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Rocafort M, Gootenberg DB, Luévano JM, Paer JM, Hayward MR, Bramante JT, Ghebremichael MS, Xu J, Rogers ZH, Munoz AR, Okello S, Kim JH, Sentongo R, Wagubi R, Lankowski A, Maruapula S, Zhao G, Handley SA, Mosepele M, Siedner MJ, Kwon DS. HIV-associated gut microbial alterations are dependent on host and geographic context. Nat Commun 2024; 15:1055. [PMID: 38316748 PMCID: PMC10844288 DOI: 10.1038/s41467-023-44566-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 12/19/2023] [Indexed: 02/07/2024] Open
Abstract
HIV-associated changes in intestinal microbiota are believed to be important drivers of disease progression. However, the majority of studies have focused on populations in high-income countries rather than in developing regions where HIV burden is greatest. To better understand the impact of HIV on fecal microbiota globally, we compare the fecal microbial community of individuals in the U.S., Uganda, and Botswana. We identify significant bacterial taxa alterations with both treated and untreated HIV infection with a high degree of uniqueness in each cohort. HIV-associated taxa alterations are also significantly different between populations that report men who have sex with men (MSM) behavior and non-MSM populations. Additionally, while we find that HIV infection is consistently associated with higher soluble markers of immune activation, most specific bacterial taxa associated with these markers in each region are not shared and none are shared across all three geographic locations in our study. Our findings demonstrate that HIV-associated changes in fecal microbiota are overall distinct among geographical locations and sexual behavior groups, although a small number of taxa shared between pairs of geographic locations warrant further investigation, highlighting the importance of considering host context to fully assess the impact of the gut microbiome on human health and disease.
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Affiliation(s)
- Muntsa Rocafort
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, 02139, USA
| | - David B Gootenberg
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, 02139, USA
- Harvard Medical School, Boston, MA, 02114, USA
| | - Jesús M Luévano
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, 02139, USA
- Harvard Medical School, Boston, MA, 02114, USA
| | - Jeffrey M Paer
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, 02139, USA
| | | | | | | | - Jiawu Xu
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, 02139, USA
| | - Zoe H Rogers
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, 02139, USA
| | | | - Samson Okello
- Department of Medicine, Mbarara University of Science and Technology, 1956, Mbarara, Uganda
| | - June-Ho Kim
- Harvard Medical School, Boston, MA, 02114, USA
| | - Ruth Sentongo
- Department of Medicine, Mbarara University of Science and Technology, 1956, Mbarara, Uganda
| | - Robert Wagubi
- Department of Medicine, Mbarara University of Science and Technology, 1956, Mbarara, Uganda
| | - Alex Lankowski
- Medical Practice Evaluation Center, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Segametsi Maruapula
- Department of Family & Consumer Sciences, University of Botswana, 0022, Gaborone, Botswana
| | - Guoyan Zhao
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Scott A Handley
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Mosepele Mosepele
- Faculty of Medicine, University of Botswana, 0022, Gaborone, Botswana
| | - Mark J Siedner
- Harvard Medical School, Boston, MA, 02114, USA
- Medical Practice Evaluation Center, Massachusetts General Hospital, Boston, MA, 02114, USA
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Douglas S Kwon
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, 02139, USA.
- Harvard Medical School, Boston, MA, 02114, USA.
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, 02114, USA.
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2
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Gootenberg DB, Kurtzman N, O'Mara T, Ge JY, Chiu D, Shapiro NI, Mechanic OJ, Dagan A. Developing a pulse oximetry home monitoring protocol for patients suspected with COVID-19 after emergency department discharge. BMJ Health Care Inform 2021; 28:bmjhci-2021-100330. [PMID: 34301725 PMCID: PMC8313308 DOI: 10.1136/bmjhci-2021-100330] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 05/17/2021] [Indexed: 01/10/2023] Open
Abstract
Objectives Patients with COVID-19 can present to the emergency department (ED) without immediate indication for admission, but with concern for decompensation. Clinical experience has demonstrated that critical illness may present later in the disease course and hypoxia is often the first indication of disease progression. The objectives of this study are to (a) assess feasibility and describe a protocol for ED-based outpatient pulse-oximetry monitoring with structured follow-up and (b) determine rates of ED return, hospitalisation and hypoxia among participants. Methods Prospective observational study of patients presenting to a single academic ED in Boston with suspected COVID-19. Eligible patients were adults being discharged from the ED with presumed COVID-19. Exclusion criteria included resting oxygen saturation <92%, ambulatory oxygen saturation <90%, heart rate >110 beats per minute or inability to use the device. Study personnel made scripted phone calls on postdischarge days 1, 3 and 7 to review the pulse-oximetry readings and to evaluate for decompensation. Return visit and admission information were collected via medical record and 28-day follow-up calls. Results 81 patients were enrolled of which 10 (12%) developed hypoxia after their initial discharge from the ED. Overall, 23 (28%) of the 81 patients returned to the ED at least once and 10 of those who returned (43%) were admitted. We successfully contacted 76/81 (94%) of subjects via phone at least once for follow-up assessment. Discussion Patients are eager and willing to participate in home monitoring systems and are comfortable with using technology, which will allow providers and health systems to extend our hospitals capabilities for tracking patient populations in times of crisis. Conclusions It is feasible to implement an outpatient pulse-oximetry monitoring protocol to monitor patients discharged from the ED with confirmed or suspected COVID-19.
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Affiliation(s)
| | - Nicholas Kurtzman
- Harvard Medical School, Boston, Massachusetts, USA .,Department of Emergency Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA.,Harvard Medical Faculty Physicians at Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - Thomas O'Mara
- Department of Emergency Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Jennifer Y Ge
- Harvard Medical School, Boston, Massachusetts, USA.,Harvard-MIT Division of Health Sciences and Technology, Cambridge, Massachusetts, USA
| | - David Chiu
- Harvard Medical School, Boston, Massachusetts, USA.,Department of Emergency Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA.,Harvard Medical Faculty Physicians at Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - Nathan I Shapiro
- Harvard Medical School, Boston, Massachusetts, USA.,Department of Emergency Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA.,Harvard Medical Faculty Physicians at Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - Oren J Mechanic
- Harvard Medical Faculty Physicians at Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - Alon Dagan
- Harvard Medical School, Boston, Massachusetts, USA.,Department of Emergency Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA.,Harvard Medical Faculty Physicians at Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
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3
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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: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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Monaco CL, Gootenberg DB, Zhao G, Handley SA, Ghebremichael MS, Lim ES, Lankowski A, Baldridge MT, Wilen CB, Flagg M, Norman JM, Keller BC, Luévano JM, Wang D, Boum Y, Martin JN, Hunt PW, Bangsberg DR, Siedner MJ, Kwon DS, Virgin HW. Altered Virome and Bacterial Microbiome in Human Immunodeficiency Virus-Associated Acquired Immunodeficiency Syndrome. Cell Host Microbe 2016; 19:311-22. [PMID: 26962942 PMCID: PMC4821831 DOI: 10.1016/j.chom.2016.02.011] [Citation(s) in RCA: 264] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Revised: 12/31/2015] [Accepted: 02/19/2016] [Indexed: 02/07/2023]
Abstract
Human immunodeficiency virus (HIV) infection is associated with increased intestinal translocation of microbial products and enteropathy as well as alterations in gut bacterial communities. However, whether the enteric virome contributes to this infection and resulting immunodeficiency remains unknown. We characterized the enteric virome and bacterial microbiome in a cohort of Ugandan patients, including HIV-uninfected or HIV-infected subjects and those either treated with anti-retroviral therapy (ART) or untreated. Low peripheral CD4 T cell counts were associated with an expansion of enteric adenovirus sequences and this increase was independent of ART treatment. Additionally, the enteric bacterial microbiome of patients with lower CD4 T counts exhibited reduced phylogenetic diversity and richness with specific bacteria showing differential abundance, including increases in Enterobacteriaceae, which have been associated with inflammation. Thus, immunodeficiency in progressive HIV infection is associated with alterations in the enteric virome and bacterial microbiome, which may contribute to AIDS-associated enteropathy and disease progression.
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Affiliation(s)
- Cynthia L Monaco
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | | | - Guoyan Zhao
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Scott A Handley
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | | | - Efrem S Lim
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA; Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Alex Lankowski
- Division of Infectious Diseases, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Megan T Baldridge
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Craig B Wilen
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Meaghan Flagg
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
| | | | - Brian C Keller
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | | | - David Wang
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA; Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Yap Boum
- Médecins Sans Frontières Epicentre, 1956 Mbarara, Uganda
| | - Jeffrey N Martin
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA 94143, USA
| | - Peter W Hunt
- Department of Medicine, University of California San Francisco, San Francisco, CA 94110, USA
| | - David R Bangsberg
- Division of Infectious Diseases, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Harvard School of Public Health, Boston, MA 02114, USA
| | - Mark J Siedner
- Division of Infectious Diseases, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Douglas S Kwon
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA; Division of Infectious Diseases, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA.
| | - Herbert W Virgin
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA.
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David LA, Maurice CF, Carmody RN, Gootenberg DB, Button JE, Wolfe BE, Ling AV, Devlin AS, Varma Y, Fischbach MA, Biddinger SB, Dutton RJ, Turnbaugh PJ. Diet rapidly and reproducibly alters the human gut microbiome. Nature 2013; 505:559-63. [PMID: 24336217 PMCID: PMC3957428 DOI: 10.1038/nature12820] [Citation(s) in RCA: 5986] [Impact Index Per Article: 544.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2013] [Accepted: 10/29/2013] [Indexed: 11/10/2022]
Abstract
Long-term diet influences the structure and activity of the trillions of
microorganisms residing in the human gut1–5, but it
remains unclear how rapidly and reproducibly the human gut microbiome responds
to short-term macronutrient change. Here, we show that the short-term
consumption of diets composed entirely of animal or plant products alters
microbial community structure and overwhelms inter-individual differences in
microbial gene expression. The animal-based diet increased the abundance of
bile-tolerant microorganisms (Alistipes, Bilophila, and
Bacteroides) and decreased the levels of Firmicutes that
metabolize dietary plant polysaccharides (Roseburia, Eubacterium
rectale, and Ruminococcus bromii). Microbial
activity mirrored differences between herbivorous and carnivorous
mammals2, reflecting
trade-offs between carbohydrate and protein fermentation. Foodborne microbes
from both diets transiently colonized the gut, including bacteria, fungi, and
even viruses. Finally, increases in the abundance and activity of
Bilophila wadsworthia on the animal-based diet support a
link between dietary fat, bile acids, and the outgrowth of microorganisms
capable of triggering inflammatory bowel disease6. In concert, these results demonstrate that the
gut microbiome can rapidly respond to altered diet, potentially facilitating the
diversity of human dietary lifestyles.
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Affiliation(s)
- Lawrence A David
- 1] FAS Center for Systems Biology, Harvard University, Cambridge, Massachusetts 02138, USA [2] Society of Fellows, Harvard University, Cambridge, Massachusetts 02138, USA [3] Molecular Genetics & Microbiology and Institute for Genome Sciences & Policy, Duke University, Durham, North Carolina 27708, USA
| | - Corinne F Maurice
- FAS Center for Systems Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Rachel N Carmody
- FAS Center for Systems Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - David B Gootenberg
- FAS Center for Systems Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Julie E Button
- FAS Center for Systems Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Benjamin E Wolfe
- FAS Center for Systems Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Alisha V Ling
- Division of Endocrinology, Children's Hospital Boston, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - A Sloan Devlin
- Department of Bioengineering & Therapeutic Sciences and the California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, California 94158, USA
| | - Yug Varma
- Department of Bioengineering & Therapeutic Sciences and the California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, California 94158, USA
| | - Michael A Fischbach
- Department of Bioengineering & Therapeutic Sciences and the California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, California 94158, USA
| | - Sudha B Biddinger
- Division of Endocrinology, Children's Hospital Boston, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Rachel J Dutton
- FAS Center for Systems Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Peter J Turnbaugh
- FAS Center for Systems Biology, Harvard University, Cambridge, Massachusetts 02138, USA
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6
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Haiser HJ, Gootenberg DB, Chatman K, Sirasani G, Balskus EP, Turnbaugh PJ. Predicting and manipulating cardiac drug inactivation by the human gut bacterium Eggerthella lenta. Science 2013; 341:295-8. [PMID: 23869020 DOI: 10.1126/science.1235872] [Citation(s) in RCA: 437] [Impact Index Per Article: 39.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Despite numerous examples of the effects of the human gastrointestinal microbiome on drug efficacy and toxicity, there is often an incomplete understanding of the underlying mechanisms. Here, we dissect the inactivation of the cardiac drug digoxin by the gut Actinobacterium Eggerthella lenta. Transcriptional profiling, comparative genomics, and culture-based assays revealed a cytochrome-encoding operon up-regulated by digoxin, inhibited by arginine, absent in nonmetabolizing E. lenta strains, and predictive of digoxin inactivation by the human gut microbiome. Pharmacokinetic studies using gnotobiotic mice revealed that dietary protein reduces the in vivo microbial metabolism of digoxin, with significant changes to drug concentration in the serum and urine. These results emphasize the importance of viewing pharmacology from the perspective of both our human and microbial genomes.
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Affiliation(s)
- Henry J Haiser
- Faculty of Arts and Sciences Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA
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