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Brenchley JM, Serrano-Villar S. From dysbiosis to defense: harnessing the gut microbiome in HIV/SIV therapy. MICROBIOME 2024; 12:113. [PMID: 38907315 PMCID: PMC11193286 DOI: 10.1186/s40168-024-01825-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Accepted: 04/26/2024] [Indexed: 06/23/2024]
Abstract
BACKGROUND Although the microbiota has been extensively associated with HIV pathogenesis, the majority of studies, particularly those using omics techniques, are largely correlative and serve primarily as a basis for hypothesis generation. Furthermore, most have focused on characterizing the taxonomic composition of the bacterial component, often overlooking other levels of the microbiome. The intricate mechanisms by which the microbiota influences immune responses to HIV are still poorly understood. Interventional studies on gut microbiota provide a powerful tool to test the hypothesis of whether we can harness the microbiota to improve health outcomes in people with HIV. RESULTS Here, we review the multifaceted role of the gut microbiome in HIV/SIV disease progression and its potential as a therapeutic target. We explore the complex interplay between gut microbial dysbiosis and systemic inflammation, highlighting the potential for microbiome-based therapeutics to open new avenues in HIV management. These include exploring the efficacy of probiotics, prebiotics, fecal microbiota transplantation, and targeted dietary modifications. We also address the challenges inherent in this research area, such as the difficulty in inducing long-lasting microbiome alterations and the complexities of study designs, including variations in probiotic strains, donor selection for FMT, antibiotic conditioning regimens, and the hurdles in translating findings into clinical practice. Finally, we speculate on future directions for this rapidly evolving field, emphasizing the need for a more granular understanding of microbiome-immune interactions, the development of personalized microbiome-based therapies, and the application of novel technologies to identify potential therapeutic agents. CONCLUSIONS Our review underscores the importance of the gut microbiome in HIV/SIV disease and its potential as a target for innovative therapeutic strategies.
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Affiliation(s)
- Jason M Brenchley
- Barrier Immunity Section, Lab of Viral Diseases, NIAID, NIH, Bethesda, MA, USA.
| | - Sergio Serrano-Villar
- Department of Infectious Diseases, Hospital Universitario Ramon y Cajal, IRYCIS and CIBERInfec, Madrid, Spain.
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2
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Bai X, Sönnerborg A, Nowak P. Elite controllers microbiome: unraveling the mystery of association and causation. Curr Opin HIV AIDS 2024:01222929-990000000-00095. [PMID: 38874425 DOI: 10.1097/coh.0000000000000867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2024]
Abstract
PURPOSE OF REVIEW To unravel the current knowledge and possible link between the gut microbiome and HIV-1 virological control in elite controllers (EC), who can suppress viral replication in the absence of antiretroviral therapy. In addition, to discuss the limitations of current research and propose future research directions. RECENT FINDINGS EC possess a different gut bacterial microbiota profile in composition and functionality from that of treatment-naive HIV-1 viremic progressors (VP). Specifically, EC have a richer bacterial microbiota as compared to VP, which closely resembles the microbiota in HIV-1 negative healthy controls (HC). Differentially abundant bacteria are found between EC and VP or HC, though results vary among the few existing studies. These data imply that the gut microbiome could contribute to the natural suppression of HIV-1 infection. SUMMARY An association between the gut microbiome and HIV-1 virological control is evidenced by recent studies. Yet, there are substantial knowledge gaps, and the underlying mechanism of how the microbiome influences the EC phenotype is far from clarified. Future research should consider diverse microbial communities, the complex microbe-host interactions, as well as yet-unidentified causal links between microbiome alterations and HIV-1 disease progression.
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Affiliation(s)
- Xiangning Bai
- Department of Microbiology, Division of Laboratory Medicine, Oslo University Hospital, Oslo, Norway
- Division of Infectious Diseases, Department of Medicine Huddinge, Karolinska Institutet, Stockholm
| | - Anders Sönnerborg
- Division of Infectious Diseases, Department of Medicine Huddinge, Karolinska Institutet, Stockholm
- Department of Infectious Diseases, Karolinska University Hospital, Huddinge, Sweden
| | - Piotr Nowak
- Division of Infectious Diseases, Department of Medicine Huddinge, Karolinska Institutet, Stockholm
- Department of Infectious Diseases, Karolinska University Hospital, Huddinge, Sweden
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3
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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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4
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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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5
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Johnson M, Lazarus SK, Bennett AE, Tovar-Salazar A, Robertson CE, Kofonow JM, Li S, McCollister B, Nunes MC, Madhi SA, Frank DN, Weinberg A. Gut Microbiota and Other Factors Associated With Increased Regulatory T Cells in Hiv-exposed Uninfected Infants. RESEARCH SQUARE 2024:rs.3.rs-3909424. [PMID: 38352510 PMCID: PMC10862973 DOI: 10.21203/rs.3.rs-3909424/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
HIV-exposed uninfected infants (HEU) have higher infectious morbidity than HIV-unexposed infants (HUU). HEU have multiple immune defects of unknown origin. We hypothesized that HEU have higher regulatory T cells (Treg) than HUU, which may dampen their immune defenses against pathogens. We compared 25 Treg subsets between HEU and HUU and sought the factors that may affect Treg frequencies. At birth, 3 Treg subsets, including CD4 + FOXP3 + and CD4 + FOXP3 + CD25+, had higher frequencies in 123 HEU than 117 HUU and 3 subsets were higher in HUU. At 28 and 62 weeks of life, 5 Treg subsets were higher in HEU, and none were higher in HUU. The frequencies of the discrepant Treg subsets correlated at birth with differential abundances of bacterial taxas in maternal gut microbiome and at subsequent visits in infant gut microbiomes. In vitro, bacterial taxa most abundant in HEU expanded Treg subsets with higher frequencies in HEU, recapitulating the in vivo observations. Other factors that correlated with increased Treg were low maternal CD4 + T cells in HEU at birth and male sex in HUU at 28 weeks. We conclude that maternal and infant gut dysbiosis are central to the Treg increase in HEU and may be targeted by mitigating interventions.
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Li K, Deng J, Zhang C, Lai G, Xie B, Zhong X. Gut microbiome dysbiosis in men who have sex with men increases HIV infection risk through immunity homeostasis alteration. Front Cell Infect Microbiol 2023; 13:1260068. [PMID: 38035339 PMCID: PMC10687210 DOI: 10.3389/fcimb.2023.1260068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 10/27/2023] [Indexed: 12/02/2023] Open
Abstract
Objectives Recent studies pointed out that gut microbiome dysbiosis in HIV infection was possibly confounded in men who have sex with men (MSM), but there is a lack of evidence. It also remained unclear how MSM-associated gut microbiome dysbiosis affected human health. This study aimed to compare the differences in gut microbiome changes between HIV and MSM and reveal the potential impacts of MSM-associated gut microbiome dysbiosis on the immune system. Methods We searched available studies based on the PubMed database, and all gut microbiome changes associated with HIV infection and MSM were extracted from the enrolled studies. The gutMgene database was used to identify the target genes and metabolites of the gut microbiome. Bioinformatic technology and single-cell RNA sequencing data analysis were utilized to explore the impacts of these gut microbiome changes on human immunity. Results The results showed significant overlaps between the gut microbiome associated with HIV and that of MSM. Moreover, bioinformatic analysis revealed that gut microbiome dysbiosis in MSM had an impact on several pathways related to immunity, including the IL-17 signaling pathway and Th17 cell differentiation. Additionally, target genes of MSM-associated gut microbiome were found to be highly expressed in monocytes and lymphocytes, suggesting their potential regulatory role in immune cells. Furthermore, we found that MSM-associated gut microbiome could produce acetate and butyrate which were reported to increase the level of inflammatory factors. Conclusion In conclusion, this study highlighted that MSM-associated gut microbiome dysbiosis might increase the risk of HIV acquisition by activating the immune system. Further studies are expected to elucidate the mechanism by which gut microbiome dysbiosis in MSM modulates HIV susceptibility.
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Affiliation(s)
| | | | | | | | - Biao Xie
- College of Public Health, Chongqing Medical University, Chongqing, China
| | - Xiaoni Zhong
- College of Public Health, Chongqing Medical University, Chongqing, China
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7
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Sultana S, Elengickal A, Bensreti H, de Chantemèle EB, McGee-Lawrence ME, Hamrick MW. The kynurenine pathway in HIV, frailty and inflammaging. Front Immunol 2023; 14:1244622. [PMID: 37744363 PMCID: PMC10514395 DOI: 10.3389/fimmu.2023.1244622] [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: 08/25/2023] [Indexed: 09/26/2023] Open
Abstract
Kynurenine (Kyn) is a circulating tryptophan (Trp) catabolite generated by enzymes including IDO1 that are induced by inflammatory cytokines such as interferon-gamma. Kyn levels in circulation increase with age and Kyn is implicated in several age-related disorders including neurodegeneration, osteoporosis, and sarcopenia. Importantly, Kyn increases with progressive disease in HIV patients, and antiretroviral therapy does not normalize IDO1 activity in these subjects. Kyn is now recognized as an endogenous agonist of the aryl hydrocarbon receptor, and AhR activation itself has been found to induce muscle atrophy, increase the activity of bone-resorbing osteoclasts, decrease matrix formation by osteoblasts, and lead to senescence of bone marrow stem cells. Several IDO1 and AhR inhibitors are now in clinical trials as potential cancer therapies. We propose that some of these drugs may be repurposed to improve musculoskeletal health in older adults living with HIV.
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Affiliation(s)
| | | | | | | | | | - Mark W. Hamrick
- Medical College of Georgia, Augusta University, Augusta, GA, United States
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8
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Sánchez-Conde M, Alba C, Castro I, Dronda F, Ramírez M, Arroyo R, Moreno S, Rodríguez JM, Brañas F. Comparison of the Fecal Bacteriome of HIV-Positive and HIV-Negative Older Adults. Biomedicines 2023; 11:2305. [PMID: 37626801 PMCID: PMC10452058 DOI: 10.3390/biomedicines11082305] [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: 08/02/2023] [Revised: 08/12/2023] [Accepted: 08/16/2023] [Indexed: 08/27/2023] Open
Abstract
HIV infection is considered a scenario of accelerated aging. Previous studies have suggested a link between aging, frailty, and gut dysbiosis, but there is a knowledge gap regarding the HIV population. Our objective was to compare the fecal bacteriome of older people with HIV (PWH) and non-HIV controls, and to assess potential links between gut dysbiosis and frailty. A total of 36 fecal samples (24 from PWH and 12 from non-HIV controls) were submitted to a metataxonomic analysis targeting the V3-V4 hypervariable region of the 16S rRNA gene. High-quality reads were assembled and classified into operational taxonomic units. Alpha diversity, assessed using the Shannon index, was higher in the control group than in the HIV group (p < 0.05). The relative abundance of the genus Blautia was higher in the HIV group (p < 0.001). The presence of Blautia was also higher in PWH with depression (p = 0.004), whereas the opposite was observed for the genus Bifidobacterium (p = 0.004). Our study shows shifts in the composition of the PWH bacteriome when compared to that of healthy controls. To our knowledge, this is the first study suggesting a potential link between depression and gut dysbiosis in the HIV population.
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Affiliation(s)
- Matilde Sánchez-Conde
- Infectious Diseases Department, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), 28034 Madrid, Spain; (F.D.); (S.M.)
- CIBER de Enfermedades Infecciosas (CIBERINFECT), Instituto de Salud Carlos III, 28220 Madrid, Spain
| | - Claudio Alba
- Department of Nutrition and Food Science, Complutense University of Madrid, 28040 Madrid, Spain; (C.A.); (I.C.); (J.M.R.)
| | - Irma Castro
- Department of Nutrition and Food Science, Complutense University of Madrid, 28040 Madrid, Spain; (C.A.); (I.C.); (J.M.R.)
| | - Fernando Dronda
- Infectious Diseases Department, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), 28034 Madrid, Spain; (F.D.); (S.M.)
| | - Margarita Ramírez
- Infectious Diseases Department, Hospital General Universitario Gregorio Marañón, 28007 Madrid, Spain;
| | - Rebeca Arroyo
- Department of Nutrition and Food Science, Complutense University of Madrid, 28040 Madrid, Spain; (C.A.); (I.C.); (J.M.R.)
| | - Santiago Moreno
- Infectious Diseases Department, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), 28034 Madrid, Spain; (F.D.); (S.M.)
| | - Juan Miguel Rodríguez
- Department of Nutrition and Food Science, Complutense University of Madrid, 28040 Madrid, Spain; (C.A.); (I.C.); (J.M.R.)
| | - Fátima Brañas
- Geriatric Department, Hospital Universitario Infanta Leonor, 28031 Madrid, Spain
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9
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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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10
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Nygren E, Gonzales Strömberg L, Logenius J, Husmark U, Löfström C, Bergström B. Potential sources of contamination on textiles and hard surfaces identified as high-touch sites near the patient environment. PLoS One 2023; 18:e0287855. [PMID: 37418451 PMCID: PMC10328241 DOI: 10.1371/journal.pone.0287855] [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: 01/19/2023] [Accepted: 06/14/2023] [Indexed: 07/09/2023] Open
Abstract
The hospital environment represents an important mediator for the transmission of healthcare-associated infections through direct and indirect hand contact with hard surfaces and textiles. In this study, bacteria on high-touch sites, including textiles and hard surfaces in two care wards in Sweden, were identified using microbiological culture methods and 16S rDNA sequencing. During a cross-sectional study, 176 high-touch hard surfaces and textiles were identified and further analysed using microbiological culture for quantification of total aerobic bacteria, Staphylococcus aureus, Clostridium difficile and Enterobacteriacae. The bacterial population structures were further analysed in 26 samples using 16S rDNA sequencing. The study showed a higher frequency of unique direct hand-textile contacts (36 per hour), compared to hard surfaces (2.2 per hour). Hard surfaces met the recommended standard of ≤ 5 CFU/cm2 for aerobic bacteria and ≤ 1 CFU/cm2 for S. aureus (53% and 35%, respectively) to a higher extent compared to textiles (19% and 30%, respectively) (P = 0.0488). The number of bacterial genera was higher on textiles than on the hard surfaces. Staphylococcus (30.4%) and Corynebacterium (10.9%) were the most representative genera for textiles and Streptococcus (13.3%) for hard surfaces. The fact that a big percentage of the textiles did not fulfil the criteria for cleanliness, combined with the higher bacterial diversity, compared to hard surfaces, are indicators that textiles were bacterial reservoirs and potential risk vectors for bacterial transmission. However, since most of the bacteria found in the study belonged to the normal flora, it was not possible to draw conclusions of textiles and hard surfaces as sources of healthcare associated infections.
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Affiliation(s)
- Erik Nygren
- RISE Research Institutes of Sweden, Agriculture and Food, Borås, Sweden
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11
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Ghahari N, Telittchenko R, Loucif H, Isnard S, Routy JP, Olagnier D, van Grevenynghe J. Harnessing Autophagy to Overcome Antigen-Specific T-Cell Dysfunction: Implication for People Living with HIV-1. Int J Mol Sci 2023; 24:11018. [PMID: 37446195 DOI: 10.3390/ijms241311018] [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: 06/09/2023] [Revised: 06/29/2023] [Accepted: 07/01/2023] [Indexed: 07/15/2023] Open
Abstract
Like other chronic viral infections, HIV-1 persistence inhibits the development of antigen-specific memory T-cells, resulting in the exhaustion of the immune response and chronic inflammation. Autophagy is a major lysosome-dependent mechanism of intracellular large-target degradation such as lipid and protein aggregates, damaged organelles, and intracellular pathogens. Although it is known that autophagy may target HIV-1 for elimination, knowledge of its function as a metabolic contributor in such viral infection is only in its infancy. Recent data show that elite controllers (EC), who are HIV-1-infected subjects with natural and long-term antigen (Ag)-specific T-cell protection against the virus, are characterized by distinct metabolic autophagy-dependent features in their T-cells compared to other people living with HIV-1 (PLWH). Despite durable viral control with antiretroviral therapy (ART), HIV-1-specific immune dysfunction does not normalize in non-controller PLWH. Therefore, the hypothesis of inducing autophagy to strengthen their Ag-specific T-cell immunity against HIV-1 starts to be an enticing concept. The aim of this review is to critically analyze promises and potential limitations of pharmacological and dietary interventions to activate autophagy in an attempt to rescue Ag-specific T-cell protection among PLWH.
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Affiliation(s)
- Nazanin Ghahari
- Institut National de la Recherche Scientifique (INRS), Centre Armand-Frappier Santé Biotechnologie, 531 Boulevard des Prairies, Laval, QC H7V 1M7, Canada
| | - Roman Telittchenko
- Institut National de la Recherche Scientifique (INRS), Centre Armand-Frappier Santé Biotechnologie, 531 Boulevard des Prairies, Laval, QC H7V 1M7, Canada
| | - Hamza Loucif
- EVAH Corp., 500 Boulevard Cartier Ouest, Laval, QC H7V 5B7, Canada
| | - Stephane Isnard
- Chronic Viral Illness Service and Division of Hematology, McGill University Health Centre, Glen Site, Montreal, QC H4A 3J1, Canada
| | - Jean-Pierre Routy
- Chronic Viral Illness Service and Division of Hematology, McGill University Health Centre, Glen Site, Montreal, QC H4A 3J1, Canada
| | - David Olagnier
- Department of Biomedicine, Research Center for Innate Immunology, Aarhus University, 8000 Aarhus, Denmark
| | - Julien van Grevenynghe
- Institut National de la Recherche Scientifique (INRS), Centre Armand-Frappier Santé Biotechnologie, 531 Boulevard des Prairies, Laval, QC H7V 1M7, Canada
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12
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Bomsel M, Lopalco L. Editorial: Mucosal immunity to HIV and SARS-CoV-2 infection and vaccination. Front Immunol 2023; 14:1201650. [PMID: 37325655 PMCID: PMC10267464 DOI: 10.3389/fimmu.2023.1201650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 05/22/2023] [Indexed: 06/17/2023] Open
Affiliation(s)
- Morgane Bomsel
- Institut Cochin, INSERM, U1016, CNRS UMR8104, Université Paris Cité, Paris, France
- Laboratory Mucosal Entry of HIV and Mucosal Immunity, Institute Cochin, Paris, France
| | - Lucia Lopalco
- Immunobiology of HIV Unit, San Raffaele Scientific Institute, Milan, Italy
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13
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Van Doren VE, Smith SA, Hu YJ, Tharp G, Bosinger S, Ackerley CG, Murray PM, Amara RR, Amancha PK, Arthur RA, Johnston HR, Kelley CF. HIV, asymptomatic STI, and the rectal mucosal immune environment among young men who have sex with men. PLoS Pathog 2023; 19:e1011219. [PMID: 37253061 PMCID: PMC10256205 DOI: 10.1371/journal.ppat.1011219] [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: 02/17/2023] [Revised: 06/09/2023] [Accepted: 05/10/2023] [Indexed: 06/01/2023] Open
Abstract
Young men who have sex with men (YMSM) are disproportionately affected by HIV and bacterial sexually transmitted infections (STI) including gonorrhea, chlamydia, and syphilis; yet research into the immunologic effects of these infections is typically pursued in siloes. Here, we employed a syndemic approach to understand potential interactions of these infections on the rectal mucosal immune environment among YMSM. We enrolled YMSM aged 18-29 years with and without HIV and/or asymptomatic bacterial STI and collected blood, rectal secretions, and rectal tissue biopsies. YMSM with HIV were on suppressive antiretroviral therapy (ART) with preserved blood CD4 cell counts. We defined 7 innate and 19 adaptive immune cell subsets by flow cytometry, the rectal mucosal transcriptome by RNAseq, and the rectal mucosal microbiome by 16S rRNA sequencing and examined the effects of HIV and STI and their interactions. We measured tissue HIV RNA viral loads among YMSM with HIV and HIV replication in rectal explant challenge experiments among YMSM without HIV. HIV, but not asymptomatic STI, was associated with profound alterations in the cellular composition of the rectal mucosa. We did not detect a difference in the microbiome composition associated with HIV, but asymptomatic bacterial STI was associated with a higher probability of presence of potentially pathogenic taxa. When examining the rectal mucosal transcriptome, there was evidence of statistical interaction; asymptomatic bacterial STI was associated with upregulation of numerous inflammatory genes and enrichment for immune response pathways among YMSM with HIV, but not YMSM without HIV. Asymptomatic bacterial STI was not associated with differences in tissue HIV RNA viral loads or in HIV replication in explant challenge experiments. Our results suggest that asymptomatic bacterial STI may contribute to inflammation particularly among YMSM with HIV, and that future research should examine potential harms and interventions to reduce the health impact of these syndemic infections.
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Affiliation(s)
- Vanessa E. Van Doren
- The Hope Clinic of the Emory Vaccine Center, Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - S. Abigail Smith
- The Hope Clinic of the Emory Vaccine Center, Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Yi-Juan Hu
- Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, Georgia, United States of America
| | - Gregory Tharp
- Emory National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
| | - Steven Bosinger
- Emory National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
- Department of Microbiology and Immunology, Emory University, Atlanta, Georgia, United States of America
| | - Cassie G. Ackerley
- The Hope Clinic of the Emory Vaccine Center, Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Phillip M. Murray
- The Hope Clinic of the Emory Vaccine Center, Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Rama R. Amara
- Emory National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
- Department of Microbiology and Immunology, Emory University, Atlanta, Georgia, United States of America
| | - Praveen K. Amancha
- The Hope Clinic of the Emory Vaccine Center, Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Robert A. Arthur
- Emory Integrated Computational Core, Emory University, Atlanta, Georgia, United States of America
| | - H. Richard Johnston
- Emory Integrated Computational Core, Emory University, Atlanta, Georgia, United States of America
| | - Colleen F. Kelley
- The Hope Clinic of the Emory Vaccine Center, Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, United States of America
- Grady Health System, Atlanta, Georgia, United States of America
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14
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Cinque F, Cespiati A, Lombardi R, Guaraldi G, Sebastiani G. Nutritional and Lifestyle Therapy for NAFLD in People with HIV. Nutrients 2023; 15:nu15081990. [PMID: 37111209 PMCID: PMC10140991 DOI: 10.3390/nu15081990] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 04/17/2023] [Accepted: 04/19/2023] [Indexed: 04/29/2023] Open
Abstract
HIV infection and nonalcoholic fatty liver disease (NAFLD) are two major epidemics affecting millions of people worldwide. As people with HIV (PWH) age, there is an increased prevalence of metabolic comorbidities, along with unique HIV factors, such as HIV chronic inflammation and life-long exposure to antiretroviral therapy, which leads to a high prevalence of NAFLD. An unhealthy lifestyle, with a high dietary intake of refined carbohydrates, saturated fatty acids, fructose added beverages, and processed red meat, as well as physical inactivity, are known to trigger and promote the progression of NAFLD to nonalcoholic steatohepatitis, liver fibrosis, and hepatocellular carcinoma. Furthermore, with no currently approved pharmacotherapy and a lack of clinical trials that are inclusive of HIV, nutritional and lifestyle approaches still represent the most recommended treatments for PWH with NAFLD. While sharing common features with the general population, NAFLD in PWH displays its own peculiarities that may also reflect different impacts of nutrition and exercise on its onset and treatment. Therefore, in this narrative review, we aimed to explore the role of nutrients in the development of NAFLD in PWH. In addition, we discussed the nutritional and lifestyle approaches to managing NAFLD in the setting of HIV, with insights into the role of gut microbiota and lean NAFLD.
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Affiliation(s)
- Felice Cinque
- Division of Gastroenterology and Hepatology, and Chronic Viral Illness Service, McGill University Health Centre, Montreal, QC H4A 3J1, Canada
- Department of Pathophysiology and Transplantation, University of Milan, 20122 Milan, Italy
- Medicine and Metabolic Disease Unit, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Via F. Sforza 35, 20122 Milan, Italy
| | - Annalisa Cespiati
- Department of Pathophysiology and Transplantation, University of Milan, 20122 Milan, Italy
- Medicine and Metabolic Disease Unit, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Via F. Sforza 35, 20122 Milan, Italy
| | - Rosa Lombardi
- Department of Pathophysiology and Transplantation, University of Milan, 20122 Milan, Italy
- Medicine and Metabolic Disease Unit, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Via F. Sforza 35, 20122 Milan, Italy
| | - Giovanni Guaraldi
- Modena HIV Metabolic Clinic, Department of Surgical, Medical, Dental and Morphological Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy
- Infectious Diseases Unit, Azienda Ospedaliero-Universitaria di Modena, 41124 Modena, Italy
| | - Giada Sebastiani
- Division of Gastroenterology and Hepatology, and Chronic Viral Illness Service, McGill University Health Centre, Montreal, QC H4A 3J1, Canada
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15
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MacCann R, Landay AL, Mallon PWG. HIV and comorbidities - the importance of gut inflammation and the kynurenine pathway. Curr Opin HIV AIDS 2023; 18:102-110. [PMID: 36722199 PMCID: PMC7614535 DOI: 10.1097/coh.0000000000000782] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
PURPOSE OF REVIEW The purpose of this article is to review alterations in microbiota composition, diversity, and functional features in the context of chronic inflammation and comorbidities associated with HIV infection. RECENT FINDINGS The gut microbiome is an important mediator of host immunity, and disruption of gut homeostasis can contribute to both systemic inflammation and immune activation. Ageing and HIV share features of intestinal damage, microbial translocation and alterations in bacterial composition that contribute to a proinflammatory state and development of age-related comorbidities. One such inflammatory pathway reviewed is the nicotinamide adenine dinucleotide (NAD+) producing kynurenine pathway (KP). Kynurenine metabolites regulate many biological processes including host-microbiome communication, immunity and oxidative stress and the KP in turn is influenced by the microbiome environment. Age-associated decline in NAD+ is implicated as a driving factor in many age-associated diseases, including those seen in people with HIV (PWH). Recent studies have shown that KP can influence metabolic changes in PWH, including increased abdominal adiposity and cardiovascular disease. Furthermore, KP activity increases with age in the general population, but it is elevated in PWH at all ages compared to age-matched controls. Host or microbiome-mediated targeting of this pathway has merits to increase healthy longevity and has potential therapeutic applications in PWH. SUMMARY As a growing proportion of PWH age, many face increased risks of developing age-related comorbidities. Chronic inflammation, a pillar of geroscience, the science of ageing and of age-related disease, is influenced by the gut microbiome and its metabolites. Combined, these contribute to a systemic inflammatory signature. Advances in geroscience-based approaches and therapeutics offer a novel paradigm for addressing age-related diseases and chronic inflammation in HIV infection. Whether targeted inhibition of KP activity alleviates pathological conditions or promotes successful ageing in PWH remains to be determined.
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Affiliation(s)
- Rachel MacCann
- UCD Centre for Experimental Pathogen Host Research (CEPHR), School of Medicine, University College Dublin
- St Vincents University Hospital, Elm Park, Dublin 4, Ireland
| | - Alan L Landay
- Department of Internal Medicine, Rush University Medical Center, Chicago, Illinois, USA
| | - Patrick W G Mallon
- UCD Centre for Experimental Pathogen Host Research (CEPHR), School of Medicine, University College Dublin
- St Vincents University Hospital, Elm Park, Dublin 4, Ireland
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16
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Yuan X, Lai Y. Bibliometric and visualized analysis of elite controllers based on CiteSpace: landscapes, hotspots, and frontiers. Front Cell Infect Microbiol 2023; 13:1147265. [PMID: 37124043 PMCID: PMC10130382 DOI: 10.3389/fcimb.2023.1147265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 03/27/2023] [Indexed: 05/02/2023] Open
Abstract
Background A unique subset of people living with HIV, known as elite controllers, possess spontaneous and consistent control over viral replication and disease progression in the absence of antiviral intervention. In-depth research on elite controllers is conducive to designing better treatment strategies for HIV. However, comprehensive and illuminating bibliometric reports on elite controllers are rare. Methods Articles on elite controllers were retrieved from the Web of Science Core Collection. A visualized analysis of this domain was conducted by CiteSpace software. Taking count, betweenness centrality, and burst value as criteria, we interpreted the visualization results and predicted future new directions and emerging trends. Results By December 31, 2022, 843 articles related to elite controllers had been published. The largest contributors in terms of country, institution, and author were the United States (485), Univ Calif San Francisco (87), and Walker B.D. (65), respectively. Migueles S.A. (325) and Journal of Virology (770) were the most cocited author and journal, respectively. Additionally, by summarizing the results of our CiteSpace software analysis on references and keywords, we considered that the research hotspots and frontiers on elite controllers mainly focus on three aspects: deciphering the mechanisms of durable control, delineating the implications for the development of treatments for HIV infection, and highlighting the clinical risks faced by elite controllers and coping strategies. Conclusion This study performed a bibliometric and visual analysis of elite controllers, identified the main characteristics and emerging trends, and provided insightful references for further development of this rapidly evolving and complex field.
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Affiliation(s)
- Xingyue Yuan
- School of Clinical Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Yu Lai
- School of Basic Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- *Correspondence: Yu Lai,
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17
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Vadaq N, Zhang Y, Meeder E, Van de Wijer L, Gasem MH, Joosten LA, Netea MG, de Mast Q, Matzaraki V, Schellekens A, Fu J, van der Ven AJ. Microbiome-Related Indole and Serotonin Metabolites are Linked to Inflammation and Psychiatric Symptoms in People Living with HIV. Int J Tryptophan Res 2022; 15:11786469221126888. [PMID: 36187510 PMCID: PMC9520182 DOI: 10.1177/11786469221126888] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 08/30/2022] [Indexed: 11/18/2022] Open
Abstract
Background: People living with HIV (PLHIV) exhibit dysregulation of tryptophan metabolism. Altered gut microbiome composition in PLHIV might be involved. Mechanistic consequences within the 3 major tryptophan metabolism pathways (serotonin, kynurenine, and indoles), and functional consequences for platelet, immune and behavioral functions are unknown. We investigated plasma tryptophan metabolites, gut microbiome composition, and their association with platelet function, inflammation, and psychiatric symptoms. Methods: This study included 211 PLHIV on long-term antiretroviral treatment (ART). Plasma tryptophan pathway metabolites were measured using time-of-flight mass spectrometry. Bacterial composition was profiled using metagenomic sequencing. Platelet reactivity and serotonin levels were quantified by flowcytometry and ELISA, respectively. Circulating inflammatory markers were determined using ELISA. Symptoms of depression and impulsivity were measured by DASS-42 and BIS-11 self-report questionnaires, respectively. Results: Plasma serotonin and indole metabolites were associated with gut bacterial composition. Notably, species enriched in PLHIV were associated with 3-methyldioxyindole. Platelet serotonin concentrations were elevated in PLHIV, without effects on platelet reactivity. Plasma serotonin and indole metabolites were positively associated with plasma IL-10 and TNF-α concentrations. Finally, higher tryptophan, serotonin, and indole metabolites were associated with lower depression and anxiety, whereas higher kynurenine metabolites were associated with increased impulsivity. Conclusion: Our results suggest that gut bacterial composition and dysbiosis in PLHIV on ART contribute to tryptophan metabolism, which may have clinical consequences for immune function and behavior.
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Affiliation(s)
- Nadira Vadaq
- Department of Internal Medicine, Radboudumc Center for Infectious Diseases, Radboud Institute of Health Science (RIHS), Radboud University Medical Center, Nijmegen, The Netherlands.,Center for Tropical and Infectious Diseases (CENTRID), Faculty of Medicine, Diponegoro University, Dr. Kariadi Hospital, Semarang, Indonesia
| | - Yue Zhang
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Elise Meeder
- Department of Psychiatry, Radboud University Medical Centre, Nijmegen, The Netherlands.,Nijmegen Institute for Scientist-Practitioners in Addiction (NISPA), Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behavior, Radboud University, Nijmegen, The Netherlands
| | - Lisa Van de Wijer
- Department of Internal Medicine, Radboudumc Center for Infectious Diseases, Radboud Institute of Health Science (RIHS), Radboud University Medical Center, Nijmegen, The Netherlands
| | - Muhammad Hussein Gasem
- Center for Tropical and Infectious Diseases (CENTRID), Faculty of Medicine, Diponegoro University, Dr. Kariadi Hospital, Semarang, Indonesia.,Department of Internal Medicine, Faculty of Medicine Diponegoro University-Dr. Kariadi Hospital, Semarang, Indonesia
| | - Leo Ab Joosten
- Department of Internal Medicine, Radboudumc Center for Infectious Diseases, Radboud Institute of Health Science (RIHS), Radboud University Medical Center, Nijmegen, The Netherlands
| | - Mihai G Netea
- Department of Internal Medicine, Radboudumc Center for Infectious Diseases, Radboud Institute of Health Science (RIHS), Radboud University Medical Center, Nijmegen, The Netherlands.,Department for Immunology and Metabolism, Life and Medical Sciences Institute, University of Bonn, Bonn, Germany
| | - Quirijn de Mast
- Department of Internal Medicine, Radboudumc Center for Infectious Diseases, Radboud Institute of Health Science (RIHS), Radboud University Medical Center, Nijmegen, The Netherlands
| | - Vasiliki Matzaraki
- Department of Internal Medicine, Radboudumc Center for Infectious Diseases, Radboud Institute of Health Science (RIHS), Radboud University Medical Center, Nijmegen, The Netherlands
| | - Arnt Schellekens
- Department of Psychiatry, Radboud University Medical Centre, Nijmegen, The Netherlands.,Nijmegen Institute for Scientist-Practitioners in Addiction (NISPA), Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behavior, Radboud University, Nijmegen, The Netherlands
| | - Jingyuan Fu
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.,Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - André Jam van der Ven
- Department of Internal Medicine, Radboudumc Center for Infectious Diseases, Radboud Institute of Health Science (RIHS), Radboud University Medical Center, Nijmegen, The Netherlands
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18
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Lu X, Zhang K, Wang T, Zhang X, Zhang J, Wei H, Gao P, Wang J, Zhang H, Zhang Z. Gut Microbiome Alterations in Men Who Have Sex with Men-a Preliminary Report. Curr HIV Res 2022; 20:CHR-EPUB-126224. [PMID: 36089779 DOI: 10.2174/1570162x20666220908105918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Revised: 07/06/2022] [Accepted: 07/29/2022] [Indexed: 11/22/2022]
Abstract
BACKGROUND Studies have found that HIV is mainly transmitted through the mucosal surface, and the entrance of early progression of the disease is the rectal and colonic mucosa. So, this paper aimed to explore and analyze the structural differences of gut microbiome between men who have sex with men (MSM) and those who haven't sex with men (Non-MSM), expecting finding novel biological factors that potentially impact transmission and/or disease in MSM population. METHODS We collected a total of 33 stool samples, 16 were MSM and 17 were Non-MSM. The 16S rRNA gene amplification sequencing was used to detect the alteration and structure of the gut microbiome community in two groups. RESULTS The difference in β diversity of gut microbiome of two groups of subjects was statistically significant (P<0.001), indicating that the difference in the structure of the gut microbiome of two groups was statistically significant. Compared with the phylum and genus level of Non-MSM group, the relative abundances of Actinobacteria, Proteobacteria, genera Collinsella, Prevotella, Bifidobacterium and Ralstonia in MSM group were higher (P<0.001, P<0.05, LDA score(log10)>2), and the relative abundance of Bacteroidetes, genera Erysipelotrichaceae incertae sedis, Bilophila, Holdemania, Clostridium XIVb and Bacteroidaceae in MSM group was lower (P<0.01, LDA score(log10)>2). CONCLUSIONS There are some differences in the structure of gut microbiome between MSM group and Non-MSM group. It indicates the differences in behavior and characteristics between MSM and Non-MSM population may be related to the difference in the structure of gut microbiome.
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Affiliation(s)
- Xiaoyan Lu
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, China
| | - Kexin Zhang
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, China
| | - Tianli Wang
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, China
| | - Xueqing Zhang
- Department of Epidemiology and Biostatistics, School of Public Health,c, Hefei, China
| | - Jianghui Zhang
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, China
| | - Hongyuan Wei
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, China
| | - Pan Gao
- Qingwei Public Health Service Center of Luyang, Hefei, China
| | - Jun Wang
- Department of Maternal, Child & Adolescent Health, School of Public Health, Anhui Medical University, Hefei, China
| | - Hongbo Zhang
- Department of Maternal, Child & Adolescent Health, School of Public Health, Anhui Medical University, Hefei, China
| | - Zhihua Zhang
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, China
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19
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Borgognone A, Noguera-Julian M, Oriol B, Noël-Romas L, Ruiz-Riol M, Guillén Y, Parera M, Casadellà M, Duran C, Puertas MC, Català-Moll F, De Leon M, Knodel S, Birse K, Manzardo C, Miró JM, Clotet B, Martinez-Picado J, Moltó J, Mothe B, Burgener A, Brander C, Paredes R. Gut microbiome signatures linked to HIV-1 reservoir size and viremia control. MICROBIOME 2022; 10:59. [PMID: 35410461 PMCID: PMC9004083 DOI: 10.1186/s40168-022-01247-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 02/16/2022] [Indexed: 05/28/2023]
Abstract
BACKGROUND The potential role of the gut microbiome as a predictor of immune-mediated HIV-1 control in the absence of antiretroviral therapy (ART) is still unknown. In the BCN02 clinical trial, which combined the MVA.HIVconsv immunogen with the latency-reversing agent romidepsin in early-ART treated HIV-1 infected individuals, 23% (3/13) of participants showed sustained low-levels of plasma viremia during 32 weeks of a monitored ART pause (MAP). Here, we present a multi-omics analysis to identify compositional and functional gut microbiome patterns associated with HIV-1 control in the BCN02 trial. RESULTS Viremic controllers during the MAP (controllers) exhibited higher Bacteroidales/Clostridiales ratio and lower microbial gene richness before vaccination and throughout the study intervention when compared to non-controllers. Longitudinal assessment indicated that the gut microbiome of controllers was enriched in pro-inflammatory bacteria and depleted in butyrate-producing bacteria and methanogenic archaea. Functional profiling also showed that metabolic pathways related to fatty acid and lipid biosynthesis were significantly increased in controllers. Fecal metaproteome analyses confirmed that baseline functional differences were mainly driven by Clostridiales. Participants with high baseline Bacteroidales/Clostridiales ratio had increased pre-existing immune activation-related transcripts. The Bacteroidales/Clostridiales ratio as well as host immune-activation signatures inversely correlated with HIV-1 reservoir size. CONCLUSIONS The present proof-of-concept study suggests the Bacteroidales/Clostridiales ratio as a novel gut microbiome signature associated with HIV-1 reservoir size and immune-mediated viral control after ART interruption. Video abstract.
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Affiliation(s)
- Alessandra Borgognone
- IrsiCaixa AIDS Research Institute, Hospital Universitari Germans Trias i Pujol, Barcelona, Catalonia, Spain.
| | - Marc Noguera-Julian
- IrsiCaixa AIDS Research Institute, Hospital Universitari Germans Trias i Pujol, Barcelona, Catalonia, Spain
- CIBERINFEC, Madrid, Spain
- University of Vic-Central University of Catalonia (UVic-UCC), Vic, Catalonia, Spain
| | - Bruna Oriol
- IrsiCaixa AIDS Research Institute, Hospital Universitari Germans Trias i Pujol, Barcelona, Catalonia, Spain
- Universitat Autonoma de Barcelona (UAB), Barcelona, Catalonia, Spain
| | - Laura Noël-Romas
- Center for Global Health and Diseases, Department of Pathology, Case Western Reserve University, Cleveland, OH, USA
- Department of Obstetrics & Gynecology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Marta Ruiz-Riol
- IrsiCaixa AIDS Research Institute, Hospital Universitari Germans Trias i Pujol, Barcelona, Catalonia, Spain
- CIBERINFEC, Madrid, Spain
| | - Yolanda Guillén
- Institut Mar d'Investigacions mediques (IMIM), CIBERONC, Barcelona, Catalonia, Spain
| | - Mariona Parera
- IrsiCaixa AIDS Research Institute, Hospital Universitari Germans Trias i Pujol, Barcelona, Catalonia, Spain
| | - Maria Casadellà
- IrsiCaixa AIDS Research Institute, Hospital Universitari Germans Trias i Pujol, Barcelona, Catalonia, Spain
| | - Clara Duran
- IrsiCaixa AIDS Research Institute, Hospital Universitari Germans Trias i Pujol, Barcelona, Catalonia, Spain
- Universitat Autonoma de Barcelona (UAB), Barcelona, Catalonia, Spain
| | - Maria C Puertas
- IrsiCaixa AIDS Research Institute, Hospital Universitari Germans Trias i Pujol, Barcelona, Catalonia, Spain
- CIBERINFEC, Madrid, Spain
| | - Francesc Català-Moll
- IrsiCaixa AIDS Research Institute, Hospital Universitari Germans Trias i Pujol, Barcelona, Catalonia, Spain
| | - Marlon De Leon
- Center for Global Health and Diseases, Department of Pathology, Case Western Reserve University, Cleveland, OH, USA
| | - Samantha Knodel
- Center for Global Health and Diseases, Department of Pathology, Case Western Reserve University, Cleveland, OH, USA
- Department of Obstetrics & Gynecology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Kenzie Birse
- Center for Global Health and Diseases, Department of Pathology, Case Western Reserve University, Cleveland, OH, USA
- Department of Obstetrics & Gynecology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Christian Manzardo
- Infectious Diseases Service, Hospital Clinic-Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona, Barcelona, Catalonia, Spain
| | - José M Miró
- CIBERINFEC, Madrid, Spain
- Infectious Diseases Service, Hospital Clinic-Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona, Barcelona, Catalonia, Spain
| | - Bonaventura Clotet
- IrsiCaixa AIDS Research Institute, Hospital Universitari Germans Trias i Pujol, Barcelona, Catalonia, Spain
- CIBERINFEC, Madrid, Spain
- University of Vic-Central University of Catalonia (UVic-UCC), Vic, Catalonia, Spain
- Universitat Autonoma de Barcelona (UAB), Barcelona, Catalonia, Spain
- Fight AIDS Foundation, Infectious Diseases Department, Germans Trias i Pujol University Hospital, Barcelona, Catalonia, Spain
- Department of Infectious Diseases Service, Germans Trias i Pujol University Hospital, Barcelona, Catalonia, Spain
| | - Javier Martinez-Picado
- IrsiCaixa AIDS Research Institute, Hospital Universitari Germans Trias i Pujol, Barcelona, Catalonia, Spain
- CIBERINFEC, Madrid, Spain
- University of Vic-Central University of Catalonia (UVic-UCC), Vic, Catalonia, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Catalonia, Spain
| | - José Moltó
- CIBERINFEC, Madrid, Spain
- Fight AIDS Foundation, Infectious Diseases Department, Germans Trias i Pujol University Hospital, Barcelona, Catalonia, Spain
- Department of Infectious Diseases Service, Germans Trias i Pujol University Hospital, Barcelona, Catalonia, Spain
| | - Beatriz Mothe
- IrsiCaixa AIDS Research Institute, Hospital Universitari Germans Trias i Pujol, Barcelona, Catalonia, Spain
- CIBERINFEC, Madrid, Spain
- University of Vic-Central University of Catalonia (UVic-UCC), Vic, Catalonia, Spain
- Fight AIDS Foundation, Infectious Diseases Department, Germans Trias i Pujol University Hospital, Barcelona, Catalonia, Spain
- Department of Infectious Diseases Service, Germans Trias i Pujol University Hospital, Barcelona, Catalonia, Spain
| | - Adam Burgener
- Center for Global Health and Diseases, Department of Pathology, Case Western Reserve University, Cleveland, OH, USA
- Department of Obstetrics & Gynecology, University of Manitoba, Winnipeg, Manitoba, Canada
- Department of Medicine Solna, Center for Molecular Medicine, Karolinska Institute, Karolinska University Hospital, Stockholm, Sweden
| | - Christian Brander
- IrsiCaixa AIDS Research Institute, Hospital Universitari Germans Trias i Pujol, Barcelona, Catalonia, Spain
- CIBERINFEC, Madrid, Spain
- University of Vic-Central University of Catalonia (UVic-UCC), Vic, Catalonia, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Catalonia, Spain
| | - Roger Paredes
- IrsiCaixa AIDS Research Institute, Hospital Universitari Germans Trias i Pujol, Barcelona, Catalonia, Spain.
- CIBERINFEC, Madrid, Spain.
- University of Vic-Central University of Catalonia (UVic-UCC), Vic, Catalonia, Spain.
- Universitat Autonoma de Barcelona (UAB), Barcelona, Catalonia, Spain.
- Center for Global Health and Diseases, Department of Pathology, Case Western Reserve University, Cleveland, OH, USA.
- Fight AIDS Foundation, Infectious Diseases Department, Germans Trias i Pujol University Hospital, Barcelona, Catalonia, Spain.
- Department of Infectious Diseases Service, Germans Trias i Pujol University Hospital, Barcelona, Catalonia, Spain.
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20
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Zaongo SD, Harypursat V, Chen Y. Single-Cell Sequencing Facilitates Elucidation of HIV Immunopathogenesis: A Review of Current Literature. Front Immunol 2022; 13:828860. [PMID: 35185920 PMCID: PMC8850777 DOI: 10.3389/fimmu.2022.828860] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Accepted: 01/18/2022] [Indexed: 12/18/2022] Open
Abstract
Knowledge gaps remain in the understanding of HIV disease establishment and progression. Scientists continue to strive in their endeavor to elucidate the precise underlying immunopathogenic mechanisms of HIV-related disease, in order to identify possible preventive and therapeutic targets. A useful tool in the quest to reveal some of the enigmas related to HIV infection and disease is the single-cell sequencing (scRNA-seq) technique. With its proven capacity to elucidate critical processes in cell formation and differentiation, to decipher critical hematopoietic pathways, and to understand the regulatory gene networks that predict immune function, scRNA-seq is further considered to be a potentially useful tool to explore HIV immunopathogenesis. In this article, we provide an overview of single-cell sequencing platforms, before delving into research findings gleaned from the use of single cell sequencing in HIV research, as published in recent literature. Finally, we describe two important avenues of research that we believe should be further investigated using the single-cell sequencing technique.
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Affiliation(s)
- Silvere D Zaongo
- Division of Infectious Diseases, Chongqing Public Health Medical Center, Chongqing, China
| | - Vijay Harypursat
- Division of Infectious Diseases, Chongqing Public Health Medical Center, Chongqing, China
| | - Yaokai Chen
- Division of Infectious Diseases, Chongqing Public Health Medical Center, Chongqing, China
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21
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Alexandrova Y, Costiniuk CT, Jenabian MA. Pulmonary Immune Dysregulation and Viral Persistence During HIV Infection. Front Immunol 2022; 12:808722. [PMID: 35058937 PMCID: PMC8764194 DOI: 10.3389/fimmu.2021.808722] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 12/10/2021] [Indexed: 12/12/2022] Open
Abstract
Despite the success of antiretroviral therapy (ART), people living with HIV continue to suffer from high burdens of respiratory infections, lung cancers and chronic lung disease at a higher rate than the general population. The lung mucosa, a previously neglected HIV reservoir site, is of particular importance in this phenomenon. Because ART does not eliminate the virus, residual levels of HIV that remain in deep tissues lead to chronic immune activation and pulmonary inflammatory pathologies. In turn, continuous pulmonary and systemic inflammation cause immune cell exhaustion and pulmonary immune dysregulation, creating a pro-inflammatory environment ideal for HIV reservoir persistence. Moreover, smoking, gut and lung dysbiosis and co-infections further fuel the vicious cycle of residual viral replication which, in turn, contributes to inflammation and immune cell proliferation, further maintaining the HIV reservoir. Herein, we discuss the recent evidence supporting the notion that the lungs serve as an HIV viral reservoir. We will explore how smoking, changes in the microbiome, and common co-infections seen in PLWH contribute to HIV persistence, pulmonary immune dysregulation, and high rates of infectious and non-infectious lung disease among these individuals.
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Affiliation(s)
- Yulia Alexandrova
- Infectious Diseases and Immunity in Global Health Program, Research Institute of McGill University Health Centre, Montreal, QC, Canada
- Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada
- Department of Biological Sciences and CERMO-FC Research Centre, Université du Québec à Montréal, Montreal, QC, Canada
| | - Cecilia T. Costiniuk
- Infectious Diseases and Immunity in Global Health Program, Research Institute of McGill University Health Centre, Montreal, QC, Canada
- Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada
- Division of Infectious Diseases and Chronic Viral Illness Service, McGill University Health Centre, Montreal, QC, Canada
| | - Mohammad-Ali Jenabian
- Department of Biological Sciences and CERMO-FC Research Centre, Université du Québec à Montréal, Montreal, QC, Canada
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22
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Yan J, Ouyang J, Isnard S, Zhou X, Harypursat V, Routy JP, Chen Y. Alcohol Use and Abuse Conspires With HIV Infection to Aggravate Intestinal Dysbiosis and Increase Microbial Translocation in People Living With HIV: A Review. Front Immunol 2021; 12:741658. [PMID: 34975838 PMCID: PMC8718428 DOI: 10.3389/fimmu.2021.741658] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 11/30/2021] [Indexed: 12/12/2022] Open
Abstract
The intestinal microbiome is an essential so-called human "organ", vital for the induction of innate immunity, for metabolizing nutrients, and for maintenance of the structural integrity of the intestinal barrier. HIV infection adversely influences the richness and diversity of the intestinal microbiome, resulting in structural and functional impairment of the intestinal barrier and an increased intestinal permeability. Pathogens and metabolites may thus cross the "leaky" intestinal barrier and enter the systemic circulation, which is a significant factor accounting for the persistent underlying chronic inflammatory state present in people living with HIV (PLWH). Additionally, alcohol use and abuse has been found to be prevalent in PLWH and has been strongly associated with the incidence and progression of HIV/AIDS. Recently, converging evidence has indicated that the mechanism underlying this phenomenon is related to intestinal microbiome and barrier function through numerous pathways. Alcohol acts as a "partner" with HIV in disrupting microbiome ecology, and thus impairing of the intestinal barrier. Optimizing the microbiome and restoring the integrity of the intestinal barrier is likely to be an effective adjunctive therapeutic strategy for PLWH. We herein critically review the interplay among HIV, alcohol, and the gut barrier, thus setting the scene with regards to development of effective strategies to counteract the dysregulated gut microbiome and the reduction of microbial translocation and inflammation in PLWH.
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Affiliation(s)
- Jiangyu Yan
- Clinical Research Center, Chongqing Public Health Medical Center, Chongqing, China
| | - Jing Ouyang
- Clinical Research Center, Chongqing Public Health Medical Center, Chongqing, China
| | - Stéphane Isnard
- Infectious Diseases and Immunity in Global Health Program, Research Institute, McGill University Health Centre, Montréal, QC, Canada
- Chronic Viral Illness Service, McGill University Health Centre, Montréal, QC, Canada
- Canadian HIV Trials Network (CTN), Canadian Institutes of Health Research (CIHR), Vancouver, BC, Canada
| | - Xin Zhou
- Clinical Research Center, Chongqing Public Health Medical Center, Chongqing, China
| | - Vijay Harypursat
- Clinical Research Center, Chongqing Public Health Medical Center, Chongqing, China
| | - Jean-Pierre Routy
- Infectious Diseases and Immunity in Global Health Program, Research Institute, McGill University Health Centre, Montréal, QC, Canada
- Chronic Viral Illness Service, McGill University Health Centre, Montréal, QC, Canada
- Division of Hematology, McGill University Health Centre, Montréal, QC, Canada
| | - Yaokai Chen
- Clinical Research Center, Chongqing Public Health Medical Center, Chongqing, China
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23
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Lopera TJ, Lujan JA, Zurek E, Zapata W, Hernandez JC, Toro MA, Alzate JF, Taborda NA, Rugeles MT, Aguilar-Jimenez W. A specific structure and high richness characterize intestinal microbiota of HIV-exposed seronegative individuals. PLoS One 2021; 16:e0260729. [PMID: 34855852 PMCID: PMC8638974 DOI: 10.1371/journal.pone.0260729] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 11/15/2021] [Indexed: 02/05/2023] Open
Abstract
Intestinal microbiota facilitates food breakdown for energy metabolism and influences the immune response, maintaining mucosal homeostasis. Overall, HIV infection is associated with intestinal dysbiosis and immune activation, which has been related to seroconversion in HIV-exposed individuals. However, it is unclear whether microbiota dysbiosis is the cause or the effect of immune alterations and disease progression or if it could modulate the risk of acquiring the HIV infection. We characterize the intestinal microbiota and determine its association with immune regulation in HIV-exposed seronegative individuals (HESN), HIV-infected progressors (HIV+), and healthy control (HC) subjects. For this, feces and blood were collected. The microbiota composition of HESN showed a significantly higher alpha (p = 0.040) and beta diversity (p = 0.006) compared to HC, but no differences were found compared to HIV+. A lower Treg percentage was observed in HESN (1.77%) than HC (2.98%) and HIV+ (4.02%), with enrichment of the genus Butyrivibrio (p = 0.029) being characteristic of this profile. Moreover, we found that Megasphaera (p = 0.017) and Victivallis (p = 0.0029) also are enriched in the microbiota composition in HESN compared to HC and HIV+ subjects. Interestingly, an increase in Succinivibrio and Prevotella, and a reduction in Bacteroides genus, which is typical of HIV-infected individuals, were observed in both HESN and HIV+, compared to HC. Thus, HESNs have a microbiota profile, similar to that observed in HIV+, most likely because HESN are cohabiting with their HIV+ partners.
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Affiliation(s)
- Tulio J. Lopera
- Facultad de Medicina, Grupo Inmunovirología, Universidad de Antioquia UdeA, Medellín, Colombia
| | - Jorge A. Lujan
- Facultad de Medicina, Grupo Inmunovirología, Universidad de Antioquia UdeA, Medellín, Colombia
| | - Eduardo Zurek
- Department of System Engineering, Universidad del Norte, Barranquilla, Colombia
| | - Wildeman Zapata
- Facultad de Medicina, Grupo Inmunovirología, Universidad de Antioquia UdeA, Medellín, Colombia
- Facultad de Medicina, Grupo Infettare, Universidad Cooperativa de Colombia, Medellín, Colombia
| | - Juan C. Hernandez
- Facultad de Medicina, Grupo Infettare, Universidad Cooperativa de Colombia, Medellín, Colombia
| | - Miguel A. Toro
- Facultad de Medicina, Centro Nacional de Secuenciación Genómica -CNSG, Sede de Investigación Universitaria -SIU, Universidad de Antioquia UdeA, Medellin, Colombia
- Facultad de Medicina, Grupo de Parasitología, Universidad de Antioquia, Medellín, Colombia
| | - Juan F. Alzate
- Facultad de Medicina, Centro Nacional de Secuenciación Genómica -CNSG, Sede de Investigación Universitaria -SIU, Universidad de Antioquia UdeA, Medellin, Colombia
| | - Natalia A. Taborda
- Facultad de Medicina, Grupo Inmunovirología, Universidad de Antioquia UdeA, Medellín, Colombia
- Facultad de Ciencias de la Salud, Grupo de Investigaciones Biomédicas Uniremington, Programa de Medicina, Corporación Universitaria Remington, Medellín, Colombia
| | - Maria T. Rugeles
- Facultad de Medicina, Grupo Inmunovirología, Universidad de Antioquia UdeA, Medellín, Colombia
| | - Wbeimar Aguilar-Jimenez
- Facultad de Medicina, Grupo Inmunovirología, Universidad de Antioquia UdeA, Medellín, Colombia
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24
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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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25
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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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26
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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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27
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Bai X, Narayanan A, Nowak P, Ray S, Neogi U, Sönnerborg A. Whole-Genome Metagenomic Analysis of the Gut Microbiome in HIV-1-Infected Individuals on Antiretroviral Therapy. Front Microbiol 2021; 12:667718. [PMID: 34248876 PMCID: PMC8267369 DOI: 10.3389/fmicb.2021.667718] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Accepted: 05/31/2021] [Indexed: 01/14/2023] Open
Abstract
Gut microbiome plays a significant role in HIV-1 immunopathogenesis and HIV-1-associated complications. Previous studies have mostly been based on 16S rRNA gene sequencing, which is limited in taxonomic resolution at the genus level and inferred functionality. Herein, we performed a deep shotgun metagenomics study with the aim to obtain a more precise landscape of gut microbiome dysbiosis in HIV-1 infection. A reduced tendency of alpha diversity and significantly higher beta diversity were found in HIV-1-infected individuals on antiretroviral therapy (ART) compared to HIV-1-negative controls. Several species, such as Streptococcus anginosus, Actinomyces odontolyticus, and Rothia mucilaginosa, were significantly enriched in the HIV-1-ART group. Correlations were observed between the degree of immunodeficiency and gut microbiome in terms of microbiota composition and metabolic pathways. Furthermore, microbial shift in HIV-1-infected individuals was found to be associated with changes in microbial virulome and resistome. From the perspective of methodological evaluations, our study showed that different DNA extraction protocols significantly affect the genomic DNA quantity and quality. Moreover, whole metagenome sequencing depth affects critically the recovery of microbial genes, including virulome and resistome, while less than 5 million reads per sample is sufficient for taxonomy profiling in human fecal metagenomic samples. These findings advance our understanding of human gut microbiome and their potential associations with HIV-1 infection. The methodological assessment assists in future study design to accurately assess human gut microbiome.
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Affiliation(s)
- Xiangning Bai
- Division of Clinical Microbiology, Department of Laboratory Medicine, ANA Futura, Karolinska Institutet, Stockholm, Sweden.,Division of Infectious Diseases, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden.,State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.,Division of Laboratory Medicine, Oslo University Hospital, Oslo, Norway
| | - Aswathy Narayanan
- Division of Infectious Diseases, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Piotr Nowak
- Division of Infectious Diseases, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden.,Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden.,The Laboratory for Molecular Infection Medicine Sweden MIMS, Umeå University, Umeå, Sweden
| | - Shilpa Ray
- Division of Clinical Microbiology, Department of Laboratory Medicine, ANA Futura, Karolinska Institutet, Stockholm, Sweden.,The Laboratory for Molecular Infection Medicine Sweden MIMS, Umeå University, Umeå, Sweden
| | - Ujjwal Neogi
- Division of Clinical Microbiology, Department of Laboratory Medicine, ANA Futura, Karolinska Institutet, Stockholm, Sweden
| | - Anders Sönnerborg
- Division of Clinical Microbiology, Department of Laboratory Medicine, ANA Futura, Karolinska Institutet, Stockholm, Sweden.,Division of Infectious Diseases, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden.,Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
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28
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Nozza S, Ferrarese R, Poli A, Galli L, Sampaolo M, Bigoloni A, Galli A, Muccini C, Spagnuolo V, Lazzarin A, Clementi M, Mancini N, Castagna A. Analysis of the faecal microbiome during analytical treatment interruption in people with chronic HIV infection and long-lasting virological suppression (APACHE study). J Antimicrob Chemother 2021; 75:2700-2702. [PMID: 32542322 DOI: 10.1093/jac/dkaa231] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Affiliation(s)
- S Nozza
- San Raffaele Scientific Institute, Milan, Italy
| | - R Ferrarese
- San Raffaele Scientific Institute, Milan, Italy
| | - A Poli
- San Raffaele Scientific Institute, Milan, Italy
| | - L Galli
- San Raffaele Scientific Institute, Milan, Italy
| | - M Sampaolo
- San Raffaele Scientific Institute, Milan, Italy
| | - A Bigoloni
- San Raffaele Scientific Institute, Milan, Italy
| | - A Galli
- San Raffaele Scientific Institute, Milan, Italy
| | - C Muccini
- University Vita-Salute San Raffaele, Milan, Italy
| | - V Spagnuolo
- University Vita-Salute San Raffaele, Milan, Italy
| | - A Lazzarin
- San Raffaele Scientific Institute, Milan, Italy.,University Vita-Salute San Raffaele, Milan, Italy
| | - M Clementi
- San Raffaele Scientific Institute, Milan, Italy.,University Vita-Salute San Raffaele, Milan, Italy
| | - N Mancini
- San Raffaele Scientific Institute, Milan, Italy.,University Vita-Salute San Raffaele, Milan, Italy
| | - A Castagna
- San Raffaele Scientific Institute, Milan, Italy.,University Vita-Salute San Raffaele, Milan, Italy
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29
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Pastor-Ibáñez R, Díez-Fuertes F, Sánchez-Palomino S, Alcamí J, Plana M, Torrents D, Leal L, García F. Impact of Transcriptome and Gut Microbiome on the Response of HIV-1 Infected Individuals to a Dendritic Cell-Based HIV Therapeutic Vaccine. Vaccines (Basel) 2021; 9:vaccines9070694. [PMID: 34202658 PMCID: PMC8310021 DOI: 10.3390/vaccines9070694] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 06/16/2021] [Accepted: 06/21/2021] [Indexed: 01/08/2023] Open
Abstract
Therapeutic vaccines based on dendritic cells offer a good approach to HIV-specific T-cell responses and partial control of the viral load after antiretroviral therapy interruption. The aim of the present study was to identify mRNA expression profiles and to assess the impact of the gut microbiome composition for predicting the viral load control after antiretroviral therapy interruption. We enrolled 29 patients to receive either placebo or a monocyte-derived dendritic cell vaccine. Patients with a decrease in their viral load of >0.5 log10 copies/mL by 12 weeks after antiretroviral therapy interruption were considered responders. In total, 66 genes were considered differentially expressed between responders and non-responders. Enrichment analysis revealed several upregulated pathways involved in the host defense response to a virus via the type I interferon signaling pathway. Regarding the gut microbiota, responders showed enriched levels of Bacteroidetes (p < 0.005) and Verrucomicrobia (p = 0.017), while non-responders were enriched with Tenericutes (p = 0.049) and Actinobacteria (p < 0.005). We also found important differences at the genus level. However, we did not discover any effect of the dendritic cell vaccine on the transcriptome or the gut microbiota. An alternative analysis did characterize that the microbiota from responders were associated with the metabolic production of short-chain fatty acids, which are key metabolites in the regulation of intestinal homeostasis. The evidence now consistently shows that short-chain fatty acid depletion occurs in HIV-infected individuals receiving antiretroviral treatment.
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Affiliation(s)
- Roque Pastor-Ibáñez
- AIDS Research Group, IDIBAPS, Hospital Clinic, University of Barcelona, 170, 08036 Barcelona, Spain; (R.P.-I.); (S.S.-P.); (J.A.); (M.P.); (F.G.)
| | | | - Sonsoles Sánchez-Palomino
- AIDS Research Group, IDIBAPS, Hospital Clinic, University of Barcelona, 170, 08036 Barcelona, Spain; (R.P.-I.); (S.S.-P.); (J.A.); (M.P.); (F.G.)
| | - Jose Alcamí
- AIDS Research Group, IDIBAPS, Hospital Clinic, University of Barcelona, 170, 08036 Barcelona, Spain; (R.P.-I.); (S.S.-P.); (J.A.); (M.P.); (F.G.)
- Instituto de Salud Carlos III, Ctra. de Pozuelo, 28, Majadahonda, 28222 Madrid, Spain;
| | - Montserrat Plana
- AIDS Research Group, IDIBAPS, Hospital Clinic, University of Barcelona, 170, 08036 Barcelona, Spain; (R.P.-I.); (S.S.-P.); (J.A.); (M.P.); (F.G.)
| | - David Torrents
- Computational Genomics Groups, Barcelona Supercomputing Center (BSC), Plaça d’Eusebi Güell, 1-3, 08034 Barcelona, Spain;
| | - Lorna Leal
- AIDS Research Group, IDIBAPS, Hospital Clinic, University of Barcelona, 170, 08036 Barcelona, Spain; (R.P.-I.); (S.S.-P.); (J.A.); (M.P.); (F.G.)
- Infectious Diseases—Department, Hospital Clínic, IDIBAPS, University of Barcelona, Villarroel, 170, 08036 Barcelona, Spain
- Correspondence: ; Tel.: +34-932-275-586; Fax: +34-934-514-438
| | - Felipe García
- AIDS Research Group, IDIBAPS, Hospital Clinic, University of Barcelona, 170, 08036 Barcelona, Spain; (R.P.-I.); (S.S.-P.); (J.A.); (M.P.); (F.G.)
- Infectious Diseases—Department, Hospital Clínic, IDIBAPS, University of Barcelona, Villarroel, 170, 08036 Barcelona, Spain
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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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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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Xiong D, Muema C, Zhang X, Pan X, Xiong J, Yang H, Yu J, Wei H. Enriched Opportunistic Pathogens Revealed by Metagenomic Sequencing Hint Potential Linkages between Pharyngeal Microbiota and COVID-19. Virol Sin 2021; 36:924-933. [PMID: 33978940 PMCID: PMC8114661 DOI: 10.1007/s12250-021-00391-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 03/15/2021] [Indexed: 02/07/2023] Open
Abstract
As a respiratory tract virus, SARS-CoV-2 infected people through contacting with the upper respiratory tract first. Previous studies indicated that microbiota could modulate immune response against pathogen infection. In the present study, we performed metagenomic sequencing of pharyngeal swabs from eleven patients with COVID-19 and eleven Non-COVID-19 patients who had similar symptoms such as fever and cough. Through metagenomic analysis of the above two groups and a healthy group from the public data, there are 6502 species identified in the samples. Specifically, the Pielou index indicated a lower evenness of the microbiota in the COVID-19 group than that in the Non-COVID-19 group. Combined with the linear discriminant analysis (LDA) and the generalized linear model, eighty-one bacterial species were found with increased abundance in the COVID-19 group, where 51 species were enriched more than 8 folds. The top three enriched genera were Streptococcus, Prevotella and Campylobacter containing some opportunistic pathogens. More interestingly, through experiments, we found that two Streptococcus strains, S. suis and S. agalactiae, could stimulate the expression of ACE2 of Vero cells in vitro, which may promote SARS-CoV-2 infection. Therefore, these enriched pathogens in the pharynxes of COVID-19 patients may involve in the virus-host interactions to affect SARS-CoV-2 infection and cause potential secondary bacterial infections through changing the expression of the viral receptor ACE2 and/or modulate the host’s immune system.
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Affiliation(s)
- Dongyan Xiong
- CAS Key Laboratory of Special Pathogens and Biosafety, Centre for Biosafety Mega-Sciences, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Caroline Muema
- CAS Key Laboratory of Special Pathogens and Biosafety, Centre for Biosafety Mega-Sciences, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaoxu Zhang
- CAS Key Laboratory of Special Pathogens and Biosafety, Centre for Biosafety Mega-Sciences, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xinming Pan
- Jiangxia District Center for Disease Control and Prevention, Wuhan, 430200, China
| | - Jin Xiong
- CAS Key Laboratory of Special Pathogens and Biosafety, Centre for Biosafety Mega-Sciences, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Hang Yang
- CAS Key Laboratory of Special Pathogens and Biosafety, Centre for Biosafety Mega-Sciences, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Junping Yu
- CAS Key Laboratory of Special Pathogens and Biosafety, Centre for Biosafety Mega-Sciences, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China.
| | - Hongping Wei
- CAS Key Laboratory of Special Pathogens and Biosafety, Centre for Biosafety Mega-Sciences, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China.
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Pastor-Ibáñez R, Blanco-Heredia J, Etcheverry F, Sánchez-Palomino S, Díez-Fuertes F, Casas R, Navarrete-Muñoz MÁ, Castro-Barquero S, Lucero C, Fernández I, Leal L, Benito JM, Noguera-Julian M, Paredes R, Rallón N, Estruch R, Torrents D, García F. Adherence to a Supplemented Mediterranean Diet Drives Changes in the Gut Microbiota of HIV-1-Infected Individuals. Nutrients 2021; 13:nu13041141. [PMID: 33808476 PMCID: PMC8067262 DOI: 10.3390/nu13041141] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 03/19/2021] [Accepted: 03/24/2021] [Indexed: 12/12/2022] Open
Abstract
Objective: The health effects of a supplemented Mediterranean diet (SMD) with extra-virgin olive oil (EVOO) and nuts are well documented in non-HIV-infected individuals. We hypothesised that the benefits of an SMD could be mediated by changes in the gut microbiota, even in those with an altered intestinal microbiota such as people living with HIV. Design: Individuals living with HIV (n = 102) were randomised to receive an SMD with 50 g/day of EVOO and 30 g/day of walnuts (SMD group) or continue with their regular diet (control group) for 12 weeks. Methods: Adherence to the Mediterranean diet was assessed using the validated 14-item MD-Adherence-Screener (MEDAS) from the PREDIMED study. A sub-study classifying the participants according to their MEDAS scores was performed. Results: The lipid profile was improved in the SMD group vs. that in the control group (delta-total cholesterol and delta-B-lipoprotein). The immune activation (CD4+HLADR+CD38+ and CD8+HLADR+CD38+ cells) and IFN-γ-producing T-cells significantly decreased at week 12 compared to the baseline in the SMD group but not in the control group. The gut microbiota in those from the high-adherence group presented significantly high diversity and richness at the end of the intervention. Succinivibrio and Bifidobacterium abundances were influenced by the adherence to the MD and significantly correlated with Treg cells. Conclusion: The Mediterranean diet improved metabolic parameters, immune activation, Treg function, and the gut microbiota composition in HIV-1-infected individuals. Further, Mediterranean diet increased the Bifidobacterium abundances after the intervention, and it was associated to a beneficial profile.
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Affiliation(s)
- Roque Pastor-Ibáñez
- AIDS Research Group, IDIBAPS, Hospital Clinic, University of Barcelona, 08036 Barcelona, Spain; (R.P.-I.); (F.E.); (S.S.-P.); (F.D.-F.); (C.L.); (I.F.); (L.L.)
| | - Juan Blanco-Heredia
- IrsiCaixa AIDS Research Institute, Germans Trias i Pujol University Hospital, 08916 Badalona, Spain;
- Germans Trias i Pujol Research Institute (IGTP), 08916 Badalona, Spain
- Barcelona Supercomputing Center, 08034 Barcelona, Spain
| | - Florencia Etcheverry
- AIDS Research Group, IDIBAPS, Hospital Clinic, University of Barcelona, 08036 Barcelona, Spain; (R.P.-I.); (F.E.); (S.S.-P.); (F.D.-F.); (C.L.); (I.F.); (L.L.)
- Infectious Diseases Department, Hospital Clínic, IDIBAPS, University of Barcelona, 08036 Barcelona, Spain
| | - Sonsoles Sánchez-Palomino
- AIDS Research Group, IDIBAPS, Hospital Clinic, University of Barcelona, 08036 Barcelona, Spain; (R.P.-I.); (F.E.); (S.S.-P.); (F.D.-F.); (C.L.); (I.F.); (L.L.)
| | - Francisco Díez-Fuertes
- AIDS Research Group, IDIBAPS, Hospital Clinic, University of Barcelona, 08036 Barcelona, Spain; (R.P.-I.); (F.E.); (S.S.-P.); (F.D.-F.); (C.L.); (I.F.); (L.L.)
| | - Rosa Casas
- Department of Internal Medicine, Hospital Clinic, Institut d’Investigació Biomèdica August Pi i Sunyer (IDIBAPS), University of Barcelona, Villarroel, 170, 08036 Barcelona, Spain; (R.C.); (S.C.-B.); (R.E.)
- CIBER 06/03: Fisiopatología de la Obesidady la Nutrición, Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - María Ángeles Navarrete-Muñoz
- HIV and Viral Hepatitis Research Laboratory, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28040 Madrid, Spain; (M.Á.N.-M.); (J.M.B.); (N.R.)
- Hospital Universitario Rey Juan Carlos, Móstoles, 28933 Madrid, Spain
| | - Sara Castro-Barquero
- Department of Internal Medicine, Hospital Clinic, Institut d’Investigació Biomèdica August Pi i Sunyer (IDIBAPS), University of Barcelona, Villarroel, 170, 08036 Barcelona, Spain; (R.C.); (S.C.-B.); (R.E.)
- CIBER 06/03: Fisiopatología de la Obesidady la Nutrición, Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Constanza Lucero
- AIDS Research Group, IDIBAPS, Hospital Clinic, University of Barcelona, 08036 Barcelona, Spain; (R.P.-I.); (F.E.); (S.S.-P.); (F.D.-F.); (C.L.); (I.F.); (L.L.)
| | - Irene Fernández
- AIDS Research Group, IDIBAPS, Hospital Clinic, University of Barcelona, 08036 Barcelona, Spain; (R.P.-I.); (F.E.); (S.S.-P.); (F.D.-F.); (C.L.); (I.F.); (L.L.)
- Infectious Diseases Department, Hospital Clínic, IDIBAPS, University of Barcelona, 08036 Barcelona, Spain
| | - Lorna Leal
- AIDS Research Group, IDIBAPS, Hospital Clinic, University of Barcelona, 08036 Barcelona, Spain; (R.P.-I.); (F.E.); (S.S.-P.); (F.D.-F.); (C.L.); (I.F.); (L.L.)
- Infectious Diseases Department, Hospital Clínic, IDIBAPS, University of Barcelona, 08036 Barcelona, Spain
| | - José Miguel Benito
- HIV and Viral Hepatitis Research Laboratory, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28040 Madrid, Spain; (M.Á.N.-M.); (J.M.B.); (N.R.)
- Hospital Universitario Rey Juan Carlos, Móstoles, 28933 Madrid, Spain
| | - Marc Noguera-Julian
- Hospital Universitari Germans Trias i Pujol, IrsiCaixa, 08916 Badalona, Spain; (M.N.-J.); (R.P.)
| | - Roger Paredes
- Hospital Universitari Germans Trias i Pujol, IrsiCaixa, 08916 Badalona, Spain; (M.N.-J.); (R.P.)
| | - Norma Rallón
- HIV and Viral Hepatitis Research Laboratory, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28040 Madrid, Spain; (M.Á.N.-M.); (J.M.B.); (N.R.)
- Hospital Universitario Rey Juan Carlos, Móstoles, 28933 Madrid, Spain
| | - Ramón Estruch
- Department of Internal Medicine, Hospital Clinic, Institut d’Investigació Biomèdica August Pi i Sunyer (IDIBAPS), University of Barcelona, Villarroel, 170, 08036 Barcelona, Spain; (R.C.); (S.C.-B.); (R.E.)
- CIBER 06/03: Fisiopatología de la Obesidady la Nutrición, Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - David Torrents
- Computational Genomics Groups, Barcelona Supercomputing Center (BSC), 08034 Barcelona, Spain;
- Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
| | - Felipe García
- AIDS Research Group, IDIBAPS, Hospital Clinic, University of Barcelona, 08036 Barcelona, Spain; (R.P.-I.); (F.E.); (S.S.-P.); (F.D.-F.); (C.L.); (I.F.); (L.L.)
- Infectious Diseases Department, Hospital Clínic, IDIBAPS, University of Barcelona, 08036 Barcelona, Spain
- Correspondence: ; Tel.: +34-932275586; Fax: +34-934514438
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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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35
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Long Y, Liang F, Guo R, Zhu C, Zhao X, Wang X, Liu F, Jiang M, Liang Q, Zeng S, Han M, Qin J, Li S, Li S, Yang H. Gut Microbiota Signatures in Gestational Anemia. Front Cell Infect Microbiol 2021; 11:549678. [PMID: 33718259 PMCID: PMC7947918 DOI: 10.3389/fcimb.2021.549678] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 01/06/2021] [Indexed: 12/30/2022] Open
Abstract
Gestational diseases are associated with altered intestinal microbiota in pregnant women. Characterizing the gut microbiota of gestational anemia (GA) may describe a novel role of gut microbial abnormality in GA. In this study, we investigated differences in gut microbiota between GA patients and healthy pregnant women from the first trimester (n = 24 vs. 54) and the third trimester (n = 30 vs. 56) based on the 16S rRNA gene sequencing method. No statistically significant differences in α-diversity were identified between GA patients and controls in the first trimester of pregnancy, whereas the Shannon index and observed OTUs were significantly lower in GA patients than in healthy controls in the third trimester. Distance-based redundancy analysis revealed striking differences in microbial communities in the third trimester between GA patients and controls. Four genera were significantly different in relative abundance between GA patients and healthy controls, while 12 genera differentiated significantly between GA patients and healthy controls in the third trimester. At the operational taxonomic unit (OTU) level, 17 OTUs and 30 OTUs were identified to be different between GA patients and healthy controls in the first and third trimesters, respectively. Changes in gut microbial composition of GA patients suggest a potential relation with GA, and provide insights into the prediction and intervention of gestational anemia.
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Affiliation(s)
- Yan Long
- Department of Laboratory, Guangzhou Women and Children's Medical Centre, Guangzhou Medical University, Guangzhou, China
| | - Fang Liang
- Shenzhen Promegene Technology Co., Ltd, Shenzhen, China
| | - Ruochun Guo
- Shenzhen Promegene Technology Co., Ltd, Shenzhen, China
| | - Chunyan Zhu
- School of Public Health, Guangzhou Medical University, Guangzhou, China
| | - Xueqin Zhao
- Department of Laboratory, Guangzhou Women and Children's Medical Centre, Guangzhou Medical University, Guangzhou, China
| | - Xifan Wang
- Shenzhen Promegene Technology Co., Ltd, Shenzhen, China
| | - Fei Liu
- Department of Laboratory, Guangzhou Women and Children's Medical Centre, Guangzhou Medical University, Guangzhou, China
| | - Min Jiang
- Department of Laboratory, Guangzhou Women and Children's Medical Centre, Guangzhou Medical University, Guangzhou, China
| | - Qihua Liang
- Department of Laboratory, Guangzhou Women and Children's Medical Centre, Guangzhou Medical University, Guangzhou, China
| | - Shanshui Zeng
- Department of Laboratory, Guangzhou Women and Children's Medical Centre, Guangzhou Medical University, Guangzhou, China
| | - Mengru Han
- Department of Laboratory, Guangzhou Women and Children's Medical Centre, Guangzhou Medical University, Guangzhou, China
| | - Junjie Qin
- Shenzhen Promegene Technology Co., Ltd, Shenzhen, China
| | - Shenghui Li
- Shenzhen Promegene Technology Co., Ltd, Shenzhen, China
| | - Shaochuan Li
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Hongling Yang
- Department of Laboratory, Guangzhou Women and Children's Medical Centre, Guangzhou Medical University, Guangzhou, China
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Gut Microbiome Profiles and Associated Metabolic Pathways in HIV-Infected Treatment-Naïve Patients. Cells 2021; 10:cells10020385. [PMID: 33668457 PMCID: PMC7917727 DOI: 10.3390/cells10020385] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 02/09/2021] [Accepted: 02/09/2021] [Indexed: 12/18/2022] Open
Abstract
The normal composition of the intestinal microbiota is a key factor for maintaining healthy homeostasis, and accordingly, dysbiosis is well known to be present in HIV-1 patients. This article investigates the gut microbiota profile of antiretroviral therapy-naive HIV-1 patients and healthy donors living in Latin America in a cohort of 13 HIV positive patients (six elite controllers, EC, and seven non-controllers, NC) and nine healthy donors (HD). Microbiota compositions in stool samples were determined by sequencing the V3-V4 region of the bacterial 16S rRNA, and functional prediction was inferred using PICRUSt. Several taxa were enriched in EC compared to NC or HD groups, including Acidaminococcus, Clostridium methylpentosum, Barnesiella, Eubacterium coprostanoligenes, and Lachnospiraceae UCG-004. In addition, our data indicate that the route of infection is an important factor associated with changes in gut microbiome composition, and we extend these results by identifying several metabolic pathways associated with each route of infection. Importantly, we observed several bacterial taxa that might be associated with different viral subtypes, such as Succinivibrio, which were more abundant in patients infected by HIV subtype B, and Streptococcus enrichment in patients infected by subtype C. In conclusion, our data brings a significant contribution to the understanding of dysbiosis-associated changes in HIV infection and describes, for the first time, differences in microbiota composition according to HIV subtypes. These results warrant further confirmation in a larger cohort of patients.
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Mehta SD, Okal D, Otieno F, Green SJ, Nordgren RK, Huibner S, Bailey RC, Bhaumik DK, Landay A, Kaul R. Schistosomiasis is associated with rectal mucosal inflammation among Kenyan men who have sex with men. Int J STD AIDS 2021; 32:694-703. [PMID: 33533314 DOI: 10.1177/0956462420985973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Background: Schistosoma mansoni infection is hyperendemic in Lake Victoria communities and associated with cervicovaginal immune alterations and HIV acquisition. We assessed the hypothesis that schistosomiasis correlates with greater rectal inflammation in men who have sex with men (MSM) in Kisumu, Kenya. Methods: In this cross-sectional study of 38 HIV-negative MSM aged 18-35 years, schistosomiasis was diagnosed by urine circulating cathodic antigen (CCA). Microbiome was assessed in rectal swabs by 16S rRNA gene amplicon sequencing, and rectal inflammation by quartile normalized summative score of inflammatory cytokines (IL-1α, IL-1β, IL-8, and TNF-α). Elastic net (EN) regression identified taxa associated with inflammation. Multivariable linear regression estimated the association between inflammation score and schistosomiasis and bacteria identified in EN. Results: Most men were CCA positive (24/38; 63%), and median rectal inflammation score was significantly higher in these participants (11 vs. 8, p = 0.04). In multivariable regression, CCA-positive men had 2.85-point greater inflammation score (p = 0.009). The relative abundance of Succinivibrio (coefficient = -1.13, p = 0.002) and Pseudomonas (coefficient = -1.04, p = 0.001) were negatively associated with inflammation. Discussion: CCA positivity was associated with rectal mucosal inflammation, controlling for rectal microbiome composition. Given its high prevalence and contribution to inflammation, schistosomiasis may have important implications for HIV transmission in this vulnerable population.
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Affiliation(s)
- Supriya D Mehta
- Division of Epidemiology & Biostatistics, 14681University of Illinois at Chicago School of Public Health, Chicago, USA
| | - Duncan Okal
- Nyanza Reproductive Health Society, Kisumu, Kenya
| | | | - Stefan J Green
- Sequencing Core, Research Resources Center, 14681University of Illinois at Chicago, Chicago, USA
| | - Rachel K Nordgren
- Division of Epidemiology & Biostatistics, 14681University of Illinois at Chicago School of Public Health, Chicago, USA
| | - Sanja Huibner
- Division of Infectious Diseases, University of Toronto School of Medicine, Toronto, Canada
| | - Robert C Bailey
- Division of Epidemiology & Biostatistics, 14681University of Illinois at Chicago School of Public Health, Chicago, USA
| | - Dulal K Bhaumik
- Division of Epidemiology & Biostatistics, 14681University of Illinois at Chicago School of Public Health, Chicago, USA
| | - Alan Landay
- Department of Internal Medicine, 2468Rush University, Chicago, USA
| | - Rupert Kaul
- Division of Infectious Diseases, University of Toronto School of Medicine, Toronto, Canada
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38
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Illanes-Álvarez F, Márquez-Ruiz D, Márquez-Coello M, Cuesta-Sancho S, Girón-González JA. Similarities and differences between HIV and SARS-CoV-2. Int J Med Sci 2021; 18:846-851. [PMID: 33437221 PMCID: PMC7797543 DOI: 10.7150/ijms.50133] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 11/17/2020] [Indexed: 12/12/2022] Open
Abstract
In the last 50 years we have experienced two big pandemics, the HIV pandemic and the pandemic caused by SARS-CoV-2. Both pandemics are caused by RNA viruses and have reached us from animals. These two viruses are different in the transmission mode and in the symptoms they generate. However, they have important similarities: the fear in the population, increase in proinflammatory cytokines that generate intestinal microbiota modifications or NETosis production by polymorphonuclear neutrophils, among others. They have been implicated in the clinical, prognostic and therapeutic attitudes.
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Affiliation(s)
| | | | | | - Sara Cuesta-Sancho
- Unidad de Enfermedades Infecciosas, Servicio de Medicina Interna, Hospital Universitario Puerta del Mar, Facultad de Medicina, Universidad de Cádiz, Cádiz, Spain. Instituto de Investigación e Innovación en Ciencias Biomédicas de la Provincia de Cádiz (INiBICA)
| | - José Antonio Girón-González
- Unidad de Enfermedades Infecciosas, Servicio de Medicina Interna, Hospital Universitario Puerta del Mar, Facultad de Medicina, Universidad de Cádiz, Cádiz, Spain. Instituto de Investigación e Innovación en Ciencias Biomédicas de la Provincia de Cádiz (INiBICA)
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Wang Z, Usyk M, Sollecito CC, Qiu Y, Williams-Nguyen J, Hua S, Gradissimo A, Wang T, Xue X, Kurland IJ, Ley K, Landay AL, Anastos K, Knight R, Kaplan RC, Burk RD, Qi Q. Altered Gut Microbiota and Host Metabolite Profiles in Women With Human Immunodeficiency Virus. Clin Infect Dis 2020; 71:2345-2353. [PMID: 31748797 PMCID: PMC7713676 DOI: 10.1093/cid/ciz1117] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 11/20/2019] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Alterations in gut microbiota (GMB) and host metabolites have been noted in individuals with HIV. However, it remains unclear whether alterations in GMB and related functional groups contribute to disrupted host metabolite profiles in these individuals. METHODS This study included 185 women (128 with longstanding HIV infection, 88% under antiretroviral therapy; and 57 women without HIV from the same geographic location with comparable characteristics). Stool samples were analyzed by 16S rRNA V4 region sequencing, and GMB function was inferred by PICRUSt. Plasma metabolomic profiling was performed using liquid chromatography-tandem mass spectrometry, and 133 metabolites (amino acids, biogenic amines, acylcarnitines, and lipids) were analyzed. RESULTS Four predominant bacterial genera were identified as associated with HIV infection, with higher abundances of Ruminococcus and Oscillospira and lower abundances of Bifidobacterium and Collinsella in women with HIV than in those without. Women with HIV showed a distinct plasma metabolite profile, which featured elevated glycerophospholipid levels compared with those without HIV. Functional analyses also indicated that GMB lipid metabolism was enriched in women with HIV. Ruminococcus and Oscillospira were among the top bacterial genera contributing to the GMB glycerophospholipid metabolism pathway and showed positive correlations with host plasma glycerophospholipid levels. One bacterial functional capacity in the acetate and propionate biosynthesis pathway was identified to be mainly contributed by Bifidobacterium; this functional capacity was lower in women with HIV than in women without HIV. CONCLUSIONS Our integrative analyses identified altered GMB with related functional capacities that might be associated with disrupted plasma metabolite profiles in women with HIV.
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Affiliation(s)
- Zheng Wang
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Mykhaylo Usyk
- Department of Pediatrics, Albert Einstein College of Medicine, Bronx, New York, USA
| | | | - Yunping Qiu
- Department of Medicine, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Jessica Williams-Nguyen
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Simin Hua
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Ana Gradissimo
- Department of Pediatrics, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Tao Wang
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Xiaonan Xue
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Irwin J Kurland
- Department of Medicine, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Klaus Ley
- Division of Inflammation Biology, La Jolla Institute for Immunology, La Jolla, California, USA
- Department of Bioengineering, University of California, San Diego, La Jolla, California, USA
| | - Alan L Landay
- Department of Internal Medicine, Rush Medical College, Chicago, Illinois, USA
| | - Kathryn Anastos
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, New York, USA
- Department of Medicine, Albert Einstein College of Medicine, Bronx, New York, USA
- Department of Obstetrics and Gynecology and Women’s Health, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Rob Knight
- Department of Bioengineering, University of California, San Diego, La Jolla, California, USA
- Department of Pediatrics, University of California, San Diego, La Jolla, California, USA
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, California, USA
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, California, USA
| | - Robert C Kaplan
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, New York, USA
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Robert D Burk
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, New York, USA
- Department of Pediatrics, Albert Einstein College of Medicine, Bronx, New York, USA
- Department of Obstetrics and Gynecology and Women’s Health, Albert Einstein College of Medicine, Bronx, New York, USA
- Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Qibin Qi
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, New York, USA
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Tamalet C, Devaux C, Dubourg G, Colson P. Resistance to human immunodeficiency virus infection: a rare but neglected state. Ann N Y Acad Sci 2020; 1485:22-42. [PMID: 33009659 DOI: 10.1111/nyas.14452] [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: 04/15/2020] [Revised: 06/25/2020] [Accepted: 07/07/2020] [Indexed: 11/29/2022]
Abstract
The natural history of human immunodeficiency virus (HIV) infection is well understood. In most individuals sexually exposed to HIV, the risk of becoming infected depends on the viral load and on sexual practices and gender. However, a low percentage of individuals who practice frequent unprotected sexual intercourse with HIV-infected partners remain uninfected. Although the systematic study of these individuals has made it possible to identify HIV resistance factors including protective genetic patterns, such epidemiological situations remain paradoxical and not fully understood. In vitro experiments have demonstrated that peripheral blood mononuclear cells (PBMCs) from HIV-free, unexposed blood donors are not equally susceptible to HIV infection; in addition, PBMCs from highly exposed seronegative individuals are generally resistant to infection by primary HIV clinical isolates. We review the literature on permissiveness of PBMCs from healthy blood donors and uninfected hyperexposed individuals to sustained infection and replication of HIV-1 in vitro. In addition, we focus on recent evidence indicating that the gut microbiota may either contribute to natural resistance to or delay replication of HIV infected individuals.
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Affiliation(s)
- Catherine Tamalet
- IHU Méditerranée Infection and Aix-Marseille University, Institut de Recherche pour le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France
| | - Christian Devaux
- IHU Méditerranée Infection and Aix-Marseille University, Institut de Recherche pour le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France
| | - Gregory Dubourg
- IHU Méditerranée Infection and Aix-Marseille University, Institut de Recherche pour le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France
| | - Philippe Colson
- IHU Méditerranée Infection and Aix-Marseille University, Institut de Recherche pour le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France
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41
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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: 8] [Impact Index Per Article: 2.0] [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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Isnard S, Lin J, Fombuena B, Ouyang J, Varin TV, Richard C, Marette A, Ramendra R, Planas D, Raymond Marchand L, Messaoudene M, Van der Ley CP, Kema IP, Sohail Ahmed D, Zhang Y, Finkelman M, Routy B, Angel J, Ancuta P, Routy JP. Repurposing Metformin in Nondiabetic People With HIV: Influence on Weight and Gut Microbiota. Open Forum Infect Dis 2020; 7:ofaa338. [PMID: 32964062 PMCID: PMC7489545 DOI: 10.1093/ofid/ofaa338] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 08/03/2020] [Indexed: 12/13/2022] Open
Abstract
Background People with HIV (PWH) taking antiretroviral therapy (ART) may experience weight gain, dyslipidemia, increased risk of non-AIDS comorbidities, and long-term alteration of the gut microbiota. Both low CD4/CD8 ratio and chronic inflammation have been associated with changes in the gut microbiota of PWH. The antidiabetic drug metformin has been shown to improve gut microbiota composition while decreasing weight and inflammation in diabetes and polycystic ovary syndrome. Nevertheless, it remains unknown whether metformin may benefit PWH receiving ART, especially those with a low CD4/CD8 ratio. Methods In the Lilac pilot trial, we recruited 23 nondiabetic PWH receiving ART for more than 2 years with a low CD4/CD8 ratio (<0.7). Blood and stool samples were collected during study visits at baseline, after a 12-week metformin treatment, and 12 weeks after discontinuation. Microbiota composition was analyzed by 16S rDNA gene sequencing, and markers of inflammation were assessed in plasma. Results Metformin decreased weight in PWH, and weight loss was inversely correlated with plasma levels of the satiety factor GDF-15. Furthermore, metformin changed the gut microbiota composition by increasing the abundance of anti-inflammatory bacteria such as butyrate-producing species and the protective Akkermansia muciniphila. Conclusions Our study provides the first evidence that a 12-week metformin treatment decreased weight and favored anti-inflammatory bacteria abundance in the microbiota of nondiabetic ART-treated PWH. Larger randomized placebo-controlled clinical trials with longer metformin treatment will be needed to further investigate the role of metformin in reducing inflammation and the risk of non-AIDS comorbidities in ART-treated PWH.
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Affiliation(s)
- Stéphane Isnard
- Infectious Diseases and Immunity in Global Health Program, Research Institute, McGill University Health Centre, Montreal, Québec, Canada.,Chronic Viral Illness Service, McGill University Health Centre, Montreal, Québec, Canada.,CIHR Canadian HIV Trials Network, Vancouver, British Columbia, Canada
| | - John Lin
- Infectious Diseases and Immunity in Global Health Program, Research Institute, McGill University Health Centre, Montreal, Québec, Canada.,Chronic Viral Illness Service, McGill University Health Centre, Montreal, Québec, Canada
| | - Brandon Fombuena
- Infectious Diseases and Immunity in Global Health Program, Research Institute, McGill University Health Centre, Montreal, Québec, Canada.,Chronic Viral Illness Service, McGill University Health Centre, Montreal, Québec, Canada
| | - Jing Ouyang
- Infectious Diseases and Immunity in Global Health Program, Research Institute, McGill University Health Centre, Montreal, Québec, Canada.,Chronic Viral Illness Service, McGill University Health Centre, Montreal, Québec, Canada.,Chongqing Public Health Medical Center, Chongqing, China
| | - Thibault V Varin
- Institute of Nutrition and Functional Foods, Laval University, Québec City, Québec, Canada
| | - Corentin Richard
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal, Montréal, Québec, Canada
| | - André Marette
- Institute of Nutrition and Functional Foods, Laval University, Québec City, Québec, Canada.,Department of Medicine, Faculty of Medicine, Cardiology Axis of the Québec Heart and Lung Institute, Laval University, Québec City, Québec, Canada
| | - Rayoun Ramendra
- Infectious Diseases and Immunity in Global Health Program, Research Institute, McGill University Health Centre, Montreal, Québec, Canada.,Chronic Viral Illness Service, McGill University Health Centre, Montreal, Québec, Canada.,Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Delphine Planas
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal, Montréal, Québec, Canada.,Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université de Montréal, Montréal, Québec, Canada
| | | | - Meriem Messaoudene
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal, Montréal, Québec, Canada
| | - Claude P Van der Ley
- Department of Laboratory Medicine, University Medical Center Groningen, University of Groningen, the Netherlands
| | - Ido P Kema
- Department of Laboratory Medicine, University Medical Center Groningen, University of Groningen, the Netherlands
| | - Darakhshan Sohail Ahmed
- Infectious Diseases and Immunity in Global Health Program, Research Institute, McGill University Health Centre, Montreal, Québec, Canada.,Chronic Viral Illness Service, McGill University Health Centre, Montreal, Québec, Canada
| | - Yonglong Zhang
- Associates of Cape Cod Inc., Falmouth, Massachusetts, USA
| | | | - Bertrand Routy
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal, Montréal, Québec, Canada.,Division of Medicine, Department of Hemato-Oncology, University of Montreal Healthcare Center, Montreal, Quebec, Canada
| | - Jonathan Angel
- The Ottawa Hospital, University of Ottawa, Ottawa, Ontario, Canada
| | - Petronela Ancuta
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal, Montréal, Québec, Canada.,Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université de Montréal, Montréal, Québec, Canada
| | - Jean-Pierre Routy
- Infectious Diseases and Immunity in Global Health Program, Research Institute, McGill University Health Centre, Montreal, Québec, Canada.,Chronic Viral Illness Service, McGill University Health Centre, Montreal, Québec, Canada.,Division of Hematology, McGill University Health Centre, Montreal, Québec, Canada
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Piggott DA, Tuddenham S. The gut microbiome and frailty. Transl Res 2020; 221:23-43. [PMID: 32360945 PMCID: PMC8487348 DOI: 10.1016/j.trsl.2020.03.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Revised: 03/26/2020] [Accepted: 03/27/2020] [Indexed: 12/12/2022]
Abstract
The human microbiome is constituted by an extensive network of organisms that lie at the host/environment interface and transduce signals that play vital roles in human health and disease across the lifespan. Frailty is a critical aging-related syndrome marked by diminished physiological reserve and heightened vulnerability to stress, predictive of major adverse clinical outcomes including death. While recent studies suggest the microbiome may impact key pathways critical to frailty pathophysiology, direct evaluation of the microbiome-frailty relationship remains limited. In this article, we review the complex interplay of biological, behavioral, and environmental factors that may influence shifts in gut microbiome composition and function in aging populations and the putative implications of such shifts for progression to frailty. We discuss HIV infection as a key prototype for elucidating the complex pathways via which the microbiome may precipitate frailty. Finally, we review considerations for future research efforts.
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Affiliation(s)
- Damani A Piggott
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Epidemiology, Johns Hopkins University School of Public Health, Baltimore, Maryland.
| | - Susan Tuddenham
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
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44
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Abstract
Early in the HIV epidemic, lipodystrophy, characterized by subcutaneous fat loss (lipoatrophy), with or without central fat accumulation (lipohypertrophy), was recognized as a frequent condition among people living with HIV (PLWH) receiving combination antiretroviral therapy. The subsequent identification of thymidine analogue nucleoside reverse transcriptase inhibitors as the cause of lipoatrophy led to the development of newer antiretroviral agents; however, studies have demonstrated continued abnormalities in fat and/or lipid storage in PLWH treated with newer drugs (including integrase inhibitor-based regimens), with fat gain due to restoration to health in antiretroviral therapy-naive PLWH, which is compounded by the rising rates of obesity. The mechanisms of fat alterations in PLWH are complex, multifactorial and not fully understood, although they are known to result in part from the direct effects of HIV proteins and antiretroviral agents on adipocyte health, genetic factors, increased microbial translocation, changes in the adaptive immune milieu after infection, increased tissue inflammation and accelerated fibrosis. Management includes classical lifestyle alterations with a role for pharmacological therapies and surgery in some patients. Continued fat alterations in PLWH will have an important effect on lifespan, healthspan and quality of life as patients age worldwide, highlighting the need to investigate the critical uncertainties regarding pathophysiology, risk factors and management.
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45
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Gabuzda D, Jamieson BD, Collman RG, Lederman MM, Burdo TH, Deeks SG, Dittmer DP, Fox HS, Funderburg NT, Pahwa SG, Pandrea I, Wilson CC, Hunt PW. Pathogenesis of Aging and Age-related Comorbidities in People with HIV: Highlights from the HIV ACTION Workshop. Pathog Immun 2020; 5:143-174. [PMID: 32856008 PMCID: PMC7449259 DOI: 10.20411/pai.v5i1.365] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 03/10/2020] [Indexed: 12/12/2022] Open
Abstract
People with HIV (PWH) experience accentuated biological aging, as defined by markers of inflammation, immune dysfunction, and the epigenetic clock. They also have an elevated risk of multiple age-associated comorbidities. To discuss current knowledge, research gaps, and priorities in aging and age-related comorbidities in treated HIV infection, the NIH program staff organized a workshop held in Bethesda, Maryland in September 2019. This review article describes highlights of discussions led by the Pathogenesis/Basic Science Research working group that focused on three high priority topics: immunopathogenesis; the microbiome/virome; and aging and senescence. We summarize knowledge in these fields and describe key questions for research on the pathogenesis of aging and age-related comorbidities in PWH. Understanding the drivers and mechanisms underlying accentuated biological aging is a high priority that will help identify potential therapeutic targets to improve healthspan in older PWH.
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Affiliation(s)
- Dana Gabuzda
- Department of Cancer Immunology and Virology; Dana-Farber Cancer Institute; Boston, Massachusetts; Department of Neurology; Harvard Medical School; Boston, Massachusetts
| | - Beth D Jamieson
- Department of Medicine; David Geffen School of Medicine; University of California; Los Angeles, California
| | - Ronald G Collman
- Department of Medicine; University of Pennsylvania School of Medicine; Philadelphia, Pennsylvania
| | - Michael M Lederman
- Department of Medicine; Case Western Reserve University School of Medicine; Cleveland, Ohio
| | - Tricia H Burdo
- Department of Neuroscience; Lewis Katz School of Medicine; Temple University; Philadelphia, Pennsylvania
| | - Steven G Deeks
- Department of Medicine; University of California; San Francisco, California
| | - Dirk P Dittmer
- Department of Microbiology and Immunology; University of North Carolina School of Medicine; Chapel Hill, North Carolina
| | - Howard S Fox
- Department of Pharmacology and Experimental Neuroscience; University of Nebraska Medical Center; Omaha, Nebraska
| | - Nicholas T Funderburg
- Division of Medical Laboratory Science; School of Health and Rehabilitation Sciences; Ohio State University College of Medicine; Columbus, Ohio
| | - Savita G Pahwa
- Department of Microbiology and Immunology; University of Miami Miller School of Medicine; Miami, Florida
| | - Ivona Pandrea
- Department of Microbiology and Molecular Genetics; School of Medicine; University of Pittsburgh; Pittsburgh, Pennsylvania
| | - Cara C Wilson
- Department of Medicine; Division of Infectious Diseases; University of Colorado Anschutz Medical Campus; Aurora, Colorado
| | - Peter W Hunt
- Department of Medicine; University of California; San Francisco, California
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46
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Vujkovic-Cvijin I, Somsouk M. HIV and the Gut Microbiota: Composition, Consequences, and Avenues for Amelioration. Curr HIV/AIDS Rep 2020; 16:204-213. [PMID: 31037552 DOI: 10.1007/s11904-019-00441-w] [Citation(s) in RCA: 89] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
PURPOSE OF REVIEW We discuss recent advances in understanding of gut bacterial microbiota composition in HIV-infected subjects and comment on controversies. We discuss the putative effects of microbiota shifts on systemic inflammation and HIV disease progression and potential mechanisms, as well as ongoing strategies being developed to modulate the gut microbiota in humans for amelioration of infectious and inflammatory diseases. RECENT FINDINGS Lifestyle and behavioral factors relevant to HIV infection studies have independent effects on the microbiota. Microbial metabolism of immunomodulatory compounds and direct immune stimulation by translocation of microbes are putative mechanisms contributing to HIV disease. Fecal microbiota transplantation, microbial enzyme inhibition, phage therapy, and rationally selected probiotic cocktails have emerged as promising strategies for microbiota modulation. Numerous surveys of the HIV gut microbiota matched for lifestyle factors suggest consistent shifts in gut microbiota composition among HIV-infected subjects. Evidence exists for a complex pathogenic role of the gut microbiota in HIV disease progression, warranting further study.
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Affiliation(s)
- Ivan Vujkovic-Cvijin
- Metaorganism Immunity Section, National Institute of Allergy & Infectious Disease, National Institutes of Health, Bethesda, MD, USA.
| | - Ma Somsouk
- Division of Gastroenterology, University of California, San Francisco, CA, USA.
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47
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Abstract
Recent studies have raised interest in the possibility that dysbiosis of the gut microbiome (i.e., the communities of bacteria residing in the intestine) in HIV-infected patients could contribute to chronic immune activation, and, thus, to elevated mortality and increased risk of inflammation-related clinical diseases (e.g., stroke, cardiovascular disease, cancer, long-bone fractures, and renal dysfunction) found even in those on effective antiretroviral therapy. Yet, to date, a consistent pattern of HIV-associated dysbiosis has not been identified. What is becoming clear, however, is that status as a man who has sex with men (MSM) may profoundly impact the structure of the gut microbiota, and that this factor likely confounded many HIV-related intestinal microbiome studies. However, what factor associated with MSM status drives these gut microbiota-related changes is unclear, and what impact, if any, these changes may have on the health of MSM is unknown. In this review, we outline available data on changes in the structure of the gut microbiome in HIV, based on studies that controlled for MSM status. We then examine what is known regarding the gut microbiota in MSM, and consider possible implications for research and the health of this population. Lastly, we discuss knowledge gaps and needed future studies.
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Affiliation(s)
- Susan Tuddenham
- Division of Infectious Diseases, Johns Hopkins School of
Medicine, Baltimore, MD
| | - Wei Li Koay
- Department of Infectious Disease, Children’s
National Hospital, Washington, D.C.;,School of Medicine and Health Sciences, George Washington
University, Washington, D.C
| | - Cynthia Sears
- Division of Infectious Diseases, Johns Hopkins School of
Medicine, Baltimore, MD
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48
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Luján JA, Rugeles MT, Taborda NA. Contribution of the Microbiota to Intestinal Homeostasis and its Role in the Pathogenesis of HIV-1 Infection. Curr HIV Res 2020; 17:13-25. [PMID: 30854974 DOI: 10.2174/1570162x17666190311114808] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 02/25/2019] [Accepted: 03/06/2019] [Indexed: 12/18/2022]
Abstract
During HIV infection, massive destruction of CD4+ T cells ensues, preferentially depleting the Th17 subset at the gut-associated lymphoid tissue (GALT), leading to a loss of mucosal integrity and an increase in cell permeability. This process favors microbial translocation between the intestinal lumen and the circulatory system, contributing to persistent immune activation and chronic inflammation characteristic of HIV infection. Thus, the gut microbiota plays an integral role in maintaining the structure and function of the mucosal barrier, a critical factor for immune homeostasis. However, in the context of HIV infection, changes in the gut microbiota have been reported and have been linked to disease progression. Here, we review evidence for the role of the gut microbiota in intestinal homeostasis, its contribution to HIV pathogenesis, as well as its use in the development of therapeutic strategies.
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Affiliation(s)
- Jorge A Luján
- Grupo Inmunovirologia, Facultad de Medicina. Universidad de Antioquia, Medellin, Colombia
| | - Maria T Rugeles
- Grupo Inmunovirologia, Facultad de Medicina. Universidad de Antioquia, Medellin, Colombia
| | - Natalia A Taborda
- Grupo Inmunovirologia, Facultad de Medicina. Universidad de Antioquia, Medellin, Colombia.,Grupo de Investigaciones Biomédicas, Facultad de Ciencias de la Salud, Corporación Universitaria Remington, Medellín, Colombia
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49
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Tuddenham SA, Koay WLA, Zhao N, White JR, Ghanem KG, Sears CL. The Impact of Human Immunodeficiency Virus Infection on Gut Microbiota α-Diversity: An Individual-level Meta-analysis. Clin Infect Dis 2020; 70:615-627. [PMID: 30921452 PMCID: PMC7319268 DOI: 10.1093/cid/ciz258] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Accepted: 03/22/2019] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Whether human immunodeficiency virus (HIV) infection impacts gut microbial α-diversity is controversial. We reanalyzed raw 16S ribosomal RNA (rRNA) gene sequences and metadata from published studies to examine α-diversity measures between HIV-uninfected (HIV-) and HIV-infected (HIV+) individuals. METHODS We conducted a systematic review and individual level meta-analysis by searching Embase, Medline, and Scopus for original research studies (inception to 31 December 2017). Included studies reported 16S rRNA gene sequences of fecal samples from HIV+ patients. Raw sequence reads and metadata were obtained from public databases or from study authors. Raw reads were processed through standardized pipelines with use of a high-resolution taxonomic classifier. The χ2 test, paired t tests, and generalized linear mixed models were used to relate α-diversity measures and clinical metadata. RESULTS Twenty-two studies were identified with 17 datasets available for analysis, yielding 1032 samples (311 HIV-, 721 HIV+). HIV status was associated with a decrease in measures of α-diversity (P < .001). However, in stratified analysis, HIV status was associated with decreased α-diversity only in women and in men who have sex with women (MSW) but not in men who have sex with men (MSM). In analyses limited to women and MSW, controlling for HIV status, women displayed increased α-diversity compared with MSW. CONCLUSIONS Our study suggests that HIV status, sexual risk category, and gender impact gut microbial community α-diversity. Future studies should consider MSM status in gut microbiome analyses.
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Affiliation(s)
| | - Wei Li A Koay
- Children’s National Medical Center, Baltimore, Maryland
- George Washington University, Washington, District of Columbia, Baltimore, Maryland
| | - Ni Zhao
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | | | - Khalil G Ghanem
- Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Cynthia L Sears
- Johns Hopkins University School of Medicine, Baltimore, Maryland
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50
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Gabrielli S, Furzi F, Fontanelli Sulekova L, Taliani G, Mattiucci S. Occurrence of Blastocystis-subtypes in patients from Italy revealed association of ST3 with a healthy gut microbiota. Parasite Epidemiol Control 2020; 9:e00134. [PMID: 32258445 PMCID: PMC7096745 DOI: 10.1016/j.parepi.2020.e00134] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 12/27/2019] [Accepted: 12/30/2019] [Indexed: 12/18/2022] Open
Abstract
An epidemiological survey on Blastocystis was carried out enrolling a total of 2524 subjects referred to the Umberto I Academic Hospital in Rome, for the routine parasitological exams, during 2017–2018. The studied population included a sample of immunocompromised individuals (N = 130) followed at the same hospital. DNA sequencing of the small subunit rRNA gene (SSU rDNA) locus was performed on samples positive to the coproparasitological analysis to molecular characterize the Blastocystis-subtypes. Microscopical analysis detected Blastocystis in 192/2524 (7.6%) of the enrolled subjects. It was the organism most frequently identified in the analysed faecal samples diagnosed in single infection (5.6%) or in co-infection with other enteric protozoa (2%). Furthermore, it was found mainly in immunocompromised patients (22.3%) compared to immunocompetent ones (6.8%). As expected, ST3 was the most occurring subtype identified in 40% of the subjects, followed by ST1 (29%), ST2 (16%), ST4 (12%), and ST7 (3%). Next-generation sequencing (NGS) of the 16S rDNA was performed on a sub-sample of Blastocystis-ST3-carriers, homogenous by age and gender, as well as on Blastocystis-free subjects, to profile and compare their gut bacterial composition. A higher bacterial diversity was found in ST3-Blastocystis-carriers, which exhibited a high abundance of Prevotella, Methanobrevibacter and Ruminococcus while, a high percentage of Bacteroides was found in Blastocystis-free subjects. This study evidenced the presence of Blastocystis in 7.6% of faecal samples in Italy and a high circulation of the protist among immunocompromised patients (22.3%). Molecular characterization of positive samples evidenced the occurrence of five different subtypes, including zoonotic ST such as the ST7, highlighting the risk of transmission from animals. Study of the gut microbiota composition confirms previous evidences according to which, the colonisation by Blastocystis would be linked with an eubiotic gut characterized by potentially beneficial species such as Prevotella and Ruminococcus, rather than with a dysbiotic state, with a high abundance of Enterobacteriaceae, and corroborated the role of the protist as “an old friend” of the human gut. Microscopical analysis detected Blastocystis in 7.6% subjects in Italy. Molecular methods allowed the identification of 5 STs (ST1, ST2, ST3, ST4, ST7). ST3 resulted the most frequent subtype. NGS of the 16S rDNA gene was performed in Blastocystis-ST3-carriers. Blastocystis-ST3 resulted correlated to an eubiotic gut characterized by potentially beneficial species.
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Affiliation(s)
- Simona Gabrielli
- Department of Public Health and Infectious Diseases, "Sapienza-University of Rome", Piazzale Aldo Moro 5, 00185 Rome, Italy
- Diagnostic Parasitology laboratory, Academic Hospital "Policlinico Umberto I", Rome, Viale del Policlinico 155, 00185 Rome, Italy
| | - Federica Furzi
- Department of Public Health and Infectious Diseases, "Sapienza-University of Rome", Piazzale Aldo Moro 5, 00185 Rome, Italy
| | | | - Gloria Taliani
- Department of Translation and Precision Medicine, "Sapienza University of Rome", 00185 Rome, Italy
| | - Simonetta Mattiucci
- Department of Public Health and Infectious Diseases, "Sapienza-University of Rome", Piazzale Aldo Moro 5, 00185 Rome, Italy
- Diagnostic Parasitology laboratory, Academic Hospital "Policlinico Umberto I", Rome, Viale del Policlinico 155, 00185 Rome, Italy
- Corresponding author at: Department of Public Health and Infectious Diseases, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy.
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