Profiling skin microbiome and metabolome has been utilised to gain further insight into wound healing processes. The aims of this multi-part temporal study in 11 volunteers were to analytically ...profile the dynamic wound tissue and headspace metabolome and sequence microbial communities in acute wound healing at days 0, 7, 14, 21 and 28, and to investigate their relationship to wound healing, using non-invasive quantitative devices. Metabolites were obtained using tissue extraction, sorbent and polydimethylsiloxane patches and analysed using GCMS. PCA of wound tissue metabolome clearly separated time points with 10 metabolites of 346 being involved in separation. Analysis of variance-simultaneous component analysis identified a statistical difference between the wound headspace metabolome, sites (P = 0.0024) and time points (P<0.0001), with 10 out of the 129 metabolites measured involved with this separation between sites and time points. A reciprocal relationship between Staphylococcus spp. and Propionibacterium spp. was observed at day 21 (P<0.05) with a statistical correlation between collagen and Propionibacterium (r = 0.417; P = 0.038) and Staphylococcus (r = -0.434; P = 0.03). Procrustes analysis showed a statistically significant similarity between wound headspace and tissue metabolome with non-invasive wound devices. This exploratory study demonstrates the temporal and dynamic nature of acute wound metabolome and microbiome presenting a novel class of biomarkers that correspond to wound healing, with further confirmatory studies now necessary.
Inflammation is strongly implicated in both injury and repair processes occurring after stroke. In this exploratory study we assessed the feasibility of repeated sampling of exhaled volatile organic ...compounds and performed an untargeted metabolomic analysis of plasma collected at multiple time periods after stroke. Metabolic profiles were compared with the time course of the inflammatory markers C-reactive protein (CRP) and interleukin-6 (IL-6). Serial breath sampling was well-tolerated by all patients and the measurement appears feasible in this group. We found that exhaled decanal tracks CRP and IL-6 levels post-stroke and correlates with several metabolic pathways associated with a post-stroke inflammatory response. This suggests that measurement of breath and blood metabolites could facilitate development of novel therapeutic and diagnostic strategies. Results are discussed in relation to the utility of breath analysis in stroke care, such as in monitoring recovery and complications including stroke associated infection.
The use of next generation sequencing (NGS) to identify novel viral sequences from eukaryotic tissue samples is challenging. Issues can include the low proportion and copy number of viral reads and ...the high number of contigs (post-assembly), making subsequent viral analysis difficult. Comparison of assembly algorithms with pre-assembly host-mapping subtraction using a short-read mapping tool, a k-mer frequency based filter and a low complexity filter, has been validated for viral discovery with Illumina data derived from naturally infected liver tissue and simulated data. Assembled contig numbers were significantly reduced (up to 99.97%) by the application of these pre-assembly filtering methods. This approach provides a validated method for maximizing viral contig size as well as reducing the total number of assembled contigs that require down-stream analysis as putative viral nucleic acids.
Metabolomics refers to study of the metabolome, the entire set of metabolites produced by a biological system. The application of metabolomics to exhaled breath samples - breathomics - is a rapidly ...growing field with potential application to asthma diagnosis and management.
We aimed to review the adult asthma breathomic literature and present a comprehensive list of volatile organic compounds identified by asthma breathomic models.
We undertook a systematic search for literature on exhaled volatile organic compounds in adult asthma. We assessed the quality of studies and performed a qualitative synthesis.
We identified twenty studies; these were methodologically heterogenous with a variable risk of bias. Studies almost universally reported breathomics to be capable of differentiating - with moderate or greater accuracy - between samples from healthy controls and those with asthma; and to be capable of phenotyping disease. However, there was little concordance in the compounds upon which discriminatory models were based.
Results to-date are promising but validation in independent prospective cohorts is needed. This may be challenging given the high levels of inter-individual variation. However, large-scale, multi-centre studies are underway and validation efforts have been aided by the publication of technical standards likely to increase inter-study comparability. Successful validation of breathomic models for diagnosis and phenotyping would constitute an important step towards personalised medicine in asthma.
•The majority of published studies report breathomics capable of differentiating between samples from healthy controls, those with asthma, and those with other respiratory disease.•Of the seventy six volatile organic compounds cited as significant in the literature, nine were reported in more than one paper.•Validation ofthese findings in independent prospective cohorts is the next step in developing disease biomarkers.
Offline breath analysis by thermal desorption gas chromatography mass spectrometry (TD-GC-MS) requires the use of sorbent traps to concentrate and store volatile compounds. The selection of which ...sorbent to use and best practices for managing high relative humidity are important considerations to allow for reproducible, untargeted, biomarker discovery in water saturated breath samples. This work aims to assess three commonly used sorbent materials for their use in breath volatile sampling and determine how the high relative humidity inherent in such samples effects the capture of volatile compounds of interest. TenaxGR, TenaxTA/Carbograph1TD and TenaxTA/Carbograph5TD tubes were selected as they are the most commonly used sorbents in the breath sampling literature. The recovery of 29 compounds in a standard mix loaded using high humidity gas was tested for each sorbent and compared to loading in dry gas. Water retention and dry purge rates were determined for each sorbent for 500 ml and 1000 ml breath collections. Finally, breath samples were collected simultaneously on to each sorbent type using the ReCIVA and analysed by TD-GC-MS. All three sorbents exhibited acceptable reproducibility when loaded with the standard mix in dry gas (RSD < 10%). Loading the standard mix in humid gas led to reduced recovery of compounds based on their chemical properties. Dry purging performance for each sorbent material was assessed and was shown to be 1.14, 1.13 and 0.89 mg H2O min−1 for TenaxGR, TenaxTA/Carbograph1TD and TenaxTA/Carbograph5TD respectively when flushed with 50 ml min−1 of N2. A comparison of breath profiles on different sorbents showed differences in background artefacts (sulfur dioxide, cyclopenten-1-one and 3-nonene) and endogenous breath compounds (2-methyl-furan and furfural). This work demonstrates that high relative humidity during sampling reduces the ability of sorbent tubes to capture volatile compounds and could impact method detection limits during breath sampling. Sufficient water to impair accurate analysis was retained on all tubes. Minimal differences were observed between sorbent materials when used to sample breath, however, suggestions are provided for sorbent selection for future studies.
Abstract
EBI metagenomics (http://www.ebi.ac.uk/metagenomics) provides a free to use platform for the analysis and archiving of sequence data derived from the microbial populations found in a ...particular environment. Over the past two years, EBI metagenomics has increased the number of datasets analysed 10-fold. In addition to increased throughput, the underlying analysis pipeline has been overhauled to include both new or updated tools and reference databases. Of particular note is a new workflow for taxonomic assignments that has been extended to include assignments based on both the large and small subunit RNA marker genes and to encompass all cellular micro-organisms. We also describe the addition of metagenomic assembly as a new analysis service. Our pilot studies have produced over 2400 assemblies from datasets in the public domain. From these assemblies, we have produced a searchable, non-redundant protein database of over 50 million sequences. To provide improved access to the data stored within the resource, we have developed a programmatic interface that provides access to the analysis results and associated sample metadata. Finally, we have integrated the results of a series of statistical analyses that provide estimations of diversity and sample comparisons.
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