The use of next generation sequencing for improving food safety: Translation into practice.

Next Generation Sequencing (NGS) combined with powerful bioinformatic approaches are revolutionising food microbiology. Whole genome sequencing (WGS) of single isolates allows the most detailed comparison possible hitherto of individual strains. The two principle approaches for strain discrimination, single nucleotide polymorphism (SNP) analysis and genomic multi-locus sequence typing (MLST) are showing concordant results for phylogenetic clustering and are complementary to each other. Metabarcoding and metagenomics, applied to total DNA isolated from either food materials or the production environment, allows the identification of complete microbial populations. Metagenomics identifies the entire gene content and when coupled to transcriptomics or proteomics, allows the identification of functional capacity and biochemical activity of microbial populations. The focus of this review is on the recent use and future potential of NGS in food microbiology and on current challenges. Guidance is provided for new users, such as public health departments and the food industry, on the implementation of NGS and how to critically interpret results and place them in a broader context. The review aims to promote the broader application of NGS technologies within the food industry as well as highlight knowledge gaps and novel applications of NGS with the aim of driving future research and increasing food safety outputs from its wider use.

In situ microstructure and rheological behavior of yeast biofilms from the juice processing industries.

The factors affecting the mechanical properties of biofilms formed by yeast species (Rhodotorula mucilaginosa, Candida krusei, C. kefyr and C. tropicalis) isolated from the juice processing industries have been investigated. Variables studied were: the food matrix (apple/pear juice), the sugar concentration (6/12 °Bx) and the hydrodynamic conditions (static/turbulent flow). A range of environmental cues were included as the mechanical properties of biofilms are complex. Yeast counts were significantly higher in turbulent flow compared with under static conditions. The thickness of the biofilm ranged from 38 to 148 µm, from static to turbulent flow. Yeast biofilms grown under turbulent flow conditions were viscoelastic with a predominant solid-like behavior and were structurally stronger than those grown under static conditions, indicating gel-type structures. Only the type of flow had a significant effect on [Formula: see text] and G*. Flow velocity and nutrient status modulated the biofilm thickness, the biomass and the mechanical properties. A better knowledge of the factors controlling biofilm formation will help in the development of control strategies.

Desiccation: An environmental and food industry stress that bacteria commonly face.

Water is essential for all living organisms, for animals as well as for plants and micro-organisms. For these latter, the presence of water or a humid environment with a high air relative humidity (RH) is necessary for their survival and growth. Thus, variations in the availability of water or in the air relative humidity constitute widespread environmental stresses which challenge microorganisms, and especially bacteria. Indeed, in their direct environment, bacteria are often faced with conditions that remove cell-bound water through air-drying of the atmosphere. Bacterial cells are subject to daily or seasonal environmental variations, sometimes going through periods of severe desiccation. This is also the case in the food industry, where air dehumidification treatments are applied after the daily cleaning-disinfection procedures. In plants producing low-water activity products, it is also usual to significantly reduce or eliminate water usage. Periodic desiccation exposure affects bacteria viability and so they require strategies to persist. Negative effects of desiccation are wide ranging and include direct cellular damage but also changes in the biochemical and biophysical properties of cells for which planktonic cells are more exposed than cells in biofilm. Understanding the mechanisms of desiccation adaptation and tolerance has a biological and biotechnological interest. This review gives an overview of the factors influencing desiccation tolerance and the biological mechanisms involved in this stress response.

Anaerobic treatment of blended sugar industry and ethanol distillery wastewater through biphasic high rate reactor.

This study aimed to investigate the physicochemical properties of sugar industry and ethanol distillery wastewater and the treatment of the blended wastewater through a two-stage anaerobic reactor. For this treatment, different initial chemical oxygen demand (COD) concentrations (5-20 g/L) and hydraulic retention times (HRTs) (2-10 days) were applied. The sugar industry effluent characteristics obtained in terms of organic matter (mg/L) were as follows: 5 days biochemical oxygen demand (BOD5): 654.5-1,968; COD: 1,100-2,148.9; total solids (TS): 2,467-4,012 mg/L; and pH: 6.93-8.43. The ethanol distillery spent wash strengths obtained were: BOD5: 27,600-42,921 mg/L; COD: 126,000-167,534 mg/L; TS: 140,160-170,000 mg/L; and pH: 3.9-4.2. Maximum COD removal of 65% was obtained at optimum condition (initial COD concentration of 10 g/L and HRT of 10 days), and maximum color removal of 79% was recorded under similar treatment conditions. Hence, the performance of the two-stage anaerobic reactor for simultaneous removal of COD and color from high-strength blended wastewater is promising for scaling up in order to mitigate environmental problems of untreated effluent discharge.

Whole genome sequencing analyses of Listeria monocytogenes that persisted in a milkshake machine for a year and caused illnesses in Washington State.

BACKGROUND: In 2015, in addition to a United States multistate outbreak linked to contaminated ice cream, another outbreak linked to ice cream was reported in the Pacific Northwest of the United States. It was a hospital-acquired outbreak linked to milkshakes, made from contaminated ice cream mixes and milkshake maker, served to patients. Here we performed multiple analyses on isolates associated with this outbreak: pulsed-field gel electrophoresis (PFGE), whole genome single nucleotide polymorphism (SNP) analysis, species-specific core genome multilocus sequence typing (cgMLST), lineage-specific cgMLST and whole genome-specific MLST (wgsMLST)/outbreak-specific cgMLST. We also analyzed the prophages and virulence genes. RESULTS: The outbreak isolates belonged to sequence type 1038, clonal complex 101, genetic lineage II. There were no pre-mature stop codons in inlA. Isolates contained Listeria Pathogenicity Island 1 and multiple internalins. PFGE and multiple whole genome sequencing (WGS) analyses all clustered together food, environmental and clinical isolates when compared to outgroup from the same clonal complex, which supported the finding that L. monocytogenes likely persisted in the soft serve ice cream/milkshake maker from November 2014 to November 2015 and caused 3 illnesses, and that the outbreak strain was transmitted between two ice cream production facilities. The whole genome SNP analysis, one of the two species-specific cgMLST, the lineage II-specific cgMLST and the wgsMLST/outbreak-specific cgMLST showed that L. monocytogenes cells persistent in the milkshake maker for a year formed a unique clade inside the outbreak cluster. This clustering was consistent with the cleaning practice after the outbreak was initially recognized in late 2014 and early 2015. Putative prophages were conserved among prophage-containing isolates. The loss of a putative prophage in two isolates resulted in the loss of the AscI restriction site in the prophage, which contributed to their AscI-PFGE banding pattern differences from other isolates. CONCLUSIONS: The high resolution of WGS analyses allowed the differentiation of epidemiologically unrelated isolates, as well as the elucidation of the microevolution and persistence of isolates within the scope of one outbreak. We applied a wgsMLST scheme which is essentially the outbreak-specific cgMLST. This scheme can be combined with lineage-specific cgMLST and species-specific cgMLST to maximize the resolution of WGS.

Rapid sensory-directed methodology for the selection of high-quality aroma wines.

BACKGROUND: The present work contributes by developing a rapid sensory-directed methodology for the screening and selection of high-quality wines with different sensory profiles. Verdejo and Tempranillo musts were fermented with 50 different yeasts each under controlled laboratory conditions. Resulting samples were firstly categorised according to five levels of quality by a panel of wine professionals. Higher quality samples were described by flash profiling by a semi-trained panel and most distinctive samples were screened by gas chromatography-olfactometry (GC-O). RESULTS: Seven Verdejo and five Tempranillo samples were classified in the highest quality category, presenting different aroma profiles such as citrus, fruit in syrup, boxtree/vegetal, tropical or wet grain aromas for Verdejo and red fruit or fruit in syrup for Tempranillo. ß-Damascenone, 3-mercaptohexyl acetate and ethyl butyrate appeared as distinctive quality compounds linked to dried, tropical and red fruit aromas, respectively. CONCLUSIONS: The categorisation task followed by flash profiling and GC-O analysis was shown to be a rapid and effective sensory-directed methodology for the screening of distinctive and quality wine aroma profiles in a case study of yeast selection. The wine industry could benefit from the use of this methodology as a complementary tool for optimising different technical processes. © 2016 Society of Chemical Industry.

Membrane processing technology in the food industry: food processing, wastewater treatment, and effects on physical, microbiological, organoleptic, and nutritional properties of foods.

Membrane processing technology (MPT) is increasingly used nowadays in a wide range of applications (demineralization, desalination, stabilization, separation, deacidification, reduction of microbial load, purification, etc.) in food industries. The most frequently applied techniques are electrodialysis (ED), reverse osmosis (RO), nanofiltration (NF), ultrafiltration (UF), and microfiltration (MF). Several membrane characteristics, such as pore size, flow properties, and the applied hydraulic pressure mainly determine membranes' potential uses. In this review paper the basic membrane techniques, their potential applications in a large number of fields and products towards the food industry, the main advantages and disadvantages of these methods, fouling phenomena as well as their effects on the organoleptic, qualitative, and nutritional value of foods are synoptically described. Some representative examples of traditional and modern membrane applications both in tabular and figural form are also provided.

Technologies that affect the weaning rate in beef cattle production systems.

We investigated the differences between weaning rates and technologies adopted by farmers in cow-calf production systems in Rio Grande do Sul State, Brazil. Interviews were carried out with 73 farmers about 48 technologies that could affect reproductive performance. Data were analyzed by multivariate analysis using a non-hierarchical cluster method. The level of significance was set at P < 0.05. Three distinct clusters of farmers were created (R (2) = 0.90), named as low (LWR), intermediate (IWR), and high (HWR) weaning rate, with 100, 91, and 96 % of the farmers identified within their respective groups and average weaning rates of 59, 72, and 83 %, respectively. IWR and HWR farmers used more improved natural pasture, fixed-time artificial insemination, selection for birth weight, and proteinated salt compared to LWR. HWR farmers used more stocking rate control, and IWR farmers used more ultrasound to evaluate reproductive performance compared to the LWR group. IWR and HWR adopted more technologies related to nutrition and reproductive aspects of the herd in comparison to LWR. We concluded that farmers with higher technology use on farm had higher weaning rates which could be used to benefit less efficient farmers.

Arcobacter butzleri in sheep ricotta cheese at retail and related sources of contamination in an industrial dairy plant.

This study aimed to evaluate Arcobacter species contamination of industrial sheep ricotta cheese purchased at retail and to establish if the dairy plant environment may represent a source of contamination. A total of 32 sheep ricotta cheeses (1.5 kg/pack) packed in a modified atmosphere were purchased at retail, and 30 samples were collected in two sampling sessions performed in the cheese factory from surfaces in contact with food and from surfaces not in contact with food. Seven out of 32 samples (21.9%) of ricotta cheese collected at retail tested positive for Arcobacter butzleri at cultural examination; all positive samples were collected during the same sampling and belonged to the same batch. Ten surface samples (33.3%) collected in the dairy plant were positive for A. butzleri. Cluster analysis identified 32 pulsed-field gel electrophoresis (PFGE) patterns. The same PFGE pattern was isolated from more than one ricotta cheese sample, indicating a common source of contamination, while more PFGE patterns could be isolated in single samples, indicating different sources of contamination. The results of the environmental sampling showed that A. butzleri may be commonly isolated from the dairy processing plant investigated and may survive over time, as confirmed by the isolation of the same PFGE pattern in different industrial plant surface samples. Floor contamination may represent a source of A. butzleri spread to different areas of the dairy plant, as demonstrated by isolation of the same PFGE pattern in different production areas. Isolation of the same PFGE pattern from surface samples in the dairy plant and from ricotta cheese purchased at retail showed that plant surfaces may represent a source of A. butzleri postprocessing contamination in cheeses produced in industrial dairy plants.

Personalized nutrition with 3D-printed foods: A systematic review on the impact of different additives.

Three-dimensional (3D) printing is one of the world's top novel technologies in the food industry due to the production of food in different conditions and places (restaurants, homes, catering, schools, for dysphagia patients, and astronauts' food) and the production of personalized food. Nowadays, 3D printers are used in the main food industries, including meat, dairy, cereals, fruits, and vegetables, and have been able to produce successfully on a small scale. However, due to the expansion of this technology, it has challenges such as high-scale production, selection of printable food, formulation optimization, and food production according to the consumer's opinion. Food additives (gums, enzymes, proteins, starches, polyphenols, spices, probiotics, algae, edible insects, oils, salts, vitamins, flavors, and by-products) are one of the main components of the formulation that can be effective in food production according to the consumer's attitude. Food additives can have the highest impact on textural and sensory characteristics, which can be effective in improving consumer attitudes and reducing food neophobia. Most of the 3D-printed food cannot be printed without the presence of hydrocolloids, because the proper flow of the selected formulation is one of the key factors in improving the quality of the printed product. Functional additives such as probiotics can be useful for specific purposes and functional food production. Food personalization for specific diseases with 3D printing technology requires a change in the formulation, which is closely related to the selection of correct food additives. For example, the production of 3D-printed plant-based steaks is not possible without the presence of additives, or the production of food for dysphagia patients is possible in many cases by adding hydrocolloids. In general, additives can improve the textural, rheological, nutritional, and sensory characteristics of 3D printed foods; so, investigating the mechanism of the additives on all the characteristics of the printed product can provide a wide perspective for industrial production and future studies.

Diverse applications of electronic-nose technologies in agriculture and forestry.

Electronic-nose (e-nose) instruments, derived from numerous types of aroma-sensor technologies, have been developed for a diversity of applications in the broad fields of agriculture and forestry. Recent advances in e-nose technologies within the plant sciences, including improvements in gas-sensor designs, innovations in data analysis and pattern-recognition algorithms, and progress in material science and systems integration methods, have led to significant benefits to both industries. Electronic noses have been used in a variety of commercial agricultural-related industries, including the agricultural sectors of agronomy, biochemical processing, botany, cell culture, plant cultivar selections, environmental monitoring, horticulture, pesticide detection, plant physiology and pathology. Applications in forestry include uses in chemotaxonomy, log tracking, wood and paper processing, forest management, forest health protection, and waste management. These aroma-detection applications have improved plant-based product attributes, quality, uniformity, and consistency in ways that have increased the efficiency and effectiveness of production and manufacturing processes. This paper provides a comprehensive review and summary of a broad range of electronic-nose technologies and applications, developed specifically for the agriculture and forestry industries over the past thirty years, which have offered solutions that have greatly improved worldwide agricultural and agroforestry production systems.

Foreign object detection by sub-terahertz quasi-Bessel beam imaging.

Food quality monitoring, particularly foreign object detection, has recently become a critical issue for the food industry. In contrast to X-ray imaging, terahertz imaging can provide a safe and ionizing-radiation-free nondestructive inspection method for foreign object sensing. In this work, a quasi-Bessel beam (QBB) known to be nondiffracting was generated by a conical dielectric lens to detect foreign objects in food samples. Using numerical evaluation via the finite-difference time-domain (FDTD) method, the beam profiles of a QBB were evaluated and compared with the results obtained via analytical calculation and experimental characterization (knife edge method, point scanning method). The FDTD method enables a more precise estimation of the beam profile. Foreign objects in food samples, namely crickets, were then detected with the QBB, which had a deep focus and a high spatial resolution at 210 GHz. Transmitted images using a Gaussian beam obtained with a conventional lens were compared in the sub-terahertz frequency experimentally with those using a QBB generated using an axicon.

Intelligent color vision system for ripeness classification of oil palm fresh fruit bunch.

Ripeness classification of oil palm fresh fruit bunches (FFBs) during harvesting is important to ensure that they are harvested during optimum stage for maximum oil production. This paper presents the application of color vision for automated ripeness classification of oil palm FFB. Images of oil palm FFBs of type DxP Yangambi were collected and analyzed using digital image processing techniques. Then the color features were extracted from those images and used as the inputs for Artificial Neural Network (ANN) learning. The performance of the ANN for ripeness classification of oil palm FFB was investigated using two methods: training ANN with full features and training ANN with reduced features based on the Principal Component Analysis (PCA) data reduction technique. Results showed that compared with using full features in ANN, using the ANN trained with reduced features can improve the classification accuracy by 1.66% and is more effective in developing an automated ripeness classifier for oil palm FFB. The developed ripeness classifier can act as a sensor in determining the correct oil palm FFB ripeness category.

Treatment of fruit-juice industry wastewater in a two-stage anaerobic hybrid (AH) reactor system followed by a sequencing batch reactor (SBR).

This study has been carried out to assess the performance of a combined system consisting of an anaerobic hybrid (AH) reactor followed by a sequencing batch reactor (SBR) for treatment of fruit-juice industry wastewater at a temperature of 26 degrees C. Three experimental runs were conducted in this investigation. In the first experiment, a single-stage AH reactor was operated at a hydraulic retention time (HRT) of 10.2 h and organic loading rate (OLR) of 11.8 kg COD m(-3) d(-1). The reactor achieved a removal efficiency of 42% for chemical oxygen demand (COD), 50.8% for biochemical oxygen demand (BOD5), 50.3% for volatile fatty acids (VFA) and 56.4% for total suspended solids (TSS). In the second experiment, two AH reactors connected in series achieved a higher removal efficiency for COD (67.4%), BOD5 (77%), and TSS (71.5%) at a total HRT of 20 h and an OLR of 5.9 kg COD m(-3) d(-1). For removal of the remaining portions of COD, BOD5 and TSS from the effluent of the two-stage AH system, a sequencing batch reactor (SBR) was investigated as a post-treatment unit. The reactor achieved a substantial reduction in total COD, resulting in an average effluent concentration of 50 mg L(-1) at an HRT of 11 h and OLR of 5.3 kg COD m(-3) d(-1). Almost complete removal of total BOD5 and oil and grease was achieved, i.e. 10 mg L(-1) and 1.2 mg L(-1), respectively, remained in the final effluent of the SBR.

Electronic noses and tongues: applications for the food and pharmaceutical industries.

The electronic nose (e-nose) is designed to crudely mimic the mammalian nose in that most contain sensors that non-selectively interact with odor molecules to produce some sort of signal that is then sent to a computer that uses multivariate statistics to determine patterns in the data. This pattern recognition is used to determine that one sample is similar or different from another based on headspace volatiles. There are different types of e-nose sensors including organic polymers, metal oxides, quartz crystal microbalance and even gas-chromatography (GC) or combined with mass spectroscopy (MS) can be used in a non-selective manner using chemical mass or patterns from a short GC column as an e-nose or "Z" nose. The electronic tongue reacts similarly to non-volatile compounds in a liquid. This review will concentrate on applications of e-nose and e-tongue technology for edible products and pharmaceutical uses.

[Assessment of dairy products quality by means of electronic nose]. / Evaluación de la calidad de productos lácteos por medio de la nariz electrónica.

The electronic nose, instrument that uses a group of sensors and a system of pattern recognition for the qualitative analysis of aroma, has found many applications in the food industry, because of its versatility. In this work a brief description of the electronic nose, its operation mode and its advantages and disadvantages were carried out. Moreover, the main applications of this instrument in the food industry, with special emphasis on the dairy industry, have been reviewed. These applications include the detection of microorganisms in milk, the identification of off-flavours in milk, the shelf life of milk and various types ofcheeses, the identification of mastitic milk, the classification of cheeses according to their time of ripening, the discrimination of cheeses by geographic origin and the control of the milk fermentation, among other. The results of this review indicate that electronic nose could be used as an instrument for the rapid quality control of dairy products.

Reliability and maintainability analysis of bread production line.

The statistical analysis of the bread production line of the failure and repair data at machine and line levels was displayed. The experiment covers a period of twenty-five months. The best fit of the failure data between the common theoretical distributions was found and its parameters were computed. The reliability and hazard rate modes for all machines and the entire production line were calculated as well. The models could prove to be a useful tool to assess the current conditions, and to predict the reliability for upgrading the maintenance policy of the production line. It was pointed out that (a) the availability of the bread production line is 90.74% and went down to 86.76% because the equipment's failures cause an additional production gap in the line, (b) the 53.5% of all failures occurred at the bread machine, cooling tower machine, and volumetric-divider machine, and (c) the machines of the bread production line that displayed increasing hazard rate functions were identified. This analysis will be very useful in terms of identifying the occurring and latent problems in manufacturing process of bread and improve it.

The use of near-infrared spectrometry in the olive oil industry.

The enormous possibilities offered by near-infrared (NIR) spectroscopy for the (on/in/at-line) quality control process of olive fruits, pastes, and oils are summarized throughout this paper. Special attention has been paid to the combination of NIR and chemometric treatments for the on-line analysis of olive fruits and also for the quality parameters evaluation on olive oils and pastes which can enhance the production of a high quality olive oil and the selection of olive fruit with superior properties. The implementation of NIR sensors in olive mills with successful results has also been reviewed and the commercial olive fruit and oil analyzers highlighted.

Reduction of Salmonella on alfalfa seeds using peroxyacetic acid and a commercial seed washer is as effective as treatment with 20 000 ppm of Ca(OCl)2.

AIMS: The efficacy of a commercial seed washer and 1 and 3% peroxyacetic acid or 20 000 ppm calcium hypochlorite for reducing Salmonella on alfalfa seeds was investigated. METHODS AND RESULTS: Alfalfa seeds were inoculated with Salmonella Stanley to achieve c. 5 log CFU g(-1). Seeds were then treated with 1 or 3% peroxyacetic acid or 20 000 ppm calcium hypochlorite for 15 min in a commercial seed washer that uses air to enhance contact of the sanitizer with the seed. Experiments were also conducted using industry and laboratory methods. An c. 1-log reduction in number of Salm. Stanley was demonstrated regardless of the chemical treatment or method of treatment. Although this 1-log reduction was significant (P < 0.05), differences among the treatments were not significant. Treating the seed with 1 and 3% peroxyacetic acid resulted in similar Salm. Stanley reductions of 1.77 and 1.34 log, respectively, not being statistically significant (P > 0.05). CONCLUSIONS: These results suggest that under conditions tested, 1 or 3% peroxyacetic acid solutions are equally effective as 20 000 ppm of Ca(OCl)2 in the reduction of Salm. Stanley on alfalfa seed when used in conjunction with a commercial seed washer. SIGNIFICANCE AND IMPACT OF THE STUDY: A 1% peroxyacetic acid solution could potentially be used in place of 20 000 ppm of Ca(OCl)2 for treatment of seeds used for sprouting. The commercial seed washer did not enhance removal of Salm. Stanley from alfalfa seeds, but did facilitate removal of excess soil from seeds.

Biosensors as analytical tools in food fermentation industry.

The food industries need rapid and affordable methods to assure the quality ofproducts and process control. Biosensors, combining a biological recognition element and a sensitive transducer, are versatile analytical tools that offer advantages as classical analytical methods due to their inherent specificity, selectivity and simplicity. This paper reviews the recent trends in the development and applications of biosensors used in food fermentation industry, focusing on amperometric enzymatic and microbial sensors.