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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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2
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Lippincott RA, O’Connor J, Neff CP, Lozupone C, Palmer BE. Deciphering HIV-associated inflammation: microbiome's influence and experimental insights. Curr Opin HIV AIDS 2024; 19:228-233. [PMID: 38884255 PMCID: PMC11305906 DOI: 10.1097/coh.0000000000000866] [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: 06/18/2024]
Abstract
PURPOSE OF REVIEW To review novel experimental approaches for studying host:microbe interactions and their role in intestinal and systemic inflammation in people living with HIV (PLWH). RECENT FINDINGS Inflammation in PLWH is impacted by interactions between the microbiome, the intestinal epithelium, and immune cells. This complex interplay is not fully understood and requires a variety of analytical techniques to study. Using a multiomic systems biology approach provides hypothesis generating data on host:microbe interactions that can be used to guide further investigation. The direct interactions between host cells and microbes can be elucidated using peripheral blood mononuclear cells (PBMCs), lamina propria mononuclear cells (LPMC's) or human intestinal organoids (HIO). Additionally, the broader relationship between the host and the microbiome can be explored using animal models such as nonhuman primates and germ-free and double humanized mice. SUMMARY To explore complex host:microbe relationships, hypotheses are generated and investigations are guided by multiomic data, while causal components are identified using in-vitro and in-vivo assays.
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Affiliation(s)
| | - John O’Connor
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | | | - Catherine Lozupone
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, 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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Chen X, Wei J, Li Z, Zhang Y, Zhang X, Zhang L, Wang X, Zhang Y, Zhang T. Dysregulation of Gut Microbiota-Derived Neuromodulatory Amino Acid Metabolism in Human Immunodeficiency Virus-Associated Neurocognitive Disorder: An Integrative Metagenomic and Metabolomic Analysis. Ann Neurol 2024; 96:306-320. [PMID: 38752697 DOI: 10.1002/ana.26963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 04/20/2024] [Accepted: 04/27/2024] [Indexed: 07/11/2024]
Abstract
OBJECTIVE Although accumulating evidence implicating altered gut microbiota in human immunodeficiency virus (HIV) infection and neurodegenerative disorders; however, the association between dysbiosis of the gut microbiota and metabolites in the pathogenesis of HIV-associated neurocognitive disorder (HAND) remains unclear. METHODS Fecal and plasma samples were obtained from 3 cohorts (HAND, HIV-non-HAND, and healthy controls), metagenomic analysis and metabolomic profiling were performed to investigate alterations in the gut microbial composition and circulating metabolites in HAND. RESULTS The gut microbiota of people living with HIV (PLWH) had an increased relative abundance of Prevotella and a decreased relative abundance of Bacteroides. In contrast, Prevotella and Megamonas were substantially decreased, and Bacteroides and Phocaeicola were increased in HAND patients. Moreover, untargeted metabolomics identified several neurotransmitters and certain amino acids associated with neuromodulation, and the differential metabolic pathways of amino acids associated with neurocognition were depleted in HAND patients. Notably, most neuromodulatory metabolites are associated with an altered abundance of specific gut bacteria. INTERPRETATION Our findings provide new insights into the intricate interplay between the gut and microbiome-brain axis in the pathogenesis of HAND, highlighting the potential for developing novel therapeutic strategies that specifically target the gut microbiota. ANN NEUROL 2024;96:306-320.
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Affiliation(s)
- Xue Chen
- Clinical and Research Center for Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing, China
- Beijing Key Laboratory for HIV/AIDS Research, Beijing Youan Hospital, Capital Medical University, Beijing, China
- Beijing Institute of Hepatology, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Jiaqi Wei
- Clinical and Research Center for Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing, China
- Beijing Key Laboratory for HIV/AIDS Research, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Zhen Li
- Beijing Key Laboratory for HIV/AIDS Research, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Yang Zhang
- Clinical and Research Center for Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing, China
- Beijing Key Laboratory for HIV/AIDS Research, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Xin Zhang
- Beijing Key Laboratory for HIV/AIDS Research, Beijing Youan Hospital, Capital Medical University, Beijing, China
- Beijing Institute of Hepatology, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Ling Zhang
- Beijing Institute of Hepatology, Beijing Youan Hospital, Capital Medical University, Beijing, China
- Department of Respiratory and Critical Care Medicine, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Xia Wang
- Beijing Key Laboratory for HIV/AIDS Research, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Yulin Zhang
- Department of Respiratory and Critical Care Medicine, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Tong Zhang
- Clinical and Research Center for Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing, China
- Beijing Key Laboratory for HIV/AIDS Research, Beijing Youan Hospital, Capital Medical University, Beijing, China
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5
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Cai Y, Podlaha O, Deeks SG, Brinson C, Ramgopal MN, DeJesus E, Mills A, Shalit P, Abdel-Mohsen M, Zhang L, de Vries CR, Vendrame E, SenGupta D, Wallin JJ. HIV rebound in HIV controllers is associated with a specific fecal microbiome profile. Eur J Immunol 2024; 54:e2350809. [PMID: 38727191 DOI: 10.1002/eji.202350809] [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: 02/27/2024] [Revised: 04/19/2024] [Accepted: 04/30/2024] [Indexed: 08/09/2024]
Abstract
HIV infection is associated with gut dysbiosis, and microbiome variability may affect HIV control when antiretroviral therapy (ART) is stopped. The TLR7 agonist, vesatolimod, was previously associated with a modest delay in viral rebound following analytical treatment interruption in HIV controllers (HCs). Using a retrospective analysis of fecal samples from HCs treated with vesatolimod or placebo (NCT03060447), people with chronic HIV (CH; NCT02858401) or without HIV (PWOH), we examined fecal microbiome profile in HCs before/after treatment, and in CH and PWOH. Microbiome diversity and abundance were compared between groups to investigate the association between specific phyla/species, immune biomarkers, and viral outcomes during treatment interruption. Although there were no significant differences in gut microbiome diversity between people with and without HIV, HCs, and CH shared common features that distinguished them from PWOH. there was a trend toward greater microbiome diversity among HCs. Treatment with vesatolimod reduced dysbiosis in HCs. Firmicutes positively correlated with T-cell activation, while Bacteroidetes and Euryarchaeota inversely correlated with TLR7-mediated immune activation. Specific types of fecal microbiome abundance (e.g. Alistipes putredinis) positively correlated with HIV rebound. In conclusion, variability in the composition of the fecal microbiome is associated with markers of immune activation following vesatolimod treatment and ART interruption.
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Affiliation(s)
- Yanhui Cai
- Gilead Sciences, Inc., Foster City, California, USA
| | | | - Steven G Deeks
- Department of Medicine, University of California San Francisco, San Francisco, California, USA
| | | | - Moti N Ramgopal
- Midway Immunology and Research Center, Fort Pierce, Florida, USA
| | | | - Anthony Mills
- Men's Health Foundation, West Hollywood, California, USA
| | - Peter Shalit
- Peter Shalit MD and Associates, Seattle, Washington, USA
| | - Mohamed Abdel-Mohsen
- Vaccine and Immunotherapy Center, The Wistar Institute, Philadelphia, Pennsylvania, USA
| | - Liao Zhang
- Gilead Sciences, Inc., Foster City, California, USA
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6
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Hmiel L, Zhang S, Obare LM, Santana MADO, Wanjalla CN, Titanji BK, Hileman CO, Bagchi S. Inflammatory and Immune Mechanisms for Atherosclerotic Cardiovascular Disease in HIV. Int J Mol Sci 2024; 25:7266. [PMID: 39000373 PMCID: PMC11242562 DOI: 10.3390/ijms25137266] [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: 06/01/2024] [Revised: 06/26/2024] [Accepted: 06/28/2024] [Indexed: 07/16/2024] Open
Abstract
Atherosclerotic vascular disease disproportionately affects persons living with HIV (PLWH) compared to those without. The reasons for the excess risk include dysregulated immune response and inflammation related to HIV infection itself, comorbid conditions, and co-infections. Here, we review an updated understanding of immune and inflammatory pathways underlying atherosclerosis in PLWH, including effects of viral products, soluble mediators and chemokines, innate and adaptive immune cells, and important co-infections. We also present potential therapeutic targets which may reduce cardiovascular risk in PLWH.
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Affiliation(s)
- Laura Hmiel
- Department of Medicine, Division of Infectious Disease, MetroHealth Medical Center and Case Western Reserve University, Cleveland, OH 44109, USA
| | - Suyu Zhang
- Department of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Laventa M. Obare
- Division of Infectious Diseases, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | | | - Celestine N. Wanjalla
- Division of Infectious Diseases, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Boghuma K. Titanji
- Division of Infectious Diseases, Emory University, Atlanta, GA 30322, USA
| | - Corrilynn O. Hileman
- Department of Medicine, Division of Infectious Disease, MetroHealth Medical Center and Case Western Reserve University, Cleveland, OH 44109, USA
| | - Shashwatee Bagchi
- Division of Infectious Diseases, Washington University in St. Louis, St. Louis, MO 63110, USA
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7
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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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8
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Moodley S, Kroon E, Naidoo CC, Nyawo GR, Wu BG, Naidoo S, Chiyaka TL, Tshivhula H, Singh S, Li Y, Warren RM, Hoal EG, Schurr E, Clemente JC, Segal LN, Möller M, Theron G. Latent Tuberculosis Infection Is Associated with an Enrichment of Short-Chain Fatty Acid-Producing Bacteria in the Stool of Women Living with HIV. Microorganisms 2024; 12:1048. [PMID: 38930430 PMCID: PMC11205370 DOI: 10.3390/microorganisms12061048] [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: 04/12/2024] [Revised: 05/10/2024] [Accepted: 05/14/2024] [Indexed: 06/28/2024] Open
Abstract
Latent tuberculosis infection (LTBI) is common in people living with HIV (PLHIV) in high-TB-burden settings. Active TB is associated with specific stool taxa; however, little is known about the stool microbiota and LTBI in PLHIV. We characterised the stool microbiota of PLHIV with [interferon-γ release assay (IGRA)- and tuberculin skin test (TST)-positive] or without (IGRA- and TST-negative) LTBI (n = 25 per group). The 16S rRNA DNA sequences were analysed using QIIME2, Dirichlet-Multinomial Mixtures, DESeq2, and PICRUSt2. No α- or β-diversity differences occurred by LTBI status; however, LTBI-positive people were Faecalibacterium-, Blautia-, Gemmiger-, and Bacteroides-enriched and Moryella-, Atopobium-, Corynebacterium-, and Streptococcus-depleted. Inferred metagenome data showed that LTBI-negative-enriched pathways included several metabolite degradation pathways. Stool from LTBI-positive people demonstrated differential taxa abundance based on a quantitative response to antigen stimulation. In LTBI-positive people, older people had different β-diversities than younger people, whereas in LTBI-negative people, no differences occurred across age groups. Amongst female PLHIV, those with LTBI were, vs. those without LTBI, Faecalibacterium-, Blautia-, Gemmiger-, and Bacteriodes-enriched, which are producers of short-chain fatty acids. Taxonomic differences amongst people with LTBI occurred according to quantitative response to antigen stimulation and age. These data enhance our understanding of the microbiome's potential role in LTBI.
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Affiliation(s)
- Suventha Moodley
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town 7505, South Africa; (S.M.); (E.K.); (C.C.N.); (G.R.N.); (S.N.); (T.L.C.); (H.T.); (R.M.W.); (E.G.H.); (M.M.)
- African Microbiome Institute, Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 7505, South Africa
| | - Elouise Kroon
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town 7505, South Africa; (S.M.); (E.K.); (C.C.N.); (G.R.N.); (S.N.); (T.L.C.); (H.T.); (R.M.W.); (E.G.H.); (M.M.)
| | - Charissa C. Naidoo
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town 7505, South Africa; (S.M.); (E.K.); (C.C.N.); (G.R.N.); (S.N.); (T.L.C.); (H.T.); (R.M.W.); (E.G.H.); (M.M.)
- African Microbiome Institute, Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 7505, South Africa
| | - Georgina R. Nyawo
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town 7505, South Africa; (S.M.); (E.K.); (C.C.N.); (G.R.N.); (S.N.); (T.L.C.); (H.T.); (R.M.W.); (E.G.H.); (M.M.)
- African Microbiome Institute, Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 7505, South Africa
| | - Benjamin G. Wu
- Division of Pulmonary and Critical Care Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY 10016, USA; (B.G.W.); (S.S.); (Y.L.); (L.N.S.)
| | - Selisha Naidoo
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town 7505, South Africa; (S.M.); (E.K.); (C.C.N.); (G.R.N.); (S.N.); (T.L.C.); (H.T.); (R.M.W.); (E.G.H.); (M.M.)
| | - Tinaye L. Chiyaka
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town 7505, South Africa; (S.M.); (E.K.); (C.C.N.); (G.R.N.); (S.N.); (T.L.C.); (H.T.); (R.M.W.); (E.G.H.); (M.M.)
- African Microbiome Institute, Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 7505, South Africa
| | - Happy Tshivhula
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town 7505, South Africa; (S.M.); (E.K.); (C.C.N.); (G.R.N.); (S.N.); (T.L.C.); (H.T.); (R.M.W.); (E.G.H.); (M.M.)
- African Microbiome Institute, Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 7505, South Africa
| | - Shivani Singh
- Division of Pulmonary and Critical Care Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY 10016, USA; (B.G.W.); (S.S.); (Y.L.); (L.N.S.)
| | - Yonghua Li
- Division of Pulmonary and Critical Care Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY 10016, USA; (B.G.W.); (S.S.); (Y.L.); (L.N.S.)
| | - Robin M. Warren
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town 7505, South Africa; (S.M.); (E.K.); (C.C.N.); (G.R.N.); (S.N.); (T.L.C.); (H.T.); (R.M.W.); (E.G.H.); (M.M.)
| | - Eileen G. Hoal
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town 7505, South Africa; (S.M.); (E.K.); (C.C.N.); (G.R.N.); (S.N.); (T.L.C.); (H.T.); (R.M.W.); (E.G.H.); (M.M.)
| | - Erwin Schurr
- Department of Biochemistry, McGill University, Montreal, QC H3A 1Y6, Canada;
- Program in Infectious Diseases and Immunity in Global Health, The Research Institute of the McGill University Health Centre, 1001 Boul Décarie, Site Glen Block E, Room EM3.3210, Montréal, QC H4A 3J1, Canada
- McGill International TB Centre, McGill University, Montréal, QC H3A3J1, Canada
- Departments of Medicine and Human Genetics, McGill University, Montréal, QC H3A0C7, Canada
| | - Jose C. Clemente
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA;
| | - Leopoldo N. Segal
- Division of Pulmonary and Critical Care Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY 10016, USA; (B.G.W.); (S.S.); (Y.L.); (L.N.S.)
| | - Marlo Möller
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town 7505, South Africa; (S.M.); (E.K.); (C.C.N.); (G.R.N.); (S.N.); (T.L.C.); (H.T.); (R.M.W.); (E.G.H.); (M.M.)
| | - Grant Theron
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town 7505, South Africa; (S.M.); (E.K.); (C.C.N.); (G.R.N.); (S.N.); (T.L.C.); (H.T.); (R.M.W.); (E.G.H.); (M.M.)
- African Microbiome Institute, Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 7505, South Africa
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9
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Moodley S, Kroon E, Naidoo CC, Nyawo GR, Wu BG, Naidoo S, Chiyaka TL, Tshivhula H, Singh S, Li Y, Warren RM, Hoal EG, Schurr E, Clemente J, Segal LN, Möller M, Theron G. Latent tuberculosis infection is associated with an enrichment of short chain fatty acid producing bacteria in the stool of women living with HIV. RESEARCH SQUARE 2024:rs.3.rs-4182285. [PMID: 38645218 PMCID: PMC11030539 DOI: 10.21203/rs.3.rs-4182285/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: 04/23/2024]
Abstract
Background Latent tuberculosis infection (LTBI) is common in people living with HIV (PLHIV) in high TB burden settings. Active TB is associated with specific stool taxa; however, little is known about the stool microbiota and LTBI, including in PLHIV. Method Within a parent study that recruited adult females with HIV from Cape Town, South Africa into predefined age categories (18-25, 35-60 years), we characterised the stool microbiota of those with [interferon-γ release assay (IGRA)- and tuberculin skin test (TST)-positive] or without (IGRA- and TST- negative) LTBI (n=25 per group). 16S rRNA DNA sequences were analysed using QIIME2, Dirichlet Multinomial Mixtures, DESeq2 and PICRUSt2. Results No α- or β-diversity differences occurred by LTBI status; however, LTBI-positives were Faecalibacterium-, Blautia-, Gemmiger-, Bacteroides-enriched and Moryella-, Atopobium-, Corynebacterium-, Streptococcus-depleted. Inferred metagenome data showed LTBI-negative-enriched pathways included several involved in methylglyoxal degradation, L-arginine, putrescine, 4-aminobutanoate degradation and L-arginine and ornithine degradation. Stool from LTBI-positives demonstrated differential taxa abundance based on a quantitative response to antigen stimulation (Acidaminococcus-enrichment and Megamonas-, Alistipes-, and Paraprevotella-depletion associated with higher IGRA or TST responses, respectively). In LTBI-positives, older people had different β-diversities than younger people whereas, in LTBI-negatives, no differences occurred across age groups. Conclusion Amongst female PLHIV, those with LTBI had, vs. those without LTBI, Faecalibacterium, Blautia, Gemmiger, Bacteriodes-enriched, which are producers of short chain fatty acids. Taxonomic differences amongst people with LTBI occurred according to quantitative response to antigen stimulation and age. These data enhance our understanding of the microbiome's potential role in LTBI.
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10
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Nazari I, Feinstein MJ. Evolving mechanisms and presentations of cardiovascular disease in people with HIV: implications for management. Clin Microbiol Rev 2024; 37:e0009822. [PMID: 38299802 PMCID: PMC10938901 DOI: 10.1128/cmr.00098-22] [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: 02/02/2024] Open
Abstract
People with HIV (PWH) are at elevated risk for cardiovascular diseases (CVDs), including myocardial infarction, heart failure, and sudden cardiac death, among other CVD manifestations. Chronic immune dysregulation resulting in persistent inflammation is common among PWH, particularly those with sustained viremia and impaired CD4+ T cell recovery. This inflammatory milieu is a major contributor to CVDs among PWH, in concert with common comorbidities (such as dyslipidemia and smoking) and, to a lesser extent, off-target effects of antiretroviral therapy. In this review, we discuss the clinical and mechanistic evidence surrounding heightened CVD risks among PWH, implications for specific CVD manifestations, and practical guidance for management in the setting of evolving data.
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Affiliation(s)
- Ilana Nazari
- Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Matthew J. Feinstein
- Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
- Division of Cardiology in the Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
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11
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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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12
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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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13
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Burke Schinkel SC, Barros PO, Berthoud T, Byrareddy SN, McGuinty M, Cameron DW, Angel JB. Comparative analysis of human gut- and blood-derived mononuclear cells: contrasts in function and phenotype. Front Immunol 2024; 15:1336480. [PMID: 38444848 PMCID: PMC10912472 DOI: 10.3389/fimmu.2024.1336480] [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: 11/10/2023] [Accepted: 02/05/2024] [Indexed: 03/07/2024] Open
Abstract
Introduction Alterations in the gut immune system have been implicated in various diseases.The challenge of obtaining gut tissues from healthy individuals, commonly performed via surgical explants, has limited the number of studies describing the phenotype and function of gut-derived immune cells in health. Methods Here, by means of recto-sigmoid colon biopsies obtained during routine care (colon cancer screening in healthy adults), the phenotype and function of immune cells present in the gut were described and compared to those found in blood. Results The proportion of CD4+, CD8+, MAIT, γδ+ T, and NK cells phenotype, expression of integrins, and ability to produce cytokine in response to stimulation with PMA and ionomycin. T cells in the gut were found to predominantly have a memory phenotype as compared to T cells in blood where a naïve phenotype predominates. Recto-sigmoid mononuclear cells also had higher PD-1 and Ki67 expression. Furthermore, integrin expression and cytokine production varied by cell type and location in blood vs. gut. Discussion These findings demonstrate the differences in functionality of these cells when compared to their blood counterparts and validate previous studies on phenotype within gut-derived immune cells in humans (where cells have been obtained through surgical means). This study suggests that recto-sigmoid biopsies collected during colonoscopy can be a reliable yet more accessible sampling method for follow up of alterations of gut derived immune cells in clinical settings.
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Affiliation(s)
| | - Priscila O Barros
- Chronic Diseases Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - Tamara Berthoud
- Chronic Diseases Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - Siddappa N Byrareddy
- Department of Pharmacology and Experimental Neuroscience, College of Medicine, University of Nebraska Medical Center, Omaha, NE, United States
| | - Michaeline McGuinty
- Department of Medicine, Division of Infectious Diseases, The Ottawa Hospital, University of Ottawa, Ottawa, ON, Canada
| | - D William Cameron
- Department of Medicine, Division of Infectious Diseases, The Ottawa Hospital, University of Ottawa, Ottawa, ON, Canada
| | - Jonathan B Angel
- Chronic Diseases Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada
- Department of Medicine, Division of Infectious Diseases, The Ottawa Hospital, University of Ottawa, Ottawa, ON, Canada
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada
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14
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Chen X, Wei J, Zhang Y, Zhang Y, Zhang T. Crosstalk between gut microbiome and neuroinflammation in pathogenesis of HIV-associated neurocognitive disorder. J Neurol Sci 2024; 457:122889. [PMID: 38262196 DOI: 10.1016/j.jns.2024.122889] [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: 09/26/2023] [Revised: 12/14/2023] [Accepted: 01/11/2024] [Indexed: 01/25/2024]
Abstract
HIV-associated neurocognitive disorder (HAND) has become a chronic neurodegenerative disease affecting the quality of life in people living with HIV (PLWH). Despite an established association between HAND and neuroinflammation induced by HIV proteins (gp120, Tat, Rev., Nef, and Vpr), the pathogenesis of HAND remains to be fully elucidated. Accumulating evidence demonstrated that the gut microbiome is emerging as a critical regulator of various neurodegenerative diseases (e.g., Parkinson's disease, Alzheimer's disease), suggesting that the crosstalk between the gut microbiome and neuroinflammation may contribute to the development of these diseases, for example, gut dysbiosis and microbiota-derived metabolites can trigger inflammation in the brain. However, the potential role of the gut microbiome in the pathogenesis of HAND remains largely unexplored. In this review, we aim to discuss and elucidate the HAND pathogenesis correlated with gut microbiome and neuroinflammation, and intend to explore the probable intervention strategies for HAND.
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Affiliation(s)
- Xue Chen
- Beijing Key Laboratory for HIV/AIDS Research, Clinical and Research Center for Infectious Diseases, Beijing Institute of Hepatology, Beijing Youan Hospital, Capital Medical University, Beijing 100069, China
| | - Jiaqi Wei
- Beijing Key Laboratory for HIV/AIDS Research, Clinical and Research Center for Infectious Diseases, Beijing Institute of Hepatology, Beijing Youan Hospital, Capital Medical University, Beijing 100069, China
| | - Yang Zhang
- Beijing Key Laboratory for HIV/AIDS Research, Clinical and Research Center for Infectious Diseases, Beijing Institute of Hepatology, Beijing Youan Hospital, Capital Medical University, Beijing 100069, China
| | - Yulin Zhang
- Beijing Key Laboratory for HIV/AIDS Research, Clinical and Research Center for Infectious Diseases, Beijing Institute of Hepatology, Beijing Youan Hospital, Capital Medical University, Beijing 100069, China.
| | - Tong Zhang
- Beijing Key Laboratory for HIV/AIDS Research, Clinical and Research Center for Infectious Diseases, Beijing Institute of Hepatology, Beijing Youan Hospital, Capital Medical University, Beijing 100069, China.
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15
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Yang Q, Zaongo SD, Zhu L, Yan J, Yang J, Ouyang J. The Potential of Clostridium butyricum to Preserve Gut Health, and to Mitigate Non-AIDS Comorbidities in People Living with HIV. Probiotics Antimicrob Proteins 2024:10.1007/s12602-024-10227-1. [PMID: 38336953 DOI: 10.1007/s12602-024-10227-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/02/2024] [Indexed: 02/12/2024]
Abstract
A dramatic reduction in mortality among people living with HIV (PLWH) has been achieved during the modern antiretroviral therapy (ART) era. However, ART does not restore gut barrier function even after long-term viral suppression, allowing microbial products to enter the systemic blood circulation and induce chronic immune activation. In PLWH, a chronic state of systemic inflammation exists and persists, which increases the risk of development of inflammation-associated non-AIDS comorbidities such as metabolic disorders, cardiovascular diseases, and cancer. Clostridium butyricum is a human butyrate-producing symbiont present in the gut microbiome. Convergent evidence has demonstrated favorable effects of C. butyricum for gastrointestinal health, including maintenance of the structural and functional integrity of the gut barrier, inhibition of pathogenic bacteria within the intestine, and reduction of microbial translocation. Moreover, C. butyricum supplementation has been observed to have a positive effect on various inflammation-related diseases such as diabetes, ulcerative colitis, and cancer, which are also recognized as non-AIDS comorbidities associated with epithelial gut damage. There is currently scant published research in the literature, focusing on the influence of C. butyricum in the gut of PLWH. In this hypothesis review, we speculate the use of C. butyricum as a probiotic oral supplementation may well emerge as a potential future synergistic adjunctive strategy in PLWH, in tandem with ART, to restore and consolidate intestinal barrier integrity, repair the leaky gut, prevent microbial translocation from the gut, and reduce both gut and systemic inflammation, with the ultimate objective of decreasing the risk for development of non-AIDS comorbidities in PLWH.
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Affiliation(s)
- Qiyu Yang
- Department of Radiation Oncology, Chongqing University Cancer Hospital & Chongqing Cancer Institute & Chongqing Cancer Hospital, Chongqing, China
| | - Silvere D Zaongo
- Department of Infectious Diseases, Chongqing Public Health Medical Center, Chongqing, China
- Clinical Research Center, Chongqing Public Health Medical Center, Chongqing, China
| | - Lijiao Zhu
- Clinical Research Center, Chongqing Public Health Medical Center, Chongqing, China
| | - Jiangyu Yan
- Clinical Research Center, Chongqing Public Health Medical Center, Chongqing, China
| | - Jiadan Yang
- Department of Pharmacy, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China.
| | - Jing Ouyang
- Clinical Research Center, Chongqing Public Health Medical Center, Chongqing, China.
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16
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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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Hishiya N, Uno K, Nakano A, Konishi M, Higashi S, Eguchi S, Ariyoshi T, Matsumoto A, Oka K, Takahashi M, Suzuki Y, Horiuchi S, Hirai N, Ogawa Y, Ogawa T, Nakano R, Mikasa K, Kasahara K, Yano H. Association between the gut microbiome and organic acid profiles in a Japanese population with HIV infection. J Infect Chemother 2024; 30:58-66. [PMID: 37708940 DOI: 10.1016/j.jiac.2023.09.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 09/04/2023] [Accepted: 09/12/2023] [Indexed: 09/16/2023]
Abstract
INTRODUCTION An increased incidence of metabolic syndrome has been observed in human immunodeficiency virus (HIV)-infected individuals. In contrast, gut dysbiosis is involved in various pathogeneses, including vascular endothelial disorders. Organic acids, including short-chain fatty acids (SCFAs), are essential for maintaining gut homeostasis. Therefore, this study aimed to explore the gut microbiome profile and organic acids in a Japanese population infected with HIV. METHODS Forty-nine patients with HIV infection on combination antiretroviral therapy (cART) were enrolled and divided into the high and low CD4 groups based on a CD4 cutoff of 350 cells/μL. Stool samples were analyzed by 16S ribosomal RNA next-generation sequencing and high-performance liquid chromatography. The association between the gut microbiome, including bacterial taxa and organic acids, was statistically analyzed. RESULTS The fecal microbial community composition was significantly different between HIV patients with CD4 counts above and below 350 cells/μL. The relative abundance of Roseburia, Prevotella, Prevotella_9, and [Clostridium]_methylpentosum_group were significantly enriched in the high CD4 group. Fecal succinic acid tended to be more abundant in the low CD4 group, and acetic, propionic, and butyric acids tended to be more abundant in the high CD4 group. Roseburia was positively correlated with butyric acid levels. Prevotella_9 and Prevotella were negatively correlated with succinic acid levels and positively correlated with acetic and propionic acid levels. CONCLUSIONS This study showed intestinal dysbiosis bordering on a CD4 count of 350 in patients with HIV infection undergoing cART. These findings might help in understanding intestinal damage and systemic inflammation in HIV infection.
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Affiliation(s)
- Naokuni Hishiya
- Department of Microbiology and Infectious Diseases, Nara Medical University, 840 Shijo-cho, Kashihara, Nara, 634-8521, Japan; Department of Infectious Diseases, Nara City Hospital, 1-50-1 Higashikidera-cho, Nara-Shi, Nara, 630-8305, Japan
| | - Kenji Uno
- Department of Infectious Diseases, Minami-Nara General Medical Center, 8-1 Fukugami, Oyodo-Cho, Yoshino-Gun, Nara, 638-8551, Japan
| | - Akiyo Nakano
- Department of Microbiology and Infectious Diseases, Nara Medical University, 840 Shijo-cho, Kashihara, Nara, 634-8521, Japan.
| | - Mitsuru Konishi
- Center for Health Control, Nara Medical University, 840 Shijo-cho, Kashihara, Nara, 634-8521, Japan; Center for Infectious Diseases, Nara Medical University, 840 Shijo-cho, Kashihara, Nara, 634-8521, Japan
| | - Seiya Higashi
- R&D Division, Miyarisan Pharmaceutical Co., Ltd., 2-22-9 Toro-Cho, Kita-Ku, Saitama-Shi, Saitama, 331-0804, Japan
| | - Shuhei Eguchi
- R&D Division, Miyarisan Pharmaceutical Co., Ltd., 2-22-9 Toro-Cho, Kita-Ku, Saitama-Shi, Saitama, 331-0804, Japan
| | - Tadashi Ariyoshi
- R&D Division, Miyarisan Pharmaceutical Co., Ltd., 2-22-9 Toro-Cho, Kita-Ku, Saitama-Shi, Saitama, 331-0804, Japan
| | - Asami Matsumoto
- R&D Division, Miyarisan Pharmaceutical Co., Ltd., 2-22-9 Toro-Cho, Kita-Ku, Saitama-Shi, Saitama, 331-0804, Japan
| | - Kentaro Oka
- R&D Division, Miyarisan Pharmaceutical Co., Ltd., 2-22-9 Toro-Cho, Kita-Ku, Saitama-Shi, Saitama, 331-0804, Japan
| | - Motomichi Takahashi
- R&D Division, Miyarisan Pharmaceutical Co., Ltd., 2-22-9 Toro-Cho, Kita-Ku, Saitama-Shi, Saitama, 331-0804, Japan
| | - Yuki Suzuki
- Department of Microbiology and Infectious Diseases, Nara Medical University, 840 Shijo-cho, Kashihara, Nara, 634-8521, Japan
| | - Saori Horiuchi
- Department of Microbiology and Infectious Diseases, Nara Medical University, 840 Shijo-cho, Kashihara, Nara, 634-8521, Japan
| | - Nobuyasu Hirai
- Department of Microbiology and Infectious Diseases, Nara Medical University, 840 Shijo-cho, Kashihara, Nara, 634-8521, Japan; Department of Gastroenterology, Seichokai Fuchu Hospital, 1-10-17 Hiko-Cho, Izumi, Osaka, 594-0076, Japan
| | - Yoshihiko Ogawa
- Department of Infectious Diseases, Sakai City Medical Center, 1-1-1 Ebaraji-Cho, Nishi-Ku, Sakai, Osaka, 593-8304, Japan
| | - Taku Ogawa
- Department of Microbiology and Infection Control, Osaka Medical and Pharmaceutical University, 2-7 Daigaku-machi, Takatsuki, Osaka, 569-8686, Japan
| | - Ryuichi Nakano
- Department of Microbiology and Infectious Diseases, Nara Medical University, 840 Shijo-cho, Kashihara, Nara, 634-8521, Japan
| | - Keiichi Mikasa
- Center for Infectious Diseases, Nara Medical University, 840 Shijo-cho, Kashihara, Nara, 634-8521, Japan; Department of Internal Medicine, Nara Koseikai Hospital, 769-3 Shigi-cho, Yamatokoriyama, Nara, 639-1039, Japan
| | - Kei Kasahara
- Center for Infectious Diseases, Nara Medical University, 840 Shijo-cho, Kashihara, Nara, 634-8521, Japan
| | - Hisakazu Yano
- Department of Microbiology and Infectious Diseases, Nara Medical University, 840 Shijo-cho, Kashihara, Nara, 634-8521, Japan
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Ray S, Narayanan A, Vesterbacka J, Blennow O, Chen P, Gao Y, Gabarrini G, Ljunggren HG, Buggert M, Manoharan L, Chen MS, Aleman S, Sönnerborg A, Nowak P. Impact of the gut microbiome on immunological responses to COVID-19 vaccination in healthy controls and people living with HIV. NPJ Biofilms Microbiomes 2023; 9:104. [PMID: 38123600 PMCID: PMC10733305 DOI: 10.1038/s41522-023-00461-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 11/20/2023] [Indexed: 12/23/2023] Open
Abstract
Although mRNA SARS-CoV-2 vaccines are generally safe and effective, in certain immunocompromised individuals they can elicit poor immunogenic responses. Among these individuals, people living with HIV (PLWH) have poor immunogenicity to several oral and parenteral vaccines. As the gut microbiome is known to affect vaccine immunogenicity, we investigated whether baseline gut microbiota predicts immune responses to the BNT162b2 mRNA SARS-CoV-2 vaccine in healthy controls and PLWH after two doses of BNT162b2. Individuals with high spike IgG titers and high spike-specific CD4+ T-cell responses against SARS-CoV-2 showed low α-diversity in the gut. Here, we investigated and presented initial evidence that the gut microbial composition influences the response to BNT162b2 in PLWH. From our predictive models, Bifidobacterium and Faecalibacterium appeared to be microbial markers of individuals with higher spike IgG titers, while Cloacibacillus was associated with low spike IgG titers. We therefore propose that microbiome modulation could optimize immunogenicity of SARS-CoV-2 mRNA vaccines.
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Affiliation(s)
- Shilpa Ray
- Department of Medicine Huddinge, Division of Infectious Diseases, Karolinska Institutet, Stockholm, Sweden.
| | - Aswathy Narayanan
- Department of Medicine Huddinge, Division of Infectious Diseases, Karolinska Institutet, 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
| | - Ola Blennow
- Department of Medicine Huddinge, Division of Infectious Diseases, Karolinska Institutet, Stockholm, Sweden
- Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Puran Chen
- Department of Medicine Huddinge, Center for Infectious Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Yu Gao
- Department of Medicine Huddinge, Center for Infectious Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Giorgio Gabarrini
- Department of Dental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Hans-Gustaf Ljunggren
- Department of Medicine Huddinge, Center for Infectious Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Marcus Buggert
- Department of Medicine Huddinge, Center for Infectious Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Lokeshwaran Manoharan
- National Bioinformatics Infrastructure Sweden (NBIS), SciLifeLab, Department of Laboratory Medicine, Lund University, Lund, 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, Stockholm, 141 52, 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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19
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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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20
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Munjoma PT, Chandiwana P, Wyss J, Mazhandu AJ, Jordi SBU, Gutsire R, Katsidzira L, Yilmaz B, Misselwitz B, Duri K. Immune activation and inflammation in lactating women on combination antiretroviral therapy: role of gut dysfunction and gut microbiota imbalance. Front Immunol 2023; 14:1280262. [PMID: 38045684 PMCID: PMC10693333 DOI: 10.3389/fimmu.2023.1280262] [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: 08/21/2023] [Accepted: 10/17/2023] [Indexed: 12/05/2023] Open
Abstract
Introduction Combination antiretroviral therapy (cART) effectively controls HIV; however, chronic low-level viremia and gut microbiota dysbiosis remain significant drivers of gut and systemic inflammation. In this study, we explored the relationship between gut microbiota composition, intestinal inflammation, microbial translocation, and systemic inflammation in women on cART in Sub-Saharan Africa. Methods We conducted a study in HIV-infected and HIV-uninfected lactating women followed up at 6 weeks and 6 months postpartum in Harare, Zimbabwe. We used 16S ribosomal Ribonucleic Acid (rRNA) sequencing and MesoScale Discovery V-Plex assays to examine the gut microbiome and to quantify plasma inflammatory biomarkers, respectively. In addition, we measured fecal calprotectin, plasma lipopolysaccharide-binding protein (LBP), and soluble cluster of differentiation 14 (sCD14) by enzyme-linked immunosorbent assay to assess gut inflammation, microbial translocation, and monocyte/macrophage activation. Results A group of 77 lactating women were studied, of which 35% were HIV-infected. Fecal calprotectin levels were similar by HIV status at both follow-up time points. In the HIV-infected group at 6 weeks postpartum, fecal calprotectin was elevated: median (interquartile range) [158.1 µg/g (75.3-230.2)] in women who had CD4+ T-lymphocyte counts <350 cells/µL compared with those with ≥350 cells/µL [21.1 µg/g (0-58.4)], p = 0.032. Plasma sCD14 levels were significantly higher in the HIV-infected group at both 6 weeks and 6 months postpartum, p < 0.001. Plasma LBP levels were similar, but higher levels were observed in HIV-infected women with elevated fecal calprotectin. We found significant correlations between fecal calprotectin, LBP, and sCD14 with proinflammatory cytokines. Gut microbial alpha diversity was not affected by HIV status and was not affected by use of antibiotic prophylaxis. HIV significantly affected microbial beta diversity, and significant differences in microbial composition were noted. The genera Slackia and Collinsella were relatively more abundant in the HIV-infected group, whereas a lower relative abundance of Clostriduim sensu_stricto_1 was observed. Our study also found correlations between gut microbial taxa abundance and systemic inflammatory biomarkers. Discussion and conclusion HIV-infected lactating women had increased immune activation and increased microbial translocation associated with increased gut inflammation. We identified correlations between the gut inflammation and microbial composition, microbial translocation, and systemic inflammation. The interplay of these parameters might affect the health of this vulnerable population.
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Affiliation(s)
- Privilege Tendai Munjoma
- Immunology Unit, Department of Laboratory Diagnostic and Investigative Sciences, University of Zimbabwe Faculty of Medicine and Health Sciences (UZ-FMHS), Harare, Zimbabwe
| | - Panashe Chandiwana
- Immunology Unit, Department of Laboratory Diagnostic and Investigative Sciences, University of Zimbabwe Faculty of Medicine and Health Sciences (UZ-FMHS), Harare, Zimbabwe
| | - Jacqueline Wyss
- Department of Visceral Surgery and Medicine, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
- Department for Biomedical Research, Maurice Müller Laboratories, University of Bern, Bern, Switzerland
| | - Arthur John Mazhandu
- Immunology Unit, Department of Laboratory Diagnostic and Investigative Sciences, University of Zimbabwe Faculty of Medicine and Health Sciences (UZ-FMHS), Harare, Zimbabwe
| | - Sebastian Bruno Ulrich Jordi
- Department of Visceral Surgery and Medicine, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
- Department for Biomedical Research, Maurice Müller Laboratories, University of Bern, Bern, Switzerland
| | - Rutendo Gutsire
- Immunology Unit, Department of Laboratory Diagnostic and Investigative Sciences, University of Zimbabwe Faculty of Medicine and Health Sciences (UZ-FMHS), Harare, Zimbabwe
| | - Leolin Katsidzira
- Department of Internal Medicine, University of Zimbabwe Faculty of Medicine and Health Sciences (UZ-FMHS), Harare, Zimbabwe
| | - Bahtiyar Yilmaz
- Department of Visceral Surgery and Medicine, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
- Department for Biomedical Research, Maurice Müller Laboratories, University of Bern, Bern, Switzerland
| | - Benjamin Misselwitz
- Department of Visceral Surgery and Medicine, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
- Department for Biomedical Research, Maurice Müller Laboratories, University of Bern, Bern, Switzerland
| | - Kerina Duri
- Immunology Unit, Department of Laboratory Diagnostic and Investigative Sciences, University of Zimbabwe Faculty of Medicine and Health Sciences (UZ-FMHS), Harare, Zimbabwe
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21
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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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22
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Xia C, Zhang X, Harypursat V, Ouyang J, Chen Y. The role of pyroptosis in incomplete immune reconstitution among people living with HIV:Potential therapeutic targets. Pharmacol Res 2023; 197:106969. [PMID: 37866704 DOI: 10.1016/j.phrs.2023.106969] [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: 06/06/2023] [Revised: 09/07/2023] [Accepted: 10/20/2023] [Indexed: 10/24/2023]
Abstract
Globally, HIV infection causes significant morbidity and mortality, and is a major public health problem. Despite the fact that widespread use of antiretroviral therapy (ART) has substantially altered the natural history of HIV infection from originally being a universally lethal disease to now being a chronic medical condition for those taking appropriate treatment, approximately 10-40% of people living with HIV (PLWH) who take effective ART and maintain long-term viral suppression fail to achieve normalization of CD4 + T-cell counts. This phenomenon is referred to as incomplete immune reconstitution or immunological non-response. Although the precise mechanisms underlying this outcome have not been elucidated, recent evidence indicates that excessive pyroptosis may play a crucial role in the development of incomplete immune reconstitution. Pyroptosis is characterized by the formation of pores in the cell membrane, cell rupture, and secretion of intracellular contents and pro-inflammatory cytokines, including IL-1β and IL-18. This excessive inflammation-induced programmed cell death leads to a massive loss of CD4 + T-cells, and inflammatory consequences that may promote and sustain incomplete immune reconstitution. Herein, we review the possible pathways activated in HIV infection by inflammasomes that act as switches of pyroptosis, and the role of pyroptosis in HIV, as well as the relevance of CD4 + T-cells in incomplete immune reconstitution. We also highlight the possible mechanisms of pyroptosis involved in incomplete immune reconstitution, thus paving the way for the development of potential targets for the treatment of incomplete immune reconstitution.
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Affiliation(s)
- Chao Xia
- Clinical Research Center, Chongqing Public Health Medical Center, Chongqing, China
| | - Xue Zhang
- Department of Pharmacy, The People's Hospital of Yubei District of Chongqing City, Chongqing, China
| | - Vijay Harypursat
- Clinical Research Center, Chongqing Public Health Medical Center, Chongqing, China; Department of Infectious Diseases, Chongqing Public Health Medical Center, Chongqing, China
| | - Jing Ouyang
- Clinical Research Center, Chongqing Public Health Medical Center, Chongqing, China.
| | - Yaokai Chen
- Clinical Research Center, Chongqing Public Health Medical Center, Chongqing, China; Department of Infectious Diseases, Chongqing Public Health Medical Center, Chongqing, China.
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23
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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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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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25
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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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Naz S, Ali Z, Minhas A, Fatima A, Waseem S. Generation of dysbiotic microbiota in cutaneous Leishmaniasis and enhancement of skin inflammation. Microb Pathog 2023; 181:106202. [PMID: 37327948 DOI: 10.1016/j.micpath.2023.106202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 06/12/2023] [Accepted: 06/13/2023] [Indexed: 06/18/2023]
Abstract
Cutaneous Leishmaniasis (CL) affects millions of people globally and has a significant impact on morbidity and mortality. Innate immune mediators are likely to influence the clinical phenotype of CL through primary responses that restrict or facilitate parasite spread. The aim of the study was to bring to attention the significance of microbiota in the development of CL and emphasized the necessity of including the role of microbiota in CL while promoting a One Health approach for managing diseases. To achieve this, we used 16S amplicon metagenome sequencing and QIIME2 pipeline to analyze the microbiome composition of CL-infected patients compared to non-infected, healthy subjects. 16S sequencing analysis showed serum microbiome was dominated by Firmicutes, Proteobacteria, Bacteroidota, and Actinobacteria. CL-infected individuals, Proteobacteria were the most prevalent (27.63 ± 9.79), with the relative abundance (10.73 ± 5.33) of Proteobacteria in control. Bacilli class was found to be the most prevalent in healthy controls (30.71 ± 8.44) while (20.57 ± 9.51) in CL-infected individuals. The class Alphaproteobacteria was found to be more in CL-infected individuals (5.47 ± 2.07) as compared to healthy controls (1.85 ± 0.39). The CL-infected individuals had a significantly lower relative abundance of the Clostridia class (p < 0.0001). An altered serum microbiome of CL infection and higher microbial abundance in the serum of healthy individuals was observed.
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Affiliation(s)
- Shumaila Naz
- Department of Biological Sciences, National University of Medical Sciences (NUMS), Rawalpindi, 46000, Pakistan.
| | - Zain Ali
- ABO SCIENTIFIC, Chakri Road, Rawalpindi, Pakistan
| | - Azhar Minhas
- Department of Dermatology, Combined Military Hospital (CMH), Quetta, 87300, Pakistan
| | - Anam Fatima
- Department of Medicine, Polyclinic Hospital, Islamabad, Pakistan
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28
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Goosen C, Proost S, Baumgartner J, Mallick K, Tito RY, Barnabas SL, Cotton MF, Zimmermann MB, Raes J, Blaauw R. Associations of HIV and iron status with gut microbiota composition, gut inflammation and gut integrity in South African school-age children: a two-way factorial case-control study. J Hum Nutr Diet 2023; 36:819-832. [PMID: 36992541 PMCID: PMC10946596 DOI: 10.1111/jhn.13171] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Accepted: 03/19/2023] [Indexed: 03/31/2023]
Abstract
BACKGROUND Human immunodeficiency virus (HIV) and iron deficiency (ID) affect many African children. Both HIV and iron status interact with gut microbiota composition and related biomarkers. The study's aim was to determine the associations of HIV and iron status with gut microbiota composition, gut inflammation and gut integrity in South African school-age children. METHODS In this two-way factorial case-control study, 8- to 13-year-old children were enrolled into four groups based on their HIV and iron status: (1) With HIV (HIV+) and ID (n = 43), (2) HIV+ and iron-sufficient nonanaemic (n = 41), (3) without HIV (HIV-) and ID (n = 44) and (4) HIV- and iron-sufficient nonanaemic (n = 38). HIV+ children were virally suppressed (<50 HIV RNA copies/ml) on antiretroviral therapy (ART). Microbial composition of faecal samples (16S rRNA sequencing) and markers of gut inflammation (faecal calprotectin) and gut integrity (plasma intestinal fatty acid-binding protein [I-FABP]) were assessed. RESULTS Faecal calprotectin was higher in ID versus iron-sufficient nonanaemic children (p = 0.007). I-FABP did not significantly differ by HIV or iron status. ART-treated HIV (redundancy analysis [RDA] R2 = 0.009, p = 0.029) and age (RDA R2 = 0.013 p = 0.004) explained the variance in the gut microbiota across the four groups. Probabilistic models showed that the relative abundance of the butyrate-producing genera Anaerostipes and Anaerotruncus was lower in ID versus iron-sufficient children. Fusicatenibacter was lower in HIV+ and in ID children versus their respective counterparts. The prevalence of the inflammation-associated genus Megamonas was 42% higher in children with both HIV and ID versus HIV- and iron-sufficient nonanaemic counterparts. CONCLUSIONS In our sample of 8- to 13-year-old virally suppressed HIV+ and HIV- children with or without ID, ID was associated with increased gut inflammation and changes in the relative abundance of specific microbiota. Moreover, in HIV+ children, ID had a cumulative effect that further shifted the gut microbiota to an unfavourable composition.
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Affiliation(s)
- Charlene Goosen
- Division of Human Nutrition, Department of Global Health, Faculty of Medicine and Health SciencesStellenbosch UniversityCape TownSouth Africa
| | - Sebastian Proost
- Laboratory of Molecular Bacteriology, Department of Microbiology and ImmunologyRega Institute, KU LeuvenLeuvenBelgium
- Center for Microbiology, VIBLeuvenBelgium
| | - Jeannine Baumgartner
- Laboratory of Human Nutrition, Department of Health Sciences and TechnologyETH ZurichZurichSwitzerland
- Department of Nutritional SciencesKing's College LondonLondonUK
| | - Kashish Mallick
- Laboratory of Human Nutrition, Department of Health Sciences and TechnologyETH ZurichZurichSwitzerland
| | - Raul Y. Tito
- Laboratory of Molecular Bacteriology, Department of Microbiology and ImmunologyRega Institute, KU LeuvenLeuvenBelgium
- Center for Microbiology, VIBLeuvenBelgium
| | - Shaun L. Barnabas
- Department of Paediatrics and Child Health, Family Centre for Research with UbuntuStellenbosch UniversityCape TownSouth Africa
| | - Mark F. Cotton
- Department of Paediatrics and Child Health, Family Centre for Research with UbuntuStellenbosch UniversityCape TownSouth Africa
| | - Michael B. Zimmermann
- Laboratory of Human Nutrition, Department of Health Sciences and TechnologyETH ZurichZurichSwitzerland
| | - Jeroen Raes
- Laboratory of Molecular Bacteriology, Department of Microbiology and ImmunologyRega Institute, KU LeuvenLeuvenBelgium
- Center for Microbiology, VIBLeuvenBelgium
| | - Renée Blaauw
- Division of Human Nutrition, Department of Global Health, Faculty of Medicine and Health SciencesStellenbosch UniversityCape TownSouth Africa
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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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Wang S, Singh M, Yang H, Morrell CN, Mohamad LA, Xu JJ, Nguyen T, Ture S, Tyrell A, Maggirwar SB, Schifitto G, Pang J. Monocyte-derived Dll4 is a novel contributor to persistent systemic inflammation in HIV patients. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.18.537330. [PMID: 37131726 PMCID: PMC10153122 DOI: 10.1101/2023.04.18.537330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Background In people living with HIV (PLWH) on combination antiretroviral therapy (cART), persistent systemic inflammation is a driving force for the progression of comorbidities, such as cardiovascular and cerebrovascular diseases. In this context, monocyte- and macrophage-related inflammation rather than T cell activation is a major cause of chronic inflammation. However, the underlying mechanism of how monocytes cause persistent systemic inflammation in PLWH is elusive. Methods and Results In vitro, we demonstrated that lipopolysaccharides (LPS) or tumor necrosis factor alpha (TNFα), induced a robust increase of Delta-like ligand 4 (Dll4) mRNA and protein expression in human monocytes and Dll4 secretion (extracellular Dll4, exDll4) from monocytes. Enhanced membrane-bound Dll4 (mDll4) expression in monocytes triggered Notch1 activation to promote pro-inflammatory factors expression. Dll4 silencing and inhibition of Nocth1 activation diminished the LPS or TNFα -induced inflammation. exDll4 releases in response to cytokines occurred in monocytes but not endothelial cells or T cells. In clinical specimens, we found that PLWH, both male and female, on cART, showed a significant increase in mDll4 expression, activation of Dll4-Notch1 signaling, and inflammatory markers in monocytes. Although there was no sex effect on mDII4 in PLWH, plasma exDll4 was significantly elevated in males but not females compared to HIV uninfected individuals. Furthermore, exDll4 plasma levels paralleled with monocytes mDll4 in male PLWH. Circulating exDll4 was also positively associated with pro-inflammatory monocytes phenotype and negatively associated with classic monocytes phenotype in male PLWH. Conclusion Pro-inflammatory stimuli increase Dll4 expression and Dll4-Notch1 signaling activation in monocytes and enhance monocyte proinflammatory phenotype, contributing to persistent systemic inflammation in male and female PLWH. Therefore, monocyte mDll4 could be a potential biomarker and therapeutic target of systemic inflammation. Plasma exDll4 may also play an additional role in systemic inflammation but primarily in men.
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31
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Cinque F, Cespiati A, Lombardi R, Guaraldi G, Sebastiani G. Nutritional and Lifestyle Therapy for NAFLD in People with HIV. Nutrients 2023; 15:nu15081990. [PMID: 37111209 PMCID: PMC10140991 DOI: 10.3390/nu15081990] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 04/17/2023] [Accepted: 04/19/2023] [Indexed: 04/29/2023] Open
Abstract
HIV infection and nonalcoholic fatty liver disease (NAFLD) are two major epidemics affecting millions of people worldwide. As people with HIV (PWH) age, there is an increased prevalence of metabolic comorbidities, along with unique HIV factors, such as HIV chronic inflammation and life-long exposure to antiretroviral therapy, which leads to a high prevalence of NAFLD. An unhealthy lifestyle, with a high dietary intake of refined carbohydrates, saturated fatty acids, fructose added beverages, and processed red meat, as well as physical inactivity, are known to trigger and promote the progression of NAFLD to nonalcoholic steatohepatitis, liver fibrosis, and hepatocellular carcinoma. Furthermore, with no currently approved pharmacotherapy and a lack of clinical trials that are inclusive of HIV, nutritional and lifestyle approaches still represent the most recommended treatments for PWH with NAFLD. While sharing common features with the general population, NAFLD in PWH displays its own peculiarities that may also reflect different impacts of nutrition and exercise on its onset and treatment. Therefore, in this narrative review, we aimed to explore the role of nutrients in the development of NAFLD in PWH. In addition, we discussed the nutritional and lifestyle approaches to managing NAFLD in the setting of HIV, with insights into the role of gut microbiota and lean NAFLD.
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Affiliation(s)
- Felice Cinque
- Division of Gastroenterology and Hepatology, and Chronic Viral Illness Service, McGill University Health Centre, Montreal, QC H4A 3J1, Canada
- Department of Pathophysiology and Transplantation, University of Milan, 20122 Milan, Italy
- Medicine and Metabolic Disease Unit, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Via F. Sforza 35, 20122 Milan, Italy
| | - Annalisa Cespiati
- Department of Pathophysiology and Transplantation, University of Milan, 20122 Milan, Italy
- Medicine and Metabolic Disease Unit, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Via F. Sforza 35, 20122 Milan, Italy
| | - Rosa Lombardi
- Department of Pathophysiology and Transplantation, University of Milan, 20122 Milan, Italy
- Medicine and Metabolic Disease Unit, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Via F. Sforza 35, 20122 Milan, Italy
| | - Giovanni Guaraldi
- Modena HIV Metabolic Clinic, Department of Surgical, Medical, Dental and Morphological Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy
- Infectious Diseases Unit, Azienda Ospedaliero-Universitaria di Modena, 41124 Modena, Italy
| | - Giada Sebastiani
- Division of Gastroenterology and Hepatology, and Chronic Viral Illness Service, McGill University Health Centre, Montreal, QC H4A 3J1, Canada
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32
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Li L, Zhao X, He JJ. HIV Tat Expression and Cocaine Exposure Lead to Sex- and Age-Specific Changes of the Microbiota Composition in the Gut. Microorganisms 2023; 11:799. [PMID: 36985373 PMCID: PMC10054272 DOI: 10.3390/microorganisms11030799] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 03/08/2023] [Accepted: 03/17/2023] [Indexed: 03/30/2023] Open
Abstract
The balance of microbial communities in the gut is extremely important for normal physiological function. Disruption of the balance is often associated with various disorders and diseases. Both HIV infection and cocaine use are known to change the gut microbiota and the epithelial barrier integrity, which contribute to inflammation and immune activation. Our recent study shows that Tat expression and cocaine exposure result in changes of genome-wide DNA methylation and gene expression and lead to worsen the learning and memory impairments. In the current study, we extended the study to determine effects of Tat and cocaine on the gut microbiota composition. We found that both Tat expression and cocaine exposure increased Alteromonadaceae in 6-month-old female/male mice. In addition, we found that Tat, cocaine, or both increased Alteromonadaceae, Bacteroidaceae, Cyanobiaceae, Erysipelotrichaceae, and Muribaculaceae but decreased Clostridiales_vadinBB60_group, Desulfovibrionaceae, Helicobacteraceae, Lachnospiraceae, and Ruminococcaceae in 12-month-old female mice. Lastly, we analyzed changes of metabolic pathways and found that Tat decreased energy metabolism and nucleotide metabolism, and increased lipid metabolism and metabolism of other amino acids while cocaine increased lipid metabolism in 12-month-old female mice. These results demonstrated that Tat expression and cocaine exposure resulted in significant changes of the gut microbiota in an age- and sex-dependent manner and provide additional evidence to support the bidirectional gut-brain axis hypothesis.
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Affiliation(s)
- Lu Li
- Department of Microbiology and Immunology, Chicago Medical School, Rosalind Franklin University, 3333 Green Bay Road, North Chicago, IL 60064, USA
- Center for Cancer Cell Biology, Immunology and Infection, Rosalind Franklin University, North Chicago, IL 60064, USA
- School of Graduate and Postdoctoral Studies, Rosalind Franklin University, North Chicago, IL 60064, USA
| | - Xiaojie Zhao
- Department of Microbiology and Immunology, Chicago Medical School, Rosalind Franklin University, 3333 Green Bay Road, North Chicago, IL 60064, USA
- Center for Cancer Cell Biology, Immunology and Infection, Rosalind Franklin University, North Chicago, IL 60064, USA
- School of Graduate and Postdoctoral Studies, Rosalind Franklin University, North Chicago, IL 60064, USA
| | - Johnny J. He
- Department of Microbiology and Immunology, Chicago Medical School, Rosalind Franklin University, 3333 Green Bay Road, North Chicago, IL 60064, USA
- Center for Cancer Cell Biology, Immunology and Infection, Rosalind Franklin University, North Chicago, IL 60064, USA
- School of Graduate and Postdoctoral Studies, Rosalind Franklin University, North Chicago, IL 60064, USA
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Hov JR, Karlsen TH. The microbiota and the gut-liver axis in primary sclerosing cholangitis. Nat Rev Gastroenterol Hepatol 2023; 20:135-154. [PMID: 36352157 DOI: 10.1038/s41575-022-00690-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/13/2022] [Indexed: 11/11/2022]
Abstract
Primary sclerosing cholangitis (PSC) offers unique opportunities to explore the gut-liver axis owing to the close association between liver disease and colonic inflammation. It is well established that the gut microbiota in people with PSC differs from that of healthy individuals, but details of the microbial factors that demarcate PSC from inflammatory bowel disease (IBD) without PSC are poorly understood. In this Review, we aim to provide an overview of the latest literature on the gut microbiome in PSC and PSC with IBD, critically examining hypotheses on how microorganisms could contribute to the pathogenesis of PSC. A particular emphasis will be put on pathogenic features of the gut microbiota that might explain the occurrence of bile duct inflammation and liver disease in the context of IBD, and we postulate the potential existence of a specific yet unknown factor related to the gut-liver axis as causative in PSC. Available data are scrutinized in the perspective of therapeutic approaches related to the gut-liver axis.
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Affiliation(s)
- Johannes R Hov
- Norwegian PSC Research Center and Section of gastroenterology and Research Institute of Internal Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital, Oslo, Norway.,Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Tom H Karlsen
- Norwegian PSC Research Center and Section of gastroenterology and Research Institute of Internal Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital, Oslo, Norway. .,Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway.
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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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Gut microbiota alterations after switching from a protease inhibitor or efavirenz to raltegravir in a randomized, controlled study. AIDS 2023; 37:323-332. [PMID: 36541643 DOI: 10.1097/qad.0000000000003419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
OBJECTIVE To study gut microbiota before and 24 weeks after a single antiretroviral agent switch. DESIGN HIV-positive patients with efavirenz (EFV) or a protease inhibitor (PI)-based antiretroviral therapy (ART) were randomized to switch EFV or PI to raltegravir (RAL group, n = 19) or to continue unchanged ART (EFV/PI group, n = 22). Age and weight-matched HIV-negative participants (n = 10) were included for comparison. METHODS Microbiota was analyzed using 16S rRNA sequencing. Serum intestinal fatty acid-binding protein (I-FABP) and serum lipopolysaccharide-binding protein (LBP) were measured as gut permeability markers. Three-day food diaries were collected. RESULTS At week 24, microbiota diversity (Chao1 index) was higher in RAL than the EFV/PI group (P = 0.014), and RAL group did not differ from HIV-negative participants. In subgroup analysis switching from EFV (P = 0.043), but not from a PI to RAL increased Chao1. At week 24, RAL and EFV/PI group differed in the relative abundance of Prevotella 9 (higher in RAL, P = 0.01), Phascolarctobacterium and Bacteroides (lower in RAL, P = 0.01 and P = 0.03). Dietary intakes did not change during the study and do not explain microbiota differences. Also, I-FABP and LBP remained unchanged. CONCLUSION Here we demonstrate that a single ART agent switch caused microbiota alterations, most importantly, an increase in diversity with EFV to RAL switch. Previously, we reported weight gain, yet reduced inflammation in this cohort. The observed microbiota differences between RAL and EFV/PI groups may be associated with reduced inflammation and/or increase in weight. Further studies are needed to evaluate inflammatory and metabolic capacity of microbiota with ART switches.
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Chandiwana P, Munjoma PT, Mazhandu AJ, Li J, Baertschi I, Wyss J, Jordi SBU, Mazengera LR, Yilmaz B, Misselwitz B, Duri K. Antenatal gut microbiome profiles and effect on pregnancy outcome in HIV infected and HIV uninfected women in a resource limited setting. BMC Microbiol 2023; 23:4. [PMID: 36604616 PMCID: PMC9817306 DOI: 10.1186/s12866-022-02747-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 12/23/2022] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Human immunodeficiency virus (HIV) severely damages the epithelial cells of the gut lining leading to an inflamed leaky gut, translocation of microbial products, and dysbiosis resulting in systemic immune activation. Also, microbiota composition and maternal gut function can be altered in pregnancy through changes in the immune system and intestinal physiology. The aim of this study was to investigate the gut microbiota in HIV-infected and HIV-uninfected pregnant women and to compare and identify the association between gut microbial composition and adverse birth outcomes. RESULTS A total of 94 pregnant women (35 HIV-infected and 59 HIV-uninfected controls) were recruited in Harare from 4 polyclinics serving populations with relatively poor socioeconomic status. Women were of a median age of 28 years (interquartile range, IQR: 22.3-32.0) and 55% of women were 35 weeks gestational age at enrolment (median 35.0 weeks, IQR: 32.5-37.2). Microbiota profiling in these participants showed that species richness was significantly lower in the HIV-infected pregnant women compared to their HIV-uninfected peers and significant differences in β-diversity using Bray-Curtis dissimilarity were observed. In contrast, there was no significant difference in α-diversity between immune-compromised (CD4+ < 350 cells/µL) and immune-competent HIV-infected women (CD4+ ≥ 350 cells/µL) even after stratification by viral load suppression. HIV infection was significantly associated with a reduced abundance of Clostridium, Turicibacter, Ruminococcus, Parabacteroides, Bacteroides, Bifidobacterium, Treponema, Oscillospira, and Faecalibacterium and a higher abundance of Actinomyces, and Succinivibrio. Low infant birth weight (< 2500 g) was significantly associated with high abundances of the phylum Spirochaetes, the families Spirochaeteceae, Veillonellaceae, and the genus Treponema. CONCLUSION The results reported here show that the species richness and taxonomy composition of the gut microbiota is altered in HIV-infected pregnant women, possibly reflecting intestinal dysbiosis. Some of these taxa were also associated with low infant birth weight.
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Affiliation(s)
- Panashe Chandiwana
- grid.13001.330000 0004 0572 0760Immunology Unit, Department of Laboratory Diagnostic and Investigative Sciences, University of Zimbabwe Faculty of Medicine and Health Sciences, Harare, Zimbabwe
| | - Privilege Tendai Munjoma
- grid.13001.330000 0004 0572 0760Immunology Unit, Department of Laboratory Diagnostic and Investigative Sciences, University of Zimbabwe Faculty of Medicine and Health Sciences, Harare, Zimbabwe
| | - Arthur John Mazhandu
- grid.13001.330000 0004 0572 0760Immunology Unit, Department of Laboratory Diagnostic and Investigative Sciences, University of Zimbabwe Faculty of Medicine and Health Sciences, Harare, Zimbabwe
| | - Jiaqi Li
- grid.411656.10000 0004 0479 0855Department of Visceral Surgery and Medicine, Inselspital, Bern University Hospital, University of Bern, 3010 Bern, Switzerland ,grid.5734.50000 0001 0726 5157Department for Biomedical Research, Maurice Müller Laboratories, University of Bern, 3008 Bern, Switzerland ,grid.5734.50000 0001 0726 5157Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Isabel Baertschi
- grid.411656.10000 0004 0479 0855Department of Visceral Surgery and Medicine, Inselspital, Bern University Hospital, University of Bern, 3010 Bern, Switzerland ,grid.5734.50000 0001 0726 5157Department for Biomedical Research, Maurice Müller Laboratories, University of Bern, 3008 Bern, Switzerland ,grid.5734.50000 0001 0726 5157Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Jacqueline Wyss
- grid.411656.10000 0004 0479 0855Department of Visceral Surgery and Medicine, Inselspital, Bern University Hospital, University of Bern, 3010 Bern, Switzerland ,grid.5734.50000 0001 0726 5157Department for Biomedical Research, Maurice Müller Laboratories, University of Bern, 3008 Bern, Switzerland
| | - Sebastian Bruno Ulrich Jordi
- grid.411656.10000 0004 0479 0855Department of Visceral Surgery and Medicine, Inselspital, Bern University Hospital, University of Bern, 3010 Bern, Switzerland ,grid.5734.50000 0001 0726 5157Department for Biomedical Research, Maurice Müller Laboratories, University of Bern, 3008 Bern, Switzerland ,grid.5734.50000 0001 0726 5157Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Lovemore Ronald Mazengera
- grid.13001.330000 0004 0572 0760Immunology Unit, Department of Laboratory Diagnostic and Investigative Sciences, University of Zimbabwe Faculty of Medicine and Health Sciences, Harare, Zimbabwe
| | - Bahtiyar Yilmaz
- grid.411656.10000 0004 0479 0855Department of Visceral Surgery and Medicine, Inselspital, Bern University Hospital, University of Bern, 3010 Bern, Switzerland ,grid.5734.50000 0001 0726 5157Department for Biomedical Research, Maurice Müller Laboratories, University of Bern, 3008 Bern, Switzerland
| | - Benjamin Misselwitz
- grid.411656.10000 0004 0479 0855Department of Visceral Surgery and Medicine, Inselspital, Bern University Hospital, University of Bern, 3010 Bern, Switzerland ,grid.5734.50000 0001 0726 5157Department for Biomedical Research, Maurice Müller Laboratories, University of Bern, 3008 Bern, Switzerland
| | - Kerina Duri
- grid.13001.330000 0004 0572 0760Immunology Unit, Department of Laboratory Diagnostic and Investigative Sciences, University of Zimbabwe Faculty of Medicine and Health Sciences, Harare, Zimbabwe
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Zhang Y, Xie Z, Zhou J, Li Y, Ning C, Su Q, Ye L, Ai S, Lai J, Pan P, Liu N, Liao Y, Su Q, Li Z, Liang H, Cui P, Huang J. The altered metabolites contributed by dysbiosis of gut microbiota are associated with microbial translocation and immune activation during HIV infection. Front Immunol 2023; 13:1020822. [PMID: 36685491 PMCID: PMC9845923 DOI: 10.3389/fimmu.2022.1020822] [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: 08/16/2022] [Accepted: 11/28/2022] [Indexed: 01/05/2023] Open
Abstract
Background The immune activation caused by microbial translocation has been considered to be a major driver of HIV infection progression. The dysbiosis of gut microbiota has been demonstrated in HIV infection, but the interplay between gut microbiota and its metabolites in the pathogenesis of HIV is seldom reported. Methods We conducted a case-controlled study including 41 AIDS patients, 39 pre-AIDS patients and 34 healthy controls. Both AIDS group and pre-AIDS group were divided according to clinical manifestations and CD4 + T cell count. We collected stool samples for 16S rDNA sequencing and untargeted metabolomics analysis, and examined immune activation and microbial translocation for blood samples. Results The pre-AIDS and AIDS groups had higher levels of microbial translocation and immune activation. There were significant differences in gut microbiota and metabolites at different stages of HIV infection. Higher abundances of pathogenic bacteria or opportunistic pathogen, as well as lower abundances of butyrate-producing bacteria and bacteria with anti-inflammatory potential were associated with HIV severity. The metabolism of tryptophan was disordered after HIV infection. Lower level of anti-inflammatory metabolites and phosphonoacetate, and higher level of phenylethylamine and polyamines were observed in HIV infection. And microbial metabolic pathways related to altered metabolites differed. Moreover, disrupted metabolites contributed by altered microbiota were found to be correlated to microbial translocation and immune activation. Conclusions Metabolites caused by dysbiosis of gut microbiota and related metabolic function are correlated to immune activation and microbial translocation, suggesting that the effect of microbiota on metabolites is related to intestinal barrier disruption in HIV infection.
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Affiliation(s)
- Yu Zhang
- Guangxi Key Laboratory of AIDS Prevention and Treatment and Guangxi Universities Key Laboratory of Prevention and Control of Highly Prevalent Disease, Nanning, China
- School of Public Health, Guangxi Medical University, Nanning, China
- The Tenth Affiliated Hospital of Guangxi Medical University, Qinzhou, China
| | - Zhiman Xie
- Department of Infectious Diseases, The Fourth People's Hospital of Nanning, Nanning, China
| | - Jie Zhou
- Guangxi Key Laboratory of AIDS Prevention and Treatment and Guangxi Universities Key Laboratory of Prevention and Control of Highly Prevalent Disease, Nanning, China
- School of Public Health, Guangxi Medical University, Nanning, China
| | - Yanjun Li
- Department of Infectious Diseases, The Fourth People's Hospital of Nanning, Nanning, China
| | - Chuanyi Ning
- Guangxi Key Laboratory of AIDS Prevention and Treatment and Guangxi Universities Key Laboratory of Prevention and Control of Highly Prevalent Disease, Nanning, China
| | - Qisi Su
- Department of Infectious Diseases, The Fourth People's Hospital of Nanning, Nanning, China
| | - Li Ye
- Guangxi Key Laboratory of AIDS Prevention and Treatment and Guangxi Universities Key Laboratory of Prevention and Control of Highly Prevalent Disease, Nanning, China
- School of Public Health, Guangxi Medical University, Nanning, China
| | - Sufang Ai
- Department of Infectious Diseases, The Fourth People's Hospital of Nanning, Nanning, China
| | - Jingzhen Lai
- Guangxi Key Laboratory of AIDS Prevention and Treatment and Guangxi Universities Key Laboratory of Prevention and Control of Highly Prevalent Disease, Nanning, China
- Life Science Institute, Guangxi Medical University, Nanning, China
| | - Peijiang Pan
- Guangxi Key Laboratory of AIDS Prevention and Treatment and Guangxi Universities Key Laboratory of Prevention and Control of Highly Prevalent Disease, Nanning, China
- Life Science Institute, Guangxi Medical University, Nanning, China
| | - Ningmei Liu
- Department of Infectious Diseases, The Fourth People's Hospital of Nanning, Nanning, China
| | - Yanyan Liao
- Guangxi Key Laboratory of AIDS Prevention and Treatment and Guangxi Universities Key Laboratory of Prevention and Control of Highly Prevalent Disease, Nanning, China
- Life Science Institute, Guangxi Medical University, Nanning, China
| | - Qijian Su
- The Tenth Affiliated Hospital of Guangxi Medical University, Qinzhou, China
| | - Zhuoxin Li
- Guangxi Key Laboratory of AIDS Prevention and Treatment and Guangxi Universities Key Laboratory of Prevention and Control of Highly Prevalent Disease, Nanning, China
- School of Public Health, Guangxi Medical University, Nanning, China
| | - Hao Liang
- Guangxi Key Laboratory of AIDS Prevention and Treatment and Guangxi Universities Key Laboratory of Prevention and Control of Highly Prevalent Disease, Nanning, China
- School of Public Health, Guangxi Medical University, Nanning, China
- Life Science Institute, Guangxi Medical University, Nanning, China
| | - Ping Cui
- Guangxi Key Laboratory of AIDS Prevention and Treatment and Guangxi Universities Key Laboratory of Prevention and Control of Highly Prevalent Disease, Nanning, China
- Life Science Institute, Guangxi Medical University, Nanning, China
| | - Jiegang Huang
- Guangxi Key Laboratory of AIDS Prevention and Treatment and Guangxi Universities Key Laboratory of Prevention and Control of Highly Prevalent Disease, Nanning, China
- School of Public Health, Guangxi Medical University, Nanning, China
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Yan L, Xu K, Xiao Q, Tuo L, Luo T, Wang S, Yang R, Zhang F, Yang X. Cellular and molecular insights into incomplete immune recovery in HIV/AIDS patients. Front Immunol 2023; 14:1152951. [PMID: 37205108 PMCID: PMC10185893 DOI: 10.3389/fimmu.2023.1152951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Accepted: 04/18/2023] [Indexed: 05/21/2023] Open
Abstract
Highly active antiretroviral therapy (ART) can effectively inhibit virus replication and restore immune function in most people living with human immunodeficiency virus (HIV). However, an important proportion of patients fail to achieve a satisfactory increase in CD4+ T cell counts. This state is called incomplete immune reconstitution or immunological nonresponse (INR). Patients with INR have an increased risk of clinical progression and higher rates of mortality. Despite widespread attention to INR, the precise mechanisms remain unclear. In this review, we will discuss the alterations in the quantity and quality of CD4+ T as well as multiple immunocytes, changes in soluble molecules and cytokines, and their relationship with INR, aimed to provide cellular and molecular insights into incomplete immune reconstitution.
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Affiliation(s)
- Liting Yan
- Department of Infectious Disease, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
- Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, Chengdu, China
- *Correspondence: Xingxiang Yang, ; Fujie Zhang, ; Liting Yan,
| | - Kaiju Xu
- Department of Infectious Disease, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
- Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, Chengdu, China
| | - Qing Xiao
- Clinical and Research Center for Infectious Diseases, Beijing Ditan Hospital, Beijing, China
| | - Lin Tuo
- Department of Infectious Disease, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
- Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, Chengdu, China
| | - Tingting Luo
- Department of Infectious Disease, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
- Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, Chengdu, China
| | - Shuqiang Wang
- Department of Infectious Disease, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
- Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, Chengdu, China
| | - Renguo Yang
- Department of Infectious Disease, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
- Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, Chengdu, China
| | - Fujie Zhang
- Clinical and Research Center for Infectious Diseases, Beijing Ditan Hospital, Beijing, China
- *Correspondence: Xingxiang Yang, ; Fujie Zhang, ; Liting Yan,
| | - Xingxiang Yang
- Department of Infectious Disease, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
- Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, Chengdu, China
- *Correspondence: Xingxiang Yang, ; Fujie Zhang, ; Liting Yan,
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Littlefield KM, Schneider JM, Neff CP, Soesanto V, Siebert JC, Nusbacher NM, Moreno-Huizar N, Cartwright IM, Armstrong AJS, Colgen SP, Lozupone CA, Palmer BE. Elevated inflammatory fecal immune factors in men who have sex with men with HIV associate with microbiome composition and gut barrier function. Front Immunol 2022; 13:1072720. [PMID: 36605218 PMCID: PMC9808389 DOI: 10.3389/fimmu.2022.1072720] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 11/30/2022] [Indexed: 12/24/2022] Open
Abstract
Introduction People living with HIV infection (PLWH) exhibit elevated levels of gastrointestinal inflammation. Potential causes of this inflammation include HIV infection and associated immune dysfunction, sexual behaviors among men who have sex with men (MSM) and gut microbiome composition. Methods To better understand the etiology of gastrointestinal inflammation we examined levels of 28 fecal soluble immune factors (sIFs) and the fecal microbiome in well-defined cohorts of HIV seronegative MSM (MSM-SN), MSM with untreated HIV infection (MSM-HIV) and MSM with HIV on anti-retroviral treatment (MSMART). Additionally, fecal solutes from these participants were used to stimulate T-84 colonic epithelial cells to assess barrier function. Results Both MSM cohorts with HIV had elevated levels of fecal calprotectin, a clinically relevant marker of GI inflammation, and nine inflammatory fecal sIFs (GM-CSF, ICAM-1, IL-1β, IL-12/23, IL-15, IL-16, TNF-β, VCAM-1, and VEGF). Interestingly, four sIFs (GM-CSF, ICAM-1, IL-7 and IL-12/23) were significantly elevated in MSM-SN compared to seronegative male non-MSM. Conversely, IL-22 and IL-13, cytokines beneficial to gut health, were decreased in all MSM with HIV and MSM-SN respectively. Importantly, all of these sIFs significantly correlated with calprotectin, suggesting they play a role in GI inflammation. Principal coordinate analysis revealed clustering of fecal sIFs by MSM status and significant associations with microbiome composition. Additionally, fecal solutes from participants in the MSM-HIV cohort significantly decreased colonic transcellular fluid transport in vitro, compared to non-MSM-SN, and this decrease associated with overall sIF composition and increased concentrations of eight inflammatory sIFs in participants with HIV. Lastly, elevated levels of plasma, sCD14 and sCD163, directly correlated with decreased transcellular transport and microbiome composition respectively, indicating that sIFs and the gut microbiome are associated with, and potentially contribute to, bacterial translocation. Conclusion Taken together, these data demonstrate that inflammatory sIFs are elevated in MSM, regardless of HIV infection status, and are associated with the gut microbiome and intestinal barrier function.
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Affiliation(s)
| | | | - Charles P. Neff
- Department of Medicine, University of Colorado, Aurora, CO, United States
| | - Victoria Soesanto
- Department of Medicine, University of Colorado, Aurora, CO, United States
| | - Janet C. Siebert
- Department of Medicine, University of Colorado, Aurora, CO, United States
- CytoAnalytics, Denver, CO, United States
| | - Nichole M. Nusbacher
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Nancy Moreno-Huizar
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Ian M. Cartwright
- Department of Medicine, University of Colorado, Aurora, CO, United States
| | - Abigail J. S. Armstrong
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Sean P. Colgen
- Department of Medicine, University of Colorado, Aurora, CO, United States
| | - Catherine A. Lozupone
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Brent E. Palmer
- Department of Medicine, University of Colorado, Aurora, CO, United States
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Impact of HIV infection and integrase strand transfer inhibitors-based treatment on the gut virome. Sci Rep 2022; 12:21658. [PMID: 36522388 PMCID: PMC9755154 DOI: 10.1038/s41598-022-25979-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 12/07/2022] [Indexed: 12/23/2022] Open
Abstract
Viruses are the most abundant components of the human gut microbiome with a significant impact on health and disease. The effects of human immunodeficiency virus (HIV) infection on gut virome has been scarcely analysed. Several studies suggested that integrase strand transfers inhibitors (INSTIs) are associated with a healthier gut. Thus, the objective of this work was to evaluate the effects of HIV infection and INSTIs on gut virome composition. 26 non-HIV-infected volunteers, 15 naive HIV-infected patients and 15 INSTIs-treated HIV-infected patients were recruited and their gut virome composition was analysed using shotgun sequencing. Bacteriophages were the most abundant and diverse viruses present in gut. HIV infection was accompanied by a decrease in phage richness which was reverted after INSTIs-based treatment. β-diversity of phages revealed that samples from HIV-infected patients clustered separately from those belonging to the control group. Differential abundant analysis showed an increase in phages belonging to Caudoviricetes class in the naive group and a decrease of Malgrandaviricetes class phages in the INSTIs-treated group compared to the control group. Besides, it was observed that INSTIs-based treatment was not able to reverse the increase of lysogenic phages associated with HIV infection or to modify the decrease observed on the relative abundance of Proteobacteria-infecting phages. Our study describes for the first time the impact of HIV and INSTIs on gut virome and demonstrates that INSTIs-based treatments are able to partially restore gut dysbiosis at the viral level, which opens several opportunities for new studies focused on microbiota-based therapies.
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Xiao Q, Yu F, Yan L, Zhao H, Zhang F. Alterations in circulating markers in HIV/AIDS patients with poor immune reconstitution: Novel insights from microbial translocation and innate immunity. Front Immunol 2022; 13:1026070. [PMID: 36325329 PMCID: PMC9618587 DOI: 10.3389/fimmu.2022.1026070] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 09/29/2022] [Indexed: 11/13/2022] Open
Abstract
After long-term anti-retroviral therapy (ART) treatment, most human immunodeficiency virus (HIV)/Acquired Immure Deficiency Syndrome (AIDS) patients can achieve virological suppression and gradual recovery of CD4+ T-lymphocyte (CD4+ T cell) counts. However, some patients still fail to attain normal CD4+ T cell counts; this group of patients are called immune non-responders (INRs), and these patients show severe immune dysfunction. The potential mechanism of poor immune reconstitution (PIR) remains unclear and the identification of uniform biomarkers to predict the occurrence of PIR is particularly vital. But limited information is available on the relationship between circulating markers of INRs and immune recovery. Hence, this review summarises alterations in the intestine microbiota and associated markers in the setting of PIR to better understand host-microbiota-metabolite interactions in HIV immune reconstitution and to identify biomarkers that can predict recovery of CD4+ T cell counts in INRs.
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Affiliation(s)
- Qing Xiao
- Beijing Ditan Hospital, Capital Medical University, Beijing, China
- Clinical Center for HIV/AIDS, Capital Medical University, Beijing, China
| | - Fengting Yu
- Beijing Ditan Hospital, Capital Medical University, Beijing, China
- Clinical Center for HIV/AIDS, Capital Medical University, Beijing, China
| | - Liting Yan
- Infectious Disease Department, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Hongxin Zhao
- Beijing Ditan Hospital, Capital Medical University, Beijing, China
- Clinical Center for HIV/AIDS, Capital Medical University, Beijing, China
| | - Fujie Zhang
- Beijing Ditan Hospital, Capital Medical University, Beijing, China
- Clinical Center for HIV/AIDS, Capital Medical University, Beijing, China
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Carrico AW, Cherenack EM, Rubin LH, McIntosh R, Ghanooni D, Chavez JV, Klatt NR, Paul RH. Through the Looking-Glass: Psychoneuroimmunology and the Microbiome-Gut-Brain Axis in the Modern Antiretroviral Therapy Era. Psychosom Med 2022; 84:984-994. [PMID: 36044613 PMCID: PMC9553251 DOI: 10.1097/psy.0000000000001133] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 08/18/2022] [Indexed: 11/26/2022]
Abstract
OBJECTIVE Depression, substance use disorders, and other neuropsychiatric comorbidities are common in people with HIV (PWH), but the underlying mechanisms are not sufficiently understood. HIV-induced damage to the gastrointestinal tract potentiates residual immune dysregulation in PWH receiving effective antiretroviral therapy. However, few studies among PWH have examined the relevance of microbiome-gut-brain axis: bidirectional crosstalk between the gastrointestinal tract, immune system, and central nervous system. METHODS A narrative review was conducted to integrate findings from 159 articles relevant to psychoneuroimmunology (PNI) and microbiome-gut-brain axis research in PWH. RESULTS Early PNI studies demonstrated that neuroendocrine signaling via the hypothalamic-pituitary-adrenal axis and autonomic nervous system could partially account for the associations of psychological factors with clinical HIV progression. This review highlights the need for PNI studies examining the mechanistic relevance of the gut microbiota for residual immune dysregulation, tryptophan catabolism, and oxytocin release as key biological determinants of neuropsychiatric comorbidities in PWH (i.e., body-to-mind pathways). It also underscores the continued relevance of neuroendocrine signaling via the hypothalamic-pituitary-adrenal axis, autonomic nervous system, and oxytocin release in modifying microbiome-gut-brain axis functioning (i.e., mind-to-body pathways). CONCLUSIONS Advancing our understanding of PNI and microbiome-gut-brain axis pathways relevant to depression, substance use disorders, and other neuropsychiatric comorbidities in PWH can guide the development of novel biobehavioral interventions to optimize health outcomes. Recommendations are provided for biobehavioral and neurobehavioral research investigating bidirectional PNI and microbiome-gut-brain axis pathways among PWH in the modern antiretroviral therapy era.
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Affiliation(s)
- Adam W Carrico
- From the Department of Public Health Sciences (Carrico, Cherenack, Ghanooni, Chavez), University of Miami Miller School of Medicine, Miami, Florida; Departments of Neurology (Rubin) and Psychiatry and Behavioral Sciences (Rubin), Johns Hopkins University School of Medicine; Department of Epidemiology (Rubin), Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland; Department of Psychology (McIntosh), University of Miami College of Arts and Sciences, Coral Gables, Florida; Department of Surgery (Klatt), University of Minnesota School of Medicine, Minneapolis, Minnesota; and Department of Psychological Sciences (Paul), University of Missouri St. Louis, St. Louis, Missouri
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Lavinder TR, Fachko DN, Stanton J, Varco-Merth B, Smedley J, Okoye AA, Skalsky RL. Effects of Early Antiretroviral Therapy on the Composition and Diversity of the Fecal Microbiome of SIV-infected Rhesus Macaques ( Macaca mulatta). Comp Med 2022; 72:287-297. [PMID: 36162961 PMCID: PMC9827599 DOI: 10.30802/aalas-cm-22-000020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
HIV-infected people develop reproducible disruptions in their gastrointestinal microbiota. Despite the suppression of HIV viremia via long-term antiretroviral therapy (ART), alterations still occur in gut microbial diversity and the commensal microbiota. Mounting evidence suggests these microbial changes lead to the development of gut dysbiosis-persistent inflammation that damages the gut mucosa-and correlate with various immune defects. In this study, we examined how early ART intervention influences microbial diversity in SIV-infected rhesus macaques. Using 16S rRNA sequencing, we defined the fecal microbiome in macaques given daily ART beginning on either 3 or 7 d after SIV infection (dpi) and characterized changes in composition, α diversity, and β diversity from before infection through 112 dpi. The dominant phyla in the fecal samples before infection were Bacteroidetes, Firmicutes, Spirochaetes, and Proteobacteria. After SIV infection and ART, the relative abundance of Firmicutes and Bacteroidetes did not change significantly. Significant reductions in α diversity occurred across time when ART was initiated at 3 dpi but not at 7 dpi. Principal coordinate analysis of samples revealed a divergence in β diversity in both treatment groups after SIV infection, with significant differences depending on the timing of ART administration. These results indicate that although administration of ART at 3 or 7 dpi did not substantially alter fecal microbial composition, the timing of early ART measurably altered phylogenetic diversity.
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Affiliation(s)
- Tiffany R Lavinder
- Division of Comparative Medicine, Oregon National Primate Research Center, Oregon Health and Science University,,Corresponding authors. ,
| | - Devin N Fachko
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, and
| | - Jeffrey Stanton
- Division of Comparative Medicine, Oregon National Primate Research Center, Oregon Health and Science University
| | - Benjamin Varco-Merth
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, and,Division of Pathobiology and Immunology, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, Oregon
| | - Jeremy Smedley
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, and,Division of Pathobiology and Immunology, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, Oregon
| | - Afam A Okoye
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, and,Division of Pathobiology and Immunology, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, Oregon
| | - Rebecca L Skalsky
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, and,Division of Pathobiology and Immunology, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, Oregon,Corresponding authors. ,
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Vestad B, Ueland T, Lerum TV, Dahl TB, Holm K, Barratt-Due A, Kåsine T, Dyrhol-Riise AM, Stiksrud B, Tonby K, Hoel H, Olsen IC, Henriksen KN, Tveita A, Manotheepan R, Haugli M, Eiken R, Berg Å, Halvorsen B, Lekva T, Ranheim T, Michelsen AE, Kildal AB, Johannessen A, Thoresen L, Skudal H, Kittang BR, Olsen RB, Ystrøm CM, Skei NV, Hannula R, Aballi S, Kvåle R, Skjønsberg OH, Aukrust P, Hov JR, Trøseid M. Respiratory dysfunction three months after severe COVID-19 is associated with gut microbiota alterations. J Intern Med 2022; 291:801-812. [PMID: 35212063 PMCID: PMC9115297 DOI: 10.1111/joim.13458] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
BACKGROUND Although coronavirus disease 2019 (COVID-19) is primarily a respiratory infection, mounting evidence suggests that the gastrointestinal tract is involved in the disease, with gut barrier dysfunction and gut microbiota alterations being related to disease severity. Whether these alterations persist and are related to long-term respiratory dysfunction remains unknown. METHODS Plasma was collected during hospital admission and after 3 months from the NOR-Solidarity trial (n = 181) and analyzed for markers of gut barrier dysfunction and inflammation. At the 3-month follow-up, pulmonary function was assessed by measuring the diffusing capacity of the lungs for carbon monoxide (DLCO ). Rectal swabs for gut microbiota analyses were collected (n = 97) and analyzed by sequencing the 16S rRNA gene. RESULTS Gut microbiota diversity was reduced in COVID-19 patients with respiratory dysfunction, defined as DLCO below the lower limit of normal 3 months after hospitalization. These patients also had an altered global gut microbiota composition, with reduced relative abundance of 20 bacterial taxa and increased abundance of five taxa, including Veillonella, potentially linked to fibrosis. During hospitalization, increased plasma levels of lipopolysaccharide-binding protein (LBP) were strongly associated with respiratory failure, defined as pO2 /fiO2 (P/F ratio) <26.6 kPa. LBP levels remained elevated during and after hospitalization and were associated with low-grade inflammation and respiratory dysfunction after 3 months. CONCLUSION Respiratory dysfunction after COVID-19 is associated with altered gut microbiota and persistently elevated LBP levels. Our results should be regarded as hypothesis generating, pointing to a potential gut-lung axis that should be further investigated in relation to long-term pulmonary dysfunction and long COVID.
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Affiliation(s)
- Beate Vestad
- Research Institute of Internal Medicine, Oslo University Hospital, Oslo, Norway.,Norwegian PSC Research Center, Department of Transplantation Medicine, Oslo University Hospital, Oslo, Norway
| | - Thor Ueland
- Research Institute of Internal Medicine, Oslo University Hospital, Oslo, Norway.,Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Tøri Vigeland Lerum
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway.,Department of Pulmonary Medicine, Oslo University Hospital Ullevål, Oslo, Norway
| | - Tuva Børresdatter Dahl
- Research Institute of Internal Medicine, Oslo University Hospital, Oslo, Norway.,Division of Critical Care and Emergencies, Oslo University Hospital, Oslo, Norway
| | - Kristian Holm
- Research Institute of Internal Medicine, Oslo University Hospital, Oslo, Norway.,Norwegian PSC Research Center, Department of Transplantation Medicine, Oslo University Hospital, Oslo, Norway.,Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Andreas Barratt-Due
- Division of Critical Care and Emergencies, Oslo University Hospital, Oslo, Norway.,Division of Laboratory Medicine, Department of Immunology, Oslo University Hospital, Oslo, Norway
| | - Trine Kåsine
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway.,Division of Critical Care and Emergencies, Oslo University Hospital, Oslo, Norway
| | - Anne Ma Dyrhol-Riise
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway.,Department of Infectious Diseases, Oslo University Hospital, Oslo, Norway
| | - Birgitte Stiksrud
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway.,Department of Infectious Diseases, Oslo University Hospital, Oslo, Norway
| | - Kristian Tonby
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway.,Department of Infectious Diseases, Oslo University Hospital, Oslo, Norway
| | - Hedda Hoel
- Research Institute of Internal Medicine, Oslo University Hospital, Oslo, Norway.,Institute of Clinical Medicine, University of Oslo, Oslo, Norway.,Medical Department, Lovisenberg Diaconal Hospital, Oslo, Norway
| | - Inge Christoffer Olsen
- Department of Research Support for Clinical Trials, Oslo University Hospital, Oslo, Norway
| | - Katerina Nezvalova Henriksen
- Department of Haematology, Oslo University Hospital, Oslo, Norway.,Hospital Pharmacies, South-Eastern Norway Enterprise, Oslo, Norway
| | - Anders Tveita
- Medical Department, Baerum Hospital, Vestre Viken Hospital Trust, Drammen, Norway
| | | | - Mette Haugli
- Department of Infectious Diseases, Sørlandet Hospital SSK, Kristiansand, Norway
| | - Ragnhild Eiken
- Department of Infectious Diseases, Innlandet Hospital Trust, Lillehammer, Norway
| | - Åse Berg
- Department of Infectious Diseases, Stavanger University Hospital, Stavanger, Norway
| | - Bente Halvorsen
- Research Institute of Internal Medicine, Oslo University Hospital, Oslo, Norway.,Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Tove Lekva
- Research Institute of Internal Medicine, Oslo University Hospital, Oslo, Norway
| | - Trine Ranheim
- Research Institute of Internal Medicine, Oslo University Hospital, Oslo, Norway
| | - Annika Elisabeth Michelsen
- Research Institute of Internal Medicine, Oslo University Hospital, Oslo, Norway.,Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Anders Benjamin Kildal
- Department of Anesthesiology and Intensive Care, University Hospital of North Norway, Tromsø, Norway
| | - Asgeir Johannessen
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway.,Department of Infectious Diseases, Vestfold Hospital Trust, Tønsberg, Norway
| | - Lars Thoresen
- Department of Medicine, Ringerike Hospital, Vestre Viken Hospital Trust, Ringerike, Norway
| | - Hilde Skudal
- Division of Infectious Diseases, Telemark Hospital Trust, Skien, Norway
| | | | | | | | - Nina Vibeche Skei
- Department of Anesthesia and Intensive Care, Levanger Hospital, Nord-Trøndelag Hospital Trust, Levanger, Norway
| | - Raisa Hannula
- Department of Infectious Diseases, Trondheim University Hospital, Trondheim, Norway
| | - Saad Aballi
- Department of Infectious Diseases, Østfold Hospital Kalnes, Grålum, Norway
| | - Reidar Kvåle
- Department of Anesthesia and Intensive Care, Haukeland University Hospital, Bergen, Norway
| | - Ole Henning Skjønsberg
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway.,Department of Pulmonary Medicine, Oslo University Hospital Ullevål, Oslo, Norway
| | - Pål Aukrust
- Research Institute of Internal Medicine, Oslo University Hospital, Oslo, Norway.,Institute of Clinical Medicine, University of Oslo, Oslo, Norway.,Section of Clinical Immunology and Infectious Diseases, Oslo University Hospital, Oslo, Norway
| | - Johannes Roksund Hov
- Research Institute of Internal Medicine, Oslo University Hospital, 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
| | - Marius Trøseid
- Research Institute of Internal Medicine, Oslo University Hospital, Oslo, Norway.,Institute of Clinical Medicine, University of Oslo, Oslo, Norway.,Section of Clinical Immunology and Infectious Diseases, Oslo University Hospital, Oslo, Norway
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Tamanai-Shacoori Z, Le Gall-David S, Moussouni F, Sweidan A, Polard E, Bousarghin L, Jolivet-Gougeon A. SARS-CoV-2 and Prevotella spp.: friend or foe? A systematic literature review. J Med Microbiol 2022; 71. [PMID: 35511246 DOI: 10.1099/jmm.0.001520] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
During this global pandemic of the COVID-19 disease, a lot of information has arisen in the media and online without scientific validation, and among these is the possibility that this disease could be aggravated by a secondary bacterial infection such as Prevotella, as well as the interest or not in using azithromycin, a potentially active antimicrobial agent. The aim of this study was to carry out a systematic literature review, to prove or disprove these allegations by scientific arguments. The search included Medline, PubMed, and Pubtator Central databases for English-language articles published 1999-2021. After removing duplicates, a total of final eligible studies (n=149) were selected. There were more articles showing an increase of Prevotella abundance in the presence of viral infection like that related to Human Immunodeficiency Virus (HIV), Papillomavirus (HPV), Herpesviridae and respiratory virus, highlighting differences according to methodologies and patient groups. The arguments for or against the use of azithromycin are stated in light of the results of the literature, showing the role of intercurrent factors, such as age, drug consumption, the presence of cancer or periodontal diseases. However, clinical trials are lacking to prove the direct link between the presence of Prevotella spp. and a worsening of COVID-19, mainly those using azithromycin alone in this indication.
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Affiliation(s)
- Zohreh Tamanai-Shacoori
- Univ Rennes, INSERM, INRAE, CHU Rennes, Institut NUMECAN (Nutrition Metabolisms and Cancer), F-35000 Rennes, France
| | - Sandrine Le Gall-David
- Univ Rennes, INSERM, INRAE, CHU Rennes, Institut NUMECAN (Nutrition Metabolisms and Cancer), F-35000 Rennes, France
| | - Fouzia Moussouni
- Univ Rennes, INSERM, INRAE, CHU Rennes, Institut NUMECAN (Nutrition Metabolisms and Cancer), F-35000 Rennes, France
| | - Alaa Sweidan
- Laboratory of Microbiology, Department of Life and Earth Sciences, Faculty of Sciences, Lebanese University, Hadath Campus, Beirut, Lebanon
| | - Elisabeth Polard
- Teaching Hospital Rennes, Service de Pharmacovigilance, F-35033 Rennes, France
| | - Latifa Bousarghin
- Univ Rennes, INSERM, INRAE, CHU Rennes, Institut NUMECAN (Nutrition Metabolisms and Cancer), F-35000 Rennes, France
| | - Anne Jolivet-Gougeon
- Univ Rennes, INSERM, INRAE, CHU Rennes, Institut NUMECAN (Nutrition Metabolisms and Cancer), F-35000 Rennes, France
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46
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Maqsood R, Skidmore PT, Holland LA, Au JL, Khan AK, Wu LI, Ma N, Begnel ER, Chohan BH, Adhiambo J, John-Stewart G, Kiarie J, Kinuthia J, Chung MH, Richardson BA, Slyker J, Lehman DA, Lim ES. Dynamic Changes in Breast Milk Microbiome in the Early Postpartum Period of Kenyan Women Living with HIV Are Influenced by Antibiotics but Not Antiretrovirals. Microbiol Spectr 2022; 10:e0208021. [PMID: 35384692 PMCID: PMC9045247 DOI: 10.1128/spectrum.02080-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 03/11/2022] [Indexed: 11/26/2022] Open
Abstract
Shared bacteria between maternal breast milk and infant stool, infers that transfer of maternal breast milk microbiota through breastfeeding seeds the establishment of the infant gut microbiome. Whether combination antiretroviral therapy (cART) impacts the breast milk microbiota in women living with HIV is unknown. Since current standard of care for people living with HIV includes cART, it has been difficult to evaluate the impact of cART on the microbiome. Here, we performed a next-generation sequencing retrospective study from pre-ART era clinical trials in Nairobi, Kenya (between 2003-2006 before cART was standard of care) that tested the effects of ART regimens to prevent mother-to-child HIV transmission. Kenyan women living with HIV were randomized to receive either no ART during breastfeeding (n = 24) or cART (zidovudine, nevirapine, lamivudine; n = 25) postpartum. Using linear mixed-effects models, we found that alpha diversity and beta diversity of the breast milk bacterial microbiome changed significantly over time during the first 4 weeks postpartum (alpha diversity P < 0.0007; beta diversity P = 0.005). There was no statistically significant difference in diversity, richness, and composition of the bacterial microbiome between cART-exposed and cART-unexposed women. In contrast, antibiotic use influenced the change of beta diversity of the bacterial microbiome over time. Our results indicate that while early postpartum time predicts breast milk microbiome composition, cART does not substantially alter the breast milk microbiota in women living with HIV. Hence, cART has minimal impact on the breast milk microbiome compared to antibiotics use. IMPORTANCE Breastfeeding has important benefits for long-term infant health, particularly in establishing and shaping the infant gut microbiome. However, the impact of combination antiretroviral therapy exposure and antibiotics on the breast milk microbiome in women living with HIV is not known. Here, in a longitudinal retrospective study of Kenyan women living with HIV from the pre-antiretroviral therapy era, we found that antibiotic use significantly influenced breast milk microbiome beta diversity, but antiretrovirals exposure did not substantially alter the microbiome. Given the protective role of breastfeeding in maternal-infant health, these findings fill an important knowledge gap of the impact of combination antiretroviral therapy on the microbiome of women living with HIV.
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Affiliation(s)
- Rabia Maqsood
- Center for Fundamental and Applied Microbiomics, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Peter T. Skidmore
- College of Health Solutions, Arizona State University, Tempe, Arizona, USA
| | - LaRinda A. Holland
- Center for Fundamental and Applied Microbiomics, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Joshua L. Au
- Center for Fundamental and Applied Microbiomics, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
- College of Health Solutions, Arizona State University, Tempe, Arizona, USA
| | - Adam K. Khan
- Center for Fundamental and Applied Microbiomics, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
| | - Lily I. Wu
- Center for Fundamental and Applied Microbiomics, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Ningxin Ma
- Division of Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
- Department of Biostatistics, University of Washington, Seattle, Washington, USA
| | - Emily R. Begnel
- Department of Global Health, University of Washington, Seattle, Washington, USA
| | - Bhavna H. Chohan
- Department of Global Health, University of Washington, Seattle, Washington, USA
- Kenya Medical Research Institute, Nairobi, Kenya
| | - Judith Adhiambo
- Department of Paediatrics and Child Health, University of Nairobi, Nairobi, Kenya
| | - Grace John-Stewart
- Department of Global Health, University of Washington, Seattle, Washington, USA
- Department of Epidemiology, University of Washington, Seattle, Washington, USA
- Department of Medicine, University of Washington, Seattle, Washington, USA
- Department of Pediatrics, University of Washington, Seattle, Washington, USA
| | - James Kiarie
- Department of Research and Programs, Kenyatta National Hospital, Nairobi, Kenya
| | - John Kinuthia
- Department of Research and Programs, Kenyatta National Hospital, Nairobi, Kenya
| | - Michael H. Chung
- Department of Global Health, University of Washington, Seattle, Washington, USA
- Department of Medicine, Emory University, Atlanta, Georgia, USA
| | - Barbra A. Richardson
- Department of Biostatistics, University of Washington, Seattle, Washington, USA
- Department of Global Health, University of Washington, Seattle, Washington, USA
| | - Jennifer Slyker
- Department of Global Health, University of Washington, Seattle, Washington, USA
- Department of Epidemiology, University of Washington, Seattle, Washington, USA
| | - Dara A. Lehman
- Department of Global Health, University of Washington, Seattle, Washington, USA
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Efrem S. Lim
- Center for Fundamental and Applied Microbiomics, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
- College of Health Solutions, Arizona State University, Tempe, Arizona, USA
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
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47
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Zaongo SD, Harypursat V, Chen Y. Single-Cell Sequencing Facilitates Elucidation of HIV Immunopathogenesis: A Review of Current Literature. Front Immunol 2022; 13:828860. [PMID: 35185920 PMCID: PMC8850777 DOI: 10.3389/fimmu.2022.828860] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Accepted: 01/18/2022] [Indexed: 12/18/2022] Open
Abstract
Knowledge gaps remain in the understanding of HIV disease establishment and progression. Scientists continue to strive in their endeavor to elucidate the precise underlying immunopathogenic mechanisms of HIV-related disease, in order to identify possible preventive and therapeutic targets. A useful tool in the quest to reveal some of the enigmas related to HIV infection and disease is the single-cell sequencing (scRNA-seq) technique. With its proven capacity to elucidate critical processes in cell formation and differentiation, to decipher critical hematopoietic pathways, and to understand the regulatory gene networks that predict immune function, scRNA-seq is further considered to be a potentially useful tool to explore HIV immunopathogenesis. In this article, we provide an overview of single-cell sequencing platforms, before delving into research findings gleaned from the use of single cell sequencing in HIV research, as published in recent literature. Finally, we describe two important avenues of research that we believe should be further investigated using the single-cell sequencing technique.
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Affiliation(s)
- Silvere D Zaongo
- Division of Infectious Diseases, Chongqing Public Health Medical Center, Chongqing, China
| | - Vijay Harypursat
- Division of Infectious Diseases, Chongqing Public Health Medical Center, Chongqing, China
| | - Yaokai Chen
- Division of Infectious Diseases, Chongqing Public Health Medical Center, Chongqing, China
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48
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Russo E, Nannini G, Sterrantino G, Kiros ST, Di Pilato V, Coppi M, Baldi S, Niccolai E, Ricci F, Ramazzotti M, Pallecchi M, Lagi F, Rossolini GM, Bartoloni A, Bartolucci G, Amedei A. Effects of viremia and CD4 recovery on gut “microbiome-immunity” axis in treatment-naïve HIV-1-infected patients undergoing antiretroviral therapy. World J Gastroenterol 2022; 28:635-652. [PMID: 35317423 PMCID: PMC8900548 DOI: 10.3748/wjg.v28.i6.635] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 07/30/2021] [Accepted: 01/12/2022] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Human immunodeficiency virus type 1 (HIV-1) infection is characterized by persistent systemic inflammation and immune activation, even in patients receiving effective antiretroviral therapy (ART). Converging data from many cross-sectional studies suggest that gut microbiota (GM) changes can occur throughout including human immunodeficiency virus (HIV) infection, treated by ART; however, the results are contrasting. For the first time, we compared the fecal microbial composition, serum and fecal microbial metabolites, and serum cytokine profile of treatment-naïve patients before starting ART and after reaching virological suppression, after 24 wk of ART therapy. In addition, we compared the microbiota composition, microbial metabolites, and cytokine profile of patients with CD4/CD8 ratio < 1 (immunological non-responders [INRs]) and CD4/CD8 > 1 (immunological responders [IRs]), after 24 wk of ART therapy.
AIM To compare for the first time the fecal microbial composition, serum and fecal microbial metabolites, and serum cytokine profile of treatment-naïve patients before starting ART and after reaching virological suppression (HIV RNA < 50 copies/mL) after 24 wk of ART.
METHODS We enrolled 12 treatment-naïve HIV-infected patients receiving ART (mainly based on integrase inhibitors). Fecal microbiota composition was assessed through next generation sequencing. In addition, a comprehensive analysis of a blood broad-spectrum cytokine panel was performed through a multiplex approach. At the same time, serum free fatty acid (FFA) and fecal short chain fatty acid levels were obtained through gas chromatography-mass spectrometry.
RESULTS We first compared microbiota signatures, FFA levels, and cytokine profile before starting ART and after reaching virological suppression. Modest alterations were observed in microbiota composition, in particular in the viral suppression condition, we detected an increase of Ruminococcus and Succinivibrio and a decrease of Intestinibacter. Moreover, in the same condition, we also observed augmented levels of serum propionic and butyric acids. Contemporarily, a reduction of serum IP-10 and an increase of IL-8 levels were detected in the viral suppression condition. In addition, the same components were compared between IRs and INRs. Concerning the microflora population, we detected a reduction of Faecalibacterium and an increase of Alistipes in INRs. Simultaneously, fecal isobutyric, isovaleric, and 2-methylbutyric acids were also increased in INRs.
CONCLUSION Our results provided an additional perspective about the impact of HIV infection, ART, and immune recovery on the “microbiome-immunity axis” at the metabolism level. These factors can act as indicators of the active processes occurring in the gastrointestinal tract. Individuals with HIV-1 infection, before ART and after reaching virological suppression with 24 wk of ART, displayed a microbiota with unchanged overall bacterial diversity; moreover, their systemic inflammatory status seems not to be completely restored. In addition, we confirmed the role of the GM metabolites in immune reconstitution.
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Affiliation(s)
- Edda Russo
- Department of Clinical and Experimental Medicine, University of Florence, Florence 50134, Italy
| | - Giulia Nannini
- Department of Clinical and Experimental Medicine, University of Florence, Florence 50134, Italy
| | - Gaetana Sterrantino
- Department of Clinical and Experimental Medicine, University of Florence, Florence 50134, Italy
| | - Seble Tekle Kiros
- Department of Clinical and Experimental Medicine, University of Florence, Florence 50134, Italy
| | - Vincenzo Di Pilato
- Department of Surgical Sciences and Integrated Diagnostics, University of Genoa, Genoa 16126, Italy
| | - Marco Coppi
- Department of Clinical and Experimental Medicine, University of Florence, Florence 50134, Italy
| | - Simone Baldi
- Department of Clinical and Experimental Medicine, University of Florence, Florence 50134, Italy
| | - Elena Niccolai
- Department of Clinical and Experimental Medicine, University of Florence, Florence 50134, Italy
| | - Federica Ricci
- Department of Clinical and Experimental Medicine, University of Florence, Florence 50134, Italy
| | - Matteo Ramazzotti
- Department of Biomedical, Experimental and Clinical "Mario Serio", University of Florence, Florence 50134, Italy
| | - Marco Pallecchi
- Department of Biomedical, Experimental and Clinical "Mario Serio", University of Florence, Florence 50134, Italy
| | - Filippo Lagi
- Department of Clinical and Experimental Medicine, University of Florence, Florence 50134, Italy
| | - Gian Maria Rossolini
- Microbiology and Virology Unit, Florence Careggi University Hospital, University of Florence, Florence 50134, Italy
| | - Alessandro Bartoloni
- Department of Clinical and Experimental Medicine, University of Florence, Florence 50134, Italy
| | - Gianluca Bartolucci
- Department of Neurosciences, Psychology, Drug Research and Child Health, University of Florence, Florence 50019, Italy
| | - Amedeo Amedei
- Department of Clinical and Experimental Medicine, University of Florence, Florence 50134, Italy
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49
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Ouyang J, Zaongo SD, Zhang X, Qi M, Hu A, Wu H, Chen Y. Microbiota-Meditated Immunity Abnormalities Facilitate Hepatitis B Virus Co-Infection in People Living With HIV: A Review. Front Immunol 2022; 12:755890. [PMID: 35069530 PMCID: PMC8770824 DOI: 10.3389/fimmu.2021.755890] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 12/17/2021] [Indexed: 12/12/2022] Open
Abstract
Hepatitis B virus (HBV) co-infection is fairly common in people living with HIV (PLWH) and affects millions of people worldwide. Identical transmission routes and HIV-induced immune suppression have been assumed to be the main factors contributing to this phenomenon. Moreover, convergent evidence has shown that people co-infected with HIV and HBV are more likely to have long-term serious medical problems, suffer more from liver-related diseases, and have higher mortality rates, compared to individuals infected exclusively by either HIV or HBV. However, the precise mechanisms underlying the comorbid infection of HIV and HBV have not been fully elucidated. In recent times, the human gastrointestinal microbiome is progressively being recognized as playing a pivotal role in modulating immune function, and is likely to also contribute significantly to critical processes involving systemic inflammation. Both antiretroviral therapy (ART)-naïve HIV-infected subjects and ART-treated individuals are now known to be characterized by having gut microbiomic dysbiosis, which is associated with a damaged intestinal barrier, impaired mucosal immunological functioning, increased microbial translocation, and long-term immune activation. Altered microbiota-related products in PLWH, such as lipopolysaccharide (LPS) and short-chain fatty acids (SCFA), have been associated with the development of leaky gut syndrome, favoring microbial translocation, which in turn has been associated with a chronically activated underlying host immune response and hence the facilitated pathogenesis of HBV infection. Herein, we critically review the interplay among gut microbiota, immunity, and HIV and HBV infection, thus laying down the groundwork with respect to the future development of effective strategies to efficiently restore normally diversified gut microbiota in PLWH with a dysregulated gut microbiome, and thus potentially reduce the prevalence of HBV infection in this population.
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Affiliation(s)
- Jing Ouyang
- Division of Infectious Diseases, Chongqing Public Health Medical Center, Chongqing, China
| | - Silvere D Zaongo
- Division of Infectious Diseases, Chongqing Public Health Medical Center, Chongqing, China
| | - Xue Zhang
- Division of Infectious Diseases, Chongqing Public Health Medical Center, Chongqing, China
| | - Miaomiao Qi
- Division of Infectious Diseases, Chongqing Public Health Medical Center, Chongqing, China
| | - Aizhen Hu
- Division of Infectious Diseases, Chongqing Public Health Medical Center, Chongqing, China
| | - Hao Wu
- Department of Infectious Diseases, You'an Hospital, Capital Medical University, Beijing, China
| | - Yaokai Chen
- Division of Infectious Diseases, Chongqing Public Health Medical Center, Chongqing, China
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50
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Mechanisms of immune aging in HIV. Clin Sci (Lond) 2022; 136:61-80. [PMID: 34985109 DOI: 10.1042/cs20210344] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 12/13/2021] [Accepted: 12/14/2021] [Indexed: 12/11/2022]
Abstract
Massive CD4+ T-cell depletion as well as sustained immune activation and inflammation are hallmarks of Human Immunodeficiency Virus (HIV)-1 infection. In recent years, an emerging concept draws an intriguing parallel between HIV-1 infection and aging. Indeed, many of the alterations that affect innate and adaptive immune subsets in HIV-infected individuals are reminiscent of the process of immune aging, characteristic of old age. These changes, of which the presumed cause is the systemic immune activation established in patients, likely participate in the immuno-incompetence described with HIV progression. With the success of antiretroviral therapy (ART), HIV-seropositive patients can now live for many years despite chronic viral infection. However, acquired immunodeficiency syndrome (AIDS)-related opportunistic infections have given way to chronic diseases as the leading cause of death since HIV infection. Therefore, the comparison between HIV-1 infected patients and uninfected elderly individuals goes beyond the sole onset of immunosenescence and extends to the deterioration of several physiological functions related to inflammation and systemic aging. In light of this observation, it is interesting to understand the precise link between immune activation and aging in HIV-1 infection to figure out how to best care for people living with HIV (PLWH).
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