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Girard L, Birse K, Holm JB, Gajer P, Humphrys MS, Garber D, Guenthner P, Noël-Romas L, Abou M, McCorrister S, Westmacott G, Wang L, Rohan LC, Matoba N, McNicholl J, Palmer KE, Ravel J, Burgener AD. Impact of the griffithsin anti-HIV microbicide and placebo gels on the rectal mucosal proteome and microbiome in non-human primates. Sci Rep 2018; 8:8059. [PMID: 29795295 PMCID: PMC5966460 DOI: 10.1038/s41598-018-26313-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 05/10/2018] [Indexed: 12/26/2022] Open
Abstract
Topical microbicides are being explored as an HIV prevention method for individuals who practice receptive anal intercourse. In vivo studies of these microbicides are critical to confirm safety. Here, we evaluated the impact of a rectal microbicide containing the antiviral lectin, Griffithsin (GRFT), on the rectal mucosal proteome and microbiome. Using a randomized, crossover placebo-controlled design, six rhesus macaques received applications of hydroxyethylcellulose (HEC)- or carbopol-formulated 0.1% GRFT gels. Rectal mucosal samples were then evaluated by label-free tandem MS/MS and 16 S rRNA gene amplicon sequencing, for proteomics and microbiome analyses, respectively. Compared to placebo, GRFT gels were not associated with any significant changes to protein levels at any time point (FDR < 5%), but increased abundances of two common and beneficial microbial taxa after 24 hours were observed in HEC-GRFT gel (p < 2E-09). Compared to baseline, both placebo formulations were associated with alterations to proteins involved in proteolysis, activation of the immune response and inflammation after 2 hours (p < 0.0001), and increases in beneficial Faecalibacterium spp. after 24 hours in HEC placebo gel (p = 4.21E-15). This study supports the safety profile of 0.1% GRFT gel as an anti-HIV microbicide and demonstrates that current placebo formulations may associate with changes to rectal proteome and microbiota.
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Affiliation(s)
- Lauren Girard
- National HIV and Retrovirology Labs, JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, Winnipeg, Canada
- Department of Medical Microbiology, University of Manitoba, Winnipeg, Canada
| | - Kenzie Birse
- National HIV and Retrovirology Labs, JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, Winnipeg, Canada
- Department of Medical Microbiology, University of Manitoba, Winnipeg, Canada
| | - Johanna B Holm
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, USA
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, USA
| | - Pawel Gajer
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, USA
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, USA
| | - Mike S Humphrys
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, USA
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, USA
| | - David Garber
- Laboratory Branch, Division of HIV/AIDS Prevention, National Centre for HIV/AIDS, Viral Hepatitis, Sexually Transmitted Disease and Tuberculosis Prevention, CDC, Atlanta, USA
| | - Patricia Guenthner
- Laboratory Branch, Division of HIV/AIDS Prevention, National Centre for HIV/AIDS, Viral Hepatitis, Sexually Transmitted Disease and Tuberculosis Prevention, CDC, Atlanta, USA
| | - Laura Noël-Romas
- National HIV and Retrovirology Labs, JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, Winnipeg, Canada
- Department of Medical Microbiology, University of Manitoba, Winnipeg, Canada
| | - Max Abou
- National HIV and Retrovirology Labs, JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, Winnipeg, Canada
| | - Stuart McCorrister
- Mass Spectrometry and Proteomics Core Facility, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
| | - Garrett Westmacott
- Mass Spectrometry and Proteomics Core Facility, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
| | - Lin Wang
- Magee Women's Research Institute, Pittsburgh, USA
- School of Pharmacy, University of Pittsburgh, Pittsburgh, USA
| | - Lisa C Rohan
- Magee Women's Research Institute, Pittsburgh, USA
- School of Pharmacy, University of Pittsburgh, Pittsburgh, USA
| | - Nobuyuki Matoba
- Center for Predictive Medicine, University of Louisville, Louisville, USA
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, USA
- James Graham Brown Cancer Centre, University of Louisville, Louisville, USA
| | - Janet McNicholl
- Laboratory Branch, Division of HIV/AIDS Prevention, National Centre for HIV/AIDS, Viral Hepatitis, Sexually Transmitted Disease and Tuberculosis Prevention, CDC, Atlanta, USA
| | - Kenneth E Palmer
- Center for Predictive Medicine, University of Louisville, Louisville, USA
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, USA
- James Graham Brown Cancer Centre, University of Louisville, Louisville, USA
| | - Jacques Ravel
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, USA
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, USA
| | - Adam D Burgener
- National HIV and Retrovirology Labs, JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, Winnipeg, Canada.
- Department of Medical Microbiology, University of Manitoba, Winnipeg, Canada.
- Unit of Infectious Diseases, Department of Medicine Solna, Centre for Molecular Medicine, Karolinska Institute, Karolinska University Hospital, Stockholm, Sweden.
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253
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Impact of HIV and Type 2 diabetes on Gut Microbiota Diversity, Tryptophan Catabolism and Endothelial Dysfunction. Sci Rep 2018; 8:6725. [PMID: 29712976 PMCID: PMC5928109 DOI: 10.1038/s41598-018-25168-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 04/10/2018] [Indexed: 01/04/2023] Open
Abstract
HIV infection and type 2 diabetes are associated with altered gut microbiota, chronic inflammation, and increased cardiovascular risk. We aimed to investigate the combined effect of these diseases on gut microbiota composition and related metabolites, and a potential relation to endothelial dysfunction in individuals with HIV-infection only (n = 23), diabetes only (n = 16) or both conditions (n = 21), as well as controls (n = 24). Fecal microbiota was analyzed by Illumina sequencing of the 16 S rRNA gene. Markers of endothelial dysfunction (asymmetric dimethylarginine [ADMA]), tryptophan catabolism (kynurenine/tryptophan [KT]-ratio), and inflammation (neopterin) were measured by liquid chromatography-tandem mass spectrometry. The combination of HIV and type 2 diabetes was associated with reduced gut microbiota diversity, increased plasma KT-ratio and neopterin. Microbial genes related to tryptophan metabolism correlated with KT-ratio and low alpha diversity, in particular in HIV-infected with T2D. In multivariate analyses, KT-ratio associated with ADMA (β = 4.58 [95% CI 2.53–6.63], p < 0.001), whereas microbiota composition per se was not associated with endothelial dysfunction. Our results indicate that tryptophan catabolism may be related to endothelial dysfunction, with a potentially detrimental interaction between HIV and diabetes. The potential contribution of gut microbiota and the impact for cardiovascular risk should be further explored in prospective studies powered for clinical end points.
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254
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Pólvora TLS, Nobre ÁVV, Tirapelli C, Taba M, Macedo LDD, Santana RC, Pozzetto B, Lourenço AG, Motta ACF. Relationship between human immunodeficiency virus (HIV-1) infection and chronic periodontitis. Expert Rev Clin Immunol 2018; 14:315-327. [PMID: 29595347 DOI: 10.1080/1744666x.2018.1459571] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
INTRODUCTION Current studies show that, even in the era of antiretroviral therapies, HIV-1 infection is associated with more severe and frequent refractory chronic periodontitis. Areas covered: This review, based on a systematic analysis of the literature, intends to provide an update on factors that may be involved in the pathogenesis of periodontal disease in HIV-1-infected patients, including local immunosuppression, oral microbial factors, systemic inflammation, salivary markers, and the role of gingival tissue as a possible reservoir of HIV-1. Expert commentary: The therapeutic revolution of ART made HIV-1 infection a chronic controllable disease, reduced HIV-1 mortality rate, restored at least partially the immune response and dramatically increased life expectancy of HIV-1-infected patients. Despite all these positive aspects, chronic periodontitis assumes an important role in the HIV-1 infection status for activating systemic inflammation favoring viral replication and influencing HIV-1 status, and also acting as a possible reservoir of HIV-1. All these issues still need to be clarified and validated, but have important clinical implications that certainly will benefit the diagnosis and management of chronic periodontitis in HIV-1-infected patients, and also contributes to HIV-1 eradication.
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Affiliation(s)
| | - Átila Vinícius V Nobre
- b Department of Oral & Maxillofacial Surgery, and Periodontology, School of Dentistry of Ribeirão Preto , University of São Paulo , Ribeirão Preto , Brazil
| | - Camila Tirapelli
- c Department of Dental Material and Prosthesis, School of Dentistry of Ribeirão Preto , USP - University of São Paulo , Ribeirão Preto , Brazil
| | - Mário Taba
- b Department of Oral & Maxillofacial Surgery, and Periodontology, School of Dentistry of Ribeirão Preto , University of São Paulo , Ribeirão Preto , Brazil
| | - Leandro Dorigan de Macedo
- d Division of Dentistry and Stomatology, Clinical Hospital, Ribeirão Preto Medical School , University of São Paulo , Ribeirão Preto , Brazil
| | - Rodrigo Carvalho Santana
- e Department of Internal Medicine, Ribeirão Preto Medical School , USP - University of São Paulo , Ribeirão Preto , Brazil
| | - Bruno Pozzetto
- f GIMAP EA 3064 (Groupe Immunité des Muqueuses et Agents Pathogènes) , University of Lyon , Saint-Etienne , France
| | - Alan Grupioni Lourenço
- g Department of Stomatology, Public Oral Health and Forensic Dentistry, School of Dentistry of Ribeirão Preto , University of São Paulo , Ribeirão Preto , Brazil
| | - Ana Carolina F Motta
- g Department of Stomatology, Public Oral Health and Forensic Dentistry, School of Dentistry of Ribeirão Preto , University of São Paulo , Ribeirão Preto , Brazil
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255
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Klatt NR, Manuzak JA. Microbial Effects on Immunity in HIV: Virus, Gender or Sexual Preference Induced? EBioMedicine 2018; 31:7-8. [PMID: 29655995 PMCID: PMC6014573 DOI: 10.1016/j.ebiom.2018.04.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 04/05/2018] [Indexed: 02/06/2023] Open
Affiliation(s)
- Nichole R Klatt
- Department of Pediatrics, Miller School of Medicine, University of Miami, Miami, FL, USA; Department of Pharmaceutics, School of Pharmacy, University of Washington, Seattle, WA, USA; Washington National Primate Research Center, University of Washington, Seattle, WA, USA
| | - Jennifer A Manuzak
- Department of Pediatrics, Miller School of Medicine, University of Miami, Miami, FL, USA; Department of Pharmaceutics, School of Pharmacy, University of Washington, Seattle, WA, USA; Washington National Primate Research Center, University of Washington, Seattle, WA, USA.
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256
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Scagnolari C, Antonelli G. Type I interferon and HIV: Subtle balance between antiviral activity, immunopathogenesis and the microbiome. Cytokine Growth Factor Rev 2018; 40:19-31. [PMID: 29576284 PMCID: PMC7108411 DOI: 10.1016/j.cytogfr.2018.03.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 02/23/2018] [Accepted: 03/08/2018] [Indexed: 02/06/2023]
Abstract
Type I interferon (IFN) response initially limits HIV-1 spread and may delay disease progression by stimulating several immune system components. Nonetheless, persistent exposure to type I IFN in the chronic phase of HIV-1 infection is associated with desensitization and/or detrimental immune activation, thereby hindering immune recovery and fostering viral persistence. This review provides a basis for understanding the complexity and function of IFN pleiotropic activity in HIV-1 infection. In particular, the dichotomous role of the IFN response in HIV-1 immunopathogenesis will be discussed, highlighting recent advances in the dynamic modulation of IFN production in acute versus chronic infection, expression signatures of IFN subtypes, and viral and host factors affecting the magnitude of IFN response during HIV-1 infection. Lastly, the review gives a forward-looking perspective on the interplay between microbiome compositions and IFN response.
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Affiliation(s)
- Carolina Scagnolari
- Department of Molecular Medicine, Laboratory of Virology Affiliated to Istituto Pasteur Italia - Fondazione Cenci Bolognetti, Sapienza University, Rome, Italy.
| | - Guido Antonelli
- Department of Molecular Medicine, Laboratory of Virology Affiliated to Istituto Pasteur Italia - Fondazione Cenci Bolognetti, Sapienza University, Rome, Italy
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257
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Neff CP, Krueger O, Xiong K, Arif S, Nusbacher N, Schneider JM, Cunningham AW, Armstrong A, Li S, McCarter MD, Campbell TB, Lozupone CA, Palmer BE. Fecal Microbiota Composition Drives Immune Activation in HIV-infected Individuals. EBioMedicine 2018; 30:192-202. [PMID: 29650491 PMCID: PMC5952409 DOI: 10.1016/j.ebiom.2018.03.024] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 03/12/2018] [Accepted: 03/20/2018] [Indexed: 02/08/2023] Open
Abstract
The inflammatory properties of the enteric microbiota of Human Immunodeficiency Virus (HIV)-infected individuals are of considerable interest because of strong evidence that bacterial translocation contributes to chronic immune activation and disease progression. Altered enteric microbiota composition occurs with HIV infection but whether altered microbiota composition or increased intestinal permeability alone drives peripheral immune activation is controversial. To comprehensively assess the inflammatory properties of HIV-associated enteric microbiota and relate these to systemic immune activation, we developed methods to purify whole fecal bacterial communities (FBCs) from stool for use in in vitro immune stimulation assays with human cells. We show that the enteric microbiota of untreated HIV-infected subjects induce significantly higher levels of activated monocytes and T cells compared to seronegative subjects. FBCs from anti-retroviral therapy (ART)-treated HIV-infected individuals induced intermediate T cell activation, indicating an only partial correction of adaptive immune cell activation capacity of the microbiome with ART. In vitro activation levels correlated with activation levels and viral load in blood and were particularly high in individuals harboring specific gram-positive opportunistic pathogens. Blockade experiments implicated Tumor Necrosis Factor (TNF)-α and Toll-Like Receptor-2 (TLR2), which recognizes peptidoglycan, as strong mediators of T cell activation; This may contradict a previous focus on lipopolysaccharide as a primary mediator of chronic immune activation. These data support that increased inflammatory properties of the enteric microbiota and not increased permeability alone drives chronic inflammation in HIV.
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Affiliation(s)
- Charles Preston Neff
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Owen Krueger
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Kathy Xiong
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Sabrina Arif
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Nichole Nusbacher
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Jennifer M Schneider
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Annie W Cunningham
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Abigail Armstrong
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Sam Li
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Martin D McCarter
- Department of Surgery, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Thomas B Campbell
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Catherine A Lozupone
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA.
| | - Brent E Palmer
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA.
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258
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San-Juan-Vergara H, Zurek E, Ajami NJ, Mogollon C, Peña M, Portnoy I, Vélez JI, Cadena-Cruz C, Diaz-Olmos Y, Hurtado-Gómez L, Sanchez-Sit S, Hernández D, Urruchurtu I, Di-Ruggiero P, Guardo-García E, Torres N, Vidal-Orjuela O, Viasus D, Petrosino JF, Cervantes-Acosta G. A Lachnospiraceae-dominated bacterial signature in the fecal microbiota of HIV-infected individuals from Colombia, South America. Sci Rep 2018; 8:4479. [PMID: 29540734 PMCID: PMC5852036 DOI: 10.1038/s41598-018-22629-7] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 02/05/2018] [Indexed: 02/08/2023] Open
Abstract
HIV infection has a tremendous impact on the immune system's proper functioning. The mucosa-associated lymphoid tissue (MALT) is significantly disarrayed during HIV infection. Compositional changes in the gut microbiota might contribute to the mucosal barrier disruption, and consequently to microbial translocation. We performed an observational, cross-sectional study aimed at evaluating changes in the fecal microbiota of HIV-infected individuals from Colombia. We analyzed the fecal microbiota of 37 individuals via 16S rRNA gene sequencing; 25 HIV-infected patients and 12 control (non-infected) individuals, which were similar in body mass index, age, gender balance and socioeconomic status. To the best of our knowledge, no such studies have been conducted in Latin American countries. Given its compositional nature, microbiota data were normalized and transformed using Aitchison's Centered Log-Ratio. Overall, a change in the network structure in HIV-infected patients was revealed by using the SPIEC-EASI MB tool. Genera such as Blautia, Dorea, Yersinia, Escherichia-Shigella complex, Staphylococcus, and Bacteroides were highly relevant in HIV-infected individuals. Differential abundance analysis by both sparse Partial Least Square-Discriminant Analysis and Random Forest identified a greater abundance of Lachnospiraceae-OTU69, Blautia, Dorea, Roseburia, and Erysipelotrichaceae in HIV-infected individuals. We show here, for the first time, a predominantly Lachnospiraceae-based signature in HIV-infected individuals.
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Affiliation(s)
| | - Eduardo Zurek
- División de Ingenierías, Fundación Universidad del Norte, Barranquilla, Colombia
| | - Nadim J Ajami
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | | | - Mario Peña
- División Ciencias de la Salud, Fundación Universidad del Norte, Barranquilla, Colombia
| | - Ivan Portnoy
- División de Ingenierías, Fundación Universidad del Norte, Barranquilla, Colombia
| | - Jorge I Vélez
- División de Ingenierías, Fundación Universidad del Norte, Barranquilla, Colombia
| | - Christian Cadena-Cruz
- División Ciencias de la Salud, Fundación Universidad del Norte, Barranquilla, Colombia
| | - Yirys Diaz-Olmos
- División Ciencias de la Salud, Fundación Universidad del Norte, Barranquilla, Colombia
| | - Leidy Hurtado-Gómez
- División Ciencias de la Salud, Fundación Universidad del Norte, Barranquilla, Colombia
| | - Silvana Sanchez-Sit
- Maestría en Estadística Aplicada, Universidad del Norte, Barranquilla, Colombia
| | | | | | | | | | | | - Oscar Vidal-Orjuela
- División Ciencias de la Salud, Fundación Universidad del Norte, Barranquilla, Colombia
| | - Diego Viasus
- División Ciencias de la Salud, Fundación Universidad del Norte, Barranquilla, Colombia
| | - Joseph F Petrosino
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
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A Pilot Study of the Immunologic, Virologic, and Pathologic Consequences of Intra-anal 5% Imiquimod in HIV-1-Infected Men With High-Grade Squamous Intraepithelial Lesions. Dis Colon Rectum 2018; 61:298-305. [PMID: 29360679 DOI: 10.1097/dcr.0000000000000991] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
BACKGROUND Imiquimod can be used to treat internal anal high-grade squamous intraepithelial lesions. In HIV-1-infected individuals there is a theoretical concern for increased HIV replication in anorectal tissue secondary to imiquimod-induced mucosal inflammation. OBJECTIVE The purpose of this study was to assess local virologic, immunologic, and pathologic effects of imiquimod treatment in HIV-infected individuals. DESIGN This was a pilot study at a single academic center. SETTINGS The study was conducted at the University of Pittsburgh Anal Dysplasia Clinic. PATIENTS HIV-1-infected individuals with biopsy-confirmed internal anal high-grade squamous intraepithelial lesions were included. INTERVENTION Imiquimod cream was prescribed for intra-anal use 3 times per week for 9 weeks. MAIN OUTCOME MEASURES Anal human papillomavirus typing, anal and rectal tissue HIV-1 RNA and DNA quantification, cytokine gene expression, and anal histology were measured. RESULTS Nine evaluable participants (1 participant was lost to follow-up) were all white men with a median age of 46 years (interquartile range = 12 y) and a median CD4 T-cell count of 480 cells per cubic millimeter (interquartile range = 835). All were taking antiretroviral therapy, and 7 of 9 had HIV-1 RNA <50 copies per milliliter. The median dose of imiquimod used was 27.0 (interquartile range = 3.5), and there was a median of 11 days (interquartile range = 10 d) from last dose to assessment. There was no progression to cancer, no significant change in the number of human papillomavirus types detected, and no significant change in quantifiable cytokines/HIV-1 RNA or DNA levels in anal or rectal tissue. Seven (35%) of 20 high-grade lesions resolved to low-grade squamous intraepithelial lesions. LIMITATIONS The study was limited by the small number of participants and variable time to final assessment. CONCLUSIONS Intra-anal imiquimod showed no evidence of immune activation or increase in HIV-1 viral replication in anal and rectal tissue and confirmed efficacy for intra-anal high-grade squamous intraepithelial lesion treatment morbidity. See Video Abstract at http://links.lww.com/DCR/A498.
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260
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Duvallet C. Meta-analysis generates and prioritizes hypotheses for translational microbiome research. Microb Biotechnol 2018; 11:273-276. [PMID: 29349912 PMCID: PMC5812236 DOI: 10.1111/1751-7915.13047] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Affiliation(s)
- Claire Duvallet
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- MIT Center for Microbiome Informatics and Therapeutics, Cambridge, MA, 02139, USA
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261
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Pescatore NA, Pollak R, Kraft CS, Mulle JG, Kelley CF. Short Communication: Anatomic Site of Sampling and the Rectal Mucosal Microbiota in HIV Negative Men Who Have Sex with Men Engaging in Condomless Receptive Anal Intercourse. AIDS Res Hum Retroviruses 2018; 34:277-281. [PMID: 29308654 DOI: 10.1089/aid.2017.0206] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Rectal transmission accounts for the majority of HIV transmissions among men who have sex with men (MSM). We previously demonstrated a distinct rectal mucosal immune environment in MSM engaging in condomless receptive anal intercourse (CRAI) compared with men who do not engage in anal intercourse, including enrichment of the microbiota for the Prevotellaceae family as compared with Bacteroidaceae. Here, we expand upon these previous findings to determine differences by anatomic site of collection (anal vs. rectal mucosa) and examine associations of the predominant taxa with other genera. We analyzed 16SrRNA gene sequences of the V1-V2 region generated on an Illumina MiSeq® from 35 MSM engaging in CRAI and 20 male controls. Observation by principal coordinates analysis and analysis of similarities test showed differing composition of the microbiota by anatomic site of collection. When analyzing the top 10 abundant genera from each anatomic site by generalized linear models, the predominant genera (Prevotella enrichment among MSM engaging in CRAI vs. Bacteroides among controls) were consistent; however, the two sites shared only four common genera. In addition, associations between the relative abundance of Prevotella and Bacteroides with other prevalent genera, by Spearman's rank correlations, were inconsistent when stratifying by study group. Prevotella versus Bacteroides predominant microbiota may not define a consistent underlying microbial community, and our data underline the importance of anatomic sampling site. Understanding the rectal mucosal immune environment, of which the microbiota is a critical component, will enable a better understanding of rectal HIV transmission.
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Affiliation(s)
- Nicole A. Pescatore
- Division of Infectious Diseases, Emory University School of Medicine, Atlanta, Georgia
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, Georgia
| | - Rebecca Pollak
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia
| | - Colleen S. Kraft
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, Georgia
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia
| | - Jennifer G. Mulle
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, Georgia
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia
| | - Colleen F. Kelley
- Division of Infectious Diseases, Emory University School of Medicine, Atlanta, Georgia
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, Georgia
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262
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Dillon SM, Castleman MJ, Frank DN, Austin GL, Gianella S, Cogswell AC, Landay AL, Barker E, Wilson CC. Brief Report: Inflammatory Colonic Innate Lymphoid Cells Are Increased During Untreated HIV-1 Infection and Associated With Markers of Gut Dysbiosis and Mucosal Immune Activation. J Acquir Immune Defic Syndr 2018; 76:431-437. [PMID: 28825942 DOI: 10.1097/qai.0000000000001523] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
BACKGROUND HIV-1 infection is associated with intestinal inflammation, changes in the enteric microbiota (dysbiosis), and intestinal epithelial cell damage. NKp44 innate lymphoid cells (ILCs) play an important role in epithelial barrier maintenance through the production of interleukin (IL)-22 but also display functional plasticity and can produce inflammatory cytokines [eg, interferon gamma (IFNγ)] in response to cytokine milieu and stimulatory signals. The objective of this pilot study was to enumerate frequencies of IL-22 and IFNγ-expressing colonic NKp44 ILCs during untreated, chronic HIV-1 infection. SETTING A cross-sectional study was performed to compare numbers of cytokine-expressing ILCs in colonic biopsies of untreated, chronic HIV-1 infected (n = 22), and uninfected (n = 10) study participants. Associations between cytokine ILC and previously established measures of virological, immunological, and microbiome indices were analyzed. METHODS Multicolor flow cytometry was used to measure the absolute number of colonic CD3NKp44CD56 ILCs expressing IL-22 or IFNγ after in vitro mitogenic stimulation. RESULTS Numbers of colonic NKp44 ILCs that expressed IFNγ were significantly higher in HIV-1 infected versus uninfected persons and positively correlated with relative abundances of dysbiotic bacterial species in the Xanthomonadaceae and Prevotellaceae bacterial families and with colonic myeloid dendritic cell and T-cell activation. CONCLUSION Higher numbers of inflammatory colonic ILCs during untreated chronic HIV-1 infection that associated with dysbiosis and colonic myeloid dendritic cell and T-cell activation suggest that inflammatory ILCs may contribute to gut mucosal inflammation and epithelial barrier breakdown, important features of HIV-1 mucosal pathogenesis.
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Affiliation(s)
- Stephanie M Dillon
- *Department of Medicine, Division of Infectious Diseases, University of Colorado Anschutz Medical Campus, Aurora, CO; †University of Colorado Microbiome Research Consortium, Aurora, CO; ‡Division of Gastroenterology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO; §Division of Infectious Diseases, School of Medicine, University of California, San Diego, La Jolla, CA; and ‖Department of Immunity and Emerging Pathogens, Rush University Medical Center, Chicago, IL
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Zhou Y, Ou Z, Tang X, Zhou Y, Xu H, Wang X, Li K, He J, Du Y, Wang H, Chen Y, Nie Y. Alterations in the gut microbiota of patients with acquired immune deficiency syndrome. J Cell Mol Med 2018; 22:2263-2271. [PMID: 29411528 PMCID: PMC5867062 DOI: 10.1111/jcmm.13508] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 11/27/2017] [Indexed: 01/02/2023] Open
Abstract
Acquired immune deficiency syndrome (AIDS), caused by infection with human immunodeficiency virus (HIV), is associated with gastrointestinal disease, systemic immune activation and changes in the gut microbiota. Here, we aim to investigate the gut microbiota patterns of HIV‐infected individuals and HIV‐uninfected individuals in populations from South China. We enrolled 33 patients with HIV (14 participants treated with highly active antiretroviral therapy [HAART] for more than 3 months; the remaining 19 individuals had not received treatment) and 35 healthy controls (HC) for a cross‐sectional comparison of gut microbiota using stool samples. Gut microbial communities were profiled by sequencing the bacterial 16S rRNA genes. Dysbiosis was more common among patients with AIDS compared with healthy individuals. Dysbiosis was characterized by decreased α‐diversity, low mean counts of Bacteroidetes, Faecalibacterium, Prevotella, Bacteroides vulgatus, Dialister and Roseburia inulnivorans, and high mean counts of Proteobacteria, Enterococcus, Streptococcus, Lactobacillus, Lachnociostridium, Ruminococcus gnavus and Streptococcus vestibularis. Increased abundance of Bacilli was observed in homosexual patients. Proteobacteria were higher among heterosexual patients with HIV infections. Tenericutes were higher among patients with history of intravenous drug abuse. Restoration of gut microbiota diversity and a significant increase in abundance of Faecalibacterium, Blautia and Bacteroides were found in patients receiving HAART compared to those who did not receive. HIV infection‐associated dysbiosis is characterized by decreased levels of α‐diversity and Bacteroidetes, increased levels of Proteobacteria and the alterations of gut microbiota correlate with the route of HIV transmission. The imbalanced faecal microbiota of HIV infection is partially restored after therapy.
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Affiliation(s)
- Youlian Zhou
- Department of Gastroenterology, Guangzhou Digestive Disease Center, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, China
| | - Zhitao Ou
- Department of Internal Medicine, Guangzhou No. 8 People's Hospital, Guangzhou, China
| | - Xiaoping Tang
- Institute for Infectious Diseases, Guangzhou No. 8 People's Hospital, Guangzhou, China
| | - Yongjian Zhou
- Department of Gastroenterology, Guangzhou Digestive Disease Center, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, China
| | - Haoming Xu
- Department of Gastroenterology, Guangzhou Digestive Disease Center, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, China
| | - Xianfei Wang
- Department of Gastroenterology, Guangzhou Digestive Disease Center, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, China.,Department of Gastroenterology, Affiliated Hospital of North Sichuan Medical College, Nanchong, China
| | - Kang Li
- Department of Gastroenterology, Guangzhou Digestive Disease Center, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, China
| | - Jie He
- Department of Gastroenterology, Guangzhou Digestive Disease Center, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, China
| | - Yanlei Du
- Department of Gastroenterology, Guangzhou Digestive Disease Center, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, China
| | - Hong Wang
- Department of Gastroenterology, Guangzhou Digestive Disease Center, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, China
| | - Ye Chen
- State Key Laboratory of Organ Failure Research, Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yuqiang Nie
- Department of Gastroenterology, Guangzhou Digestive Disease Center, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, China
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Complementary Methodologies To Investigate Human Gut Microbiota in Host Health, Working towards Integrative Systems Biology. J Bacteriol 2018; 200:JB.00376-17. [PMID: 28874411 DOI: 10.1128/jb.00376-17] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
In 1680, Antonie van Leeuwenhoek noted compositional differences in his oral and fecal microbiota, pioneering the study of the diversity of the human microbiome. From Leeuwenhoek's time to successful modern attempts at changing the gut microbial landscape to cure disease, there has been an exponential increase in the recognition of our resident microbes as part of ourselves. Thus, the human host and microbiome have evolved in parallel to configure a balanced system in which microbes survive in homeostasis with our innate and acquired immune systems, unless disease occurs. A growing number of studies have demonstrated a correlation between the presence/absence of microbial taxa and some of their functional molecules (i.e., genes, proteins, and metabolites) with health and disease states. Nevertheless, misleading experimental design on human subjects and the cost and lack of standardized animal models pose challenges to answering the question of whether changes in microbiome composition are cause or consequence of a certain biological state. In this review, we evaluate the state of the art of methodologies that enable the study of the gut microbiome, encouraging a change in broadly used analytic strategies by choosing effector molecules (proteins and metabolites) in combination with coding nucleic acids. We further explore microbial and effector microbial product imbalances that relate to disease and health.
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265
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Gootenberg DB, Paer JM, Luevano JM, Kwon DS. HIV-associated changes in the enteric microbial community: potential role in loss of homeostasis and development of systemic inflammation. Curr Opin Infect Dis 2018; 30:31-43. [PMID: 27922852 PMCID: PMC5325247 DOI: 10.1097/qco.0000000000000341] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Supplemental Digital Content is available in the text Purpose of review Despite HIV therapy advances, average life expectancy in HIV-infected individuals on effective treatment is significantly decreased relative to uninfected persons, largely because of increased incidence of inflammation-related diseases, such as cardiovascular disease and renal dysfunction. The enteric microbial community could potentially cause this inflammation, as HIV-driven destruction of gastrointestinal CD4+ T cells may disturb the microbiota–mucosal immune system balance, disrupting the stable gut microbiome and leading to further deleterious host outcomes. Recent findings Varied enteric microbiome changes have been reported during HIV infection, but unifying patterns have emerged. Community diversity is decreased, similar to pathologies such as inflammatory bowel disease, obesity, and Clostridium difficile infection. Many taxa frequently enriched in HIV-infected individuals, such as Enterobacteriaceae and Erysipelotrichaceae, have pathogenic potential, whereas depleted taxa, such as Bacteroidaceae and Ruminococcaceae, are more linked with anti-inflammatory properties and maintenance of gut homeostasis. The gut viral community in HIV has been found to contain a greater abundance of pathogenesis-associated Adenoviridae and Anelloviridae. These bacterial and viral changes correlate with increased systemic inflammatory markers, such as serum sCD14, sCD163, and IL-6. Summary Enteric microbial community changes may contribute to chronic HIV pathogenesis, but more investigation is necessary, especially in the developing world population with the greatest HIV burden (Video, Supplemental Digital Content 1, which includes the authors’ summary of the importance of the work).
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Affiliation(s)
- David B Gootenberg
- aRagon Institute of MGH, MIT, and Harvard, Massachusetts General Hospital, Cambridge bHarvard Medical School, Boston cDivision of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
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266
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Pinto-Cardoso S, Klatt NR, Reyes-Terán G. Impact of antiretroviral drugs on the microbiome: unknown answers to important questions. Curr Opin HIV AIDS 2018; 13:53-60. [PMID: 29028667 PMCID: PMC5718259 DOI: 10.1097/coh.0000000000000428] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
PURPOSE OF REVIEW Little is known on how different antiretroviral (ARV) drugs affect the gut microbiome in HIV infection; and conflicting data exists on the effect of ARV drugs on residual inflammation/immune activation and microbial translocation. RECENT FINDINGS Gut microbiome involvement in the transmission and pathogenesis of HIV infection is increasingly being recognized. Various studies have shown that antiretroviral therapy (ART) is unable to restore gut health despite effective suppression of plasma HIV viremia. Indeed, the resolution of residual inflammation and gut microbial translocation is partial under ART. Very recent studies have provided new evidence that ARV combinations can differentially affect the gut microbiome, immune activation and microbial translocation. Furthermore, a recent article uncovered a link between drug metabolism and specific microbial species indicating that microbes can directly metabolically degrade ARV drugs when administered topically. SUMMARY There are still many unanswered questions regarding ARVs and the gut microbiome. It is, therefore, critical for researchers to address the effect of distinct ARV drugs on the microbiome and vice versa: the effects of the microbiome on ARV drug metabolism, and speculate about possible therapeutic avenues.
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Affiliation(s)
- Sandra Pinto-Cardoso
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Mexico City, Mexico
| | - Nichole R. Klatt
- Department of Pharmaceutics, Washington National Primate Research Center, University of Washington, Seattle, Washington, USA
| | - Gustavo Reyes-Terán
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Mexico City, Mexico
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267
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Enterotypes in the landscape of gut microbial community composition. Nat Microbiol 2017; 3:8-16. [PMID: 29255284 DOI: 10.1038/s41564-017-0072-8] [Citation(s) in RCA: 584] [Impact Index Per Article: 83.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 10/27/2017] [Indexed: 12/16/2022]
Abstract
Population stratification is a useful approach for a better understanding of complex biological problems in human health and wellbeing. The proposal that such stratification applies to the human gut microbiome, in the form of distinct community composition types termed enterotypes, has been met with both excitement and controversy. In view of accumulated data and re-analyses since the original work, we revisit the concept of enterotypes, discuss different methods of dividing up the landscape of possible microbiome configurations, and put these concepts into functional, ecological and medical contexts. As enterotypes are of use in describing the gut microbial community landscape and may become relevant in clinical practice, we aim to reconcile differing views and encourage a balanced application of the concept.
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268
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Duvallet C, Gibbons SM, Gurry T, Irizarry RA, Alm EJ. Meta-analysis of gut microbiome studies identifies disease-specific and shared responses. Nat Commun 2017; 8:1784. [PMID: 29209090 PMCID: PMC5716994 DOI: 10.1038/s41467-017-01973-8] [Citation(s) in RCA: 590] [Impact Index Per Article: 84.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 10/30/2017] [Indexed: 12/16/2022] Open
Abstract
Hundreds of clinical studies have demonstrated associations between the human microbiome and disease, yet fundamental questions remain on how we can generalize this knowledge. Results from individual studies can be inconsistent, and comparing published data is further complicated by a lack of standard processing and analysis methods. Here we introduce the MicrobiomeHD database, which includes 28 published case–control gut microbiome studies spanning ten diseases. We perform a cross-disease meta-analysis of these studies using standardized methods. We find consistent patterns characterizing disease-associated microbiome changes. Some diseases are associated with over 50 genera, while most show only 10–15 genus-level changes. Some diseases are marked by the presence of potentially pathogenic microbes, whereas others are characterized by a depletion of health-associated bacteria. Furthermore, we show that about half of genera associated with individual studies are bacteria that respond to more than one disease. Thus, many associations found in case–control studies are likely not disease-specific but rather part of a non-specific, shared response to health and disease. Reported associations between the human microbiome and disease are often inconsistent. Here, Duvallet et al. perform a meta-analysis of 28 gut microbiome studies spanning ten diseases, and find associations that are likely not disease-specific but potentially part of a shared response to disease.
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Affiliation(s)
- Claire Duvallet
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.,Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Sean M Gibbons
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.,Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.,The Broad Institute of MIT and Harvard, Cambridge, MA, 02139, USA
| | - Thomas Gurry
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.,Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.,The Broad Institute of MIT and Harvard, Cambridge, MA, 02139, USA
| | - Rafael A Irizarry
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.,Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Eric J Alm
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA. .,Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA. .,The Broad Institute of MIT and Harvard, Cambridge, MA, 02139, USA.
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Mehraj V, Ghali P, Ramendra R, Costiniuk C, Lebouché B, Ponte R, Reinhard R, Sousa J, Chomont N, Cohen EA, Ancuta P, Routy JP. The evaluation of risk-benefit ratio for gut tissue sampling in HIV cure research. J Virus Erad 2017; 3:212-217. [PMID: 29057085 PMCID: PMC5632548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
INTRODUCTION Antiretroviral therapy (ART) does not cure HIV infection due to the persistence of HIV reservoirs in long-lived memory CD4 T cells present in the blood, lymph nodes, intestinal tract, and other tissues. Interest grows in obtaining gut-tissue samples for HIV persistence studies, which poses an ethical challenge to provide study volunteers with adequate information on risks and benefits. Herein we assess the risks and benefits of undergoing gut biopsy procedures for HIV pathogenesis and reservoir studies. METHODS A group discussion was organised with physicians and community representatives on performing either a flexible sigmoidoscopy or a colonoscopy. Consensus was reached on conducting colonoscopy in persons ≥50 years. Thirty HIV-infected, ART-treated and nine uninfected participants were recruited. Colonoscopy was performed to collect 30 gut mucosal biopsies. When present, polyps were removed and abnormal mucosal findings were biopsied for pathological analysis. Participants were interviewed on potential discomfort following colonoscopic examination. RESULTS The HIV-infected and uninfected groups were comparable in terms of age and gender with more men who have sex with men (MSM) in the former group. Abnormal colonoscopic findings were observed in 43.6% of all the participants and did not differ by HIV status. In total, 24 polyps were removed with a higher mean number of polyps removed in HIV-infected versus uninfected participants (1.7 vs 1.0, P=0.013). The number of polyps marginally correlated with inverted CD4:CD8 ratio. Based on our findings, colonoscopic examination was safe to use for gut biopsy procedures where almost half of the participants had polyps removed. CONCLUSION Participation in the study provided colon cancer screening as an ancillary benefit that participants could have received in standard medical care, thus mitigating burdens of invasive procedures. Dialogue between community representatives and clinical researchers can increase participation and advance HIV cure research.
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Affiliation(s)
| | - Peter Ghali
- Division of Gastroenterology and Hepatology, McGill University Health Centre,
Montreal, QC,
Canada
| | | | | | | | | | - Robert Reinhard
- Community Liaison, Canadian HIV Cure Enterprise (CanCURE),
Montreal, QC,
Canada
| | - Jose Sousa
- Community Advisory Committee, CIHR/CTN,
Canada
| | | | | | | | - Jean-Pierre Routy
- Corresponding author: Jean-Pierre Routy,
McGill University Health Centre: Glen siteResearch Institute, Block E, Suite EM 3-3232, Mezzanine 3M1001 Boulevard Décarie,
Montréal,
QCH4A 3J1,
Canada
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271
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Gianella S, Chaillon A, Mutlu EA, Engen PA, Voigt RM, Keshavarzian A, Losurdo J, Chakradeo P, Lada SM, Nakazawa M, Landay AL. Effect of cytomegalovirus and Epstein-Barr virus replication on intestinal mucosal gene expression and microbiome composition of HIV-infected and uninfected individuals. AIDS 2017; 31:2059-2067. [PMID: 28906277 PMCID: PMC5654609 DOI: 10.1097/qad.0000000000001579] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
BACKGROUND HIV-infection is associated with dramatic changes in the intestinal mucosa. The impact of other viral pathogens is unclear. METHODS One hundred and eight (108) biopsies from left and right colon (n = 79) and terminal ileum (n = 29) were collected from 19 HIV-infected and 22 HIV-uninfected participants. Levels of cytomegalovirus (CMV) and Epstein-Barr virus (EBV) DNA were measured by droplet digital PCR. Mucosal gene expression was measured via multiplex-assay. Microbiome analysis was performed using bacterial 16S-rDNA-pyrosequencing. The effect of CMV and EBV replication on the microbiome composition and mRNA-expression of selected cytokines (IL-6, IFN-γ, IL-1β, CCL2, IL-8, and IFN-β1) was evaluated. RESULTS Overall, CMV and EBV were detected in at least one intestinal site in 60.5 and 78.9% of participants, respectively. HIV-infected individuals demonstrated less detectable CMV (PB = 0.02); CMV was more frequently detected in terminal ileum than colon (PB = 0.05). Detectable EBV was more frequent among HIV-infected (P B= 0.04) without differences by intestinal site. The number of operational taxonomic units did not differ by CMV or EBV detection status. Among HIV-infected participants, higher CMV was only associated with lower relative abundance of Actinobacteria in the ileum (P = 0.03). Presence of CMV was associated with upregulated expression of all selected cytokines in the ileum (all P < 0.02) and higher expression of IL-8 and IFN-β1 in the colon (all P < 0.05) of HIV-uninfected participants, but not among HIV-infected. EBV had no effect on cytokine expression or microbiome composition whatsoever. CONCLUSION These results illustrate a complex interplay among HIV-infection, intestinal CMV replication, and mucosal gut environment, and highlight a possible modulatory effect of CMV on the microbial and immune homeostasis.
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Affiliation(s)
- Sara Gianella
- Division of Infectious Diseases, University of California, San Diego, La Jolla, California, USA
| | - Antoine Chaillon
- Division of Infectious Diseases, University of California, San Diego, La Jolla, California, USA
| | - Ece A. Mutlu
- Department of Internal Medicine, Division of Gastroenterology, Rush University Medical Center, Chicago, Illinois, USA
| | - Phillip A. Engen
- Department of Internal Medicine, Division of Gastroenterology, Rush University Medical Center, Chicago, Illinois, USA
| | - Robin M. Voigt
- Department of Internal Medicine, Division of Gastroenterology, Rush University Medical Center, Chicago, Illinois, USA
| | - Ali Keshavarzian
- Department of Internal Medicine, Division of Gastroenterology, Rush University Medical Center, Chicago, Illinois, USA
| | - John Losurdo
- Department of Internal Medicine, Division of Gastroenterology, Rush University Medical Center, Chicago, Illinois, USA
| | - Prachi Chakradeo
- Department of Internal Medicine, Division of Gastroenterology, Rush University Medical Center, Chicago, Illinois, USA
| | - Steven M. Lada
- Division of Infectious Diseases, University of California, San Diego, La Jolla, California, USA
| | - Masato Nakazawa
- Division of Infectious Diseases, University of California, San Diego, La Jolla, California, USA
| | - Alan L. Landay
- Department of Immunology-Microbiology, Rush University Medical Center, Chicago, Illinois, USA
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Differential effects of antiretrovirals on microbial translocation and gut microbiota composition of HIV-infected patients. J Int AIDS Soc 2017; 20:21526. [PMID: 28362071 PMCID: PMC5467634 DOI: 10.7448/ias.20.1.21526] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
INTRODUCTION Increased bacterial translocation and alterations to gut microbiota composition have been described in HIV infection and contribute to immune activation and inflammation. These effects persist despite combined antiretroviral therapy (cART). However, the contribution of different cART combinations has not yet been investigated. The aim of this study was to analyse the long-term effects of different combinations of cART on bacterial translocation and gut microbiota composition in HIV-infected patients. METHODS We carried out a cross-sectional study of 45 HIV-infected patients on cART, classified as nucleoside reverse transcriptase inhibitors (NRTIs)+ protease inhibitors (PIs) (n = 15), NRTIs+ non-nucleoside reverse transcriptase inhibitors (NNRTIs) (n = 22), and NRTIs+ integrase strand transfer inhibitors (INSTIs) (n = 8). Untreated HIV-infected patients (n = 5) and non-infected volunteers (n = 21) were also included. Soluble markers of bacterial translocation and inflammation were measured and gut microbiota composition was analysed using 16S rDNA pyrosequencing (Illumina MiSeq). RESULTS The NRTIs+INSTIs regimen was associated with levels of systemic inflammation that were similar to uninfected controls. The reduction in faecal bacterial diversity induced by HIV infection was also restored by this regimen. HIV infection was more closely related to changes in lower taxonomic units and diversity rather than at the phylum level. The NRTIs+PIs regimen showed the highest reduction in bacterial species, whereas NRTIs+INSTIs induced a minor loss of bacterial species and a significant increase in others. CONCLUSION Our study demonstrated that INSTI-based ART was associated with levels of systemic inflammation and microbial diversity similar to that of uninfected controls. The role of INSTIs other than raltegravir needs to be further investigated. Patients on the NRTIs+PIs regimen presented the highest reduction in bacterial species compared with other antiretrovirals and naive patients. Thus, different cART regimens are associated with diverse profiles in gut microbiota composition. Longitudinal and functional studies are needed to better understand these findings.
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273
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Serrano-Villar S, Vázquez-Castellanos JF, Vallejo A, Latorre A, Sainz T, Ferrando-Martínez S, Rojo D, Martínez-Botas J, Del Romero J, Madrid N, Leal M, Mosele JI, Motilva MJ, Barbas C, Ferrer M, Moya A, Moreno S, Gosalbes MJ, Estrada V. The effects of prebiotics on microbial dysbiosis, butyrate production and immunity in HIV-infected subjects. Mucosal Immunol 2017; 10:1279-1293. [PMID: 28000678 DOI: 10.1038/mi.2016.122] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 11/19/2016] [Indexed: 02/06/2023]
Abstract
Altered interactions between the gut mucosa and bacteria during HIV infection seem to contribute to chronic immune dysfunction. A deeper understanding of how nutritional interventions could ameliorate gut dysbiosis is needed. Forty-four subjects, including 12 HIV+ viremic untreated (VU) patients, 23 antiretroviral therapy-treated (ART+) virally suppressed patients (15 immunological responders and 8 non-responders) and 9 HIV- controls (HIV-), were blindly randomized to receive either prebiotics (scGOS/lcFOS/glutamine) or placebo (34/10) over 6 weeks in this pilot study. We assessed fecal microbiota composition using deep 16S rRNA gene sequencing and several immunological and genetic markers involved in HIV immunopathogenesis. The short dietary supplementation attenuated HIV-associated dysbiosis, which was most apparent in VU individuals but less so in ART+ subjects, whose gut microbiota was found more resilient. This compositional shift was not observed in the placebo arm. Significantly, declines in indirect markers of bacterial translocation and T-cell activation, improvement of thymic output, and changes in butyrate production were observed. Increases in the abundance of Faecalibacterium and Lachnospira strongly correlated with moderate but significant increases of butyrate production and amelioration of the inflammatory biomarkers soluble CD14 and high-sensitivity C-reactive protein, especially among VU. Hence, the bacterial butyrate synthesis pathway holds promise as a viable target for interventions.
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Affiliation(s)
- S Serrano-Villar
- Department of Infectious Diseases, Hospital Universitario Ramón y Cajal, Facultad de Medicina, Universidad de Alcalá (IRYCIS), Madrid, Spain
| | - J F Vázquez-Castellanos
- Unidad Mixta de Investigación en Genómica y Salud de la Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO-Salud Pública) y el Instituto Cavanilles de Biodiversidad y Biología Evolutiva (Universidad de Valencia), Valencia, Spain
- CIBER en Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - A Vallejo
- Department of Infectious Diseases, Hospital Universitario Ramón y Cajal, Facultad de Medicina, Universidad de Alcalá (IRYCIS), Madrid, Spain
| | - A Latorre
- Unidad Mixta de Investigación en Genómica y Salud de la Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO-Salud Pública) y el Instituto Cavanilles de Biodiversidad y Biología Evolutiva (Universidad de Valencia), Valencia, Spain
- CIBER en Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - T Sainz
- Department of Pediatric Infectious Diseases, University Hospital La Paz, and La Paz Research Institute, Madrid, Spain
| | - S Ferrando-Martínez
- Laboratory of Immunovirology, Biomedicine Institute of Seville (IBIS), Department of Infectious Diseases, University Hospital Virgen del Rocío, Sevilla, Spain
| | - D Rojo
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, CEU San Pablo University, Madrid, Spain
| | - J Martínez-Botas
- Department of Biochemistry, University Hospital Ramón y Cajal-IRYCIS, Madrid, Spain
- CIBER of Obesity and Nutrition Pathophysiology (CIBEROBN), Madrid, Spain
| | | | - N Madrid
- Department of Infectious Diseases, Hospital Universitario Ramón y Cajal, Facultad de Medicina, Universidad de Alcalá (IRYCIS), Madrid, Spain
| | - M Leal
- Laboratory of Immunovirology, Biomedicine Institute of Seville (IBIS), Department of Infectious Diseases, University Hospital Virgen del Rocío, Sevilla, Spain
| | - J I Mosele
- Food Technology Department, Agrotecnio Center, University of Lleida, Spain
| | - M J Motilva
- Food Technology Department, Agrotecnio Center, University of Lleida, Spain
| | - C Barbas
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, CEU San Pablo University, Madrid, Spain
| | - M Ferrer
- Institute of Catalysis, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - A Moya
- Unidad Mixta de Investigación en Genómica y Salud de la Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO-Salud Pública) y el Instituto Cavanilles de Biodiversidad y Biología Evolutiva (Universidad de Valencia), Valencia, Spain
- CIBER en Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - S Moreno
- Department of Infectious Diseases, Hospital Universitario Ramón y Cajal, Facultad de Medicina, Universidad de Alcalá (IRYCIS), Madrid, Spain
| | - M J Gosalbes
- Unidad Mixta de Investigación en Genómica y Salud de la Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO-Salud Pública) y el Instituto Cavanilles de Biodiversidad y Biología Evolutiva (Universidad de Valencia), Valencia, Spain
- CIBER en Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - V Estrada
- HIV Unit, Department of Internal Medicine, University Hospital Clínico San Carlos, Madrid, Spain
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Ribeiro ABDTM, Heimesaat MM, Bereswill S. Changes of the Intestinal Microbiome-Host Homeostasis in HIV-Infected Individuals - A Focus on the Bacterial Gut Microbiome. Eur J Microbiol Immunol (Bp) 2017; 7:158-167. [PMID: 29034105 PMCID: PMC5632743 DOI: 10.1556/1886.2017.00016] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 07/24/2017] [Indexed: 01/17/2023] Open
Abstract
Human immunodeficiency virus (HIV) infections cause severe CD4+ T cell depletion leading to chronic inflammation and immune activation, impaired barrier function, and microbial translocation. Even under effective antiretroviral therapy, these processes persist, leading to gut microbiome dysbiosis and disturbance of microbiome–host homeostasis. This systematic review aims at analyzing how gut microbiome and host immune system influence each other during HIV pathogenesis. An online search applying the PubMed database was conducted. The number of total results (n = 35) was narrowed down to 5 relevant studies focusing on the interaction between the host and gut microbiome, whereas strict exclusion criteria were applied, thereby assuring that no other comorbidities impacted study results. Our analyses revealed that gut microbiome diversity correlated positively with CD4+ T cell counts and negatively with microbial translocation markers. However, quantitative changes in bacterial richness did not consistently correlate with the numbers of metabolically active bacterial populations. Despite the reported increase in potentially pathogenic bacteria and, conversely, decrease in protective populations, the gut microbiota exhibited immune-modulating qualities given that mucosal inflammatory sequelae were dampened by decreasing pro-inflammatory and accelerating anti-inflammatory cytokine responses. Future research is needed to further elucidate these findings, to gain a deeper insight into host–microbiota interactions and to develop novel therapeutic strategies.
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Affiliation(s)
| | - Markus M Heimesaat
- Department of Microbiology and Hygiene, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Stefan Bereswill
- Department of Microbiology and Hygiene, Charité - Universitätsmedizin Berlin, Berlin, Germany
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275
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Petersen LM, Bautista EJ, Nguyen H, Hanson BM, Chen L, Lek SH, Sodergren E, Weinstock GM. Community characteristics of the gut microbiomes of competitive cyclists. MICROBIOME 2017; 5:98. [PMID: 28797298 PMCID: PMC5553673 DOI: 10.1186/s40168-017-0320-4] [Citation(s) in RCA: 193] [Impact Index Per Article: 27.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2017] [Accepted: 08/01/2017] [Indexed: 05/04/2023]
Abstract
BACKGROUND Changes in diet and exercise can alter the gut microbiome of humans and mice; however, few studies to date have assessed the microbiomes of highly fit athletes. In this pilot study, we used metagenomic whole genome shotgun (mWGS) and metatranscriptomic (RNA-Seq) sequencing to show what organisms are both present and active in the gut microbiomes of both professional and amateur level competitive cyclists and to determine if any significant differences exist between these two groups. RESULTS Using mWGS sequencing data, we showed that the gut microbiomes of 33 cyclists split into three taxonomic clusters, characterized by either high Prevotella, high Bacteroides or a mix of many genera including Bacteroides, Prevotella, Eubacterium, Ruminococcus, and Akkermansia. While no significant correlations could be found between taxonomic cluster and being either a professional or amateur level cyclist, high abundance of the genus Prevotella (≥2.5%) was significantly correlated with time reported exercising during an average week. Increased abundance of Prevotella was correlated with a number of amino acid and carbohydrate metabolism pathways, including branched chain amino acid metabolism. Further analysis of the metatranscriptome revealed significant taxonomic differences when compared to the metagenome. There was increased abundance of Methanobrevibacter smithii transcripts in a number of professional cyclists in comparison to amateur cyclists and this archaeon had upregulation of genes involved in the production of methane. Furthermore, when methane metabolism was upregulated, there was similar upregulation of energy and carbohydrate metabolism pathways. CONCLUSIONS These results provide a framework for common constituents of the gut community in individuals who follow an exercise-rich lifestyle. These data also suggest how certain organisms such as M. smithii may beneficially influence the metabolic efficiency of the gut community in professional cyclists due to synergistic metabolic cross-feeding events.
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Affiliation(s)
- Lauren M. Petersen
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT 06032 USA
| | - Eddy J. Bautista
- Corporación Colombiana de Investigación Agropecuaria, Km 14 Vía Mosquera-Bogotá, Mosquera, Cundinamarca Colombia
| | - Hoan Nguyen
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT 06032 USA
| | - Blake M. Hanson
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT 06032 USA
| | - Lei Chen
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT 06032 USA
| | - Sai H. Lek
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT 06032 USA
| | - Erica Sodergren
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT 06032 USA
| | - George M. Weinstock
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT 06032 USA
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276
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Liu J, Williams B, Frank D, Dillon SM, Wilson CC, Landay AL. Inside Out: HIV, the Gut Microbiome, and the Mucosal Immune System. THE JOURNAL OF IMMUNOLOGY 2017; 198:605-614. [PMID: 28069756 DOI: 10.4049/jimmunol.1601355] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 10/04/2016] [Indexed: 12/13/2022]
Abstract
The components of the human gut microbiome have been found to influence a broad array of pathologic conditions ranging from heart disease to diabetes and even to cancer. HIV infection upsets the delicate balance in the normal host-microbe interaction both through alterations in the taxonomic composition of gut microbial communities as well as through disruption of the normal host response mechanisms. In this article we review the current methods of gut microbiome analysis and the resulting data regarding how HIV infection might change the balance of commensal bacteria in the gut. Additionally, we cover the various effects gut microbes have on host immune homeostasis and the preliminary but intriguing data on how HIV disrupts those mechanisms. Finally, we briefly describe some of the important biomolecules produced by gut microbiota and the role that they may play in maintaining host immune homeostasis with and without HIV infection.
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Affiliation(s)
- Jay Liu
- Division of Infectious Disease, Department of Medicine, Anschutz Medical Campus, University of Colorado, Aurora, CO 80045
| | - Brett Williams
- Division of Infectious Disease, Department of Medicine, Rush Medical College, Chicago, IL 60612; and
| | - Daniel Frank
- Division of Infectious Disease, Department of Medicine, Anschutz Medical Campus, University of Colorado, Aurora, CO 80045
| | - Stephanie M Dillon
- Division of Infectious Disease, Department of Medicine, Anschutz Medical Campus, University of Colorado, Aurora, CO 80045
| | - Cara C Wilson
- Division of Infectious Disease, Department of Medicine, Anschutz Medical Campus, University of Colorado, Aurora, CO 80045
| | - Alan L Landay
- Department of Immunology and Microbiology, Rush Medical College, Chicago, IL 60612
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277
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Fulcher JA, Romas L, Hoffman JC, Elliott J, Saunders T, Burgener AD, Anton PA, Yang OO. Highly Human Immunodeficiency Virus-Exposed Seronegative Men Have Lower Mucosal Innate Immune Reactivity. AIDS Res Hum Retroviruses 2017; 33:788-795. [PMID: 28503933 DOI: 10.1089/aid.2017.0014] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Risk of HIV acquisition varies, and some individuals are highly HIV-1-exposed, yet, persistently seronegative (HESN). The immunologic mechanisms contributing to this phenomenon are an area of intense interest. As immune activation and inflammation facilitate disease progression in HIV-1-infected persons and gastrointestinal-associated lymphoid tissue is a highly susceptible site for transmission, we hypothesized that reduced gut mucosal immune reactivity may contribute to reduced HIV-1 susceptibility in HESN men with a history of numerous rectal sexual exposures. To test this, we used ex vivo mucosal explants from freshly acquired colorectal biopsies from healthy control and HESN subjects who were stimulated with specific innate immune ligands and inactivated whole pathogens. Immune reactivity was then assessed via cytokine arrays and proteomic analysis. Mucosal immune cell compositions were quantified via immunohistochemistry. We found that explants from HESN subjects produced less proinflammatory cytokines compared with controls following innate immune stimulation; while noninflammatory cytokines were similar between groups. Proteomic analysis identified several immune response proteins to be differentially expressed between HIV-1-stimulated HESN and control explants. Immunohistochemical examination of colorectal mucosa showed similar amounts of T cells, macrophages, and dendritic cells between groups. The results of this pilot study suggest that mucosal innate immune reactivity is dampened in HESN versus control groups, despite presence of similar densities of immune cells in the colorectal mucosa. This observed modulation of the rectal mucosal immune response may contribute to lower risk of mucosal HIV-1 transmission in these individuals.
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Affiliation(s)
- Jennifer A. Fulcher
- Division of Infectious Diseases, Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, California
| | - Laura Romas
- National HIV and Retrovirology Labs, JC Wilt Center for Infectious Diseases, Public Health Agency of Canada, Winnipeg, Canada
- Department of Medical Microbiology, University of Manitoba, Winnipeg, Canada
| | - Jennifer C. Hoffman
- Division of Infectious Diseases, Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, California
| | - Julie Elliott
- Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, California
| | - Terry Saunders
- Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, California
| | - Adam D. Burgener
- National HIV and Retrovirology Labs, JC Wilt Center for Infectious Diseases, Public Health Agency of Canada, Winnipeg, Canada
- Department of Medical Microbiology, University of Manitoba, Winnipeg, Canada
- Unit of Infectious Diseases, Department of Medicine, Solna, Center for Molecular Medicine, Karolinska Institute, Karolinska University Hospital, Stockholm, Sweden
| | - Peter A. Anton
- Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, California
| | - Otto O. Yang
- Division of Infectious Diseases, Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, California
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278
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Richer gut microbiota with distinct metabolic profile in HIV infected Elite Controllers. Sci Rep 2017; 7:6269. [PMID: 28740260 PMCID: PMC5524949 DOI: 10.1038/s41598-017-06675-1] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Accepted: 06/15/2017] [Indexed: 12/11/2022] Open
Abstract
Gut microbiota dysbiosis features progressive HIV infection and is a potential target for intervention. Herein, we explored the microbiome of 16 elite controllers (EC), 32 antiretroviral therapy naive progressors and 16 HIV negative controls. We found that the number of observed genera and richness indices in fecal microbiota were significantly higher in EC versus naive. Genera Succinivibrio, Sutterella, Rhizobium, Delftia, Anaerofilum and Oscillospira were more abundant in EC, whereas Blautia and Anaerostipes were depleted. Additionally, carbohydrate metabolism and secondary bile acid synthesis pathway related genes were less represented in EC. Conversely, fatty acid metabolism, PPAR-signalling and lipid biosynthesis proteins pathways were enriched in EC vs naive. The kynurenine pathway of tryptophan metabolism was altered during progressive HIV infection, and inversely associated with microbiota richness. In conclusion, EC have richer gut microbiota than untreated HIV patients, with unique bacterial signatures and a distinct metabolic profile which may contribute to control of HIV.
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279
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Amato KR, Van Belle S, Di Fiore A, Estrada A, Stumpf R, White B, Nelson KE, Knight R, Leigh SR. Patterns in Gut Microbiota Similarity Associated with Degree of Sociality among Sex Classes of a Neotropical Primate. MICROBIAL ECOLOGY 2017; 74:250-258. [PMID: 28124727 DOI: 10.1007/s00248-017-0938-6] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 01/11/2017] [Indexed: 06/06/2023]
Abstract
Studies of human and domestic animal models indicate that related individuals and those that spend the most time in physical contact typically have more similar gut microbial communities. However, few studies have examined these factors in wild mammals where complex social dynamics and a variety of interacting environmental factors may impact the patterns observed in controlled systems. Here, we explore the effect of host kinship and time spent in social contact on the gut microbiota of wild, black howler monkeys (Alouatta pigra). Our results indicate that closely related individuals had less similar gut microbial communities than non-related individuals. However, the effect was small. In contrast, as previously reported in baboons and chimpanzees, individuals that spent more time in contact (0 m) and close proximity (0-1 m) had more similar gut microbial communities. This pattern was driven by adult female-adult female dyads, which generally spend more time in social contact than adult male-adult male dyads or adult male-adult female dyads. Relative abundances of individual microbial genera such as Bacteroides, Clostridium, and Streptococcus were also more similar in individuals that spent more time in contact or close proximity. Overall, our data suggest that even in arboreal primates that live in small social groups and spend a relatively low proportion of their time in physical contact, social interactions are associated with variation in gut microbiota composition. Additionally, these results demonstrate that within a given host species, subgroups of individuals may interact with the gut microbiota differently.
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Affiliation(s)
- Katherine R Amato
- Department of Anthropology, Northwestern University, 1810 Hinman Ave, Evanston, IL, 60208, USA.
| | - Sarie Van Belle
- Department of Anthropology, University of Texas, Austin, TX, USA
| | - Anthony Di Fiore
- Department of Anthropology, University of Texas, Austin, TX, USA
| | - Alejandro Estrada
- Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Rebecca Stumpf
- Department of Anthropology, University of Illinois, Urbana, IL, USA
- Institute for Genomic Biology, University of Illinois, Urbana, IL, USA
| | - Bryan White
- Institute for Genomic Biology, University of Illinois, Urbana, IL, USA
- Department of Animal Sciences, University of Illinois, Urbana, IL, USA
| | | | - Rob Knight
- School of Medicine, University of California, San Diego, CA, USA
| | - Steven R Leigh
- Department of Anthropology, University of Colorado, Boulder, CO, USA
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280
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Kelley CF, Kraft CS, de Man TJ, Duphare C, Lee HW, Yang J, Easley KA, Tharp GK, Mulligan MJ, Sullivan PS, Bosinger SE, Amara RR. The rectal mucosa and condomless receptive anal intercourse in HIV-negative MSM: implications for HIV transmission and prevention. Mucosal Immunol 2017; 10:996-1007. [PMID: 27848950 PMCID: PMC5433931 DOI: 10.1038/mi.2016.97] [Citation(s) in RCA: 127] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 09/23/2016] [Indexed: 02/04/2023]
Abstract
Most HIV transmissions among men who have sex with men (MSM), the group that accounted for 67% of new US infections in 2014, occur via exposure to the rectal mucosa. However, it is unclear how the act of condomless receptive anal intercourse (CRAI) may alter the mucosal immune environment in HIV-negative MSM. Here, we performed a comprehensive characterization of the rectal mucosal immune environment for the phenotype and production of pro-inflammatory cytokines by CD4 and CD8 T cells, global transcriptomic analyses, and the composition of microbiota in HIV-negative MSM. Our results show that compared with men who had never engaged in anal intercourse, the rectal mucosa of MSM engaging in CRAI has a distinct phenotype characterized by higher levels of Th17 cells, greater CD8+ T cell proliferation and production of pro-inflammatory cytokines, molecular signatures associated with mucosal injury and repair likely mediated by innate immune cells, and a microbiota enriched for the Prevotellaceae family. These data provide a high-resolution model of the immunological, molecular, and microbiological perturbations induced by CRAI, will have direct utility in understanding rectal HIV transmission among MSM, and will enhance the design of future biomedical prevention interventions, including candidate HIV vaccines.
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Affiliation(s)
- Colleen F. Kelley
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine,Department of Epidemiology, Rollins School of Public Health, Emory University,Corresponding author;
| | - Colleen S. Kraft
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine,Department of Pathology, Emory University School of Medicine
| | - Tom J.B. de Man
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention
| | - Chandni Duphare
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University
| | - Hyun-Woo Lee
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University
| | - Jing Yang
- Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University
| | - Kirk A. Easley
- Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University
| | - Gregory K. Tharp
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University
| | - Mark J. Mulligan
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine
| | - Patrick S. Sullivan
- Department of Epidemiology, Rollins School of Public Health, Emory University
| | - Steven E. Bosinger
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University
| | - Rama R. Amara
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University,Department of Microbiology and Immunology, Emory University School of Medicine
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281
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Vujkovic-Cvijin I, Rutishauser RL, Pao M, Hunt PW, Lynch SV, McCune JM, Somsouk M. Limited engraftment of donor microbiome via one-time fecal microbial transplantation in treated HIV-infected individuals. Gut Microbes 2017; 8:440-450. [PMID: 28541799 PMCID: PMC5628639 DOI: 10.1080/19490976.2017.1334034] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Many HIV-infected individuals on antiretroviral therapy (ART) exhibit persistent systemic inflammation, which predicts morbidity and mortality. ART-treated subjects concurrently exhibit marked compositional alterations in the gut bacterial microbiota and the degree of dysbiosis correlates with systemic inflammation. Whether interventions to modulate the microbiome can affect systemic inflammation is unknown. An open-label fecal microbial transplantation (FMT) was delivered by colonoscopy to asymptomatic HIV-infected ART-suppressed individuals without antibiotic pre-treatment. Stool was assessed before and after FMT for engraftment of donor microbes, and peripheral blood was assayed for immune activation biomarkers. Six participants received FMT and 2 participants served as controls. No serious adverse effects occurred during 24 weeks of follow-up. At baseline, HIV-infected individuals exhibited microbiota profiles distinct from uninfected donors. During the 8 weeks post-FMT, recipients demonstrated partial engraftment of the donor microbiome (P < 0.05). Recipient microbiota remained significantly distant from donors, unlike that observed following FMT for treatment of C. difficile infection. Systemic inflammatory markers showed no significant change post-FMT. FMT was well-tolerated in ART-treated, HIV-infected individuals. Engraftment was detectable but modest, and appeared to be limited to specific bacterial taxa. Whether antibiotic conditioning can enhance engraftment and the capacity of microbiota to modulate inflammation remains to be investigated.
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Affiliation(s)
- Ivan Vujkovic-Cvijin
- Division of Experimental Medicine, University of California, San Francisco, San Francisco, CA, United States
| | - Rachel L. Rutishauser
- Division of Experimental Medicine, University of California, San Francisco, San Francisco, CA, United States
| | - Montha Pao
- Division of HIV, AIDS, and Global Medicine, University of California, San Francisco, San Francisco, CA, United States
| | - Peter W. Hunt
- Division of Experimental Medicine, University of California, San Francisco, San Francisco, CA, United States
| | - Susan V. Lynch
- Division of Gastroenterology, University of California, San Francisco, San Francisco, CA, United States
| | - Joseph M. McCune
- Division of Experimental Medicine, University of California, San Francisco, San Francisco, CA, United States
| | - Ma Somsouk
- Division of Gastroenterology, University of California, San Francisco, San Francisco, CA, United States,CONTACT Ma Somsouk .Division of Gastroenterology, University of CaliforniaSan Francisco, 1001 Potrero Ave., 3D2, San Francisco, CA 94110
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282
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Mudd JC, Brenchley JM. Gut Mucosal Barrier Dysfunction, Microbial Dysbiosis, and Their Role in HIV-1 Disease Progression. J Infect Dis 2017; 214 Suppl 2:S58-66. [PMID: 27625432 DOI: 10.1093/infdis/jiw258] [Citation(s) in RCA: 108] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Distinct pathological events occur within the gastrointestinal (GI) tract of Asian macaques with progressive simian immunodeficiency virus (SIV) infection and humans with human immunodeficiency virus type 1 (HIV-1) infection that are critical in shaping disease course. These events include depletion and functional alteration of GI-resident CD4(+) T cells, loss of antigen-presenting cells, loss of innate lymphocytes, and possible alterations to the composition of the gut microbiota. These contribute to structural damage to the GI tract and systemic translocation of GI tract microbial products. These translocated microbial products directly stimulate the immune system, and there is now overwhelming evidence that this drives chronic immune activation in HIV-1 and SIV infection. While combined antiretroviral therapy (cART) in HIV-1-infected subjects generally allows for immune reconstitution in peripheral blood, reconstitution of the GI tract occurs at a much slower pace, and both immunological and structural abnormalities persist in the GI tract. Importantly, studies of large cohorts of individuals have linked suboptimal GI reconstitution to residual inflammation and heightened morbidities in HIV-1-infected cART recipients. As a result, current era treatments aimed at augmenting restoration of the GI tract hold promise in returning cART recipients to full health.
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Affiliation(s)
- Joseph C Mudd
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Jason M Brenchley
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
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283
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Kim D, Hofstaedter CE, Zhao C, Mattei L, Tanes C, Clarke E, Lauder A, Sherrill-Mix S, Chehoud C, Kelsen J, Conrad M, Collman RG, Baldassano R, Bushman FD, Bittinger K. Optimizing methods and dodging pitfalls in microbiome research. MICROBIOME 2017; 5:52. [PMID: 28476139 PMCID: PMC5420141 DOI: 10.1186/s40168-017-0267-5] [Citation(s) in RCA: 335] [Impact Index Per Article: 47.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2016] [Accepted: 04/21/2017] [Indexed: 05/09/2023]
Abstract
Research on the human microbiome has yielded numerous insights into health and disease, but also has resulted in a wealth of experimental artifacts. Here, we present suggestions for optimizing experimental design and avoiding known pitfalls, organized in the typical order in which studies are carried out. We first review best practices in experimental design and introduce common confounders such as age, diet, antibiotic use, pet ownership, longitudinal instability, and microbial sharing during cohousing in animal studies. Typically, samples will need to be stored, so we provide data on best practices for several sample types. We then discuss design and analysis of positive and negative controls, which should always be run with experimental samples. We introduce a convenient set of non-biological DNA sequences that can be useful as positive controls for high-volume analysis. Careful analysis of negative and positive controls is particularly important in studies of samples with low microbial biomass, where contamination can comprise most or all of a sample. Lastly, we summarize approaches to enhancing experimental robustness by careful control of multiple comparisons and to comparing discovery and validation cohorts. We hope the experimental tactics summarized here will help researchers in this exciting field advance their studies efficiently while avoiding errors.
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Affiliation(s)
- Dorothy Kim
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania 19104 USA
| | - Casey E. Hofstaedter
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania 19104 USA
| | - Chunyu Zhao
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania 19104 USA
| | - Lisa Mattei
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania 19104 USA
| | - Ceylan Tanes
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania 19104 USA
| | - Erik Clarke
- Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania 19104 USA
| | - Abigail Lauder
- Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania 19104 USA
| | - Scott Sherrill-Mix
- Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania 19104 USA
| | - Christel Chehoud
- Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania 19104 USA
| | - Judith Kelsen
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania 19104 USA
| | - Máire Conrad
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania 19104 USA
| | - Ronald G. Collman
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104 USA
| | - Robert Baldassano
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania 19104 USA
| | - Frederic D. Bushman
- Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania 19104 USA
| | - Kyle Bittinger
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania 19104 USA
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284
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Presti RM, Flores SC, Palmer BE, Atkinson JJ, Lesko CR, Lau B, Fontenot AP, Roman J, McDyer JF, Twigg HL. Mechanisms Underlying HIV-Associated Noninfectious Lung Disease. Chest 2017; 152:1053-1060. [PMID: 28427967 DOI: 10.1016/j.chest.2017.04.154] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Revised: 02/28/2017] [Accepted: 04/05/2017] [Indexed: 01/15/2023] Open
Abstract
Pulmonary disease remains a primary source of morbidity and mortality in persons living with HIV (PLWH), although the advent of potent combination antiretroviral therapy has resulted in a shift from predominantly infectious to noninfectious pulmonary complications. PLWH are at high risk for COPD, pulmonary hypertension, and lung cancer even in the era of combination antiretroviral therapy. The underlying mechanisms of this are incompletely understood, but recent research in both human and animal models suggests that oxidative stress, expression of matrix metalloproteinases, and genetic instability may result in lung damage, which predisposes PLWH to these conditions. Some of the factors that drive these processes include tobacco and other substance use, direct HIV infection and expression of specific HIV proteins, inflammation, and shifts in the microbiome toward pathogenic and opportunistic organisms. Further studies are needed to understand the relative importance of these factors to the development of lung disease in PLWH.
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Affiliation(s)
- Rachel M Presti
- Department of Medicine, Washington University School of Medicine, St. Louis, MO.
| | - Sonia C Flores
- Department of Medicine, University of Colorado Denver, Aurora, CO
| | - Brent E Palmer
- Department of Medicine, University of Colorado Denver, Aurora, CO
| | - Jeffrey J Atkinson
- Department of Medicine, Washington University School of Medicine, St. Louis, MO
| | - Catherine R Lesko
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, School of Medicine, Johns Hopkins University, Baltimore, MD
| | - Bryan Lau
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, School of Medicine, Johns Hopkins University, Baltimore, MD
| | | | - Jesse Roman
- Department of Medicine, University of Louisville, Health Sciences Center and Robley Rex VA Medical Center, Louisville, KY
| | - John F McDyer
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA
| | - Homer L Twigg
- Department of Medicine, Indiana University, Indianapolis, IN
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285
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Faner R, Sibila O, Agustí A, Bernasconi E, Chalmers JD, Huffnagle GB, Manichanh C, Molyneaux PL, Paredes R, Pérez Brocal V, Ponomarenko J, Sethi S, Dorca J, Monsó E. The microbiome in respiratory medicine: current challenges and future perspectives. Eur Respir J 2017; 49:49/4/1602086. [PMID: 28404649 DOI: 10.1183/13993003.02086-2016] [Citation(s) in RCA: 152] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 02/08/2017] [Indexed: 12/15/2022]
Abstract
The healthy lung has previously been considered to be a sterile organ because standard microbiological culture techniques consistently yield negative results. However, culture-independent techniques report that large numbers of microorganisms coexist in the lung. There are many unknown aspects in the field, but available reports show that the lower respiratory tract microbiota: 1) is similar in healthy subjects to the oropharyngeal microbiota and dominated by members of the Firmicutes, Bacteroidetes and Proteobacteria phyla; 2) shows changes in smokers and well-defined differences in chronic respiratory diseases, although the temporal and spatial kinetics of these changes are only partially known; and 3) shows relatively abundant non-cultivable bacteria in chronic obstructive pulmonary disease, idiopathic pulmonary fibrosis, cystic fibrosis and bronchiectasis, with specific patterns for each disease. In all of these diseases, a loss of diversity, paralleled by an over-representation of Proteobacteria (dysbiosis), has been related to disease severity and exacerbations. However, it is unknown whether dysbiosis is a cause or a consequence of the damage to bronchoalveolar surfaces.Finally, little is known about bacterial functionality and the interactions between viruses, fungi and bacteria. It is expected that future research in bacterial gene expressions, metagenomics longitudinal analysis and host-microbiome animal models will help to move towards targeted microbiome interventions in respiratory diseases.
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Affiliation(s)
- Rosa Faner
- Hospital Clinic, IDIBAPS, Universitat de Barcelona, Barcelona, Spain.,CIBER de Enfermedades Respiratorias - CIBERES, Madrid, Spain.,These co-primary authors contributed equally to this work
| | - Oriol Sibila
- Hospital Universitari de la Santa Creu i Sant Pau, Universitat Autónoma Barcelona, Barcelona, Spain.,These co-primary authors contributed equally to this work
| | - Alvar Agustí
- Hospital Clinic, IDIBAPS, Universitat de Barcelona, Barcelona, Spain.,CIBER de Enfermedades Respiratorias - CIBERES, Madrid, Spain
| | - Eric Bernasconi
- Service de Pneumologie, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | | | | | - Chaysavanh Manichanh
- Dept of Gastroenterology, Vall d'Hebron Research Institute, Barcelona, Spain.,CIBER de Enfermedades Hepáticas y Digestivas (CIBEREHD), Madrid, Spain
| | | | - Roger Paredes
- Hospital Universitari Germans Trias i Pujol, Universitat Autónoma Barcelona, Barcelona, Spain
| | - Vicente Pérez Brocal
- CIBER en Epidemiología y Salud Pública (CIBERESP), Madrid, Spain.,Joint Research Unit on Genomics and Health, Foundation for the Promotion of Health and Biomedical Research of Valencia Region (FISABIO-Public Health) and Cavanilles Institute for Biodiversity and Evolutionary Biology, University of Valencia, Valencia, Spain
| | - Julia Ponomarenko
- Centro de Regulación Genómica, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | | | - Jordi Dorca
- Hospital Universitari de Bellvitge, IDIBELL, Universitat de Barcelona, Hospitalet del Llobregat, Barcelona, Spain.,These co-senior authors contributed equally to this work
| | - Eduard Monsó
- CIBER de Enfermedades Respiratorias - CIBERES, Madrid, Spain .,Hospital Universitari Parc Taulí, Universitat Autònoma de Barcelona, Barcelona, Spain.,These co-senior authors contributed equally to this work
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286
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Abstract
OBJECTIVE Untreated advanced HIV infection alters the gut microbiota, but it is unclear whether antiretroviral therapy (ART) reverses these changes. We compared the composition of the rectal microbiota among three groups of men who have sex with men (MSM): HIV-uninfected, untreated HIV, and ART-treated HIV-infected. DESIGN A cross-sectional study was conducted among 130 MSM (55 HIV-uninfected, 41 untreated HIV, and 34 ART-treated HIV) in Abuja, Nigeria. METHODS Bacterial 16S rRNA genes were amplified from rectal swabs, sequenced and clustered into Genera-level operational taxonomic units. Alpha diversity was quantified using the Shannon index and compared among groups using the Kruskal-Wallis test; associations with other scale variables were quantified using Spearman's rank correlation (Rs). The relative abundance of the top 15 taxa was compared according to HIV infection/treatment status using the Wilcoxon rank sum test. RESULTS HIV-treated MSM had a decrease in a commensal phylum, Bacteroidetes (P < 0.01). Alpha diversity was positively correlated with viral loads (Rs = 0.32, P < 0.01). Statistically significant shifts in relative abundance of rectal microbiota for the HIV-treated group included a decrease in the most abundant bacteria, Prevotella (P = 0.02) and an increase in pathogenic bacteria, Peptoniphilus (P = 0.04), Finegoldia (P = 0.01), Anaerococcus (P = 0.03), and Campylobacter (P = 0.03) compared with the other groups. CONCLUSION Untreated HIV infection does not significantly alter the rectal microbiota, whereas prior treatment is associated with a shift toward a more pathogenic pattern of microbiota. Treatment with an antibiotic, co-trimoxazole, in conjunction with ART may have contributed to this shift.
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287
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Pinto-Cardoso S, Lozupone C, Briceño O, Alva-Hernández S, Téllez N, Adriana A, Murakami-Ogasawara A, Reyes-Terán G. Fecal Bacterial Communities in treated HIV infected individuals on two antiretroviral regimens. Sci Rep 2017; 7:43741. [PMID: 28262770 PMCID: PMC5338340 DOI: 10.1038/srep43741] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 01/30/2017] [Indexed: 12/19/2022] Open
Abstract
Intestinal microbiome changes that occur in HIV positive individuals on different antiretroviral therapy (ART) regimens are important to understand, as they are potentially linked with chronic inflammation and microbiome-linked comorbidities that occur at increased incidence in this population. We conducted a cross-sectional study comparing the fecal microbiomes of HIV-uninfected (HIV SN) to HIV-infected individuals on long-term ART (HIV+ LTART) from Mexico using 16S ribosomal RNA (16sRNA) targeted sequencing. These individuals were on two ART regimens based on either Non-Nucleoside Reverse Transcriptase Inhibitors (EFV) or ritonavir-boosted Protease Inhibitors (PI) with the same backbone of Nucleoside Reverse Transcriptase Inhibitors. Microbiome diversity was reduced in treated HIV infection compared to HIV SN (p < 0.05). Several operational taxonomic units (OTUs) related to the Ruminococcaceae family including Faecalibacterium prausnitzii were depleted in EFV and PI compared to HIV SN and negatively correlated with intestinal gut dysfunction as measured by the intestinal fatty binding protein (p < 0.05). This is the first report to address the fecal bacterial communities in HIV-infected individuals on two ARV regimens from Mexico.
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Affiliation(s)
- Sandra Pinto-Cardoso
- Center for Research in Infectious Diseases, National Institute of Respiratory Diseases, Mexico City, Mexico
| | | | - Olivia Briceño
- Center for Research in Infectious Diseases, National Institute of Respiratory Diseases, Mexico City, Mexico
| | - Selma Alva-Hernández
- Center for Research in Infectious Diseases, National Institute of Respiratory Diseases, Mexico City, Mexico
| | - Norma Téllez
- Center for Research in Infectious Diseases, National Institute of Respiratory Diseases, Mexico City, Mexico
| | - Aguilar Adriana
- Center for Research in Infectious Diseases, National Institute of Respiratory Diseases, Mexico City, Mexico
| | - Akio Murakami-Ogasawara
- Center for Research in Infectious Diseases, National Institute of Respiratory Diseases, Mexico City, Mexico
| | - Gustavo Reyes-Terán
- Center for Research in Infectious Diseases, National Institute of Respiratory Diseases, Mexico City, Mexico
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288
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Noguera-Julian M, Guillén Y, Peterson J, Reznik D, Harris EV, Joseph SJ, Rivera J, Kannanganat S, Amara R, Nguyen ML, Mutembo S, Paredes R, Read TD, Marconi VC. Oral microbiome in HIV-associated periodontitis. Medicine (Baltimore) 2017; 96:e5821. [PMID: 28328799 PMCID: PMC5371436 DOI: 10.1097/md.0000000000005821] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
HIV-associated periodontal diseases (PD) could serve as a source of chronic inflammation. Here, we sought to characterize the oral microbial signatures of HIV+ and HIV- individuals at different levels of PD severity.This cross-sectional study included both HIV+ and HIV- patients with varying degrees of PD. Two tooth, 2 cheek, and 1 saliva samples were obtained for microbiome analysis. Mothur/SILVADB were used to classify sequences. R/Bioconductor (Vegan, PhyloSeq, and DESeq2) was employed to assess overall microbiome structure differences and differential abundance of bacterial genera between groups. Polychromatic flow cytometry was used to assess immune activation in CD4 and CD8 cell populations.Around 250 cheek, tooth, and saliva samples from 50 participants (40 HIV+ and 10 HIV-) were included. Severity of PD was classified clinically as None/Mild (N), Moderate (M), and Severe (S) with 18 (36%), 16 (32%), and 16 (32%) participants in each category, respectively. Globally, ordination analysis demonstrated clustering by anatomic site (R2 = 0.25, P < 0.001). HIV status and PD severity showed a statistically significant impact on microbiome composition but only accounted for a combined 2% of variation. HIV+ samples were enriched in genera Abiotrophia, Neisseria, Kingella, and unclassified Neisseriaceae and depleted in Leptotrichia and Selenomonas. The Neisseria genus was consistently enriched in HIV+ participants regardless of sampling site and PD level. Immune markers were altered in HIV+ participants but did not show association with the oral microbiome.HIV-associated changes in oral microbiome result in subtle microbial signatures along different stages of PD that are common in independent oral anatomic sites.
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Affiliation(s)
- Marc Noguera-Julian
- IrsiCaixa AIDS Research Institute, Badalona
- University Autònoma de Barcelona, Bellaterra
- University de Vic-University Central de Catalunya, Vic, Catalonia, Spain
| | - Yolanda Guillén
- IrsiCaixa AIDS Research Institute, Badalona
- University Autònoma de Barcelona, Bellaterra
| | - Jessica Peterson
- Division of Infectious Diseases, Emory University School of Medicine
| | - David Reznik
- Division of Infectious Diseases, Emory University School of Medicine
- Infectious Diseases Program, Grady Health System
| | - Erica V. Harris
- Department of Biology, Emory University, O. Wayne Rollins Research Center
| | - Sandeep J. Joseph
- Division of Infectious Diseases, Emory University School of Medicine
| | - Javier Rivera
- IrsiCaixa AIDS Research Institute, Badalona
- University de Vic-University Central de Catalunya, Vic, Catalonia, Spain
| | - Sunil Kannanganat
- Division of Infectious Diseases, Emory University School of Medicine
- Department of Global Health, Emory University Rollins School of Public Health, Atlanta, GA
| | - Rama Amara
- Division of Infectious Diseases, Emory University School of Medicine
- Department of Global Health, Emory University Rollins School of Public Health, Atlanta, GA
| | - Minh Ly Nguyen
- Division of Infectious Diseases, Emory University School of Medicine
| | | | - Roger Paredes
- IrsiCaixa AIDS Research Institute, Badalona
- University Autònoma de Barcelona, Bellaterra
- University de Vic-University Central de Catalunya, Vic, Catalonia, Spain
- Unitat VIH, Hosp. University Germans Trias i Pujol, Badalona, Catalonia, Spain
| | - Timothy D. Read
- Division of Infectious Diseases, Emory University School of Medicine
| | - Vincent C. Marconi
- Division of Infectious Diseases, Emory University School of Medicine
- Department of Global Health, Emory University Rollins School of Public Health, Atlanta, GA
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289
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Yoder AC, Guo K, Dillon SM, Phang T, Lee EJ, Harper MS, Helm K, Kappes JC, Ochsenbauer C, McCarter MD, Wilson CC, Santiago ML. The transcriptome of HIV-1 infected intestinal CD4+ T cells exposed to enteric bacteria. PLoS Pathog 2017; 13:e1006226. [PMID: 28241075 PMCID: PMC5344538 DOI: 10.1371/journal.ppat.1006226] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Revised: 03/09/2017] [Accepted: 02/08/2017] [Indexed: 01/01/2023] Open
Abstract
Global transcriptome studies can help pinpoint key cellular pathways exploited by viruses to replicate and cause pathogenesis. Previous data showed that laboratory-adapted HIV-1 triggers significant gene expression changes in CD4+ T cell lines and mitogen-activated CD4+ T cells from peripheral blood. However, HIV-1 primarily targets mucosal compartments during acute infection in vivo. Moreover, early HIV-1 infection causes extensive depletion of CD4+ T cells in the gastrointestinal tract that herald persistent inflammation due to the translocation of enteric microbes to the systemic circulation. Here, we profiled the transcriptome of primary intestinal CD4+ T cells infected ex vivo with transmitted/founder (TF) HIV-1. Infections were performed in the presence or absence of Prevotella stercorea, a gut microbe enriched in the mucosa of HIV-1-infected individuals that enhanced both TF HIV-1 replication and CD4+ T cell death ex vivo. In the absence of bacteria, HIV-1 triggered a cellular shutdown response involving the downregulation of HIV-1 reactome genes, while perturbing genes linked to OX40, PPAR and FOXO3 signaling. However, in the presence of bacteria, HIV-1 did not perturb these gene sets or pathways. Instead, HIV-1 enhanced granzyme expression and Th17 cell function, inhibited G1/S cell cycle checkpoint genes and triggered downstream cell death pathways in microbe-exposed gut CD4+ T cells. To gain insights on these differential effects, we profiled the gene expression landscape of HIV-1-uninfected gut CD4+ T cells exposed to bacteria. Microbial exposure upregulated genes involved in cellular proliferation, MAPK activation, Th17 cell differentiation and type I interferon signaling. Our findings reveal that microbial exposure influenced how HIV-1 altered the gut CD4+ T cell transcriptome, with potential consequences for HIV-1 susceptibility, cell survival and inflammation. The HIV-1- and microbe-altered pathways unraveled here may serve as a molecular blueprint to gain basic insights in mucosal HIV-1 pathogenesis.
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Affiliation(s)
- Alyson C. Yoder
- Department of Medicine, University of Colorado School of Medicine, Aurora, CO, United States of America
| | - Kejun Guo
- Department of Medicine, University of Colorado School of Medicine, Aurora, CO, United States of America
- RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, CO, United States of America
| | - Stephanie M. Dillon
- Department of Medicine, University of Colorado School of Medicine, Aurora, CO, United States of America
| | - Tzu Phang
- Department of Medicine, University of Colorado School of Medicine, Aurora, CO, United States of America
- The Cancer Center, University of Colorado School of Medicine, Aurora, CO, United States of America
| | - Eric J. Lee
- Department of Medicine, University of Colorado School of Medicine, Aurora, CO, United States of America
| | - Michael S. Harper
- Department of Medicine, University of Colorado School of Medicine, Aurora, CO, United States of America
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, United States of America
| | - Karen Helm
- The Cancer Center, University of Colorado School of Medicine, Aurora, CO, United States of America
| | - John C. Kappes
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States of America
- Center for AIDS Research, University of Alabama at Birmingham, Birmingham, AL, United States of America
| | - Christina Ochsenbauer
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States of America
- Center for AIDS Research, University of Alabama at Birmingham, Birmingham, AL, United States of America
| | - Martin D. McCarter
- Department of Surgery, University of Colorado School of Medicine, Aurora, CO, United States of America
| | - Cara C. Wilson
- Department of Medicine, University of Colorado School of Medicine, Aurora, CO, United States of America
- RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, CO, United States of America
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, United States of America
- * E-mail: (MLS); (CCW)
| | - Mario L. Santiago
- Department of Medicine, University of Colorado School of Medicine, Aurora, CO, United States of America
- RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, CO, United States of America
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, United States of America
- * E-mail: (MLS); (CCW)
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290
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Low abundance of colonic butyrate-producing bacteria in HIV infection is associated with microbial translocation and immune activation. AIDS 2017; 31:511-521. [PMID: 28002063 DOI: 10.1097/qad.0000000000001366] [Citation(s) in RCA: 109] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
OBJECTIVE Gut microbial translocation is a major driving force behind chronic immune activation during HIV-1 infection. HIV-1-related intestinal dysbiosis, including increases in mucosa-associated pathobionts, may influence microbial translocation and contribute to mucosal and systemic inflammation. Thus, it is critical to understand the mechanisms by which gut microbes and their metabolic products, such as butyrate, influence immune cell function during HIV-1 infection. DESIGN A cross-sectional study was performed to compare the relative abundance of butyrate-producing bacterial (BPB) species in colonic biopsies and stool of untreated, chronic HIV-1-infected (n = 18) and HIV-1-uninfected (n = 14) study participants. The effect of exogenously added butyrate on gut T-cell activation and HIV-1 infection was evaluated using an ex-vivo human intestinal cell culture model. METHODS Species were identified in 16S ribosomal RNA sequence datasets. Ex-vivo isolated lamina propria mononuclear cells were infected with C-C chemokine receptor type 5-tropic HIV-1Bal, cultured with enteric gram-negative bacteria and a range of butyrate doses, and lamina propria T-cell activation and HIV-1 infection levels measured. RESULTS Relative abundance of total BPB and specifically of Roseburia intestinalis, were lower in colonic mucosa of HIV-1-infected versus HIV-1-uninfected individuals. In HIV-1-infected study participants, R. intestinalis relative abundance inversely correlated with systemic indicators of microbial translocation, immune activation, and vascular inflammation. Exogenous butyrate suppressed enteric gram-negative bacteria-driven lamina propria T-cell activation and HIV-1 infection levels in vitro. CONCLUSION Reductions in mucosal butyrate from diminished colonic BPB may exacerbate pathobiont-driven gut T-cell activation and HIV replication, thereby contributing to HIV-associated mucosal pathogenesis.
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291
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Villar-García J, Güerri-Fernández R, Moya A, González A, Hernández JJ, Lerma E, Guelar A, Sorli L, Horcajada JP, Artacho A, D´Auria G, Knobel H. Impact of probiotic Saccharomyces boulardii on the gut microbiome composition in HIV-treated patients: A double-blind, randomised, placebo-controlled trial. PLoS One 2017; 12:e0173802. [PMID: 28388647 PMCID: PMC5384743 DOI: 10.1371/journal.pone.0173802] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Accepted: 02/22/2017] [Indexed: 02/07/2023] Open
Abstract
Dysbalance in gut microbiota has been linked to increased microbial translocation, leading to chronic inflammation in HIV-patients, even under effective HAART. Moreover, microbial translocation is associated with insufficient reconstitution of CD4+T cells, and contributes to the pathogenesis of immunologic non-response. In a double-blind, randomised, placebo-controlled trial, we recently showed that, compared to placebo, 12 weeks treatment with probiotic Saccharomyces boulardii significantly reduced plasma levels of bacterial translocation (Lipopolysaccharide-binding protein or LBP) and systemic inflammation (IL-6) in 44 HIV virologically suppressed patients, half of whom (n = 22) had immunologic non-response to antiretroviral therapy (<270 CD4+Tcells/μL despite long-term suppressed viral load). The aim of the present study was to investigate if this beneficial effect of the probiotic Saccharomyces boulardii is due to modified gut microbiome composition, with a decrease of some species associated with higher systemic levels of microbial translocation and inflammation. In this study, we used 16S rDNA gene amplification and parallel sequencing to analyze the probiotic impact on the composition of the gut microbiome (faecal samples) in these 44 patients randomized to receive oral supplementation with probiotic or placebo for 12 weeks. Compared to the placebo group, in individuals treated with probiotic we observed lower concentrations of some gut species, such as those of the Clostridiaceae family, which were correlated with systemic levels of bacterial translocation and inflammation markers. In a sub-study of these patients, we observed significantly higher parameters of microbial translocation (LBP, soluble CD14) and systemic inflammation in immunologic non-responders than in immunologic responders, which was correlated with a relative abundance of specific gut bacterial groups (Lachnospiraceae genus and Proteobacteria). Thus, in this work, we propose a new therapeutic strategy using the probiotic yeast S. boulardii to modify gut microbiome composition. Identifying pro-inflammatory species in the gut microbiome could also be a useful new marker of poor immune response and a new therapeutic target.
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Affiliation(s)
- Judit Villar-García
- Department of Infectious Diseases, Hospital del Mar, Barcelona, Spain
- IMIM (Hospital del Mar Medical Research Institute, Institut Hospital del Mar d'Investigacions Mediques), Barcelona, Spain
- Department of Medicine, Universitat Autònoma de Barcelona, Spain
- * E-mail:
| | - Robert Güerri-Fernández
- Department of Infectious Diseases, Hospital del Mar, Barcelona, Spain
- IMIM (Hospital del Mar Medical Research Institute, Institut Hospital del Mar d'Investigacions Mediques), Barcelona, Spain
- Department of Medicine, Universitat Autònoma de Barcelona, Spain
| | - Andrés Moya
- Joint Unit of Research in Genomics and Health, Foundation for the Promotion of Health and Biomedical Research in the Valencian Community (FISABIO) and Cavanilles Institute of Biodiversity and Evolutionary Biology (Universitat de València), València, Spain
- CIBER en Epidemiología y Salud Pública, Madrid, Spain
| | - Alicia González
- Department of Infectious Diseases, Hospital del Mar, Barcelona, Spain
- IMIM (Hospital del Mar Medical Research Institute, Institut Hospital del Mar d'Investigacions Mediques), Barcelona, Spain
| | | | - Elisabet Lerma
- Department of Infectious Diseases, Hospital del Mar, Barcelona, Spain
- IMIM (Hospital del Mar Medical Research Institute, Institut Hospital del Mar d'Investigacions Mediques), Barcelona, Spain
| | - Ana Guelar
- Department of Infectious Diseases, Hospital del Mar, Barcelona, Spain
- IMIM (Hospital del Mar Medical Research Institute, Institut Hospital del Mar d'Investigacions Mediques), Barcelona, Spain
| | - Luisa Sorli
- Department of Infectious Diseases, Hospital del Mar, Barcelona, Spain
- IMIM (Hospital del Mar Medical Research Institute, Institut Hospital del Mar d'Investigacions Mediques), Barcelona, Spain
| | - Juan P. Horcajada
- Department of Infectious Diseases, Hospital del Mar, Barcelona, Spain
- IMIM (Hospital del Mar Medical Research Institute, Institut Hospital del Mar d'Investigacions Mediques), Barcelona, Spain
- Department of Medicine, Universitat Autònoma de Barcelona, Spain
| | - Alejandro Artacho
- Joint Unit of Research in Genomics and Health, Foundation for the Promotion of Health and Biomedical Research in the Valencian Community (FISABIO) and Cavanilles Institute of Biodiversity and Evolutionary Biology (Universitat de València), València, Spain
| | - Giuseppe D´Auria
- Joint Unit of Research in Genomics and Health, Foundation for the Promotion of Health and Biomedical Research in the Valencian Community (FISABIO) and Cavanilles Institute of Biodiversity and Evolutionary Biology (Universitat de València), València, Spain
- CIBER en Epidemiología y Salud Pública, Madrid, Spain
| | - Hernando Knobel
- Department of Infectious Diseases, Hospital del Mar, Barcelona, Spain
- IMIM (Hospital del Mar Medical Research Institute, Institut Hospital del Mar d'Investigacions Mediques), Barcelona, Spain
- Department of Medicine, Universitat Autònoma de Barcelona, Spain
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292
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Williams B, Landay A, Presti RM. Microbiome alterations in HIV infection a review. Cell Microbiol 2016; 18:645-51. [PMID: 26945815 DOI: 10.1111/cmi.12588] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Revised: 02/28/2016] [Accepted: 03/03/2016] [Indexed: 12/25/2022]
Abstract
Recent developments in molecular techniques have allowed researchers to identify previously uncultured organisms, which has propelled a vast expansion of our knowledge regarding our commensal microbiota. Interest in the microbiome specific to HIV grew from earlier findings suggesting that bacterial translocation from the intestines is the cause of persistent immune activation despite effective viral suppression with antiretroviral therapy (ART). Studies of SIV infected primates have demonstrated that Proteobacteria preferentially translocate and that mucosal immunity can be restored with probiotics. Pathogenic SIV infection results in a massive expansion of the virome, whereas non-pathogenic SIV infection does not. Human HIV infected cohorts have been shown to have microbiota distinctive from that of HIV negative controls and efforts to restore the intestinal microbiome via probiotics have often had positive results on host markers. The microbiota of the genital tract may play a significant role in acquisition and transmission of HIV. Modification of commensal microbial communities likely represents an important therapeutic adjunct to treatment of HIV. Here we review the literature regarding human microbiome in HIV infection.
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Affiliation(s)
- Brett Williams
- Division of Infectious Diseases, Rush University Medical Center, USA
| | - Alan Landay
- Department of Immunology/microbiology, Rush University Medical Center, USA
| | - Rachel M Presti
- Division of Infectious Disease, Washington University School of Medicine, USA
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293
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Abstract
HIV-1 infection is associated with substantial damage to the gastrointestinal tract resulting in structural impairment of the epithelial barrier and a disruption of intestinal homeostasis. The accompanying translocation of microbial products and potentially microbes themselves from the lumen into systemic circulation has been linked to immune activation, inflammation, and HIV-1 disease progression. The importance of microbial translocation in the setting of HIV-1 infection has led to a recent focus on understanding how the communities of microbes that make up the intestinal microbiome are altered during HIV-1 infection and how they interact with mucosal immune cells to contribute to inflammation. This review details the dysbiotic intestinal communities associated with HIV-1 infection and their potential link to HIV-1 pathogenesis. We detail studies that begin to address the mechanisms driving microbiota-associated immune activation and inflammation and the various treatment strategies aimed at correcting dysbiosis and improving the overall health of HIV-1-infected individuals. Finally, we discuss how this relatively new field of research can advance to provide a more comprehensive understanding of the contribution of the gut microbiome to HIV-1 pathogenesis.
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294
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Ling Z, Jin C, Xie T, Cheng Y, Li L, Wu N. Alterations in the Fecal Microbiota of Patients with HIV-1 Infection: An Observational Study in A Chinese Population. Sci Rep 2016; 6:30673. [PMID: 27477587 PMCID: PMC4967929 DOI: 10.1038/srep30673] [Citation(s) in RCA: 121] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Accepted: 07/08/2016] [Indexed: 02/06/2023] Open
Abstract
The available evidence suggests that alterations in gut microbiota may be tightly linked to the increase in microbial translocation and systemic inflammation in patients with human immunodeficiency virus 1 (HIV-1) infection. We profiled the fecal microbiota as a proxy of gut microbiota by parallel barcoded 454-pyrosequencing in 67 HIV-1-infected patients (32 receiving highly active antiretroviral therapy [HAART] and 35 HAART naïve) and 16 healthy controls from a Chinese population. We showed that α-diversity indices did not differ significantly between the healthy control and HIV-1-infected patients. The ratio of Firmicutes/Bacteroidetes increased significantly in HIV-1-infected patients. Several key bacterial phylotypes, including Prevotella, were prevalent in HIV-1-infected patients; whereas Phascolarctobacterium, Clostridium XIVb, Dialister and Megamonas were significantly correlated with systemic inflammatory cytokines. After short-term, effective HAART, the viral loads of HIV-1 were reduced; however, the diversity and composition of the fecal microbiota were not completely restored. and the dysbiosis remained among HIV-1-infected subjects undergoing HAART. Our detailed analysis demonstrated that dysbiosis of fecal microbiota might play an active role in HIV-1 infection. Thus, new insights may be provided into therapeutics that target the microbiota to attenuate the progression of HIV disease and to reduce the risk of gut-linked disease in HIV-1-infected patients.
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Affiliation(s)
- Zongxin Ling
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310003, China
| | - Changzhong Jin
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310003, China
| | - Tiansheng Xie
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310003, China
| | - Yiwen Cheng
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310003, China
| | - Lanjuan Li
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310003, China
| | - Nanping Wu
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310003, China
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295
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Palmer BE, Li SX, Lozupone CA. The HIV-Associated Enteric Microbiome Has Gone Viral. Cell Host Microbe 2016; 19:270-2. [PMID: 26962936 DOI: 10.1016/j.chom.2016.02.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
HIV infection is associated with dramatic alterations in enteric bacteria, but little is known about other microbiome components. In this issue of Cell Host & Microbe, studies by Monaco et al. (2016) and Handley et al. (2016) reveal an under-appreciated role of the enteric virome in HIV-associated gastroenteritis and pathogenesis.
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Affiliation(s)
- Brent E Palmer
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA.
| | - Sam X Li
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Catherine A Lozupone
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA.
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296
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Serrano-Villar S, Rojo D, Martínez-Martínez M, Deusch S, Vázquez-Castellanos JF, Bargiela R, Sainz T, Vera M, Moreno S, Estrada V, Gosalbes MJ, Latorre A, Seifert J, Barbas C, Moya A, Ferrer M. Gut Bacteria Metabolism Impacts Immune Recovery in HIV-infected Individuals. EBioMedicine 2016; 8:203-216. [PMID: 27428431 PMCID: PMC4919658 DOI: 10.1016/j.ebiom.2016.04.033] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Revised: 04/01/2016] [Accepted: 04/25/2016] [Indexed: 02/07/2023] Open
Abstract
While changes in gut microbial populations have been described in human immuno-deficiency virus (HIV)-infected patients undergoing antiretroviral therapy (ART), the mechanisms underlying the contributions of gut bacteria and their molecular agents (metabolites and proteins) to immune recovery remain unexplored. To study this, we examined the active fraction of the gut microbiome, through examining protein synthesis and accumulation of metabolites inside gut bacteria and in the bloodstream, in 8 healthy controls and 29 HIV-infected individuals (6 being longitudinally studied). We found that HIV infection is associated to dramatic changes in the active set of gut bacteria simultaneously altering the metabolic outcomes. Effects were accentuated among immunological ART responders, regardless diet, subject characteristics, clinical variables other than immune recovery, the duration and type of ART and sexual preferences. The effect was found at quantitative levels of several molecular agents and active bacteria which were herein identified and whose abundance correlated with HIV immune pathogenesis markers. Although, we cannot rule out the possibility that some changes are partially a random consequence of the disease status, our data suggest that most likely reduced inflammation and immune recovery is a joint solution orchestrated by both the active fraction of the gut microbiota and the host.
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Affiliation(s)
- Sergio Serrano-Villar
- Department of Infectious Diseases, University Hospital Ramón y Cajal and Ramón y Cajal Health Research Institute (IRYCIS), Madrid, Spain
| | - David Rojo
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad CEU San Pablo, Campus Montepríncipe, Madrid, Spain
| | | | - Simon Deusch
- Institute of Animal Science, Universität Hohenheim, Stuttgart, Germany
| | - Jorge F Vázquez-Castellanos
- Foundation for the Promotion of Health and Biomedical Research in the Valencian Community (FISABIO) - Public Health, Valencia, Spain; Network Research Center for Epidemiology and Public Health (CIBER-ESP), Madrid, Spain
| | - Rafael Bargiela
- Institute of Catalysis, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Talía Sainz
- Department of Pediatric Infectious Diseases, University Hospital La Paz, and La Paz Research Institute (IdiPAZ), Madrid, Spain
| | - Mar Vera
- Centro Sanitario Sandoval, Madrid, Spain
| | - Santiago Moreno
- Department of Infectious Diseases, University Hospital Ramón y Cajal and Ramón y Cajal Health Research Institute (IRYCIS), Madrid, Spain
| | - Vicente Estrada
- HIV Unit, Department of Internal Medicine, University Hospital Clínico San Carlos, Madrid, Spain
| | - María José Gosalbes
- Foundation for the Promotion of Health and Biomedical Research in the Valencian Community (FISABIO) - Public Health, Valencia, Spain; Network Research Center for Epidemiology and Public Health (CIBER-ESP), Madrid, Spain
| | - Amparo Latorre
- Foundation for the Promotion of Health and Biomedical Research in the Valencian Community (FISABIO) - Public Health, Valencia, Spain; Network Research Center for Epidemiology and Public Health (CIBER-ESP), Madrid, Spain; Instituto Cavanilles de Biodiversidad y Biología Evolutiva (Universidad de Valencia), Valencia, Spain
| | - Jana Seifert
- Institute of Animal Science, Universität Hohenheim, Stuttgart, Germany
| | - Coral Barbas
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad CEU San Pablo, Campus Montepríncipe, Madrid, Spain.
| | - Andrés Moya
- Foundation for the Promotion of Health and Biomedical Research in the Valencian Community (FISABIO) - Public Health, Valencia, Spain; Network Research Center for Epidemiology and Public Health (CIBER-ESP), Madrid, Spain; Instituto Cavanilles de Biodiversidad y Biología Evolutiva (Universidad de Valencia), Valencia, Spain.
| | - Manuel Ferrer
- Institute of Catalysis, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain.
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297
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Li SX, Armstrong A, Neff CP, Shaffer M, Lozupone CA, Palmer BE. Complexities of Gut Microbiome Dysbiosis in the Context of HIV Infection and Antiretroviral Therapy. Clin Pharmacol Ther 2016; 99:600-11. [PMID: 26940481 DOI: 10.1002/cpt.363] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Revised: 02/26/2016] [Accepted: 02/28/2016] [Indexed: 12/14/2022]
Abstract
Human immunodeficiency virus (HIV) infection is associated with an altered gut microbiome that is not consistently restored with effective antiretroviral therapy (ART). Interpretation of the specific microbiome changes observed during HIV infection is complicated by factors like population, sample type, and ART-each of which may have dramatic effects on gut bacteria. Understanding how these factors shape the microbiome during HIV infection (which we refer to as the HIV-associated microbiome) is critical for defining its role in HIV disease, and for developing therapies that restore gut health during infection.
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Affiliation(s)
- S X Li
- Department of Medicine, University of Colorado Denver, Anschutz Medical Campus, Aurora, Colorado, USA
| | - Ajs Armstrong
- Department of Medicine, University of Colorado Denver, Anschutz Medical Campus, Aurora, Colorado, USA.,Department of Immunology and Microbiology, University of Colorado Denver, Anschutz Medical Campus, Aurora, Colorado, USA
| | - C P Neff
- Department of Medicine, University of Colorado Denver, Anschutz Medical Campus, Aurora, Colorado, USA
| | - M Shaffer
- Department of Medicine, University of Colorado Denver, Anschutz Medical Campus, Aurora, Colorado, USA.,Computational Bioscience Program, University of Colorado Denver, Anschutz Medical Campus, Aurora, Colorado, USA
| | - C A Lozupone
- Department of Medicine, University of Colorado Denver, Anschutz Medical Campus, Aurora, Colorado, USA
| | - B E Palmer
- Department of Medicine, University of Colorado Denver, Anschutz Medical Campus, Aurora, Colorado, USA
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298
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Goedert JJ. Effects of HIV, Immune Deficiency, and Confounding on the Distal Gut Microbiota. EBioMedicine 2016; 5:14-5. [PMID: 27077101 PMCID: PMC4816843 DOI: 10.1016/j.ebiom.2016.01.034] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 01/28/2016] [Indexed: 01/13/2023] Open
Affiliation(s)
- James J Goedert
- Infections and Immunoepidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
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