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Zimmermann P, Pittet LF, Jakob W, Messina NL, Falquet L, Curtis N. The Effect of Bacille Calmette-Guérin Vaccination on the Composition of the Intestinal Microbiome in Neonates From the MIS BAIR Trial. Pediatr Infect Dis J 2024; 43:378-389. [PMID: 38145402 DOI: 10.1097/inf.0000000000004223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/26/2023]
Abstract
INTRODUCTION The early-life intestinal microbiome plays an important role in the development and regulation of the immune system. It is unknown whether the administration of vaccines influences the composition of the intestinal microbiome. OBJECTIVE To investigate whether Bacille Calmette-Guérin (BCG) vaccine given in the first few days of life influences the abundance of bacterial taxa and metabolic pathways in the intestinal microbiome at 1 week of age. METHODS Healthy, term-born neonates were randomized at birth to receive BCG or no vaccine within the first few days of life. Stool samples were collected at 1 week of age from 335 neonates and analyzed using shotgun metagenomic sequencing and functional analyses. RESULTS The composition of the intestinal microbiome was different between neonates born by cesarean section (CS) and those born vaginally. Differences in the composition between BCG-vaccinated and BCG-naïve neonates were only minimal. CS-born BCG-vaccinated neonates had a higher abundance of Staphylococcus lugdunensis compared with CS-born BCG-naïve neonates. The latter had a higher abundance of Streptococcus infantis and Trabulsiella guamensis . Vaginally-born BCG-vaccinated neonates had a higher abundance of Clostridiaceae and Streptococcus parasanguinis compared with vaginally-born BCG-naïve neonates, and a lower abundance of Veillonella atypica and Butyricimonas faecalis. Metabolic pathways that were differently abundant between BCG-vaccinated and BCG-naïve neonates were mainly those involved in sugar degradation and nucleotide/nucleoside biosynthesis. CONCLUSION BCG given in the first few days of life has little effect on the composition of the intestinal microbiome at 1 week of age but does influence the abundance of certain metabolic pathways.
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Affiliation(s)
- Petra Zimmermann
- From the Department for Community Health, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland
- Department of Paediatrics, Fribourg Hospital, Fribourg, Switzerland
- Department of Paediatrics, The University of Melbourne, Parkville, Australia
- Infectious Diseases Research Group, Murdoch Children's Research Institute, Parkville, Australia
| | - Laure F Pittet
- Department of Paediatrics, The University of Melbourne, Parkville, Australia
- Infectious Diseases Research Group, Murdoch Children's Research Institute, Parkville, Australia
- Pediatric Infectious Diseases Unit, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland
| | - William Jakob
- Microbiology Laboratory, Fribourg Hospital, Fribourg, Switzerland
| | - Nicole L Messina
- Department of Paediatrics, The University of Melbourne, Parkville, Australia
- Infectious Diseases Research Group, Murdoch Children's Research Institute, Parkville, Australia
| | - Laurent Falquet
- Department of Biology, University of Fribourg and Swiss Institute of Bioinformatics, Fribourg, Switzerland
| | - Nigel Curtis
- Department of Paediatrics, The University of Melbourne, Parkville, Australia
- Infectious Diseases Research Group, Murdoch Children's Research Institute, Parkville, Australia
- Infectious Diseases Unit, The Royal Children's Hospital Melbourne, Parkville, Australia
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Brochu HN, Smith E, Jeong S, Carlson M, Hansen SG, Tisoncik-Go J, Law L, Picker LJ, Gale M, Peng X. Pre-challenge gut microbial signature predicts RhCMV/SIV vaccine efficacy in rhesus macaques. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.27.582186. [PMID: 38464179 PMCID: PMC10925241 DOI: 10.1101/2024.02.27.582186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Background RhCMV/SIV vaccines protect ∼59% of vaccinated rhesus macaques against repeated limiting-dose intra-rectal exposure with highly pathogenic SIVmac239M, but the exact mechanism responsible for the vaccine efficacy is not known. It is becoming evident that complex interactions exist between gut microbiota and the host immune system. Here we aimed to investigate if the rhesus gut microbiome impacts RhCMV/SIV vaccine-induced protection. Methods Three groups of 15 rhesus macaques naturally pre-exposed to RhCMV were vaccinated with RhCMV/SIV vaccines. Rectal swabs were collected longitudinally both before SIV challenge (after vaccination) and post challenge and were profiled using 16S rRNA based microbiome analysis. Results We identified ∼2,400 16S rRNA amplicon sequence variants (ASVs), representing potential bacterial species/strains. Global gut microbial profiles were strongly associated with each of the three vaccination groups, and all animals tended to maintain consistent profiles throughout the pre-challenge phase. Despite vaccination group differences, using newly developed compositional data analysis techniques we identified a common gut microbial signature predictive of vaccine protection outcome across the three vaccination groups. Part of this microbial signature persisted even after SIV challenge. We also observed a strong correlation between this microbial signature and an early signature derived from whole blood transcriptomes in the same animals. Conclusions Our findings indicate that changes in gut microbiomes are associated with RhCMV/SIV vaccine-induced protection and early host response to vaccination in rhesus macaques.
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Meng P, Zhang G, Ma X, Ding X, Song X, Dang S, Yang R, Xu L. Traditional Chinese medicine (Xielikang) reduces diarrhea symptoms in acquired immune deficiency syndrome (AIDS) patients by regulating the intestinal microbiota. Front Microbiol 2024; 15:1346955. [PMID: 38435694 PMCID: PMC10904582 DOI: 10.3389/fmicb.2024.1346955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 02/05/2024] [Indexed: 03/05/2024] Open
Abstract
Diarrheal acquired immune deficiency syndrome (AIDS) seriously affects the quality of life of patients. In this study, we analyzed the differences in the intestinal microbiota among healthy individuals, AIDS patients without diarrhea and AIDS patients with diarrhea through high-throughput sequencing. The microbial diversity in the intestines of patients in the AIDS diarrhea group was significantly increased, and after treatment with Xielikang, the intestinal microbial diversity returned to the baseline level. At the phylum level, compared those in to the healthy (ZC) and AIDS non diarrhea (FN) groups, the relative abundances of Bacteroidetes and Verrucomirobia in the AIDS diarrhea (FA) group before treatment were significantly increased, while the relative abundance of Firmicutes was significantly decreased. Similarly, compared with those in the FA group, the relative abundances of Bacteroidea and Firmicutes in the AIDS diarrhea (FB) group after treatment were significantly increased, while the relative abundance of Firmicutes was significantly decreased after treatment. Additionally, there was no significant difference between the ZC and FN groups. At the genus level, compared with those in the ZC group, the relative abundance of Prevotella and Escherichia_Shigella in the FA group was significantly increased, while the relative abundances of Megamonas and Bifidobacterium was significantly decreased compared to that in the ZC group. After treatment with Xielikang, the relative abundance of Prevotella and Escherichia_Shigella in the FB group were significantly decreased, while the relative abundances of Megamonas and Bifidobacteria were significantly increased than those in the FA group; moreover, there was no significant difference between the ZC and FN groups. The functional prediction results showed that the ketodeoxyoctonate (Kdo) transfer to lipid IVA III and the superpathway of N-acetylglucosamine pathways in the AIDS diarrhea group were significantly altered. The correlation analysis results showed that Dorea was positively correlated with inflammatory factors, while Streptococcus and Lactobacillus were negatively correlated with inflammatory factors. The composition and function of the intestinal microbiota changed significantly in AIDS diarrhea patients, which affected the immune function of the host. The Xielikang capsule modulated the composition of the intestinal microbiota in AIDS diarrhea patients and thus improved immune function and reduced diarrheal symptoms.
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Affiliation(s)
- Pengfei Meng
- Henan University of Chinese Medicine, Zhengzhou, China
- The First Affiliated Hospital of Henan University of Chinese Medicine, Zhengzhou, China
| | - Guichun Zhang
- The First Affiliated Hospital of Henan University of Chinese Medicine, Zhengzhou, China
| | - Xiuxia Ma
- The First Affiliated Hospital of Henan University of Chinese Medicine, Zhengzhou, China
| | - Xue Ding
- The First Affiliated Hospital of Henan University of Chinese Medicine, Zhengzhou, China
| | - Xiyuan Song
- The First Affiliated Hospital of Henan University of Chinese Medicine, Zhengzhou, China
| | - Shuyuan Dang
- Henan University of Chinese Medicine, Zhengzhou, China
| | - Ruihan Yang
- Henan University of Chinese Medicine, Zhengzhou, China
| | - Liran Xu
- Henan University of Chinese Medicine, Zhengzhou, China
- The First Affiliated Hospital of Henan University of Chinese Medicine, Zhengzhou, China
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Tibbs-Cortes BW, Rahic-Seggerman FM, Schmitz-Esser S, Boggiatto PM, Olsen S, Putz EJ. Fecal and vaginal microbiota of vaccinated and non-vaccinated pregnant elk challenged with Brucella abortus. Front Vet Sci 2024; 11:1334858. [PMID: 38352039 PMCID: PMC10861794 DOI: 10.3389/fvets.2024.1334858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 01/02/2024] [Indexed: 02/16/2024] Open
Abstract
Introduction Brucella abortus is the causative agent of brucellosis in cattle and in humans, resulting in economic losses in the agricultural sector and representing a major threat to public health. Elk populations in the American Northwest are reservoirs for this bacterium and transmit the agent to domestic cattle herds. One potential strategy to mitigate the transmission of brucellosis by elk is vaccination of elk populations against B. abortus; however, elk appear to be immunologically distinct from cattle in their responses to current vaccination strategies. The differences in host response to B. abortus between cattle and elk could be attributed to differences between the cattle and elk innate and adaptive immune responses. Because species-specific interactions between the host microbiome and the immune system are also known to affect immunity, we sought to investigate interactions between the elk microbiome and B. abortus infection and vaccination. Methods We analyzed the fecal and vaginal microbial communities of B. abortus-vaccinated and unvaccinated elk which were challenged with B. abortus during the periparturient period. Results We observed that the elk fecal and vaginal microbiota are similar to those of other ruminants, and these microbial communities were affected both by time of sampling and by vaccination status. Notably, we observed that taxa representing ruminant reproductive tract pathogens tended to increase in abundance in the elk vaginal microbiome following parturition. Furthermore, many of these taxa differed significantly in abundance depending on vaccination status, indicating that vaccination against B. abortus affects the elk vaginal microbiota with potential implications for animal reproductive health. Discussion This study is the first to analyze the vaginal microbiota of any species of the genus Cervus and is also the first to assess the effects of B. abortus vaccination and challenge on the vaginal microbiome.
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Affiliation(s)
- Bienvenido W. Tibbs-Cortes
- Infectious Bacterial Diseases Research Unit, United States Department of Agriculture, Ames, IA, United States
| | - Faith M. Rahic-Seggerman
- Interdepartmental Microbiology Graduate Program, Iowa State University, Ames, IA, United States
- Department of Animal Science, Iowa State University, Ames, IA, United States
| | - Stephan Schmitz-Esser
- Interdepartmental Microbiology Graduate Program, Iowa State University, Ames, IA, United States
- Department of Animal Science, Iowa State University, Ames, IA, United States
| | - Paola M. Boggiatto
- Infectious Bacterial Diseases Research Unit, United States Department of Agriculture, Ames, IA, United States
| | - Steven Olsen
- Infectious Bacterial Diseases Research Unit, United States Department of Agriculture, Ames, IA, United States
| | - Ellie J. Putz
- Infectious Bacterial Diseases Research Unit, United States Department of Agriculture, Ames, IA, United States
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Dickstein DR, Edwards CR, Lehrer EJ, Tarras ES, Gallitto M, Sfakianos J, Galsky MD, Stock R, Safer JD, Rosser BRS, Marshall DC. Sexual health and treatment-related sexual dysfunction in sexual and gender minorities with prostate cancer. Nat Rev Urol 2023; 20:332-355. [PMID: 37217695 PMCID: PMC10389287 DOI: 10.1038/s41585-023-00778-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/03/2023] [Indexed: 05/24/2023]
Abstract
Prostate cancer treatment has substantial effects on sexual health and function. Sexual function is a vital aspect of human health and a critical component of cancer survivorship, and understanding the potential effects of different treatment modalities on sexual health is crucial. Existing research has extensively described the effects of treatment on male erectile tissues necessary for heterosexual intercourse; however, evidence regarding their effects on sexual health and function in sexual and gender minority populations is minimal. These groups include sexual minority - gay and bisexual - men, and transgender women or trans feminine people in general. Such unique effects in these groups might include altered sexual function in relation to receptive anal and neovaginal intercourse and changes to patients' role-in-sex. Sexual dysfunctions following prostate cancer treatment affecting quality of life in sexual minority men include climacturia, anejaculation, decreased penile length, erectile dysfunction, and problematic receptive anal intercourse, including anodyspareunia and altered pleasurable sensation. Notably, clinical trials investigating sexual outcomes after prostate cancer treatment do not collect sexual orientation and gender identity demographic data or outcomes specific to members of these populations, which perpetuates the uncertainty regarding optimal management. Providing clinicians with a solid evidence base is essential to communicate recommendations and tailor interventions for sexual and gender minority patients with prostate cancer.
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Affiliation(s)
- Daniel R Dickstein
- Department of Radiation Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Collin R Edwards
- Department of Radiology, Vagelos College of Physicians and Surgeons of Columbia University, New York, NY, USA
| | - Eric J Lehrer
- Department of Radiation Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Elizabeth S Tarras
- Department of Pulmonology, Critical Care, and Sleep Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Matthew Gallitto
- Department of Radiation Oncology, Vagelos College of Physicians and Surgeons of Columbia University, New York, NY, USA
| | - John Sfakianos
- Department of Urology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Matthew D Galsky
- Department of Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Richard Stock
- Department of Radiation Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Joshua D Safer
- Center for Transgender Medicine and Surgery, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - B R Simon Rosser
- Division of Epidemiology and Community Health, School of Public Health at University of Minnesota, Minneapolis, MN, USA
| | - Deborah C Marshall
- Department of Radiation Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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Zimmermann P. The immunological interplay between vaccination and the intestinal microbiota. NPJ Vaccines 2023; 8:24. [PMID: 36823142 PMCID: PMC9947885 DOI: 10.1038/s41541-023-00627-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 02/16/2023] [Indexed: 02/25/2023] Open
Affiliation(s)
- Petra Zimmermann
- Department for Community Health, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland. .,Department of Paediatrics, Fribourg Hospital, Fribourg, Switzerland. .,Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia. .,Infectious Diseases Research Group, Murdoch Children's Research Institute, Parkville, VIC, Australia.
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7
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Vaccination with an HIV T-cell immunogen induces alterations in the mouse gut microbiota. NPJ Biofilms Microbiomes 2022; 8:104. [PMID: 36585401 PMCID: PMC9801356 DOI: 10.1038/s41522-022-00368-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 12/12/2022] [Indexed: 12/31/2022] Open
Abstract
The gut microbiota is emerging as a crucial factor modulating vaccine responses; however, few studies have investigated if vaccines, in turn, can alter the microbiota and to what extent such changes may improve vaccine efficacy. To understand the effect of T-cell vaccination on the gut microbiome, we administered an HIV-1 T-cell immunogen (HTI arm) or PBS (control, Mock arm) to C57Bl/6 mice following a heterologous prime-boost scheme. The longitudinal dynamics of the mice gut microbiota was characterized by 16 S ribosomal RNA sequencing in fecal samples collected from cages, as well as from three gut sections (cecum, small and large intestine). Serum and spleen cells were obtained at the last time point of the study to assess immune correlates using IFNγ ELISPOT and cytokine Luminex® assays. Compared with Mock, HTI-vaccinated mice were enriched in Clostridiales genera (Eubacterium xylanophilum group, Roseburia and Ruminococcus) known as primary contributors of anti-inflammatory metabolites, such as short-chain fatty acids. Such shift was observed after the first HTI dose and remained throughout the study follow-up (18 weeks). However, the enriched Clostridiales genera were different between feces and gut sections. The abundance of bacteria enriched in vaccinated animals positively correlated with HTI-specific T-cell responses and a set of pro-inflammatory cytokines, such as IL-6. This longitudinal analysis indicates that, in mice, T-cell vaccination may promote an increase in gut bacteria known to produce anti-inflammatory molecules, which in turn correlate with proinflammatory cytokines, suggesting an adaptation of the gut microbial milieu to T-cell-induced systemic inflammation.
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Abstract
The microorganisms associated with an organism, the microbiome, have a strong and wide impact in their host biology. In particular, the microbiome modulates both the host defense responses and immunity, thus influencing the fate of infections by pathogens. Indeed, this immune modulation and/or interaction with pathogenic viruses can be essential to define the outcome of viral infections. Understanding the interplay between the microbiome and pathogenic viruses opens future venues to fight viral infections and enhance the efficacy of antiviral therapies. An increasing number of researchers are focusing on microbiome-virus interactions, studying diverse combinations of microbial communities, hosts, and pathogenic viruses. Here, we aim to review these studies, providing an integrative overview of the microbiome impact on viral infection across different pathosystems.
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Affiliation(s)
- Rubén González
- Instituto de Biología Integrativa de Sistemas, Consejo Superior de Investigaciones Científicas-Universitat de València, Paterna, Valencia, Spain
| | - Santiago F. Elena
- Instituto de Biología Integrativa de Sistemas, Consejo Superior de Investigaciones Científicas-Universitat de València, Paterna, Valencia, Spain
- The Santa Fe Institute, Santa Fe, New Mexico, USA
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9
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Methodological advances and challenges in probiotic bacteria production: Ongoing strategies and future perspectives. Biochem Eng J 2021. [DOI: 10.1016/j.bej.2021.108199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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10
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Abstract
Purpose of Review Observations of differing bacterial, intestinal microbiomes in people living with HIV have propelled interest in contributions of the microbiome to HIV disease. Non-human primate (NHP) models of HIV infection provide a controlled setting for assessing contributions of the microbiome by standardizing environmental confounders. We provide an overview of the findings of microbiome contributions to aspects of HIV disease derived from these animal models. Recent Findings Observations of differing bacterial, intestinal microbiomes are inconsistently observed in the NHP model following SIV infection. Differences in lentiviral susceptibility and vaccine efficacy have been attributed to variations in the intestinal microbiome; however, by-and-large, these differences have not been experimentally assessed. Summary Although compelling associations exist, clearly defined contributions of the microbiome to HIV and SIV disease are lacking. The empirical use of comprehensive multi-omics assessments and longitudinal and interventional study designs in NHP models is necessary to define this contribution more clearly.
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Affiliation(s)
- Jason M Brenchley
- Barrier Immunity Section, Laboratory of Viral Diseases, National Institutes of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, USA
| | - Alexandra M Ortiz
- Barrier Immunity Section, Laboratory of Viral Diseases, National Institutes of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, USA.
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Sobia P, Archary D. Preventive HIV Vaccines-Leveraging on Lessons from the Past to Pave the Way Forward. Vaccines (Basel) 2021; 9:vaccines9091001. [PMID: 34579238 PMCID: PMC8472969 DOI: 10.3390/vaccines9091001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 09/01/2021] [Accepted: 09/03/2021] [Indexed: 12/05/2022] Open
Abstract
Almost four decades on, since the 1980’s, with hundreds of HIV vaccine candidates tested in both non-human primates and humans, and several HIV vaccines trials later, an efficacious HIV vaccine continues to evade us. The enormous worldwide genetic diversity of HIV, combined with HIV’s inherent recombination and high mutation rates, has hampered the development of an effective vaccine. Despite the advent of antiretrovirals as pre-exposure prophylaxis and preventative treatment, which have shown to be effective, HIV infections continue to proliferate, highlighting the great need for a vaccine. Here, we provide a brief history for the HIV vaccine field, with the most recent disappointments and advancements. We also provide an update on current passive immunity trials, testing proof of the concept of the most clinically advanced broadly neutralizing monoclonal antibodies for HIV prevention. Finally, we include mucosal immunity, the importance of vaccine-elicited immune responses and the challenges thereof in the most vulnerable environment–the female genital tract and the rectal surfaces of the gastrointestinal tract for heterosexual and men who have sex with men transmissions, respectively.
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Affiliation(s)
- Parveen Sobia
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Nelson Mandela School of Medicine, University of KwaZulu-Natal, Durban 4001, South Africa;
| | - Derseree Archary
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Nelson Mandela School of Medicine, University of KwaZulu-Natal, Durban 4001, South Africa;
- Department of Medical Microbiology, University of KwaZulu-Natal, Durban 4001, South Africa
- Correspondence: ; Tel.: +27-(0)-31-655-0540
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Ishizaka A, Koga M, Mizutani T, Parbie PK, Prawisuda D, Yusa N, Sedohara A, Kikuchi T, Ikeuchi K, Adachi E, Koibuchi T, Furukawa Y, Tojo A, Imoto S, Suzuki Y, Tsutsumi T, Kiyono H, Matano T, Yotsuyanagi H. Unique Gut Microbiome in HIV Patients on Antiretroviral Therapy (ART) Suggests Association with Chronic Inflammation. Microbiol Spectr 2021; 9:e0070821. [PMID: 34378948 PMCID: PMC8552706 DOI: 10.1128/spectrum.00708-21] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Accepted: 07/13/2021] [Indexed: 02/07/2023] Open
Abstract
Chronic inflammation is a hallmark of human immunodeficiency virus (HIV) infection and a risk factor for the development and progression of age-related comorbidities. Although HIV-associated gut dysbiosis has been suggested to be involved in sustained chronic inflammation, there remains a limited understanding of the association between gut dysbiosis and chronic inflammation during HIV infection. Here, we investigated compositional changes in the gut microbiome and its role in chronic inflammation in patients infected with HIV. We observed that the gut microbiomes of patients with low CD4 counts had reduced alpha diversity compared to those in uninfected controls. Following CD4 recovery, alpha diversity was restored, but intergroup dissimilarity of bacterial composition remained unchanged between patients and uninfected controls. Patients with HIV had higher abundance of the classes Negativicutes, Bacilli, and Coriobacteriia, as well as depletion of the class Clostridia. These relative abundances positively correlated with inflammatory cytokines and negatively correlated with anti-inflammatory cytokines. We found that gut dysbiosis accompanying HIV infection was characterized by a depletion of obligate anaerobic Clostridia and enrichment of facultative anaerobic bacteria, reflecting increased intestinal oxygen levels and intestinal permeability. Furthermore, it is likely that HIV-associated dysbiosis shifts the immunological balance toward inflammatory Th1 responses and encourages proinflammatory cytokine production. Our results suggest that gut dysbiosis contributes to sustaining chronic inflammation in patients with HIV infection despite effective antiretroviral therapy and that correcting gut dysbiosis will be effective in improving long-term outcomes in patients. IMPORTANCE Chronic inflammation is a hallmark of HIV infection and is associated with the development and progression of age-related comorbidities. Although the gastrointestinal tract is a major site of HIV replication and CD4+ T-cell depletion, the role of HIV-associated imbalance of gut microbiome in chronic inflammation is unclear. Here, we aimed to understand the causal relationship between abnormalities in the gut microbiome and chronic inflammation in patients with HIV. Our results suggest HIV-associated gut dysbiosis presents a more aerobic environment than that of healthy individuals, despite prolonged viral suppression. This dysbiosis likely results from a sustained increase in intestinal permeability, which supports sustained bacterial translocation in HIV patients, despite effective therapy. Additionally, we observed that several bacterial taxa enriched in HIV patients were associated with increased expression of inflammatory cytokines. Collectively, these results suggest that gut dysbiosis plays an important role in chronic inflammation in HIV patients.
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Affiliation(s)
- Aya Ishizaka
- Division of Infectious Diseases, Advanced Clinical Research Center, the Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- International Research and Development Center for Mucosal Vaccines, the Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Michiko Koga
- Division of Infectious Diseases, Advanced Clinical Research Center, the Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Taketoshi Mizutani
- Division of Infectious Diseases, Advanced Clinical Research Center, the Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- International Research and Development Center for Mucosal Vaccines, the Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Prince Kofi Parbie
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Diki Prawisuda
- Division of Infectious Diseases, Advanced Clinical Research Center, the Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Nozomi Yusa
- Department of Applied Genomics, Research Hospital, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Ayako Sedohara
- Division of Infectious Diseases, Advanced Clinical Research Center, the Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Tadashi Kikuchi
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan
- Department of Infectious Diseases and Applied Immunology, IMSUT Hospital of Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Kazuhiko Ikeuchi
- Department of Infectious Diseases and Applied Immunology, IMSUT Hospital of Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Eisuke Adachi
- Department of Infectious Diseases and Applied Immunology, IMSUT Hospital of Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Tomohiko Koibuchi
- Department of Infectious Diseases and Applied Immunology, IMSUT Hospital of Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Yoichi Furukawa
- Department of Applied Genomics, Research Hospital, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Arinobu Tojo
- Department of Laboratory Medicine, Research Hospital, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Seiya Imoto
- Division of Health Medical Data Science, Health Intelligence Center, the Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Takeya Tsutsumi
- Division of Infectious Diseases, Advanced Clinical Research Center, the Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Hiroshi Kiyono
- International Research and Development Center for Mucosal Vaccines, the Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Tetsuro Matano
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan
- Department of AIDS Vaccine Development, IMSUT Hospital, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Hiroshi Yotsuyanagi
- Division of Infectious Diseases, Advanced Clinical Research Center, the Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Department of Infectious Diseases and Applied Immunology, IMSUT Hospital of Institute of Medical Science, The University of Tokyo, Tokyo, Japan
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Nunez N, Réot L, Menu E. Neonatal Immune System Ontogeny: The Role of Maternal Microbiota and Associated Factors. How Might the Non-Human Primate Model Enlighten the Path? Vaccines (Basel) 2021; 9:584. [PMID: 34206053 PMCID: PMC8230289 DOI: 10.3390/vaccines9060584] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 05/26/2021] [Accepted: 05/28/2021] [Indexed: 12/23/2022] Open
Abstract
Interactions between the immune system and the microbiome play a crucial role on the human health. These interactions start in the prenatal period and are critical for the maturation of the immune system in newborns and infants. Several factors influence the composition of the infant's microbiota and subsequently the development of the immune system. They include maternal infection, antibiotic treatment, environmental exposure, mode of delivery, breastfeeding, and food introduction. In this review, we focus on the ontogeny of the immune system and its association to microbial colonization from conception to food diversification. In this context, we give an overview of the mother-fetus interactions during pregnancy, the impact of the time of birth and the mode of delivery, the neonate gastrointestinal colonization and the role of breastfeeding, weaning, and food diversification. We further review the impact of the vaccination on the infant's microbiota and the reciprocal case. Finally, we discuss several potential therapeutic interventions that might help to improve the newborn and infant's health and their responses to vaccination. Throughout the review, we underline the main scientific questions that are left to be answered and how the non-human primate model could help enlighten the path.
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Affiliation(s)
- Natalia Nunez
- CEA, Université Paris-Sud, Inserm, U1184 “Immunology of Viral Infections and Autoimmune Diseases” (IMVA-HB), IDMIT Department, IBFJ, 92265 Fontenay-aux-Roses, France; (N.N.); (L.R.)
| | - Louis Réot
- CEA, Université Paris-Sud, Inserm, U1184 “Immunology of Viral Infections and Autoimmune Diseases” (IMVA-HB), IDMIT Department, IBFJ, 92265 Fontenay-aux-Roses, France; (N.N.); (L.R.)
| | - Elisabeth Menu
- CEA, Université Paris-Sud, Inserm, U1184 “Immunology of Viral Infections and Autoimmune Diseases” (IMVA-HB), IDMIT Department, IBFJ, 92265 Fontenay-aux-Roses, France; (N.N.); (L.R.)
- MISTIC Group, Department of Virology, Institut Pasteur, 75015 Paris, France
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A Prime/Boost Vaccine Regimen Alters the Rectal Microbiome and Impacts Immune Responses and Viremia Control Post-Simian Immunodeficiency Virus Infection in Male and Female Rhesus Macaques. J Virol 2020; 94:JVI.01225-20. [PMID: 32967951 DOI: 10.1128/jvi.01225-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 09/15/2020] [Indexed: 12/22/2022] Open
Abstract
An efficacious human immunodeficiency virus (HIV) vaccine will likely require induction of both mucosal and systemic immune responses. We compared the immunogenicity and protective efficacy of two mucosal/systemic vaccine regimens and investigated their effects on the rectal microbiome. Rhesus macaques were primed twice mucosally with replication-competent adenovirus type 5 host range mutant (Ad5hr)-simian immunodeficiency virus (SIV) recombinants and boosted twice intramuscularly with ALVAC-SIV recombinant plus SIV gp120 protein or with DNA for SIV genes and rhesus interleukin-12 plus SIV gp120 protein. Controls received empty Ad5hr vector and alum adjuvant only. Both regimens elicited strong, comparable mucosal and systemic cellular and humoral immunity. Prevaccination rectal microbiomes of males and females differed and significantly changed over the course of immunization, most strongly in females after Ad5hr immunizations. Following repeated low-dose intrarectal SIV challenges, both vaccine groups exhibited modestly but significantly reduced acute viremia. Male and female controls exhibited similar acute viral loads; however, vaccinated females, but not males, exhibited lower levels of acute viremia, compared to same-sex controls. Few differences in adaptive immune responses were observed between the sexes. Striking differences in correlations of the rectal microbiome of males and females with acute viremia and immune responses associated with protection were seen and point to effects of the microbiome on vaccine-induced immunity and viremia control. Our study clearly demonstrates direct effects of a mucosal SIV vaccine regimen on the rectal microbiome and validates our previously reported SIV vaccine-induced sex bias. Sex and the microbiome are critical factors that should not be overlooked in vaccine design and evaluation.IMPORTANCE Differences in HIV pathogenesis between males and females, including immunity postinfection, have been well documented, as have steroid hormone effects on the microbiome, which is known to influence mucosal immune responses. Few studies have applied this knowledge to vaccine trials. We investigated two SIV vaccine regimens combining mucosal priming immunizations and systemic protein boosting. We again report a vaccine-induced sex bias, with female rhesus macaques but not males displaying significantly reduced acute viremia. The vaccine regimens, especially the mucosal primes, significantly altered the rectal microbiome. The greatest effects were in females. Striking differences between female and male macaques in correlations of prevalent rectal bacteria with viral loads and potentially protective immune responses were observed. Effects of the microbiome on vaccine-induced immunity and viremia control require further study by microbiome transfer. However, the findings presented highlight the critical importance of considering effects of sex and the microbiome in vaccine design and evaluation.
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15
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Zhang Y, Wu Q, Zhou M, Luo Z, Lv L, Pei J, Wang C, Chai B, Sui B, Huang F, Fu ZF, Zhao L. Composition of the murine gut microbiome impacts humoral immunity induced by rabies vaccines. Clin Transl Med 2020; 10:e161. [PMID: 32898335 PMCID: PMC7443138 DOI: 10.1002/ctm2.161] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 08/12/2020] [Accepted: 08/12/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Gut microbiome plays a crucial role in modulating human and animal immune responses. Rabies is a fatal zoonosis causing encephalitis in mammals and vaccination is the most effective method to control and eliminate rabies. The relationship between the gut microbiome and humoral immunity post rabies vaccination has not been investigated yet. METHODS Mice orally administrated with a cocktail of broad-spectrum antibiotics were inoculated with rabies vaccines, and humoral immune response was analyzed at indicated time points. The 16S ribosomal RNA (16S rRNA) gene sequencing was performed on fecal samples from groups in vancomycin-treated and untreated mice. Mice were immunized with rabies vaccines and virus-neutralizing antibody (VNA) levels were measured, resulting in VNA high (H) and low (L) groups. Then 16S rRNA gene sequencing was performed on fecal samples from H and L group mice. RESULTS After antibiotic (Abx) treatment, mice had decreased levels of rabies virus (RABV)-specific IgM, IgG, and virus-neutralizing antibody compared with untreated mice. Abx-treated mice had fewer T follicular helper cells, germinal center B cells, and antibody secreting cells (ASCs) in lymph nodes than did untreated mice. Gut microbiome facilitated secondary immune responses by increasing the generation of ASCs. Treatment with vancomycin alone had a similarly impaired effect on the humoral immune responses compared with Abx-treated mice. From the natural population group of mice received rabies vaccines, VNA titers vary significantly and the abundance of Clostridiales and Lachnospiraceae was positively associated with the antibody titers in mice. CONCLUSIONS Our results provide the evidence that the gut microbiome impacts humoral immunity post rabies vaccination, and further investigation of the mechanism will help the development of novel adjuvants and vaccines.
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Affiliation(s)
- Yachun Zhang
- State Key Laboratory of Agricultural MicrobiologyHuazhong Agricultural UniversityWuhanChina
- Key Laboratory of Preventive Veterinary Medicine of Hubei ProvinceCollege of Veterinary MedicineHuazhong Agricultural UniversityWuhanChina
| | - Qiong Wu
- State Key Laboratory of Agricultural MicrobiologyHuazhong Agricultural UniversityWuhanChina
- Key Laboratory of Preventive Veterinary Medicine of Hubei ProvinceCollege of Veterinary MedicineHuazhong Agricultural UniversityWuhanChina
| | - Ming Zhou
- State Key Laboratory of Agricultural MicrobiologyHuazhong Agricultural UniversityWuhanChina
- Key Laboratory of Preventive Veterinary Medicine of Hubei ProvinceCollege of Veterinary MedicineHuazhong Agricultural UniversityWuhanChina
| | - Zhaochen Luo
- State Key Laboratory of Agricultural MicrobiologyHuazhong Agricultural UniversityWuhanChina
- Key Laboratory of Preventive Veterinary Medicine of Hubei ProvinceCollege of Veterinary MedicineHuazhong Agricultural UniversityWuhanChina
| | - Lei Lv
- State Key Laboratory of Agricultural MicrobiologyHuazhong Agricultural UniversityWuhanChina
- Key Laboratory of Preventive Veterinary Medicine of Hubei ProvinceCollege of Veterinary MedicineHuazhong Agricultural UniversityWuhanChina
| | - Jie Pei
- State Key Laboratory of Agricultural MicrobiologyHuazhong Agricultural UniversityWuhanChina
- Key Laboratory of Preventive Veterinary Medicine of Hubei ProvinceCollege of Veterinary MedicineHuazhong Agricultural UniversityWuhanChina
| | - Caiqian Wang
- State Key Laboratory of Agricultural MicrobiologyHuazhong Agricultural UniversityWuhanChina
- Key Laboratory of Preventive Veterinary Medicine of Hubei ProvinceCollege of Veterinary MedicineHuazhong Agricultural UniversityWuhanChina
| | - Benjie Chai
- State Key Laboratory of Agricultural MicrobiologyHuazhong Agricultural UniversityWuhanChina
- Key Laboratory of Preventive Veterinary Medicine of Hubei ProvinceCollege of Veterinary MedicineHuazhong Agricultural UniversityWuhanChina
| | - Baokun Sui
- State Key Laboratory of Agricultural MicrobiologyHuazhong Agricultural UniversityWuhanChina
- Key Laboratory of Preventive Veterinary Medicine of Hubei ProvinceCollege of Veterinary MedicineHuazhong Agricultural UniversityWuhanChina
| | - Fei Huang
- State Key Laboratory of Agricultural MicrobiologyHuazhong Agricultural UniversityWuhanChina
- Key Laboratory of Preventive Veterinary Medicine of Hubei ProvinceCollege of Veterinary MedicineHuazhong Agricultural UniversityWuhanChina
| | - Zhen F. Fu
- State Key Laboratory of Agricultural MicrobiologyHuazhong Agricultural UniversityWuhanChina
- Key Laboratory of Preventive Veterinary Medicine of Hubei ProvinceCollege of Veterinary MedicineHuazhong Agricultural UniversityWuhanChina
| | - Ling Zhao
- State Key Laboratory of Agricultural MicrobiologyHuazhong Agricultural UniversityWuhanChina
- Key Laboratory of Preventive Veterinary Medicine of Hubei ProvinceCollege of Veterinary MedicineHuazhong Agricultural UniversityWuhanChina
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