Transcription profiling reveals potential mechanisms of dysbiosis in the oral microbiome of rhesus macaques with chronic untreated SIV infection.

A majority of individuals infected with human immunodeficiency virus (HIV) have inadequate access to antiretroviral therapy and ultimately develop debilitating oral infections that often correlate with disease progression. Due to the impracticalities of conducting host-microbe systems-based studies in HIV infected patients, we have evaluated the potential of simian immunodeficiency virus (SIV) infected rhesus macaques to serve as a non-human primate model for oral manifestations of HIV disease. We present the first description of the rhesus macaque oral microbiota and show that a mixture of human commensal bacteria and "macaque versions" of human commensals colonize the tongue dorsum and dental plaque. Our findings indicate that SIV infection results in chronic activation of antiviral and inflammatory responses in the tongue mucosa that may collectively lead to repression of epithelial development and impact the microbiome. In addition, we show that dysbiosis of the lingual microbiome in SIV infection is characterized by outgrowth of Gemella morbillorum that may result from impaired macrophage function. Finally, we provide evidence that the increased capacity of opportunistic pathogens (e.g. E. coli) to colonize the microbiome is associated with reduced production of antimicrobial peptides

Transcription profiling reveals potential mechanisms of dysbiosis in the oral microbiome of rhesus macaques with chronic untreated SIV infection.

A majority of individuals infected with human immunodeficiency virus (HIV) have inadequate access to antiretroviral therapy and ultimately develop debilitating oral infections that often correlate with disease progression. Due to the impracticalities of conducting host-microbe systems-based studies in HIV infected patients, we have evaluated the potential of simian immunodeficiency virus (SIV) infected rhesus macaques to serve as a non-human primate model for oral manifestations of HIV disease. We present the first description of the rhesus macaque oral microbiota and show that a mixture of human commensal bacteria and "macaque versions" of human commensals colonize the tongue dorsum and dental plaque. Our findings indicate that SIV infection results in chronic activation of antiviral and inflammatory responses in the tongue mucosa that may collectively lead to repression of epithelial development and impact the microbiome. In addition, we show that dysbiosis of the lingual microbiome in SIV infection is characterized by outgrowth of Gemella morbillorum that may result from impaired macrophage function. Finally, we provide evidence that the increased capacity of opportunistic pathogens (e.g. E. coli) to colonize the microbiome is associated with reduced production of antimicrobial peptides

Transcriptional profile of genes in up-regulated functional categories.

<p>Heat maps are shown detailing the transcription levels of genes associated with A) antiviral response, B) viral replication, C) epithelial cell death, D) epithelial hyperplasia, E) interferon response, F) keratinocyte differentiation, and G) quantity of lymphocytes that were up-regulated in the tongue mucosa of SIV infected macaques.</p

Validation of microarray data by quantitative real-time PCR.

<p>A) Comparison of fold changes in expression of BST2, MX1, STAT1, and IL1β in the tongue of SIV infected animals as determined by quantitative real-time PCR (RT-PCR) and microarray-based assays. B) Comparison of microarray and RT-PCR-based changes in expression of pro-inflammatory cytokines IFNγ, IFNα, and TNFα in the tongue of SIV infected macaques. Notes: error bars denote standard deviation of fold change in each system. RT-PCR data were generated from comparison of 3 SIV infected animals to 3 uninfected controls, and microarray data from comparison of 5 SIV infected animals to 3 uninfected controls.</p

Transcriptional profiling of the macaque tongue epithelium.

<p>A) Representative images of rhesus macaque tongue tissue sections “before” and “after” laser capture microdissection of the epithelial layer. B) Hierarchical clustering of genes up- and down-regulated specifically in the tongue epithelium of SIV infected macaques (35804, 34030) in comparison to uninfected controls (36792, 33832). C) IPA^©-based pathway analysis of genes up- and down-modulated in the tongue epithelium of SIV infected macaques. Statistically over-represented biological functions were identified in the list of differentially expressed genes in the tongue epithelium and are shown as stacked bar graphs with the contribution (# genes) from up-regulated transcripts in red and down-regulated transcripts in green. D) Comparison of fold changes in genes associated with epithelial proliferation and differentiation identified through analysis of epithelium purified by laser capture microdissection versus analysis of whole lingual tissues.</p

Neighbor-joining tree for rhesus macaque tongue and dental plaque taxa.

<p>The oral taxon number follows the name of each taxon. Bacterial species common to the human oral microbiome are shown in black text and species unique to the macaque in red.</p

Correlation between expression of macrophage biomarkers and colonization of <i>Gemella morbillorum</i>.

<p>The relationship between the proportions of G. morbillorum in the lingual microbiome and the expression level of macrophage biomarkers IL1B, ICAM1, CCL2, and CCL6 in the lingual mucosa was evaluated in 9 macaques (3 uninfected and 6 SIV infected) by correlative analysis using Graph Pad Prism, version 6.0b. <i>P</i>-values are also shown for each correlation.</p