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Small RNAs from plants, bacteria and fungi within the order Hypocreales are ubiquitous in human plasma.

Beatty M, Guduric-Fuchs J, Brown E, Bridgett S, Chakravarthy U, Hogg RE, Simpson DA - BMC Genomics (2014)

Bottom Line: The human microbiome plays a significant role in maintaining normal physiology.The source and functions of these molecules remain to be determined, but the specific profiles are likely to reflect health status.The potential to provide biomarkers of diet and for the diagnosis and prognosis of human disease is immense.

View Article: PubMed Central - PubMed

Affiliation: Centre for Experimental Medicine, Queen's University Belfast, Belfast, Northern Ireland, UK. David.Simpson@qub.ac.uk.

ABSTRACT

Background: The human microbiome plays a significant role in maintaining normal physiology. Changes in its composition have been associated with bowel disease, metabolic disorders and atherosclerosis. Sequences of microbial origin have been observed within small RNA sequencing data obtained from blood samples. The aim of this study was to characterise the microbiome from which these sequences are derived.

Results: Abundant non-human small RNA sequences were identified in plasma and plasma exosomal samples. Assembly of these short sequences into longer contigs was the pivotal novel step in ascertaining their origin by BLAST searches. Most reads mapped to rRNA sequences. The taxonomic profiles of the microbes detected were very consistent between individuals but distinct from microbiomes reported at other sites. The majority of bacterial reads were from the phylum Proteobacteria, whilst for 5 of 6 individuals over 90% of the more abundant fungal reads were from the phylum Ascomycota; of these over 90% were from the order Hypocreales. Many contigs were from plants, presumably of dietary origin. In addition, extremely abundant small RNAs derived from human Y RNAs were detected.

Conclusions: A characteristic profile of a subset of the human microbiome can be obtained by sequencing small RNAs present in the blood. The source and functions of these molecules remain to be determined, but the specific profiles are likely to reflect health status. The potential to provide biomarkers of diet and for the diagnosis and prognosis of human disease is immense.

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Related in: MedlinePlus

Schema of the strategy for analysis of sequencing data. Reads that did not align to human sequences or other known microRNAs were assembled into contigs. These were annotated by BLAST alignment to the NCBI nr database and phylogenetic analysis performed with the gi numbers of the top resulting hits.
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Fig1: Schema of the strategy for analysis of sequencing data. Reads that did not align to human sequences or other known microRNAs were assembled into contigs. These were annotated by BLAST alignment to the NCBI nr database and phylogenetic analysis performed with the gi numbers of the top resulting hits.

Mentions: RNA was extracted from three plasma samples and small RNA libraries prepared using an Illumina kit. Each library was sequenced on a MiSeq (Illumina). The unique reads and raw sequencing data have been deposited in Gene Expression Omnibus (GEO), accession number GSE52981. Sequencing data for three plasma exosomal small RNA libraries prepared with a kit from Bioo Scientific were downloaded from GEO[28]. For one of these samples data from libraries prepared with an NEB kit and an Illumina kit (as used in this study) were also available. The strategy for analysis of the sequencing data was to filter out reads derived from human genes, assemble the remaining reads into contigs, annotate these by alignment to known sequences and perform a phylogenetic classification (FigureĀ 1).Figure 1


Small RNAs from plants, bacteria and fungi within the order Hypocreales are ubiquitous in human plasma.

Beatty M, Guduric-Fuchs J, Brown E, Bridgett S, Chakravarthy U, Hogg RE, Simpson DA - BMC Genomics (2014)

Schema of the strategy for analysis of sequencing data. Reads that did not align to human sequences or other known microRNAs were assembled into contigs. These were annotated by BLAST alignment to the NCBI nr database and phylogenetic analysis performed with the gi numbers of the top resulting hits.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4230795&req=5

Fig1: Schema of the strategy for analysis of sequencing data. Reads that did not align to human sequences or other known microRNAs were assembled into contigs. These were annotated by BLAST alignment to the NCBI nr database and phylogenetic analysis performed with the gi numbers of the top resulting hits.
Mentions: RNA was extracted from three plasma samples and small RNA libraries prepared using an Illumina kit. Each library was sequenced on a MiSeq (Illumina). The unique reads and raw sequencing data have been deposited in Gene Expression Omnibus (GEO), accession number GSE52981. Sequencing data for three plasma exosomal small RNA libraries prepared with a kit from Bioo Scientific were downloaded from GEO[28]. For one of these samples data from libraries prepared with an NEB kit and an Illumina kit (as used in this study) were also available. The strategy for analysis of the sequencing data was to filter out reads derived from human genes, assemble the remaining reads into contigs, annotate these by alignment to known sequences and perform a phylogenetic classification (FigureĀ 1).Figure 1

Bottom Line: The human microbiome plays a significant role in maintaining normal physiology.The source and functions of these molecules remain to be determined, but the specific profiles are likely to reflect health status.The potential to provide biomarkers of diet and for the diagnosis and prognosis of human disease is immense.

View Article: PubMed Central - PubMed

Affiliation: Centre for Experimental Medicine, Queen's University Belfast, Belfast, Northern Ireland, UK. David.Simpson@qub.ac.uk.

ABSTRACT

Background: The human microbiome plays a significant role in maintaining normal physiology. Changes in its composition have been associated with bowel disease, metabolic disorders and atherosclerosis. Sequences of microbial origin have been observed within small RNA sequencing data obtained from blood samples. The aim of this study was to characterise the microbiome from which these sequences are derived.

Results: Abundant non-human small RNA sequences were identified in plasma and plasma exosomal samples. Assembly of these short sequences into longer contigs was the pivotal novel step in ascertaining their origin by BLAST searches. Most reads mapped to rRNA sequences. The taxonomic profiles of the microbes detected were very consistent between individuals but distinct from microbiomes reported at other sites. The majority of bacterial reads were from the phylum Proteobacteria, whilst for 5 of 6 individuals over 90% of the more abundant fungal reads were from the phylum Ascomycota; of these over 90% were from the order Hypocreales. Many contigs were from plants, presumably of dietary origin. In addition, extremely abundant small RNAs derived from human Y RNAs were detected.

Conclusions: A characteristic profile of a subset of the human microbiome can be obtained by sequencing small RNAs present in the blood. The source and functions of these molecules remain to be determined, but the specific profiles are likely to reflect health status. The potential to provide biomarkers of diet and for the diagnosis and prognosis of human disease is immense.

Show MeSH
Related in: MedlinePlus