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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; 19:261-267. [PMID: 38874425 DOI: 10.1097/coh.0000000000000867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 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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Ortiz AM, Brenchley JM. Untangling the role of the microbiome across the stages of HIV disease. Curr Opin HIV AIDS 2024; 19:221-227. [PMID: 38935047 PMCID: PMC11305932 DOI: 10.1097/coh.0000000000000870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2024]
Abstract
PURPOSE OF REVIEW The primate microbiome consists of bacteria, eukaryotes, and viruses that dynamically shape and respond to host health and disease. Understanding how the symbiotic relationship between the host and microbiome responds to HIV has implications for therapeutic design. RECENT FINDINGS Advances in microbiome identification technologies have expanded our ability to identify constituents of the microbiome and to infer their functional capacity. The dual use of these technologies and animal models has allowed interrogation into the role of the microbiome in lentiviral acquisition, vaccine efficacy, and the response to antiretrovirals. Lessons learned from such studies are now being harnessed to design microbiome-based interventions. SUMMARY Previous studies considering the role of the microbiome in people living with HIV largely described viral acquisition as an intrusion on the host:microbiome interface. Re-framing this view to consider HIV as a novel, albeit unwelcome, component of the microbiome may better inform the research and development of pre and postexposure prophylaxes.
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Affiliation(s)
- Alexandra M Ortiz
- Barrier Immunity Section, Laboratory of Viral Diseases, Division of Intramural Research, NIAID, NIH, Bethesda, Maryland, USA
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3
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Narayanan A, Kieri O, Vesterbacka J, Manoharan L, Chen P, Ghorbani M, Ljunggren HG, Sällberg Chen M, Aleman S, Sönnerborg A, Ray S, Nowak P. Exploring the interplay between antiretroviral therapy and the gut-oral microbiome axis in people living with HIV. Sci Rep 2024; 14:17820. [PMID: 39090139 PMCID: PMC11294597 DOI: 10.1038/s41598-024-68479-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Accepted: 07/24/2024] [Indexed: 08/04/2024] Open
Abstract
The gut and oral microbiome is altered in people living with HIV (PLWH). While antiretroviral treatment (ART) is pivotal in restoring immune function in PLWH, several studies have identified an association between specific antiretrovirals, particularly integrase inhibitors (INSTI), and weight gain. In our study, we explored the differences in the oral and gut microbiota of PLWH under different ART regimens, and its correlation to Body Mass Index (BMI). Fecal and salivary samples were collected from PLWH (n = 69) and healthy controls (HC, n = 80). We performed taxonomy analysis to determine the microbial composition and relationship between microbial abundance and ART regimens, BMI, CD4+T-cell count, CD4/CD8 ratio, and ART duration. PLWH showed significantly lower richness compared to HC in both the oral and gut environment. The gut microbiome composition of INSTI-treated individuals was enriched with Faecalibacterium and Bifidobacterium, whereas non-nucleotide reverse transcriptase inhibitor (NNRTI)-treated individuals were enriched with Gordonibacter, Megasphaera, and Staphylococcus. In the oral microenvironment, Veillonella was significantly more abundant in INSTI-treated individuals and Fusobacterium and Alloprevotella in the NNRTI-treated individuals. Furthermore, Bifidobacterium and Dorea were enriched in gut milieu of PLWH with high BMI. Collectively, our findings identify distinct microbial profiles, which are associated with different ART regimens and BMI in PLWH on successful ART, thereby highlighting significant effects of specific antiretrovirals on the microbiome.
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Affiliation(s)
- Aswathy Narayanan
- Department of Medicine Huddinge, Division of Infectious Diseases, Karolinska Institutet, Stockholm, Sweden.
| | - Oscar Kieri
- Department of Medicine Huddinge, Division of Infectious Diseases, Karolinska Institutet, Stockholm, Sweden
- Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Jan Vesterbacka
- Department of Medicine Huddinge, Division of Infectious Diseases, Karolinska Institutet, Stockholm, Sweden
- Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Lokeshwaran Manoharan
- Department of Laboratory Medicine, National Bioinformatics Infrastructure Sweden (NBIS), SciLife, Lund University, Lund, Sweden
| | - Puran Chen
- Department of Medicine Huddinge, Center for Infectious Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Mahin Ghorbani
- Department of Dental Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Laboratory Medicine, Division of Pathology, ANA Futura, Karolinska Institutet, 141 52, Stockholm, Sweden
| | - Hans-Gustaf Ljunggren
- Department of Medicine Huddinge, Center for Infectious Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Margaret Sällberg Chen
- Department of Dental Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Laboratory Medicine, Division of Pathology, ANA Futura, Karolinska Institutet, 141 52, Stockholm, Sweden
| | - Soo Aleman
- Department of Medicine Huddinge, Division of Infectious Diseases, Karolinska Institutet, Stockholm, Sweden
- Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Anders Sönnerborg
- Department of Medicine Huddinge, Division of Infectious Diseases, Karolinska Institutet, Stockholm, Sweden
- Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
- Department of Laboratory Medicine, Division of Clinical Microbiology, ANA Futura, Karolinska Institutet, 141 52, Stockholm, Sweden
| | - Shilpa Ray
- Department of Medicine Huddinge, Division of Infectious Diseases, Karolinska Institutet, Stockholm, Sweden.
| | - Piotr Nowak
- Department of Medicine Huddinge, Division of Infectious Diseases, Karolinska Institutet, Stockholm, Sweden
- Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
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4
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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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Trøseid M, Nielsen SD, Vujkovic-Cvijin I. Gut microbiome and cardiometabolic comorbidities in people living with HIV. MICROBIOME 2024; 12:106. [PMID: 38877521 PMCID: PMC11177534 DOI: 10.1186/s40168-024-01815-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 04/12/2024] [Indexed: 06/16/2024]
Abstract
BACKGROUND Despite modern antiretroviral therapy (ART), people living with HIV (PLWH) have increased relative risk of inflammatory-driven comorbidities, including cardiovascular disease (CVD). The gut microbiome could be one of several driving factors, along with traditional risk factors and HIV-related risk factors such as coinfections, ART toxicity, and past immunodeficiency. RESULTS PLWH have an altered gut microbiome, even after adjustment for known confounding factors including sexual preference. The HIV-related microbiome has been associated with cardiometabolic comorbidities, and shares features with CVD-related microbiota profiles, in particular reduced capacity for short-chain fatty acid (SCFA) generation. Substantial inter-individual variation has so far been an obstacle for applying microbiota profiles for risk stratification. This review covers updated knowledge and recent advances in our understanding of the gut microbiome and comorbidities in PLWH, with specific focus on cardiometabolic comorbidities and inflammation. It covers a comprehensive overview of HIV-related and comorbidity-related dysbiosis, microbial translocation, and microbiota-derived metabolites. It also contains recent data from studies in PLWH on circulating metabolites related to comorbidities and underlying gut microbiota alterations, including circulating levels of the SCFA propionate, the histidine-analogue imidazole propionate, and the protective metabolite indole-3-propionic acid. CONCLUSIONS Despite recent advances, the gut microbiome and related metabolites are not yet established as biomarkers or therapeutic targets. The review gives directions for future research needed to advance the field into clinical practice, including promises and pitfalls for precision medicine. Video Abstract.
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Affiliation(s)
- Marius Trøseid
- Research Institute of Internal Medicine, Oslo University Hospital Rikshospitalet, Oslo, Norway.
- Section for Clinical Immunology and Infectious Diseases, Oslo University Hospital Rikshospitalet, Oslo, Norway.
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway.
| | - Susanne Dam Nielsen
- Department of Infectious Diseases, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, Blegdamsvej 3B, Copenhagen, 2200, Denmark
- Department of Surgical Gastroenterology and Transplantation, Rigshospitalet, University of Copenhagen, Blegdamsvej 9, Copenhagen Oe, 2100, Denmark
| | - Ivan Vujkovic-Cvijin
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Karsh Division of Gastroenterology & Hepatology, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- F. Widjaja Inflammatory Bowel Disease Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
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6
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Rubio Garcia E, Casadellà M, Parera M, Vila J, Paredes R, Noguera-Julian M. Gut resistome linked to sexual preference and HIV infection. BMC Microbiol 2024; 24:201. [PMID: 38851693 PMCID: PMC11162057 DOI: 10.1186/s12866-024-03335-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 05/16/2024] [Indexed: 06/10/2024] Open
Abstract
BACKGROUND People living with HIV (PLWH) are at increased risk of acquisition of multidrug resistant organisms due to higher rates of predisposing factors. The gut microbiome is the main reservoir of the collection of antimicrobial resistance determinants known as the gut resistome. In PLWH, changes in gut microbiome have been linked to immune activation and HIV-1 associated complications. Specifically, gut dysbiosis defined by low microbial gene richness has been linked to low Nadir CD4 + T-cell counts. Additionally, sexual preference has been shown to strongly influence gut microbiome composition in PLWH resulting in different Prevotella or Bacteroides enriched enterotypes, in MSM (men-who-have-sex-with-men) or no-MSM, respectively. To date, little is known about gut resistome composition in PLWH due to the scarcity of studies using shotgun metagenomics. The present study aimed to detect associations between different microbiome features linked to HIV-1 infection and gut resistome composition. RESULTS Using shotgun metagenomics we characterized the gut resistome composition of 129 HIV-1 infected subjects showing different HIV clinical profiles and 27 HIV-1 negative controls from a cross-sectional observational study conducted in Barcelona, Spain. Most no-MSM showed a Bacteroides-enriched enterotype and low microbial gene richness microbiomes. We did not identify differences in resistome diversity and composition according to HIV-1 infection or immune status. However, gut resistome was more diverse in MSM group, Prevotella-enriched enterotype and gut micorbiomes with high microbial gene richness compared to no-MSM group, Bacteroides-enriched enterotype and gut microbiomes with low microbial gene richness. Additionally, gut resistome beta-diversity was different according to the defined groups and we identified a set of differentially abundant antimicrobial resistance determinants based on the established categories. CONCLUSIONS Our findings reveal a significant correlation between gut resistome composition and various host variables commonly associated with gut microbiome, including microbiome enterotype, microbial gene richness, and sexual preference. These host variables have been previously linked to immune activation and lower Nadir CD4 + T-Cell counts, which are prognostic factors of HIV-related comorbidities. This study provides new insights into the relationship between antibiotic resistance and clinical characteristics of PLWH.
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Affiliation(s)
- Elisa Rubio Garcia
- Department of Microbiology, CDB, Hospital Clinic, University of Barcelona, Barcelona, Spain.
- Molecuar Core Facilty, Hospital Clínic de Barcelona, Barcelona, Spain.
- ISGlobal Barcelona Institute for Global Health, Barcelona, Spain.
| | | | | | - Jordi Vila
- Department of Microbiology, CDB, Hospital Clinic, University of Barcelona, Barcelona, Spain
- ISGlobal Barcelona Institute for Global Health, Barcelona, Spain
- Infectious Disease Networking Biomedical Research Center (CIBERINFEC), Carlos III Health Institute, Madrid, Spain
| | - Roger Paredes
- IrsiCaixa, Ctra de Canyet S/N, 08916, Badalona, Spain
- Universitat de Vic-Universitat Central de Catalunya, Vic, Spain
- Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
- Department of Infectious Diseasest &, Lluita Contra La SIDA Foundation, Hospital Universitari Germans Trias I Pujol, Badalona, Spain
- Infectious Disease Networking Biomedical Research Center (CIBERINFEC), Carlos III Health Institute, Madrid, Spain
| | - Marc Noguera-Julian
- IrsiCaixa, Ctra de Canyet S/N, 08916, Badalona, Spain
- Universitat de Vic-Universitat Central de Catalunya, Vic, Spain
- Infectious Disease Networking Biomedical Research Center (CIBERINFEC), Carlos III Health Institute, Madrid, Spain
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Nganou-Makamdop K, Douek DC. The Gut and the Translocated Microbiomes in HIV Infection: Current Concepts and Future Avenues. Pathog Immun 2024; 9:168-194. [PMID: 38807656 PMCID: PMC11132393 DOI: 10.20411/pai.v9i1.693] [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: 03/05/2024] [Accepted: 05/03/2024] [Indexed: 05/30/2024] Open
Abstract
It is widely acknowledged that HIV infection results in disruption of the gut's mucosal integrity partly due a profound loss of gastrointestinal CD4+ T cells that are targets of the virus. In addition, systemic inflammation and immune activation that drive disease pathogenesis are reduced but not normalized by antiretroviral therapy (ART). It has long been postulated that through the process of microbial translocation, the gut microbiome acts as a key driver of systemic inflammation and immune recovery in HIV infection. As such, many studies have aimed at characterizing the gut microbiota in order to unravel its influence in people with HIV and have reported an association between various bacterial taxa and inflammation. This review assesses both contra-dictory and consistent findings among several studies in order to clarify the overall mechanisms by which the gut microbiota in adults may influence immune recovery in HIV infection. Independently of the gut microbiome, observations made from analysis of microbial products in the blood provide direct insight into how the translocated microbiome may drive immune recovery. To help better understand strengths and limitations of the findings reported, this review also highlights the numerous factors that can influence microbiome studies, be they experimental methodologies, and host-intrinsic or host-extrinsic factors. Altogether, a fuller understanding of the interplay between the gut microbiome and immunity in HIV infection may contribute to preventive and therapeutic approaches.
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Affiliation(s)
| | - Daniel C. Douek
- Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
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Cossarini F, Shang J, Krek A, Al-Taie Z, Hou R, Canales-Herrerias P, Tokuyama M, Tankelevich M, Tillowiz A, Jha D, Livanos AE, Leyre L, Uzzan M, Martinez-Delgado G, Tylor M, Sharma K, Bourgonje AR, Cruz M, Ioannou G, Dawson T, D'Souza D, Kim-Schulze S, Akm A, Aberg JA, Chen BK, Gnjatic S, Polydorides AD, Cerutti A, Argmann C, Vujkovic-Cvijin I, Suarez-Farinas M, Petralia F, Faith JJ, Mehandru S. HIV-1 infection is associated with depletion of germinal center B cells and a decrease in IgA + plasma cells in the GI tract. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.17.590425. [PMID: 38826293 PMCID: PMC11142040 DOI: 10.1101/2024.05.17.590425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Gastrointestinal (GI) B cells and plasma cells (PCs), critical to mucosal homeostasis, play an important role in the host response to HIV-1 infection. Here, high resolution mapping of human B cells and PCs from colon and ileum during both viremic and suppressed HIV-1 infection identified a significant reduction in germinal center (GC) B cells and Follicular Dendritic Cells (FDCs) during HIV-1 viremia. Further, IgA + PCs, the major cellular output of intestinal GCs were significantly reduced during viremic HIV-1 infection. PC-associated transcriptional perturbations, including type I interferon signaling persisted in antiretroviral therapy (ART) treated individuals, suggesting ongoing disruption of the intestinal immune milieu during ART. GI humoral immune perturbations associated with changes in intestinal microbiome composition and systemic inflammation. Herein, we highlight a key immune defect in the GI mucosa due to HIV-1 viremia, with major implications. One Sentence Summary Major perturbations in intestinal GC dynamics in viremic HIV-1 infection relate to reduced IgA + plasma cells, systemic inflammation and microbiota changes.
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Salvador PBU, Altavas PJDR, del Rosario MAS, Ornos EDB, Dalmacio LMM. Alterations in the Gut Microbiome Composition of People Living with HIV in the Asia-Pacific Region: A Systematic Review. Clin Pract 2024; 14:846-861. [PMID: 38804398 PMCID: PMC11130874 DOI: 10.3390/clinpract14030066] [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: 04/03/2024] [Revised: 04/25/2024] [Accepted: 05/06/2024] [Indexed: 05/29/2024] Open
Abstract
Human immunodeficiency virus (HIV) infection continues to present a global health issue. Recent studies have explored the potential role of the gut microbiome in HIV infection for novel therapeutic approaches. We investigated the gut microbiome composition of people living with HIV (PLHIV) in the Asia-Pacific region. This review was conducted following the Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) guidelines. An electronic search was conducted in the PubMed/MEDLINE, Scopus, and ScienceDirect databases using keywords such as "HIV", "PLHIV", "AIDS", "gut microbiome", "gut dysbiosis", and "metagenomics". Only peer-reviewed and full-text studies published in English were included. A total of 15 studies from the Asia-Pacific region were included for analysis. Compared to healthy controls, PLHIV showed an increased abundance of Proteobacteria and its genera, which may be considered pathobionts, and decreased abundances of Bacteroidetes and several genera under Firmicutes with known short-chain fatty acid and immunoregulatory activities. Predominant taxa such as Ruminococcaceae and Prevotellaceae were also associated with clinical factors such as CD4 count, the CD4/CD8 ratio, and inflammatory cytokines. This review highlights gut microbiome changes among PLHIV in the Asia-Pacific region, indicating potential bacterial signatures for prognostication. The partial restoration of the microbiome toward beneficial taxa may ensure the long-term success of treatment, promoting immune recovery while maintaining viral load suppression.
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Affiliation(s)
- Paul Benedic U. Salvador
- Department of Biochemistry and Molecular Biology, College of Medicine, University of the Philippines Manila, Manila 1000, Philippines; (P.J.d.R.A.); (L.M.M.D.)
| | - Patrick Josemaria d. R. Altavas
- Department of Biochemistry and Molecular Biology, College of Medicine, University of the Philippines Manila, Manila 1000, Philippines; (P.J.d.R.A.); (L.M.M.D.)
| | - Mark Angelo S. del Rosario
- Multi-Omics Research Program for Health, College of Medicine, University of the Philippines Manila, Manila 1000, Philippines; (M.A.S.d.R.); (E.D.B.O.)
| | - Eric David B. Ornos
- Multi-Omics Research Program for Health, College of Medicine, University of the Philippines Manila, Manila 1000, Philippines; (M.A.S.d.R.); (E.D.B.O.)
- Department of Medical Microbiology, College of Public Health, University of the Philippines Manila, Manila 1000, Philippines
| | - Leslie Michelle M. Dalmacio
- Department of Biochemistry and Molecular Biology, College of Medicine, University of the Philippines Manila, Manila 1000, Philippines; (P.J.d.R.A.); (L.M.M.D.)
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Guo Y, Wang W, Yu Y, Sun X, Zhang B, Wang Y, Cao J, Wen S, Wang X, Li Y, Cai S, Wu R, Duan W, Xia W, Wei F, Duan J, Dong H, Guo S, Zhang F, Sun Z, Huang X. Crosstalk between human immunodeficiency virus infection and salivary bacterial function in men who have sex with men. Front Cell Infect Microbiol 2024; 14:1341545. [PMID: 38779561 PMCID: PMC11109444 DOI: 10.3389/fcimb.2024.1341545] [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: 11/20/2023] [Accepted: 04/22/2024] [Indexed: 05/25/2024] Open
Abstract
Background Engaging in anal sexual intercourse markedly increases the risk of developing HIV among men who have sex with men (MSM); oral sexual activities tend to uniquely introduce gut-derived microbes to salivary microbiota, which, combined with an individual's positive HIV status, may greatly perturb oral microecology. However, till date, only a few published studies have addressed this aspect. Methods Based on 16S rRNA sequencing data of bacterial taxa, MicroPITA picks representative samples for metagenomic analysis, effectively revealing how the development and progression of the HIV disease influences oral microbiota in MSM. Therefore, we collected samples from 11 HIV-negative and 44 HIV-positive MSM subjects (stage 0 was defined by HIV RNA positivity, but negative or indeterminate antibody status; stages 1, 2, and 3 were defined by CD4+ T lymphocyte counts ≥ 500, 200-499, and ≤ 200 or opportunistic infection) and selected 25 representative saliva samples (5 cases/stage) using MicroPITA. Metagenomic sequencing analysis were performed to explore whether positive HIV status changes salivary bacterial KEGG function and metabolic pathway in MSM. Results The core functions of oral microbiota were maintained across each of the five groups, including metabolism, genetic and environmental information processing. All HIV-positive groups displayed KEGG functions of abnormal proliferation, most prominently at stage 0, and others related to metabolism. Clustering relationship analysis tentatively identified functional relationships between groups, with bacterial function being more similar between stage 0-control groups and stage 1-2 groups, whereas the stage 3 group exhibited large functional changes. Although we identified most metabolic pathways as being common to all five groups, several unique pathways formed clusters for certain groups; the stage 0 group had several, while the stage 2 and 3 groups had few, such clusters. The abundance of K03046 was positively correlated with CD4 counts. Conclusion As HIV progresses, salivary bacterial function and metabolic pathways in MSM progressively changes, which may be related to HIV promoting abnormal energy metabolism and exacerbate pathogen virulence. Further, infection and drug resistance of acute stage and immune cell destruction of AIDS stage were abnormally increased, predicting an increased risk for MSM individuals to develop systemic and oral diseases.
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Affiliation(s)
- Ying Guo
- Department of Stomatology, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Wenjing Wang
- Clinical and Research Center for Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Yixi Yu
- Department of Stomatology, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Xintong Sun
- Department of Stomatology, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Baojin Zhang
- Department of Stomatology, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Yan Wang
- Department of Stomatology, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Jie Cao
- Department of Stomatology, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Shuo Wen
- Department of Stomatology, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Xin Wang
- Department of Stomatology, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Yuchen Li
- Department of Stomatology, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Siyu Cai
- Center for Clinical Epidemiology and Evidence-Based Medicine, Beijing Children’s Hospital, Capital Medical University, Beijing, China
| | - Ruojun Wu
- Harvard School of Dental Medicine, Boston, MA, United States
| | - Wenshan Duan
- Clinical and Research Center for Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Wei Xia
- Clinical and Research Center for Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Feili Wei
- Beijing Institute of Hepatology, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Junyi Duan
- Clinical and Research Center for Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Haozhi Dong
- Department of Stomatology, Beijing Daxing District Hospital of Integrated Chinese and Western Medicine, Beijing, China
| | - Shan Guo
- Beijing Institute of Hepatology, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Fengqiu Zhang
- Department of Periodontology, Beijing Stomatological Hospital, Capital Medical University, Beijing, China
| | - Zheng Sun
- Department of Oral Medicine, Beijing Stomatological Hospital, Capital Medical University, Beijing, China
| | - Xiaojie Huang
- Clinical and Research Center for Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing, China
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Wang Z, Zhen C, Guo X, Qu M, Zhang C, Song J, Fan X, Huang H, Xu R, Zhang J, Yuan J, Hong W, Li J, Wang F, Jiao Y, Linghu E. Landscape of gut mucosal immune cells showed gap of follicular or memory B cells into plasma cells in immunological non-responders. Clin Transl Med 2024; 14:e1699. [PMID: 38783408 PMCID: PMC11116468 DOI: 10.1002/ctm2.1699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 04/24/2024] [Accepted: 04/29/2024] [Indexed: 05/25/2024] Open
Abstract
BACKGROUND The gut is an important site for human immunodeficiency virus (HIV) infection and immune responses. The role of gut mucosal immune cells in immune restoration in patients infected with HIV undergoing antiretroviral therapy remains unclear. METHODS Ileocytes, including 54 475 immune cells, were obtained from colonoscopic biopsies of five HIV-negative controls, nine immunological responders (IRs), and three immunological non-responders (INRs) and were analyzed using single-cell RNA sequencing. Immunohistochemical assays were performed for validation. The 16S rRNA gene was amplified using PCR in faecal samples to analyze faecal microbiota. Flow cytometry was used to analyze CD4+ T-cell counts and the activation of T cells. RESULTS This study presents a global transcriptomic profile of the gut mucosal immune cells in patients infected with HIV. Compared with the IRs, the INRs exhibited a lower proportion of gut plasma cells, especially the IGKC+IgA+ plasma cell subpopulation. IGKC+IgA+ plasma cells were negatively associated with enriched f. Prevotellaceae the INRs and negatively correlated with the overactivation of T cells, but they were positively correlated with CD4+ T-cell counts. The INRs exhibited a higher proportion of B cells than the IRs. Follicular and memory B cells were significantly higher in the INRs. Reduced potential was observed in the differentiation of follicular or memory B cells into gut plasma cells in INRs. In addition, the receptor-ligand pairs CD74_MIF and CD74_COPA of memory B/ follicular helper T cells were significantly reduced in the INRs, which may hinder the differentiation of memory and follicular B cells into plasma cells. CONCLUSIONS Our study shows that plasma cells are dysregulated in INRs and provides an extensive resource for deciphering the immune pathogenesis of HIV in INRs. KEY POINTS An investigation was carried out at the single-cell-level to analyze gut mucosal immune cells alterations in PLWH after ART. B cells were significantly increased and plasma cells were significantly decreased in the INRs compared to the IRs and NCs. There are gaps in the transition from gut follicular or memory B cellsinto plasma cells in INRs.
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Affiliation(s)
- Zerui Wang
- Senior Department of Gastroenterologythe First Medical Center of Chinese PLA General HospitalBeijingChina
| | - Cheng Zhen
- Senior Department of Infectious Diseasesthe Fifth Medical Centre of Chinese PLA General HospitalNational Clinical Research Center for Infectious DiseasesBeijingChina
| | - Xiaoyan Guo
- Senior Department of Infectious Diseasesthe Fifth Medical Centre of Chinese PLA General HospitalNational Clinical Research Center for Infectious DiseasesBeijingChina
| | - Mengmeng Qu
- Senior Department of Infectious Diseasesthe Fifth Medical Centre of Chinese PLA General HospitalNational Clinical Research Center for Infectious DiseasesBeijingChina
| | - Chao Zhang
- Senior Department of Infectious Diseasesthe Fifth Medical Centre of Chinese PLA General HospitalNational Clinical Research Center for Infectious DiseasesBeijingChina
| | - Jinwen Song
- Senior Department of Infectious Diseasesthe Fifth Medical Centre of Chinese PLA General HospitalNational Clinical Research Center for Infectious DiseasesBeijingChina
| | - Xing Fan
- Senior Department of Infectious Diseasesthe Fifth Medical Centre of Chinese PLA General HospitalNational Clinical Research Center for Infectious DiseasesBeijingChina
| | - Huihuang Huang
- Senior Department of Infectious Diseasesthe Fifth Medical Centre of Chinese PLA General HospitalNational Clinical Research Center for Infectious DiseasesBeijingChina
| | - Ruonan Xu
- Senior Department of Infectious Diseasesthe Fifth Medical Centre of Chinese PLA General HospitalNational Clinical Research Center for Infectious DiseasesBeijingChina
| | - Jiyuan Zhang
- Senior Department of Infectious Diseasesthe Fifth Medical Centre of Chinese PLA General HospitalNational Clinical Research Center for Infectious DiseasesBeijingChina
| | - Jinhong Yuan
- Senior Department of Infectious Diseasesthe Fifth Medical Centre of Chinese PLA General HospitalNational Clinical Research Center for Infectious DiseasesBeijingChina
| | - Weiguo Hong
- Senior Department of Infectious Diseasesthe Fifth Medical Centre of Chinese PLA General HospitalNational Clinical Research Center for Infectious DiseasesBeijingChina
| | - Jiaying Li
- Senior Department of Infectious Diseasesthe Fifth Medical Centre of Chinese PLA General HospitalNational Clinical Research Center for Infectious DiseasesBeijingChina
| | - Fu‐Sheng Wang
- Senior Department of Infectious Diseasesthe Fifth Medical Centre of Chinese PLA General HospitalNational Clinical Research Center for Infectious DiseasesBeijingChina
| | - Yan‐Mei Jiao
- Senior Department of Infectious Diseasesthe Fifth Medical Centre of Chinese PLA General HospitalNational Clinical Research Center for Infectious DiseasesBeijingChina
| | - Enqiang Linghu
- Senior Department of Gastroenterologythe First Medical Center of Chinese PLA General HospitalBeijingChina
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12
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Baltazar-Díaz TA, Andrade-Villanueva JF, Sánchez-Álvarez P, Amador-Lara F, Holguín-Aguirre T, Sánchez-Reyes K, Álvarez-Zavala M, López-Roa RI, Bueno-Topete MR, González-Hernández LA. A Two-Faced Gut Microbiome: Butyrogenic and Proinflammatory Bacteria Predominate in the Intestinal Milieu of People Living with HIV from Western Mexico. Int J Mol Sci 2024; 25:4830. [PMID: 38732048 PMCID: PMC11084381 DOI: 10.3390/ijms25094830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 04/12/2024] [Accepted: 04/15/2024] [Indexed: 05/13/2024] Open
Abstract
HIV infection results in marked alterations in the gut microbiota (GM), such as the loss of microbial diversity and different taxonomic and metabolic profiles. Despite antiretroviral therapy (ART) partially ablating gastrointestinal alterations, the taxonomic profile after successful new ART has shown wide variations. Our objective was to determine the GM composition and functions in people living with HIV (PLWHIV) under ART in comparison to seronegative controls (SC). Fecal samples from 21 subjects (treated with integrase strand-transfer inhibitors, INSTIs) and 18 SC were included. We employed 16S rRNA amplicon sequencing, coupled with PICRUSt2 and fecal short-chain fatty acid (SCFA) quantification by gas chromatography. The INSTI group showed a decreased α-diversity (p < 0.001) compared to the SC group, at the expense of increased amounts of Pseudomonadota (Proteobacteria), Segatella copri, Lactobacillus, and Gram-negative bacteria. Concurrently, we observed an enrichment in Megasphaera and Butyricicoccus, both SCFA-producing bacteria, and significant elevations in fecal butyrate in this group (p < 0.001). Interestingly, gut dysbiosis in PLWHIV was characterized by a proinflammatory environment orchestrated by Pseudomonadota and elevated levels of butyrate associated with bacterial metabolic pathways, as well as the evident presence of butyrogenic bacteria. The role of this unique GM in PLWHIV should be evaluated, as well as the use of butyrate-based supplements and ART regimens that contain succinate, such as tenofovir disoproxil succinate. This mixed profile is described for the first time in PLWHIV from Mexico.
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Affiliation(s)
- Tonatiuh Abimael Baltazar-Díaz
- Instituto de Investigación en Enfermedades Crónico-Degenerativas, Departamento de Biología Molecular y Genómica, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Sierra Mojada 950, Guadalajara 44340, Mexico;
- Instituto de Investigación en Inmunodeficiencias y VIH, Departamento de Clínicas Médicas, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Hospital 278, Guadalajara 44280, Mexico; (J.F.A.-V.); (K.S.-R.); (M.Á.-Z.)
| | - Jaime F. Andrade-Villanueva
- Instituto de Investigación en Inmunodeficiencias y VIH, Departamento de Clínicas Médicas, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Hospital 278, Guadalajara 44280, Mexico; (J.F.A.-V.); (K.S.-R.); (M.Á.-Z.)
- Unidad de VIH, Hospital Civil de Guadalajara Fray Antonio Alcalde, Hospital 278, Guadalajara 44280, Mexico; (P.S.-Á.); (F.A.-L.); (T.H.-A.)
| | - Paulina Sánchez-Álvarez
- Unidad de VIH, Hospital Civil de Guadalajara Fray Antonio Alcalde, Hospital 278, Guadalajara 44280, Mexico; (P.S.-Á.); (F.A.-L.); (T.H.-A.)
| | - Fernando Amador-Lara
- Unidad de VIH, Hospital Civil de Guadalajara Fray Antonio Alcalde, Hospital 278, Guadalajara 44280, Mexico; (P.S.-Á.); (F.A.-L.); (T.H.-A.)
| | - Tania Holguín-Aguirre
- Unidad de VIH, Hospital Civil de Guadalajara Fray Antonio Alcalde, Hospital 278, Guadalajara 44280, Mexico; (P.S.-Á.); (F.A.-L.); (T.H.-A.)
| | - Karina Sánchez-Reyes
- Instituto de Investigación en Inmunodeficiencias y VIH, Departamento de Clínicas Médicas, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Hospital 278, Guadalajara 44280, Mexico; (J.F.A.-V.); (K.S.-R.); (M.Á.-Z.)
| | - Monserrat Álvarez-Zavala
- Instituto de Investigación en Inmunodeficiencias y VIH, Departamento de Clínicas Médicas, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Hospital 278, Guadalajara 44280, Mexico; (J.F.A.-V.); (K.S.-R.); (M.Á.-Z.)
| | - Rocío Ivette López-Roa
- Laboratorio de Investigación y Desarrollo Farmacéutico, Centro Universitario de Ciencias Exactas e Ingenierías, Universidad de Guadalajara, Marcelino García Barragán 1421, Guadalajara 44430, Mexico;
| | - Miriam Ruth Bueno-Topete
- Instituto de Investigación en Enfermedades Crónico-Degenerativas, Departamento de Biología Molecular y Genómica, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Sierra Mojada 950, Guadalajara 44340, Mexico;
| | - Luz Alicia González-Hernández
- Instituto de Investigación en Inmunodeficiencias y VIH, Departamento de Clínicas Médicas, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Hospital 278, Guadalajara 44280, Mexico; (J.F.A.-V.); (K.S.-R.); (M.Á.-Z.)
- Unidad de VIH, Hospital Civil de Guadalajara Fray Antonio Alcalde, Hospital 278, Guadalajara 44280, Mexico; (P.S.-Á.); (F.A.-L.); (T.H.-A.)
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13
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Zhou J, Yang Y, Xie Z, Lu D, Huang J, Lan L, Guo B, Yang X, Wang Q, Li Z, Zhang Y, Yang X, Ai S, Liu N, Cui P, Liang H, Ye L, Huang J. Dysbiosis of gut microbiota and metabolites during AIDS: implications for CD4 + T cell reduction and immune activation. AIDS 2024; 38:633-644. [PMID: 38061029 PMCID: PMC10942204 DOI: 10.1097/qad.0000000000003812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 10/11/2023] [Accepted: 11/29/2023] [Indexed: 03/16/2024]
Abstract
OBJECTIVE Identifying the gut microbiota associated with host immunity in the AIDS stage. DESIGN We performed a cross-sectional study. METHODS We recruited people with HIV (PWH) in the AIDS or non-AIDS stage and evaluated their gut microbiota and metabolites by using 16S ribosomal RNA (rRNA) sequencing and liquid chromatography-mass spectrometry (LC-MS). Machine learning models were used to analyze the correlations between key bacteria and CD4 + T cell count, CD4 + T cell activation, bacterial translocation, gut metabolites, and KEGG functional pathways. RESULTS We recruited 114 PWH in the AIDS stage and 203 PWH in the non-AIDS stage. The α-diversity of gut microbiota was downregulated in the AIDS stage ( P < 0.05). Several machine learning models could be used to identify key gut microbiota associated with AIDS, including the logistic regression model with area under the curve (AUC), sensitivity, specificity, and Brier scores of 0.854, 0.813, 0.813, and 0.160, respectively. The decreased key bacteria ASV1 ( Bacteroides sp.), ASV8 ( Fusobacterium sp.), ASV30 ( Roseburia sp.), ASV37 ( Bacteroides sp.), and ASV41 ( Lactobacillus sp.) in the AIDS stage were positively correlated with the CD4 + T cell count, the EndoCAb IgM level, 4-hydroxyphenylpyruvic acid abundance, and the predicted cell growth pathway, and negatively correlated with the CD3 + CD4 + CD38 + HLA-DR + T cell count and the sCD14 level. CONCLUSION Machine learning has the potential to recognize key gut microbiota related to AIDS. The key five bacteria in the AIDS stage and their metabolites might be related to CD4 + T cell reduction and immune activation.
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Affiliation(s)
- Jie Zhou
- Guangxi Key Laboratory of AIDS Prevention and Treatment & School of Public Health, Guangxi Medical University
- Guangxi Universities Key Laboratory of Prevention and Control of Highly Prevalent Disease
| | - Yuecong Yang
- Guangxi Key Laboratory of AIDS Prevention and Treatment & School of Public Health, Guangxi Medical University
- Guangxi Universities Key Laboratory of Prevention and Control of Highly Prevalent Disease
| | | | - Dongjia Lu
- Guangxi Key Laboratory of AIDS Prevention and Treatment & School of Public Health, Guangxi Medical University
- Guangxi Universities Key Laboratory of Prevention and Control of Highly Prevalent Disease
| | | | - Liuyang Lan
- Guangxi Key Laboratory of AIDS Prevention and Treatment & School of Public Health, Guangxi Medical University
- Guangxi Universities Key Laboratory of Prevention and Control of Highly Prevalent Disease
| | - Baodong Guo
- Guangxi Key Laboratory of AIDS Prevention and Treatment & School of Public Health, Guangxi Medical University
- Guangxi Universities Key Laboratory of Prevention and Control of Highly Prevalent Disease
| | - Xiping Yang
- Guangxi Key Laboratory of AIDS Prevention and Treatment & School of Public Health, Guangxi Medical University
- Guangxi Universities Key Laboratory of Prevention and Control of Highly Prevalent Disease
| | - Qing Wang
- Guangxi Key Laboratory of AIDS Prevention and Treatment & School of Public Health, Guangxi Medical University
- Guangxi Universities Key Laboratory of Prevention and Control of Highly Prevalent Disease
| | - Zhuoxin Li
- Guangxi Key Laboratory of AIDS Prevention and Treatment & School of Public Health, Guangxi Medical University
- Guangxi Universities Key Laboratory of Prevention and Control of Highly Prevalent Disease
| | - Yu Zhang
- Guangxi Key Laboratory of AIDS Prevention and Treatment & School of Public Health, Guangxi Medical University
- Guangxi Universities Key Laboratory of Prevention and Control of Highly Prevalent Disease
| | - Xing Yang
- Guangxi Key Laboratory of AIDS Prevention and Treatment & School of Public Health, Guangxi Medical University
- Guangxi Universities Key Laboratory of Prevention and Control of Highly Prevalent Disease
| | - Sufang Ai
- The Fourth People's Hospital of Nanning
| | | | - Ping Cui
- Guangxi Key Laboratory of AIDS Prevention and Treatment & School of Public Health, Guangxi Medical University
- Life Science Institute, Guangxi Medical University, Nanning, Guangxi, China
| | - Hao Liang
- Guangxi Key Laboratory of AIDS Prevention and Treatment & School of Public Health, Guangxi Medical University
- Guangxi Universities Key Laboratory of Prevention and Control of Highly Prevalent Disease
- Life Science Institute, Guangxi Medical University, Nanning, Guangxi, China
| | - Li Ye
- Guangxi Key Laboratory of AIDS Prevention and Treatment & School of Public Health, Guangxi Medical University
- Guangxi Universities Key Laboratory of Prevention and Control of Highly Prevalent Disease
- Life Science Institute, Guangxi Medical University, Nanning, Guangxi, China
| | - Jiegang Huang
- Guangxi Key Laboratory of AIDS Prevention and Treatment & School of Public Health, Guangxi Medical University
- Guangxi Universities Key Laboratory of Prevention and Control of Highly Prevalent Disease
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14
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Huang KD, Amend L, Gálvez EJC, Lesker TR, de Oliveira R, Bielecka A, Blanco-Míguez A, Valles-Colomer M, Ruf I, Pasolli E, Buer J, Segata N, Esser S, Strowig T, Kehrmann J. Establishment of a non-Westernized gut microbiota in men who have sex with men is associated with sexual practices. Cell Rep Med 2024; 5:101426. [PMID: 38366600 PMCID: PMC10982974 DOI: 10.1016/j.xcrm.2024.101426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 09/07/2023] [Accepted: 01/22/2024] [Indexed: 02/18/2024]
Abstract
The human gut microbiota is influenced by various factors, including health status and environmental conditions, yet considerable inter-individual differences remain unexplained. Previous studies identified that the gut microbiota of men who have sex with men (MSM) is distinct from that of non-MSM. Here, we reveal through species-level microbiota analysis using shotgun metagenomics that the gut microbiota of many MSM with Western origin resembles gut microbial communities of non-Westernized populations. Specifically, MSM gut microbiomes are frequently dominated by members of the Prevotellaceae family, including co-colonization of species from the Segatella copri complex and unknown Prevotellaceae members. Questionnaire-based analysis exploring inter-individual differences in MSM links specific sexual practices to microbiota composition. Moreover, machine learning identifies microbial features associated with sexual activities in MSM. Together, this study shows associations of sexual activities with gut microbiome alterations in MSM, which may have a large impact on population-based microbiota studies.
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Affiliation(s)
- Kun D Huang
- Department of Microbial Immune Regulation, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Lena Amend
- Department of Microbial Immune Regulation, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Eric J C Gálvez
- Department of Microbial Immune Regulation, Helmholtz Centre for Infection Research, Braunschweig, Germany; Hannover Medical School, Hannover, Germany; Roche Pharma Research and Early Development, Roche Innovation Center, Basel, Switzerland
| | - Till-Robin Lesker
- Department of Microbial Immune Regulation, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Romulo de Oliveira
- Department of Microbial Immune Regulation, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Agata Bielecka
- Department of Microbial Immune Regulation, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | | | - Mireia Valles-Colomer
- Department CIBIO, University of Trento, Trento, Italy; Department of Medicine and Life Sciences, University Pompeu Fabra, Barcelona, Spain
| | - Isabel Ruf
- Institute of Medical Microbiology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Edoardo Pasolli
- Department of Agricultural Sciences, University of Naples, Naples, Italy
| | - Jan Buer
- Institute of Medical Microbiology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Nicola Segata
- Department CIBIO, University of Trento, Trento, Italy
| | - Stefan Esser
- Department of Dermatology and Venerology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Till Strowig
- Department of Microbial Immune Regulation, Helmholtz Centre for Infection Research, Braunschweig, Germany; Hannover Medical School, Hannover, Germany; Centre for Individualized Infection Medicine, Hannover, Germany.
| | - Jan Kehrmann
- Institute of Medical Microbiology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany.
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15
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Lohani SC, Ramer-Tait AE, Li Q. High-fat diet feeding exacerbates HIV-1 rectal transmission. mSystems 2024; 9:e0132223. [PMID: 38303112 PMCID: PMC10949459 DOI: 10.1128/msystems.01322-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 01/07/2024] [Indexed: 02/03/2024] Open
Abstract
High-fat diet (HFD) is well known to impact various aspects of gut health and has been associated with many diseases and inflammation. However, the impact of HFD feeding on HIV-1 rectal transmission has not yet been well addressed. With an increasing threat of HIV-1 infection in men who have sex with men (MSM), where the rectal route is the primary mode of infection, it is imperative to understand the impact of HFD on gut microbiota and inflammation and consequently, its effect on HIV-1 rectal transmission. Here, we utilized our double humanized bone marrow, liver, thymus (dHu-BLT) mouse model to assess the impact of HFD feeding on the host's susceptibility to HIV-1 rectal transmission. We found that feeding an HFD successfully altered the gut microbial composition within 3 weeks in the dHu-BLT mouse model. In addition, levels of inflammatory mediators, specifically IL-12p70, IP-10, ICAM-1, and fecal calprotectin, were significantly higher in HFD-fed mice compared to control mice on a regular chow diet. We also observed that significantly different inflammatory markers (IL-12p70 and ICAM-1) were negatively correlated with the number of observed ASVs, Shannon diversity, and Faith's diversity in the HFD-fed group. Notably, when repeatedly challenged with a low dose of HIV-1 via a rectal route, mice receiving an HFD were significantly more susceptible to HIV-1 rectal infection than control mice. Together, these results underscore the impact of HFD feeding on the gut microbiota and inflammation and suggest the significance of diet-induced gut microbial dysbiosis and inflammation in promoting viral infection.IMPORTANCEHFD induces gut microbial dysbiosis and inflammation and has been associated with many infections and disease progression; however, its impact on HIV-1 rectal transmission is largely unknown. Given the increasing threat of HIV-1 incidence in men who have sex with men (MSM), it has become crucial to comprehend the impact of factors associated with gut health, like HFD consumption, on host susceptibility to HIV-1 rectal transmission. This is particularly important since anal intercourse remains the primary mode of HIV transmission within the MSM group. In this study, utilizing our unique mouse model, featuring both the human immune system and gut microbiota, we showed that HFD feeding led to gut microbial dysbiosis, induced inflammation, and increased HIV-1 rectal transmission. Collectively, our study highlights the significant impact of HFD on gut microbiota and inflammation and suggests an HFD consumption as a potential risk factor for promoting HIV-1 rectal susceptibility.
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Affiliation(s)
- Saroj Chandra Lohani
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
- Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Amanda E. Ramer-Tait
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
- Nebraska Food for Health Center, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Qingsheng Li
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
- Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
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16
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Trøseid M, Molinaro A, Gelpi M, Vestad B, Kofoed KF, Fuchs A, Køber L, Holm K, Benfield T, Ueland PM, Hov JR, Nielsen SD, Knudsen AD. Gut Microbiota Alterations and Circulating Imidazole Propionate Levels Are Associated With Obstructive Coronary Artery Disease in People With HIV. J Infect Dis 2024; 229:898-907. [PMID: 38195204 PMCID: PMC10938217 DOI: 10.1093/infdis/jiad604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 12/13/2023] [Accepted: 12/21/2023] [Indexed: 01/11/2024] Open
Abstract
BACKGROUND The impact of gut microbiota and its metabolites on coronary artery disease (CAD) in people with human immunodeficiency virus (PWH) is unknown. Emerging evidence suggests that imidazole propionate (ImP), a microbial metabolite, is linked with cardiometabolic diseases. METHODS Fecal samples from participants of the Copenhagen Comorbidity in HIV infection (COCOMO) study were processed for 16S rRNA sequencing and ImP measured with liquid chromatography-tandem mass spectrometry. CAD severity was investigated by coronary computed tomography-angiography, and participants grouped according to obstructive CAD (n = 60), nonobstructive CAD (n = 80), or no CAD (n = 114). RESULTS Participants with obstructive CAD had a gut microbiota with lower diversity and distinct compositional shift, with increased abundance of Rumiococcus gnavus and Veillonella, known producers of ImP. ImP plasma levels were associated with this dysbiosis, and significantly elevated in participants with obstructive CAD. However, gut dysbiosis but not plasma ImP was independently associated with obstructive CAD after adjustment for traditional and HIV-related risk factors (adjusted odds ratio, 2.7; 95% confidence interval, 1.1-7.2; P = .048). CONCLUSIONS PWH with obstructive CAD displays a distinct gut microbiota profile and increased circulating ImP plasma levels. Future studies should determine whether gut dysbiosis and related metabolites such as ImP are predictive of incident cardiovascular events.
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Affiliation(s)
- Marius Trøseid
- Research Institute of Internal Medicine, Oslo University Hospital Rikshospitalet, Oslo, Norway
- Section for Clinical Immunology and Infectious Diseases, Oslo University Hospital Rikshospitalet, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Antonio Molinaro
- Research Institute of Internal Medicine, Oslo University Hospital Rikshospitalet, Oslo, Norway
- Norwegian PSC Research Center, Department of Transplantation Medicine, Oslo University Hospital, Oslo, Norway
| | - Marco Gelpi
- Department of Infectious Diseases, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Beate Vestad
- Research Institute of Internal Medicine, Oslo University Hospital Rikshospitalet, Oslo, Norway
| | - Klaus Fuglsang Kofoed
- Department of Cardiology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
- Department of Radiology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Andreas Fuchs
- Department of Cardiology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Lars Køber
- Department of Cardiology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Kristian Holm
- Research Institute of Internal Medicine, Oslo University Hospital Rikshospitalet, Oslo, Norway
- Norwegian PSC Research Center, Department of Transplantation Medicine, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Thomas Benfield
- Department of Infectious Diseases, Copenhagen University Hospital—Amager and Hvidovre, Hvidovre, Denmark
| | | | - Johannes R Hov
- Research Institute of Internal Medicine, Oslo University Hospital Rikshospitalet, Oslo, Norway
- Norwegian PSC Research Center, Department of Transplantation Medicine, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Section of Gastroenterology, Department of Transplantation Medicine, Oslo University Hospital, Oslo, Norway
| | - Susanne Dam Nielsen
- Department of Infectious Diseases, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
- Department of Surgical Gastroenterology and Transplantation, Rigshospitalet, University of Copenhagen Copenhagen, Denmark
| | - Andreas Dehlbæk Knudsen
- Department of Infectious Diseases, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
- Department of Cardiology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
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17
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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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18
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Yerke A, Fry Brumit D, Fodor AA. Proportion-based normalizations outperform compositional data transformations in machine learning applications. MICROBIOME 2024; 12:45. [PMID: 38443997 PMCID: PMC10913632 DOI: 10.1186/s40168-023-01747-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 12/22/2023] [Indexed: 03/07/2024]
Abstract
BACKGROUND Normalization, as a pre-processing step, can significantly affect the resolution of machine learning analysis for microbiome studies. There are countless options for normalization scheme selection. In this study, we examined compositionally aware algorithms including the additive log ratio (alr), the centered log ratio (clr), and a recent evolution of the isometric log ratio (ilr) in the form of balance trees made with the PhILR R package. We also looked at compositionally naïve transformations such as raw counts tables and several transformations that are based on relative abundance, such as proportions, the Hellinger transformation, and a transformation based on the logarithm of proportions (which we call "lognorm"). RESULTS In our evaluation, we used 65 metadata variables culled from four publicly available datasets at the amplicon sequence variant (ASV) level with a random forest machine learning algorithm. We found that different common pre-processing steps in the creation of the balance trees made very little difference in overall performance. Overall, we found that the compositionally aware data transformations such as alr, clr, and ilr (PhILR) performed generally slightly worse or only as well as compositionally naïve transformations. However, relative abundance-based transformations outperformed most other transformations by a small but reliably statistically significant margin. CONCLUSIONS Our results suggest that minimizing the complexity of transformations while correcting for read depth may be a generally preferable strategy in preparing data for machine learning compared to more sophisticated, but more complex, transformations that attempt to better correct for compositionality. Video Abstract.
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Affiliation(s)
- Aaron Yerke
- Department of Bioinformatics and Genomics, Bioinformatics Building, UNC Charlotte, The University of North Carolina, Charlotte 9331 Robert D. Snyder Rd, Charlotte, USA
- Food Components and Health Laboratory, USDA, ARS, Beltsville Human Nutrition Research Center, Beltsville, USA
| | - Daisy Fry Brumit
- Department of Bioinformatics and Genomics, Bioinformatics Building, UNC Charlotte, The University of North Carolina, Charlotte 9331 Robert D. Snyder Rd, Charlotte, USA
| | - Anthony A Fodor
- Department of Bioinformatics and Genomics, Bioinformatics Building, UNC Charlotte, The University of North Carolina, Charlotte 9331 Robert D. Snyder Rd, Charlotte, USA.
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19
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Li K, Zhang C, Deng J, Zeng H, Zhang Y, Lai G, Zhong X, Xie B. Causal effects of gut microbiome on HIV infection: a two-sample mendelian randomization analysis. BMC Infect Dis 2024; 24:280. [PMID: 38438963 PMCID: PMC10913272 DOI: 10.1186/s12879-024-09176-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 02/26/2024] [Indexed: 03/06/2024] Open
Abstract
BACKGROUND The causal association between gut microbiome and HIV infection remains to be elucidated. We conducted a two-sample mendelian randomization analysis to estimate the causality between gut microbiome and HIV infection. METHODS Publicly released genome-wide association studies summary data were collected to perform the mendelian analysis. The GWAS summary data of gut microbiome was retrieved from the MiBioGen consortium, which contains 18 340 samples from 24 cohorts. GWAS summary data of HIV infection was collected from the R5 release of FinnGen consortium, including 357 HIV infected cases and 218 435 controls. The SNPs were selected as instrumental variables according to our selection rules. And SNPs with a F-statistics less than ten were regarded as weak instrumental variables and excluded. Mendelian randomization analysis was conducted by five methods, including inverse variance weighted (IVW), MR-Egger, weighted median, weighted mode, and simple mode. The Cochran's Q test and MR-Egger intercept test were performed to identify heterogeneity and pleiotropy. Leave-one-out analysis were used to test the sensitivity of the results. RESULTS Fifteen gut microbiota taxa showed causal effects on HIV infection according to the MR methods. Four taxa were observed to increase the risk of HIV infection, including Ruminococcaceae (OR: 2.468[1.043, 5.842], P: 0.039), Ruminococcaceae UCG005 (OR: 2.051[1.048, 4.011], P: 0.036), Subdoligranulum (OR: 3.957[1.762, 8.887], P < 0.001) and Victivallis (OR: 1.605[1.012, 2.547], P=0.044). Erysipelotrichaceae was protective factor of HIV infection (OR: 0.278[0.106, 0.731], P < 0.001) and Methanobrevibacter was also found to be associated with reduced risk of HIV infection (OR: 0.509[0.265, 0.980], P=0.043). Horizontal pleiotropy was found for Fusicatenibacter (P<0.05) according to the MR-Egger regression intercept analysis. No heterogeneity was detected. CONCLUSION Our results demonstrate significant causal effects of gut microbiome on HIV infection. These findings facilitate future studies to develop better strategies for HIV prophylaxis through gut microbiome regulation. Further explorations are also warranted to dissect the mechanism of how gut microbiome affects HIV susceptibility.
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Affiliation(s)
- Kangjie Li
- College of Public Health, Chongqing Medical University, Chongqing, China
| | - Cong Zhang
- College of Public Health, Chongqing Medical University, Chongqing, China
| | - Jielian Deng
- College of Public Health, Chongqing Medical University, Chongqing, China
| | - Haijiao Zeng
- College of Public Health, Chongqing Medical University, Chongqing, China
| | - Yuan Zhang
- College of Public Health, Chongqing Medical University, Chongqing, China
| | - Guichuan Lai
- College of Public Health, Chongqing Medical University, Chongqing, China
| | - Xiaoni Zhong
- College of Public Health, Chongqing Medical University, Chongqing, China.
| | - Biao Xie
- College of Public Health, Chongqing Medical University, Chongqing, China.
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20
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Singh S, Giron LB, Shaikh MW, Shankaran S, Engen PA, Bogin ZR, Bambi SA, Goldman AR, Azevedo JLLC, Orgaz L, de Pedro N, González P, Giera M, Verhoeven A, Sánchez-López E, Pandrea I, Kannan T, Tanes CE, Bittinger K, Landay AL, Corley MJ, Keshavarzian A, Abdel-Mohsen M. Distinct intestinal microbial signatures linked to accelerated systemic and intestinal biological aging. MICROBIOME 2024; 12:31. [PMID: 38383483 PMCID: PMC10882811 DOI: 10.1186/s40168-024-01758-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 01/05/2024] [Indexed: 02/23/2024]
Abstract
BACKGROUND People living with HIV (PLWH), even when viral replication is controlled through antiretroviral therapy (ART), experience persistent inflammation. This inflammation is partly attributed to intestinal microbial dysbiosis and translocation, which may lead to non-AIDS-related aging-associated comorbidities. The extent to which living with HIV - influenced by the infection itself, ART usage, sexual orientation, or other associated factors - affects the biological age of the intestines is unclear. Furthermore, the role of microbial dysbiosis and translocation in the biological aging of PLWH remains to be elucidated. To investigate these uncertainties, we used a systems biology approach, analyzing colon and ileal biopsies, blood samples, and stool specimens from PLWH on ART and people living without HIV (PLWoH) as controls. RESULTS PLWH exhibit accelerated biological aging in the colon, ileum, and blood, as measured by various epigenetic aging clocks, compared to PLWoH. Investigating the relationship between microbial translocation and biological aging, PLWH had decreased levels of tight junction proteins in the intestines, along with increased microbial translocation. This intestinal permeability correlated with faster biological aging and increased inflammation. When investigating the relationship between microbial dysbiosis and biological aging, the intestines of PLWH had higher abundance of specific pro-inflammatory bacteria, such as Catenibacterium and Prevotella. These bacteria correlated with accelerated biological aging. Conversely, the intestines of PLWH had lower abundance of bacteria known for producing the anti-inflammatory short-chain fatty acids, such as Subdoligranulum and Erysipelotrichaceae, and these bacteria were associated with slower biological aging. Correlation networks revealed significant links between specific microbial genera in the colon and ileum (but not in feces), increased aging, a rise in pro-inflammatory microbe-related metabolites (e.g., those in the tryptophan metabolism pathway), and a decrease in anti-inflammatory metabolites like hippuric acid. CONCLUSIONS We identified specific microbial compositions and microbiota-related metabolic pathways that are intertwined with intestinal and systemic biological aging. This microbial signature of biological aging is likely reflecting various factors including the HIV infection itself, ART usage, sexual orientation, and other aspects associated with living with HIV. A deeper understanding of the mechanisms underlying these connections could offer potential strategies to mitigate accelerated aging and its associated health complications. Video Abstract.
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Affiliation(s)
- Shalini Singh
- Vaccine and Immunotherapy Center, The Wistar Institute, 3601 Spruce Street, Philadelphia, PA, 19104, USA
| | - Leila B Giron
- Vaccine and Immunotherapy Center, The Wistar Institute, 3601 Spruce Street, Philadelphia, PA, 19104, USA
| | - Maliha W Shaikh
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush University, Chicago, IL, USA
| | - Shivanjali Shankaran
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush University, Chicago, IL, USA
- Department of Medicine, Rush University, Chicago, IL, USA
| | - Phillip A Engen
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush University, Chicago, IL, USA
| | - Zlata R Bogin
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush University, Chicago, IL, USA
| | - Simona A Bambi
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush University, Chicago, IL, USA
| | - Aaron R Goldman
- Vaccine and Immunotherapy Center, The Wistar Institute, 3601 Spruce Street, Philadelphia, PA, 19104, USA
| | - Joao L L C Azevedo
- Vaccine and Immunotherapy Center, The Wistar Institute, 3601 Spruce Street, Philadelphia, PA, 19104, USA
| | | | | | | | - Martin Giera
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Aswin Verhoeven
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Elena Sánchez-López
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Toshitha Kannan
- Vaccine and Immunotherapy Center, The Wistar Institute, 3601 Spruce Street, Philadelphia, PA, 19104, USA
| | - Ceylan E Tanes
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Kyle Bittinger
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Alan L Landay
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush University, Chicago, IL, USA
- Department of Medicine, Rush University, Chicago, IL, USA
| | | | - Ali Keshavarzian
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush University, Chicago, IL, USA
- Department of Medicine, Rush University, Chicago, IL, USA
| | - Mohamed Abdel-Mohsen
- Vaccine and Immunotherapy Center, The Wistar Institute, 3601 Spruce Street, Philadelphia, PA, 19104, USA.
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21
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Qiao NN, Fang Q, Zhang XH, Ke SS, Wang ZW, Tang G, Leng RX, Fan YG. Effects of alcohol on the composition and metabolism of the intestinal microbiota among people with HIV: a cross-sectional study. Alcohol 2024:S0741-8329(24)00019-3. [PMID: 38387693 DOI: 10.1016/j.alcohol.2024.02.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Revised: 02/08/2024] [Accepted: 02/09/2024] [Indexed: 02/24/2024]
Abstract
OBJECTIVES Alcohol consumption is not uncommon among people with HIV (PWH) and may exacerbate HIV-induced intestinal damage, and further lead to dysbiosis and increased intestinal permeability. This study aimed to determine the changes in the faecal microbiota and its association with alcohol consumption in HIV-infected patients. METHODS A cross-sectional survey was conducted between November 2021 and May 2022, and 93 participants were recruited. To investigate the alterations of alcohol misuse on fecal microbiology in HIV-infected individuals, we performed 16s rDNA gene sequencing on fecal samples from the low to moderate drinking (n=21) and non-drinking (n=72) groups. RESULTS Comparison between groups using alpha and beta diversity showed that the diversity of stool microbiota in the low to moderate drinkinge group did not differ from that of the non-drinking group (all P>0.05). The Linear discriminant Analysis effect size (LEfSe) algorithm was to determine the bacterial taxa associated with alcohol consumption, and the results showed altered fecal bacterial composition in HIV-infected patients who consumed alcohol, with Coprobacillus, Pseudobutyrivibrio and Peptostreptococcaceae enriched, and Pasteurellaceae and Xanthomonadaceae were depleted. In addition, by using the Kyoto Encyclopedia of Genes and Genomes (KEGG) functional microbiome features were also found to be altered in the low to moderate drinking group, showing a reduction in metabolic pathways (P=0.036) and cardiovascular disease pathway (P=0.006). CONCLUSION Low to moderate drinking will change the composition, metabolism and cardiovascular disease pathway of the gut microbiota of HIV-infected patients.
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Affiliation(s)
- Ni-Ni Qiao
- Department of Epidemiology and Health Statistics, Anhui Medical University, Hefei, 230032 Anhui People's Republic of China
| | - Quan Fang
- Department of Epidemiology and Health Statistics, Anhui Medical University, Hefei, 230032 Anhui People's Republic of China
| | - Xin-Hong Zhang
- Department of Epidemiology and Health Statistics, Anhui Medical University, Hefei, 230032 Anhui People's Republic of China
| | - Su-Su Ke
- Department of Epidemiology and Health Statistics, Anhui Medical University, Hefei, 230032 Anhui People's Republic of China
| | - Zi-Wei Wang
- Department of Epidemiology and Health Statistics, Anhui Medical University, Hefei, 230032 Anhui People's Republic of China
| | - Gan Tang
- Department of Epidemiology and Health Statistics, Anhui Medical University, Hefei, 230032 Anhui People's Republic of China
| | - Rui-Xue Leng
- Department of Epidemiology and Health Statistics, Anhui Medical University, Hefei, 230032 Anhui People's Republic of China.
| | - Yin-Guang Fan
- Department of Epidemiology and Health Statistics, Anhui Medical University, Hefei, 230032 Anhui People's Republic of China.
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22
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Runtuwene LR, Parbie PK, Mizutani T, Ishizaka A, Matsuoka S, Abana CZY, Kushitor D, Bonney EY, Ofori SB, Kiyono H, Ishikawa K, Ampofo WK, Matano T. Longitudinal analysis of microbiome composition in Ghanaians living with HIV-1. Front Microbiol 2024; 15:1359402. [PMID: 38426062 PMCID: PMC10902004 DOI: 10.3389/fmicb.2024.1359402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 01/18/2024] [Indexed: 03/02/2024] Open
Abstract
Human immunodeficiency virus (HIV) 1 infection is known to cause gut microbiota dysbiosis. Among the causes is the direct infection of HIV-1 in gut-resident CD4+ T cells, causing a cascade of phenomena resulting in the instability of the gut mucosa. The effect of HIV infection on gut microbiome dysbiosis remains unresolved despite antiretroviral therapy. Here, we show the results of a longitudinal study of microbiome analysis of people living with HIV (PLWH). We contrasted the diversity and composition of the microbiome of patients with HIV at the first and second time points (baseline_case and six months later follow-up_case, respectively) with those of healthy individuals (baseline_control). We found that despite low diversity indices in the follow-up_case, the abundance of some genera was recovered but not completely, similar to baseline_control. Some genera were consistently in high abundance in PLWH. Furthermore, we found that the CD4+ T-cell count and soluble CD14 level were significantly related to high and low diversity indices, respectively. We also found that the abundance of some genera was highly correlated with clinical features, especially with antiretroviral duration. This includes genera known to be correlated with worse HIV-1 progression (Achromobacter and Stenotrophomonas) and a genus associated with gut protection (Akkermansia). The fact that a protector of the gut and genera linked to a worse progression of HIV-1 are both enriched may signify that despite the improvement of clinical features, the gut mucosa remains compromised.
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Affiliation(s)
- Lucky Ronald Runtuwene
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
| | - Prince Kofi Parbie
- Department of Virology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
- Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO, United States
| | - Taketoshi Mizutani
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
- The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Aya Ishizaka
- The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Saori Matsuoka
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Christopher Zaab-Yen Abana
- Department of Virology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Dennis Kushitor
- Department of Virology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Evelyn Yayra Bonney
- Department of Virology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Sampson Badu Ofori
- Department of Internal Medicine, Eastern Regional Hospital Koforidua, Ghana Health Service, Koforidua, Ghana
| | - Hiroshi Kiyono
- The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Institute for Global Prominent Research, Graduate School of Medicine, Chiba University, Chiba, Japan
- Department of Medicine, Chiba University-University of California San Diego Center for Mucosal Immunology, Allergy and Vaccines (cMAV), University of California San Diego, San Diego, CA, United States
| | - Koichi Ishikawa
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - William Kwabena Ampofo
- Department of Virology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Tetsuro Matano
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan
- The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
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23
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Rocafort M, Gootenberg DB, Luévano JM, Paer JM, Hayward MR, Bramante JT, Ghebremichael MS, Xu J, Rogers ZH, Munoz AR, Okello S, Kim JH, Sentongo R, Wagubi R, Lankowski A, Maruapula S, Zhao G, Handley SA, Mosepele M, Siedner MJ, Kwon DS. HIV-associated gut microbial alterations are dependent on host and geographic context. Nat Commun 2024; 15:1055. [PMID: 38316748 PMCID: PMC10844288 DOI: 10.1038/s41467-023-44566-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 12/19/2023] [Indexed: 02/07/2024] Open
Abstract
HIV-associated changes in intestinal microbiota are believed to be important drivers of disease progression. However, the majority of studies have focused on populations in high-income countries rather than in developing regions where HIV burden is greatest. To better understand the impact of HIV on fecal microbiota globally, we compare the fecal microbial community of individuals in the U.S., Uganda, and Botswana. We identify significant bacterial taxa alterations with both treated and untreated HIV infection with a high degree of uniqueness in each cohort. HIV-associated taxa alterations are also significantly different between populations that report men who have sex with men (MSM) behavior and non-MSM populations. Additionally, while we find that HIV infection is consistently associated with higher soluble markers of immune activation, most specific bacterial taxa associated with these markers in each region are not shared and none are shared across all three geographic locations in our study. Our findings demonstrate that HIV-associated changes in fecal microbiota are overall distinct among geographical locations and sexual behavior groups, although a small number of taxa shared between pairs of geographic locations warrant further investigation, highlighting the importance of considering host context to fully assess the impact of the gut microbiome on human health and disease.
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Affiliation(s)
- Muntsa Rocafort
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, 02139, USA
| | - David B Gootenberg
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, 02139, USA
- Harvard Medical School, Boston, MA, 02114, USA
| | - Jesús M Luévano
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, 02139, USA
- Harvard Medical School, Boston, MA, 02114, USA
| | - Jeffrey M Paer
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, 02139, USA
| | | | | | | | - Jiawu Xu
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, 02139, USA
| | - Zoe H Rogers
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, 02139, USA
| | | | - Samson Okello
- Department of Medicine, Mbarara University of Science and Technology, 1956, Mbarara, Uganda
| | - June-Ho Kim
- Harvard Medical School, Boston, MA, 02114, USA
| | - Ruth Sentongo
- Department of Medicine, Mbarara University of Science and Technology, 1956, Mbarara, Uganda
| | - Robert Wagubi
- Department of Medicine, Mbarara University of Science and Technology, 1956, Mbarara, Uganda
| | - Alex Lankowski
- Medical Practice Evaluation Center, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Segametsi Maruapula
- Department of Family & Consumer Sciences, University of Botswana, 0022, Gaborone, Botswana
| | - Guoyan Zhao
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Scott A Handley
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Mosepele Mosepele
- Faculty of Medicine, University of Botswana, 0022, Gaborone, Botswana
| | - Mark J Siedner
- Harvard Medical School, Boston, MA, 02114, USA
- Medical Practice Evaluation Center, Massachusetts General Hospital, Boston, MA, 02114, USA
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Douglas S Kwon
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, 02139, USA.
- Harvard Medical School, Boston, MA, 02114, USA.
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, 02114, USA.
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24
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Burkhart Colorado AS, Lazzaro A, Neff CP, Nusbacher N, Boyd K, Fiorillo S, Martin C, Siebert JC, Campbell TB, Borok M, Palmer BE, Lozupone C. Differential effects of antiretroviral treatment on immunity and gut microbiome composition in people living with HIV in rural versus urban Zimbabwe. MICROBIOME 2024; 12:18. [PMID: 38310301 PMCID: PMC10837999 DOI: 10.1186/s40168-023-01718-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Accepted: 11/09/2023] [Indexed: 02/05/2024]
Abstract
BACKGROUND The widespread availability of antiretroviral therapy (ART) has dramatically reduced mortality and improved life expectancy for people living with HIV (PLWH). However, even with HIV-1 suppression, chronic immune activation and elevated inflammation persist and have been linked to a pro-inflammatory gut microbiome composition and compromised intestinal barrier integrity. PLWH in urban versus rural areas of sub-Saharan Africa experience differences in environmental factors that may impact the gut microbiome and immune system, in response to ART, yet this has not previously been investigated in these groups. To address this, we measured T cell activation/exhaustion/trafficking markers, plasma inflammatory markers, and fecal microbiome composition in PLWH and healthy participants recruited from an urban clinic in the city of Harare, Zimbabwe, and a district hospital that services surrounding rural villages. PLWH were either ART naïve at baseline and sampled again after 24 weeks of first-line ART and the antibiotic cotrimoxazole or were ART-experienced at both timepoints. RESULTS Although expected reductions in the inflammatory marker IL-6, T-cell activation, and exhaustion were observed with ART-induced viral suppression, these changes were much more pronounced in the urban versus the rural area. Gut microbiome composition was the most highly altered from healthy controls in ART experienced PLWH, and characterized by both reduced alpha diversity and altered composition. However, gut microbiome composition showed a pronounced relationship with T cell activation and exhaustion in ART-naïve PLWH, suggesting a particularly significant role for the gut microbiome in disease progression in uncontrolled infection. Elevated immune exhaustion after 24 weeks of ART did correlate with both living in the rural location and a more Prevotella-rich/Bacteroides-poor microbiome type, suggesting a potential role for rural-associated microbiome differences or their co-variates in the muted improvements in immune exhaustion in the rural area. CONCLUSION Successful ART was less effective at reducing gut microbiome-associated inflammation and T cell activation in PLWH in rural versus urban Zimbabwe, suggesting that individuals on ART in rural areas of Zimbabwe may be more vulnerable to co-morbidity related to sustained immune dysfunction in treated infection. Video Abstract.
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Affiliation(s)
| | - Alessandro Lazzaro
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, 00185, Rome, Italy
| | - Charles Preston Neff
- Department Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Nichole Nusbacher
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Kathryn Boyd
- Department of Clinical Research, London School of Hygiene and Tropical Medicine, Keppel St, London, WC1E 7HT, England
| | - Suzanne Fiorillo
- Department Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Casey Martin
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Janet C Siebert
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Thomas B Campbell
- Department Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Margaret Borok
- Faculty of Medicine and Health Sciences, University of Zimbabwe, Harare, Zimbabwe
| | - Brent E Palmer
- Department Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA.
| | - Catherine Lozupone
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA.
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25
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Wang Q, Fan X, Wu S, Su X. PM-CNN: microbiome status recognition and disease detection model based on phylogeny and multi-path neural network. BIOINFORMATICS ADVANCES 2024; 4:vbae013. [PMID: 38371919 PMCID: PMC10873578 DOI: 10.1093/bioadv/vbae013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 02/15/2024] [Accepted: 02/15/2024] [Indexed: 02/20/2024]
Abstract
Motivation The human microbiome, found throughout various body parts, plays a crucial role in health dynamics and disease development. Recent research has highlighted microbiome disparities between patients with different diseases and healthy individuals, suggesting the microbiome's potential in recognizing health states. Traditionally, microbiome-based status classification relies on pre-trained machine learning (ML) models. However, most ML methods overlook microbial relationships, limiting model performance. Results To address this gap, we propose PM-CNN (Phylogenetic Multi-path Convolutional Neural Network), a novel phylogeny-based neural network model for multi-status classification and disease detection using microbiome data. PM-CNN organizes microbes based on their phylogenetic relationships and extracts features using a multi-path convolutional neural network. An ensemble learning method then fuses these features to make accurate classification decisions. We applied PM-CNN to human microbiome data for status and disease detection, demonstrating its significant superiority over existing ML models. These results provide a robust foundation for microbiome-based state recognition and disease prediction in future research and applications. Availability and implementation PM-CNN software is available at https://github.com/qdu-bioinfo/PM_CNN.
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Affiliation(s)
- Qiangqiang Wang
- College of Computer Science and Technology, Qingdao University, Qingdao 266071, China
| | - Xiaoqian Fan
- Department of Gastroenterology, Shouguang Hospital of Traditional Chinese Medicine, Weifang 262700, China
| | - Shunyao Wu
- College of Computer Science and Technology, Qingdao University, Qingdao 266071, China
| | - Xiaoquan Su
- College of Computer Science and Technology, Qingdao University, Qingdao 266071, China
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26
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Lin H, Chen Y, Abror G, Price M, Morris A, Sun J, Palella F, Chew KW, Brown TT, Rinaldo CR, Peddada SD. The effect of sexual behavior on HIV-1 seroconversion is mediated by the gut microbiome and proinflammatory cytokines. RESEARCH SQUARE 2024:rs.3.rs-3868545. [PMID: 38343862 PMCID: PMC10854284 DOI: 10.21203/rs.3.rs-3868545/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
The association between HIV-1 seroconversion and gut dysbiosis is well documented, and its association with sexual activity is also widely recognized. However, it is not known whether the gut dysbiosis mediates the effects of high-risk sexual behavior on HIV-1 seroconversion. In this report we focused on men who engaged in high-risk sexual behavior where they had receptive anal intercourse with multiple men. We demonstrate that proinflammatory cytokines, sCD14 and sCD163, and gut microbiota mediate the effects of this high-risk sexual behavior on subsequent HIV seroconversion. We discovered changes in the gut microbial ecology, prior to seroconversion, both in terms of the composition as well as inter-relationships among the commensal species. Furthermore, these changes correlate with future HIV seroconversion. Specifically, as the number of sexual partners increased, we discovered in a "dose-response" manner, a decrease in the abundance of commensal and short-chain fatty acid-producing species, A. muciniphila, B. caccae, B. fragilis, B. uniformis, Bacteroides spp., Butyricimonas spp., and Odoribacter spp, and an increase in proinflammatory species Dehalobacterium spp. and Methanobrevibacter spp. These changes were also observed among subsequent HIV seroconverters. Interestingly, we also discovered a reduction in correlations among these commensal and short-chain fatty acid producing bacteria in a "dose-response" manner with the number of sexual partners. Our mediation analysis not only provides a conceptual model for the disease process but also provides clues for future clinical interventions that will manipulate the gut microbiota to treat high-risk subjects to prevent HIV seroconversion.
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Affiliation(s)
- Huang Lin
- Co-first authors
- Biostatistics and Computational Biology, National Institute of Environmental Health Sciences (NIH), Research Triangle Park, NC USA
| | - Yue Chen
- Co-first authors
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh, Pittsburgh, PA USA
| | - Grace Abror
- Department of Infectious Diseases and Microbiology, School of Public Health, University of Pittsburgh, Pittsburgh, PA USA
| | - Meaghan Price
- Department of Infectious Diseases and Microbiology, School of Public Health, University of Pittsburgh, Pittsburgh, PA USA
| | - Alison Morris
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA USA
| | - Jing Sun
- Department of Epidemiology, The Johns Hopkins Bloomberg School of Public Health, Baltimore, MD USA
| | - Frank Palella
- Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL USA
| | - Kara W Chew
- School of Medicine, University of California at Los Angeles, Los Angeles, CA, USA
| | - Todd T Brown
- Department of Epidemiology, The Johns Hopkins Bloomberg School of Public Health, Baltimore, MD USA
| | - Charles R Rinaldo
- Co-senior authors
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh, Pittsburgh, PA USA
| | - Shyamal D Peddada
- Co-senior authors
- Biostatistics and Computational Biology, National Institute of Environmental Health Sciences (NIH), Research Triangle Park, NC USA
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Ishizaka A, Koga M, Mizutani T, Yamayoshi S, Iwatsuki-Horimoto K, Adachi E, Suzuki Y, Kawaoka Y, Yotsuyanagi H. Association of gut microbiota with the pathogenesis of SARS-CoV-2 Infection in people living with HIV. BMC Microbiol 2024; 24:6. [PMID: 38172680 PMCID: PMC10763188 DOI: 10.1186/s12866-023-03157-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 12/12/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND People living with HIV (PLWH) with chronic inflammation may have an increasing risk for coronavirus disease 2019 (COVID-19) severity; however, the impact of their gut microbiota on COVID-19 is not fully elucidated. Here, we analyzed the temporal changes in the gut microbiota composition of hospitalized severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-infected PLWH (PLWH-CoV) and their correlation with COVID-19 severity. RESULT The 16S rRNA analysis results using stool samples (along the timeline from disease onset) from 12 hospitalized PLWH-CoV, whose median CD4 + T cell count was 671 cells/µl, were compared to those of 19 healthy people and 25 PLWH. Bacterial diversity in PLWH-CoV is not significantly different from that of healthy people and SARS-CoV-2 non-infected PLWH, but a significant difference in the microbiota diversity was observed in the classification according to the disease severity. Immediately after the disease onset, remarkable changes were observed in the gut microbiota of PLWH-CoV, and the changing with a decrease in some short-chain fatty acid-producing bacteria and an increase in colitis-related pathobiont. In the second week after disease onset, relative amounts of specific bacteria distinguished between disease severity. One month after the disease onset, dysbiosis of the gut microbiota persisted, and the number of Enterobacteriaceae, mainly Escherichia-Shigella, which is potentially pathogenic, increased and were enriched in patients who developed post-acute sequelae of COVID-19 (PASC). CONCLUSION The changes in the gut microbiota associated with SARS-CoV-2 infection observed in PLWH in this study indicated a persistent decrease in SCFA-producing bacteria and an intestinal environment with an increase in opportunistic pathogens associated with enteritis. This report demonstrates that the intestinal environment in PLWH tends to show delayed improvement even after COVID-19 recovery, and highlights the importance of the dysbiosis associated with SARS-CoV-2 infection as a potential factor in the COVID-19 severity and the PASC in PLWH.
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Affiliation(s)
- Aya Ishizaka
- Division of Infectious Diseases, Advanced Clinical Research Center, the Institute of Medical Science, the University of Tokyo, Tokyo, Japan
| | - Michiko Koga
- Division of Infectious Diseases, Advanced Clinical Research Center, the Institute of Medical Science, the University of Tokyo, Tokyo, Japan
| | - Taketoshi Mizutani
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, the University of Tokyo, Chiba, Japan.
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, the University of Tokyo, 6-2-3 Kashiwanoha, 277-0882, Kashiwa-shi, Chiba, Japan.
| | - Seiya Yamayoshi
- Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- The Research Center for Global Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo, Japan
| | - Kiyoko Iwatsuki-Horimoto
- Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Eisuke Adachi
- Department of Infectious Diseases and Applied Immunology, IMSUT Hospital of Institute of Medical Science, the University of Tokyo, Tokyo, Japan
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, the University of Tokyo, Chiba, Japan
| | - Yoshihiro Kawaoka
- Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- The Research Center for Global Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo, Japan
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA
- Pandemic Preparedness, Infection and Advanced Research Center, The University of Tokyo, Tokyo, Japan
| | - Hiroshi Yotsuyanagi
- Division of Infectious Diseases, Advanced Clinical Research Center, the Institute of Medical Science, the University of Tokyo, Tokyo, Japan.
- Department of Infectious Diseases and Applied Immunology, IMSUT Hospital of Institute of Medical Science, the University of Tokyo, Tokyo, Japan.
- Division of Infectious Diseases, Advanced Clinical Research Center, Institute of Medical Science, the University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, 108-8639, Tokyo, Japan.
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Morgan E, Manuzak JA, Broedlow C, Hudson H, D'Aquila R, Carrico AW, Klatt NR, Mustanski B. Problematic Cannabis Use Is Associated with Reduced Rectal Microbial Species Richness and Diversity Among a Pilot Sample of Young Sexual and Gender Minorities. AIDS Res Hum Retroviruses 2024; 40:1-6. [PMID: 37022787 PMCID: PMC10790549 DOI: 10.1089/aid.2022.0143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023] Open
Abstract
Compared to young heterosexual men, young sexual and gender minorities (YSGM) have elevated systemic inflammation and unique intestinal microbial profiles, influenced by HIV infection and substance use. However, links between cannabis use and microbial dysbiosis in this population have not been well described. In this pilot study, we aimed to characterize the complex interrelationships between cannabis use and microbial community structure in YSGM in relationship to HIV status. Cannabis use was assessed by self-administered Cannabis Use Disorder Identification Test (CUDIT) questionnaires and rectal microbial community alpha-diversity metrics were assessed via 16S ribosomal ribonucleic acid (rRNA) sequencing in a subset of YSGM (n = 42) in the RADAR cohort (aged 16-29) in Chicago. Multivariable regression models were used to assess the relationship between cannabis use and microbiome alpha-diversity metrics, adjusting for HIV status and other risk characteristics, including inflammation, which was evaluated by plasma levels of C-reactive protein (CRP). Problematic cannabis use, but not general use, was significantly inversely associated with microbial community richness (Adj. Beta = -8.13; 95% confidence interval [CI]: -15.68 to -0.59) and Shannon diversity (Adj. Beta = -0.04; 95% CI: -0.07 to 0.009). No significant association was observed between CUDIT score and community evenness, nor was any significant moderation observed by HIV status. We observed that problematic cannabis use was associated with reduced microbial community richness and Shannon diversity, adjusting for within population differences in inflammation and HIV status. Future research should aim to assess how cannabis use contributes to microbiome-related health factors among YSGM and if decreasing cannabis use can restore gut microbial community structure.
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Affiliation(s)
- Ethan Morgan
- College of Nursing, and The Ohio State University, Columbus, Ohio, USA
- Infectious Disease Institute, The Ohio State University, Columbus, Ohio, USA
| | - Jennifer A. Manuzak
- Division of Immunology, Tulane National Primate Research Center, Tulane University, Covington, Louisiana, USA
- Department of Pediatrics, Miller School of Medicine, University of Miami, Miami, Florida, USA
| | - Courtney Broedlow
- Department of Pediatrics, Miller School of Medicine, University of Miami, Miami, Florida, USA
- Division of Surgical Outcomes and Precision Medicine Research, Department of Surgery, University of Minnesota, Minneapolis, Minnesota, USA
| | - Hannah Hudson
- Division of Infectious Diseases, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Richard D'Aquila
- Division of Infectious Diseases, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Adam W. Carrico
- Department of Public Health Sciences, Miller School of Medicine, University of Miami, Miami, Florida, USA
| | - Nichole R. Klatt
- Department of Pediatrics, Miller School of Medicine, University of Miami, Miami, Florida, USA
- Division of Surgical Outcomes and Precision Medicine Research, Department of Surgery, University of Minnesota, Minneapolis, Minnesota, USA
| | - Brian Mustanski
- Institute for Sexual and Gender Minority Health and Wellbeing, and Northwestern University, Chicago, Illinois, USA
- Department of Medical Social Sciences, Northwestern University, Chicago, Illinois, USA
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29
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Lembas A, Załęski A, Peller M, Mikuła T, Wiercińska-Drapało A. Human Immunodeficiency Virus as a Risk Factor for Cardiovascular Disease. Cardiovasc Toxicol 2024; 24:1-14. [PMID: 37982976 PMCID: PMC10838226 DOI: 10.1007/s12012-023-09815-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Accepted: 11/10/2023] [Indexed: 11/21/2023]
Abstract
The developments in HIV treatments have increased the life expectancy of people living with HIV (PLWH), a situation that makes cardiovascular disease (CVD) in that population as relevant as ever. PLWH are at increased risk of CVD, and our understanding of the underlying mechanisms is continually increasing. HIV infection is associated with elevated levels of multiple proinflammatory molecules, including IL-6, IL-1β, VCAM-1, ICAM-1, TNF-α, TGF-β, osteopontin, sCD14, hs-CRP, and D-dimer. Other currently examined mechanisms include CD4 + lymphocyte depletion, increased intestinal permeability, microbial translocation, and altered cholesterol metabolism. Antiretroviral therapy (ART) leads to decreases in the concentrations of the majority of proinflammatory molecules, although most remain higher than in the general population. Moreover, adverse effects of ART also play an important role in increased CVD risk, especially in the era of rapid advancement of new therapeutical options. Nevertheless, it is currently believed that HIV plays a more significant role in the development of metabolic syndromes than treatment-associated factors. PLWH being more prone to develop CVD is also due to the higher prevalence of smoking and chronic coinfections with viruses such as HCV and HBV. For these reasons, it is crucial to consider HIV a possible causal factor in CVD occurrence, especially among young patients or individuals without common CVD risk factors.
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Affiliation(s)
- Agnieszka Lembas
- Department of Infectious and Tropical Diseases and Hepatology, Medical University of Warsaw, Warsaw, Poland
- Hospital for Infectious Diseases, Warsaw, Poland
| | - Andrzej Załęski
- Department of Infectious and Tropical Diseases and Hepatology, Medical University of Warsaw, Warsaw, Poland.
- Hospital for Infectious Diseases, Warsaw, Poland.
| | - Michał Peller
- 1st Department of Cardiology, Medical University of Warsaw, Warsaw, Poland
| | - Tomasz Mikuła
- Department of Infectious and Tropical Diseases and Hepatology, Medical University of Warsaw, Warsaw, Poland
- Hospital for Infectious Diseases, Warsaw, Poland
| | - Alicja Wiercińska-Drapało
- Department of Infectious and Tropical Diseases and Hepatology, Medical University of Warsaw, Warsaw, Poland
- Hospital for Infectious Diseases, Warsaw, Poland
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30
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Sereti I, Verburgh ML, Gifford J, Lo A, Boyd A, Verheij E, Verhoeven A, Wit FWNM, Schim van der Loeff MF, Giera M, Kootstra NA, Reiss P, Vujkovic-Cvijin I. Impaired gut microbiota-mediated short-chain fatty acid production precedes morbidity and mortality in people with HIV. Cell Rep 2023; 42:113336. [PMID: 37918403 PMCID: PMC10872975 DOI: 10.1016/j.celrep.2023.113336] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 08/28/2023] [Accepted: 10/10/2023] [Indexed: 11/04/2023] Open
Abstract
Antiretroviral therapy (ART) has dramatically lengthened lifespan among people with HIV (PWH), but this population experiences heightened rates of inflammation-related comorbidities. HIV-associated inflammation is linked with an altered microbiome; whether such alterations precede inflammation-related comorbidities or occur as their consequence remains unknown. We find that ART-treated PWH exhibit depletion of gut-resident bacteria that produce short-chain fatty acids (SCFAs)-crucial microbial metabolites with anti-inflammatory properties. Prior reports establish that fecal SCFA concentrations are not depleted in PWH. We find that gut-microbiota-mediated SCFA production capacity is better reflected in serum than in feces and that PWH exhibit reduced serum SCFA, which associates with inflammatory markers. Leveraging stool and serum samples collected prior to comorbidity onset, we find that HIV-specific microbiome alterations precede morbidity and mortality in ART-treated PWH. Among these microbiome alterations, reduced microbiome-mediated conversion of lactate to propionate precedes mortality in PWH. Thus, gut microbial fiber/lactate conversion to SCFAs may modulate HIV-associated comorbidity risk.
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Affiliation(s)
- Irini Sereti
- HIV Pathogenesis Section, Laboratory of Immunoregulation, NIAID/NIH, Rockville, MD, USA; Amsterdam Institute for Global Health and Development, Amsterdam, the Netherlands
| | - Myrthe L Verburgh
- Amsterdam University Medical Centers, University of Amsterdam, Infectious Diseases, Amsterdam, the Netherlands; Amsterdam Institute for Infection and Immunity, Amsterdam, the Netherlands; Amsterdam Institute for Global Health and Development, Amsterdam, the Netherlands
| | - Jacob Gifford
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Karsh Division of Gastroenterology & Hepatology, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA; F. Widjaja Inflammatory Bowel Disease Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Alice Lo
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Karsh Division of Gastroenterology & Hepatology, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA; F. Widjaja Inflammatory Bowel Disease Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Anders Boyd
- Amsterdam University Medical Centers, University of Amsterdam, Infectious Diseases, Amsterdam, the Netherlands; Amsterdam Institute for Infection and Immunity, Amsterdam, the Netherlands; HIV Monitoring Foundation, Amsterdam, the Netherlands; Public Health Service of Amsterdam, Infectious Diseases, Amsterdam, the Netherlands
| | - Eveline Verheij
- Amsterdam University Medical Centers, University of Amsterdam, Infectious Diseases, Amsterdam, the Netherlands; Amsterdam Institute for Infection and Immunity, Amsterdam, the Netherlands; Amsterdam Institute for Global Health and Development, Amsterdam, the Netherlands
| | - Aswin Verhoeven
- Leiden University Medical Center, Center for Proteomics & Metabolomics, Leiden, the Netherlands
| | - Ferdinand W N M Wit
- Amsterdam University Medical Centers, University of Amsterdam, Infectious Diseases, Amsterdam, the Netherlands; Amsterdam Institute for Infection and Immunity, Amsterdam, the Netherlands; HIV Monitoring Foundation, Amsterdam, the Netherlands
| | - Maarten F Schim van der Loeff
- Amsterdam University Medical Centers, University of Amsterdam, Infectious Diseases, Amsterdam, the Netherlands; Amsterdam Institute for Infection and Immunity, Amsterdam, the Netherlands; Public Health Service of Amsterdam, Infectious Diseases, Amsterdam, the Netherlands
| | - Martin Giera
- Leiden University Medical Center, Center for Proteomics & Metabolomics, Leiden, the Netherlands
| | - Neeltje A Kootstra
- Amsterdam Institute for Infection and Immunity, Amsterdam, the Netherlands; Amsterdam UMC, University of Amsterdam, Experimental Immunology, Amsterdam, the Netherlands
| | - Peter Reiss
- Amsterdam University Medical Centers, University of Amsterdam, Infectious Diseases, Amsterdam, the Netherlands; Amsterdam Institute for Infection and Immunity, Amsterdam, the Netherlands; Amsterdam Institute for Global Health and Development, Amsterdam, the Netherlands; Amsterdam University Medical Centers, University of Amsterdam, Department of Global Health, Meibergdreef 9, Amsterdam, the Netherlands
| | - Ivan Vujkovic-Cvijin
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Karsh Division of Gastroenterology & Hepatology, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA; F. Widjaja Inflammatory Bowel Disease Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
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31
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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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32
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Singh S, Giron LB, Shaikh MW, Shankaran S, Engen PA, Bogin ZR, Bambi SA, Goldman AR, Azevedo JLLC, Orgaz L, de Pedro N, González P, Giera M, Verhoeven A, Sánchez-López E, Pandrea IV, Kannan T, Tanes CE, Bittinger K, Landay AL, Corley MJ, Keshavarzian A, Abdel-Mohsen M. Distinct Intestinal Microbial Signatures Linked to Accelerated Biological Aging in People with HIV. RESEARCH SQUARE 2023:rs.3.rs-3492242. [PMID: 37961645 PMCID: PMC10635386 DOI: 10.21203/rs.3.rs-3492242/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Background People with HIV (PWH), even with controlled viral replication through antiretroviral therapy (ART), experience persistent inflammation. This is partly due to intestinal microbial dysbiosis and translocation. Such ongoing inflammation may lead to the development of non-AIDS-related aging-associated comorbidities. However, there remains uncertainty regarding whether HIV affects the biological age of the intestines and whether microbial dysbiosis and translocation influence the biological aging process in PWH on ART. To fill this knowledge gap, we utilized a systems biology approach, analyzing colon and ileal biopsies, blood samples, and stool specimens from PWH on ART and their matched HIV-negative counterparts. Results Despite having similar chronological ages, PWH on ART exhibit accelerated biological aging in the colon, ileum, and blood, as measured by various epigenetic aging clocks, compared to HIV-negative controls. Investigating the relationship between microbial translocation and biological aging, PWH on ART had decreased levels of tight junction proteins in the colon and ileum, along with increased microbial translocation. This increased intestinal permeability correlated with faster intestinal and systemic biological aging, as well as increased systemic inflammation. When investigating the relationship between microbial dysbiosis and biological aging, the intestines of PWH on ART had higher abundance of specific pro-inflammatory bacterial genera, such as Catenibacterium and Prevotella. These bacteria significantly correlated with accelerated local and systemic biological aging. Conversely, the intestines of PWH on ART had lower abundance of bacterial genera known for producing short-chain fatty acids and exhibiting anti-inflammatory properties, such as Subdoligranulum and Erysipelotrichaceae, and these bacteria taxa were associated with slower biological aging. Correlation networks revealed significant links between specific microbial genera in the colon and ileum (but not in feces), increased aging, a rise in pro-inflammatory microbial-related metabolites (e.g., those in the tryptophan metabolism pathway), and a decrease in anti-inflammatory metabolites like hippuric acid and oleic acid. Conclusions We identified a specific microbial composition and microbiome-related metabolic pathways that are intertwined with both intestinal and systemic biological aging in PWH on ART. A deeper understanding of the mechanisms underlying these connections could potentially offer strategies to counteract premature aging and its associated health complications in PWH.
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Burke FF, Hinks M, Salia S, Sparkes KM, Swift-Gallant A. Using Animal Models to Study the Interplay Between the Biodevelopmental Pathways Underlying Human Sexual Orientation. ARCHIVES OF SEXUAL BEHAVIOR 2023; 52:2979-2984. [PMID: 36477673 DOI: 10.1007/s10508-022-02499-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 11/22/2022] [Accepted: 11/23/2022] [Indexed: 06/17/2023]
Affiliation(s)
- Francine F Burke
- Department of Psychology, Memorial University of Newfoundland, 230 Elizabeth Ave., St John's, NL, A1B 3X9, Canada
| | - Meagan Hinks
- Department of Psychology, Memorial University of Newfoundland, 230 Elizabeth Ave., St John's, NL, A1B 3X9, Canada
| | - Stephanie Salia
- Department of Psychology, Memorial University of Newfoundland, 230 Elizabeth Ave., St John's, NL, A1B 3X9, Canada
| | - Kerri M Sparkes
- Department of Psychology, Memorial University of Newfoundland, 230 Elizabeth Ave., St John's, NL, A1B 3X9, Canada
| | - Ashlyn Swift-Gallant
- Department of Psychology, Memorial University of Newfoundland, 230 Elizabeth Ave., St John's, NL, A1B 3X9, Canada.
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34
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Mouliou DS. C-Reactive Protein: Pathophysiology, Diagnosis, False Test Results and a Novel Diagnostic Algorithm for Clinicians. Diseases 2023; 11:132. [PMID: 37873776 PMCID: PMC10594506 DOI: 10.3390/diseases11040132] [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: 08/09/2023] [Revised: 09/15/2023] [Accepted: 09/19/2023] [Indexed: 10/25/2023] Open
Abstract
The current literature provides a body of evidence on C-Reactive Protein (CRP) and its potential role in inflammation. However, most pieces of evidence are sparse and controversial. This critical state-of-the-art monography provides all the crucial data on the potential biochemical properties of the protein, along with further evidence on its potential pathobiology, both for its pentameric and monomeric forms, including information for its ligands as well as the possible function of autoantibodies against the protein. Furthermore, the current evidence on its potential utility as a biomarker of various diseases is presented, of all cardiovascular, respiratory, hepatobiliary, gastrointestinal, pancreatic, renal, gynecological, andrological, dental, oral, otorhinolaryngological, ophthalmological, dermatological, musculoskeletal, neurological, mental, splenic, thyroid conditions, as well as infections, autoimmune-supposed conditions and neoplasms, including other possible factors that have been linked with elevated concentrations of that protein. Moreover, data on molecular diagnostics on CRP are discussed, and possible etiologies of false test results are highlighted. Additionally, this review evaluates all current pieces of evidence on CRP and systemic inflammation, and highlights future goals. Finally, a novel diagnostic algorithm to carefully assess the CRP level for a precise diagnosis of a medical condition is illustrated.
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35
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Bulygin I, Shatov V, Rykachevskiy A, Raiko A, Bernstein A, Burnaev E, Gelfand MS. Absence of enterotypes in the human gut microbiomes reanalyzed with non-linear dimensionality reduction methods. PeerJ 2023; 11:e15838. [PMID: 37701837 PMCID: PMC10494839 DOI: 10.7717/peerj.15838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 07/12/2023] [Indexed: 09/14/2023] Open
Abstract
Enterotypes of the human gut microbiome have been proposed to be a powerful prognostic tool to evaluate the correlation between lifestyle, nutrition, and disease. However, the number of enterotypes suggested in the literature ranged from two to four. The growth of available metagenome data and the use of exact, non-linear methods of data analysis challenges the very concept of clusters in the multidimensional space of bacterial microbiomes. Using several published human gut microbiome datasets of variable 16S rRNA regions, we demonstrate the presence of a lower-dimensional structure in the microbiome space, with high-dimensional data concentrated near a low-dimensional non-linear submanifold, but the absence of distinct and stable clusters that could represent enterotypes. This observation is robust with regard to diverse combinations of dimensionality reduction techniques and clustering algorithms.
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Affiliation(s)
- Ivan Bulygin
- Skolkovo Institute of Science and Technology, Moscow, Russia
| | | | | | - Arsenii Raiko
- Skolkovo Institute of Science and Technology, Moscow, Russia
| | | | - Evgeny Burnaev
- Skolkovo Institute of Science and Technology, Moscow, Russia
- Artificial Intelligence Research Institute (AIRI), Moscow, Russia
| | - Mikhail S. Gelfand
- Skolkovo Institute of Science and Technology, Moscow, Russia
- Institute for Information Transmission Problems, Moscow, Russia
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Rosel-Pech C, Pinto-Cardoso S, Chávez-Torres M, Montufar N, Osuna-Padilla I, Ávila-Ríos S, Reyes-Terán G, Aguirre-Alvarado C, Matías Juan NA, Pérez-Lorenzana H, Vázquez-Rosales JG, Bekker-Méndez VC. Distinct fecal microbial signatures are linked to sex and chronic immune activation in pediatric HIV infection. Front Immunol 2023; 14:1244473. [PMID: 37711620 PMCID: PMC10497879 DOI: 10.3389/fimmu.2023.1244473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 08/09/2023] [Indexed: 09/16/2023] Open
Abstract
Introduction Our understanding of HIV-associated gut microbial dysbiosis in children perinatally-infected with HIV (CLWH) lags behind that of adults living with HIV. Childhood represents a critical window for the gut microbiota. Any disturbances, including prolonged exposure to HIV, antiretroviral drugs, and antibiotics are likely to have a significant impact on long-term health, resulting in a less resilient gut microbiome. The objective of our study was to characterize the gut microbiota in CLWH, and compare it with HIV-unexposed and -uninfected children. Methods We enrolled 31 children aged 3 to 15 years; 15 were CLWH and 16 were HUU. We assessed dietary patterns and quality; quantified soluble and cellular markers of HIV disease progression by flow cytometry, enzyme-linked immunosorbent and multiplex-bead assays, and profiled the gut microbiota by 16S rRNA sequencing. We explored relationships between the gut microbiota, antibiotic exposure, dietary habits, soluble and cellular markers and host metadata. Results Children had a Western-type diet, their median health eating index score was 67.06 (interquartile range 58.76-74.66). We found no discernable impact of HIV on the gut microbiota. Alpha diversity metrics did not differ between CLWH and HUU. Sex impacted the gut microbiota (R-squared= 0.052, PERMANOVA p=0.024). Male children had higher microbial richness compared with female children. Two taxa were found to discriminate female from male children independently from HIV status: Firmicutes for males, and Bacteroides for females. Markers of HIV disease progression were comparable between CLWH and HUU, except for the frequency of exhausted CD4+ T cells (PD-1+) which was increased in CLWH (p=0.0024 after adjusting for confounders). Both the frequency of exhausted CD4+ and activated CD4+ T cells (CD38+ HLADR+) correlated positively with the relative abundance of Proteobacteria (rho=0.568. false discovery rate (FDR)-adjusted p= 0.029, and rho=0.62, FDR-adjusted p=0.0126, respectively). Conclusion The gut microbiota of CLWH appears similar to that of HUU, and most markers of HIV disease progression are normalized with long-term ART, suggesting a beneficial effect of the latter on the gut microbial ecology. The relationship between exhausted and activated CD4+ T cells and Proteobacteria suggests a connection between the gut microbiome, and premature aging in CLWH.
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Affiliation(s)
- Cecilia Rosel-Pech
- Posgrado en Ciencias Biológicas, Unidad de Posgrado, Universidad Nacional Autónoma de México (UNAM), Ciudad de México, Mexico
- Unidad de Investigación Médica en Inmunología e Infectología, Hospital de Infectología “Dr. Daniel Méndez Hernández”, Centro Médico Nacional “La Raza”, Instituto Mexicano del Seguro Social (IMSS), Ciudad de México, Mexico
| | - Sandra Pinto-Cardoso
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Ciudad de México, Mexico
| | - Monserrat Chávez-Torres
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Ciudad de México, Mexico
| | - Nadia Montufar
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Ciudad de México, Mexico
| | - Iván Osuna-Padilla
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Ciudad de México, Mexico
| | - Santiago Ávila-Ríos
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Ciudad de México, Mexico
| | - Gustavo Reyes-Terán
- Posgrado en Ciencias Biológicas, Unidad de Posgrado, Universidad Nacional Autónoma de México (UNAM), Ciudad de México, Mexico
| | - Charmina Aguirre-Alvarado
- Unidad de Investigación Médica en Inmunología e Infectología, Hospital de Infectología “Dr. Daniel Méndez Hernández”, Centro Médico Nacional “La Raza”, Instituto Mexicano del Seguro Social (IMSS), Ciudad de México, Mexico
| | - Norma Angelica Matías Juan
- Hospital de Infectología “Dr. Daniel Méndez Hernández”, Centro Médico Nacional “La Raza”, Instituto Mexicano del Seguro Social (IMSS), Ciudad de México, Mexico
| | - Héctor Pérez-Lorenzana
- UMAE Hospital General Dr. Gaudencio González Garza, Centro Médico Nacional La Raza, Instituto Mexicano del Seguro Social (IMSS), Ciudad de México, Mexico
| | - José Guillermo Vázquez-Rosales
- Hospital de Pediatría “Doctor Silvestre Frenk Freund”, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, México, Mexico
| | - Vilma Carolina Bekker-Méndez
- Unidad de Investigación Médica en Inmunología e Infectología, Hospital de Infectología “Dr. Daniel Méndez Hernández”, Centro Médico Nacional “La Raza”, Instituto Mexicano del Seguro Social (IMSS), Ciudad de México, Mexico
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Schuetz A, Corley MJ, Sacdalan C, Phuang-Ngern Y, Nakpor T, Wansom T, Ehrenberg PK, Sriplienchan S, Thomas R, Ratnaratorn N, Sukhumvittaya S, Tragonlugsana N, Slike BM, Akapirat S, Pinyakorn S, Rerknimitr R, Pang AP, Kroon E, Teeratakulpisan N, Krebs SJ, Phanuphak N, Ndhlovu LC, Vasan S. Distinct mucosal and systemic immunological characteristics in transgender women potentially relating to HIV acquisition. JCI Insight 2023; 8:e169272. [PMID: 37432754 PMCID: PMC10543719 DOI: 10.1172/jci.insight.169272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 07/06/2023] [Indexed: 07/12/2023] Open
Abstract
Transgender women (TGW) are disproportionally affected by HIV infection, with a global estimated prevalence of 19.9%, often attributed to behavioral risk factors, with less known about biological factors. We evaluated potential biological risk factors for HIV acquisition in TGW at the sites of viral entry by assessing immune parameters of the neovaginal surface and gut mucosa. The neovagina in TGW, compared with the vagina in cisgender women (CW), shows distinct cell composition and may pose a more inflammatory environment, evidenced by increased CD4+ T cell activation and higher levels of soluble markers of inflammation (C-reactive protein, soluble CD30). Increased inflammation may be driven by microbiome composition, as shown by a greater abundance of Prevotella and a higher Shannon Diversity Index. In addition, we have observed higher frequency of CD4+CCR5+ target cells and decreased DNA methylation of the CCR5 gene in the gut mucosa of TGW compared with CW and men who have sex with men, which was inversely correlated with testosterone levels. The rectal microbiome composition in TGW appears to favor a proinflammatory milieu as well as mucosal barrier disruption. Thus, it is possible that increased inflammation and higher frequencies of CCR5-expressing target cells at sites of mucosal viral entry may contribute to increased risk of HIV acquisition in TGW, with further validation in larger studies warranted.
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Affiliation(s)
- Alexandra Schuetz
- Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, Maryland, USA
| | - Michael J. Corley
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, New York, USA
| | | | | | | | - Tanyaporn Wansom
- Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, Maryland, USA
| | - Philip K. Ehrenberg
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | | | - Rasmi Thomas
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | | | | | | | - Bonnie M. Slike
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, Maryland, USA
| | - Siriwat Akapirat
- Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Suteeraporn Pinyakorn
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, Maryland, USA
| | - Rungsun Rerknimitr
- Department of Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Alina P.S. Pang
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Eugène Kroon
- Institute of HIV Research and Innovation, Bangkok, Thailand
| | | | - Shelly J. Krebs
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, Maryland, USA
| | | | - Lishomwa C. Ndhlovu
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Sandhya Vasan
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, Maryland, USA
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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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Mansoor E, Martin SA, Perez A, Nguyen VQ, Katz JA, Gupta S, Cominelli F. Epidemiology of inflammatory bowel disease in men with high-risk homosexual activity. Gut 2023; 72:1624-1625. [PMID: 36170381 DOI: 10.1136/gutjnl-2022-328218] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 08/20/2022] [Indexed: 12/19/2022]
Affiliation(s)
- Emad Mansoor
- Digestive Health Institute, Case Western Reserve University/University Hospitals Cleveland Medical Center, Cleveland, Ohio, USA
| | - Scott A Martin
- Clinical Research Center, University Hospitals Cleveland Medical Center, Cleveland, Ohio, USA
| | - Abe Perez
- Clinical Research Center, University Hospitals Cleveland Medical Center, Cleveland, Ohio, USA
| | - Vu Quang Nguyen
- Digestive Health Institute, Case Western Reserve University/University Hospitals Cleveland Medical Center, Cleveland, Ohio, USA
| | - Jeffry A Katz
- Digestive Health Institute, Case Western Reserve University/University Hospitals Cleveland Medical Center, Cleveland, Ohio, USA
| | - Shubham Gupta
- Division of Reconstructive Urology, Case Western Reserve University/University Hospitals Cleveland Medical Center, Cleveland, Ohio, USA
| | - Fabio Cominelli
- Digestive Health Institute, Case Western Reserve University/University Hospitals Cleveland Medical Center, Cleveland, Ohio, USA
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40
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Zhang Y, Andreu-Sánchez S, Vadaq N, Wang D, Matzaraki V, van der Heijden WA, Gacesa R, Weersma RK, Zhernakova A, Vandekerckhove L, de Mast Q, Joosten LAB, Netea MG, van der Ven AJAM, Fu J. Gut dysbiosis associates with cytokine production capacity in viral-suppressed people living with HIV. Front Cell Infect Microbiol 2023; 13:1202035. [PMID: 37583444 PMCID: PMC10425223 DOI: 10.3389/fcimb.2023.1202035] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 07/06/2023] [Indexed: 08/17/2023] Open
Abstract
Background People living with human immunodeficiency virus (PLHIV) are exposed to chronic immune dysregulation, even when virus replication is suppressed by antiretroviral therapy (ART). Given the emerging role of the gut microbiome in immunity, we hypothesized that the gut microbiome may be related to the cytokine production capacity of PLHIV. Methods To test this hypothesis, we collected metagenomic data from 143 ART-treated PLHIV and assessed the ex vivo production capacity of eight different cytokines [interleukin-1β (IL-1β), IL-6, IL-1Ra, IL-10, IL-17, IL-22, tumor necrosis factor, and interferon-γ] in response to different stimuli. We also characterized CD4+ T-cell counts, HIV reservoir, and other clinical parameters. Results Compared with 190 age- and sex-matched controls and a second independent control cohort, PLHIV showed microbial dysbiosis that was correlated with viral reservoir levels (CD4+ T-cell-associated HIV-1 DNA), cytokine production capacity, and sexual behavior. Notably, we identified two genetically different P. copri strains that were enriched in either PLHIV or healthy controls. The control-related strain showed a stronger negative association with cytokine production capacity than the PLHIV-related strain, particularly for Pam3Cys-incuded IL-6 and IL-10 production. The control-related strain is also positively associated with CD4+ T-cell level. Conclusions Our findings suggest that modulating the gut microbiome may be a strategy to modulate immune response in PLHIV.
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Affiliation(s)
- Yue Zhang
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
- Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Sergio Andreu-Sánchez
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
- Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Nadira Vadaq
- Department of Internal Medicine, Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands
| | - Daoming Wang
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
- Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Vasiliki Matzaraki
- Department of Internal Medicine, Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands
| | - Wouter A. van der Heijden
- Department of Internal Medicine, Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands
| | - Ranko Gacesa
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
- Department of Gastroenterology and Hepatology, University Medical Center Groningen, Groningen, Netherlands
| | - Rinse K. Weersma
- Department of Gastroenterology and Hepatology, University Medical Center Groningen, Groningen, Netherlands
| | - Alexandra Zhernakova
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Linos Vandekerckhove
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Faculty of Medicine and Health Sciences, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Quirijn de Mast
- Department of Internal Medicine, Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands
| | - Leo A. B. Joosten
- Department of Internal Medicine, Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands
- Department of Medical Genetics, Iuliu Hațieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Mihai G. Netea
- Department of Internal Medicine, Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands
- Department of Immunology and Metabolism, Life and Medical Sciences Institute, University of Bonn, Bonn, Germany
| | - André J. A. M. van der Ven
- Department of Internal Medicine, Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands
| | - Jingyuan Fu
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
- Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
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Lacunza E, Fink V, Salas ME, Canzoneri R, Naipauer J, Williams S, Coso O, Sued O, Cahn P, Mesri EA, Abba MC. Oral and anal microbiome from HIV-exposed individuals: role of host-associated factors in taxa composition and metabolic pathways. NPJ Biofilms Microbiomes 2023; 9:48. [PMID: 37438354 DOI: 10.1038/s41522-023-00413-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 06/20/2023] [Indexed: 07/14/2023] Open
Abstract
Evidence indicates that the microbiome plays a significant role in HIV immunopathogenesis and associated complications. This study aimed to characterize the oral and anal microbiome of Men who have Sex with Men (MSM) and Transgender Women (TGW), with and without HIV. One hundred and thirty oral and anal DNA-derived samples were obtained from 78 participants and subjected to shotgun metagenomics sequencing for further microbiome analysis. Significant differences in the microbiome composition were found among subjects associated with HIV infection, gender, sex behavior, CD4+ T-cell counts, antiretroviral therapy (ART), and the presence of HPV-associated precancerous anal lesions. Results confirm the occurrence of oncogenic viromes in this high HIV-risk population. The oral microbiome in HIV-associated cases exhibited an enrichment of bacteria associated with periodontal disease pathogenesis. Conversely, anal bacteria showed a significant decrease in HIV-infected subjects (Coprococcus comes, Finegoldia magna, Blautia obeum, Catenibacterium mitsuokai). TGW showed enrichment in species related to sexual transmission, which concurs that most recruited TGW are or have been sex workers. Prevotella bivia and Fusobacterium gonidiaformans were positively associated with anal precancerous lesions among HIV-infected subjects. The enrichment of Holdemanella biformis and C. comes was associated with detectable viral load and ART-untreated patients. Metabolic pathways were distinctly affected by predominant factors linked to sexual behavior or HIV pathogenesis. Gene family analysis identified bacterial gene signatures as potential prognostic and predictive biomarkers for HIV/AIDS-associated malignancies. Conclusions: Identified microbial features at accessible sites are potential biomarkers for predicting precancerous anal lesions and therapeutic targets for HIV immunopathogenesis.
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Affiliation(s)
- Ezequiel Lacunza
- Centro de Investigaciones Inmunológicas Básicas y Aplicadas (CINIBA), Facultad de Ciencias Médicas, Universidad Nacional de La Plata, La Plata, Argentina.
| | - Valeria Fink
- Dirección de Investigaciones, Fundación Huésped, Buenos Aires, Argentina
| | - María E Salas
- Centro de Investigaciones Inmunológicas Básicas y Aplicadas (CINIBA), Facultad de Ciencias Médicas, Universidad Nacional de La Plata, La Plata, Argentina
| | - Romina Canzoneri
- Centro de Investigaciones Inmunológicas Básicas y Aplicadas (CINIBA), Facultad de Ciencias Médicas, Universidad Nacional de La Plata, La Plata, Argentina
| | - Julián Naipauer
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), CONICET - Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Sion Williams
- University of Miami - Center for AIDS Research (UM-CFAR) / Sylvester Comprehensive Cancer Center (CCC), University of Miami Miller School of Medicine, Miami, FL, USA
| | - Omar Coso
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), CONICET - Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Omar Sued
- Pan American Health Organization, Washington, USA
| | - Pedro Cahn
- Dirección de Investigaciones, Fundación Huésped, Buenos Aires, Argentina
| | - Enrique A Mesri
- University of Miami - Center for AIDS Research (UM-CFAR) / Sylvester Comprehensive Cancer Center (CCC), University of Miami Miller School of Medicine, Miami, FL, USA
| | - Martín C Abba
- Centro de Investigaciones Inmunológicas Básicas y Aplicadas (CINIBA), Facultad de Ciencias Médicas, Universidad Nacional de La Plata, La Plata, Argentina.
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Duarte MJ, Tien PC, Somsouk M, Price JC. The human microbiome and gut-liver axis in people living with HIV. Curr HIV/AIDS Rep 2023; 20:170-180. [PMID: 37129834 PMCID: PMC10232565 DOI: 10.1007/s11904-023-00657-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/05/2023] [Indexed: 05/03/2023]
Abstract
PURPOSE OF REVIEW Chronic liver disease is a major cause of morbidity and mortality amongst people living with HIV (PLWH). Emerging data suggests that gut microbial translocation may play a role in driving and modulating liver disease, a bi-directional relationship termed the gut-liver axis. While it is recognized that PLWH have a high degree of dysbiosis and gut microbial translocation, little is known about the gut-liver axis in PLWH. RECENT FINDINGS Recent studies have shown that microbial translocation can directly lead to hepatic inflammation, and have linked gut microbial signatures, dysbiosis, and translocation to liver disease in PLWH. Additionally, multiple trials have explored interventions targeting the microbiome in PLWH. Emerging research supports the interaction between the gut microbiome and liver disease in PLWH. This offers new opportunities to expand our understanding of the pathophysiology of liver disease in this population, as well as to explore possible clinical interventions.
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Affiliation(s)
- Maria J Duarte
- Division of Gastroenterology and Hepatology, Department of Medicine, University of California, San Francisco, CA, USA
| | - Phyllis C Tien
- Division of Infectious Diseases, Department of Medicine, University of California, San Francisco, CA, USA
- Department of Veterans Affairs Medical Center, San Francisco, CA, USA
| | - Ma Somsouk
- Division of Gastroenterology and Hepatology, Department of Medicine, University of California, San Francisco, CA, USA
| | - Jennifer C Price
- Division of Gastroenterology and Hepatology, Department of Medicine, University of California, San Francisco, CA, USA.
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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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44
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Satish S, Abu Y, Gomez D, Kumar Dutta R, Roy S. HIV, opioid use, and alterations to the gut microbiome: elucidating independent and synergistic effects. Front Immunol 2023; 14:1156862. [PMID: 37168868 PMCID: PMC10164749 DOI: 10.3389/fimmu.2023.1156862] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 03/22/2023] [Indexed: 05/13/2023] Open
Abstract
Background The microbiome is essential to immune development, defense against pathogens, and modulation of inflammation. Microbial dysbiosis has been reported in various diseases including human immunodeficiency virus (HIV) and opioid use disorder (OUD). Notably, people living with HIV (PLWH) have been reported to both have higher rates of OUD and use opioids at higher rates than the general public. Thus, studying gut microbial alterations in people living with HIV and with OUD could elucidate mechanisms pertaining to how these conditions both shape and are shaped by the microbiome. However, to date few studies have investigated how HIV and OUD in combination impact the microbiome. Aim of review Here, we review previous studies outlining interactions between HIV, opioid use, and microbial dysbiosis and describe attempts to treat this dysbiosis with fecal microbial transplantation, probiotics, and dietary changes. Key scientific concepts of review While the limited number of studies prevent overgeneralizations; accumulating data suggest that HIV and opioid use together induce distinct alterations in the gut microbiome. Among the three existing preclinical studies of HIV and opioid use, two studies reported a decrease in Lachnospiraceae and Ruminococcaceae, and one study reported a decrease in Muribaculaceae in the combined HIV and opioid group relative to HIV-alone, opioid-alone, or control groups. These bacteria are known to modulate immune function, decrease colonic inflammation, and maintain gut epithelial barrier integrity in healthy individuals. Accordingly, modulation of the gut microbiome to restore gut homeostasis may be attempted to improve both conditions. While mixed results exist regarding treating dysbiosis with microbial restoration in PLWH or in those with opioid dependency, larger well-defined studies that can improve microbial engraftment in hosts hold much promise and should still be explored.
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Affiliation(s)
- Sanjana Satish
- Department of Medical Education, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Yaa Abu
- Department of Medical Education, University of Miami Miller School of Medicine, Miami, FL, United States
- Department of Surgery, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Daniel Gomez
- Department of Medical Education, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Rajib Kumar Dutta
- Department of Surgery, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Sabita Roy
- Department of Surgery, University of Miami Miller School of Medicine, Miami, FL, United States
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Baltazar-Díaz TA, Amador-Lara F, Andrade-Villanueva JF, González-Hernández LA, Cabrera-Silva RI, Sánchez-Reyes K, Álvarez-Zavala M, Valenzuela-Ramírez A, Del Toro-Arreola S, Bueno-Topete MR. Gut Bacterial Communities in HIV-Infected Individuals with Metabolic Syndrome: Effects of the Therapy with Integrase Strand Transfer Inhibitor-Based and Protease Inhibitor-Based Regimens. Microorganisms 2023; 11:microorganisms11040951. [PMID: 37110374 PMCID: PMC10146710 DOI: 10.3390/microorganisms11040951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 03/27/2023] [Accepted: 04/04/2023] [Indexed: 04/29/2023] Open
Abstract
Antiretroviral therapies (ART) are strongly associated with weight gain and metabolic syndrome (MetS) development in HIV-infected patients. Few studies have evaluated the association between gut microbiota and integrase strand transfer inhibitor (INSTI)-based and protease inhibitor (PI)-based regimens in HIV-infected patients with MetS. To assess this, fecal samples were obtained from HIV-infected patients treated with different regimens (16 PI + MetS or 30 INSTI + MetS) and 18 healthy controls (HCs). The microbial composition was characterized using 16S rRNA amplicon sequencing. The INSTI-based and PI-based regimens were associated with a significant decrease in α-diversity compared to HCs. The INSTI + MetS group showed the lowest α-diversity between both regimens. A significant increase in the abundance of short-chain fatty acid (SCFA)-producing genera (Roseburia, Dorea, Ruminococcus torques, and Coprococcus) was observed in the PI + MetS group, while Prevotella, Fusobacterium, and Succinivibrio were significantly increased in the INSTI + MetS group. Moreover, the Proteobacteria/Firmicutes ratio was overrepresented, and functional pathways related to the biosynthesis of LPS components were increased in the INSTI + MetS group. The gut microbiota of patients receiving INSTIs showed a more pronounced dysbiosis orchestrated by decreased bacterial richness and diversity, with an almost complete absence of SCFA-producing bacteria and alterations in gut microbiota functional pathways. These findings have not been previously observed.
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Affiliation(s)
- Tonatiuh Abimael Baltazar-Díaz
- Departamento de Biología Molecular y Genómica, Instituto de Investigación en Enfermedades Crónico-Degenerativas, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara 44350, Mexico
| | - Fernando Amador-Lara
- Unidad de VIH, Hospital Civil de Guadalajara "Fray Antonio Alcalde", Guadalajara 44350, Mexico
- Departamento de Clínicas Médicas, Instituto de Investigación en Inmunodeficiencias y VIH, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara 44350, Mexico
| | - Jaime F Andrade-Villanueva
- Unidad de VIH, Hospital Civil de Guadalajara "Fray Antonio Alcalde", Guadalajara 44350, Mexico
- Departamento de Clínicas Médicas, Instituto de Investigación en Inmunodeficiencias y VIH, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara 44350, Mexico
| | - Luz Alicia González-Hernández
- Unidad de VIH, Hospital Civil de Guadalajara "Fray Antonio Alcalde", Guadalajara 44350, Mexico
- Departamento de Clínicas Médicas, Instituto de Investigación en Inmunodeficiencias y VIH, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara 44350, Mexico
| | - Rodolfo Ismael Cabrera-Silva
- Departamento de Clínicas Médicas, Instituto de Investigación en Inmunodeficiencias y VIH, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara 44350, Mexico
| | - Karina Sánchez-Reyes
- Departamento de Clínicas Médicas, Instituto de Investigación en Inmunodeficiencias y VIH, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara 44350, Mexico
| | - Monserrat Álvarez-Zavala
- Departamento de Clínicas Médicas, Instituto de Investigación en Inmunodeficiencias y VIH, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara 44350, Mexico
| | - Aldo Valenzuela-Ramírez
- Unidad de VIH, Hospital Civil de Guadalajara "Fray Antonio Alcalde", Guadalajara 44350, Mexico
| | - Susana Del Toro-Arreola
- Departamento de Biología Molecular y Genómica, Instituto de Investigación en Enfermedades Crónico-Degenerativas, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara 44350, Mexico
| | - Miriam Ruth Bueno-Topete
- Departamento de Biología Molecular y Genómica, Instituto de Investigación en Enfermedades Crónico-Degenerativas, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara 44350, Mexico
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Ancona G, Alagna L, Alteri C, Palomba E, Tonizzo A, Pastena A, Muscatello A, Gori A, Bandera A. Gut and airway microbiota dysbiosis and their role in COVID-19 and long-COVID. Front Immunol 2023; 14:1080043. [PMID: 36969243 PMCID: PMC10030519 DOI: 10.3389/fimmu.2023.1080043] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 02/13/2023] [Indexed: 03/29/2023] Open
Abstract
The gut microbiota plays a crucial role in human health and disease. Gut dysbiosis is known to be associated with increased susceptibility to respiratory diseases and modifications in the immune response and homeostasis of the lungs (the so-called gut-lung axis). Furthermore, recent studies have highlighted the possible role of dysbiosis in neurological disturbances, introducing the notion of the "gut-brain axis." During the last 2 years, several studies have described the presence of gut dysbiosis during coronavirus disease 2019 (COVID-19) and its relationship with disease severity, SARS-CoV-2 gastrointestinal replication, and immune inflammation. Moreover, the possible persistence of gut dysbiosis after disease resolution may be linked to long-COVID syndrome and particularly to its neurological manifestations. We reviewed recent evidence on the association between dysbiosis and COVID-19, investigating the possible epidemiologic confounding factors like age, location, sex, sample size, the severity of disease, comorbidities, therapy, and vaccination status on gut and airway microbial dysbiosis in selected studies on both COVID-19 and long-COVID. Moreover, we analyzed the confounding factors strictly related to microbiota, specifically diet investigation and previous use of antibiotics/probiotics, and the methodology used to study the microbiota (α- and β-diversity parameters and relative abundance tools). Of note, only a few studies focused on longitudinal analyses, especially for long-term observation in long-COVID. Lastly, there is a lack of knowledge regarding the role of microbiota transplantation and other therapeutic approaches and their possible impact on disease progression and severity. Preliminary data seem to suggest that gut and airway dysbiosis might play a role in COVID-19 and in long-COVID neurological symptoms. Indeed, the development and interpretation of these data could have important implications for future preventive and therapeutic strategies.
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Affiliation(s)
- Giuseppe Ancona
- Infectious Diseases Unit, Foundation IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Laura Alagna
- Infectious Diseases Unit, Foundation IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Claudia Alteri
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
- Multimodal Research Area, Bambino Gesù Children Hospital (IRCCS), Rome, Italy
| | - Emanuele Palomba
- Infectious Diseases Unit, Foundation IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
- Department of Pathophysiology and Transplantation, Centre for Multidisciplinary Research in Health Science (MACH), University of Milan, Milan, Italy
| | - Anna Tonizzo
- Infectious Diseases Unit, Foundation IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
- Department of Pathophysiology and Transplantation, Centre for Multidisciplinary Research in Health Science (MACH), University of Milan, Milan, Italy
| | - Andrea Pastena
- Infectious Diseases Unit, Foundation IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
- Department of Pathophysiology and Transplantation, Centre for Multidisciplinary Research in Health Science (MACH), University of Milan, Milan, Italy
| | - Antonio Muscatello
- Infectious Diseases Unit, Foundation IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Andrea Gori
- Infectious Diseases Unit, Foundation IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
- Department of Pathophysiology and Transplantation, Centre for Multidisciplinary Research in Health Science (MACH), University of Milan, Milan, Italy
| | - Alessandra Bandera
- Infectious Diseases Unit, Foundation IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
- Department of Pathophysiology and Transplantation, Centre for Multidisciplinary Research in Health Science (MACH), University of Milan, Milan, Italy
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47
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Castillo-Rozas G, Lopez MN, Soto-Rifo R, Vidal R, Cortes CP. Enteropathy and gut dysbiosis as obstacles to achieve immune recovery in undetectable people with HIV: a clinical view of evidence, successes, and projections. AIDS 2023; 37:367-378. [PMID: 36695354 DOI: 10.1097/qad.0000000000003450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Immune performance following antiretroviral therapy initiation varies among patients. Despite achieving viral undetectability, a subgroup of patients fails to restore CD4+ T-cell counts during follow-up, which exposes them to non-AIDS defining comorbidities and increased mortality. Unfortunately, its mechanisms are incompletely understood, and no specific treatment is available. In this review, we address some of the pathophysiological aspects of the poor immune response from a translational perspective, with emphasis in the interaction between gut microbiome, intestinal epithelial dysfunction, and immune system, and we also discuss some studies attempting to improve immune performance by intervening in this vicious cycle.
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Affiliation(s)
- Gabriel Castillo-Rozas
- Molecular and Cellular Virology Laboratory, Virology Program
- Cancer Regulation and Immunoediting Laboratory, Immunology Program
- Center for HIV/AIDS Integral Research -CHAIR, Universidad de Chile, Santiago
- Millennium Institute on Immunology and Immunotherapy, Santiago, Chile
| | - Mercedes N Lopez
- Cancer Regulation and Immunoediting Laboratory, Immunology Program
| | - Ricardo Soto-Rifo
- Molecular and Cellular Virology Laboratory, Virology Program
- Center for HIV/AIDS Integral Research -CHAIR, Universidad de Chile, Santiago
- Millennium Institute on Immunology and Immunotherapy, Santiago, Chile
| | - Roberto Vidal
- Microbiology and Mycology Program, Institute of Biomedical Sciences
| | - Claudia P Cortes
- Internal Medicine Department, Faculty of Medicine, Universidad de Chile
- Center for HIV/AIDS Integral Research -CHAIR, Universidad de Chile, Santiago
- Millennium Institute on Immunology and Immunotherapy, Santiago, Chile
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48
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Mikaeloff F, Gelpi M, Benfeitas R, Knudsen AD, Vestad B, Høgh J, Hov JR, Benfield T, Murray D, Giske CG, Mardinoglu A, Trøseid M, Nielsen SD, Neogi U. Network-based multi-omics integration reveals metabolic at-risk profile within treated HIV-infection. eLife 2023; 12:82785. [PMID: 36794912 PMCID: PMC10017104 DOI: 10.7554/elife.82785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 02/15/2023] [Indexed: 02/17/2023] Open
Abstract
Multiomics technologies improve the biological understanding of health status in people living with HIV on antiretroviral therapy (PWH). Still, a systematic and in-depth characterization of metabolic risk profile during successful long-term treatment is lacking. Here, we used multi-omics (plasma lipidomic, metabolomic, and fecal 16 S microbiome) data-driven stratification and characterization to identify the metabolic at-risk profile within PWH. Through network analysis and similarity network fusion (SNF), we identified three groups of PWH (SNF-1-3): healthy (HC)-like (SNF-1), mild at-risk (SNF-3), and severe at-risk (SNF-2). The PWH in the SNF-2 (45%) had a severe at-risk metabolic profile with increased visceral adipose tissue, BMI, higher incidence of metabolic syndrome (MetS), and increased di- and triglycerides despite having higher CD4+ T-cell counts than the other two clusters. However, the HC-like and the severe at-risk group had a similar metabolic profile differing from HIV-negative controls (HNC), with dysregulation of amino acid metabolism. At the microbiome profile, the HC-like group had a lower α-diversity, a lower proportion of men having sex with men (MSM) and was enriched in Bacteroides. In contrast, in at-risk groups, there was an increase in Prevotella, with a high proportion of MSM, which could potentially lead to higher systemic inflammation and increased cardiometabolic risk profile. The multi-omics integrative analysis also revealed a complex microbial interplay of the microbiome-associated metabolites in PWH. Those severely at-risk clusters may benefit from personalized medicine and lifestyle intervention to improve their dysregulated metabolic traits, aiming to achieve healthier aging.
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Affiliation(s)
- Flora Mikaeloff
- The Systems Virology Lab, Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska InstituteStockholmSweden
| | - Marco Gelpi
- Copenhagen University Hospital RigshospitaletCopenhagenDenmark
| | - Rui Benfeitas
- National Bioinformatics Infrastructure Sweden (NBIS), Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm UniversityStockholmSweden
| | | | - Beate Vestad
- Research Institute of Internal Medicine, Oslo University Hospital RikshospitaletOsloNorway
- Norwegian PSC Research Center, Oslo University Hospital RikshospitaletOsloNorway
| | - Julie Høgh
- Copenhagen University Hospital RigshospitaletCopenhagenDenmark
| | - Johannes R Hov
- Research Institute of Internal Medicine, Oslo University Hospital RikshospitaletOsloNorway
- Norwegian PSC Research Center, Oslo University Hospital RikshospitaletOsloNorway
- Institute of Clinical Medicine, University of OsloOsloNorway
| | - Thomas Benfield
- Department of Infectious Diseases, Copenhagen University Hospital – Amager and HvidovreHvidovreDenmark
| | - Daniel Murray
- Centre of Excellence for Health, Immunity and Infections (CHIP), Rigshospitalet, University of CopenhagenCopenhagenDenmark
| | - Christian G Giske
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska InstitutetStockholmSweden
| | - Adil Mardinoglu
- Science for Life Laboratory, KTH - Royal Institute of TechnologyStockholmSweden
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College LondonLondonUnited Kingdom
| | - Marius Trøseid
- Research Institute of Internal Medicine, Oslo University Hospital RikshospitaletOsloNorway
- Institute of Clinical MedicineOsloNorway
| | | | - Ujjwal Neogi
- The Systems Virology Lab, Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska InstituteStockholmSweden
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49
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Flynn JK, Ortiz AM, Herbert R, Brenchley JM. Host Genetics and Environment Shape the Composition of the Gastrointestinal Microbiome in Nonhuman Primates. Microbiol Spectr 2023; 11:e0213922. [PMID: 36475838 PMCID: PMC9927375 DOI: 10.1128/spectrum.02139-22] [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: 06/07/2022] [Accepted: 11/16/2022] [Indexed: 12/13/2022] Open
Abstract
The bacterial component of the gastrointestinal tract microbiome is comprised of hundreds of species, the majority of which live in symbiosis with the host. The bacterial microbiome is influenced by host diet and disease history, and host genetics may additionally play a role. To understand the degree to which host genetics shapes the gastrointestinal tract microbiome, we studied fecal microbiomes in 4 species of nonhuman primates (NHPs) held in separate facilities but fed the same base diet. These animals include Chlorocebus pygerythrus, Chlorocebus sabaeus, Macaca mulatta, and Macaca nemestrina. We also followed gastrointestinal tract microbiome composition in 20 Macaca mulatta (rhesus macaques [RMs]) as they transitioned from an outdoor to indoor environment and compared 6 Chlorocebus pygerythrus monkeys that made the outdoor to indoor transition to their 9 captive-born offspring. We found that genetics can influence microbiome composition, with animals of different genera (Chlorocebus versus Macaca) having significantly different gastrointestinal (GI) microbiomes despite controlled diets. Animals within the same genera have more similar microbiomes, although still significantly different, and animals within the same species have even more similar compositions that are not significantly different. Significant differences were also not observed between wild-born and captive-born Chlorocebus pygerythrus, while there were significant changes in RMs as they transitioned into captivity. Together, these results suggest that the effects of captivity have a larger impact on the microbiome than other factors we examined within a single NHP species, although host genetics does significantly influence microbiome composition between NHP genera and species. IMPORTANCE Our data point to the degree to which host genetics can influence GI microbiome composition and suggest, within primate species, that individual host genetics is unlikely to significantly alter the microbiome. These data are important for the development of therapeutics aimed at altering the microbiome within populations of genetically disparate members of primate species.
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Affiliation(s)
- Jacob K. Flynn
- Barrier Immunity Section, Lab of Viral Diseases, NIAID, NIH, Bethesda, Maryland, USA
| | - Alexandra M. Ortiz
- Barrier Immunity Section, Lab of Viral Diseases, NIAID, NIH, Bethesda, Maryland, USA
| | - Richard Herbert
- Comparative Medicine Branch, NIAID, NIH, Bethesda, Maryland, USA
| | - Jason M. Brenchley
- Barrier Immunity Section, Lab of Viral Diseases, NIAID, NIH, Bethesda, Maryland, USA
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50
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Meng J, Tao J, Abu Y, Sussman DA, Girotra M, Franceschi D, Roy S. HIV-Positive Patients on Antiretroviral Therapy Have an Altered Mucosal Intestinal but Not Oral Microbiome. Microbiol Spectr 2023; 11:e0247222. [PMID: 36511710 PMCID: PMC9927552 DOI: 10.1128/spectrum.02472-22] [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: 06/29/2022] [Accepted: 11/27/2022] [Indexed: 12/15/2022] Open
Abstract
This study characterized compositional and functional shifts in the intestinal and oral microbiome in HIV-positive patients on antiretroviral therapy compared to HIV-negative individuals. Seventy-nine specimens were collected from 5 HIV-positive and 12 control subjects from five locations (colon brush, colon wash, terminal ileum [TI] brush, TI wash, and saliva) during colonoscopy and at patient visits. Microbiome composition was characterized using 16S rRNA sequencing, and microbiome function was predicted using bioinformatics tools (PICRUSt and BugBase). Our analysis indicated that the β-diversity of all intestinal samples (colon brush, colon wash, TI brush, and TI wash) from patients with HIV was significantly different from patients without HIV. Specifically, bacteria from genera Prevotella, Fusobacterium, and Megasphaera were more abundant in samples from HIV-positive patients. On the other hand, bacteria from genera Ruminococcus, Blautia, and Clostridium were more abundant in samples from HIV-negative patients. Additionally, HIV-positive patients had higher abundances of biofilm-forming and pathogenic bacteria. Furthermore, pathways related to translation and nucleotide metabolism were elevated in HIV-positive patients, whereas pathways related to lipid and carbohydrate metabolism were positively correlated with samples from HIV-negative patients. Our analyses further showed variations in microbiome composition in HIV-positive and negative patients by sampling site. Samples from colon wash, colon brush, and TI wash were significant between groups, while samples from TI brush and saliva were not significant. Taken together, here, we report altered intestinal microbiome composition and predicted function in patients with HIV compared to uninfected patients, though we found no changes in the oral microbiome. IMPORTANCE Over 37 million people worldwide are living with HIV. Although the availability of antiretroviral therapy has significantly reduced the number of AIDS-related deaths, individuals living with HIV are at increased risk for opportunistic infections. We now know that HIV interacts with the trillions of bacteria, fungi, and viruses in the human body termed the microbiome. Only a limited number of previous studies have compared variations in the oral and gastrointestinal microbiome with HIV infection. Here, we detail how the oral and gastrointestinal microbiome changes with HIV infection, having used 5 different sampling sites to gain a more comprehensive view of these changes by location. Our results show site-specific changes in the intestinal microbiome associated with HIV infection. Additionally, we show that while there were significant changes in the intestinal microbiome, there were no significant changes in the oral microbiome.
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Affiliation(s)
- Jingjing Meng
- Department of Surgery, Sylvester Comprehensive Cancer Center, University of Miami, Miami, Florida, USA
| | - Junyi Tao
- Department of Surgery, Sylvester Comprehensive Cancer Center, University of Miami, Miami, Florida, USA
| | - Yaa Abu
- Department of Surgery, Sylvester Comprehensive Cancer Center, University of Miami, Miami, Florida, USA
| | - Daniel Andrew Sussman
- Department of Gastroenterology, University of Miami Medical Group, Miami, Florida, USA
| | - Mohit Girotra
- Department of Gastroenterology, University of Miami Medical Group, Miami, Florida, USA
| | - Dido Franceschi
- Department of Surgery, Sylvester Comprehensive Cancer Center, University of Miami, Miami, Florida, USA
| | - Sabita Roy
- Department of Surgery, Sylvester Comprehensive Cancer Center, University of Miami, Miami, Florida, USA
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