Effect of Advanced HIV Infection on the Respiratory Microbiome

Twigg, Homer L.; Knox, Kenneth S.; Zhou, Jin; Crothers, Kristina; Nelson, David E.; Day, Richard B.; Lin, Huaiying; Gao, Xiang; Dong, Qunfeng; Mi, Deming; Katz, Barry P.; Sodergren, Erica; Weinstock, George M.

doi:10.1164/rccm.201509-1875oc

Cited by 83 publications

(103 citation statements)

References 36 publications

(33 reference statements)

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“…Two recent LHMP studies characterized the lower respiratory tract microbiome at different stages of HIV disease [23, 26]. Beck and colleagues evaluated a cohort of HIV-uninfected individuals, HAART naïve HIV-infected individuals and HAART-treated HIV-infected individuals [23].…”

Section: The Lower Respiratory Tractmentioning

confidence: 99%

“…Twigg and colleagues recently examined the lung microbiome in 20 HIV-uninfected persons and 26 HIV-infected persons sampled by BAL at baseline (pre-HAART), 1 year and 3 years post-HAART initiation [26]. In contrast to the LHMP study above, the median CD4 count at baseline was 280 cells/μL and 375 cells/ μL at 3 years.…”

Section: The Lower Respiratory Tractmentioning

confidence: 99%

“…At baseline, the lower airways of HIV-infected participants were characterized by decreased richness (α diversity), but increased β diversity of microbial communities. Taxonomic differences at baseline included elevated abundance of Streptococcus in HIV-infected subjects and increased abundance of Flavobacterium in uninfected controls [26]. Although these findings are in contrast with results from Beck et al [23], the differences are likely due to differences in the immune status of the cohorts.…”

Section: The Lower Respiratory Tractmentioning

confidence: 99%

“…The differences in relative abundance of Streptococcus and Flavobacterium persisted at pre-HAART levels. Interestingly, the frequency of Veillonella and Prevotella increased in the HIV-infected group at this time point [26]. At the 3-year time point, the differences in abundance of Streptococcus and Flavobacterium were less pronounced.…”

Section: The Lower Respiratory Tractmentioning

confidence: 99%

“…Much of what is currently known about the lung microbiome in HIV has been reported by members of the Lung HIV Microbiome Project (LHMP), a multi-center research consortium that investigated the microbiome of the upper and lower respiratory tract in various populations of HIV-infected individuals [6, 13, 22–26]. In this review, we summarize the immune changes in HIV infection that may alter the lung microbiome, discuss existing data from the LHMP and other groups on the microbiome of the various components of the respiratory tract, and speculate on how these changes may influence disease.…”

Section: Introductionmentioning

confidence: 99%

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The respiratory microbiome of HIV-infected individuals

Lawani

Morris

2016

Expert Review of Anti-infective Therapy

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Introduction The respiratory tract is constantly exposed to various environmental and endogenous microbes; however, unlike other similar mucosal surfaces, there has been limited investigation of the microbiome of the respiratory tract. Areas Covered In this review, we summarize the current state of knowledge of the bacterial, fungal, and viral respiratory microbiomes during HIV infection and how the microbiome might relate to HIV-associated lung disease. Expert Commentary HIV infection is associated with alterations in the respiratory microbiome. The clinical implications of lung microbial dysbiosis are however currently unknown. Mechanistic studies are needed to establish causality between shifts in the respiratory microbiome and pulmonary complications in HIV-infected individuals.

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Section: The Lower Respiratory Tractmentioning

confidence: 99%

Section: The Lower Respiratory Tractmentioning

confidence: 99%

Section: The Lower Respiratory Tractmentioning

confidence: 99%

Section: The Lower Respiratory Tractmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

The respiratory microbiome of HIV-infected individuals

Lawani

Morris

2016

Expert Review of Anti-infective Therapy

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Exact variance component tests for longitudinal microbiome studies

Zhai

Knox

Twigg

et al. 2019

Genetic Epidemiology

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In metagenomic studies, testing the association between microbiome composition and clinical outcomes translates to testing the nullity of variance components. Motivated by a lung human immunodeficiency virus (HIV) microbiome project, we study longitudinal microbiome data by using variance component models with more than two variance components. Current testing strategies only apply to models with exactly two variance components and when sample sizes are large. Therefore, they are not applicable to longitudinal microbiome studies. In this paper, we propose exact tests (score test, likelihood ratio test, and restricted likelihood ratio test) to (a) test the association of the overall microbiome composition in a longitudinal design and (b) detect the association of one specific microbiome cluster while adjusting for the effects from related clusters. Our approach combines the exact tests for null hypothesis with a single variance component with a strategy of reducing multiple variance components to a single one. Simulation studies demonstrate that our method has a correct type I error rate and superior power compared to existing methods at small sample sizes and weak signals. Finally, we apply our method to a longitudinal pulmonary microbiome study of HIV‐infected patients and reveal two interesting genera Prevotella and Veillonella associated with forced vital capacity. Our findings shed light on the impact of the lung microbiome on HIV complexities. The method is implemented in the open‐source, high‐performance computing language Julia and is freely available at https://github.com/JingZhai63/VCmicrobiome.

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The human lung microbiome—A hidden link between microbes and human health and diseases

Gao

Wang

2022

iMeta

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Once thought to be sterile, the human lung is now well recognized to harbor a consortium of microorganisms collectively known as the lung microbiome.The lung microbiome is altered in an array of lung diseases, including chronic lung diseases such as chronic obstructive pulmonary disease, asthma, and bronchiectasis, acute lung diseases caused by pneumonia, sepsis, and COVID-19, and other lung complications such as those related to lung transplantation, lung cancer, and human immunodeficiency virus. The effects of lung microbiome in modulating host immunity and inflammation in the lung and distal organs are being elucidated. However, the precise mechanism by which members of microbiota produce structural ligands that interact with host genes and pathways remains largely uncharacterized. Multiple unique challenges, both technically and biologically, exist in the field of lung microbiome, necessitating the development of tailored experimental and analytical approaches to overcome the bottlenecks. In this review, we first provide an overview of the principles and methodologies in studying the lung microbiome. We next review current knowledge of the roles of lung microbiome in human diseases, highlighting mechanistic insights. We finally discuss critical challenges in the field and share our thoughts on broad topics for future investigation.

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Effect of Advanced HIV Infection on the Respiratory Microbiome

Abstract: Rationale: Previous work found the lung microbiome in healthy subjects infected with HIV was similar to that in uninfected subjects.

Cited by 83 publications

References 36 publications

The respiratory microbiome of HIV-infected individuals

The respiratory microbiome of HIV-infected individuals

Exact variance component tests for longitudinal microbiome studies

The human lung microbiome—A hidden link between microbes and human health and diseases

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