The microbiome of diabetic foot ulcers: a comparison of swab and tissue biopsy wound sampling techniques using 16S rRNA gene sequencing.

BACKGROUND: Health-care professionals need to collect wound samples to identify potential pathogens that contribute to wound infection. Obtaining appropriate samples from diabetic foot ulcers (DFUs) where there is a suspicion of infection is of high importance. Paired swabs and tissue biopsies were collected from DFUs and both sampling techniques were compared using 16S rRNA gene sequencing. RESULTS: Mean bacterial abundance determined using quantitative polymerase chain reaction (qPCR) was significantly lower in tissue biopsies (p = 0.03). The mean number of reads across all samples was significantly higher in wound swabs [Formula: see text] = 32,014) compared to tissue ([Formula: see text] = 15,256, p = 0.001). Tissue biopsies exhibited greater overall diversity of bacteria relative to swabs (Shannon's H diversity p = 0.009). However, based on a presence/absence analysis of all paired samples, the frequency of occurrence of bacteria from genera of known and potential pathogens was generally higher in wound swabs than tissue biopsies. Multivariate analysis identified significantly different bacterial communities in swabs compared to tissue (p = 0.001). There was minimal correlation between paired wound swabs and tissue biopsies in the number and types of microorganisms. RELATE analysis revealed low concordance between paired DFU swab and tissue biopsy samples (Rho = 0.043, p = 0.34). CONCLUSIONS: Using 16S rRNA gene sequencing this study identifies the potential for using less invasive swabs to recover high relative abundances of known and potential pathogen genera from DFUs when compared to the gold standard collection method of tissue biopsy.

Metabolite mapping by consecutive nanostructure and silver-assisted mass spectrometry imaging on tissue sections.

RATIONALE: Nanostructure-based mass spectrometry imaging (MSI) is a promising technology for molecular imaging of small molecules, without the complex chemical background typically encountered in matrix-assisted molecular imaging approaches. Here, we have enhanced these surfaces with silver (Ag) to provide a second tier of MSI data from a single sample. METHODS: MSI data was acquired through the application of laser desorption/ionization mass spectrometry to biological samples imprinted onto desorption/ionization on silicon (DIOS) substrates. Following initial analysis, ultra-thin Ag layers were overlaid onto the followed by MSI analysis (Ag-DIOS MSI). This approach was first demonstrated for fingermark small molecules including environmental contaminants and sebum components. Subsequently, this bimodal method was translated to lipids and metabolites in fore-stomach sections from a 6-bromoisatin chemopreventative murine mouse model. RESULTS: DIOS MSI allowed mapping of common ions in fingermarks as well as 6-bromoisatin metabolites and lipids in murine fore-stomach. Furthermore, DIOS MSI was complemented by the Ag-DIOS MSI of Ag-adductable lipids such as wax esters in fingermarks and cholesterol in murine fore-stomach. Gastrointestinal acid condensation products of 6-bromoisatin, such as the 6,6'-dibromoindirubin mapped herein, are very challenging to isolate and characterize. By re-analyzing the same tissue imprints, this metabolite was readily detected by DIOS, placed in a tissue-specific spatial context, and subsequently overlaid with additional lipid distributions acquired using Ag-DIOS MSI. CONCLUSIONS: The ability to place metabolite and lipid classes in a tissue-specific context makes this novel method suited to MSI analyses where the collection of additional information from the same sample maximises resource use, and also maximises the number of annotated small molecules, in particular for metabolites that are typically undetectable with traditional platforms. Copyright © 2017 John Wiley & Sons, Ltd.

Arbuscular mycorrhizal fungi: effects on plant terpenoid accumulation.

Arbuscular mycorrhizal fungi (AMF) are a diverse group of soil-dwelling fungi that form symbiotic associations with land plants. AMF-plant associations promote the accumulation of plant terpenoids beneficial to human health, although how AMF mediate terpenoid accumulation is not fully understood. A critical assessment and discussion of the literature relating to mechanisms by which AMF influence plant terpenoid accumulation, and whether this symbiosis can be harnessed in horticultural ecosystems was performed. Modification of plant morphology, phosphorus availability and gene transcription involved with terpenoid biosynthetic pathways were identified as key mechanisms associated with terpenoid accumulation in AMF-colonised plants. In order to exploit AMF-plant symbioses in horticultural ecosystems it is important to consider the specificity of the AMF-plant association, the predominant factor affecting terpenoid accumulation, as well as the end use application of the harvested plant material. Future research should focus on resolving the relationship between ecologically matched AMF genotypes and terpenoid accumulation in plants to establish if these associations are effective in promoting mechanisms favourable for plant terpenoid accumulation.

A quantitative survey of mycosporine-like amino acids (MAAS) in intertidal egg masses from temperate rocky shores.

Mycosporine-like amino acids (MAAs) have been reported as functional chemical sunscreens in a variety of marine organisms, but their role in development of marine embryos and larvae remains largely unexplored. In this study, we quantified MAAs from intertidal egg masses of 46 species of mollusks, two species of polychaetes, and one species of fish from southeastern Australia. We aimed to elucidate potential patterns of occurrence and variation based on egg mass maturity, adult diet, spawning habitat, phylogeny, and viability. Our analyses revealed that maturity and spawning habitat did not affect MAA composition within egg masses. In contrast, adult diet, phylogeny, and viability affected MAA composition. Herbivores had higher levels of certain MAAs than carnivores; similarly, viable egg masses had higher levels of some MAAs than inviable ones. MAA composition varied according to the taxonomic group, with nudibranchs and anaspids showing different MAA composition compared to that of neogastropods, sacoglossans, and polychaetes. Basommatophoran egg masses had more porphyra-334 than the other taxa, and anaspids had more mycosporine-2-glycine than the other groups. MAAs occurred in relatively high concentrations in intertidal molluskan egg masses when compared to adult mollusks and other common intertidal organisms. Despite the complexity of factors affecting MAA composition, the prevalence of MAAs in some species is consistent with protection afforded to offspring against negative effects of UV radiation.

Chemical defense in the egg masses of benthic invertebrates: an assessment of antibacterial activity in 39 mollusks and 4 polychaetes.

Many marine invertebrates deposit benthic egg masses that are potentially vulnerable to microbial infection. To help counter this threat these species may have evolved some form of chemical protection for their encapsulated embryos. In this study the egg masses from 7 marine mollusks were tested for antibacterial activity against 4 marine pathogens: Enterococcus sericolicida, Vibrio anguillarum, Vibrio alginolyticus, and Vibrio harveyi. Extracts from all of these egg masses were found to inhibit the growth of at least 1 marine bacterium at concentrations that approximate the natural concentration of extract in the egg masses. The egg masses of 39 mollusks and 4 polychaetes were then tested for antibacterial activity against 3 human pathogenic bacteria; Escherichia coli, Staphylococcus aureus, and Pseudomonas aeruginosa. Activity was detected in the egg masses from 34 species, including 2 polychaetes and mollusks from two classes and 18 families. Antibacterial activity in molluskan egg masses was found to extend across the marine, estuarine, freshwater, and terrestrial environments. Both gelatinous egg masses and tough egg capsules were found to inhibit microbial growth, suggesting that physical protection alone may not be sufficient to protect the eggs. Antimicrobial activity was observed in the fresh egg masses but not in the well-developed egg masses of a subset of species. The results of this study indicate that a wide range of invertebrates use chemical defense to protect their early stage embryos against bacterial infection.