In silico analyses of metagenomes from human atherosclerotic plaque samples

Suparna Mitra; Daniela I Drautz-Moses; Morten Alhede; Myat T Maw; Yang Liu; Rikky W Purbojati; Zhei H Yap; Kavita K Kushwaha; Alexandra G Gheorghe; Thomas Bjarnsholt; Gorm M Hansen; Henrik Sillesen; Hans P Hougen; Peter R Hansen; Liang Yang; Tim Tolker-Nielsen; Stephan C Schuster; Michael Givskov

doi:10.1186/s40168-015-0100-y

In silico analyses of metagenomes from human atherosclerotic plaque samples

Suparna Mitra, Daniela I Drautz-Moses, Morten Alhede, Myat T Maw, Yang Liu, Rikky W Purbojati, Zhei H Yap, Kavita K Kushwaha, Alexandra G Gheorghe, Thomas Bjarnsholt, Gorm M Hansen, Henrik Sillesen, Hans P Hougen, Peter R Hansen, Liang Yang, Tim Tolker-Nielsen, Stephan C Schuster, Michael Givskov

38 Citations (Scopus)

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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.

Original language	English
Article number	38
Journal	Microbiome
Volume	3
Pages (from-to)	1-14
ISSN	2049-2618
DOIs	https://doi.org/10.1186/s40168-015-0100-y
Publication status	Published - 3 Sept 2015

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Mitra, S., Drautz-Moses, D. I., Alhede, M., Maw, M. T., Liu, Y., Purbojati, R. W., Yap, Z. H., Kushwaha, K. K., Gheorghe, A. G., Bjarnsholt, T., Hansen, G. M., Sillesen, H., Hougen, H. P., Hansen, P. R., Yang, L., Tolker-Nielsen, T., Schuster, S. C., & Givskov, M. (2015). In silico analyses of metagenomes from human atherosclerotic plaque samples. Microbiome, 3, 1-14. Article 38. https://doi.org/10.1186/s40168-015-0100-y

Mitra, S, Drautz-Moses, DI, Alhede, M, Maw, MT, Liu, Y, Purbojati, RW, Yap, ZH, Kushwaha, KK, Gheorghe, AG , Bjarnsholt, T, Hansen, GM, Sillesen, H, Hougen, HP, Hansen, PR, Yang, L, Tolker-Nielsen, T, Schuster, SC & Givskov, M 2015, 'In silico analyses of metagenomes from human atherosclerotic plaque samples', Microbiome, vol. 3, 38, pp. 1-14. https://doi.org/10.1186/s40168-015-0100-y

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title = "In silico analyses of metagenomes from human atherosclerotic plaque samples",

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.",

author = "Suparna Mitra and Drautz-Moses, {Daniela I} and Morten Alhede and Maw, {Myat T} and Yang Liu and Purbojati, {Rikky W} and Yap, {Zhei H} and Kushwaha, {Kavita K} and Gheorghe, {Alexandra G} and Thomas Bjarnsholt and Hansen, {Gorm M} and Henrik Sillesen and Hougen, {Hans P} and Hansen, {Peter R} and Liang Yang and Tim Tolker-Nielsen and Schuster, {Stephan C} and Michael Givskov",

year = "2015",

month = sep,

day = "3",

doi = "10.1186/s40168-015-0100-y",

language = "English",

volume = "3",

pages = "1--14",

journal = "Microbiome",

issn = "2049-2618",

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TY - JOUR

T1 - In silico analyses of metagenomes from human atherosclerotic plaque samples

AU - Mitra, Suparna

AU - Drautz-Moses, Daniela I

AU - Alhede, Morten

AU - Maw, Myat T

AU - Liu, Yang

AU - Purbojati, Rikky W

AU - Yap, Zhei H

AU - Kushwaha, Kavita K

AU - Gheorghe, Alexandra G

AU - Bjarnsholt, Thomas

AU - Hansen, Gorm M

AU - Sillesen, Henrik

AU - Hougen, Hans P

AU - Hansen, Peter R

AU - Yang, Liang

AU - Tolker-Nielsen, Tim

AU - Schuster, Stephan C

AU - Givskov, Michael

PY - 2015/9/3

Y1 - 2015/9/3

N2 - 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.

AB - 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.

U2 - 10.1186/s40168-015-0100-y

DO - 10.1186/s40168-015-0100-y

M3 - Journal article

C2 - 26334731

SN - 2049-2618

VL - 3

SP - 1

EP - 14

JO - Microbiome

JF - Microbiome

M1 - 38

ER -

In silico analyses of metagenomes from human atherosclerotic plaque samples

Abstract

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