Limits...
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.

Show MeSH

Related in: MedlinePlus

Alignment of contigs with sequences that could potentially be derived from food. Selected BLAST hits aligned using MAFFT and visualised with Jalview, coloured by BLOSUM62 score. A) Contig 2129 exhibits complete identity across the kingdom Viridiplantae 28S rRNA. Alignment with potential dietary plant and meat foodstuffs and the human rRNA gene. B) Contig 2062 is very similar to many chloroplast rRNA sequences and is shown aligned to several of the best hits and potential dietary sources. 1 - Pseudendoclonium akinetum: 2 - Trichosarcina mucosa: 3 - Lycopodium clavatum: 4 - Zygnema: 5 - Solanum Lycopersicum: 6 - Solanum tuberosum: C) All the lineages to which Contig 1748 has a perfect match, including many potential food sources. Representative sequences from each species are aligned and coloured by percentage identity (1: Fragaria vesca, 2: Medicago truncatula, 3: Lotus japonicus, 4: Glycine max, 5: Arabidopsis thaliana, 6: Solanum lycopersicum, NB: A 30 bp insertion present in Glycine max immediately 5 prime of the contig 1748 sequence is omitted to facilitate visualisation). Full lineage of core eudicotyledons is [root; cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; eudicotyledons].
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig4: Alignment of contigs with sequences that could potentially be derived from food. Selected BLAST hits aligned using MAFFT and visualised with Jalview, coloured by BLOSUM62 score. A) Contig 2129 exhibits complete identity across the kingdom Viridiplantae 28S rRNA. Alignment with potential dietary plant and meat foodstuffs and the human rRNA gene. B) Contig 2062 is very similar to many chloroplast rRNA sequences and is shown aligned to several of the best hits and potential dietary sources. 1 - Pseudendoclonium akinetum: 2 - Trichosarcina mucosa: 3 - Lycopodium clavatum: 4 - Zygnema: 5 - Solanum Lycopersicum: 6 - Solanum tuberosum: C) All the lineages to which Contig 1748 has a perfect match, including many potential food sources. Representative sequences from each species are aligned and coloured by percentage identity (1: Fragaria vesca, 2: Medicago truncatula, 3: Lotus japonicus, 4: Glycine max, 5: Arabidopsis thaliana, 6: Solanum lycopersicum, NB: A 30 bp insertion present in Glycine max immediately 5 prime of the contig 1748 sequence is omitted to facilitate visualisation). Full lineage of core eudicotyledons is [root; cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; eudicotyledons].

Mentions: A small percentage of contigs matched plant sequences, but due to the conservation of rRNA across the kingdom Viridiplantae, the top blast hits did not reliably identify their source, but rather reflected the composition of the database (a preponderance of algal sequences was observed). However, in most instances the sequences were sufficiently divergent from human rRNA to support the notion that they are derived from dietary plant material (Figure 4).Figure 4


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)

Alignment of contigs with sequences that could potentially be derived from food. Selected BLAST hits aligned using MAFFT and visualised with Jalview, coloured by BLOSUM62 score. A) Contig 2129 exhibits complete identity across the kingdom Viridiplantae 28S rRNA. Alignment with potential dietary plant and meat foodstuffs and the human rRNA gene. B) Contig 2062 is very similar to many chloroplast rRNA sequences and is shown aligned to several of the best hits and potential dietary sources. 1 - Pseudendoclonium akinetum: 2 - Trichosarcina mucosa: 3 - Lycopodium clavatum: 4 - Zygnema: 5 - Solanum Lycopersicum: 6 - Solanum tuberosum: C) All the lineages to which Contig 1748 has a perfect match, including many potential food sources. Representative sequences from each species are aligned and coloured by percentage identity (1: Fragaria vesca, 2: Medicago truncatula, 3: Lotus japonicus, 4: Glycine max, 5: Arabidopsis thaliana, 6: Solanum lycopersicum, NB: A 30 bp insertion present in Glycine max immediately 5 prime of the contig 1748 sequence is omitted to facilitate visualisation). Full lineage of core eudicotyledons is [root; cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; eudicotyledons].
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig4: Alignment of contigs with sequences that could potentially be derived from food. Selected BLAST hits aligned using MAFFT and visualised with Jalview, coloured by BLOSUM62 score. A) Contig 2129 exhibits complete identity across the kingdom Viridiplantae 28S rRNA. Alignment with potential dietary plant and meat foodstuffs and the human rRNA gene. B) Contig 2062 is very similar to many chloroplast rRNA sequences and is shown aligned to several of the best hits and potential dietary sources. 1 - Pseudendoclonium akinetum: 2 - Trichosarcina mucosa: 3 - Lycopodium clavatum: 4 - Zygnema: 5 - Solanum Lycopersicum: 6 - Solanum tuberosum: C) All the lineages to which Contig 1748 has a perfect match, including many potential food sources. Representative sequences from each species are aligned and coloured by percentage identity (1: Fragaria vesca, 2: Medicago truncatula, 3: Lotus japonicus, 4: Glycine max, 5: Arabidopsis thaliana, 6: Solanum lycopersicum, NB: A 30 bp insertion present in Glycine max immediately 5 prime of the contig 1748 sequence is omitted to facilitate visualisation). Full lineage of core eudicotyledons is [root; cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; eudicotyledons].
Mentions: A small percentage of contigs matched plant sequences, but due to the conservation of rRNA across the kingdom Viridiplantae, the top blast hits did not reliably identify their source, but rather reflected the composition of the database (a preponderance of algal sequences was observed). However, in most instances the sequences were sufficiently divergent from human rRNA to support the notion that they are derived from dietary plant material (Figure 4).Figure 4

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