, and in the genera Acholeplasma and uncultured Eubacteriaceae bacterium in the INTIs-treated HIV-infected patients compared to controls). These differences seem to be partially independent of smoking habit. HIV infection and INSTIs effects on oral microbiota seem not to be very potent, probably due to the modulation of other factors such as smoking and the greatest outward exposure of the oral cavity.
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Affiliation(s)
- Pablo Villoslada-Blanco
- Infectious Diseases, Microbiota and Metabolism Unit, Infectious Diseases Department, Center for Biomedical Research of La Rioja (CIBIR), C/Piqueras 98, CIBIR Building, Third Floor, 26006, Logroño, La Rioja, Spain
| | - Patricia Pérez-Matute
- Infectious Diseases, Microbiota and Metabolism Unit, Infectious Diseases Department, Center for Biomedical Research of La Rioja (CIBIR), C/Piqueras 98, CIBIR Building, Third Floor, 26006, Logroño, La Rioja, Spain.
| | - Emma Recio-Fernández
- Infectious Diseases, Microbiota and Metabolism Unit, Infectious Diseases Department, Center for Biomedical Research of La Rioja (CIBIR), C/Piqueras 98, CIBIR Building, Third Floor, 26006, Logroño, La Rioja, Spain
| | - María Íñiguez
- Infectious Diseases, Microbiota and Metabolism Unit, Infectious Diseases Department, Center for Biomedical Research of La Rioja (CIBIR), C/Piqueras 98, CIBIR Building, Third Floor, 26006, Logroño, La Rioja, Spain
| | | | - Luis Metola
- Infectious Diseases Department, Hospital Universitario San Pedro, Logroño, La Rioja, Spain
| | - Valvanera Ibarra
- Infectious Diseases Department, Hospital Universitario San Pedro, Logroño, La Rioja, Spain
| | - Jorge Alba
- Infectious Diseases Department, Hospital Universitario San Pedro, Logroño, La Rioja, Spain
| | - María de Toro
- Genomics and Bioinformatics Platform, Center for Biomedical Research of La Rioja (CIBIR), Logroño, La Rioja, Spain
| | - José A Oteo
- Infectious Diseases, Microbiota and Metabolism Unit, Infectious Diseases Department, Center for Biomedical Research of La Rioja (CIBIR), C/Piqueras 98, CIBIR Building, Third Floor, 26006, Logroño, La Rioja, Spain
- Infectious Diseases Department, Hospital Universitario San Pedro, Logroño, La Rioja, Spain
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12
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Rosel-Pech C, Pinto-Cardoso S, Chávez-Torres M, Montufar N, Osuna-Padilla I, Ávila-Ríos S, Reyes-Terán G, Aguirre-Alvarado C, Matías Juan NA, Pérez-Lorenzana H, Vázquez-Rosales JG, Bekker-Méndez VC. Distinct fecal microbial signatures are linked to sex and chronic immune activation in pediatric HIV infection. Front Immunol 2023; 14:1244473. [PMID: 37711620 PMCID: PMC10497879 DOI: 10.3389/fimmu.2023.1244473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 08/09/2023] [Indexed: 09/16/2023] Open
Abstract
Introduction Our understanding of HIV-associated gut microbial dysbiosis in children perinatally-infected with HIV (CLWH) lags behind that of adults living with HIV. Childhood represents a critical window for the gut microbiota. Any disturbances, including prolonged exposure to HIV, antiretroviral drugs, and antibiotics are likely to have a significant impact on long-term health, resulting in a less resilient gut microbiome. The objective of our study was to characterize the gut microbiota in CLWH, and compare it with HIV-unexposed and -uninfected children. Methods We enrolled 31 children aged 3 to 15 years; 15 were CLWH and 16 were HUU. We assessed dietary patterns and quality; quantified soluble and cellular markers of HIV disease progression by flow cytometry, enzyme-linked immunosorbent and multiplex-bead assays, and profiled the gut microbiota by 16S rRNA sequencing. We explored relationships between the gut microbiota, antibiotic exposure, dietary habits, soluble and cellular markers and host metadata. Results Children had a Western-type diet, their median health eating index score was 67.06 (interquartile range 58.76-74.66). We found no discernable impact of HIV on the gut microbiota. Alpha diversity metrics did not differ between CLWH and HUU. Sex impacted the gut microbiota (R-squared= 0.052, PERMANOVA p=0.024). Male children had higher microbial richness compared with female children. Two taxa were found to discriminate female from male children independently from HIV status: Firmicutes for males, and Bacteroides for females. Markers of HIV disease progression were comparable between CLWH and HUU, except for the frequency of exhausted CD4+ T cells (PD-1+) which was increased in CLWH (p=0.0024 after adjusting for confounders). Both the frequency of exhausted CD4+ and activated CD4+ T cells (CD38+ HLADR+) correlated positively with the relative abundance of Proteobacteria (rho=0.568. false discovery rate (FDR)-adjusted p= 0.029, and rho=0.62, FDR-adjusted p=0.0126, respectively). Conclusion The gut microbiota of CLWH appears similar to that of HUU, and most markers of HIV disease progression are normalized with long-term ART, suggesting a beneficial effect of the latter on the gut microbial ecology. The relationship between exhausted and activated CD4+ T cells and Proteobacteria suggests a connection between the gut microbiome, and premature aging in CLWH.
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Affiliation(s)
- Cecilia Rosel-Pech
- Posgrado en Ciencias Biológicas, Unidad de Posgrado, Universidad Nacional Autónoma de México (UNAM), Ciudad de México, Mexico
- Unidad de Investigación Médica en Inmunología e Infectología, Hospital de Infectología “Dr. Daniel Méndez Hernández”, Centro Médico Nacional “La Raza”, Instituto Mexicano del Seguro Social (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
| | - Monserrat Chávez-Torres
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Ciudad de México, Mexico
| | - Nadia Montufar
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Ciudad de México, Mexico
| | - Iván Osuna-Padilla
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Ciudad de México, Mexico
| | - Santiago Ávila-Ríos
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Ciudad de México, Mexico
| | - Gustavo Reyes-Terán
- Posgrado en Ciencias Biológicas, Unidad de Posgrado, Universidad Nacional Autónoma de México (UNAM), Ciudad de México, Mexico
| | - Charmina Aguirre-Alvarado
- Unidad de Investigación Médica en Inmunología e Infectología, Hospital de Infectología “Dr. Daniel Méndez Hernández”, Centro Médico Nacional “La Raza”, Instituto Mexicano del Seguro Social (IMSS), Ciudad de México, Mexico
| | - Norma Angelica Matías Juan
- Hospital de Infectología “Dr. Daniel Méndez Hernández”, Centro Médico Nacional “La Raza”, Instituto Mexicano del Seguro Social (IMSS), Ciudad de México, Mexico
| | - Héctor Pérez-Lorenzana
- UMAE Hospital General Dr. Gaudencio González Garza, Centro Médico Nacional La Raza, Instituto Mexicano del Seguro Social (IMSS), Ciudad de México, Mexico
| | - José Guillermo Vázquez-Rosales
- Hospital de Pediatría “Doctor Silvestre Frenk Freund”, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, 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”, Instituto Mexicano del Seguro Social (IMSS), Ciudad de México, Mexico
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13
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Rodriguez MT, McLaurin KA, Shtutman M, Kubinak JL, Mactutus CF, Booze RM. Therapeutically targeting the consequences of HIV-1-associated gastrointestinal dysbiosis: Implications for neurocognitive and affective alterations. Pharmacol Biochem Behav 2023; 229:173592. [PMID: 37390973 PMCID: PMC10494709 DOI: 10.1016/j.pbb.2023.173592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 06/16/2023] [Accepted: 06/26/2023] [Indexed: 07/02/2023]
Abstract
Approximately 50 % of the individuals living with human immunodeficiency virus type 1 (HIV-1) are plagued by debilitating neurocognitive impairments (NCI) and/or affective alterations. Sizeable alterations in the composition of the gut microbiome, or gastrointestinal dysbiosis, may underlie, at least in part, the NCI, apathy, and/or depression observed in this population. Herein, two interrelated aims will be critically addressed, including: 1) the evidence for, and functional implications of, gastrointestinal microbiome dysbiosis in HIV-1 seropositive individuals; and 2) the potential for therapeutically targeting the consequences of this dysbiosis for the treatment of HIV-1-associated NCI and affective alterations. First, gastrointestinal microbiome dysbiosis in HIV-1 seropositive individuals is characterized by decreased alpha (α) diversity, a decreased relative abundance of bacterial species belonging to the Bacteroidetes phylum, and geographic-specific alterations in Bacillota (formerly Firmicutes) spp. Fundamentally, changes in the relative abundance of Bacteroidetes and Bacillota spp. may underlie, at least in part, the deficits in γ-aminobutyric acid and serotonin neurotransmission, as well as prominent synaptodendritic dysfunction, observed in this population. Second, there is compelling evidence for the therapeutic utility of targeting synaptodendritic dysfunction as a method to enhance neurocognitive function and improve motivational dysregulation in HIV-1. Further research is needed to determine whether the therapeutics enhancing synaptic efficacy exert their effects by altering the gut microbiome. Taken together, understanding gastrointestinal microbiome dysbiosis resulting from chronic HIV-1 viral protein exposure may afford insight into the mechanisms underlying HIV-1-associated neurocognitive and/or affective alterations; mechanisms which can be subsequently targeted via novel therapeutics.
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Affiliation(s)
- Mason T Rodriguez
- Cognitive and Neural Science Program, Department of Psychology, Barnwell College, 1512 Pendleton Street, University of South Carolina, Columbia, SC 29208, United States of America
| | - Kristen A McLaurin
- Cognitive and Neural Science Program, Department of Psychology, Barnwell College, 1512 Pendleton Street, University of South Carolina, Columbia, SC 29208, United States of America
| | - Michael Shtutman
- Drug Discovery and Biomedical Sciences, College of Pharmacy, 715 Sumter Street, University of South Carolina, Columbia, SC 29208, United States of America
| | - Jason L Kubinak
- Pathology, Microbiology & Immunology, School of Medicine Columbia, 6311 Garners Ferry Road, Building 2, Columbia, SC 29209, United States of America
| | - Charles F Mactutus
- Cognitive and Neural Science Program, Department of Psychology, Barnwell College, 1512 Pendleton Street, University of South Carolina, Columbia, SC 29208, United States of America
| | - Rosemarie M Booze
- Cognitive and Neural Science Program, Department of Psychology, Barnwell College, 1512 Pendleton Street, University of South Carolina, Columbia, SC 29208, United States of America.
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14
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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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15
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Goosen C, Proost S, Baumgartner J, Mallick K, Tito RY, Barnabas SL, Cotton MF, Zimmermann MB, Raes J, Blaauw R. Associations of HIV and iron status with gut microbiota composition, gut inflammation and gut integrity in South African school-age children: a two-way factorial case-control study. J Hum Nutr Diet 2023; 36:819-832. [PMID: 36992541 PMCID: PMC10946596 DOI: 10.1111/jhn.13171] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Accepted: 03/19/2023] [Indexed: 03/31/2023]
Abstract
BACKGROUND Human immunodeficiency virus (HIV) and iron deficiency (ID) affect many African children. Both HIV and iron status interact with gut microbiota composition and related biomarkers. The study's aim was to determine the associations of HIV and iron status with gut microbiota composition, gut inflammation and gut integrity in South African school-age children. METHODS In this two-way factorial case-control study, 8- to 13-year-old children were enrolled into four groups based on their HIV and iron status: (1) With HIV (HIV+) and ID (n = 43), (2) HIV+ and iron-sufficient nonanaemic (n = 41), (3) without HIV (HIV-) and ID (n = 44) and (4) HIV- and iron-sufficient nonanaemic (n = 38). HIV+ children were virally suppressed (<50 HIV RNA copies/ml) on antiretroviral therapy (ART). Microbial composition of faecal samples (16S rRNA sequencing) and markers of gut inflammation (faecal calprotectin) and gut integrity (plasma intestinal fatty acid-binding protein [I-FABP]) were assessed. RESULTS Faecal calprotectin was higher in ID versus iron-sufficient nonanaemic children (p = 0.007). I-FABP did not significantly differ by HIV or iron status. ART-treated HIV (redundancy analysis [RDA] R2 = 0.009, p = 0.029) and age (RDA R2 = 0.013 p = 0.004) explained the variance in the gut microbiota across the four groups. Probabilistic models showed that the relative abundance of the butyrate-producing genera Anaerostipes and Anaerotruncus was lower in ID versus iron-sufficient children. Fusicatenibacter was lower in HIV+ and in ID children versus their respective counterparts. The prevalence of the inflammation-associated genus Megamonas was 42% higher in children with both HIV and ID versus HIV- and iron-sufficient nonanaemic counterparts. CONCLUSIONS In our sample of 8- to 13-year-old virally suppressed HIV+ and HIV- children with or without ID, ID was associated with increased gut inflammation and changes in the relative abundance of specific microbiota. Moreover, in HIV+ children, ID had a cumulative effect that further shifted the gut microbiota to an unfavourable composition.
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Affiliation(s)
- Charlene Goosen
- Division of Human Nutrition, Department of Global Health, Faculty of Medicine and Health SciencesStellenbosch UniversityCape TownSouth Africa
| | - Sebastian Proost
- Laboratory of Molecular Bacteriology, Department of Microbiology and ImmunologyRega Institute, KU LeuvenLeuvenBelgium
- Center for Microbiology, VIBLeuvenBelgium
| | - Jeannine Baumgartner
- Laboratory of Human Nutrition, Department of Health Sciences and TechnologyETH ZurichZurichSwitzerland
- Department of Nutritional SciencesKing's College LondonLondonUK
| | - Kashish Mallick
- Laboratory of Human Nutrition, Department of Health Sciences and TechnologyETH ZurichZurichSwitzerland
| | - Raul Y. Tito
- Laboratory of Molecular Bacteriology, Department of Microbiology and ImmunologyRega Institute, KU LeuvenLeuvenBelgium
- Center for Microbiology, VIBLeuvenBelgium
| | - Shaun L. Barnabas
- Department of Paediatrics and Child Health, Family Centre for Research with UbuntuStellenbosch UniversityCape TownSouth Africa
| | - Mark F. Cotton
- Department of Paediatrics and Child Health, Family Centre for Research with UbuntuStellenbosch UniversityCape TownSouth Africa
| | - Michael B. Zimmermann
- Laboratory of Human Nutrition, Department of Health Sciences and TechnologyETH ZurichZurichSwitzerland
| | - Jeroen Raes
- Laboratory of Molecular Bacteriology, Department of Microbiology and ImmunologyRega Institute, KU LeuvenLeuvenBelgium
- Center for Microbiology, VIBLeuvenBelgium
| | - Renée Blaauw
- Division of Human Nutrition, Department of Global Health, Faculty of Medicine and Health SciencesStellenbosch UniversityCape TownSouth Africa
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16
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Taylor BC, Sheikh Andalibi M, Wandro S, Weldon KC, Sepich-Poore GD, Carpenter CS, Fraraccio S, Franklin D, Iudicello JE, Letendre S, Gianella S, Grant I, Ellis RJ, Heaton RK, Knight R, Swafford AD. Signatures of HIV and Major Depressive Disorder in the Plasma Microbiome. Microorganisms 2023; 11:1022. [PMID: 37110445 PMCID: PMC10146336 DOI: 10.3390/microorganisms11041022] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Revised: 04/08/2023] [Accepted: 04/10/2023] [Indexed: 04/29/2023] Open
Abstract
Inter-individual differences in the gut microbiome are linked to alterations in inflammation and blood-brain barrier permeability, which may increase the risk of depression in people with HIV (PWH). The microbiome profile of blood, which is considered by many to be typically sterile, remains largely unexplored. We aimed to characterize the blood plasma microbiome composition and assess its association with major depressive disorder (MDD) in PWH and people without HIV (PWoH). In this cross-sectional, observational cohort, we used shallow-shotgun metagenomic sequencing to characterize the plasma microbiome of 151 participants (84 PWH and 67 PWoH), all of whom underwent a comprehensive neuropsychiatric assessment. The microbial composition did not differ between PWH and PWoH or between participants with MDD and those without it. Using the songbird model, we computed the log ratio of the highest and lowest 30% of the ranked classes associated with HIV and MDD. We found that HIV infection and lifetime MDD were enriched in a set of differentially abundant inflammatory classes, such as Flavobacteria and Nitrospira. Our results suggest that the circulating plasma microbiome may increase the risk of MDD related to dysbiosis-induced inflammation in PWH. If confirmed, these findings may indicate new biological mechanisms that could be targeted to improve treatment of MDD in PWH.
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Affiliation(s)
- Bryn C. Taylor
- Biomedical Sciences Graduate Program, University of California San Diego, San Diego, CA 92093, USA
| | - Mohammadsobhan Sheikh Andalibi
- Departments of Neurosciences and Psychiatry, HIV Neurobehavioral Research Center, University of California, San Diego, CA 92093, USA; (M.S.A.)
| | - Stephen Wandro
- Center for Microbiome Innovation, University of California San Diego, San Diego, CA 92093, USA
| | - Kelly C. Weldon
- Center for Microbiome Innovation, University of California San Diego, San Diego, CA 92093, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA 92093, USA
| | | | - Carolina S. Carpenter
- Center for Microbiome Innovation, University of California San Diego, San Diego, CA 92093, USA
| | - Serena Fraraccio
- Center for Microbiome Innovation, University of California San Diego, San Diego, CA 92093, USA
| | - Donald Franklin
- Department of Psychiatry, School of Medicine, University of California, San Diego, CA 92093, USA
| | - Jennifer E. Iudicello
- Department of Psychiatry, School of Medicine, University of California, San Diego, CA 92093, USA
| | - Scott Letendre
- Departments of Medicine and Psychiatry, University of California San Diego, San Diego, CA 92093, USA
| | - Sara Gianella
- Division of Infectious Diseases and Global Public Health, University of California San Diego, San Diego, CA 92093, USA
| | - Igor Grant
- Department of Psychiatry, School of Medicine, University of California, San Diego, CA 92093, USA
| | - Ronald J. Ellis
- Departments of Neurosciences and Psychiatry, HIV Neurobehavioral Research Center, University of California, San Diego, CA 92093, USA; (M.S.A.)
| | - Robert K. Heaton
- Department of Psychiatry, School of Medicine, University of California, San Diego, CA 92093, USA
| | - Rob Knight
- Center for Microbiome Innovation, University of California San Diego, San Diego, CA 92093, USA
- Department of Bioengineering, University of California San Diego, San Diego, CA 92093, USA
- Department of Pediatrics, School of Medicine, University of California San Diego, San Diego, CA 92093, USA
- Department of Computer Science and Engineering, University of California San Diego, San Diego, CA 92093, USA
| | - Austin D. Swafford
- Center for Microbiome Innovation, University of California San Diego, San Diego, CA 92093, USA
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17
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Baltazar-Díaz TA, Amador-Lara F, Andrade-Villanueva JF, González-Hernández LA, Cabrera-Silva RI, Sánchez-Reyes K, Álvarez-Zavala M, Valenzuela-Ramírez A, Del Toro-Arreola S, Bueno-Topete MR. Gut Bacterial Communities in HIV-Infected Individuals with Metabolic Syndrome: Effects of the Therapy with Integrase Strand Transfer Inhibitor-Based and Protease Inhibitor-Based Regimens. Microorganisms 2023; 11:microorganisms11040951. [PMID: 37110374 PMCID: PMC10146710 DOI: 10.3390/microorganisms11040951] [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: 03/08/2023] [Revised: 03/27/2023] [Accepted: 04/04/2023] [Indexed: 04/29/2023] Open
Abstract
Antiretroviral therapies (ART) are strongly associated with weight gain and metabolic syndrome (MetS) development in HIV-infected patients. Few studies have evaluated the association between gut microbiota and integrase strand transfer inhibitor (INSTI)-based and protease inhibitor (PI)-based regimens in HIV-infected patients with MetS. To assess this, fecal samples were obtained from HIV-infected patients treated with different regimens (16 PI + MetS or 30 INSTI + MetS) and 18 healthy controls (HCs). The microbial composition was characterized using 16S rRNA amplicon sequencing. The INSTI-based and PI-based regimens were associated with a significant decrease in α-diversity compared to HCs. The INSTI + MetS group showed the lowest α-diversity between both regimens. A significant increase in the abundance of short-chain fatty acid (SCFA)-producing genera (Roseburia, Dorea, Ruminococcus torques, and Coprococcus) was observed in the PI + MetS group, while Prevotella, Fusobacterium, and Succinivibrio were significantly increased in the INSTI + MetS group. Moreover, the Proteobacteria/Firmicutes ratio was overrepresented, and functional pathways related to the biosynthesis of LPS components were increased in the INSTI + MetS group. The gut microbiota of patients receiving INSTIs showed a more pronounced dysbiosis orchestrated by decreased bacterial richness and diversity, with an almost complete absence of SCFA-producing bacteria and alterations in gut microbiota functional pathways. These findings have not been previously observed.
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Affiliation(s)
- Tonatiuh Abimael Baltazar-Díaz
- Departamento de Biología Molecular y Genómica, Instituto de Investigación en Enfermedades Crónico-Degenerativas, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara 44350, Mexico
| | - Fernando Amador-Lara
- Unidad de VIH, Hospital Civil de Guadalajara "Fray Antonio Alcalde", Guadalajara 44350, Mexico
- Departamento de Clínicas Médicas, Instituto de Investigación en Inmunodeficiencias y VIH, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara 44350, Mexico
| | - Jaime F Andrade-Villanueva
- Unidad de VIH, Hospital Civil de Guadalajara "Fray Antonio Alcalde", Guadalajara 44350, Mexico
- Departamento de Clínicas Médicas, Instituto de Investigación en Inmunodeficiencias y VIH, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara 44350, Mexico
| | - Luz Alicia González-Hernández
- Unidad de VIH, Hospital Civil de Guadalajara "Fray Antonio Alcalde", Guadalajara 44350, Mexico
- Departamento de Clínicas Médicas, Instituto de Investigación en Inmunodeficiencias y VIH, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara 44350, Mexico
| | - Rodolfo Ismael Cabrera-Silva
- Departamento de Clínicas Médicas, Instituto de Investigación en Inmunodeficiencias y VIH, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara 44350, Mexico
| | - Karina Sánchez-Reyes
- Departamento de Clínicas Médicas, Instituto de Investigación en Inmunodeficiencias y VIH, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara 44350, Mexico
| | - Monserrat Álvarez-Zavala
- Departamento de Clínicas Médicas, Instituto de Investigación en Inmunodeficiencias y VIH, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara 44350, Mexico
| | - Aldo Valenzuela-Ramírez
- Unidad de VIH, Hospital Civil de Guadalajara "Fray Antonio Alcalde", Guadalajara 44350, Mexico
| | - Susana Del Toro-Arreola
- Departamento de Biología Molecular y Genómica, Instituto de Investigación en Enfermedades Crónico-Degenerativas, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara 44350, Mexico
| | - Miriam Ruth Bueno-Topete
- Departamento de Biología Molecular y Genómica, Instituto de Investigación en Enfermedades Crónico-Degenerativas, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara 44350, Mexico
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18
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Distinct inflammatory profiles linked to cardiovascular disease risk in HIV infection: implications for the design of preventive and therapeutic interventions. AIDS 2023; 37:693-695. [PMID: 36815523 DOI: 10.1097/qad.0000000000003475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
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19
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Castillo-Rozas G, Lopez MN, Soto-Rifo R, Vidal R, Cortes CP. Enteropathy and gut dysbiosis as obstacles to achieve immune recovery in undetectable people with HIV: a clinical view of evidence, successes, and projections. AIDS 2023; 37:367-378. [PMID: 36695354 DOI: 10.1097/qad.0000000000003450] [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: 01/26/2023]
Abstract
Immune performance following antiretroviral therapy initiation varies among patients. Despite achieving viral undetectability, a subgroup of patients fails to restore CD4+ T-cell counts during follow-up, which exposes them to non-AIDS defining comorbidities and increased mortality. Unfortunately, its mechanisms are incompletely understood, and no specific treatment is available. In this review, we address some of the pathophysiological aspects of the poor immune response from a translational perspective, with emphasis in the interaction between gut microbiome, intestinal epithelial dysfunction, and immune system, and we also discuss some studies attempting to improve immune performance by intervening in this vicious cycle.
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Affiliation(s)
- Gabriel Castillo-Rozas
- Molecular and Cellular Virology Laboratory, Virology Program
- Cancer Regulation and Immunoediting Laboratory, Immunology Program
- Center for HIV/AIDS Integral Research -CHAIR, Universidad de Chile, Santiago
- Millennium Institute on Immunology and Immunotherapy, Santiago, Chile
| | - Mercedes N Lopez
- Cancer Regulation and Immunoediting Laboratory, Immunology Program
| | - Ricardo Soto-Rifo
- Molecular and Cellular Virology Laboratory, Virology Program
- Center for HIV/AIDS Integral Research -CHAIR, Universidad de Chile, Santiago
- Millennium Institute on Immunology and Immunotherapy, Santiago, Chile
| | - Roberto Vidal
- Microbiology and Mycology Program, Institute of Biomedical Sciences
| | - Claudia P Cortes
- Internal Medicine Department, Faculty of Medicine, Universidad de Chile
- Center for HIV/AIDS Integral Research -CHAIR, Universidad de Chile, Santiago
- Millennium Institute on Immunology and Immunotherapy, Santiago, Chile
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20
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Chan P, Yoon B, Colby D, Kroon E, Sacdalan C, Sriplienchan S, Pinyakorn S, Ananworanich J, Valcour V, Vasan S, Hsu D, Phanuphak N, Paul R, Spudich S. Immunological, Cognitive, and Psychiatric Outcomes After Initiating Efavirenz- and Dolutegravir-based Antiretroviral Therapy During Acute Human Immunodeficiency Virus Infection. Clin Infect Dis 2023; 76:e718-e726. [PMID: 35687498 PMCID: PMC9907536 DOI: 10.1093/cid/ciac466] [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: 02/11/2022] [Revised: 05/27/2022] [Accepted: 06/03/2022] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Efavirenz (EFV)- and dolutegravir (DTG)-based antiretroviral therapy (ART) is the former and current recommended regimen for treatment-naive individuals with human immunodeficiency virus type 1 (HIV-1). Whether they impact the immunological and neuropsychiatric profile differentially remains unclear. METHODS This retrospective analysis included 258 participants enrolled during acute HIV-1 infection (AHI). Participants initiated 1 of 3 ART regimens during AHI: EFV-based (n = 131), DTG-based (n = 92), or DTG intensified with maraviroc (DTG/MVC, n = 35). All regimens included 2 nucleoside reverse-transcriptase inhibitors and were maintained for 96 weeks. CD4+ and CD8+ T-cell counts, mood symptoms, and composite score on a 4-test neuropsychological battery (NPZ-4) were compared. RESULTS At baseline, the median age was 26 years, 99% were male, and 36% were enrolled during Fiebig stage I-II. Plasma viral suppression at weeks 24 and 96 was similar between the groups. Compared with the EFV group, the DTG group showed greater increments of CD4+ (P < .001) and CD8+ (P = .015) T-cell counts but a similar increment of CD4/CD8 ratio at week 96. NPZ-4 improvement was similar between the 2 groups at week 24 but greater in the DTG group at week 96 (P = .005). Depressive mood and distress symptoms based on the Patient Health Questionnaire and distress thermometer were similar between the 2 groups at follow-up. Findings for the DTG/MVC group were comparable to those for the DTG group vs the EFV group. CONCLUSIONS Among individuals with AHI, 96 weeks of DTG-based ART was associated with greater increments of CD4+ and CD8+ T-cell counts and improvement in cognitive performance.
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Affiliation(s)
- Phillip Chan
- South East Asia Research Collaboration in HIV, Institute of HIV Research and Innovation, Bangkok, Thailand
- Department of Neurology, Yale School of Medicine, New Haven, Connecticut, USA
| | - Bohyung Yoon
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, Bethesda, Maryland, USA
| | - Donn Colby
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, Bethesda, Maryland, USA
| | - Eugène Kroon
- South East Asia Research Collaboration in HIV, Institute of HIV Research and Innovation, Bangkok, Thailand
| | - Carlo Sacdalan
- South East Asia Research Collaboration in HIV, Institute of HIV Research and Innovation, Bangkok, Thailand
| | - Somchai Sriplienchan
- South East Asia Research Collaboration in HIV, Institute of HIV Research and Innovation, Bangkok, Thailand
| | - Suteeraporn Pinyakorn
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, Bethesda, Maryland, USA
| | - Jintanat Ananworanich
- Department of Global Health, Amsterdam University Medical Centers, Amsterdam Institute for Global Health and Development, University of Amsterdam, Amsterdam, The Netherlands
| | - Victor Valcour
- Department of Neurology, Memory and Aging Center, University of California–San Francisco, San Francisco,California, USA
| | - Sandhya Vasan
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, Bethesda, Maryland, USA
| | - Denise Hsu
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, Bethesda, Maryland, USA
| | - Nittaya Phanuphak
- South East Asia Research Collaboration in HIV, Institute of HIV Research and Innovation, Bangkok, Thailand
| | - Robert Paul
- Faculty of Psychological Sciences, Missouri Institute of Mental Health, University of Missouri-St. Louis, St. Louis, Missouri, USA
| | - Serena Spudich
- Department of Neurology, Yale School of Medicine, New Haven, Connecticut, USA
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21
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Gut microbiota alterations after switching from a protease inhibitor or efavirenz to raltegravir in a randomized, controlled study. AIDS 2023; 37:323-332. [PMID: 36541643 DOI: 10.1097/qad.0000000000003419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
OBJECTIVE To study gut microbiota before and 24 weeks after a single antiretroviral agent switch. DESIGN HIV-positive patients with efavirenz (EFV) or a protease inhibitor (PI)-based antiretroviral therapy (ART) were randomized to switch EFV or PI to raltegravir (RAL group, n = 19) or to continue unchanged ART (EFV/PI group, n = 22). Age and weight-matched HIV-negative participants (n = 10) were included for comparison. METHODS Microbiota was analyzed using 16S rRNA sequencing. Serum intestinal fatty acid-binding protein (I-FABP) and serum lipopolysaccharide-binding protein (LBP) were measured as gut permeability markers. Three-day food diaries were collected. RESULTS At week 24, microbiota diversity (Chao1 index) was higher in RAL than the EFV/PI group (P = 0.014), and RAL group did not differ from HIV-negative participants. In subgroup analysis switching from EFV (P = 0.043), but not from a PI to RAL increased Chao1. At week 24, RAL and EFV/PI group differed in the relative abundance of Prevotella 9 (higher in RAL, P = 0.01), Phascolarctobacterium and Bacteroides (lower in RAL, P = 0.01 and P = 0.03). Dietary intakes did not change during the study and do not explain microbiota differences. Also, I-FABP and LBP remained unchanged. CONCLUSION Here we demonstrate that a single ART agent switch caused microbiota alterations, most importantly, an increase in diversity with EFV to RAL switch. Previously, we reported weight gain, yet reduced inflammation in this cohort. The observed microbiota differences between RAL and EFV/PI groups may be associated with reduced inflammation and/or increase in weight. Further studies are needed to evaluate inflammatory and metabolic capacity of microbiota with ART switches.
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22
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Impact of HIV infection and integrase strand transfer inhibitors-based treatment on the gut virome. Sci Rep 2022; 12:21658. [PMID: 36522388 PMCID: PMC9755154 DOI: 10.1038/s41598-022-25979-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 12/07/2022] [Indexed: 12/23/2022] Open
Abstract
Viruses are the most abundant components of the human gut microbiome with a significant impact on health and disease. The effects of human immunodeficiency virus (HIV) infection on gut virome has been scarcely analysed. Several studies suggested that integrase strand transfers inhibitors (INSTIs) are associated with a healthier gut. Thus, the objective of this work was to evaluate the effects of HIV infection and INSTIs on gut virome composition. 26 non-HIV-infected volunteers, 15 naive HIV-infected patients and 15 INSTIs-treated HIV-infected patients were recruited and their gut virome composition was analysed using shotgun sequencing. Bacteriophages were the most abundant and diverse viruses present in gut. HIV infection was accompanied by a decrease in phage richness which was reverted after INSTIs-based treatment. β-diversity of phages revealed that samples from HIV-infected patients clustered separately from those belonging to the control group. Differential abundant analysis showed an increase in phages belonging to Caudoviricetes class in the naive group and a decrease of Malgrandaviricetes class phages in the INSTIs-treated group compared to the control group. Besides, it was observed that INSTIs-based treatment was not able to reverse the increase of lysogenic phages associated with HIV infection or to modify the decrease observed on the relative abundance of Proteobacteria-infecting phages. Our study describes for the first time the impact of HIV and INSTIs on gut virome and demonstrates that INSTIs-based treatments are able to partially restore gut dysbiosis at the viral level, which opens several opportunities for new studies focused on microbiota-based therapies.
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23
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Lavinder TR, Fachko DN, Stanton J, Varco-Merth B, Smedley J, Okoye AA, Skalsky RL. Effects of Early Antiretroviral Therapy on the Composition and Diversity of the Fecal Microbiome of SIV-infected Rhesus Macaques ( Macaca mulatta). Comp Med 2022; 72:287-297. [PMID: 36162961 PMCID: PMC9827599 DOI: 10.30802/aalas-cm-22-000020] [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: 01/27/2023]
Abstract
HIV-infected people develop reproducible disruptions in their gastrointestinal microbiota. Despite the suppression of HIV viremia via long-term antiretroviral therapy (ART), alterations still occur in gut microbial diversity and the commensal microbiota. Mounting evidence suggests these microbial changes lead to the development of gut dysbiosis-persistent inflammation that damages the gut mucosa-and correlate with various immune defects. In this study, we examined how early ART intervention influences microbial diversity in SIV-infected rhesus macaques. Using 16S rRNA sequencing, we defined the fecal microbiome in macaques given daily ART beginning on either 3 or 7 d after SIV infection (dpi) and characterized changes in composition, α diversity, and β diversity from before infection through 112 dpi. The dominant phyla in the fecal samples before infection were Bacteroidetes, Firmicutes, Spirochaetes, and Proteobacteria. After SIV infection and ART, the relative abundance of Firmicutes and Bacteroidetes did not change significantly. Significant reductions in α diversity occurred across time when ART was initiated at 3 dpi but not at 7 dpi. Principal coordinate analysis of samples revealed a divergence in β diversity in both treatment groups after SIV infection, with significant differences depending on the timing of ART administration. These results indicate that although administration of ART at 3 or 7 dpi did not substantially alter fecal microbial composition, the timing of early ART measurably altered phylogenetic diversity.
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Affiliation(s)
- Tiffany R Lavinder
- Division of Comparative Medicine, Oregon National Primate Research Center, Oregon Health and Science University,,Corresponding authors. ,
| | - Devin N Fachko
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, and
| | - Jeffrey Stanton
- Division of Comparative Medicine, Oregon National Primate Research Center, Oregon Health and Science University
| | - Benjamin Varco-Merth
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, and,Division of Pathobiology and Immunology, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, Oregon
| | - Jeremy Smedley
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, and,Division of Pathobiology and Immunology, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, Oregon
| | - Afam A Okoye
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, and,Division of Pathobiology and Immunology, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, Oregon
| | - Rebecca L Skalsky
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, and,Division of Pathobiology and Immunology, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, Oregon,Corresponding authors. ,
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24
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Prasad R, Patton MJ, Floyd JL, Fortmann S, DuPont M, Harbour A, Wright J, Lamendella R, Stevens BR, Oudit GY, Grant MB. Plasma Microbiome in COVID-19 Subjects: An Indicator of Gut Barrier Defects and Dysbiosis. Int J Mol Sci 2022; 23:9141. [PMID: 36012406 PMCID: PMC9409329 DOI: 10.3390/ijms23169141] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 08/10/2022] [Accepted: 08/12/2022] [Indexed: 12/16/2022] Open
Abstract
The gut is a well-established route of infection and target for viral damage by SARS-CoV-2. This is supported by the clinical observation that about half of COVID-19 patients exhibit gastrointestinal (GI) complications. We aimed to investigate whether the analysis of plasma could provide insight into gut barrier dysfunction in patients with COVID-19 infection. Plasma samples of COVID-19 patients (n = 146) and healthy individuals (n = 47) were collected during hospitalization and routine visits. Plasma microbiome was analyzed using 16S rRNA sequencing and gut permeability markers including fatty acid binding protein 2 (FABP2), peptidoglycan (PGN), and lipopolysaccharide (LPS) in both patient cohorts. Plasma samples of both cohorts contained predominately Proteobacteria, Firmicutes, Bacteroides, and Actinobacteria. COVID-19 subjects exhibit significant dysbiosis (p = 0.001) of the plasma microbiome with increased abundance of Actinobacteria spp. (p = 0.0332), decreased abundance of Bacteroides spp. (p = 0.0003), and an increased Firmicutes:Bacteroidetes ratio (p = 0.0003) compared to healthy subjects. The concentration of the plasma gut permeability marker FABP2 (p = 0.0013) and the gut microbial antigens PGN (p < 0.0001) and LPS (p = 0.0049) were significantly elevated in COVID-19 patients compared to healthy subjects. These findings support the notion that the intestine may represent a source for bacteremia and contribute to worsening COVID-19 outcomes. Therapies targeting the gut and prevention of gut barrier defects may represent a strategy to improve outcomes in COVID-19 patients.
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Affiliation(s)
- Ram Prasad
- Department of Ophthalmology and Visual Sciences, University of Alabama at Birmingham, 1670 University BLVD, VH490, Birmingham, AL 35294, USA
| | - Michael John Patton
- Hugh Kaul Precision Medicine Institute, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Jason Levi. Floyd
- Department of Ophthalmology and Visual Sciences, University of Alabama at Birmingham, 1670 University BLVD, VH490, Birmingham, AL 35294, USA
| | - Seth Fortmann
- Department of Ophthalmology and Visual Sciences, University of Alabama at Birmingham, 1670 University BLVD, VH490, Birmingham, AL 35294, USA
| | - Mariana DuPont
- Department of Ophthalmology and Visual Sciences, University of Alabama at Birmingham, 1670 University BLVD, VH490, Birmingham, AL 35294, USA
| | - Angela Harbour
- Department of Ophthalmology and Visual Sciences, University of Alabama at Birmingham, 1670 University BLVD, VH490, Birmingham, AL 35294, USA
| | | | | | - Bruce R. Stevens
- Department of Physiology and Functional Genomics, University of Florida, Gainesville, FL 32611, USA
| | - Gavin Y. Oudit
- Division of Cardiology, Department of Medicine, University of Alberta, Mazankowski Alberta Heart Institute, Edmonton, AB T6G 2B7, Canada
| | - Maria B. Grant
- Department of Ophthalmology and Visual Sciences, University of Alabama at Birmingham, 1670 University BLVD, VH490, Birmingham, AL 35294, USA
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25
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Villoslada-Blanco P, Pérez-Matute P, Íñiguez M, Recio-Fernández E, Blanco-Navarrete P, Metola L, Ibarra V, Alba J, de Toro M, Oteo JA. Integrase Inhibitors Partially Restore Bacterial Translocation, Inflammation and Gut Permeability Induced by HIV Infection: Impact on Gut Microbiota. Infect Dis Ther 2022; 11:1541-1557. [PMID: 35618952 PMCID: PMC9334516 DOI: 10.1007/s40121-022-00654-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 05/04/2022] [Indexed: 11/30/2022] Open
Abstract
Introduction Human immunodeficiency virus (HIV) infection can be considered a chronic disease thanks to the extended use of antiretroviral treatment (ART). In this context, low-grade chronic inflammation related to gut microbiota (GM) dysbiosis and bacterial translocation (BT) among other factors has been observed despite the use of ART. In addition, different ART regimens have demonstrated differential impacts on GM. However, the role of novel integrase strand transfer inhibitors (INSTIs) has not been investigated yet. The aim of this study was to analyse the effects of INSTIs in first-line of treatment on markers of BT, inflammation, cardiovascular risk, gut permeability and GM composition and derived short-chain fatty acids. Methods Twenty-six non-HIV-infected volunteers and 30 HIV-infected patients (15 naïve and 15 under INSTIs regimen) were recruited. Blood samples were extracted to analyse biochemical parameters and markers of BT, inflammation, cardiovascular risk, gut permeability and bacterial metabolism. GM composition was analysed using 16S rRNA gene sequencing. Results Our results showed that HIV infection increased BT, inflammation, cardiovascular risk and gut permeability, whereas INSTIs counteracted these effects. Regarding GM, the reduction in bacterial richness induced by HIV infection was restored by INSTIs. Beta diversity revealed that HIV-infected people were separated from the control group independently of treatment. Conclusions Current antiretroviral regimens based on INSTIs are able to reverse the impact of HIV infection on BT, systemic inflammation, gut permeability and bacterial diversity/richness, reaching similar levels to those observed in an uninfected/control population. These results suggest a protective role of INSTIs in disease progression, subsequent immune activation and in the development of future age-related complications such as cardiovascular events. Supplementary Information The online version contains supplementary material available at 10.1007/s40121-022-00654-4.
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Affiliation(s)
- Pablo Villoslada-Blanco
- Infectious Diseases, Microbiota and Metabolism Unit. Infectious Diseases Department, Center for Biomedical Research of La Rioja (CIBIR), Logroño, La Rioja, Spain
| | - Patricia Pérez-Matute
- Infectious Diseases, Microbiota and Metabolism Unit. Infectious Diseases Department, Center for Biomedical Research of La Rioja (CIBIR), Logroño, La Rioja, Spain.
| | - María Íñiguez
- Infectious Diseases, Microbiota and Metabolism Unit. Infectious Diseases Department, Center for Biomedical Research of La Rioja (CIBIR), Logroño, La Rioja, Spain
| | - Emma Recio-Fernández
- Infectious Diseases, Microbiota and Metabolism Unit. Infectious Diseases Department, Center for Biomedical Research of La Rioja (CIBIR), Logroño, La Rioja, Spain
| | | | - Luis Metola
- Infectious Diseases Department, Hospital Universitario San Pedro, Logroño, La Rioja, Spain
| | - Valvanera Ibarra
- Infectious Diseases Department, Hospital Universitario San Pedro, Logroño, La Rioja, Spain
| | - Jorge Alba
- Infectious Diseases Department, Hospital Universitario San Pedro, Logroño, La Rioja, Spain
| | - María de Toro
- Genomics and Bioinformatics Platform, Center for Biomedical Research of La Rioja (CIBIR), Logroño, La Rioja, Spain
| | - José A Oteo
- Infectious Diseases, Microbiota and Metabolism Unit. Infectious Diseases Department, Center for Biomedical Research of La Rioja (CIBIR), Logroño, La Rioja, Spain.,Infectious Diseases Department, Hospital Universitario San Pedro, Logroño, La Rioja, Spain
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26
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Russo E, Nannini G, Sterrantino G, Kiros ST, Di Pilato V, Coppi M, Baldi S, Niccolai E, Ricci F, Ramazzotti M, Pallecchi M, Lagi F, Rossolini GM, Bartoloni A, Bartolucci G, Amedei A. Effects of viremia and CD4 recovery on gut “microbiome-immunity” axis in treatment-naïve HIV-1-infected patients undergoing antiretroviral therapy. World J Gastroenterol 2022; 28:635-652. [PMID: 35317423 PMCID: PMC8900548 DOI: 10.3748/wjg.v28.i6.635] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 07/30/2021] [Accepted: 01/12/2022] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Human immunodeficiency virus type 1 (HIV-1) infection is characterized by persistent systemic inflammation and immune activation, even in patients receiving effective antiretroviral therapy (ART). Converging data from many cross-sectional studies suggest that gut microbiota (GM) changes can occur throughout including human immunodeficiency virus (HIV) infection, treated by ART; however, the results are contrasting. For the first time, we compared the fecal microbial composition, serum and fecal microbial metabolites, and serum cytokine profile of treatment-naïve patients before starting ART and after reaching virological suppression, after 24 wk of ART therapy. In addition, we compared the microbiota composition, microbial metabolites, and cytokine profile of patients with CD4/CD8 ratio < 1 (immunological non-responders [INRs]) and CD4/CD8 > 1 (immunological responders [IRs]), after 24 wk of ART therapy.
AIM To compare for the first time the fecal microbial composition, serum and fecal microbial metabolites, and serum cytokine profile of treatment-naïve patients before starting ART and after reaching virological suppression (HIV RNA < 50 copies/mL) after 24 wk of ART.
METHODS We enrolled 12 treatment-naïve HIV-infected patients receiving ART (mainly based on integrase inhibitors). Fecal microbiota composition was assessed through next generation sequencing. In addition, a comprehensive analysis of a blood broad-spectrum cytokine panel was performed through a multiplex approach. At the same time, serum free fatty acid (FFA) and fecal short chain fatty acid levels were obtained through gas chromatography-mass spectrometry.
RESULTS We first compared microbiota signatures, FFA levels, and cytokine profile before starting ART and after reaching virological suppression. Modest alterations were observed in microbiota composition, in particular in the viral suppression condition, we detected an increase of Ruminococcus and Succinivibrio and a decrease of Intestinibacter. Moreover, in the same condition, we also observed augmented levels of serum propionic and butyric acids. Contemporarily, a reduction of serum IP-10 and an increase of IL-8 levels were detected in the viral suppression condition. In addition, the same components were compared between IRs and INRs. Concerning the microflora population, we detected a reduction of Faecalibacterium and an increase of Alistipes in INRs. Simultaneously, fecal isobutyric, isovaleric, and 2-methylbutyric acids were also increased in INRs.
CONCLUSION Our results provided an additional perspective about the impact of HIV infection, ART, and immune recovery on the “microbiome-immunity axis” at the metabolism level. These factors can act as indicators of the active processes occurring in the gastrointestinal tract. Individuals with HIV-1 infection, before ART and after reaching virological suppression with 24 wk of ART, displayed a microbiota with unchanged overall bacterial diversity; moreover, their systemic inflammatory status seems not to be completely restored. In addition, we confirmed the role of the GM metabolites in immune reconstitution.
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Affiliation(s)
- Edda Russo
- Department of Clinical and Experimental Medicine, University of Florence, Florence 50134, Italy
| | - Giulia Nannini
- Department of Clinical and Experimental Medicine, University of Florence, Florence 50134, Italy
| | - Gaetana Sterrantino
- Department of Clinical and Experimental Medicine, University of Florence, Florence 50134, Italy
| | - Seble Tekle Kiros
- Department of Clinical and Experimental Medicine, University of Florence, Florence 50134, Italy
| | - Vincenzo Di Pilato
- Department of Surgical Sciences and Integrated Diagnostics, University of Genoa, Genoa 16126, Italy
| | - Marco Coppi
- Department of Clinical and Experimental Medicine, University of Florence, Florence 50134, Italy
| | - Simone Baldi
- Department of Clinical and Experimental Medicine, University of Florence, Florence 50134, Italy
| | - Elena Niccolai
- Department of Clinical and Experimental Medicine, University of Florence, Florence 50134, Italy
| | - Federica Ricci
- Department of Clinical and Experimental Medicine, University of Florence, Florence 50134, Italy
| | - Matteo Ramazzotti
- Department of Biomedical, Experimental and Clinical "Mario Serio", University of Florence, Florence 50134, Italy
| | - Marco Pallecchi
- Department of Biomedical, Experimental and Clinical "Mario Serio", University of Florence, Florence 50134, Italy
| | - Filippo Lagi
- Department of Clinical and Experimental Medicine, University of Florence, Florence 50134, Italy
| | - Gian Maria Rossolini
- Microbiology and Virology Unit, Florence Careggi University Hospital, University of Florence, Florence 50134, Italy
| | - Alessandro Bartoloni
- Department of Clinical and Experimental Medicine, University of Florence, Florence 50134, Italy
| | - Gianluca Bartolucci
- Department of Neurosciences, Psychology, Drug Research and Child Health, University of Florence, Florence 50019, Italy
| | - Amedeo Amedei
- Department of Clinical and Experimental Medicine, University of Florence, Florence 50134, Italy
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27
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Villa C, Rivellini E, Lavitrano M, Combi R. Can SARS-CoV-2 Infection Exacerbate Alzheimer's Disease? An Overview of Shared Risk Factors and Pathogenetic Mechanisms. J Pers Med 2022; 12:29. [PMID: 35055344 PMCID: PMC8780286 DOI: 10.3390/jpm12010029] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 12/19/2021] [Accepted: 12/20/2021] [Indexed: 12/11/2022] Open
Abstract
The current coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus (SARS-CoV)-2, is affecting every aspect of global society, including public healthcare systems, medical care access, and the economy. Although the respiratory tract is primarily affected by SARS-CoV-2, emerging evidence suggests that the virus may also reach the central nervous system (CNS), leading to several neurological issues. In particular, people with a diagnosis of Alzheimer's disease (AD) are a vulnerable group at high risk of contracting COVID-19, and develop more severe forms and worse outcomes, including death. Therefore, understanding shared links between COVID-19 and AD could aid the development of therapeutic strategies against both. Herein, we reviewed common risk factors and potential pathogenetic mechanisms that might contribute to the acceleration of neurodegenerative processes in AD patients infected by SARS-CoV-2.
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Affiliation(s)
- Chiara Villa
- School of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy
| | - Eleonora Rivellini
- School of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy
| | - Marialuisa Lavitrano
- School of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy
| | - Romina Combi
- School of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy
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28
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Yanavich C, Perazzo H, Li F, Tobin N, Lee D, Zabih S, Morata M, Almeida C, Veloso VG, Grinsztejn B, Aldrovandi GM. A pilot study of microbial signatures of liver disease in those with HIV mono-infection in Rio de Janeiro, Brazil. AIDS 2022; 36:49-58. [PMID: 34873092 PMCID: PMC8667204 DOI: 10.1097/qad.0000000000003084] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
OBJECTIVE The rectal microbiome was examined to assess the relationship between the microbiome and liver disease in HIV-infection. DESIGN Eighty-two HIV-1 mono-infected individuals from the PROSPEC-HIV-study (NCT02542020) were grouped into three liver health categories based on results of controlled attenuation parameter (CAP) and liver stiffness measurement (LSM) of transient elastography: normal (n = 30), steatosis (n = 30), or fibrosis (n = 22). METHODS Liver steatosis and fibrosis were defined by CAP at least 248 dB/m and LSM at least 8.0 kPa, respectively. 16S rRNA gene and whole genome shotgun metagenomic sequencing were performed on rectal swabs. Bacterial differences were assessed using zero-inflated negative binomial regression and random forests modeling; taxonomic drivers of functional shifts were identified using FishTaco. RESULTS Liver health status explained four percentage of the overall variation (r2 = 0.04, P = 0.003) in bacterial composition. Participants with steatosis had depletions of Akkermansia muciniphila and Bacteroides dorei and enrichment of Prevotella copri, Finegoldia magna, and Ruminococcus bromii. Participants with fibrosis had depletions of Bacteroides stercoris and Parabacteroides distasonis and enrichment of Sneathia sanguinegens. In steatosis, functional analysis revealed increases in primary and secondary bile acid synthesis encoded by increased Eubacterium rectale, F. magna, and Faecalibacterium prausnitzii and decreased A. muciniphila, Bacteroides fragilis and B. dorei. Decreased folate biosynthesis was driven by similar changes in microbial composition. CONCLUSION HIV mono-infection with steatosis or fibrosis had distinct microbial profiles. Some taxa are similar to those associated with non-alcoholic fatty liver disease in HIV-negative populations. Further studies are needed to define the role of the gut microbiota in the pathogenesis of liver disease in HIV-infected persons.
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Affiliation(s)
- Carolyn Yanavich
- Laboratory of Clinical Research in STD/AIDS (LAPCLIN-AIDS), Evandro Chagas National Institute of Infectious Diseases-Oswaldo Cruz Foundation (INI/FIOCRUZ), Rio de Janeiro, Brazil
- Department of Pediatrics, University of California, Los Angeles (UCLA), Los Angeles, California, USA
| | - Hugo Perazzo
- Laboratory of Clinical Research in STD/AIDS (LAPCLIN-AIDS), Evandro Chagas National Institute of Infectious Diseases-Oswaldo Cruz Foundation (INI/FIOCRUZ), Rio de Janeiro, Brazil
| | - Fan Li
- Department of Pediatrics, University of California, Los Angeles (UCLA), Los Angeles, California, USA
| | - Nicole Tobin
- Department of Pediatrics, University of California, Los Angeles (UCLA), Los Angeles, California, USA
| | - David Lee
- Department of Pediatrics, University of California, Los Angeles (UCLA), Los Angeles, California, USA
| | - Sara Zabih
- Department of Pediatrics, University of California, Los Angeles (UCLA), Los Angeles, California, USA
| | - Michelle Morata
- Laboratory of Clinical Research in STD/AIDS (LAPCLIN-AIDS), Evandro Chagas National Institute of Infectious Diseases-Oswaldo Cruz Foundation (INI/FIOCRUZ), Rio de Janeiro, Brazil
| | - Cristiane Almeida
- Laboratory of Clinical Research in STD/AIDS (LAPCLIN-AIDS), Evandro Chagas National Institute of Infectious Diseases-Oswaldo Cruz Foundation (INI/FIOCRUZ), Rio de Janeiro, Brazil
| | - Valdilea G Veloso
- Laboratory of Clinical Research in STD/AIDS (LAPCLIN-AIDS), Evandro Chagas National Institute of Infectious Diseases-Oswaldo Cruz Foundation (INI/FIOCRUZ), Rio de Janeiro, Brazil
| | - Beatriz Grinsztejn
- Laboratory of Clinical Research in STD/AIDS (LAPCLIN-AIDS), Evandro Chagas National Institute of Infectious Diseases-Oswaldo Cruz Foundation (INI/FIOCRUZ), Rio de Janeiro, Brazil
| | - Grace M Aldrovandi
- Department of Pediatrics, University of California, Los Angeles (UCLA), Los Angeles, California, USA
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29
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Li H, Zhang L, Zhang K, Huang Y, Liu Y, Lu X, Liao W, Liu X, Zhang Q, Pan W. Gut microbiota associated with cryptococcal meningitis and dysbiosis caused by anti-fungal treatment. Front Microbiol 2022; 13:1086239. [PMID: 36909846 PMCID: PMC9994644 DOI: 10.3389/fmicb.2022.1086239] [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: 11/01/2022] [Accepted: 12/05/2022] [Indexed: 02/24/2023] Open
Abstract
The gut microbiota is a dynamic and highly diverse microbial ecosystem that affects many aspects of the host's physiology. An improved understanding of the gut microbiota could lead to better strategies for the diagnosis and therapy of cryptococcal meningitis (CM), but the impact of Cryptococcus infection and anti-fungal treatment on the gut microbiota has rarely been studied. We characterized the diversity and composition of the gut microbiota in CM patients at diagnosis and healthy controls (HCs) using metagenomic sequencing and determined the effects of anti-fungal drugs. We found that CM patients had distinct bacterial and fungal compositions compared with HCs, with eight differentially abundant fungal and 72 differentially abundant bacterial species identified between the two groups. CM patients showed an increased abundance of Enterococcus avium, Leuconostoc mesenteroides, and Weissella cibaria, and a decreased abundance of Prevotella spp. compared with HCs. However, anti-fungal treatment only led to minor changes in the intestinal microbiota. Moreover, both positive and negative correlations existed in fungal, bacterial, and clinical indicators. Our study suggests that the Cryptococcus neoformans infection caused a distinct dysbiosis of the gut microbiota and contributes valuable information implying potential links between the CM and gut microbiota.
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Affiliation(s)
- Hang Li
- Shanghai Key Laboratory of Molecular Medical Mycology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China.,Department of Dermatology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China.,Department of Dermatology, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Lei Zhang
- Department of Dermatology, The Third Affiliated Hospital of Xi'an Jiaotong University, Shaanxi Provincial People's Hospital, Xi'an, China
| | - Keming Zhang
- Shanghai Key Laboratory of Molecular Medical Mycology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China.,Department of Dermatology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Yue Huang
- Shanghai Key Laboratory of Molecular Medical Mycology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China.,Department of Dermatology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China.,Department of Dermatology, The First Naval Hospital of Southern Theater Command, Zhanjiang, China
| | - Yi Liu
- Shanghai Key Laboratory of Molecular Medical Mycology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China.,Department of Dermatology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Xiaodi Lu
- Shanghai Key Laboratory of Molecular Medical Mycology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China.,Department of Dermatology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Wanqing Liao
- Shanghai Key Laboratory of Molecular Medical Mycology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China.,Department of Dermatology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Xiaogang Liu
- Shanghai Key Laboratory of Molecular Medical Mycology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China.,Department of Dermatology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Qilong Zhang
- Department of Neurology, Jiangxi Chest Hospital, Jiangxi, China
| | - Weihua Pan
- Shanghai Key Laboratory of Molecular Medical Mycology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China.,Department of Dermatology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China
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30
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Nguyen QT, Ishizaki A, Bi X, Matsuda K, Nguyen LV, Pham HV, Phan CTT, Phung TTB, Ngo TTT, Nguyen AV, Khu DTK, Ichimura H. Alterations in children's sub-dominant gut microbiota by HIV infection and anti-retroviral therapy. PLoS One 2021; 16:e0258226. [PMID: 34634074 PMCID: PMC8504761 DOI: 10.1371/journal.pone.0258226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 09/21/2021] [Indexed: 12/05/2022] Open
Abstract
Objective We investigated the impact of human immunodeficiency virus (HIV) infection and anti-retroviral therapy (ART) on the gut microbiota of children. Design This cross-sectional study investigated the gut microbiota of children with and without HIV. Methods We collected fecal samples from 59 children with HIV (29 treated with ART [ART(+)] and 30 without ART [HIV(+)]) and 20 children without HIV [HIV(–)] in Vietnam. We performed quantitative RT-PCR to detect 14 representative intestinal bacteria targeting 16S/23S rRNA molecules. We also collected the blood samples for immunological analyses. Results In spearman’s correlation analyses, no significant correlation between the number of dominant bacteria and age was found among children in the HIV(−) group. However, the number of sub-dominant bacteria, including Streptococcus, Enterococcus, and Enterobacteriaceae, positively correlated with age in the HIV(−) group, but not in the HIV(+) group. In the HIV(+) group, Clostridium coccoides group positively associated with the CD4+ cell count and its subsets. In the ART(+) group, Staphylococcus and C. perfringens positively correlated with CD4+ cells and their subsets and negatively with activated CD8+ cells. C. coccoides group and Bacteroides fragilis group were associated with regulatory T-cell counts. In multiple linear regression analyses, ART duration was independently associated with the number of C. perfringens, and Th17 cell count with the number of Staphylococcus in the ART(+) group. Conclusions HIV infection and ART may influence sub-dominant gut bacteria, directly or indirectly, in association with immune status in children with HIV.
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Affiliation(s)
- Quynh Thi Nguyen
- Department of Viral infection and International Health, Graduate school of Medical Science, Kanazawa University, Kanazawa, Japan
| | - Azumi Ishizaki
- Department of Viral infection and International Health, Graduate school of Medical Science, Kanazawa University, Kanazawa, Japan
| | - Xiuqiong Bi
- Department of Viral infection and International Health, Graduate school of Medical Science, Kanazawa University, Kanazawa, Japan
| | | | | | | | | | | | | | - An Van Nguyen
- Vietnam National Children’s Hospital, Hanoi, Viet Nam
| | | | - Hiroshi Ichimura
- Department of Viral infection and International Health, Graduate school of Medical Science, Kanazawa University, Kanazawa, Japan
- * E-mail:
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31
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Park SY, Faraci G, Nanda S, Ter-Saakyan S, Love TMT, Mack WJ, Dubé MP, Lee HY. Gut microbiome in people living with HIV is associated with impaired thiamine and folate syntheses. Microb Pathog 2021; 160:105209. [PMID: 34563611 DOI: 10.1016/j.micpath.2021.105209] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 08/11/2021] [Accepted: 09/22/2021] [Indexed: 12/12/2022]
Abstract
People living with HIV have a high incidence of cardiovascular and neurological diseases as comorbid disorders that are commonly linked to inflammation. While microbial translocation can augment inflammation during HIV infection, functional microbiome shifts that may increase pro-inflammatory responses have not been fully characterized. In addition, defining HIV-induced microbiome changes has been complicated by high variability among individuals. Here we conducted functional annotation of previously-published 16S ribosomal RNA gene sequences of 305 HIV positive and 249 negative individuals, with adjustment for geographic region, sex, sexual behavior, and age. Metagenome profiles were inferred from these individuals' 16S data. HIV infection was associated with impaired microbial vitamin B synthesis; around half of the gene families in thiamine and folate biosynthesis pathways were significantly less abundant in the HIV positive group than the negative control. These results are consistent with the high prevalence of thiamine and folate deficiencies in HIV infections. These HIV-induced microbiota shifts have the potential to influence cardiovascular and neurocognitive diseases, given the documented associations between B-vitamin deficiencies, inflammation, and these diseases. We also observed that most essential amino acid biosynthesis pathways were downregulated in the microbiome of HIV-infected individuals. Microbial vitamin B and amino acid synthesis pathways were not significantly recovered by antiretroviral treatment when we compared 262 ART positive and 184 ART negative individuals. Our meta-analysis provides a new outlook for understanding vitamin B and amino acid deficiencies in HIV patients, suggesting that interventions for reversing HIV-induced microbiome shifts may aid in lessening the burdens of HIV comorbidities.
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Affiliation(s)
- Sung Yong Park
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Gina Faraci
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Sayan Nanda
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Sonia Ter-Saakyan
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Tanzy M T Love
- Department of Biostatistics and Computational Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Wendy J Mack
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Michael P Dubé
- Department of Medicine and Division of Infectious Diseases, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Ha Youn Lee
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
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32
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Castillo-Álvarez F, Pérez-Matute P, Oteo JA, Marzo-Sola ME. The influence of interferon β-1b on gut microbiota composition in patients with multiple sclerosis. NEUROLOGÍA (ENGLISH EDITION) 2021; 36:495-503. [PMID: 34537163 DOI: 10.1016/j.nrleng.2020.05.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 04/04/2018] [Indexed: 02/06/2023] Open
Abstract
INTRODUCTION The association between gut microbiota and animal models of multiple sclerosis has been well established; however, studies in humans are scarce. METHODS We performed a descriptive, cross-sectional study comparing the relative composition of gut microbiota in 30 patients with multiple sclerosis (15 treated with interferon β-1b, 15 not receiving this treatment) and 14 healthy controls using next generation sequencing. RESULTS Patients with multiple sclerosis and controls showed differences in the proportion of Euryarchaeota, Firmicutes, Proteobacteria, Actinobacteria, and Lentisphaerae phyla and in 17 bacterial species. More specifically, we found significant differences in the proportion of Firmicutes, Actinobacteria, and Lentisphaerae and 6 bacteria species between controls and untreated patients; however, these differences disappeared when compared with treated patients. Untreated patients showed a significant reduction in the proportion of Prevotella copri compared to controls, while the bacteria was significantly more abundant in patients treated with interferon β-1b than in untreated patients, with levels resembling those observed in the healthy control group. CONCLUSION We observed differences in gut microbiota composition between patients with multiple sclerosis and controls, and between patients treated and not treated with interferon β-1b. In most cases, no differences were observed between treated patients and healthy controls, particularly for P. copri levels. This suggests that the clinical improvements observed in patients with multiple sclerosis receiving interferon β-1b may result from the effect of the drug on gut microbiota. Longitudinal and functional studies are necessary to establish a causal relationship.
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Affiliation(s)
| | - P Pérez-Matute
- Servicio de Enfermedades Infecciosas, CIBIR-Hospital San Pedro, Logroño, La Rioja, Spain
| | - J A Oteo
- Servicio de Enfermedades Infecciosas, CIBIR-Hospital San Pedro, Logroño, La Rioja, Spain
| | - M E Marzo-Sola
- Servicio de Neurología, Hospital San Pedro, Logroño, La Rioja, Spain
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33
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Sperk M, Ambikan AT, Ray S, Singh K, Mikaeloff F, Diez RC, Narayanan A, Vesterbacka J, Nowak P, Sönnerborg A, Neogi U. Fecal Metabolome Signature in the HIV-1 Elite Control Phenotype: Enrichment of Dipeptides Acts as an HIV-1 Antagonist but a Prevotella Agonist. J Virol 2021; 95:e0047921. [PMID: 34232744 PMCID: PMC8387056 DOI: 10.1128/jvi.00479-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 06/30/2021] [Indexed: 12/21/2022] Open
Abstract
HIV-1 elite controllers (EC) are a rare group among HIV-1-infected individuals who can naturally control viral replication for a prolonged period. Due to their heterogeneous nature, no universal mechanism could be attributed to the EC status; instead, several host and viral factors have been discussed as playing a role. In this study, we investigated the fecal metabolome and microbiome in a Swedish cohort of EC (n = 14), treatment-naive viremic progressors (VP; n = 16), and HIV-negative individuals (HC; n = 12). Fecal untargeted metabolomics was performed by four ultra-high-performance liquid chromatography tandem mass spectrometry (UHPLC-MS/MS). Molecular docking and biochemical microscale thermophoresis (MST) were used to describe the peptide-metabolite interactions. Single-cycle infectivity assays were performed in TZM-Bl cell lines using CCR5- and CXCR4-tropic HIV-1 strains. The microbiome analysis was performed using 16S rRNA sequencing. Th effects of metabolites on bacterial species viability were determined using several clinical isolates. We observed an enrichment of dipeptides in EC compared to VP and HC (adjusted P < 0.05). In silico analysis by molecular docking, in vitro biochemical assays, and ex vivo infection assays identified anti-HIV-1 properties for two dipeptides (WG and VQ) that could bind to the HIV-1 gp120, of which WG was more potent. The microbiome analysis identified enrichment of the genus Prevotella in EC, and these dipeptides supported bacterial growth of the genus Prevotella in vitro. The enrichments of the dipeptides and higher abundance of Prevotella have a distinct mechanism of elite control status in HIV-1 infection that influences host metabolism. IMPORTANCE HIV-1 elite controllers (EC) are a rare group among HIV-1-infected individuals who can naturally control viral replication for a prolonged period. Due to their heterogeneous nature, no universal mechanism could be attributed to the EC status; instead, several host and viral factors have been discussed as playing a role. In this study, we investigated the fecal metabolome and microbiome in a Swedish cohort of EC, treatment-naive viremic progressors (VP), and HIV-negative individuals (HC). We observed an enrichment of dipeptides in EC compared to the other two study groups. In silico and in vitro analyses identified anti-HIV-1 properties for two dipeptides that could bind to the HIV-1 gp120 and act as an HIV-1 antagonist. Furthermore, these dipeptides supported bacterial growth of the genus Prevotella in vitro that was enriched in EC, which influences host metabolism. Thus, increased levels of both dipeptides and Prevotella could provide beneficial effects for EC.
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Affiliation(s)
- Maike Sperk
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, ANA Futura, Stockholm, Sweden
| | - Anoop T. Ambikan
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, ANA Futura, Stockholm, Sweden
| | - Shilpa Ray
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, ANA Futura, Stockholm, Sweden
| | - Kamal Singh
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, Missouri, USA, 65211, USA
| | - Flora Mikaeloff
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, ANA Futura, Stockholm, Sweden
| | - Rafael Ceña Diez
- Department of Medicine Huddinge, Division of Infectious Diseases, Karolinska Institute, Karolinska University Hospital, Huddinge, Stockholm, Sweden
| | - Ashwathy Narayanan
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, ANA Futura, Stockholm, Sweden
| | - Jan Vesterbacka
- Department of Medicine Huddinge, Division of Infectious Diseases, Karolinska Institute, Karolinska University Hospital, Huddinge, Stockholm, Sweden
| | - Piotr Nowak
- Department of Medicine Huddinge, Division of Infectious Diseases, Karolinska Institute, Karolinska University Hospital, Huddinge, Stockholm, Sweden
| | - Anders Sönnerborg
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, ANA Futura, Stockholm, Sweden
- Department of Medicine Huddinge, Division of Infectious Diseases, Karolinska Institute, Karolinska University Hospital, Huddinge, Stockholm, Sweden
| | - Ujjwal Neogi
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, ANA Futura, Stockholm, Sweden
- Manipal Institute of Virology (MIV), Manipal Academy of Higher Education, Manipal, Karnataka, India
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34
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Tanes C, Walker EM, Slisarenko N, Gerrets GL, Grasperge BF, Qin X, Jazwinski SM, Bushman FD, Bittinger K, Rout N. Gut Microbiome Changes Associated with Epithelial Barrier Damage and Systemic Inflammation during Antiretroviral Therapy of Chronic SIV Infection. Viruses 2021; 13:1567. [PMID: 34452432 PMCID: PMC8402875 DOI: 10.3390/v13081567] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 08/01/2021] [Accepted: 08/05/2021] [Indexed: 12/26/2022] Open
Abstract
Gut dysbiosis is a common feature associated with the chronic inflammation of HIV infection. Toward understanding the interplay of chronic treated HIV infection, dysbiosis, and systemic inflammation, we investigated longitudinal fecal microbiome changes and plasma inflammatory markers in the nonhuman primate model. Following simian immunodeficiency virus (SIV) infection in rhesus macaques, significant changes were observed in several members of the phylum Firmicutes along with an increase in Bacteroidetes. Viral suppression with antiretroviral therapy (ART) resulted in an early but partial recovery of compositional changes and butyrate producing genes in the gut microbiome. Over the course of chronic SIV infection and long-term ART, however, the specific loss of Faecalibacterium prausnitzii and Treponema succinifaciens significantly correlated with an increase in plasma inflammatory cytokines including IL-6, G-CSF, I-TAC, and MIG. Further, the loss of T. succinifaciens correlated with an increase in circulating biomarkers of gut epithelial barrier damage (IFABP) and microbial translocation (LBP and sCD14). As F. prausnitzii and T. succinifaciens are major short-chain fatty acid producing bacteria, their sustained loss during chronic SV-ART may contribute to gut inflammation and metabolic alterations despite effective long-term control of viremia. A better understanding of the correlations between the anti-inflammatory bacterial community and healthy gut barrier functions in the setting of long-term ART may have a major impact on the clinical management of inflammatory comorbidities in HIV-infected individuals.
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Affiliation(s)
- Ceylan Tanes
- Division of Gastroenterology, Hepatology and Nutrition, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA; (C.T.); (K.B.)
| | - Edith M. Walker
- Division of Microbiology, Tulane National Primate Research Center, Tulane University, Covington, LA 70433, USA; (E.M.W.); (N.S.); (G.L.G.)
| | - Nadia Slisarenko
- Division of Microbiology, Tulane National Primate Research Center, Tulane University, Covington, LA 70433, USA; (E.M.W.); (N.S.); (G.L.G.)
| | - Giovanni L. Gerrets
- Division of Microbiology, Tulane National Primate Research Center, Tulane University, Covington, LA 70433, USA; (E.M.W.); (N.S.); (G.L.G.)
| | - Brooke F. Grasperge
- Division of Veterinary Medicine, Tulane National Primate Research Center, Tulane University, Covington, LA 70433, USA;
| | - Xuebin Qin
- Division of Comparative Pathology, Tulane National Primate Research Center, Tulane University, Covington, LA 70433, USA;
| | - S. Michal Jazwinski
- Tulane Center for Aging, Tulane University School of Medicine, New Orleans, LA 70112, USA;
| | - Frederic D. Bushman
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA;
| | - Kyle Bittinger
- Division of Gastroenterology, Hepatology and Nutrition, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA; (C.T.); (K.B.)
| | - Namita Rout
- Division of Microbiology, Tulane National Primate Research Center, Tulane University, Covington, LA 70433, USA; (E.M.W.); (N.S.); (G.L.G.)
- Tulane Center for Aging, Tulane University School of Medicine, New Orleans, LA 70112, USA;
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35
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Lu D, Zhang JB, Wang YX, Geng ST, Zhang Z, Xu Y, Li SY, Wang KH, Kuang YQ. Association between CD4 + T cell counts and gut microbiota and serum cytokines levels in HIV-infected immunological non-responders. BMC Infect Dis 2021; 21:742. [PMID: 34344350 PMCID: PMC8336095 DOI: 10.1186/s12879-021-06491-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 07/27/2021] [Indexed: 01/05/2023] Open
Abstract
Background CD4+ T cell counts in certain human immunodeficiency virus (HIV)-infected patients called immunological non-responders (INRs) could not return to a normal level even with sustained antiretroviral therapy (ART) because of persistent immune activation, which is associated with pro-inflammatory cytokines production and an altered intestinal microbiome profile. Changes in gut bacterial composition have been linked to low CD4+ T cell counts in HIV-infected individuals. However, the association between CD4+ T cell counts and gut microbiota community composition and cytokines levels in INRs (CD4+ T cell counts < 500 cells/μL) from Yunnan Province, China, has not been previously investigated.
Methods To address this issue, we carried out a cross-sectional study of 34 HIV-infected INRs. The patients were divided into CD4 count > 200 cells/μL group and CD4 count < 200 cells/μL group. The gut microbiota composition of each subject was analyzed by 16S rRNA gene sequencing. We also compared CD8+ T cell counts, pro-inflammatory cytokines levels, and nutritional status between the two groups. Results Compared to INRs with CD4 count > 200 cells/μL, those with CD4 count < 200 cells/μL had a lower CD4/CD8 ratio, lower nutritional status and higher serum levels of tumor necrosis factor (TNF)-α, interferon-γ-inducible protein (IP)-10 and interleukin (IL)-1α. Ruminococcaceae was less abundant in the CD4 count < 200 cells/μL group than in the CD4 count > 200 cells/μL group, and difference in alpha diversity was observed between the two groups. Moreover, CD4+ T cell counts were negatively associated with TNF-α and IL-1α levels and positively associated with the relative abundance of Ruminococcaceae. Conclusions Our study demonstrated that lower CD4+ T cell counts in INRs are associated with a reduced abundance of Ruminococcaceae in the gut and elevated serum pro-inflammatory cytokines levels. Thus, interventions targeting gut microbiota to increase CD4+ T cell counts are a potential strategy for promoting immune reconstitution in HIV-infected INRs. Supplementary Information The online version contains supplementary material available at 10.1186/s12879-021-06491-z.
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Affiliation(s)
- Danfeng Lu
- NHC Key Laboratory of Drug Addiction Medicine, First Affiliated Hospital of Kunming Medical University, Kunming Medical University, 295 Xichang Road, Kunming, Yunnan, China.,Scientific Research Laboratory Center, First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Jian-Bo Zhang
- Department of Dermatology, Second People's Hospital of Dali City, Dali, China
| | - Yue-Xin Wang
- NHC Key Laboratory of Drug Addiction Medicine, First Affiliated Hospital of Kunming Medical University, Kunming Medical University, 295 Xichang Road, Kunming, Yunnan, China.,Department of Gastrointestinal and Hernia Surgery, First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Shi-Tao Geng
- NHC Key Laboratory of Drug Addiction Medicine, First Affiliated Hospital of Kunming Medical University, Kunming Medical University, 295 Xichang Road, Kunming, Yunnan, China.,Department of Gastrointestinal and Hernia Surgery, First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Zunyue Zhang
- NHC Key Laboratory of Drug Addiction Medicine, First Affiliated Hospital of Kunming Medical University, Kunming Medical University, 295 Xichang Road, Kunming, Yunnan, China.,Scientific Research Laboratory Center, First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Yu Xu
- NHC Key Laboratory of Drug Addiction Medicine, First Affiliated Hospital of Kunming Medical University, Kunming Medical University, 295 Xichang Road, Kunming, Yunnan, China.,Department of Gastrointestinal and Hernia Surgery, First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Shao-You Li
- NHC Key Laboratory of Drug Addiction Medicine, First Affiliated Hospital of Kunming Medical University, Kunming Medical University, 295 Xichang Road, Kunming, Yunnan, China.,Scientific Research Laboratory Center, First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Kun-Hua Wang
- NHC Key Laboratory of Drug Addiction Medicine, First Affiliated Hospital of Kunming Medical University, Kunming Medical University, 295 Xichang Road, Kunming, Yunnan, China. .,Department of Gastrointestinal and Hernia Surgery, First Affiliated Hospital of Kunming Medical University, Kunming, China.
| | - Yi-Qun Kuang
- NHC Key Laboratory of Drug Addiction Medicine, First Affiliated Hospital of Kunming Medical University, Kunming Medical University, 295 Xichang Road, Kunming, Yunnan, China. .,Scientific Research Laboratory Center, First Affiliated Hospital of Kunming Medical University, Kunming, China.
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36
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Torres B, Guardo AC, Squarcia M, Diaz A, Fabra A, Caballero M, Ugarte A, Leal L, Gatell JM, Plana M, Garcia F. Impact of switching to raltegravir and/or adding losartan in lymphoid tissue fibrosis and inflammation in people living with HIV. A randomized clinical trial. HIV Med 2021; 22:674-681. [PMID: 34288357 DOI: 10.1111/hiv.13114] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 03/23/2021] [Indexed: 12/19/2022]
Abstract
BACKGROUND Persistent inflammation and immune activation are associated with lymph node fibrosis and end-organ diseases in treatment-suppressed people living with HIV (PLWH). We investigated the effect of switching to raltegravir and/or adding losartan on lymphoid tissue fibrosis and on the inflammatory/immune-activation mediators in treated HIV patients. METHODS Chronic HIV-infected patients treated with two nucleoside reverse transcriptase inhibitors (2NRTI) and one non-NRTI (NNRTI) or protease inhibitor (PI) during at least 48 weeks were randomized to four groups (n = 48): 2NRTI + efavirenz (EFV), 2NRTI + EFV + losartan, 2NRTI + raltegravir and 2NRTI + raltegravir + losartan for 48 weeks. Tonsillar biopsy and peripheral blood markers of CD4 and CD8 T-lymphocyte activation and senescence, monocyte activation and soluble markers of inflammation were determined at baseline and at week 48 and compared between groups. RESULTS No changes in lymphoid tissue architecture were observed. Adding losartan had no impact on lymphocyte subsets. Conversely, patients who switched to raltegravir showed a higher decrease in all activated [CD4+CD38+HLA-DR+, -0.3 vs. 0.48 (P = 0.033); CD8+CD38+ HLA-DR+, -1.6 vs. 1.3 (P = 0.02)] and senescent [CD4+CD28-CD57+, -0.3 vs. 0.26 (P = 0.04); CD8+CD28-CD57+, -6.1 vs. 3.8 (P = 0.002)] T lymphocytes. In addition, the median CD4/CD8 ratio increased by 0.35 in patients in the raltegravir group vs. 0.03 in the other arms (P = 0.002). Differences between groups in monocyte subpopulations or soluble inflammation markers were not observed. CONCLUSIONS Losartan had no effect on lymphoid fibrosis or immune activation/inflammation. Conversely, switching to a regimen with raltegravir significantly decreased activated and senescent T-lymphocyte subpopulations and increased CD4/CD8 ratio in successfully treated PLWH.
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Affiliation(s)
- B Torres
- Infectious Diseases Department, Hospital Clínic, Barcelona, Spain.,Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - A C Guardo
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - M Squarcia
- Radiology Department, Hospital Clínic, Barcelona, Spain
| | - A Diaz
- Pathology Department, Hospital Clínic, Barcelona, Spain
| | - A Fabra
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - M Caballero
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Otorhinolaryngology Department, Hospital Clínic, Barcelona, Spain
| | - A Ugarte
- Infectious Diseases Department, Hospital Clínic, Barcelona, Spain
| | - L Leal
- Infectious Diseases Department, Hospital Clínic, Barcelona, Spain.,Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - J M Gatell
- Infectious Diseases Department, Hospital Clínic, Barcelona, Spain
| | - M Plana
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - F Garcia
- Infectious Diseases Department, Hospital Clínic, Barcelona, Spain.,Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
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37
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Perler BK, Reinhart EM, Montgomery M, Maynard M, Shapiro JM, Belenky P, Chan PA. Evaluation of the Microbiome in Men Taking Pre-exposure Prophylaxis for HIV Prevention. AIDS Behav 2021; 25:2005-2013. [PMID: 33394167 DOI: 10.1007/s10461-020-03130-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/07/2020] [Indexed: 01/04/2023]
Abstract
Tenofovir-based regimens as pre-exposure prophylaxis (PrEP) are highly effective at preventing HIV infection. The most common side-effect is gastrointestinal (GI) distress which may be associated with changes in the microbiome. Dysbiosis of the microbiome can have numerous health-related consequences. To understand the effect of PrEP on dysbiosis, we evaluated 27 individuals; 14 were taking PrEP for an average of 171 weeks. Sequencing of 16S rRNA was performed using self-collected rectal swabs. Mixed beta diversity testing demonstrated significant differences between PrEP and non-PrEP users with Bray-Curtis and unweighted UniFrac analyses (p = 0.05 and 0.049, respectively). At the genus level, there was a significant reduction in Finegoldia, along with a significant increase in Catenibacterium and Prevotella in PrEP users. Prevotella has been associated with inflammatory pathways, insulin resistance and cardiovascular disease, while Catenibacterium has been associated with morbid obesity and metabolic syndrome. Overall, these results suggest that PrEP may be associated with some degree of microbiome dysbiosis, which may contribute to GI symptoms. Long-term impact of these changes is unknown.
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38
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Lights and Shadows of Microbiota Modulation and Cardiovascular Risk in HIV Patients. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:ijerph18136837. [PMID: 34202210 PMCID: PMC8297340 DOI: 10.3390/ijerph18136837] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 06/07/2021] [Accepted: 06/16/2021] [Indexed: 12/12/2022]
Abstract
Human immunodeficiency virus (HIV) infection is associated with premature aging and the development of aging-related comorbidities, such as cardiovascular disease (CVD). Gut microbiota (GM) disturbance is involved in these comorbidities and there is currently interest in strategies focused on modulating GM composition and/or functionality. Scientific evidence based on well-designed clinical trials is needed to support the use of prebiotics, probiotics, symbiotics, and fecal transplantation (FT) to modify the GM and reduce the incidence of CVD in HIV-infected patients. We reviewed the data obtained from three clinical trials focused on prebiotics, 25 trials using probiotics, six using symbiotics, and four using FT. None of the trials investigated whether these compounds could reduce CVD in HIV patients. The huge variability observed in the type of compound as well as the dose and duration of administration makes it difficult to adopt general recommendations and raise serious questions about their application in clinical practice.
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39
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González-Cordón A, Assoumou L, Moyle G, Waters L, Johnson M, Domingo P, Fox J, Stellbrink HJ, Guaraldi G, Masiá M, Gompels M, De Wit S, Florence E, Esser S, Raffi F, Behrens G, Pozniak A, Gatell JM, Martínez E. Switching from boosted PIs to dolutegravir decreases soluble CD14 and adiponectin in high cardiovascular risk people living with HIV. J Antimicrob Chemother 2021; 76:2380-2393. [PMID: 34120186 DOI: 10.1093/jac/dkab158] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 04/23/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Switching from boosted PIs to dolutegravir in people living with HIV (PLWH) with high cardiovascular risk improved plasma lipids at 48 weeks in the NEAT022 trial. Whether this strategy may have an impact on cardiovascular biomarkers is unknown. METHODS We assessed 48 week changes in biomarkers associated with inflammation, endothelial dysfunction, monocyte immune activation, oxidation, insulin resistance, hypercoagulability, heart failure, myocardial injury, and glomerular and tubular kidney injury. RESULTS Of 415 PLWH randomized in the NEAT022 study, 313 (75.4%) remained on allocated therapy and had paired samples available. Soluble CD14 (-11%, P < 0.001) and adiponectin (-11%, P < 0.001) significantly declined and high-sensitive C-reactive protein (-13%, P = 0.069) and oxidized LDL (-13%, P = 0.084) tended to decrease with dolutegravir. Switching to dolutegravir remained significantly associated with soluble CD14 and adiponectin reductions after adjustment for baseline variables. There were inverse correlations between soluble CD14 and CD4 count changes (P = 0.05), and between adiponectin and BMI changes (P < 0.001). CONCLUSIONS Switching from boosted PIs to dolutegravir in PLWH with high cardiovascular risk led to soluble CD14 and adiponectin reductions at 48 weeks. While decreasing soluble CD14 may entail favourable health effects in PLWH, adiponectin reduction may reflect less insulin sensitivity associated with weight gain.
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Affiliation(s)
| | - Lambert Assoumou
- Sorbonne Université, INSERM, Institut Pierre Louis d'Épidémiologie et de Santé Publique, Paris, France
| | - Graeme Moyle
- Chelsea and Westminster Hospital NHS Foundation Trust, London, UK
| | - Laura Waters
- Mortimer Market Centre, Central & North West London NHS Foundation Trust, London, UK
| | | | | | - Julie Fox
- Guy's & St Thomas' NHS Foundation Trust, London, UK
| | | | | | - Mar Masiá
- Hospital General Universitario de Elche, Elche, Spain
| | | | - Stephane De Wit
- Centre Hospitalier Universitaire Saint-Pierre, Brussels, Belgium
| | | | | | | | | | - Anton Pozniak
- Chelsea and Westminster Hospital NHS Foundation Trust, London, UK
| | - José M Gatell
- Hospital Clínic-IDIBAPS, University of Barcelona, Barcelona, Spain.,ViiV Healthcare, Brentford, UK
| | - Esteban Martínez
- Hospital Clínic-IDIBAPS, University of Barcelona, Barcelona, Spain
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40
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Ray S, Narayanan A, Giske CG, Neogi U, Sönnerborg A, Nowak P. Altered Gut Microbiome under Antiretroviral Therapy: Impact of Efavirenz and Zidovudine. ACS Infect Dis 2021; 7:1104-1115. [PMID: 33346662 PMCID: PMC8154435 DOI: 10.1021/acsinfecdis.0c00536] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
![]()
Millions
of individuals currently living with HIV globally are
receiving antiretroviral therapy (ART) that suppresses viral replication
and improves host immune responses. The involvement of gut microbiome
during HIV infection has been studied, exposing correlation with immune
status and inflammation. However, the direct effect of ART on gut
commensals of HIV-infected individuals has been mostly overlooked
in microbiome studies. We used 16S rRNA sequencing (Illumina MiSeq)
for determining the microbiota composition of stool samples from 16
viremic patients before and one year after ART. We also tested the
direct effect of 15 antiretrovirals against four gut microbes, namely, Escherichia coli, Enterococcus faecalis, Bacteroides, and Prevotella to assess their in vitro antibacterial effect. 16S rRNA analysis of fecal samples showed
that effective ART for one year does not restore the microbiome diversity
in HIV-infected patients. A significant reduction in α-diversity
was observed in patients under non-nucleoside reverse transcriptase
inhibitors; (NNRTI; 2 NRTI+NNRTI; NRTIs are nucleoside reverse transcriptase
inhibitors) as compared to ritonavir-boosted protease inhibitors (PI/r;
2 NRTI+PI/r). Prevotella (P = 0.00001) showed a significantly decreased abundance in patients
after ART (n = 16). We also found the direct effect
of antivirals on gut microbes, where zidovudine (ZDV) and efavirenz
(EFV) showed in vitro antimicrobial activity against Bacteroides fragilis and Prevotella. EFV also inhibited the growth of E. faecalis. Therefore, we observed that ART does not reverse the HIV-induced
gut microbiome dysbiosis and might aggravate those microbiota alterations
due to the antibacterial effect of certain antiretrovirals (like EFV,
ZDV). Our results imply that restructuring the microbiota could be
a potential therapeutic target in HIV-1 patients under ART.
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Affiliation(s)
- Shilpa Ray
- Department of Laboratory Medicine, Division of Clinical Microbiology, ANA Futura, Karolinska Institutet, Stockholm 141 52 Sweden
- The Laboratory for Molecular Infection Medicine Sweden MIMS, Umeå University, Umeå 901 87, Sweden
| | - Aswathy Narayanan
- Department of Laboratory Medicine, Division of Clinical Microbiology, ANA Futura, Karolinska Institutet, Stockholm 141 52 Sweden
| | - Christian G. Giske
- Department of Laboratory Medicine, Division of Clinical Microbiology, ANA Futura, Karolinska Institutet, Stockholm 141 52 Sweden
- Department of Clinical Microbiology, Karolinska University Hospital, Solna, Stockholm 171 76,Sweden
| | - Ujjwal Neogi
- Department of Laboratory Medicine, Division of Clinical Microbiology, ANA Futura, Karolinska Institutet, Stockholm 141 52 Sweden
| | - Anders Sönnerborg
- Department of Laboratory Medicine, Division of Clinical Microbiology, ANA Futura, Karolinska Institutet, Stockholm 141 52 Sweden
- Department of Medicine Huddinge, Division of Infectious Diseases, Karolinska University Hospital, Huddinge, Stockholm 141 86, Sweden
| | - Piotr Nowak
- Department of Laboratory Medicine, Division of Clinical Microbiology, ANA Futura, Karolinska Institutet, Stockholm 141 52 Sweden
- The Laboratory for Molecular Infection Medicine Sweden MIMS, Umeå University, Umeå 901 87, Sweden
- Department of Medicine Huddinge, Division of Infectious Diseases, Karolinska University Hospital, Huddinge, Stockholm 141 86, Sweden
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41
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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: 0.7] [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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42
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Alteration of the gut fecal microbiome in children living with HIV on antiretroviral therapy in Yaounde, Cameroon. Sci Rep 2021; 11:7666. [PMID: 33828220 PMCID: PMC8027858 DOI: 10.1038/s41598-021-87368-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 03/15/2021] [Indexed: 02/08/2023] Open
Abstract
Multiple factors, such as immune disruption, prophylactic co-trimoxazole, and antiretroviral therapy, may influence the structure and function of the gut microbiome of children infected with HIV from birth. In order to understand whether HIV infection altered gut microbiome and to relate changes in microbiome structure and function to immune status, virological response and pediatric ART regimens, we characterized the gut microbiome of 87 HIV-infected and 82 non-exposed HIV-negative children from Yaounde, a cosmopolitan city in Cameroon. We found that children living with HIV had significantly lower alpha diversity in their gut microbiome and altered beta diversity that may not be related to CD4+ T cell count or viral load. There was an increased level of Akkermansia and Faecalibacterium genera and decreased level of Escherichia and other Gamma proteobacteria in children infected with HIV, among other differences. We noted an effect of ethnicity/geography on observed gut microbiome composition and that children on ritonavir-boosted protease inhibitor (PI/r)-based ART had gut microbiome composition that diverged more from HIV-negative controls compared to those on non-nucleoside reverse-transcriptase inhibitors-based ART. Further studies investigating the role of this altered gut microbiome in increased disease susceptibility are warranted for individuals who acquired HIV via mother-to-child transmission.
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43
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Prasad R, Patton MJ, Floyd JL, Vieira CP, Fortmann S, DuPont M, Harbour A, Jeremy CS, Wright J, Lamendella R, Stevens BR, Grant MB. Plasma microbiome in COVID-19 subjects: an indicator of gut barrier defects and dysbiosis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021. [PMID: 33851159 DOI: 10.1101/2021.04.06.438634] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The gut is a well-established route of infection and target for viral damage by SARS-CoV-2. This is supported by the clinical observation that about half of COVID-19 patients exhibit gastrointestinal ( GI ) symptoms. We asked whether the analysis of plasma could provide insight into gut barrier dysfunction in patients with COVID-19 infection. Plasma samples of COVID-19 patients (n=30) and healthy control (n=16) were collected during hospitalization. Plasma microbiome was analyzed using 16S rRNA sequencing, metatranscriptomic analysis, and gut permeability markers including FABP-2, PGN and LPS in both patient cohorts. Almost 65% (9 out 14) COVID-19 patients showed abnormal presence of gut microbes in their bloodstream. Plasma samples contained predominately Proteobacteria, Firmicutes, and Actinobacteria . The abundance of gram-negative bacteria ( Acinetobacter, Nitrospirillum, Cupriavidus, Pseudomonas, Aquabacterium, Burkholderia, Caballeronia, Parabhurkholderia, Bravibacterium, and Sphingomonas ) was higher than the gram-positive bacteria ( Staphylococcus and Lactobacillus ) in COVID-19 subjects. The levels of plasma gut permeability markers FABP2 (1282±199.6 vs 838.1±91.33; p=0.0757), PGN (34.64±3.178 vs 17.53±2.12; p<0.0001), and LPS (405.5±48.37 vs 249.6±17.06; p=0.0049) were higher in COVID-19 patients compared to healthy subjects. These findings support that the intestine may represent a source for bacteremia and may contribute to worsening COVID-19 outcomes. Therapies targeting the gut and prevention of gut barrier defects may represent a strategy to improve outcomes in COVID-19 patients.
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44
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Wilson NL, Peterson SN, Ellis RJ. Cannabis and the Gut-Brain Axis Communication in HIV Infection. Cannabis Cannabinoid Res 2021; 6:92-104. [PMID: 33912676 PMCID: PMC8064951 DOI: 10.1089/can.2020.0037] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
People living with HIV infection (PWH) disclose that cannabis is an effective strategy for alleviating symptoms associated with HIV disease. However, some medical providers feel ill-informed to engage in evidence-based conversations. HIV leads to alterations in the gut microbiome, gut-brain axis signaling, and chronic inflammation. The endocannabinoid system regulates homeostasis of multiple organ systems. When deficient, dysregulation of the gut-brain axis can result in chronic inflammation and neuroinflammation. Cannabis along with the naturally occurring endocannabinoids has antioxidant and anti-inflammatory properties that can support healing and restoration as an adjunctive therapy. The purpose of this literature review is to report the physiologic mechanisms that occur in the pathology of HIV and discuss potential benefits of cannabinoids in supporting health and reducing the negative effects of comorbidities in PWH.
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Affiliation(s)
- Natalie L. Wilson
- Department of Community Health Systems, School of Nursing, University of California, San Francisco, San Francisco, California, USA
| | - Scott N. Peterson
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, USA
| | - Ronald J. Ellis
- Departments of Neurosciences and Psychiatry, University of California, San Diego, San Diego, California, USA
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45
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Koh H, Tuddenham S, Sears CL, Zhao N. Meta-analysis methods for multiple related markers: Applications to microbiome studies with the results on multiple α-diversity indices. Stat Med 2021; 40:2859-2876. [PMID: 33768631 DOI: 10.1002/sim.8940] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 12/18/2020] [Accepted: 02/10/2021] [Indexed: 11/10/2022]
Abstract
Meta-analysis is a practical and powerful analytic tool that enables a unified statistical inference across the results from multiple studies. Notably, researchers often report the results on multiple related markers in each study (eg, various α-diversity indices in microbiome studies). However, univariate meta-analyses are limited to combining the results on a single common marker at a time, whereas existing multivariate meta-analyses are limited to the situations where marker-by-marker correlations are given in each study. Thus, here we introduce two meta-analysis methods, multi-marker meta-analysis (mMeta) and adaptive multi-marker meta-analysis (aMeta), to combine multiple studies throughout multiple related markers with no priori results on marker-by-marker correlations. mMeta is a statistical estimator for a pooled estimate and its SE across all the studies and markers, whereas aMeta is a statistical test based on the test statistic of the minimum P-value among marker-specific meta-analyses. mMeta conducts both effect estimation and hypothesis testing based on a weighted average of marker-specific pooled estimates while estimating marker-by-marker correlations non-parametrically via permutations, yet its power is only moderate. In contrast, aMeta closely approaches the highest power among marker-specific meta-analyses, yet it is limited to hypothesis testing. While their applications can be broader, we illustrate the use of mMeta and aMeta to combine microbiome studies throughout multiple α-diversity indices. We evaluate mMeta and aMeta in silico and apply them to real microbiome studies on the disparity in α-diversity by the status of human immunodeficiency virus (HIV) infection. The R package for mMeta and aMeta is freely available at https://github.com/hk1785/mMeta.
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Affiliation(s)
- Hyunwook Koh
- Department of Applied Mathematics and Statistics, The State University of New York, Korea, Incheon, South Korea
| | - Susan Tuddenham
- Department of Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Cynthia L Sears
- Department of Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Ni Zhao
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
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46
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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: 15] [Impact Index Per Article: 5.0] [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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47
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Xu H, Ou Z, Zhou Y, Li Y, Huang H, Zhao H, Xu J, Luo M, Zhou Y, Nie Y. Intestinal mucosal microbiota composition of patients with acquired immune deficiency syndrome in Guangzhou, China. Exp Ther Med 2021; 21:391. [PMID: 33680113 PMCID: PMC7918403 DOI: 10.3892/etm.2021.9822] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 07/21/2020] [Indexed: 12/12/2022] Open
Abstract
Acquired immune deficiency syndrome, caused by the human immunodeficiency virus (HIV), has been associated with intestinal dysbiosis, which includes an increase in the number of mucosa-associated pathobionts. In the present study, the intestinal mucosal microbiota patterns of HIV-infected patients were compared with those of healthy individuals in a population from Guangzhou, China. The gut microbiota of intestinal mucosal samples from 12 patients with HIV (transmission routes included sex and intravenous drug abuse) was compared with that of 12 healthy age- and sex-matched controls. Gut microbial communities were profiled via sequencing of the bacterial 16S ribosomal RNA genes. Dysbiosis in HIV-infected individuals was characterized by decreased α-diversity, decreased levels of Firmicutes and increased levels of Proteobacteria. Furthermore, low mean counts of Lachnoclostridium, Roseburia, Thauera, Dorea and Roseburia inulinivorans, and high mean counts of Halomonas and Shewanella bacteria, were indicated to be HIV-associated mucosal bacterial alterations. The relative abundance of Fusobacterium and Lachnoclostridium was significantly decreased, while that of Halomonas and Shewanella was significantly increased in patients with sexually transmitted HIV-infection compared with healthy controls. Alterations of the gut microbiota during HIV infection were also indicated to be associated with the route of HIV transmission. Certain bacteria may be potential biomarkers for HIV infection in patients from Guangzhou, China.
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Affiliation(s)
- Haoming Xu
- Department of Gastroenterology and Hepatology, Guangzhou Digestive Disease Center, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong 510180, P.R. China
| | - Zhitao Ou
- Department of Internal Medicine, Guangzhou No. 8 People's Hospital, Guangzhou, Guangdong 510180, P.R. China
| | - Yongjian Zhou
- Department of Gastroenterology and Hepatology, Guangzhou Digestive Disease Center, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong 510180, P.R. China
| | - Yingfei Li
- Department of Gastroenterology and Hepatology, Guangzhou Digestive Disease Center, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong 510180, P.R. China
| | - Hongli Huang
- Department of Gastroenterology and Hepatology, Guangzhou Digestive Disease Center, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong 510180, P.R. China
| | - Hailan Zhao
- Department of Gastroenterology and Hepatology, Guangzhou Digestive Disease Center, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong 510180, P.R. China
| | - Jing Xu
- Department of Gastroenterology and Hepatology, Guangzhou Digestive Disease Center, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong 510180, P.R. China
| | - Meijuan Luo
- Department of Pediatrics, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong 510180, P.R. China
| | - Youlian Zhou
- Department of Gastroenterology and Hepatology, Guangzhou Digestive Disease Center, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong 510180, P.R. China
| | - Yuqiang Nie
- Department of Gastroenterology and Hepatology, Guangzhou Digestive Disease Center, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong 510180, P.R. China
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48
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Impact of long-term antiretroviral therapy on gut and oral microbiotas in HIV-1-infected patients. Sci Rep 2021; 11:960. [PMID: 33441754 PMCID: PMC7806981 DOI: 10.1038/s41598-020-80247-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 12/17/2020] [Indexed: 02/06/2023] Open
Abstract
In HIV-1-infected patients, antiretroviral therapy (ART) is a key factor that may impact commensal microbiota and cause the emergence of side effects. However, it is not fully understood how long-term ART regimens have diverse impacts on the microbial compositions over time. Here, we performed 16S ribosomal RNA gene sequencing of the fecal and salivary microbiomes in patients under different long-term ART. We found that ART, especially conventional nucleotide/nucleoside reverse transcriptase inhibitor (NRTI)-based ART, has remarkable impacts on fecal microbial diversity: decreased α-diversity and increased ß-diversity over time. In contrast, dynamic diversity changes in the salivary microbiome were not observed. Comparative analysis of bacterial genus compositions showed a propensity for Prevotella-enriched and Bacteroides-poor gut microbiotas in patients with ART over time. In addition, we observed a gradual reduction in Bacteroides but drastic increases in Succinivibrio and/or Megasphaera under conventional ART. These results suggest that ART, especially NRTI-based ART, has more suppressive impacts on microbiota composition and diversity in the gut than in the mouth, which potentially causes intestinal dysbiosis in patients. Therefore, NRTI-sparing ART, especially integrase strand transfer inhibitor (INSTI)- and/or non-nucleotide reverse transcriptase inhibitor (NNRTI)-containing regimens, might alleviate the burden of intestinal dysbiosis in HIV-1-infected patients under long-term ART.
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49
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Geng ST, Zhang ZY, Wang YX, Lu D, Yu J, Zhang JB, Kuang YQ, Wang KH. Regulation of Gut Microbiota on Immune Reconstitution in Patients With Acquired Immunodeficiency Syndrome. Front Microbiol 2020; 11:594820. [PMID: 33193273 PMCID: PMC7652894 DOI: 10.3389/fmicb.2020.594820] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 09/28/2020] [Indexed: 12/12/2022] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) infection of CD4+ T cells in the gut plays an insidious role in acquired immunodeficiency syndrome (AIDS) pathogenesis. Host immune function is closely related to gut microbiota. Changes in the gut microbiota cause a different immune response. Previous studies revealed that HIV-1 infection caused changes in gut microbiota, which induced immune deficiency. HIV-1 infection results in an abnormal composition and function of the gut microbiota, which may disrupt the intestinal epithelial barrier and microbial translocation, leading to long-term immune activation, including inflammation and metabolic disorders. At the same time, an abnormal gut microbiota also hinders the effect of antiviral therapy and affects the immune reconstruction of patients. However, studies on the impact of the gut microbiota on immune reconstitution in patients with HIV/AIDS are still limited. In this review, we focus on changes in the gut microbiota caused by HIV infection, as well as the impact and regulation of the gut microbiota on immune function and immune reconstitution, while we also discuss the potential impact of probiotics/prebiotics and fecal microbiota transplantation (FMT) on immune reconstitution.
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Affiliation(s)
- Shi-Tao Geng
- NHC Key Laboratory of Drug Addiction Medicine, First Affiliated Hospital of Kunming Medical University, Kunming Medical University, Kunming, China.,Department of Gastrointestinal and Hernia Surgery, First Affiliated Hospital of Kunming Medical University, Kunming, China.,Scientific Research Laboratory Center, First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Zun-Yue Zhang
- NHC Key Laboratory of Drug Addiction Medicine, First Affiliated Hospital of Kunming Medical University, Kunming Medical University, Kunming, China.,Scientific Research Laboratory Center, First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Yue-Xin Wang
- NHC Key Laboratory of Drug Addiction Medicine, First Affiliated Hospital of Kunming Medical University, Kunming Medical University, Kunming, China.,Department of Gastrointestinal and Hernia Surgery, First Affiliated Hospital of Kunming Medical University, Kunming, China.,Scientific Research Laboratory Center, First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Danfeng Lu
- NHC Key Laboratory of Drug Addiction Medicine, First Affiliated Hospital of Kunming Medical University, Kunming Medical University, Kunming, China.,Scientific Research Laboratory Center, First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Juehua Yu
- NHC Key Laboratory of Drug Addiction Medicine, First Affiliated Hospital of Kunming Medical University, Kunming Medical University, Kunming, China.,Scientific Research Laboratory Center, First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Jian-Bo Zhang
- Department of Dermatology, Second People's Hospital of Dali City, Dali, China
| | - Yi-Qun Kuang
- NHC Key Laboratory of Drug Addiction Medicine, First Affiliated Hospital of Kunming Medical University, Kunming Medical University, Kunming, China.,Scientific Research Laboratory Center, First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Kun-Hua Wang
- NHC Key Laboratory of Drug Addiction Medicine, First Affiliated Hospital of Kunming Medical University, Kunming Medical University, Kunming, China.,Department of Gastrointestinal and Hernia Surgery, First Affiliated Hospital of Kunming Medical University, Kunming, China.,Scientific Research Laboratory Center, First Affiliated Hospital of Kunming Medical University, Kunming, China
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50
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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: 5.0] [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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