Molecular characterization of stool microbiota in hiv-infected subjects by panbacterial and order-level 16s ribosomal DNA (rDNA) quantification and correlations with immune activation

Collin L. Ellis, Zhong Min Ma, Surinder K Mann, Chin-Shang Li, Jian Wu, Thomas H. Knight, Tammy Yotter, Timothy L. Hayes, Archana Maniar, Paolo Troia-Cancio, Heather A. Overman, Natalia J Torok, Anthony Albanese, John C Rutledge, Chris J Miller, Richard B Pollard, David Asmuth

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Abstract

Background: The relationship between gut microbial community composition at the higher-taxonomic order level and local and systemic immunologic abnormalities in HIV disease may provide insight into how bacterial translocation impacts HIV disease. METHODS:: Antiretroviral-naive patients with HIV underwent upper endoscopy before and 9 months after starting antiretroviral treatment. Duodenal tissue was paraffin-embedded for immunohistochemical analysis and digested for fluorescence activated cell sorting for T-cell subsets and immune activation (CD38+/HLA-DR+) enumeration. Stool samples were provided from patients and control subjects for comparison. Metagenomic microbial DNA was extracted from feces for optimized 16S ribosomal RNA gene (rDNA) real-time quantitative polymerase chain reaction assays designed to quantify panbacterial loads and the relative abundances of proinflammatory Enterobacteriales order and the dominant Bacteroidales and Clostridiales orders. RESULTS:: Samples from 10 HIV subjects before initiating and from six subjects receiving antiretroviral treatment were available for analysis. There was a trend for a greater proportion of Enterobacteriales in HIV-positive subjects compared with control subjects (P = 0.099). There were significant negative correlations between total bacterial load and duodenal CD4 and CD8 T-cell activation levels (r =-0.74, P = 0.004 and r =-0.67, P = 0.013, respectively). The proportions of Enterobacteriales and Bacteroidales were significantly correlated with duodenal CD4 T-cell depletion and peripheral CD8 T-cell activation, respectively. Conclusions: These data represent the first report of quantitative molecular and cellular correlations between total/universal and order-level gut bacterial populations and gastrointestinal-associated lymphoid tissue levels of immune activation in HIV-infected subjects. The correlations between lower overall 16S rDNA levels and tissue immune activation suggest that the gut microbiome may contribute to immune activation and influence HIV progression.

Original languageEnglish (US)
Pages (from-to)363-370
Number of pages8
JournalJournal of Acquired Immune Deficiency Syndromes
Volume57
Issue number5
DOIs
StatePublished - Aug 15 2011

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Microbiota
Ribosomal DNA
HIV
T-Lymphocytes
16S Ribosomal RNA
Bacterial Translocation
Metagenomics
Bacterial Load
T-Lymphocyte Subsets
Lymphoid Tissue
HLA-DR Antigens
rRNA Genes
Feces
Paraffin
Endoscopy
Real-Time Polymerase Chain Reaction
Flow Cytometry
DNA
Therapeutics
Population

Keywords

  • 16S rDNA
  • CD41
  • CD81
  • duodenal tissue
  • gastrointestinal-associated lymphoid tissue
  • HIV infection
  • microbes
  • peripheral blood mononuclear cells
  • stool
  • T-cell
  • T-lymphocyte

ASJC Scopus subject areas

  • Infectious Diseases
  • Pharmacology (medical)

Cite this

@article{3af1e57e18d041a3a2d461f24e709032,
title = "Molecular characterization of stool microbiota in hiv-infected subjects by panbacterial and order-level 16s ribosomal DNA (rDNA) quantification and correlations with immune activation",
abstract = "Background: The relationship between gut microbial community composition at the higher-taxonomic order level and local and systemic immunologic abnormalities in HIV disease may provide insight into how bacterial translocation impacts HIV disease. METHODS:: Antiretroviral-naive patients with HIV underwent upper endoscopy before and 9 months after starting antiretroviral treatment. Duodenal tissue was paraffin-embedded for immunohistochemical analysis and digested for fluorescence activated cell sorting for T-cell subsets and immune activation (CD38+/HLA-DR+) enumeration. Stool samples were provided from patients and control subjects for comparison. Metagenomic microbial DNA was extracted from feces for optimized 16S ribosomal RNA gene (rDNA) real-time quantitative polymerase chain reaction assays designed to quantify panbacterial loads and the relative abundances of proinflammatory Enterobacteriales order and the dominant Bacteroidales and Clostridiales orders. RESULTS:: Samples from 10 HIV subjects before initiating and from six subjects receiving antiretroviral treatment were available for analysis. There was a trend for a greater proportion of Enterobacteriales in HIV-positive subjects compared with control subjects (P = 0.099). There were significant negative correlations between total bacterial load and duodenal CD4 and CD8 T-cell activation levels (r =-0.74, P = 0.004 and r =-0.67, P = 0.013, respectively). The proportions of Enterobacteriales and Bacteroidales were significantly correlated with duodenal CD4 T-cell depletion and peripheral CD8 T-cell activation, respectively. Conclusions: These data represent the first report of quantitative molecular and cellular correlations between total/universal and order-level gut bacterial populations and gastrointestinal-associated lymphoid tissue levels of immune activation in HIV-infected subjects. The correlations between lower overall 16S rDNA levels and tissue immune activation suggest that the gut microbiome may contribute to immune activation and influence HIV progression.",
keywords = "16S rDNA, CD41, CD81, duodenal tissue, gastrointestinal-associated lymphoid tissue, HIV infection, microbes, peripheral blood mononuclear cells, stool, T-cell, T-lymphocyte",
author = "Ellis, {Collin L.} and Ma, {Zhong Min} and Mann, {Surinder K} and Chin-Shang Li and Jian Wu and Knight, {Thomas H.} and Tammy Yotter and Hayes, {Timothy L.} and Archana Maniar and Paolo Troia-Cancio and Overman, {Heather A.} and Torok, {Natalia J} and Anthony Albanese and Rutledge, {John C} and Miller, {Chris J} and Pollard, {Richard B} and David Asmuth",
year = "2011",
month = "8",
day = "15",
doi = "10.1097/QAI.0b013e31821a603c",
language = "English (US)",
volume = "57",
pages = "363--370",
journal = "Journal of acquired immune deficiency syndromes (1999)",
issn = "1525-4135",
publisher = "Lippincott Williams and Wilkins",
number = "5",

}

TY - JOUR

T1 - Molecular characterization of stool microbiota in hiv-infected subjects by panbacterial and order-level 16s ribosomal DNA (rDNA) quantification and correlations with immune activation

AU - Ellis, Collin L.

AU - Ma, Zhong Min

AU - Mann, Surinder K

AU - Li, Chin-Shang

AU - Wu, Jian

AU - Knight, Thomas H.

AU - Yotter, Tammy

AU - Hayes, Timothy L.

AU - Maniar, Archana

AU - Troia-Cancio, Paolo

AU - Overman, Heather A.

AU - Torok, Natalia J

AU - Albanese, Anthony

AU - Rutledge, John C

AU - Miller, Chris J

AU - Pollard, Richard B

AU - Asmuth, David

PY - 2011/8/15

Y1 - 2011/8/15

N2 - Background: The relationship between gut microbial community composition at the higher-taxonomic order level and local and systemic immunologic abnormalities in HIV disease may provide insight into how bacterial translocation impacts HIV disease. METHODS:: Antiretroviral-naive patients with HIV underwent upper endoscopy before and 9 months after starting antiretroviral treatment. Duodenal tissue was paraffin-embedded for immunohistochemical analysis and digested for fluorescence activated cell sorting for T-cell subsets and immune activation (CD38+/HLA-DR+) enumeration. Stool samples were provided from patients and control subjects for comparison. Metagenomic microbial DNA was extracted from feces for optimized 16S ribosomal RNA gene (rDNA) real-time quantitative polymerase chain reaction assays designed to quantify panbacterial loads and the relative abundances of proinflammatory Enterobacteriales order and the dominant Bacteroidales and Clostridiales orders. RESULTS:: Samples from 10 HIV subjects before initiating and from six subjects receiving antiretroviral treatment were available for analysis. There was a trend for a greater proportion of Enterobacteriales in HIV-positive subjects compared with control subjects (P = 0.099). There were significant negative correlations between total bacterial load and duodenal CD4 and CD8 T-cell activation levels (r =-0.74, P = 0.004 and r =-0.67, P = 0.013, respectively). The proportions of Enterobacteriales and Bacteroidales were significantly correlated with duodenal CD4 T-cell depletion and peripheral CD8 T-cell activation, respectively. Conclusions: These data represent the first report of quantitative molecular and cellular correlations between total/universal and order-level gut bacterial populations and gastrointestinal-associated lymphoid tissue levels of immune activation in HIV-infected subjects. The correlations between lower overall 16S rDNA levels and tissue immune activation suggest that the gut microbiome may contribute to immune activation and influence HIV progression.

AB - Background: The relationship between gut microbial community composition at the higher-taxonomic order level and local and systemic immunologic abnormalities in HIV disease may provide insight into how bacterial translocation impacts HIV disease. METHODS:: Antiretroviral-naive patients with HIV underwent upper endoscopy before and 9 months after starting antiretroviral treatment. Duodenal tissue was paraffin-embedded for immunohistochemical analysis and digested for fluorescence activated cell sorting for T-cell subsets and immune activation (CD38+/HLA-DR+) enumeration. Stool samples were provided from patients and control subjects for comparison. Metagenomic microbial DNA was extracted from feces for optimized 16S ribosomal RNA gene (rDNA) real-time quantitative polymerase chain reaction assays designed to quantify panbacterial loads and the relative abundances of proinflammatory Enterobacteriales order and the dominant Bacteroidales and Clostridiales orders. RESULTS:: Samples from 10 HIV subjects before initiating and from six subjects receiving antiretroviral treatment were available for analysis. There was a trend for a greater proportion of Enterobacteriales in HIV-positive subjects compared with control subjects (P = 0.099). There were significant negative correlations between total bacterial load and duodenal CD4 and CD8 T-cell activation levels (r =-0.74, P = 0.004 and r =-0.67, P = 0.013, respectively). The proportions of Enterobacteriales and Bacteroidales were significantly correlated with duodenal CD4 T-cell depletion and peripheral CD8 T-cell activation, respectively. Conclusions: These data represent the first report of quantitative molecular and cellular correlations between total/universal and order-level gut bacterial populations and gastrointestinal-associated lymphoid tissue levels of immune activation in HIV-infected subjects. The correlations between lower overall 16S rDNA levels and tissue immune activation suggest that the gut microbiome may contribute to immune activation and influence HIV progression.

KW - 16S rDNA

KW - CD41

KW - CD81

KW - duodenal tissue

KW - gastrointestinal-associated lymphoid tissue

KW - HIV infection

KW - microbes

KW - peripheral blood mononuclear cells

KW - stool

KW - T-cell

KW - T-lymphocyte

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U2 - 10.1097/QAI.0b013e31821a603c

DO - 10.1097/QAI.0b013e31821a603c

M3 - Article

C2 - 21436711

AN - SCOPUS:80051552856

VL - 57

SP - 363

EP - 370

JO - Journal of acquired immune deficiency syndromes (1999)

JF - Journal of acquired immune deficiency syndromes (1999)

SN - 1525-4135

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ER -