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Singh S, Giron LB, Shaikh MW, Shankaran S, Engen PA, Bogin ZR, Bambi SA, Goldman AR, Azevedo JLLC, Orgaz L, de Pedro N, González P, Giera M, Verhoeven A, Sánchez-López E, Pandrea I, Kannan T, Tanes CE, Bittinger K, Landay AL, Corley MJ, Keshavarzian A, Abdel-Mohsen M. Distinct intestinal microbial signatures linked to accelerated systemic and intestinal biological aging. MICROBIOME 2024; 12:31. [PMID: 38383483 PMCID: PMC10882811 DOI: 10.1186/s40168-024-01758-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 01/05/2024] [Indexed: 02/23/2024]
Abstract
BACKGROUND People living with HIV (PLWH), even when viral replication is controlled through antiretroviral therapy (ART), experience persistent inflammation. This inflammation is partly attributed to intestinal microbial dysbiosis and translocation, which may lead to non-AIDS-related aging-associated comorbidities. The extent to which living with HIV - influenced by the infection itself, ART usage, sexual orientation, or other associated factors - affects the biological age of the intestines is unclear. Furthermore, the role of microbial dysbiosis and translocation in the biological aging of PLWH remains to be elucidated. To investigate these uncertainties, we used a systems biology approach, analyzing colon and ileal biopsies, blood samples, and stool specimens from PLWH on ART and people living without HIV (PLWoH) as controls. RESULTS PLWH exhibit accelerated biological aging in the colon, ileum, and blood, as measured by various epigenetic aging clocks, compared to PLWoH. Investigating the relationship between microbial translocation and biological aging, PLWH had decreased levels of tight junction proteins in the intestines, along with increased microbial translocation. This intestinal permeability correlated with faster biological aging and increased inflammation. When investigating the relationship between microbial dysbiosis and biological aging, the intestines of PLWH had higher abundance of specific pro-inflammatory bacteria, such as Catenibacterium and Prevotella. These bacteria correlated with accelerated biological aging. Conversely, the intestines of PLWH had lower abundance of bacteria known for producing the anti-inflammatory short-chain fatty acids, such as Subdoligranulum and Erysipelotrichaceae, and these bacteria were associated with slower biological aging. Correlation networks revealed significant links between specific microbial genera in the colon and ileum (but not in feces), increased aging, a rise in pro-inflammatory microbe-related metabolites (e.g., those in the tryptophan metabolism pathway), and a decrease in anti-inflammatory metabolites like hippuric acid. CONCLUSIONS We identified specific microbial compositions and microbiota-related metabolic pathways that are intertwined with intestinal and systemic biological aging. This microbial signature of biological aging is likely reflecting various factors including the HIV infection itself, ART usage, sexual orientation, and other aspects associated with living with HIV. A deeper understanding of the mechanisms underlying these connections could offer potential strategies to mitigate accelerated aging and its associated health complications. Video Abstract.
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Affiliation(s)
- Shalini Singh
- Vaccine and Immunotherapy Center, The Wistar Institute, 3601 Spruce Street, Philadelphia, PA, 19104, USA
| | - Leila B Giron
- Vaccine and Immunotherapy Center, The Wistar Institute, 3601 Spruce Street, Philadelphia, PA, 19104, USA
| | - Maliha W Shaikh
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush University, Chicago, IL, USA
| | - Shivanjali Shankaran
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush University, Chicago, IL, USA
- Department of Medicine, Rush University, Chicago, IL, USA
| | - Phillip A Engen
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush University, Chicago, IL, USA
| | - Zlata R Bogin
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush University, Chicago, IL, USA
| | - Simona A Bambi
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush University, Chicago, IL, USA
| | - Aaron R Goldman
- Vaccine and Immunotherapy Center, The Wistar Institute, 3601 Spruce Street, Philadelphia, PA, 19104, USA
| | - Joao L L C Azevedo
- Vaccine and Immunotherapy Center, The Wistar Institute, 3601 Spruce Street, Philadelphia, PA, 19104, USA
| | | | | | | | - Martin Giera
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Aswin Verhoeven
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Elena Sánchez-López
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Toshitha Kannan
- Vaccine and Immunotherapy Center, The Wistar Institute, 3601 Spruce Street, Philadelphia, PA, 19104, USA
| | - Ceylan E Tanes
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Kyle Bittinger
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Alan L Landay
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush University, Chicago, IL, USA
- Department of Medicine, Rush University, Chicago, IL, USA
| | | | - Ali Keshavarzian
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush University, Chicago, IL, USA
- Department of Medicine, Rush University, Chicago, IL, USA
| | - Mohamed Abdel-Mohsen
- Vaccine and Immunotherapy Center, The Wistar Institute, 3601 Spruce Street, Philadelphia, PA, 19104, USA.
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Singh S, Giron LB, Shaikh MW, Shankaran S, Engen PA, Bogin ZR, Bambi SA, Goldman AR, Azevedo JLLC, Orgaz L, de Pedro N, González P, Giera M, Verhoeven A, Sánchez-López E, Pandrea IV, Kannan T, Tanes CE, Bittinger K, Landay AL, Corley MJ, Keshavarzian A, Abdel-Mohsen M. Distinct Intestinal Microbial Signatures Linked to Accelerated Biological Aging in People with HIV. RESEARCH SQUARE 2023:rs.3.rs-3492242. [PMID: 37961645 PMCID: PMC10635386 DOI: 10.21203/rs.3.rs-3492242/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Background People with HIV (PWH), even with controlled viral replication through antiretroviral therapy (ART), experience persistent inflammation. This is partly due to intestinal microbial dysbiosis and translocation. Such ongoing inflammation may lead to the development of non-AIDS-related aging-associated comorbidities. However, there remains uncertainty regarding whether HIV affects the biological age of the intestines and whether microbial dysbiosis and translocation influence the biological aging process in PWH on ART. To fill this knowledge gap, we utilized a systems biology approach, analyzing colon and ileal biopsies, blood samples, and stool specimens from PWH on ART and their matched HIV-negative counterparts. Results Despite having similar chronological ages, PWH on ART exhibit accelerated biological aging in the colon, ileum, and blood, as measured by various epigenetic aging clocks, compared to HIV-negative controls. Investigating the relationship between microbial translocation and biological aging, PWH on ART had decreased levels of tight junction proteins in the colon and ileum, along with increased microbial translocation. This increased intestinal permeability correlated with faster intestinal and systemic biological aging, as well as increased systemic inflammation. When investigating the relationship between microbial dysbiosis and biological aging, the intestines of PWH on ART had higher abundance of specific pro-inflammatory bacterial genera, such as Catenibacterium and Prevotella. These bacteria significantly correlated with accelerated local and systemic biological aging. Conversely, the intestines of PWH on ART had lower abundance of bacterial genera known for producing short-chain fatty acids and exhibiting anti-inflammatory properties, such as Subdoligranulum and Erysipelotrichaceae, and these bacteria taxa were associated with slower biological aging. Correlation networks revealed significant links between specific microbial genera in the colon and ileum (but not in feces), increased aging, a rise in pro-inflammatory microbial-related metabolites (e.g., those in the tryptophan metabolism pathway), and a decrease in anti-inflammatory metabolites like hippuric acid and oleic acid. Conclusions We identified a specific microbial composition and microbiome-related metabolic pathways that are intertwined with both intestinal and systemic biological aging in PWH on ART. A deeper understanding of the mechanisms underlying these connections could potentially offer strategies to counteract premature aging and its associated health complications in PWH.
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Sánchez-Conde M, Alba C, Castro I, Dronda F, Ramírez M, Arroyo R, Moreno S, Rodríguez JM, Brañas F. Comparison of the Fecal Bacteriome of HIV-Positive and HIV-Negative Older Adults. Biomedicines 2023; 11:2305. [PMID: 37626801 PMCID: PMC10452058 DOI: 10.3390/biomedicines11082305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 08/12/2023] [Accepted: 08/16/2023] [Indexed: 08/27/2023] Open
Abstract
HIV infection is considered a scenario of accelerated aging. Previous studies have suggested a link between aging, frailty, and gut dysbiosis, but there is a knowledge gap regarding the HIV population. Our objective was to compare the fecal bacteriome of older people with HIV (PWH) and non-HIV controls, and to assess potential links between gut dysbiosis and frailty. A total of 36 fecal samples (24 from PWH and 12 from non-HIV controls) were submitted to a metataxonomic analysis targeting the V3-V4 hypervariable region of the 16S rRNA gene. High-quality reads were assembled and classified into operational taxonomic units. Alpha diversity, assessed using the Shannon index, was higher in the control group than in the HIV group (p < 0.05). The relative abundance of the genus Blautia was higher in the HIV group (p < 0.001). The presence of Blautia was also higher in PWH with depression (p = 0.004), whereas the opposite was observed for the genus Bifidobacterium (p = 0.004). Our study shows shifts in the composition of the PWH bacteriome when compared to that of healthy controls. To our knowledge, this is the first study suggesting a potential link between depression and gut dysbiosis in the HIV population.
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Affiliation(s)
- Matilde Sánchez-Conde
- Infectious Diseases Department, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), 28034 Madrid, Spain; (F.D.); (S.M.)
- CIBER de Enfermedades Infecciosas (CIBERINFECT), Instituto de Salud Carlos III, 28220 Madrid, Spain
| | - Claudio Alba
- Department of Nutrition and Food Science, Complutense University of Madrid, 28040 Madrid, Spain; (C.A.); (I.C.); (J.M.R.)
| | - Irma Castro
- Department of Nutrition and Food Science, Complutense University of Madrid, 28040 Madrid, Spain; (C.A.); (I.C.); (J.M.R.)
| | - Fernando Dronda
- Infectious Diseases Department, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), 28034 Madrid, Spain; (F.D.); (S.M.)
| | - Margarita Ramírez
- Infectious Diseases Department, Hospital General Universitario Gregorio Marañón, 28007 Madrid, Spain;
| | - Rebeca Arroyo
- Department of Nutrition and Food Science, Complutense University of Madrid, 28040 Madrid, Spain; (C.A.); (I.C.); (J.M.R.)
| | - Santiago Moreno
- Infectious Diseases Department, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), 28034 Madrid, Spain; (F.D.); (S.M.)
| | - Juan Miguel Rodríguez
- Department of Nutrition and Food Science, Complutense University of Madrid, 28040 Madrid, Spain; (C.A.); (I.C.); (J.M.R.)
| | - Fátima Brañas
- Geriatric Department, Hospital Universitario Infanta Leonor, 28031 Madrid, Spain
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Cai Y, Kang Y. Gut microbiota and metabolites in diabetic retinopathy: Insights into pathogenesis for novel therapeutic strategies. Biomed Pharmacother 2023; 164:114994. [PMID: 37301133 DOI: 10.1016/j.biopha.2023.114994] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 05/30/2023] [Accepted: 06/06/2023] [Indexed: 06/12/2023] Open
Abstract
Diabetic retinopathy (DR) is the most common and detrimental microvascular complication of diabetes mellitus. It has become one of the top causes of blindness and visual impairment in the working-age population. However, prevention and treatment options for DR are limited, invasive, and expensive, and most are focused on advanced-stage disease. The gut microbiota is an intricate system that alters the body's microenvironment, and its dysbiosis is strongly associated with DR. Recently, more and more investigations into the relationship between microbiota and DR have enhanced our understanding of how the gut microbiota influences the occurrence, development, prevention, and treatment of DR. In this review, we summarize the changes in the gut microbiota of animals and patients with DR and the function of metabolites and anti-diabetes drugs. Furthermore, we discuss the potential use of gut microbiota as an early diagnostic marker and targeting for DR in the healthy people and diabetic patients. Finally, the microbiota-gut-retina axis is presented to help us understand the mechanisms underlying the effect of gut microbiota on triggering or promoting DR, with a focus on the key pathways (e.g., bacterial dysbiosis and gut barrier dysfunction) that promote inflammation, insulin resistance, retinal cell and acellular capillary damage, leading to DR. Based on these data, we can hope to achieve a non-invasive, inexpensive treatment for DR by modulating the gut microbiota, either by supplementation with probiotics or by fecal transplantation. We outline the gut microbiota-targeting treatments in detail that could prevent DR progression.
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Affiliation(s)
- Yue Cai
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China; School of Medicine, Kunming University of Science and Technology, Kunming, Yunnan, China; Department of Infectious Disease and Hepatic Disease, The First People's Hospital of Yunnan Province, Kunming, Yunnan, China
| | - Yongbo Kang
- Department of Microbiology and Immunology, School of Basic Medical Sciences, Shanxi Medical University, Taiyuan, Shanxi, China.
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Meng J, Tao J, Abu Y, Sussman DA, Girotra M, Franceschi D, Roy S. HIV-Positive Patients on Antiretroviral Therapy Have an Altered Mucosal Intestinal but Not Oral Microbiome. Microbiol Spectr 2023; 11:e0247222. [PMID: 36511710 PMCID: PMC9927552 DOI: 10.1128/spectrum.02472-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 11/27/2022] [Indexed: 12/15/2022] Open
Abstract
This study characterized compositional and functional shifts in the intestinal and oral microbiome in HIV-positive patients on antiretroviral therapy compared to HIV-negative individuals. Seventy-nine specimens were collected from 5 HIV-positive and 12 control subjects from five locations (colon brush, colon wash, terminal ileum [TI] brush, TI wash, and saliva) during colonoscopy and at patient visits. Microbiome composition was characterized using 16S rRNA sequencing, and microbiome function was predicted using bioinformatics tools (PICRUSt and BugBase). Our analysis indicated that the β-diversity of all intestinal samples (colon brush, colon wash, TI brush, and TI wash) from patients with HIV was significantly different from patients without HIV. Specifically, bacteria from genera Prevotella, Fusobacterium, and Megasphaera were more abundant in samples from HIV-positive patients. On the other hand, bacteria from genera Ruminococcus, Blautia, and Clostridium were more abundant in samples from HIV-negative patients. Additionally, HIV-positive patients had higher abundances of biofilm-forming and pathogenic bacteria. Furthermore, pathways related to translation and nucleotide metabolism were elevated in HIV-positive patients, whereas pathways related to lipid and carbohydrate metabolism were positively correlated with samples from HIV-negative patients. Our analyses further showed variations in microbiome composition in HIV-positive and negative patients by sampling site. Samples from colon wash, colon brush, and TI wash were significant between groups, while samples from TI brush and saliva were not significant. Taken together, here, we report altered intestinal microbiome composition and predicted function in patients with HIV compared to uninfected patients, though we found no changes in the oral microbiome. IMPORTANCE Over 37 million people worldwide are living with HIV. Although the availability of antiretroviral therapy has significantly reduced the number of AIDS-related deaths, individuals living with HIV are at increased risk for opportunistic infections. We now know that HIV interacts with the trillions of bacteria, fungi, and viruses in the human body termed the microbiome. Only a limited number of previous studies have compared variations in the oral and gastrointestinal microbiome with HIV infection. Here, we detail how the oral and gastrointestinal microbiome changes with HIV infection, having used 5 different sampling sites to gain a more comprehensive view of these changes by location. Our results show site-specific changes in the intestinal microbiome associated with HIV infection. Additionally, we show that while there were significant changes in the intestinal microbiome, there were no significant changes in the oral microbiome.
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Affiliation(s)
- Jingjing Meng
- Department of Surgery, Sylvester Comprehensive Cancer Center, University of Miami, Miami, Florida, USA
| | - Junyi Tao
- Department of Surgery, Sylvester Comprehensive Cancer Center, University of Miami, Miami, Florida, USA
| | - Yaa Abu
- Department of Surgery, Sylvester Comprehensive Cancer Center, University of Miami, Miami, Florida, USA
| | - Daniel Andrew Sussman
- Department of Gastroenterology, University of Miami Medical Group, Miami, Florida, USA
| | - Mohit Girotra
- Department of Gastroenterology, University of Miami Medical Group, Miami, Florida, USA
| | - Dido Franceschi
- Department of Surgery, Sylvester Comprehensive Cancer Center, University of Miami, Miami, Florida, USA
| | - Sabita Roy
- Department of Surgery, Sylvester Comprehensive Cancer Center, University of Miami, Miami, Florida, USA
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Lu Y, Xing S, He L, Li C, Wang X, Zeng X, Dai Y. Characterization, High-Density Fermentation, and the Production of a Directed Vat Set Starter of Lactobacilli Used in the Food Industry: A Review. Foods 2022; 11:3063. [PMID: 36230139 PMCID: PMC9563398 DOI: 10.3390/foods11193063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 09/15/2022] [Accepted: 09/29/2022] [Indexed: 11/16/2022] Open
Abstract
Lactobacilli have been widely concerned for decades. Bacteria of the genus Lactobacillus have been commonly employed in fermented food to improve the appearance, smell, and taste of food or prolong its shelf-life. They comprise 261 species (by March 2020) that are highly diverse at the phenotypic, ecological, and genotypic levels. Some Lactobacilli strains have been documented to be essential probiotics, which are defined as a group of living microorganisms that are beneficial to the health of the host when ingested in sufficiency. However, the characterization, high-density fermentation, and the production of a directed vat set (DVS) starter of Lactobacilli strains used in the food industry have not been systematically reported. This paper mainly focuses on reviewing Lactobacilli as functional starter cultures in the food industry, including different molecular techniques for identification at the species and strain levels, methods for evaluating Lactobacilli properties, enhancing their performance and improving the cell density of Lactobacilli, and the production techniques of DVS starter of Lactobacilli strains. Moreover, this review further discussed the existing problems and future development prospects of Lactobacilli in the food industry. The viability and stability of Lactobacilli in the food industry and gastrointestinal environment are critical challenges at the industrial scale. The new production equipment and technology of DVS starter of Lactobacilli strains will have the potential for large-scale application, for example, developing low-temperature spray drying, freezing granulation drying, and spray freeze-drying.
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Affiliation(s)
- Yun Lu
- Key Laboratory of Agricultural and Animal Products Storage & Processing of Guizhou Province, Guizhou University, Guiyang 550025, China
- Department of Brewing Engineering, Moutai University, Renhuai 564507, China
| | - Shuqi Xing
- Key Laboratory of Agricultural and Animal Products Storage & Processing of Guizhou Province, Guizhou University, Guiyang 550025, China
- College of Liquor and Food Engineering, Guizhou University, Guiyang 550025, China
| | - Laping He
- Key Laboratory of Agricultural and Animal Products Storage & Processing of Guizhou Province, Guizhou University, Guiyang 550025, China
- College of Liquor and Food Engineering, Guizhou University, Guiyang 550025, China
| | - Cuiqin Li
- Key Laboratory of Agricultural and Animal Products Storage & Processing of Guizhou Province, Guizhou University, Guiyang 550025, China
- College of Liquor and Food Engineering, Guizhou University, Guiyang 550025, China
- School of Chemistry and Chemical Engineering, Guizhou University, Guiyang 550025, China
| | - Xiao Wang
- Key Laboratory of Agricultural and Animal Products Storage & Processing of Guizhou Province, Guizhou University, Guiyang 550025, China
- College of Liquor and Food Engineering, Guizhou University, Guiyang 550025, China
| | - Xuefeng Zeng
- Key Laboratory of Agricultural and Animal Products Storage & Processing of Guizhou Province, Guizhou University, Guiyang 550025, China
- College of Liquor and Food Engineering, Guizhou University, Guiyang 550025, China
| | - Yifeng Dai
- Key Laboratory of Agricultural and Animal Products Storage & Processing of Guizhou Province, Guizhou University, Guiyang 550025, China
- College of Liquor and Food Engineering, Guizhou University, Guiyang 550025, China
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Mizutani T, Ishizaka A, Koga M, Tsutsumi T, Yotsuyanagi H. Role of Microbiota in Viral Infections and Pathological Progression. Viruses 2022; 14:950. [PMID: 35632692 PMCID: PMC9144409 DOI: 10.3390/v14050950] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 04/29/2022] [Accepted: 04/29/2022] [Indexed: 02/04/2023] Open
Abstract
Viral infections are influenced by various microorganisms in the environment surrounding the target tissue, and the correlation between the type and balance of commensal microbiota is the key to establishment of the infection and pathogenicity. Some commensal microorganisms are known to resist or promote viral infection, while others are involved in pathogenicity. It is also becoming evident that the profile of the commensal microbiota under normal conditions influences the progression of viral diseases. Thus, to understand the pathogenesis underlying viral infections, it is important to elucidate the interactions among viruses, target tissues, and the surrounding environment, including the commensal microbiota, which should have different relationships with each virus. In this review, we outline the role of microorganisms in viral infections. Particularly, we focus on gaining an in-depth understanding of the correlations among viral infections, target tissues, and the surrounding environment, including the commensal microbiota and the gut virome, and discussing the impact of changes in the microbiota (dysbiosis) on the pathological progression of viral infections.
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Affiliation(s)
- Taketoshi Mizutani
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8562, Japan
- Division of Infectious Diseases, Advanced Clinical Research Center, the Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan; (A.I.); (M.K.); (T.T.); (H.Y.)
| | - Aya Ishizaka
- Division of Infectious Diseases, Advanced Clinical Research Center, the Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan; (A.I.); (M.K.); (T.T.); (H.Y.)
| | - Michiko Koga
- Division of Infectious Diseases, Advanced Clinical Research Center, the Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan; (A.I.); (M.K.); (T.T.); (H.Y.)
| | - Takeya Tsutsumi
- Division of Infectious Diseases, Advanced Clinical Research Center, the Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan; (A.I.); (M.K.); (T.T.); (H.Y.)
| | - Hiroshi Yotsuyanagi
- Division of Infectious Diseases, Advanced Clinical Research Center, the Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan; (A.I.); (M.K.); (T.T.); (H.Y.)
- Department of Infectious Diseases and Applied Immunology, IMSUT Hospital of Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
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Jiang D, Zhang L, Zhu G, Zhang P, Wu X, Yao X, Luo Y, Yang Z, Ren M, Wang X, Chen S, Wang Y. The Antiviral Effect of Isatis Root Polysaccharide against NADC30-like PRRSV by Transcriptome and Proteome Analysis. Int J Mol Sci 2022; 23:ijms23073688. [PMID: 35409050 PMCID: PMC8998840 DOI: 10.3390/ijms23073688] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Revised: 03/24/2022] [Accepted: 03/25/2022] [Indexed: 01/25/2023] Open
Abstract
(1) Background: In recent years, the porcine reproductive and respiratory syndrome virus (PRRSV) has become a virulent pathogen that has caused devastating diseases and economic losses worldwide in the swine industry. IRPS has attracted extensive attention in the field of virology. However, it is not clear that IRPS has an antiviral effect on PRRSV at gene and protein levels. (2) Methods: We used transcriptomic and proteomic analysis to investigate the antiviral effect of IRPS against PRRSV. Additionally, a microbiome was used to explore the effects of IRPS on gut microbes. (3) Results: IRPS significantly extenuated the pulmonary pathological lesions and inflammatory response. We used transcriptomic and proteomic analysis to investigate the antiviral effect of IRPS against PRRSV. In the porcine model, 1669 differentially expressed genes (DEGs) and 370 differentially expressed proteins (DEPs) were identified. Analysis of the DEG/DEP-related pathways indicated immune-system and infectious-disease (viral) pathways, such as the NOD-like receptor (NLR) signaling pathway, toll-like receptor (TLR) signaling pathway, and Influenza A-associated signaling pathways. It is noteworthy that IRPS can inhibit NLR-dependent gene expression, then reduce the inflammatory damage. IRPS could exert beneficial effects on the host by regulating the structure of intestinal flora. (4) Conclusions: The antiviral effect of IRPS on PRRSV can be directly achieved by omics techniques. Specifically, the antiviral mechanism of IPRS can be better elucidated by screening target genes and proteins using transcriptome and proteome sequencing, and then performing enrichment and classification according to DEGs and DEPs.
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Affiliation(s)
- Dike Jiang
- Key Laboratory of Animal Diseases and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China; (D.J.); (G.Z.); (P.Z.); (X.Y.); (Y.L.); (Z.Y.); (M.R.)
| | - Ling Zhang
- College of Veterinary Medicine, Jilin University, Changchun 130012, China;
| | - Guangheng Zhu
- Key Laboratory of Animal Diseases and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China; (D.J.); (G.Z.); (P.Z.); (X.Y.); (Y.L.); (Z.Y.); (M.R.)
| | - Pengfei Zhang
- Key Laboratory of Animal Diseases and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China; (D.J.); (G.Z.); (P.Z.); (X.Y.); (Y.L.); (Z.Y.); (M.R.)
| | - Xulong Wu
- Branch of Animal Husbandry and Veterinary Medicine, Chengdu Agricultural College, Chengdu 611130, China;
| | - Xueping Yao
- Key Laboratory of Animal Diseases and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China; (D.J.); (G.Z.); (P.Z.); (X.Y.); (Y.L.); (Z.Y.); (M.R.)
| | - Yan Luo
- Key Laboratory of Animal Diseases and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China; (D.J.); (G.Z.); (P.Z.); (X.Y.); (Y.L.); (Z.Y.); (M.R.)
| | - Zexiao Yang
- Key Laboratory of Animal Diseases and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China; (D.J.); (G.Z.); (P.Z.); (X.Y.); (Y.L.); (Z.Y.); (M.R.)
| | - Meishen Ren
- Key Laboratory of Animal Diseases and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China; (D.J.); (G.Z.); (P.Z.); (X.Y.); (Y.L.); (Z.Y.); (M.R.)
| | - Xinping Wang
- College of Veterinary Medicine, Jilin University, Changchun 130012, China;
- Correspondence: (X.W.); (Y.W.)
| | - Sheng Chen
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong 999077, China;
| | - Yin Wang
- Key Laboratory of Animal Diseases and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China; (D.J.); (G.Z.); (P.Z.); (X.Y.); (Y.L.); (Z.Y.); (M.R.)
- Correspondence: (X.W.); (Y.W.)
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9
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Mingjun Z, Fei M, Zhousong X, Wei X, Jian X, Yuanxue Y, Youfeng S, Zhongping C, Yiqin L, Xiaohong Z, Ying C, Zhenbing W, Zehu D, Lanjuan L. 16S rDNA sequencing analyzes differences in intestinal flora of human immunodeficiency virus (HIV) patients and association with immune activation. Bioengineered 2022; 13:4085-4099. [PMID: 35129067 PMCID: PMC8974104 DOI: 10.1080/21655979.2021.2019174] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
To clarify the influence of HIV on the intestinal flora and the interrelationship with CD4 T cells, the present study collected stool specimens from 33 HIV patients and 28 healthy subjects to compare the differences in the intestinal flora and CD4 T cells in a 16S rDNA-sequencing approach. ELISA was used to detect the expressions of interleukin 2 (IL-2), IL-8, and tumor necrosis factor-α (TNF-α). Meanwhile, correlation analysis with the different bacterial populations in each group was carried out. The results revealed that Alpha diversity indices of the intestinal flora of HIV patients were markedly lower than that of the healthy group (p < 0.05). The top five bacterial species in the HIV group were Bacteroides (23.453%), Prevotella (19.237%), Fusobacterium (12.408%), Lachnospira (3.811%), and Escherichia-Shigella (3.126%). Spearman correlation analysis results indicated that Fusobacterium_mortiferum, Fusobacterium, and Gammaproteobacteria were positively correlated with TNF-α (p < 0.05), whereas Ruminococcaceae, Bacteroidales was negatively correlated with TNF-α (p < 0.05). Additionally, Agathobacter was positively correlated with contents of IL-2 and IL-8 (p < 0.05), whereas Prevotellaceae, and Prevotella were negatively correlated with IL-8 content (p < 0.05). Furthermore, the top five strains in the CD4 high group (≥350/mm3) included Bacteroides (23.286%), Prevotella (21.943%), Fusobacterium (10.479%), Lachnospira (4.465%), and un_f_Lachnospiraceae (2.786%). Taken together, the present study identified that Fusobacterium and Escherichia-Shigella were specific and highly abundant in the HIV group and a correlation between the different bacterial flora and the contents of IL-2, IL-8, and TNF-α was revealed.
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Affiliation(s)
- Zhang Mingjun
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Department of Laboratory Medicine, People's Hospital of Jiulongpo District, Chongqing, China
| | - Mo Fei
- Department of Laboratory Medicine, People's Hospital of Jiulongpo District, Chongqing, China
| | - Xu Zhousong
- Department of Laboratory Medicine, People's Hospital of Jiulongpo District, Chongqing, China
| | - Xu Wei
- Department of Laboratory Medicine, Hangzhou Shulan Hospital, Zhejiang University, Hangzhou, China.,Department of Laboratory Medicine, Hangzhou Tongchuang Medical Laboratory Co. LTD, Hangzhou, China
| | - Xu Jian
- Department of Laboratory Medicine, Chongqing Precision Medical Industry Technology Research Institute, Chongqing, China
| | - Yi Yuanxue
- Department of Laboratory Medicine, Chongqing Precision Medical Industry Technology Research Institute, Chongqing, China.,Department of Laboratory Medicine, Chongqing D.A. Medical Laboratory, Chongqing, China
| | - Shen Youfeng
- Department of Laboratory Medicine, Chongqing Precision Medical Industry Technology Research Institute, Chongqing, China.,Department of Laboratory Medicine, Chongqing D.A. Medical Laboratory, Chongqing, China
| | - Chen Zhongping
- Department of Laboratory Medicine, People's Hospital of Jiulongpo District, Chongqing, China
| | - Long Yiqin
- Department of Laboratory Medicine, People's Hospital of Jiulongpo District, Chongqing, China
| | - Zhao Xiaohong
- Department of Laboratory Medicine, People's Hospital of Jiulongpo District, Chongqing, China
| | - Cheng Ying
- Department of Laboratory Medicine, Hangzhou Shulan Hospital, Zhejiang University, Hangzhou, China
| | - Wang Zhenbing
- Department of Laboratory Medicine, Chongqing Precision Medical Industry Technology Research Institute, Chongqing, China.,Department of Laboratory Medicine, Chongqing D.A. Medical Laboratory, Chongqing, China
| | - Deng Zehu
- Department of Laboratory Medicine, People's Hospital of Jiulongpo District, Chongqing, China
| | - Li Lanjuan
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
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10
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Lin MQ, Wu YH, Yang J, Lin HC, Liu LY, Yu YL, Yao QW, Li JC. Gut Microbiota Characteristics Are Associated With Severity of Acute Radiation-Induced Esophagitis. Front Microbiol 2022; 13:883650. [PMID: 35756007 PMCID: PMC9218355 DOI: 10.3389/fmicb.2022.883650] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 05/13/2022] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Acute radiation-induced esophagitis (ARIE) is one of the most debilitating complications in patients who receive thoracic radiotherapy, especially those with esophageal cancer (EC). There is little known about the impact of the characteristics of gut microbiota on the initiation and severity of ARIE. MATERIALS AND METHODS Gut microbiota samples of EC patients undergoing radiotherapy (n = 7) or concurrent chemoradiotherapy (n = 42) were collected at the start, middle, and end of the radiotherapy regimen. Assessment of patient-reported ARIE was also performed. Based on 16S rRNA gene sequencing, changes of the gut microbial community during the treatment regimen and correlations of the gut microbiota characteristics with the severity of ARIE were investigated. RESULTS There were significant associations of several properties of the gut microbiota with the severity of ARIE. The relative abundance of several genera in the phylum Proteobacteria increased significantly as mucositis severity increased. The predominant genera had characteristic changes during the treatment regimen, such as an increase of opportunistic pathogenic bacteria including Streptococcus. Patients with severe ARIE had significantly lower alpha diversity and a higher abundance of Fusobacterium before radiotherapy, but patients with mild ARIE were enriched in Klebsiella, Roseburia, Veillonella, Prevotella_9, Megasphaera, and Ruminococcus_2. A model combining these genera had the best performance in prediction of severe ARIE (area under the curve: 0.907). CONCLUSION The characteristics of gut microbiota before radiotherapy were associated with subsequent ARIE severity. Microbiota-based strategies have potential use for the early prediction of subsequent ARIE and for the selection of interventions that may prevent severe ARIE.
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Affiliation(s)
- Ming-qiang Lin
- College of Clinical Medicine for Oncology, Fujian Medical University, Fuzhou, China
| | - Ya-hua Wu
- College of Clinical Medicine for Oncology, Fujian Medical University, Fuzhou, China
| | - Jun Yang
- College of Clinical Medicine for Oncology, Fujian Medical University, Fuzhou, China
| | - Han-cui Lin
- College of Clinical Medicine for Oncology, Fujian Medical University, Fuzhou, China
| | - Ling-yun Liu
- College of Clinical Medicine for Oncology, Fujian Medical University, Fuzhou, China
| | - Yi-lin Yu
- College of Clinical Medicine for Oncology, Fujian Medical University, Fuzhou, China
| | - Qi-wei Yao
- College of Clinical Medicine for Oncology, Fujian Medical University, Fuzhou, China
- Fujian Medical University Cancer Hospital, Fujian Cancer Hospital, Fuzhou, China
- *Correspondence: Qi-wei Yao,
| | - Jian-cheng Li
- College of Clinical Medicine for Oncology, Fujian Medical University, Fuzhou, China
- Fujian Medical University Cancer Hospital, Fujian Cancer Hospital, Fuzhou, China
- Jian-cheng Li,
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11
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Ye P, Zhang X, Xu Y, Xu J, Song X, Yao K. Alterations of the Gut Microbiome and Metabolome in Patients With Proliferative Diabetic Retinopathy. Front Microbiol 2021; 12:667632. [PMID: 34566901 PMCID: PMC8457552 DOI: 10.3389/fmicb.2021.667632] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Accepted: 08/10/2021] [Indexed: 12/05/2022] Open
Abstract
Diabetic retinopathy (DR) has been reported to associate with gut microbiota alterations in murine models and thus “gut-retina-axis” has been proposed. However, the role of gut microbiome and the associated metabolism in DR patients still need to be elucidated. In this study, we collected fecal samples from 45 patients with proliferative diabetic retinopathy (PDR) and 90 matched diabetic patients (1:2 according to age, sex, and duration of diabetes) without DR (NDR) and performed 16S rRNA gene sequencing and untargeted metabolomics. We observed significantly lower bacterial diversity in the PDR group than that in the NDR group. Differential gut bacterial composition was also found, with significant depletion of 22 families (e.g., Coriobacteriaceae, Veillonellaceae, and Streptococcaceae) and enrichment of two families (Burkholderiaceae and Burkholderiales_unclassified) in the PDR group as compared with the NDR group. There were significantly different fecal metabolic features, which were enriched in metabolic pathways such as arachidonic acid and microbial metabolism, between the two groups. Among 36 coabundance metabolite clusters, 11 were positively/negatively contributed to PDR using logistic regression analysis. Fifteen gut microbial families were significantly correlated with the 11 metabolite clusters. Furthermore, a fecal metabolite-based classifier was constructed to distinguish PDR patients from NDR patients accurately. In conclusion, PDR is associated with reduced diversity and altered composition of gut microbiota and specific microbe-metabolite interplay. Our findings help to better understand the disease pathogenesis and provide novel diagnostic and therapeutic targets for PDR.
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Affiliation(s)
- Panpan Ye
- Eye Center, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,Eye Hospital, Zhejiang University, Hangzhou, China
| | - Xueyou Zhang
- Department of Surgery, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Yufeng Xu
- Eye Center, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,Eye Hospital, Zhejiang University, Hangzhou, China
| | - Jia Xu
- Eye Center, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,Eye Hospital, Zhejiang University, Hangzhou, China
| | - Xiaoxiao Song
- Department of Endocrinology, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Ke Yao
- Eye Center, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,Eye Hospital, Zhejiang University, Hangzhou, China
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12
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Li S, Zhu J, Su B, Wei H, Chen F, Liu H, Wei J, Yang X, Zhang Q, Xia W, Wu H, He Q, Zhang T. Alteration in Oral Microbiome Among Men Who Have Sex With Men With Acute and Chronic HIV Infection on Antiretroviral Therapy. Front Cell Infect Microbiol 2021; 11:695515. [PMID: 34336719 PMCID: PMC8317457 DOI: 10.3389/fcimb.2021.695515] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 06/24/2021] [Indexed: 12/12/2022] Open
Abstract
Despite the antiretroviral therapy (ART), human immunodeficiency virus (HIV)-related oral disease remains a common problem for people living with HIV (PLWH). Evidence suggests that impairment of immune function in HIV infection might lead to the conversion of commensal bacteria to microorganisms with increased pathogenicity. However, limited information is available about alteration in oral microbiome in PLWH on ART. We performed a longitudinal comparative study on men who have sex with men (MSM) with acute HIV infection (n=15), MSM with chronic HIV infection (n=15), and HIV-uninfected MSM controls (n=15). Throat swabs were collected when these subjects were recruited (W0) and 12 weeks after ART treatment (W12) from the patients. Genomic DNAs were extracted and 16S rRNA gene sequencing was performed. Microbiome diversity was significantly decreased in patients with acute and chronic HIV infections compared with those in controls at the sampling time of W0 and the significant difference remained at W12. An increased abundance of unidentified Prevotellaceae was found in patients with acute and chronic HIV infections. Moreover, increased abundances of Prevotella in subjects with acute HIV infection and Streptococcus in subjects with chronic HIV infection were observed. In contrast, greater abundance in Lactobacillus, Rothia, Lautropia, and Bacteroides was found in controls. After effective ART, Bradyrhizobium was enriched in both acute and chronic HIV infections, whereas in controls, Lactobacillus, Rothia, Clostridia, Actinobacteria, and Ruminococcaceae were enriched. In addition, we found that lower CD4+ T-cell counts (<200 cells/mm3) were associated with lower relative abundances of Haemophilus, Actinomyces, unidentified Ruminococcaceae, and Rothia. This study has shown alteration in oral microbiome resulting from HIV infection and ART. The results obtained warrant further studies in a large number of subjects with different ethnics. It might contribute to improved oral health in HIV-infected individuals.
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Affiliation(s)
- Shuang Li
- Beijing Key Laboratory for HIV/AIDS Research, Center for Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Junping Zhu
- Department of Medical Microbiology, Capital Medical University, Beijing, China
| | - Bin Su
- Beijing Key Laboratory for HIV/AIDS Research, Center for Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Huanhuan Wei
- Department of Medical Microbiology, Capital Medical University, Beijing, China
| | - Fei Chen
- Department of Medical Microbiology, Capital Medical University, Beijing, China
| | - Hongshan Liu
- Department of Medical Microbiology, Capital Medical University, Beijing, China
| | - Jiaqi Wei
- Beijing Key Laboratory for HIV/AIDS Research, Center for Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Xiaodong Yang
- Beijing Key Laboratory for HIV/AIDS Research, Center for Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Qiuyue Zhang
- Beijing Key Laboratory for HIV/AIDS Research, Center for Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Wei Xia
- Beijing Key Laboratory for HIV/AIDS Research, Center for Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Hao Wu
- Beijing Key Laboratory for HIV/AIDS Research, Center for Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Qiushui He
- Department of Medical Microbiology, Capital Medical University, Beijing, China.,Institute of Biomedicine, Research Center for Infections and Immunity, University of Turku, Turku, Finland
| | - Tong Zhang
- Beijing Key Laboratory for HIV/AIDS Research, Center for Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing, China
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13
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Xie Y, Sun J, Wei L, Jiang H, Hu C, Yang J, Huang Y, Ruan B, Zhu B. Altered gut microbiota correlate with different immune responses to HAART in HIV-infected individuals. BMC Microbiol 2021; 21:11. [PMID: 33407128 PMCID: PMC7789785 DOI: 10.1186/s12866-020-02074-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 12/16/2020] [Indexed: 02/08/2023] Open
Abstract
Background Although gut microbiota dysbiosis has been reported in HIV infected individuals recently, the relationship between the gut microbiota and immune activation in patients with different immune responses to highly active antiretroviral therapy (HAART) is still not well understood. Gut microbiota and immune activation were studied in 36 non-HIV-infected subjects (healthy controls) and 58 HIV-infected individuals, including 28 immunological responders (IR) and 30 immunological non-responders (INR) (≥500 and < 200 CD4+ T-cell counts/μl after 2 years of HIV-1 viral suppression respectively) without comorbidities. Results Metagenome sequencing revealed that HIV-infected immunological responders and immunological non-responders could not recover completely from the gut microbiota dysbiosis. At a 97% similarity level, the relative abundances of Fusobacterium, Ruminococcus gnavus and Megamonas were greater, whereas Faecalibacterium, Alistipes, Bifidobacterium, Eubacterium rectale and Roseburia were more depleted in the IR and INR groups than those in the healthy controls. Ruminococcaceae and Alistipes were positively correlated with nadir and current CD4+ T-cell counts, but negatively correlated with CD8 + CD57+ T-cell counts. Inflammation markers and translocation biomarkers (LPS) levels were positively correlated with the abundances of genera Ruminococcus and Fusobacterium but were negatively correlated with the genus Faecalibacterium. The relative abundances of Escherichia-Shigella and Blautia were significantly higher in the IR than those in the INR group. Escherichia-Shigella were negatively correlated with the CD4/CD8 ratio but positively correlated with the amount of CD8 + CD57+ T-cells. Roseburia and Blautia were negatively associated with nadir CD4+ T-cell and positively associated with CD8 + CD57+ T-cell counts. Conclusions Gut microbiota dysbiosis may be one of the factors contributing to different immune responses and treatment outcomes to HAART. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-020-02074-1.
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Affiliation(s)
- Yirui Xie
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The Department of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, 79, QingChun Road, Hangzhou, 310003, China.
| | - Jia Sun
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The Department of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, 79, QingChun Road, Hangzhou, 310003, China.,Ningbo Medical Center Lihuili Hospital, Ningbo, 315000, China
| | - Li Wei
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The Department of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, 79, QingChun Road, Hangzhou, 310003, China
| | - Haiyin Jiang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The Department of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, 79, QingChun Road, Hangzhou, 310003, China
| | - Caiqin Hu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The Department of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, 79, QingChun Road, Hangzhou, 310003, China
| | - Jiezuan Yang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The Department of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, 79, QingChun Road, Hangzhou, 310003, China
| | - Ying Huang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The Department of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, 79, QingChun Road, Hangzhou, 310003, China
| | - Bing Ruan
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The Department of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, 79, QingChun Road, Hangzhou, 310003, China
| | - Biao Zhu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The Department of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, 79, QingChun Road, Hangzhou, 310003, China.
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14
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Newsome RC, Gauthier J, Hernandez MC, Abraham GE, Robinson TO, Williams HB, Sloan M, Owings A, Laird H, Christian T, Pride Y, Wilson KJ, Hasan M, Parker A, Senitko M, Glover SC, Gharaibeh RZ, Jobin C. The gut microbiome of COVID-19 recovered patients returns to uninfected status in a minority-dominated United States cohort. Gut Microbes 2021; 13:1-15. [PMID: 34100340 PMCID: PMC8205023 DOI: 10.1080/19490976.2021.1926840] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 04/06/2021] [Accepted: 04/22/2021] [Indexed: 02/04/2023] Open
Abstract
To investigate the relationship between intestinal microbiota and SARS-CoV-2-mediated pathogenicity in a United States, majority African American cohort. We prospectively collected fecal samples from 50 SARS-CoV-2 infected patients, 9 SARS-CoV-2 recovered patients, and 34 uninfected subjects seen by the hospital with unrelated respiratory medical conditions (controls). 16S rRNA sequencing and qPCR analysis was performed on fecal DNA/RNA. The fecal microbial composition was found to be significantly different between SARS-CoV-2 patients and controls (PERMANOVA FDR-P = .004), independent of antibiotic exposure. Peptoniphilus, Corynebacterium and Campylobacter were identified as the three most significantly enriched genera in COVID-19 patients compared to controls. Actively infected patients were also found to have a different gut microbiota than recovered patients (PERMANOVA FDR-P = .003), and the most enriched genus in infected patients was Campylobacter, with Agathobacter and Faecalibacterium being enriched in the recovered patients. No difference in microbial community structure between recovered patients and uninfected controls was observed, nor a difference in alpha diversity between the three groups. 24 of the 50 COVID-19 patients (48%) tested positive via RT-qPCR for fecal SARS-CoV-2 RNA. A significant difference in gut microbial composition between SARS-CoV-2 positive and negative samples was observed, with Klebsiella and Agathobacter being enriched in the positive cohort. No significant associations between microbiome composition and disease severity was found. The intestinal microbiota is sensitive to the presence of SARS-CoV-2, with increased relative abundance of genera (Campylobacter, Klebsiella) associated with gastrointestinal (GI) disease. Further studies are needed to investigate the functional impact of SARS-CoV-2 on GI health.
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Affiliation(s)
- Rachel C. Newsome
- Department of Medicine, University of Florida College of Medicine, Gainesville, FL, USA
| | - Josee Gauthier
- Department of Medicine, University of Florida College of Medicine, Gainesville, FL, USA
| | - Maria C. Hernandez
- Department of Medicine, University of Florida College of Medicine, Gainesville, FL, USA
| | - George E. Abraham
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS, USA
| | - Tanya O. Robinson
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS, USA
| | - Haley B. Williams
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS, USA
| | - Meredith Sloan
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS, USA
| | - Anna Owings
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS, USA
| | - Hannah Laird
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS, USA
| | - Taylor Christian
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS, USA
| | - Yilianys Pride
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS, USA
| | - Kenneth J. Wilson
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS, USA
| | - Mohammad Hasan
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS, USA
| | - Adam Parker
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS, USA
| | - Michal Senitko
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS, USA
| | - Sarah C. Glover
- Department of Medicine, University of Florida College of Medicine, Gainesville, FL, USA
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS, USA
| | - Raad Z. Gharaibeh
- Department of Medicine, University of Florida College of Medicine, Gainesville, FL, USA
| | - Christian Jobin
- Department of Medicine, University of Florida College of Medicine, Gainesville, FL, USA
- Department of Infectious Diseases and Immunology, University of Florida College of Veterinary Medicine, Gainesville, FL, USA
- Department of Anatomy and Cell Biology, University of Florida College of Medicine, Gainesville, FL, USA
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15
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Li J, Chang S, Guo H, Ji Y, Jiang H, Ruan L, Du M. Altered Salivary Microbiome in the Early Stage of HIV Infections among Young Chinese Men Who Have Sex with Men (MSM). Pathogens 2020; 9:pathogens9110960. [PMID: 33228000 PMCID: PMC7699166 DOI: 10.3390/pathogens9110960] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 11/07/2020] [Accepted: 11/17/2020] [Indexed: 02/06/2023] Open
Abstract
Human immunodeficiency virus (HIV) infections are spiking in Chinese young men who have sex with men (MSM). To explore alterations in the salivary microbiome and its correlation with demographic characteristics, CD4+ T cell count and viral load (VL) in HIV infections, samples of unstimulated whole saliva were analyzed by 16S rRNA gene sequencing using the Illumina MiSeq platform in 20 HIV newly infected patients before the initiation of antiretroviral therapy (ART) and at three and six months after, and in 20 age- and gender-paired healthy Chinese people. The results showed that the alpha diversity of salivary microbiota in HIV infections did not show differences from the healthy controls, but was reduced after six months under ART treatment. Comparative analysis revealed that Streptococcus was enriched in HIV-infected individuals, while Neisseria was enriched in the healthy control group. After effective ART, the salivary microbiota composition was not completely restored, although some microbiota recovered. In addition, we found Provotella_7, Neisseria and Haemophilus were correlated negatively with CD4+ T cell count, while Neisseria was correlated positively with VL. We conclude that HIV infections experience a dysbiosis of the salivary microbiome. The salivary microbiome test could be a substitute for the blood tests in the diagnosis and prognosis of diseases.
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Affiliation(s)
- Jin Li
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan 430079, China; (J.L.); (S.C.); (H.G.); (Y.J.); (H.J.)
| | - Shenghua Chang
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan 430079, China; (J.L.); (S.C.); (H.G.); (Y.J.); (H.J.)
| | - Haiying Guo
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan 430079, China; (J.L.); (S.C.); (H.G.); (Y.J.); (H.J.)
| | - Yaoting Ji
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan 430079, China; (J.L.); (S.C.); (H.G.); (Y.J.); (H.J.)
| | - Han Jiang
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan 430079, China; (J.L.); (S.C.); (H.G.); (Y.J.); (H.J.)
| | - Lianguo Ruan
- Department of Infectious Diseases, Jin Yin-tan Hospital, Wuhan 430023, China
- Correspondence: (L.R.); (M.D.)
| | - Minquan Du
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan 430079, China; (J.L.); (S.C.); (H.G.); (Y.J.); (H.J.)
- Correspondence: (L.R.); (M.D.)
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16
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Jasinska AJ, Dong TS, Lagishetty V, Katzka W, Jacobs JP, Schmitt CA, Cramer JD, Ma D, Coetzer WG, Grobler JP, Turner TR, Freimer N, Pandrea I, Apetrei C. Shifts in microbial diversity, composition, and functionality in the gut and genital microbiome during a natural SIV infection in vervet monkeys. MICROBIOME 2020; 8:154. [PMID: 33158452 PMCID: PMC7648414 DOI: 10.1186/s40168-020-00928-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 10/06/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND The microbiota plays an important role in HIV pathogenesis in humans. Microbiota can impact health through several pathways such as increasing inflammation in the gut, metabolites of bacterial origin, and microbial translocation from the gut to the periphery which contributes to systemic chronic inflammation and immune activation and the development of AIDS. Unlike HIV-infected humans, SIV-infected vervet monkeys do not experience gut dysfunction, microbial translocation, and chronic immune activation and do not progress to immunodeficiency. Here, we provide the first reported characterization of the microbial ecosystems of the gut and genital tract in a natural nonprogressing host of SIV, wild vervet monkeys from South Africa. RESULTS We characterized fecal, rectal, vaginal, and penile microbiomes in vervets from populations heavily infected with SIV from diverse locations across South Africa. Geographic site, age, and sex affected the vervet microbiome across different body sites. Fecal and vaginal microbiome showed marked stratification with three enterotypes in fecal samples and two vagitypes, which were predicted functionally distinct within each body site. External bioclimatic factors, biome type, and environmental temperature influenced microbiomes locally associated with vaginal and rectal mucosa. Several fecal microbial taxa were linked to plasma levels of immune molecules, for example, MIG was positively correlated with Lactobacillus and Escherichia/Shigella and Helicobacter, and IL-10 was negatively associated with Erysipelotrichaceae, Anaerostipes, Prevotella, and Anaerovibrio, and positively correlated with Bacteroidetes and Succinivibrio. During the chronic phase of infection, we observed a significant increase in gut microbial diversity, alterations in community composition (including a decrease in Proteobacteria/Succinivibrio in the gut) and functionality (including a decrease in genes involved in bacterial invasion of epithelial cells in the gut), and partial reversibility of acute infection-related shifts in microbial abundance observed in the fecal microbiome. As part of our study, we also developed an accurate predictor of SIV infection using fecal samples. CONCLUSIONS The vervets infected with SIV and humans infected with HIV differ in microbial responses to infection. These responses to SIV infection may aid in preventing microbial translocation and subsequent disease progression in vervets, and may represent host microbiome adaptations to the virus. Video Abstract.
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Affiliation(s)
- Anna J Jasinska
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA, USA.
- Department of Molecular Genetics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland.
- Eye on Primates, Los Angeles, CA, USA.
| | - Tien S Dong
- The Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Venu Lagishetty
- The Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - William Katzka
- The Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Jonathan P Jacobs
- The Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
- Division of Gastroenterology, Hepatology and Parenteral Nutrition, VA Greater Los Angeles Healthcare System, Los Angeles, CA, USA
- UCLA Microbiome Center, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | | | - Jennifer Danzy Cramer
- Department of Sociology, Anthropology, and General Studies, American Public University System, Charles Town, WV, USA
| | - Dongzhu Ma
- Department of Orthopedic Surgery, University of Pittsburgh, Pittsburgh, PA, USA
| | - Willem G Coetzer
- Department of Genetics, University of the Free State, Bloemfontein, South Africa
| | - J Paul Grobler
- Department of Genetics, University of the Free State, Bloemfontein, South Africa
| | - Trudy R Turner
- Department of Genetics, University of the Free State, Bloemfontein, South Africa
- Department of Anthropology, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Nelson Freimer
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA, USA
| | - Ivona Pandrea
- Department of Pathology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Cristian Apetrei
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
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17
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Siddiqui S, Bao D, Doyle-Meyers L, Dufour J, Wu Y, Liu YZ, Ling B. Alterations of the gut bacterial microbiota in rhesus macaques with SIV infection and on short- or long-term antiretroviral therapy. Sci Rep 2020; 10:19056. [PMID: 33149234 PMCID: PMC7642356 DOI: 10.1038/s41598-020-76145-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 10/16/2020] [Indexed: 12/16/2022] Open
Abstract
Gut dysbiosis and microbial translocation are associated with chronic systemic immune activation and inflammation in HIV-1 infection. However, the extent of restoration of gut microbiota in HIV-1 patients with short or long-term antiretroviral therapy (ART) is unclear. To understand the impact of ART on the gut microbiota, we used the rhesus macaque model of SIV infection to characterize and compare the gut microbial community upon SIV infection and during ART. We observed altered taxonomic compositions of gut microbiota communities upon SIV infection and at different time points of ART. SIV-infected animals showed decreased diversity of gut microbiome composition, while the ART group appeared to recover towards the diversity level of the healthy control. Animals undergoing ART for various lengths of time were observed to have differential gut bacterial abundance across different time points. In addition, increased blood lipopolysaccharide (LPS) levels during SIV infection were reduced to near normal upon ART, indicating that microbial translocation and immune activation can be improved during therapy. In conclusion, while short ART may be related to transient increase of certain pathogenic bacterial microbiome, ART may promote microbiome diversity compromised by SIV infection, improve the gut microbiota towards the healthy compositions and alleviate immune activation.
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Affiliation(s)
- Summer Siddiqui
- Tulane National Primate Research Center, Covington, LA, 70433, USA
| | - Duran Bao
- Department of Biostatistics and Data Science, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, 70112, USA
| | | | - Jason Dufour
- Tulane National Primate Research Center, Covington, LA, 70433, USA
| | - Yuntao Wu
- Department of Molecular and Microbiology, National Center for Biodefense and Infectious Diseases, George Mason University, Manassas, VA, 20110, USA
| | - Yao-Zhong Liu
- Department of Biostatistics and Data Science, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, 70112, USA
| | - Binhua Ling
- Tulane National Primate Research Center, Covington, LA, 70433, USA. .,Tulane Center for Aging, School of Medicine, Tulane University, New Orleans, LA, 70112, USA. .,Department of Microbiology and Immunology, School of Medicine, Tulane University, New Orleans, LA, 70112, USA. .,Texas Biomedical Research Institute, 8715 W Military Dr, San Antonio, TX, 78227, USA.
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18
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Zhou J, Zhang Y, Cui P, Luo L, Chen H, Liang B, Jiang J, Ning C, Tian L, Zhong X, Ye L, Liang H, Huang J. Gut Microbiome Changes Associated With HIV Infection and Sexual Orientation. Front Cell Infect Microbiol 2020; 10:434. [PMID: 33102244 PMCID: PMC7546801 DOI: 10.3389/fcimb.2020.00434] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 07/15/2020] [Indexed: 12/20/2022] Open
Abstract
Background: Many studies have explored changes in the gut microbiome associated with HIV infection, but the consistent pattern of changes has not been clarified. Men who have sex with men (MSM) are very likely to be an independent influencing factor of the gut microbiome, but relevant research is still lacking. Methods: We conducted a meta-analysis by screening 12 published studies of 16S rRNA gene amplicon sequencing of gut microbiomes related to HIV/AIDS (six of these studies contain data that is relevant and available to MSM) from NCBI and EBI databases. The analysis of gut microbiomes related to HIV infection status and MSM status included 1,288 samples (HIV-positive (HIV+) individuals, n = 744; HIV-negative (HIV–) individuals, n = 544) and 632 samples (MSM, n = 328; non-MSM, n = 304), respectively. The alpha diversity indexes, beta diversity indexes, differentially enriched genera, differentially enriched species, and differentially enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) functional pathways related to gut microbiomes were calculated. Finally, the overall trend of the above indicators was evaluated. Results: Our results indicate that HIV+ status is associated with decreased alpha diversity of the gut microbiome. MSM status is an important factor that affects the study of HIV-related gut microbiomes; that is, MSM are associated with alpha diversity changes in the gut microbiome regardless of HIV infection, and the changes in the gut microbiome composition of MSM are more significant than those of HIV+ individuals. A consistent change in Bacteroides caccae, Bacteroides ovatus, Bacteroides uniformis, and Prevotella stercorea was found in HIV+ individuals and MSM. The differential expression of the gut microbiome may be accompanied by changes in functional pathways of carbohydrate metabolism, amino acid metabolism, and lipid Metabolism. Conclusions: This study shows that the changes in the gut microbiome are related to HIV and MSM status. Importantly, MSM status may have a far greater impact on the gut microbiome than HIV status.
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Affiliation(s)
- Jie Zhou
- Guangxi Key Laboratory of AIDS Prevention and Treatment, Guangxi Universities Key Laboratory of Prevention and Control of Highly Prevalent Disease, Guangxi Medical University, Nanning, China.,School of Public Health, Guangxi Medical University, Nanning, China
| | - Yu Zhang
- Guangxi Key Laboratory of AIDS Prevention and Treatment, Guangxi Universities Key Laboratory of Prevention and Control of Highly Prevalent Disease, Guangxi Medical University, Nanning, China.,School of Public Health, Guangxi Medical University, Nanning, China
| | - Ping Cui
- Guangxi Key Laboratory of AIDS Prevention and Treatment, Guangxi Universities Key Laboratory of Prevention and Control of Highly Prevalent Disease, Guangxi Medical University, Nanning, China.,Guangxi Collaborative Innovation Center for Biomedicine, Life Science Institute, Guangxi Medical University, Nanning, China
| | - Lijia Luo
- Guangxi Key Laboratory of AIDS Prevention and Treatment, Guangxi Universities Key Laboratory of Prevention and Control of Highly Prevalent Disease, Guangxi Medical University, Nanning, China.,School of Public Health, Guangxi Medical University, Nanning, China
| | - Hui Chen
- Guangxi Key Laboratory of AIDS Prevention and Treatment, Guangxi Universities Key Laboratory of Prevention and Control of Highly Prevalent Disease, Guangxi Medical University, Nanning, China.,The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Bingyu Liang
- Guangxi Key Laboratory of AIDS Prevention and Treatment, Guangxi Universities Key Laboratory of Prevention and Control of Highly Prevalent Disease, Guangxi Medical University, Nanning, China.,School of Public Health, Guangxi Medical University, Nanning, China
| | - Junjun Jiang
- Guangxi Key Laboratory of AIDS Prevention and Treatment, Guangxi Universities Key Laboratory of Prevention and Control of Highly Prevalent Disease, Guangxi Medical University, Nanning, China.,School of Public Health, Guangxi Medical University, Nanning, China
| | - Chuanyi Ning
- Guangxi Key Laboratory of AIDS Prevention and Treatment, Guangxi Universities Key Laboratory of Prevention and Control of Highly Prevalent Disease, Guangxi Medical University, Nanning, China.,Guangxi Collaborative Innovation Center for Biomedicine, Life Science Institute, Guangxi Medical University, Nanning, China
| | - Li Tian
- Guangxi Key Laboratory of AIDS Prevention and Treatment, Guangxi Universities Key Laboratory of Prevention and Control of Highly Prevalent Disease, Guangxi Medical University, Nanning, China.,The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Xiaodan Zhong
- Guangxi Key Laboratory of AIDS Prevention and Treatment, Guangxi Universities Key Laboratory of Prevention and Control of Highly Prevalent Disease, Guangxi Medical University, Nanning, China.,The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Li Ye
- Guangxi Key Laboratory of AIDS Prevention and Treatment, Guangxi Universities Key Laboratory of Prevention and Control of Highly Prevalent Disease, Guangxi Medical University, Nanning, China.,School of Public Health, Guangxi Medical University, Nanning, China.,Guangxi Collaborative Innovation Center for Biomedicine, Life Science Institute, Guangxi Medical University, Nanning, China
| | - Hao Liang
- Guangxi Key Laboratory of AIDS Prevention and Treatment, Guangxi Universities Key Laboratory of Prevention and Control of Highly Prevalent Disease, Guangxi Medical University, Nanning, China.,School of Public Health, Guangxi Medical University, Nanning, China.,Guangxi Collaborative Innovation Center for Biomedicine, Life Science Institute, Guangxi Medical University, Nanning, China
| | - Jiegang Huang
- Guangxi Key Laboratory of AIDS Prevention and Treatment, Guangxi Universities Key Laboratory of Prevention and Control of Highly Prevalent Disease, Guangxi Medical University, Nanning, China.,School of Public Health, Guangxi Medical University, Nanning, China
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19
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De Filippis F, Pasolli E, Ercolini D. The food-gut axis: lactic acid bacteria and their link to food, the gut microbiome and human health. FEMS Microbiol Rev 2020; 44:454-489. [PMID: 32556166 PMCID: PMC7391071 DOI: 10.1093/femsre/fuaa015] [Citation(s) in RCA: 104] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 05/20/2020] [Indexed: 12/18/2022] Open
Abstract
Lactic acid bacteria (LAB) are present in foods, the environment and the animal gut, although fermented foods (FFs) are recognized as the primary niche of LAB activity. Several LAB strains have been studied for their health-promoting properties and are employed as probiotics. FFs are recognized for their potential beneficial effects, which we review in this article. They are also an important source of LAB, which are ingested daily upon FF consumption. In this review, we describe the diversity of LAB and their occurrence in food as well as the gut microbiome. We discuss the opportunities to study LAB diversity and functional properties by considering the availability of both genomic and metagenomic data in public repositories, as well as the different latest computational tools for data analysis. In addition, we discuss the role of LAB as potential probiotics by reporting the prevalence of key genomic features in public genomes and by surveying the outcomes of LAB use in clinical trials involving human subjects. Finally, we highlight the need for further studies aimed at improving our knowledge of the link between LAB-fermented foods and the human gut from the perspective of health promotion.
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Affiliation(s)
- Francesca De Filippis
- Department of Agricultural Sciences, University of Naples Federico II, via Università, 100, 80055, Portici (NA)Italy
- Task Force on Microbiome Studies, Corso Umberto I, 40, 80100, Napoli, Italy
| | - Edoardo Pasolli
- Department of Agricultural Sciences, University of Naples Federico II, via Università, 100, 80055, Portici (NA)Italy
- Task Force on Microbiome Studies, Corso Umberto I, 40, 80100, Napoli, Italy
| | - Danilo Ercolini
- Department of Agricultural Sciences, University of Naples Federico II, via Università, 100, 80055, Portici (NA)Italy
- Task Force on Microbiome Studies, Corso Umberto I, 40, 80100, Napoli, Italy
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20
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Alizadehmohajer N, Shojaeifar S, Nedaeinia R, Esparvarinha M, Mohammadi F, Ferns GA, Ghayour-Mobarhan M, Manian M, Balouchi A. Association between the microbiota and women's cancers - Cause or consequences? Biomed Pharmacother 2020; 127:110203. [PMID: 32559847 DOI: 10.1016/j.biopha.2020.110203] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 04/25/2020] [Accepted: 04/28/2020] [Indexed: 02/07/2023] Open
Abstract
Breast, ovarian and uterine cancers are the most common neoplasms among women. Several mechanisms may be involved in oncogenesis and these include environmental and genetic factors. Bacteria may affect the development of some cancers, with bacterial components, their products and metabolites interacting with susceptible tissues. Commensalism and dysbiosis are important potential mechanisms involved in oncogenesis, and an effective strategy for diagnosis and treatment is required. The purpose of this review was to analyze the complex associations between these cancers in women, and the microbiota, specifically bacterial microbes. However, several cancers have an increased prevalence among individuals with HIV and HPV so the relationship between viral infections and malignancies in women is also referred to. We described how different phylum of bacteria, particularly in the gut, mammary tissue and vaginal microbiome may be involved in carcinogenesis; and we discuss the potential pathways involved: (I), that lead to cell proliferation, (II), immune system perturbation, (III), cell metabolic changes (e.g., hormonal factors), and (IV), DNA damage. Studies investigating the differences between the composition of the bacterial microbiota of healthy women compared to that present in various conditions, and the clinical trials are summarized for the few studies that have addressed the microbiota and related conditions, are also reviewed.
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Affiliation(s)
- Negin Alizadehmohajer
- Department of Medical Laboratory Science, Faculty of Medicine, Kermanshah Branch, Islamic Azad University, Kermanshah, Iran
| | - Samaneh Shojaeifar
- Department of Midwifery, Faculty of Nursing and Midwifery, Arak University of Medical Sciences, Arak, Iran
| | - Reza Nedaeinia
- Pediatric Inherited Diseases Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mojgan Esparvarinha
- Department of Immunology, School of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Forogh Mohammadi
- Department of Veterinary, Agriculture Faculty, Kermanshah Branch, Islamic Azad University, Kermanshah, Iran
| | - Gordon A Ferns
- Brighton and Sussex Medical School, Division of Medical Education, Falmer, Brighton, Sussex BN1 9PH, UK
| | - Majid Ghayour-Mobarhan
- Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mostafa Manian
- Department of Medical Laboratory Science, Faculty of Medicine, Kermanshah Branch, Islamic Azad University, Kermanshah, Iran; Department of Immunology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran.
| | - Adele Balouchi
- Department of Biology, Payame Noor University, P.O. Box 19395-3697, Tehran, Iran.
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21
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Abstract
PURPOSE OF REVIEW Aging and HIV share features of intestinal damage and alterations in the communities of enteric bacteria, termed dysbiosis. The purpose of this review is to highlight the various features of the gut microbiome in aging and in people with HIV (PWH) and to discuss how aging and HIV converge to impact the gut microbiome. The term microbiome reflects the combined genetic material of micro-organisms present including bacteria, viruses, bacteriophages, and fungi. To date, the majority of studies investigating the impact of aging and HIV on the gut microbiome have focused on bacteria, and therefore, for the purposes of this review, the term 'microbiome' is used to reflect enteric bacterial communities. RECENT FINDINGS Aging is associated with alterations in the gut bacterial microbiome. Although changes vary by the age of the population, lifestyle (diet, physical activity) and geographic location, the age-associated dysbiosis is typically characterized by an increase in facultative anaerobes with inflammatory properties and a decrease in obligate anaerobes that play critical roles in maintaining intestinal homeostasis and in regulating host immunity. PWH also have dysbiotic gut microbiomes, many features of which reflect those observed in elderly persons. In one study, the age effect on the gut microbiome differed based on HIV serostatus in older adults. SUMMARY HIV and age may interact to shape the gut microbiome. Future studies should investigate relationships between the gut microbiome and age-associated comorbidities in older PWH populations. Identifying these links will provide new avenues for treatments and interventions to improve the healthspan and lifespan of older PWH.
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22
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Luján JA, Rugeles MT, Taborda NA. Contribution of the Microbiota to Intestinal Homeostasis and its Role in the Pathogenesis of HIV-1 Infection. Curr HIV Res 2020; 17:13-25. [PMID: 30854974 DOI: 10.2174/1570162x17666190311114808] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 02/25/2019] [Accepted: 03/06/2019] [Indexed: 12/18/2022]
Abstract
During HIV infection, massive destruction of CD4+ T cells ensues, preferentially depleting the Th17 subset at the gut-associated lymphoid tissue (GALT), leading to a loss of mucosal integrity and an increase in cell permeability. This process favors microbial translocation between the intestinal lumen and the circulatory system, contributing to persistent immune activation and chronic inflammation characteristic of HIV infection. Thus, the gut microbiota plays an integral role in maintaining the structure and function of the mucosal barrier, a critical factor for immune homeostasis. However, in the context of HIV infection, changes in the gut microbiota have been reported and have been linked to disease progression. Here, we review evidence for the role of the gut microbiota in intestinal homeostasis, its contribution to HIV pathogenesis, as well as its use in the development of therapeutic strategies.
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Affiliation(s)
- Jorge A Luján
- Grupo Inmunovirologia, Facultad de Medicina. Universidad de Antioquia, Medellin, Colombia
| | - Maria T Rugeles
- Grupo Inmunovirologia, Facultad de Medicina. Universidad de Antioquia, Medellin, Colombia
| | - Natalia A Taborda
- Grupo Inmunovirologia, Facultad de Medicina. Universidad de Antioquia, Medellin, Colombia.,Grupo de Investigaciones Biomédicas, Facultad de Ciencias de la Salud, Corporación Universitaria Remington, Medellín, Colombia
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23
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Williams BB, Green SJ, Bosch RJ, Chan ES, Jacobson JM, Margolis DM, Engen P, Landay AL, Wilson CC. Four Weeks of Treatment With Rifaximin Fails to Significantly Alter Microbial Diversity in Rectal Samples of HIV-Infected Immune Non-Responders (ACTG A5286) Which May be Attributed to Rectal Swab Use. Pathog Immun 2019; 4:235-250. [PMID: 31583331 PMCID: PMC6768152 DOI: 10.20411/pai.v4i2.290] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 08/20/2019] [Indexed: 01/25/2023] Open
Abstract
INTRODUCTION HIV-infected individuals have evidence of intestinal microbial translocation which is associated with immune activation and unfavorable clinical outcomes. Rifaximin, a non-absorbable antibiotic which reduces microbial translocation in other disease states, was shown to have a marginal beneficial effect on microbial translocation, T-cell activation, and inflammation in a multisite randomized trial (ACTG A5286; NCT01466595) of HIV-infected persons with poor immunologic recovery receiving ART. Here, we report analysis of the rectal microbiome changes associated with that trial. METHODS HIV-1-infected individuals receiving ART with CD4-T cell count < 350cells/mm3 and viral suppression were randomized 2:1 to rifaximin or no therapy for 4 weeks. Rectal swabs were collected at baseline (pre-treatment) and at week 4 of rifaximin therapy. Genomic DNA extracted from rectal swab samples was analyzed using high throughput sequencing and quantitative PCR of bacterial 16S ribosomal RNA (rRNA) genes. RESULTS Forty-eight HIV-infected participants (31 received rifaximin, 17 no treatment) were included. There was broad variability in the recovery of bacterial rRNA from the specimens at baseline. No major significant (FDR P < 0.05) effects of rifaximin treatment on alpha- or beta-diversity or individual taxa were observed between or within the treatment arms, with analyses conducted at taxonomic levels from phylum to genus. CONCLUSIONS Rifaximin did not meaningfully alter the diversity or composition of the rectal microbiome of HIV-infected individuals after 4 weeks of therapy, although rectal swab specimens varied widely in their microbial load.
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Affiliation(s)
- Brett B. Williams
- Division of Infectious Disease; Rush University Medical Center; Chicago, Illinois
| | - Stefan J. Green
- Sequencing Core; University of Illinois at Chicago; Chicago, Illinois
| | - Ronald J. Bosch
- Center for Biostatistics in AIDS Research; Harvard School of Public Health; Boston, Massachusetts
| | - Ellen S. Chan
- Center for Biostatistics in AIDS Research; Harvard School of Public Health; Boston, Massachusetts
| | - Jeffrey M. Jacobson
- Division of Infectious Diseases and HIV; Drexel University; Philadelphia, Pennsylvania
| | - David M. Margolis
- Department of Medicine; University of North Carolina; Chapel Hill, North Carolina
| | - Phillip Engen
- Division of Gastroenterology, Hepatology and Nutrition; Department of Medicine; Rush University Medical Center; Chicago, Illinois
| | - Alan L. Landay
- Department of Immunology and Microbiology; Rush University Medical Center; Chicago, Illinois
| | - Cara C. Wilson
- Department of Medicine; University of Colorado at Denver; Aurora, Colorado
| | - A5286 protocol team
- Division of Infectious Disease; Rush University Medical Center; Chicago, Illinois
- Sequencing Core; University of Illinois at Chicago; Chicago, Illinois
- Center for Biostatistics in AIDS Research; Harvard School of Public Health; Boston, Massachusetts
- Division of Infectious Diseases and HIV; Drexel University; Philadelphia, Pennsylvania
- Department of Medicine; University of North Carolina; Chapel Hill, North Carolina
- Division of Gastroenterology, Hepatology and Nutrition; Department of Medicine; Rush University Medical Center; Chicago, Illinois
- Department of Immunology and Microbiology; Rush University Medical Center; Chicago, Illinois
- Department of Medicine; University of Colorado at Denver; Aurora, Colorado
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24
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The effect of pyridostigmine on small intestinal bacterial overgrowth (SIBO) and plasma inflammatory biomarkers in HIV-associated autonomic neuropathies. J Neurovirol 2019; 25:551-559. [PMID: 31098925 DOI: 10.1007/s13365-019-00756-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Indexed: 01/08/2023]
Abstract
Small intestinal bacterial overgrowth (SIBO) is common among patients with HIV-associated autonomic neuropathies (HIV-AN) and may be associated with increased bacterial translocation and elevated plasma inflammatory biomarkers. Pyridostigmine is an acetylcholinesterase inhibitor which has been used to augment autonomic signaling. We sought preliminary evidence as to whether pyridostigmine could improve proximal gastrointestinal motility, reduce SIBO, reduce plasma sCD14 (a marker of macrophage activation and indirect measure of translocation), and reduce the inflammatory cytokines IL-6 and TNFα in patients with HIV-AN. Fifteen participants with well-controlled HIV, HIV-AN, and SIBO were treated with 8 weeks of pyridostigmine (30 mg PO TID). Glucose breath testing for SIBO, gastric emptying studies (GES) to assess motility, plasma sCD14, IL-6, and TNFα, and gastrointestinal autonomic symptoms were compared before and after treatment. Thirteen participants (87%) experienced an improvement in SIBO following pyridostigmine treatment; with an average improvement of 50% (p = 0.016). There was no change in gastrointestinal motility; however, only two participants met GES criteria for gastroparesis at baseline. TNFα and sCD14 levels declined by 12% (p = 0.004) and 19% (p = 0.015), respectively; there was no significant change in IL-6 or gastrointestinal symptoms. Pyridostigmine may ameliorate SIBO and reduce levels of sCD14 and TNFα in patients with HIV-AN. Larger placebo-controlled studies are needed to definitively delineate how HIV-AN affects gastrointestinal motility, SIBO, and systemic inflammation in HIV, and whether treatment improves clinical outcomes.
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25
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Rocafort M, Noguera-Julian M, Rivera J, Pastor L, Guillén Y, Langhorst J, Parera M, Mandomando I, Carrillo J, Urrea V, Rodríguez C, Casadellà M, Calle ML, Clotet B, Blanco J, Naniche D, Paredes R. Evolution of the gut microbiome following acute HIV-1 infection. MICROBIOME 2019; 7:73. [PMID: 31078141 PMCID: PMC6511141 DOI: 10.1186/s40168-019-0687-5] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 04/22/2019] [Indexed: 05/12/2023]
Abstract
BACKGROUND In rhesus macaques, simian immunodeficiency virus infection is followed by expansion of enteric viruses but has a limited impact on the gut bacteriome. To understand the longitudinal effects of HIV-1 infection on the human gut microbiota, we prospectively followed 49 Mozambican subjects diagnosed with recent HIV-1 infection (RHI) and 54 HIV-1-negative controls for 9-18 months and compared them with 98 chronically HIV-1-infected subjects treated with antiretrovirals (n = 27) or not (n = 71). RESULTS We show that RHI is followed by increased fecal adenovirus shedding, which persists during chronic HIV-1 infection and does not resolve with ART. Recent HIV-1 infection is also followed by transient non-HIV-specific changes in the gut bacterial richness and composition. Despite early resilience to change, an HIV-1-specific signature in the gut bacteriome-featuring depletion of Akkermansia, Anaerovibrio, Bifidobacterium, and Clostridium-previously associated with chronic inflammation, CD8+ T cell anergy, and metabolic disorders, can be eventually identified in chronically HIV-1-infected subjects. CONCLUSIONS Recent HIV-1 infection is associated with increased fecal shedding of eukaryotic viruses, transient loss of bacterial taxonomic richness, and long-term reductions in microbial gene richness. An HIV-1-associated microbiome signature only becomes evident in chronically HIV-1-infected subjects.
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Affiliation(s)
- Muntsa Rocafort
- IrsiCaixa AIDS Research Institute, Ctra de Canyet s/n, 08916, Badalona, Catalonia, Spain
- Universitat Autònoma de Barcelona, 08193, Bellaterra, Catalonia, Spain
| | - Marc Noguera-Julian
- IrsiCaixa AIDS Research Institute, Ctra de Canyet s/n, 08916, Badalona, Catalonia, Spain
- Universitat Autònoma de Barcelona, 08193, Bellaterra, Catalonia, Spain
- Universitat de Vic-Universitat Central de Catalunya, C. Sagrada Família 7, 08500, Vic, Catalonia, Spain
| | - Javier Rivera
- IrsiCaixa AIDS Research Institute, Ctra de Canyet s/n, 08916, Badalona, Catalonia, Spain
- Universitat de Vic-Universitat Central de Catalunya, C. Sagrada Família 7, 08500, Vic, Catalonia, Spain
| | - Lucía Pastor
- Universitat Autònoma de Barcelona, 08193, Bellaterra, Catalonia, Spain
- ISGlobal, Barcelona Centre for International Health Research (CRESIB), Hospital Clínic-Universitat de Barcelona, 08036, Barcelona, Catalonia, Spain
- Institut Germans Trias i Pujol (IGTP), Hospital Germans Trias i Pujol, Universitat Autonoma de Barcelona, 08916, Badalona, Catalonia, Spain
- Centro de Investigação em Saúde da Manhiça (CISM), 1929, Maputo, Mozambique
| | - Yolanda Guillén
- IrsiCaixa AIDS Research Institute, Ctra de Canyet s/n, 08916, Badalona, Catalonia, Spain
- Universitat Autònoma de Barcelona, 08193, Bellaterra, Catalonia, Spain
| | - Jost Langhorst
- Integrative Gastroenterology, Kliniken Essen-Mitte, University of Duisburg-Essen, Essen, Germany
- Chair for Integrative Medicine and translationale Gastroenterology, Klinikum Bamberg, University of Duisburg-Essen, Essen, Bavaria, Germany
| | - Mariona Parera
- IrsiCaixa AIDS Research Institute, Ctra de Canyet s/n, 08916, Badalona, Catalonia, Spain
- Universitat Autònoma de Barcelona, 08193, Bellaterra, Catalonia, Spain
| | - Inacio Mandomando
- Centro de Investigação em Saúde da Manhiça (CISM), 1929, Maputo, Mozambique
| | - Jorge Carrillo
- IrsiCaixa AIDS Research Institute, Ctra de Canyet s/n, 08916, Badalona, Catalonia, Spain
- Universitat Autònoma de Barcelona, 08193, Bellaterra, Catalonia, Spain
| | - Víctor Urrea
- IrsiCaixa AIDS Research Institute, Ctra de Canyet s/n, 08916, Badalona, Catalonia, Spain
- Universitat Autònoma de Barcelona, 08193, Bellaterra, Catalonia, Spain
| | - Cristina Rodríguez
- IrsiCaixa AIDS Research Institute, Ctra de Canyet s/n, 08916, Badalona, Catalonia, Spain
- Universitat Autònoma de Barcelona, 08193, Bellaterra, Catalonia, Spain
| | - Maria Casadellà
- IrsiCaixa AIDS Research Institute, Ctra de Canyet s/n, 08916, Badalona, Catalonia, Spain
- Universitat Autònoma de Barcelona, 08193, Bellaterra, Catalonia, Spain
| | - Maria Luz Calle
- Universitat de Vic-Universitat Central de Catalunya, C. Sagrada Família 7, 08500, Vic, Catalonia, Spain
| | - Bonaventura Clotet
- IrsiCaixa AIDS Research Institute, Ctra de Canyet s/n, 08916, Badalona, Catalonia, Spain
- Universitat Autònoma de Barcelona, 08193, Bellaterra, Catalonia, Spain
- Universitat de Vic-Universitat Central de Catalunya, C. Sagrada Família 7, 08500, Vic, Catalonia, Spain
- Infectious Diseases Service, Hospital Universitari Germans Trias i Pujol, Ctra de Canyet s/n, 08916, Badalona, Catalonia, Spain
| | - Julià Blanco
- IrsiCaixa AIDS Research Institute, Ctra de Canyet s/n, 08916, Badalona, Catalonia, Spain
- Universitat Autònoma de Barcelona, 08193, Bellaterra, Catalonia, Spain
- Universitat de Vic-Universitat Central de Catalunya, C. Sagrada Família 7, 08500, Vic, Catalonia, Spain
- Institut Germans Trias i Pujol (IGTP), Hospital Germans Trias i Pujol, Universitat Autonoma de Barcelona, 08916, Badalona, Catalonia, Spain
| | - Denise Naniche
- ISGlobal, Barcelona Centre for International Health Research (CRESIB), Hospital Clínic-Universitat de Barcelona, 08036, Barcelona, Catalonia, Spain
- Centro de Investigação em Saúde da Manhiça (CISM), 1929, Maputo, Mozambique
| | - Roger Paredes
- IrsiCaixa AIDS Research Institute, Ctra de Canyet s/n, 08916, Badalona, Catalonia, Spain.
- Universitat Autònoma de Barcelona, 08193, Bellaterra, Catalonia, Spain.
- Universitat de Vic-Universitat Central de Catalunya, C. Sagrada Família 7, 08500, Vic, Catalonia, Spain.
- Infectious Diseases Service, Hospital Universitari Germans Trias i Pujol, Ctra de Canyet s/n, 08916, Badalona, Catalonia, Spain.
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26
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Wang Z, Qi Q. Gut microbial metabolites associated with HIV infection. Future Virol 2019; 14:335-347. [PMID: 31263508 PMCID: PMC6595475 DOI: 10.2217/fvl-2019-0002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 04/25/2019] [Indexed: 02/06/2023]
Abstract
HIV infection has been associated with alterations in gut microbiota and related microbial metabolite production. However, the mechanisms of how these functional microbial metabolites may affect HIV immunopathogenesis and comorbidities, such as cardiovascular disease and other metabolic diseases, remain largely unknown. Here we review the current understanding of gut microbiota and related metabolites in the context of HIV infection. We focus on several bacteria-produced metabolites, including tryptophan catabolites, short-chain fatty acids and trimethylamine-N-oxide (TMAO), and discuss their implications in HIV infection and comorbidities. We also prospect future studies using integrative multiomics approaches to better understand host-microbiota-metabolites interactions in HIV infection, and facilitate integrative medicine utilizing the microbiota in HIV infection.
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Affiliation(s)
- Zheng Wang
- Department of Epidemiology & Population Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Qibin Qi
- Department of Epidemiology & Population Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA
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27
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Hensley-McBain T, Wu MC, Manuzak JA, Cheu RK, Gustin A, Driscoll CB, Zevin AS, Miller CJ, Coronado E, Smith E, Chang J, Gale M, Somsouk M, Burgener AD, Hunt PW, Hope TJ, Collier AC, Klatt NR. Increased mucosal neutrophil survival is associated with altered microbiota in HIV infection. PLoS Pathog 2019; 15:e1007672. [PMID: 30973942 PMCID: PMC6459500 DOI: 10.1371/journal.ppat.1007672] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 03/02/2019] [Indexed: 12/21/2022] Open
Abstract
Gastrointestinal (GI) mucosal dysfunction predicts and likely contributes to non-infectious comorbidities and mortality in HIV infection and persists despite antiretroviral therapy. However, the mechanisms underlying this dysfunction remain incompletely understood. Neutrophils are important for containment of pathogens but can also contribute to tissue damage due to their release of reactive oxygen species and other potentially harmful effector molecules. Here we used a flow cytometry approach to investigate increased neutrophil lifespan as a mechanism for GI neutrophil accumulation in chronic, treated HIV infection and a potential role for gastrointestinal dysbiosis. We report that increased neutrophil survival contributes to neutrophil accumulation in colorectal biopsy tissue, thus implicating neutrophil lifespan as a new therapeutic target for mucosal inflammation in HIV infection. Additionally, we characterized the intestinal microbiome of colorectal biopsies using 16S rRNA sequencing. We found that a reduced Lactobacillus: Prevotella ratio associated with neutrophil survival, suggesting that intestinal bacteria may contribute to GI neutrophil accumulation in treated HIV infection. Finally, we provide evidence that Lactobacillus species uniquely decrease neutrophil survival and neutrophil frequency in vitro, which could have important therapeutic implications for reducing neutrophil-driven inflammation in HIV and other chronic inflammatory conditions.
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Affiliation(s)
- Tiffany Hensley-McBain
- Department of Pharmaceutics, University of Washington, Seattle, WA, United States of America
- Washington National Primate Research Center, Seattle, WA, United States of America
| | - Michael C. Wu
- Biostatistics and Biomathematics Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America
| | - Jennifer A. Manuzak
- Department of Pharmaceutics, University of Washington, Seattle, WA, United States of America
- Washington National Primate Research Center, Seattle, WA, United States of America
- Department of Pediatrics, Miller School of Medicine, University of Miami, Miami, FL, United States of America
| | - Ryan K. Cheu
- Department of Pharmaceutics, University of Washington, Seattle, WA, United States of America
- Washington National Primate Research Center, Seattle, WA, United States of America
- Department of Pediatrics, Miller School of Medicine, University of Miami, Miami, FL, United States of America
| | - Andrew Gustin
- Department of Pharmaceutics, University of Washington, Seattle, WA, United States of America
- Washington National Primate Research Center, Seattle, WA, United States of America
| | - Connor B. Driscoll
- Department of Pharmaceutics, University of Washington, Seattle, WA, United States of America
- Department of Pediatrics, Miller School of Medicine, University of Miami, Miami, FL, United States of America
- Center for Innate Immunity and Immune Disease, Department of Immunology, University of Washington School of Medicine, Seattle, WA, United States of America
| | - Alexander S. Zevin
- Department of Pharmaceutics, University of Washington, Seattle, WA, United States of America
- Washington National Primate Research Center, Seattle, WA, United States of America
| | - Charlene J. Miller
- Department of Pharmaceutics, University of Washington, Seattle, WA, United States of America
- Washington National Primate Research Center, Seattle, WA, United States of America
- Department of Pediatrics, Miller School of Medicine, University of Miami, Miami, FL, United States of America
| | - Ernesto Coronado
- Department of Pharmaceutics, University of Washington, Seattle, WA, United States of America
- Washington National Primate Research Center, Seattle, WA, United States of America
| | - Elise Smith
- Center for Innate Immunity and Immune Disease, Department of Immunology, University of Washington School of Medicine, Seattle, WA, United States of America
| | - Jean Chang
- Center for Innate Immunity and Immune Disease, Department of Immunology, University of Washington School of Medicine, Seattle, WA, United States of America
| | - Michael Gale
- Washington National Primate Research Center, Seattle, WA, United States of America
- Center for Innate Immunity and Immune Disease, Department of Immunology, University of Washington School of Medicine, Seattle, WA, United States of America
| | - Ma Somsouk
- Division of Gastroenterology, University of California, San Francisco, San Francisco, CA, United States of America
| | - Adam D. Burgener
- National HIV and Retrovirology Labs, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
- Departments of Obstetrics & Gynecology and Medical Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
- Unit of Infectious Diseases, Department of Medicine Solna, Center for Molecular Medicine, Karolinska Institute, Stockholm, Sweden
| | - Peter W. Hunt
- Division of Experimental Medicine, University of California, San Francisco, San Francisco, CA, United States of America
| | - Thomas J. Hope
- Department of Cellular and Molecular Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States of America
| | - Ann C. Collier
- Department of Medicine, University of Washington, Seattle, WA, United States of America
| | - Nichole R. Klatt
- Department of Pharmaceutics, University of Washington, Seattle, WA, United States of America
- Washington National Primate Research Center, Seattle, WA, United States of America
- Department of Pediatrics, Miller School of Medicine, University of Miami, Miami, FL, United States of America
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28
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Leung CY, Weitz JS. Not by (Good) Microbes Alone: Towards Immunocommensal Therapies. Trends Microbiol 2019; 27:294-302. [DOI: 10.1016/j.tim.2018.12.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 12/02/2018] [Accepted: 12/13/2018] [Indexed: 12/26/2022]
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29
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Kang Y, Cai Y. Altered Gut Microbiota in HIV Infection: Future Perspective of Fecal Microbiota Transplantation Therapy. AIDS Res Hum Retroviruses 2019; 35:229-235. [PMID: 29877092 DOI: 10.1089/aid.2017.0268] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
HIV infection progressively destroys CD4+ mononuclear cells, leading to profound cellular immune deficiency that manifests as life-threatening opportunistic infections and malignancies (i.e., AIDS). Gut microbiota plays key roles in the modulation of host metabolism and gene expression, maintenance of epithelial integrity, and mediation of inflammatory and immunity. Hence, the normal intestinal microbiota plays a major role in the maintenance of health and disease prevention. In fact, a large number of studies have shown that the alteration of the gut microbiota contributes to the pathogenesis of several diseases, such as inflammatory bowel diseases, irritable bowel syndrome, metabolic diseases, anorexia nervosa, autoimmune diseases, multiple sclerosis, cancer, neuropsychiatric disorders, and cardiovascular diseases. Recently, accumulating evidence has shed light on the association of dysbiosis of gut microbiota with HIV infection. Hence, the modification of gut microbiota may be a potential therapeutic tool. Fecal microbiota transplantation may improve the conditions of patients with HIV infection by manipulating the human intestinal bacteria. However, the relevant research is very limited, and a large amount of scientific research work needs to be done in the near future.
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Affiliation(s)
- Yongbo Kang
- 1 School of Basic Medical Sciences, Shanxi Medical University, Taiyuan, China
- 2 Medical Faculty, Kunming University of Science and Technology, Kunming, China
| | - Yue Cai
- 1 School of Basic Medical Sciences, Shanxi Medical University, Taiyuan, China
- 3 Genetics and Pharmacogenomics Laboratory, Kunming University of Science and Technology, Kunming, China
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30
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Williams B, Weber K, Chlipala G, Evans C, Morack R, French A. HIV Status Does Not Affect Rectal Microbiome Composition, Diversity, or Stability over Time: A Chicago Women's Interagency HIV Study. AIDS Res Hum Retroviruses 2019; 35:260-266. [PMID: 30618262 DOI: 10.1089/aid.2018.0250] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
It remains unclear whether differences in gut microbiota noted between HIV-infected and uninfected individuals are driven by HIV or sexual behavior. We evaluated rectal swab microbiota of HIV-infected and uninfected women with similar demographic, neighborhood, and diet characteristics enrolled in the Chicago Women's Interagency HIV Study (WIHS). DNA was amplified for sequencing of fragments of bacterial small subunit (SSU or 16S) ribosomal RNA (rRNA) genes. HIV-infected and uninfected women did not differ by Shannon diversity index (p = .14), non-metric multidimensional scaling (NMDS) plot of Bray-Curtis indices (p = .488, r = 0.0027), or copy number of individual taxa. Both groups demonstrated marked microbiome stability over time (p = .889).
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Affiliation(s)
- Brett Williams
- Department of Internal Medicine, Division of Infectious Disease, Rush University Medical Center, Chicago, Illinois
- Ruth M. Rothstein Core Center of Cook County, Chicago, Illinois
| | - Kathleen Weber
- Cook County Health and Hospitals System, Chicago, Illinois
| | - George Chlipala
- Center for Research Informatics, Research Resources Center, University of Illinois at Chicago, Chicago, Illinois
| | - Charlesnika Evans
- Department of Preventive Medicine, Northwestern University, Chicago, Illinois
- Center for Healthcare Studies, Northwestern University, Chicago, Illinois
- Department of Veterans Affairs, Center of Innovation for Complex Chronic Healthcare, Hines, Illinois
| | - Ralph Morack
- Cook County Health and Hospitals System, Chicago, Illinois
| | - Audrey French
- Department of Internal Medicine, Division of Infectious Disease, Rush University Medical Center, Chicago, Illinois
- Ruth M. Rothstein Core Center of Cook County, Chicago, Illinois
- Department of Medicine, Stroger Hospital of Cook County, Chicago, Illinois
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31
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Machiavelli A, Duarte RTD, Pires MMDS, Zárate-Bladés CR, Pinto AR. The impact of in utero HIV exposure on gut microbiota, inflammation, and microbial translocation. Gut Microbes 2019; 10:599-614. [PMID: 30657007 PMCID: PMC6748604 DOI: 10.1080/19490976.2018.1560768] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
HIV-exposed but uninfected (HEU) children represent a growing population and show a significantly higher number of infectious diseases, several immune alterations, compromised growth, and increased mortality rates when compared to HIV-unexposed children. Considering the impact that the gut microbiota has on general host homeostasis and immune system development and modulation, we hypothesized that HEU children present altered gut microbiota that is linked to the increased morbidity and the immune system disorders faced by them. Our experiments revealed no differences in beta and alpha diversity of the gut microbiota between HEU and unexposed children or between HIV-infected and uninfected mothers. However, there were differences in the abundance of several taxa from the gut microbiota between HEU and unexposed children and between HIV-infected and uninfected mothers. Functional prediction based on 16S rRNA sequences also indicated differences between HEU and unexposed children and between infected and uninfected mothers. In addition, we detected no differences between HEU and unexposed children in relation to weight, weight-for-age z scores, albumin serum levels, or microbial translocation and inflammation markers. In summary, HIV-infected mothers and their HIV-exposed children present alterations in the abundance of several taxa in the gut microbiome and the predicted functional metagenome when compared to uninfected mothers and unexposed children. Knowledge about the gut microbiome of HEU children in different settings is essential in order to determine better treatments for this susceptible population.
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Affiliation(s)
- Aline Machiavelli
- Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de Santa Catarina, Florianópolis, Brazil
| | - Rubens T. Delgado Duarte
- Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de Santa Catarina, Florianópolis, Brazil
| | - Maria M. de Souza Pires
- Departamento de Pediatria, Universidade Federal de Santa Catarina, Florianópolis, Brazil,Hospital Infantil Joana de Gusmão, Florianópolis, Brazil
| | - Carlos R. Zárate-Bladés
- Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de Santa Catarina, Florianópolis, Brazil
| | - Aguinaldo R. Pinto
- Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de Santa Catarina, Florianópolis, Brazil,CONTACT Aguinaldo R. Pinto Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de Santa Catarina, Florianópolis, SC, Brazil
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32
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Yang L, Hao Y, Hu J, Kelly D, Li H, Brown S, Tasker C, Roche NE, Chang TL, Pei Z. Differential effects of depot medroxyprogesterone acetate administration on vaginal microbiome in Hispanic White and Black women. Emerg Microbes Infect 2019; 8:197-210. [PMID: 30866773 PMCID: PMC6455113 DOI: 10.1080/22221751.2018.1563458] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 12/13/2018] [Accepted: 12/17/2018] [Indexed: 12/27/2022]
Abstract
The use of depot medroxyprogesterone acetate (DMPA), a 3-monthly injectable hormonal contraceptive, is associated with an increased risk of HIV acquisition possibly through alteration of the vaginal microbiome. In this longitudinal interventional study, we investigated the impact of DMPA administration on the vaginal microbiome in Hispanic White and Black women at the baseline (visit 1), 1 month (visit 2), and 3 months (visit 3) following DMPA treatment by using 16S rRNA gene sequencing. No significant changes in the vaginal microbiome were observed after DMPA treatment when Hispanic White and Black women were analysed as a combined group. However, DMPA treatment enriched total vaginosis-associated bacteria (VNAB) and Prevotella at visit 2, and simplified the correlational network in the vaginal microbiome in Black women, while increasing the network size in Hispanic White women. The microbiome in Black women became more diversified and contained more VNAB than Hispanic White women after DMPA treatment. While the Firmicutes to Bacteroidetes (F/B) ratio and Lactobacillus to Prevotella (L/P) ratio were comparable between Black and Hispanic White women at visit 1, both ratios were lower in Black women than in Hispanic White women at visit 2. In conclusion, DMPA treatment altered the community network and enriched VNAB in Black women but not in Hispanic White women. The Lactobacillus deficiency and enrichment of VNAB may contribute to the increased risk of HIV acquisition in Black women. Future studies on the impact of racial differences on the risk of HIV acquisition will offer insights into developing effective strategies for HIV prevention. Abbreviations: DMPA: depot medroxyprogesterone acetate; PCR: polymerase chain reaction; OTU: operational taxonomic unit; STI: sexually transmitted infections; VNAB: vaginosis-associated bacteria.
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Affiliation(s)
- Liying Yang
- Department of Pathology, New York University School of Medicine, New York, NY, USA
- Department of Medicine, New York University School of Medicine, New York, NY, USA
| | - Yuhan Hao
- Department of Pathology, New York University School of Medicine, New York, NY, USA
- Applied Bioinformatics Laboratories, New York University School of Medicine, New York, NY, USA
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, USA
| | - Jiyuan Hu
- Department of Population Health, New York University School of Medicine, New York, NY, USA
- Department of Environmental Medicine, New York University School of Medicine, New York, NY, USA
| | - Dervla Kelly
- Department of Pathology, New York University School of Medicine, New York, NY, USA
| | - Huilin Li
- Department of Population Health, New York University School of Medicine, New York, NY, USA
- Department of Environmental Medicine, New York University School of Medicine, New York, NY, USA
| | - Stuart Brown
- Applied Bioinformatics Laboratories, New York University School of Medicine, New York, NY, USA
| | - Carley Tasker
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers, The State University of New Jersey, New Jersey Medical School, Newark, NJ, USA
| | - Natalie E. Roche
- Department of Obstetrics, Gynecology & Women’s Health, Rutgers, the State University of New Jersey, New Jersey Medical School, Newark, NJ, USA
| | - Theresa L. Chang
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers, The State University of New Jersey, New Jersey Medical School, Newark, NJ, USA
- Public Health Research Institute, Rutgers, The State University of New Jersey, New Jersey Medical School, Newark, NJ, USA
| | - Zhiheng Pei
- Department of Medicine, New York University School of Medicine, New York, NY, USA
- Department of Veterans Affairs New York Harbor Healthcare System, New York, NY, USA
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33
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Kaur US, Shet A, Rajnala N, Gopalan BP, Moar P, D H, Singh BP, Chaturvedi R, Tandon R. High Abundance of genus Prevotella in the gut of perinatally HIV-infected children is associated with IP-10 levels despite therapy. Sci Rep 2018; 8:17679. [PMID: 30518941 PMCID: PMC6281660 DOI: 10.1038/s41598-018-35877-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 11/12/2018] [Indexed: 12/11/2022] Open
Abstract
Perinatal HIV infection is characterized by faster HIV disease progression and higher initial rate of HIV replication compared to adults. While antiretroviral therapy (ART) has greatly reduced HIV replication to undetectable levels, there is persistent elevated inflammation associated with HIV disease progression. Alteration of gut microbiota is associated with increased inflammation in chronic adult HIV infection. Here, we aim to study the gut microbiome and its role in inflammation in treated and untreated HIV-infected children. Examination of fecal microbiota revealed that perinatally infected children living with HIV had significantly higher levels of genus Prevotella that persisted despite ART. These children also had higher levels of soluble CD14 (sCD14), a marker of microbial translocation, and IP-10 despite therapy. The Prevotella positively correlated with IP-10 levels in both treated and untreated HIV-infected children, while genus Prevotella and species Prevotella copri was inversely associated with CD4 count. Relative abundance of genus Prevotella and species Prevotella copri showed positive correlation with sCD14 in ART-suppressed perinatally HIV-infected children. Our study suggests that gut microbiota may serve as one of the driving forces behind the persistent inflammation in children despite ART. Reshaping of microbiota using probiotics may be recommended as an adjunctive therapy along with ART.
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Affiliation(s)
- Urvinder S Kaur
- Laboratory of AIDS Research and Immunology, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Anita Shet
- International Vaccine Access Center, Johns Hopkins School of Public Health, Baltimore, USA
| | - Niharika Rajnala
- Division of Infectious Diseases, St. John's Research Institute, St. John's National Academy of health Sciences, Bangalore, India
| | - Bindu Parachalil Gopalan
- Division of Infectious Diseases, St. John's Research Institute, St. John's National Academy of health Sciences, Bangalore, India
| | - Preeti Moar
- Laboratory of AIDS Research and Immunology, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Himanshu D
- Department of Medicine, King Georges Medical University, Lucknow, India
| | | | - Rupesh Chaturvedi
- Host Pathogen Interaction Laboratory, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Ravi Tandon
- Laboratory of AIDS Research and Immunology, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India.
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34
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de Lorgeril J, Lucasson A, Petton B, Toulza E, Montagnani C, Clerissi C, Vidal-Dupiol J, Chaparro C, Galinier R, Escoubas JM, Haffner P, Dégremont L, Charrière GM, Lafont M, Delort A, Vergnes A, Chiarello M, Faury N, Rubio T, Leroy MA, Pérignon A, Régler D, Morga B, Alunno-Bruscia M, Boudry P, Le Roux F, Destoumieux-Garzόn D, Gueguen Y, Mitta G. Immune-suppression by OsHV-1 viral infection causes fatal bacteraemia in Pacific oysters. Nat Commun 2018; 9:4215. [PMID: 30310074 PMCID: PMC6182001 DOI: 10.1038/s41467-018-06659-3] [Citation(s) in RCA: 132] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 09/18/2018] [Indexed: 11/09/2022] Open
Abstract
Infectious diseases are mostly explored using reductionist approaches despite repeated evidence showing them to be strongly influenced by numerous interacting host and environmental factors. Many diseases with a complex aetiology therefore remain misunderstood. By developing a holistic approach to tackle the complexity of interactions, we decipher the complex intra-host interactions underlying Pacific oyster mortality syndrome affecting juveniles of Crassostrea gigas, the main oyster species exploited worldwide. Using experimental infections reproducing the natural route of infection and combining thorough molecular analyses of oyster families with contrasted susceptibilities, we demonstrate that the disease is caused by multiple infection with an initial and necessary step of infection of oyster haemocytes by the Ostreid herpesvirus OsHV-1 µVar. Viral replication leads to the host entering an immune-compromised state, evolving towards subsequent bacteraemia by opportunistic bacteria. We propose the application of our integrative approach to decipher other multifactorial diseases that affect non-model species worldwide. Pacific oyster mortality syndrome is a poorly understood cause of mortality in commercially important oyster species. Here, the authors use multiple infection experiments to show that the syndrome is caused by sequential infection by herpesvirus and opportunistic bacteria.
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Affiliation(s)
- Julien de Lorgeril
- IHPE, Université de Montpellier, CNRS, Ifremer, Université de Perpignan Via Domitia, Place E. Bataillon, 34095, Montpellier, France
| | - Aude Lucasson
- IHPE, Université de Montpellier, CNRS, Ifremer, Université de Perpignan Via Domitia, Place E. Bataillon, 34095, Montpellier, France
| | - Bruno Petton
- LEMAR UMR 6539, UBO/CNRS/IRD/Ifremer, 11 presqu'île du vivier, 29840, Argenton-en-Landunvez, France
| | - Eve Toulza
- IHPE, Université de Montpellier, CNRS, Ifremer, Université de Perpignan Via Domitia, Place E. Bataillon, 34095, Montpellier, France
| | - Caroline Montagnani
- IHPE, Université de Montpellier, CNRS, Ifremer, Université de Perpignan Via Domitia, Place E. Bataillon, 34095, Montpellier, France
| | - Camille Clerissi
- IHPE, Université de Montpellier, CNRS, Ifremer, Université de Perpignan Via Domitia, Place E. Bataillon, 34095, Montpellier, France
| | - Jeremie Vidal-Dupiol
- IHPE, Université de Montpellier, CNRS, Ifremer, Université de Perpignan Via Domitia, Place E. Bataillon, 34095, Montpellier, France
| | - Cristian Chaparro
- IHPE, Université de Montpellier, CNRS, Ifremer, Université de Perpignan Via Domitia, Place E. Bataillon, 34095, Montpellier, France
| | - Richard Galinier
- IHPE, Université de Montpellier, CNRS, Ifremer, Université de Perpignan Via Domitia, Place E. Bataillon, 34095, Montpellier, France
| | - Jean-Michel Escoubas
- IHPE, Université de Montpellier, CNRS, Ifremer, Université de Perpignan Via Domitia, Place E. Bataillon, 34095, Montpellier, France
| | - Philippe Haffner
- IHPE, Université de Montpellier, CNRS, Ifremer, Université de Perpignan Via Domitia, Place E. Bataillon, 34095, Montpellier, France
| | - Lionel Dégremont
- Laboratoire de Génétique et Pathologie des Mollusques Marins, Ifremer, Avenue du Mus de Loup, 17930, La Tremblade, France
| | - Guillaume M Charrière
- IHPE, Université de Montpellier, CNRS, Ifremer, Université de Perpignan Via Domitia, Place E. Bataillon, 34095, Montpellier, France
| | - Maxime Lafont
- IHPE, Université de Montpellier, CNRS, Ifremer, Université de Perpignan Via Domitia, Place E. Bataillon, 34095, Montpellier, France
| | - Abigaïl Delort
- IHPE, Université de Montpellier, CNRS, Ifremer, Université de Perpignan Via Domitia, Place E. Bataillon, 34095, Montpellier, France
| | - Agnès Vergnes
- IHPE, Université de Montpellier, CNRS, Ifremer, Université de Perpignan Via Domitia, Place E. Bataillon, 34095, Montpellier, France
| | - Marlène Chiarello
- Marine Biodiversity, Exploitation and Conservation (MARBEC), Université de Montpellier, CNRS, IRD, Ifremer, Place E. Bataillon, 34095, Montpellier, France
| | - Nicole Faury
- Laboratoire de Génétique et Pathologie des Mollusques Marins, Ifremer, Avenue du Mus de Loup, 17930, La Tremblade, France
| | - Tristan Rubio
- IHPE, Université de Montpellier, CNRS, Ifremer, Université de Perpignan Via Domitia, Place E. Bataillon, 34095, Montpellier, France
| | - Marc A Leroy
- IHPE, Université de Montpellier, CNRS, Ifremer, Université de Perpignan Via Domitia, Place E. Bataillon, 34095, Montpellier, France
| | - Adeline Pérignon
- CRCM, Comité de la Conchyliculture de Méditerranée, Quai Baptiste Guitard, 34140, Mèze, France
| | - Denis Régler
- CRCM, Comité de la Conchyliculture de Méditerranée, Quai Baptiste Guitard, 34140, Mèze, France
| | - Benjamin Morga
- Laboratoire de Génétique et Pathologie des Mollusques Marins, Ifremer, Avenue du Mus de Loup, 17930, La Tremblade, France
| | - Marianne Alunno-Bruscia
- LEMAR UMR 6539, UBO/CNRS/IRD/Ifremer, 11 presqu'île du vivier, 29840, Argenton-en-Landunvez, France
| | - Pierre Boudry
- LEMAR UMR6539, CNRS/UBO/IRD/Ifremer, ZI pointe du diable, CS 10070, F-29280, Plouzané, France
| | - Frédérique Le Roux
- Sorbonne Universités, UPMC Paris 06, CNRS, UMR 8227, LBI2M, Ifremer, Station Biologique de Roscoff, CS 90074, F-29680, Roscoff, France
| | - Delphine Destoumieux-Garzόn
- IHPE, Université de Montpellier, CNRS, Ifremer, Université de Perpignan Via Domitia, Place E. Bataillon, 34095, Montpellier, France
| | - Yannick Gueguen
- IHPE, Université de Montpellier, CNRS, Ifremer, Université de Perpignan Via Domitia, Place E. Bataillon, 34095, Montpellier, France.
| | - Guillaume Mitta
- IHPE, Université de Montpellier, CNRS, Ifremer, Université de Perpignan Via Domitia, Place E. Bataillon, 34095, Montpellier, France.
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Fukui Y, Aoki K, Ishii Y, Tateda K. The palatine tonsil bacteriome, but not the mycobiome, is altered in HIV infection. BMC Microbiol 2018; 18:127. [PMID: 30290791 PMCID: PMC6173881 DOI: 10.1186/s12866-018-1274-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 09/28/2018] [Indexed: 01/01/2023] Open
Abstract
Background Microbial flora in several organs of HIV-infected individuals have been characterized; however, the palatine tonsil bacteriome and mycobiome and their relationship with each other remain unclear. Determining the palatine tonsil microbiome may provide a better understanding of the pathogenesis of oral and systemic complications in HIV-infected individuals. We conducted a cross-sectional study to characterize the palatine tonsil microbiome in HIV-infected individuals. Results Palatine tonsillar swabs were collected from 46 HIV-infected and 20 HIV-uninfected individuals. The bacteriome and mycobiome were analyzed by amplicon sequencing using Illumina MiSeq. The palatine tonsil bacteriome of the HIV-infected individuals differed from that of HIV-uninfected individuals in terms of the decreased relative abundances of the commensal genera Neisseria and Haemophilus. At the species level, the relative abundances and presence of Capnocytophaga ochracea, Neisseria cinerea, and Selenomonas noxia were higher in the HIV-infected group than those in the HIV-uninfected group. In contrast, fungal diversity and composition did not differ significantly between the two groups. Microbial intercorrelation analysis revealed that Candida and Neisseria were negatively correlated with each other in the HIV-infected group. HIV immune status did not influence the palatine tonsil microbiome in the HIV-infected individuals. Conclusions HIV-infected individuals exhibit dysbiotic changes in their palatine tonsil bacteriome, independent of immunological status. Electronic supplementary material The online version of this article (10.1186/s12866-018-1274-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yuto Fukui
- Department of Microbiology and Infectious Diseases, Toho University Graduate School of Medicine, 5-21-16 Omorinishi, Ota-ku, Tokyo, 143-8540, Japan. .,Department of Infectious Diseases, Toho University Omori Medical Center, 6-11-1 Omorinishi, Ota-ku, Tokyo, 143-8541, Japan.
| | - Kotaro Aoki
- Department of Microbiology and Infectious Diseases, Toho University Graduate School of Medicine, 5-21-16 Omorinishi, Ota-ku, Tokyo, 143-8540, Japan
| | - Yoshikazu Ishii
- Department of Microbiology and Infectious Diseases, Toho University Graduate School of Medicine, 5-21-16 Omorinishi, Ota-ku, Tokyo, 143-8540, Japan
| | - Kazuhiro Tateda
- Department of Microbiology and Infectious Diseases, Toho University Graduate School of Medicine, 5-21-16 Omorinishi, Ota-ku, Tokyo, 143-8540, Japan
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36
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Nally E, Groah SL, Pérez-Losada M, Caldovic L, Ljungberg I, Chandel NJ, Sprague B, Hsieh MH, Pohl HG. Identification of Burkholderia fungorum in the urine of an individual with spinal cord injury and augmentation cystoplasty using 16S sequencing: copathogen or innocent bystander? Spinal Cord Ser Cases 2018; 4:85. [PMID: 30275977 PMCID: PMC6155001 DOI: 10.1038/s41394-018-0115-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 07/30/2018] [Accepted: 08/01/2018] [Indexed: 01/26/2023] Open
Abstract
INTRODUCTION People with neuropathic bladder (NB) secondary to spinal cord injury (SCI) are at risk for multiple genitourinary complications, the most frequent of which is urinary tract infection (UTI). Despite the high frequency with which UTI occurs, our understanding of the role of urinary microbes in health and disease is limited. In this paper, we present the first prospective case study integrating symptom reporting, urinalysis, urine cultivation, and 16S ribosomal ribonucleic acid (rRNA) sequencing of the urine microbiome. CASE PRESENTATION A 55-year-old male with NB secondary to SCI contributed 12 urine samples over an 8-month period during asymptomatic, symptomatic, and postantibiotic periods. All bacteria identified on culture were present on 16S rRNA sequencing, however, 16S rRNA sequencing revealed the presence of bacteria not isolated on culture. In particular, Burkholderia fungorum was present in three samples during both asymptomatic and symptomatic periods. White blood cells of ≥5-10/high power field and leukocyte esterase ≥2 on urinalysis was associated with the presence of symptoms. DISCUSSION In this patient, there was a predominance of pathogenic bacteria and a lack of putative probiotic bacteria during both symptomatic and asymptomatic states. Urinalysis-defined inflammatory markers were present to a greater extent during symptomatic periods compared to the asymptomatic state, which may underscore a role for urinalysis or other inflammatory markers in differentiating asymptomatic bacteriuria from UTI in patients with NB. The finding of potentially pathogenic bacteria identified by sequencing but not cultivation, suggests a need for greater understanding of the relationships amongst bacterial species in the bacteriuric neuropathic bladder.
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Affiliation(s)
- Emma Nally
- MedStar National Rehabilitation Hospital, 102 Irving St., NW, Washington, DC 20010 USA
- Department of Rehabilitation Medicine, MedStar Georgetown University Hospital, Washington, DC USA
| | - Suzanne L. Groah
- MedStar National Rehabilitation Hospital, 102 Irving St., NW, Washington, DC 20010 USA
- Department of Rehabilitation Medicine, MedStar Georgetown University Hospital, Washington, DC USA
| | - Marcos Pérez-Losada
- Computational Biology Institute, The George Washington University, Ashburn, VA USA
- Department of Integrative Systems Biology, Children’s National Health System, Washington, DC USA
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, , Universidade do Porto, 4485-661 Vairão Porto, Portugal
| | - Ljubica Caldovic
- Department of Integrative Systems Biology, Children’s National Health System, Washington, DC USA
| | - Inger Ljungberg
- MedStar National Rehabilitation Hospital, 102 Irving St., NW, Washington, DC 20010 USA
| | - Neel J. Chandel
- Montefiore Medical Center, Albert Einstein College of Medicine, New York, NY USA
| | - Bruce Sprague
- Division of Urology, Children’s National Health System, Washington, DC USA
| | - Michael H. Hsieh
- Division of Urology, Children’s National Health System, Washington, DC USA
| | - Hans G. Pohl
- Division of Urology, Children’s National Health System, Washington, DC USA
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Robinson-Papp J, Nmashie A, Pedowitz E, Benn EKT, George MC, Sharma S, Murray J, Machac J, Heiba S, Mehandru S, Kim-Schulze S, Navis A, Elicer I, Morgello S. Vagal dysfunction and small intestinal bacterial overgrowth: novel pathways to chronic inflammation in HIV. AIDS 2018; 32:1147-1156. [PMID: 29596112 PMCID: PMC5945300 DOI: 10.1097/qad.0000000000001802] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
OBJECTIVE Chronic inflammation in HIV-infected individuals drives disease progression and the development of comorbidities, despite viral suppression with combined antiretroviral therapy. Here, we sought evidence that vagal dysfunction, which occurs commonly as part of HIV-associated autonomic neuropathy, could exacerbate inflammation through gastrointestinal dysmotility, small intestinal bacterial overgrowth (SIBO), and alterations in patterns of soluble immune mediators. DESIGN This is a cross-sectional observational study. METHODS Forty participants on stable combined antiretroviral therapy with gastrointestinal symptoms, and no causes for vagal or gastrointestinal dysfunction other than HIV, underwent autonomic testing, hydrogen/methane breath testing for SIBO, and gastric emptying scintigraphy. A panel of 41 cytokines, high-mobility group box 1, and markers of bacterial translocation (lipopolysaccharide) and monocyte/macrophage activation (sCD14 and sCD163) were tested in plasma. RESULTS We found that participants with vagal dysfunction had delayed gastric emptying and higher prevalence of SIBO. SIBO was associated with IL-6, but not sCD14; lipopolysaccharide could not be detected in any participant. We also found alteration of cytokine networks in participants with vagal dysfunction, with stronger and more numerous positive correlations between cytokines. In the vagal dysfunction group, high mobility group box 1 was the only soluble mediator displaying strong negative correlations with other cytokines, especially those cytokines that had numerous other strong positive correlations. CONCLUSION The current study provides evidence that the vagal component of HIV-associated autonomic neuropathy is associated with changes in immune and gastrointestinal function in individuals with well treated HIV. Further study will be needed to understand whether therapies targeted at enhancing vagal function could be of benefit in HIV.
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Affiliation(s)
- Jessica Robinson-Papp
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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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: 58] [Impact Index Per Article: 9.7] [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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Heeney DD, Gareau MG, Marco ML. Intestinal Lactobacillus in health and disease, a driver or just along for the ride? Curr Opin Biotechnol 2018; 49:140-147. [PMID: 28866243 PMCID: PMC5808898 DOI: 10.1016/j.copbio.2017.08.004] [Citation(s) in RCA: 203] [Impact Index Per Article: 33.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 07/20/2017] [Accepted: 08/14/2017] [Indexed: 02/07/2023]
Abstract
Metagenomics and related methods have led to significant advances in our understanding of the human microbiome. Members of the genus Lactobacillus, although best understood for essential roles in food fermentations and applications as probiotics, have also come to the fore in a number of untargeted gut microbiome studies in humans and animals. Even though Lactobacillus is only a minor member of the human colonic microbiota, the proportions of those bacteria are frequently either positively or negatively correlated with human disease and chronic conditions. Recent findings on Lactobacillus species in human and animal microbiome research, together with the increased knowledge on probiotic and other ingested lactobacilli, have resulted in new perspectives on the importance of this genus to human health.
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Affiliation(s)
- Dustin D Heeney
- Department of Food Science & Technology, University of California, Davis, USA
| | - Mélanie G Gareau
- Department of Anatomy, Physiology & Cell Biology, School of Veterinary Medicine, University of California, Davis, USA
| | - Maria L Marco
- Department of Food Science & Technology, University of California, Davis, USA.
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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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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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Larsen JM. The immune response to Prevotella bacteria in chronic inflammatory disease. Immunology 2017; 151:363-374. [PMID: 28542929 DOI: 10.1111/imm.12760] [Citation(s) in RCA: 707] [Impact Index Per Article: 101.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Revised: 05/10/2017] [Accepted: 05/15/2017] [Indexed: 02/07/2023] Open
Abstract
The microbiota plays a central role in human health and disease by shaping immune development, immune responses and metabolism, and by protecting from invading pathogens. Technical advances that allow comprehensive characterization of microbial communities by genetic sequencing have sparked the hunt for disease-modulating bacteria. Emerging studies in humans have linked the increased abundance of Prevotella species at mucosal sites to localized and systemic disease, including periodontitis, bacterial vaginosis, rheumatoid arthritis, metabolic disorders and low-grade systemic inflammation. Intriguingly, Prevotella abundance is reduced within the lung microbiota of patients with asthma and chronic obstructive pulmonary disease. Increased Prevotella abundance is associated with augmented T helper type 17 (Th17) -mediated mucosal inflammation, which is in line with the marked capacity of Prevotella in driving Th17 immune responses in vitro. Studies indicate that Prevotella predominantly activate Toll-like receptor 2, leading to production of Th17-polarizing cytokines by antigen-presenting cells, including interleukin-23 (IL-23) and IL-1. Furthermore, Prevotella stimulate epithelial cells to produce IL-8, IL-6 and CCL20, which can promote mucosal Th17 immune responses and neutrophil recruitment. Prevotella-mediated mucosal inflammation leads to systemic dissemination of inflammatory mediators, bacteria and bacterial products, which in turn may affect systemic disease outcomes. Studies in mice support a causal role of Prevotella as colonization experiments promote clinical and inflammatory features of human disease. When compared with strict commensal bacteria, Prevotella exhibit increased inflammatory properties, as demonstrated by augmented release of inflammatory mediators from immune cells and various stromal cells. These findings indicate that some Prevotella strains may be clinically important pathobionts that can participate in human disease by promoting chronic inflammation.
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Affiliation(s)
- Jeppe Madura Larsen
- Department of Technology, Faculty of Health and Technology, Metropolitan University College, Copenhagen, Denmark.,National Food Institute, Technical University of Denmark, Lyngby, Denmark
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Wen L, Duffy A. Factors Influencing the Gut Microbiota, Inflammation, and Type 2 Diabetes. J Nutr 2017; 147:1468S-1475S. [PMID: 28615382 DOI: 10.3945/jn.116.240754] [Citation(s) in RCA: 214] [Impact Index Per Article: 30.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Revised: 10/12/2016] [Accepted: 01/11/2017] [Indexed: 12/17/2022] Open
Abstract
The gut microbiota is a complex community of bacteria residing in the intestine. Animal models have demonstrated that several factors contribute to and can significantly alter the composition of the gut microbiota, including genetics; the mode of delivery at birth; the method of infant feeding; the use of medications, especially antibiotics; and the diet. There may exist a gut microbiota signature that promotes intestinal inflammation and subsequent systemic low-grade inflammation, which in turn promotes the development of type 2 diabetes. There are preliminary studies that suggest that the consumption of probiotic bacteria such as those found in yogurt and other fermented milk products can beneficially alter the composition of the gut microbiome, which in turn changes the host metabolism. Obesity, insulin resistance, fatty liver disease, and low-grade peripheral inflammation are more prevalent in patients with low α diversity in the gut microbiome than they are in patients with high α diversity. Fermented milk products, such as yogurt, deliver a large number of lactic acid bacteria to the gastrointestinal tract. They may modify the intestinal environment, including inhibiting lipopolysaccharide production and increasing the tight junctions of gut epithelia cells.
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Affiliation(s)
- Li Wen
- Section of Endocrinology and
| | - Andrew Duffy
- Department of Surgery, Yale University School of Medicine, New Haven, CT
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44
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Associations of the vaginal microbiota with HIV infection, bacterial vaginosis, and demographic factors. AIDS 2017; 31:895-904. [PMID: 28121709 DOI: 10.1097/qad.0000000000001421] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
OBJECTIVE We sought to investigate the effects of HIV infection on the vaginal microbiota and associations with treatment and demographic factors. We thus compared vaginal microbiome samples from HIV-infected (HIV+) and HIV-uninfected (HIV-) women collected at two Chicago area hospitals. DESIGN We studied vaginal microbiome samples from 178 women analyzed longitudinally (n = 324 samples) and collected extensive data on clinical status and demographic factors. METHODS We used 16S rRNA gene sequencing to characterize the bacterial lineages present, then UniFrac, Shannon diversity, and other measures to compare community structure with sample metadata. RESULTS Differences in microbiota measures were modest in the comparison of HIV+ and HIV- samples, in contrast to several previous studies, consistent with effective antiretroviral therapy. Proportions of healthy Lactobacillus species were not higher in HIV- patients overall, but were significantly higher when analyzed within each hospital in isolation. Rates of bacterial vaginosis were higher among African-American women and HIV+ women. Bacterial vaginosis was associated with higher frequency of HIV+. Unexpectedly, African-American women were more likely to switch bacterial vaginosis status between sampling times; switching was not associated with HIV+ status. CONCLUSION The influence of HIV infection on the vaginal microbiome was modest for this cohort of well suppressed urban American women, consistent with effective antiretroviral therapy. HIV+ was found to be associated with bacterial vaginosis. Although bacterial vaginosis has previously been associated with HIV transmission, most of the women studied here became HIV+ many years before our test for bacterial vaginosis, thus implicating additional mechanisms linking HIV infection and bacterial vaginosis.
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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: 104] [Impact Index Per Article: 14.9] [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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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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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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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: 119] [Impact Index Per Article: 14.9] [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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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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Thomson KA, Baeten JM, Mugo NR, Bekker LG, Celum CL, Heffron R. Tenofovir-based oral preexposure prophylaxis prevents HIV infection among women. Curr Opin HIV AIDS 2016; 11:18-26. [PMID: 26417954 PMCID: PMC4705855 DOI: 10.1097/coh.0000000000000207] [Citation(s) in RCA: 86] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
PURPOSE OF REVIEW Despite tremendous promise as a female-controlled HIV prevention strategy, implementation of preexposure prophylaxis (PrEP) among women has been limited, in part because of disparate efficacy results from randomized trials in this population. This review synthesizes existing evidence regarding PrEP efficacy for preventing HIV infection in women and considerations for delivering PrEP to women. RECENT FINDINGS In three efficacy trials, conducted among men and women, tenofovir-based oral PrEP reduced HIV acquisition in subgroups of women by 49-79% in intent-to-treat analyses, and by >85% when accounting for PrEP adherence. Two trials did not demonstrate an HIV prevention benefit from PrEP in women, but substantial evidence indicates those results were compromised by very low adherence to the study medication. Qualitative research has identified risk perception, stigma, and aspects of clinical trial participation as influencing adherence to study medication. Pharmacokinetic studies provide supporting evidence that PrEP offers HIV protection in women who are adherent to the medication. SUMMARY Tenofovir-based daily oral PrEP prevents HIV acquisition in women. Offering PrEP as an HIV prevention option for women at high risk of HIV acquisition is a public health imperative and opportunities to evaluate implementation strategies for PrEP for women are needed.
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Affiliation(s)
- Kerry A. Thomson
- Department of Global Health, University of Washington, Seattle, USA
- Department of Epidemiology, University of Washington, Seattle, USA
| | - Jared M. Baeten
- Department of Global Health, University of Washington, Seattle, USA
- Department of Epidemiology, University of Washington, Seattle, USA
- Department of Medicine, University of Washington, Seattle, USA
| | - Nelly R. Mugo
- Department of Global Health, University of Washington, Seattle, USA
- Sexual Reproductive Adolescent and Child Health Program, Kenya Medical Research Institute, Nairobi, Kenya
| | - Linda-Gail Bekker
- The Desmond Tutu HIV Centre, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Connie L. Celum
- Department of Global Health, University of Washington, Seattle, USA
- Department of Epidemiology, University of Washington, Seattle, USA
- Department of Medicine, University of Washington, Seattle, USA
| | - Renee Heffron
- Department of Global Health, University of Washington, Seattle, USA
- Department of Epidemiology, University of Washington, Seattle, USA
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