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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

Order-level phylogenetic profile of fungal small RNAs. The tree illustrates the taxonomic composition of the contigs derived from small RNAs isolated from the plasma samples of six individuals. All orders within the kingdom Fungi which have matching sequences are illustrated. The numbers of contigs assigned to each taxonomic group are indicated within the tree. The numbers on the right are the total number of reads assigned to each order; the order Hypocreales, highlighted in green, is the most abundant.
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Fig5: Order-level phylogenetic profile of fungal small RNAs. The tree illustrates the taxonomic composition of the contigs derived from small RNAs isolated from the plasma samples of six individuals. All orders within the kingdom Fungi which have matching sequences are illustrated. The numbers of contigs assigned to each taxonomic group are indicated within the tree. The numbers on the right are the total number of reads assigned to each order; the order Hypocreales, highlighted in green, is the most abundant.

Mentions: The phylogenetic profile of the bacterial microbiome was remarkably similar between individuals (Figure 2C), with Proteobacteria being the most abundant phylum. This is consistent with an origin in the gut. The number of reads matching fungal sequences was higher than expected and of these, more than 90% in 5 of 6 individuals were from the phylum Ascomycetes (Figure 2D). Remarkably, it was possible to further define the origin of almost all these reads to within the class Sordariomycetes and order Hypocreales (Figure 2E-F). The predominance of sequences from the Hypocreales is illustrated when the numbers of reads mapping to each fungal order are placed on a phylogenetic tree comprising all orders with at least one matching contig (Figure 5).Figure 5


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)

Order-level phylogenetic profile of fungal small RNAs. The tree illustrates the taxonomic composition of the contigs derived from small RNAs isolated from the plasma samples of six individuals. All orders within the kingdom Fungi which have matching sequences are illustrated. The numbers of contigs assigned to each taxonomic group are indicated within the tree. The numbers on the right are the total number of reads assigned to each order; the order Hypocreales, highlighted in green, is the most abundant.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig5: Order-level phylogenetic profile of fungal small RNAs. The tree illustrates the taxonomic composition of the contigs derived from small RNAs isolated from the plasma samples of six individuals. All orders within the kingdom Fungi which have matching sequences are illustrated. The numbers of contigs assigned to each taxonomic group are indicated within the tree. The numbers on the right are the total number of reads assigned to each order; the order Hypocreales, highlighted in green, is the most abundant.
Mentions: The phylogenetic profile of the bacterial microbiome was remarkably similar between individuals (Figure 2C), with Proteobacteria being the most abundant phylum. This is consistent with an origin in the gut. The number of reads matching fungal sequences was higher than expected and of these, more than 90% in 5 of 6 individuals were from the phylum Ascomycetes (Figure 2D). Remarkably, it was possible to further define the origin of almost all these reads to within the class Sordariomycetes and order Hypocreales (Figure 2E-F). The predominance of sequences from the Hypocreales is illustrated when the numbers of reads mapping to each fungal order are placed on a phylogenetic tree comprising all orders with at least one matching contig (Figure 5).Figure 5

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