In silico analyses of metagenomes from human atherosclerotic plaque samples - PubMed (original) (raw)
doi: 10.1186/s40168-015-0100-y.
Suparna Mitra 1 2 3, Morten Alhede 5, Myat T Maw 6, Yang Liu 7, Rikky W Purbojati 8, Zhei H Yap 9, Kavita K Kushwaha 10, Alexandra G Gheorghe 11, Thomas Bjarnsholt 12 13, Gorm M Hansen 14 15, Henrik H Sillesen 16, Hans P Hougen 17, Peter R Hansen 18, Liang Yang 19, Tim Tolker-Nielsen 20, Stephan C Schuster 21, Michael Givskov 22 23
Affiliations
- PMID: 26334731
- PMCID: PMC4559171
- DOI: 10.1186/s40168-015-0100-y
In silico analyses of metagenomes from human atherosclerotic plaque samples
Suparna Mitra et al. Microbiome. 2015.
Abstract
Background: Through several observational and mechanistic studies, microbial infection is known to promote cardiovascular disease. Direct infection of the vessel wall, along with the cardiovascular risk factors, is hypothesized to play a key role in the atherogenesis by promoting an inflammatory response leading to endothelial dysfunction and generating a proatherogenic and prothrombotic environment ultimately leading to clinical manifestations of cardiovascular disease, e.g., acute myocardial infarction or stroke. There are many reports of microbial DNA isolation and even a few studies of viable microbes isolated from human atherosclerotic vessels. However, high-resolution investigation of microbial infectious agents from human vessels that may contribute to atherosclerosis is very limited. In spite of the progress in recent sequencing technologies, analyzing host-associated metagenomes remain a challenge.
Results: To investigate microbiome diversity within human atherosclerotic tissue samples, we employed high-throughput metagenomic analysis on: (1) atherosclerotic plaques obtained from a group of patients who underwent endarterectomy due to recent transient cerebral ischemia or stroke. (2) Presumed stabile atherosclerotic plaques obtained from autopsy from a control group of patients who all died from causes not related to cardiovascular disease. Our data provides evidence that suggest a wide range of microbial agents in atherosclerotic plaques, and an intriguing new observation that shows these microbiota displayed differences between symptomatic and asymptomatic plaques as judged from the taxonomic profiles in these two groups of patients. Additionally, functional annotations reveal significant differences in basic metabolic and disease pathway signatures between these groups.
Conclusions: We demonstrate the feasibility of novel high-resolution techniques aimed at identification and characterization of microbial genomes in human atherosclerotic tissue samples. Our analysis suggests that distinct groups of microbial agents might play different roles during the development of atherosclerotic plaques. These findings may serve as a reference point for future studies in this area of research.
Figures
Fig. 1
Taxonomic comparison of all DNA samples. Hierarchical clustering result of “family” level taxonomic comparisons of data from unstable atherosclerotic plaques from 15 patients with symptomatic atherosclerotic disease (unstable plaques) and stable plaques from a control group of 7 patients that died from other causes than atherosclerosis (controls). Red indicates down-regulation, green indicates up-regulation, and black indicates no change in read abundance level comparing to all samples. Hierarchical clustering was computed with average linkage, whereas Pearson correlation was used for clustering the families (rows) and Spearman correlation was used for clustering the datasets (columns), respectively
Fig. 2
Rarefaction. Rarefaction plot using annotated species profile for all 22 (unstable and stable) atherosclerotic plaque samples. These curves show the number of nodes that would be present if based on 10, 20, and up to 90 % of the reads
Fig. 3
Multiple comparison clustering. Clustering of the 22 atherosclerotic samples using a principal coordinate analyses (PCoA) and b unweighted pair group method with arithmetic mean (UPGMA) tree. The 15 unstable atherosclerotic plaque samples (cases) are displayed in white and the 7 stable plaque samples (controls) in gray
Fig. 4
Taxonomic comparison of all DNA samples. Comparative tree view of merged samples (excluding samples 233, 238, and P0613) from unstable atherosclerotic plaques (white) and control group of stable plaques (gray) at “family” level of NCBI taxonomy. The scale shows the log value of reads assigned directly to a particular node. Some of the species hits that are likely to be of human origin are marked with black crosses
Fig. 5
Top 25 abundant species. Top 25 abundant species for all (unstable and stable) atherosclerotic plaque samples (excluding samples 233, 238 and P0613) are displayed in a bar chart
Fig. 6
Functional comparison of total biome. Differences between total biome for unstable atherosclerotic plaque samples (white) and stable plaque samples (blue) are displayed with comparative bar charts. a depicts the difference of KEGG orthologies (level 2) and b provides comparison of the two groups with the top 50 SEED-level 2 subsystems
Fig. 7
FISH images of Acidovorax spp_._ and H. pylori in atherosclerotic plaque samples. Representative results of plaque samples after applying the Acidovorax spp_.-specific probe (a), H. pylori_-specific probe (b), as well as two negative control probes, i.e., Candidate division TM7 (c), and Paracoccus spp. (d), on atherosclerotic plaque material from several different patients. We observed morphogically distinct clusters of Acidovorax spp. and H. pylori cells surrounded by atherosclerotic tissue material
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