Nucleic acid-based approaches to investigate microbial-related cheese quality defects

peer-reviewedThe microbial profile of cheese is a primary determinant of cheese quality. Microorganisms can contribute to aroma and taste defects, form biogenic amines, cause gas and secondary fermentation defects, and can contribute to cheese pinking and mineral deposition issues. These defects may be as a result of seasonality and the variability in the composition of the milk supplied, variations in cheese processing parameters, as well as the nature and number of the non-starter microorganisms which come from the milk or other environmental sources. Such defects can be responsible for production and product recall costs and thus represent a significant economic burden for the dairy industry worldwide. Traditional non-molecular approaches are often considered biased and have inherently slow turnaround times. Molecular techniques can provide early and rapid detection of defects that result from the presence of specific spoilage microbes and, ultimately, assist in enhancing cheese quality and reducing costs. Here we review the DNA-based methods that are available to detect/quantify spoilage bacteria, and relevant metabolic pathways in cheeses and, in the process, highlight how these strategies can be employed to improve cheese quality and reduce the associated economic burden on cheese processors.This work was funded by the Department of Agriculture, Food and the Marine under the Food Institutional Research Measure. Daniel J. O’Sullivan is in receipt of a Teagasc Walsh Fellowship, Grant Number:2012205

Temporal and spatial differences in microbial composition during the manufacture of a Continental-type cheese

peer-reviewedWe sought to determine if the time, within a production day, that a cheese is manufactured has an influence on the microbial community present within that cheese. To facilitate this, 16S rRNA amplicon sequencing was used to elucidate the microbial community dynamics of brine salted Continental-type cheese in cheeses produced early and late in the production day. Differences in microbial composition of the core and rind of the cheese were also investigated. Throughout ripening, it was apparent that late production day cheeses had a more diverse microbial population than their early day equivalents. Spatial variation between the cheese core and rind was also noted in that cheese rinds were found to initially have a more diverse microbial population but thereafter the opposite was the case. Interestingly, the genera Thermus, Pseudoalteromonas and Bifidobacterium, not routinely associated with a Continental-type cheese produced from pasteurised milk were detected. The significance, if any, of the presence of these genera will require further attention. Ultimately, the use of high throughput sequencing has facilitated a novel and detailed analysis of the temporal and spatial distribution of microbes in this complex cheese system and established that the period during a production cycle at which a cheese is manufactured can influence its microbial composition.This work was funded by the Department of Agriculture, Food and the Marine under the Food Institutional Research Measure through the ‘Cheeseboard 2015’ project. Daniel J. O’Sullivan is in receipt of a Teagasc Walsh Fellowship, Grant Number: 201220

High-throughput DNA sequencing to survey bacterial histidine and tyrosine decarboxylases in raw milk cheeses

peer-reviewedBackground The aim of this study was to employ high-throughput DNA sequencing to assess the incidence of bacteria with biogenic amine (BA; histamine and tyramine) producing potential from among 10 different cheeses varieties. To facilitate this, a diagnostic approach using degenerate PCR primer pairs that were previously designed to amplify segments of the histidine (hdc) and tyrosine (tdc) decarboxylase gene clusters were employed. In contrast to previous studies in which the decarboxylase genes of specific isolates were studied, in this instance amplifications were performed using total metagenomic DNA extracts. Results Amplicons were initially cloned to facilitate Sanger sequencing of individual gene fragments to ensure that a variety of hdc and tdc genes were present. Once this was established, high throughput DNA sequencing of these amplicons was performed to provide a more in-depth analysis of the histamine- and tyramine-producing bacteria present in the cheeses. High-throughput sequencing resulted in generation of a total of 1,563,764 sequencing reads and revealed that Lactobacillus curvatus, Enterococcus faecium and E. faecalis were the dominant species with tyramine producing potential, while Lb. buchneri was found to be the dominant species harbouring histaminogenic potential. Commonly used cheese starter bacteria, including Streptococcus thermophilus and Lb. delbreueckii, were also identified as having biogenic amine producing potential in the cheese studied. Molecular analysis of bacterial communities was then further complemented with HPLC quantification of histamine and tyramine in the sampled cheeses. Conclusions In this study, high-throughput DNA sequencing successfully identified populations capable of amine production in a variety of cheeses. This approach also gave an insight into the broader hdc and tdc complement within the various cheeses. This approach can be used to detect amine producing communities not only in food matrices but also in the production environment itself.This work was funded by the Department of Agriculture, Food and the Marine under the Food Institutional Research Measure through the ‘Cheeseboard 2015’ project. Daniel J. O’Sullivan is in receipt of a Teagasc Walsh Fellowship, Grant Number: 2012205

Plausible Constraints on the Range of Bulk Terrestrial Exoplanet Compositions in the Solar Neighborhood

Rocky planet compositions regulate planetary evolution by affecting core sizes, mantle properties, and melting behaviors. Yet, quantitative treatments of this aspect of exoplanet studies remain generally underexplored. We attempt to constrain the range of potential bulk terrestrial exoplanet compositions in the solar neighborhood (<200 pc). We circumscribe probable rocky exoplanet compositions based on a population analysis of stellar chemical abundances from the Hypatia and GALAH catalogs. We apply a devolatilization model to simulate compositions of hypothetical, terrestrial-type exoplanets in the habitable zones around Sun-like stars, considering elements O, S, Na, Si, Mg, Fe, Ni, Ca, and Al. We further apply core-mantle differentiation by assuming constant oxygen fugacity, and model the consequent mantle mineralogy with a Gibbs energy minimization algorithm. We report statistics on several compositional parameters and propose a reference set of (21) representative planet compositions for use as end-member compositions in imminent modeling and experimental studies. We find a strong correlation between stellar Fe/Mg and metallic-core sizes, which can vary from 18 to 35 wt%. Furthermore, stellar Mg/Si gives a first-order indication of mantle mineralogy, with high-Mg/Si stars leading to weaker, ferropericlase-rich mantles, and low-Mg/Si stars leading to mechanically stronger mantles. The element Na, which modulates crustal buoyancy and mantle clinopyroxene fraction, is affected by devolatilization the most. While we find that planetary mantles mostly consist of Fe/Mg silicates, the core sizes and relative abundances of common minerals can nevertheless vary significantly among exoplanets. These differences likely lead to different evolutionary pathways among rocky exoplanets in the solar neighborhood

Sequencing of the Cheese Microbiome and Its Relevance to Industry

peer-reviewedThe microbiota of cheese plays a key role in determining its organoleptic and other physico-chemical properties. It is essential to understand the various contributions, positive or negative, of these microbial components in order to promote the growth of desirable taxa and, thus, characteristics. The recent application of high throughput DNA sequencing (HTS) facilitates an even more accurate identification of these microbes, and their functional properties, and has the potential to reveal those microbes, and associated pathways, responsible for favorable or unfavorable characteristics. This technology also facilitates a detailed analysis of the composition and functional potential of the microbiota of milk, curd, whey, mixed starters, processing environments, and how these contribute to the final cheese microbiota, and associated characteristics. Ultimately, this information can be harnessed by producers to optimize the quality, safety, and commercial value of their products. In this review we highlight a number of key studies in which HTS was employed to study the cheese microbiota, and pay particular attention to those of greatest relevance to industry

Supercapacitor Degradation: Understanding Mechanisms of Cycling-Induced Deterioration and Failure of a Pseudocapacitor

Owing to a reputation for long lifetimes and excellent cycle stability, degradation in supercapacitors has largely been overlooked. In this work, we demonstrate that significant degradation in some commercial supercapacitors can in fact occur early in their life, leading to a rapid loss in capacitance, especially when utilized in full voltage range, high charge-discharge frequency applications. By using a commercial 300 F lithium-ion pseudocapacitor rated for 100,000 charge/discharge cycles as an example system, it is shown that a ∼96 % loss in capacitance over the first ∼2000 cycles is caused by significant structural and chemical change in the cathode active material (LiMn2O4, LMO). Multi-scale in-situ and ex-situ characterization, using a combination of X-ray computed tomography, Raman spectroscopy and X-ray photoelectron spectroscopy, shows that while minimal material loss (∼5.5 %), attributed to the dissolution of Mn2+, is observed, the primary mode of degradation is due to manganese charge disproportionation (Mn3+→Mn4++Mn2+) and its physical consequences (i. e. microstrain formation, particle fragmentation, loss of conductivity etc.). In contrast to prior understanding of LMO material degradation in battery systems, negligible contributions from cubic-to-tetragonal phase transitions are observed. Hence, as supercapacitors are becoming more widely utilized in real-world applications, this work demonstrates that it is vital to understand the mechanisms by which this family of devices change during their lifetimes, not just for lithium-ion pseudocapacitors, but for a wide range of commercial chemistries

Trends in the knowledge, attitudes and practices of travel risk groups towards prevention of malaria: Results from the Dutch Schiphol airport survey 2002 to 2009

Background: Previous studies investigating the travellers knowledge, attitudes and practices (KAP) profile indicated an important educational need among those travelling to risk destinations. Initiatives to improve such education should target all groups of travellers, including business travellers, those visiting friends and relatives (VFRs), and elderly travellers. Methods: In the years 2002 to 2009, a questionnaire-based survey was conducted at the Dutch Schiphol Airport with the aim to study trends in KAP of travel risk groups towards prevention of malaria. The risk groups last-minute travellers, solo-travellers, business travellers, VFRs and elderly travellers were specifically studied. Results: A total of 3,045 respondents were included in the survey. Travellers to destinations with a high risk for malaria had significantly more accurate risk perceptions (knowledge) than travellers to low-risk destinations. The relative risk for malaria in travellers to high-risk destinations was probably mitigated by higher protection rates against malaria as compared with travellers to low risk destinations. There were no significant differences in intended risk-taking behaviour. Trend analyses showed a significant change over time in attitude towards more risk-avoiding behaviour and towards higher protection rates against malaria in travellers to high-risk destinations. The KAP profile of last-minute travellers substantially increased their relative risk for malaria, which contrasts to the slight increase in relative risk of solo travellers, business travellers and VFRs for malaria. Conclusions: The results of this sequential cohort survey in Dutch travellers suggest an annual 1.8% increase in protection rates against malaria coinciding with an annual 2.5% decrease in intended risk-seeking behaviour. This improvement may reflect the continuous efforts of travel health advice providers to create awareness and to propagate safe and healthy travel. The KAP profile of last-minute travellers, in particular, substantially increased their relative risk for malaria, underlining the continuous need for personal protective measures and malaria chemoprophylaxis for this risk group

Resolving debris discs in the far-infrared: early highlights from the DEBRIS survey

We present results from the earliest observations of DEBRIS, a Herschel Key Programme to conduct a volume- and flux-limited survey for debris discs in A-type through M-type stars. PACS images (from chop/nod or scan-mode observations) at 100 and 160 micron are presented toward two A-type stars and one F-type star: beta Leo, beta UMa and eta Corvi. All three stars are known disc hosts. Herschel spatially resolves the dust emission around all three stars (marginally, in the case of beta UMa), providing new information about discs as close as 11 pc with sizes comparable to that of the Solar System. We have combined these data with existing flux density measurements of the discs to refine the SEDs and derive estimates of the fractional luminosities, temperatures and radii of the discs.Comment: to be published in A&A, 5 pages, 2 color figure