Metagenomics reveals differences in the composition of bacterial antimicrobial resistance and antibiotic resistance genes in pasteurized yogurt and probiotic bacteria yogurt from China.

Antimicrobial resistance has become a global public health concern, and antibiotic resistance genes (ARGs) in food are a research focus. In China, probiotics and pasteurized yogurts are the 2 main types of commercially available yogurt, but the distribution and differences of antibiotic-resistant bacteria and gene types in these products are not well known. This study used a shotgun metagenomic approach to analyze 22 different types of yogurt collected from 9 main yogurt-producing areas in China, each type of yogurt includes 8 different batches of samples. The abundance and diversity of bacteria identified in probiotic yogurt were significantly higher than those in pasteurized yogurt, with Acetobacter, Raoultella, and Burkholderia identified as unique and highly abundant genera in probiotic yogurt. Similarly, ESKAPE (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp.) abundance was higher than that in pasteurized yogurt. A total of 1149 ARG subtypes belonging to 16 ARG types were identified, with the highest abundance of rifampicin, multidrug efflux pumps, and quinolone resistance genes detected. Network analysis revealed significant non-random co-occurrence relationships between different types and subtypes of ARGs in yogurt samples. Forty-four ARG subtypes in pasteurized yogurt were potentially hosted by 36 bacterial genera, and in probiotic yogurt, 63 ARGs were expected to be hosted by 86 bacterial species from 37 genera. These findings speculate on potential safety issues in fermented dairy products and emphasize the need for a more hygienic environment when processing probiotic yogurt.

Metabolomic profiles of not from concentrate orange juice after different sterilization treatments based on HS-SPME-GC-MS and UPLC-QTOF-MS.

Not from concentrate (NFC) orange juice is minimally processed, natural-appearing food, and has become more popular. Sterilization is an important stage for NFC orange juice production. Here we present a comprehensive analysis of the effect of sterilization on the metabolites of NFC orange juices, including three thermal (pasteurization, high-temperature short time, and ultra-high temperature) and one nonthermal (high hydrostatic pressure) method. A total of 108 metabolites, including 59 volatiles and 49 nonvolatiles were identified in orange juice. Of which, only butyl butanoate and 3-carene were detected in fresh orange juice. Sterilization significantly changed the metabolites of orange juice, and different methods caused various changes. Esters were downregulated by both thermal and nonthermal sterilization, while most flavonoids and terpenes were upregulated. With comparative analyses of three thermal sterilization, we found that high temperature and relatively short-time treatment preserved esters and ascorbic acid more effectively than low temperature and prolonged treatment. Aldehydes, however, were the opposite. Nonthermal sterilization is effective in preserving the metabolites of orange juice, especially for esters, terpenes, and flavonoids. In addition, 19 distinct metabolites were characterized between thermal and nonthermal samples by chemometrics analysis. These findings provide a new sight of the optimization of sterilization methods and references for different types of NFC orange juice identification. PRACTICAL APPLICATION: This study provides a reference for the optimization of sterilization methods and identification of HHP and thermal NFC orange juice and also benefits the purchase of consumers.

Quality changes of HHP orange juice during storage: Metabolomic data integration analyses.

High hydrostatic pressure (HHP) is a non-thermal method of sterilizing orange juice. However, knowledge of the quality variation during its storage is limited. This study aimed to comprehensively analyze metabolite variations during HHP orange juice storage using gas chromatography-mass spectrometer and liquid chromatography-mass spectrometry. Fifty-seven volatiles and 49 non-volatiles were identified. Partial least square analysis results showed that 21 days was a dividing point for metabolites highly varied. Results of relative odor activity value showed nonanal, methyl butanoate, and ethyl butanoate decreased after six days, which might reduce fruity flavor. After 21 days, over 60 % of metabolites such as linalool, α-pinene, and ascorbic acids decreased while α-terpineol and limonin increased, which would likely result in a change of coniferous, tarry, and bitter, as well as decreased organoleptic quality and antioxidative activities. This study provides a theoretical basis to optimize the shelf-life of HHP orange juice and advice for consumers' choices.

Effect of Roasting on the Conformational Structure and IgE Binding of Sesame Allergens.

Sesame can trigger a systemic allergic reaction. In the present study, we investigated the responses of the structure and IgE binding of sesame allergens to different roasting treatments (120, 150, and 180 °C for 5 to 30 min). We analyzed the tryptic digestion peptides using a label-free mass spectrometry method. The total amount of soluble proteins in sesame was significantly reduced by roasting at 180 °C, followed by 150 °C. Ses i 1 was the most stable protein during processing as it still possessed a higher protein abundance compared to other allergens after roasting under 180 °C. The most unstable allergens were Ses i 4 and Ses i 7, which suffered severe protein degradation at 180 °C. Roasting at 180 °C remarkably increased the secondary structure content of α-helices but decreased that of ß-sheets, whereas roasting at 120 and 150 °C had a limited effect on the secondary structure of sesame proteins. Moreover, serum pool Western blot analysis showed that the main allergens were oleosin of Ses i 4 and Ses i 5. The IgE-binding ability of sesame allergens was significantly decreased under 180 °C roasting, as well as the solubility of sesame proteins, which showed remarkable congruence in changes. Relative quantification results indicate that individual sesame allergens respond differently to the roasting process. In general, sesame allergens are unstable under roasting treatment. Therefore, the allergenic potential of sesame allergens may be minimized by selecting appropriate parameters during processing.

An Accurate and Rapid Way for Identifying Food Geographical Origin and Authenticity: Editable DNA-Traceable Barcode.

DNA offers significant advantages in information density, durability, and replication efficiency compared with information labeling solutions using electronic, magnetic, or optical devices. Synthetic DNA containing specific information via gene editing techniques is a promising identifying approach. We developed a new traceability approach to convert traditional digitized information into DNA sequence information. We used encapsulation to make it stable for storage and to enable reading and detection by DNA sequencing and PCR-capillary electrophoresis (PCR-CE). The synthesized fragment consisted of a short fragment of the mitochondrial cytochrome oxidase subunit I (COI) gene from the Holothuria fuscogilva (ID: LC593268.1), inserted geographical origin information (18 bp), and authenticity information from Citrus sinensis (20 bp). The obtained DNA-traceable barcodes were cloned into vector PMD19-T. Sanger sequencing of the DNA-traceable barcode vector was 100% accurate and provided a complete readout of the traceability information. Using selected recognition primers CAI-B, DNA-traceable barcodes were identified rapidly by PCR amplification. We encapsulated the DNA-traceable barcodes into amorphous silica spheres and improved the encapsulation procedure to ensure the durability of the DNA-traceable barcodes. To demonstrate the applicability of DNA-traceable barcodes as product labels, we selected Citrus sinensis as an example. We found that the recovered and purified DNA-traceable barcode can be analyzed by standard techniques (PCR-CE for DNA-traceable barcode identification and DNA sequencing for readout). This study provides an accurate and rapid approach to identifying and certifying products' authenticity and traceability.

Verification and applicability of endogenous reference genes for quantifying GM rice by digital PCR.

To standardize the rice-specific quantification methods, the criteria of six genes of rice (gos9, PLD, SPS, RBE4, ppi-PPF and oriazain) were compared and evaluated by ddPCR. The results revealed that SPS, RBE4 and ppi-PPF were single copy genes per haploid genome and species specificity and stable among different rice cultivars, by employing Lectin gene of soybean as internal reference gene. The established ddPCR systems were precise and reliable with an absolute LOQ of 10-20 copies/reaction. Furthermore, the robustness of these three assays was verified by performing an intra-laboratory repeatability validation and the results showed that the three endogenous genes of rice could be quantitated repeatedly and precisely above the LOQ. These ddPCR methods can reliably quantified the GM content even if the content was low to 0.1%, which were much more reliable than the results from real-time PCR using the same primers and probes.

Bacterial communities in prepared foods available at supermarkets in Beijing, China.

Prepared foods have received increasing attention owing to their convenience, rapidness, and ease of processing in a fast-paced life. The bacterial diversity and composition vary among different prepared foods and are closely related to food safety and human health. However, the knowledge on the bacterial community in prepared foods is still limited. In this study, the bacterial diversity in three kinds of prepared foods (meat, aquatic, and dish) available at supermarkets in Beijing was examined by using the high throughput sequencing technology to identify bacterial 16S rRNA genes. Alpha diversity analysis indicated that Proteobacteria and Firmicutes were the predominant bacterial phyla in prepared meat products, which accounted for 35-49% and 42-58% of the total sequences, respectively. Similar results were observed in prepared aquatic products, except salmon, which had a relatively unique bacterial community with Proteobacteria accounting for 90.72%. In prepared dishes, the proportions of Proteobacteria and Firmicutes were about 39-74% and 8-37%, respectively. The predominant bacterial genera detected in all samples within each kind of prepared foods were used to examine the differences in the bacterial community among three kinds of prepared foods. Results showed that the bacterial community in prepared meat products was much more diverse (14 genera) than those in prepared aquatic products (6 genera) and prepared dishes (2 genera). Acinetobacter was detected in all 288 prepared products. The bacterial community structures of prepared meat and aquatic products were more similar compared to those of prepared dishes. On the other hand, in prepared meat products, the bacterial communities of the samples with the same materials or brands were more similar, and further, among the sample with the same brands, the bacterial communities of the samples from the development zone were clearly different from those of the samples from the main urban area. In prepared aquatic products, the bacterial communities of the samples from the same region were also more similar. In prepared dish products, the bacterial communities of the samples with the same foodstuff or cooking style were more similar. In conclusion, this study revealed that the origin and type of prepared food ingredients, along with the sales location and processing methods, influenced microbial diversity and composition.

Metabolomic Approach for the Authentication of Berry Fruit Juice by Liquid Chromatography Quadrupole Time-of-Flight Mass Spectrometry Coupled to Chemometrics.

Berry fruit juice, which is represented by blueberry and cranberry juice, has become increasingly popular due to its reported nutritional and health benefits. However, in markets, adulteration of berry fruit juice with cheaper substitutes is frequent. In the present study, a metabolomic approach for authentication of berry fruit juices by liquid chromatography coupled with quadrupole time-of-flight mass spectrometry (LC-QTOF-MS) was established. The global characterization of the berry fruit metabolome by information dependent acquisition directed LC-MS/MS coupled to a peak mining workflow by isotope pattern matching was reported. Targeted metabolomics analysis of known juice biomarkers, such as flavonoids, anthocyanins, etc. exhibited a good separation of berry fruit juices from adulterant juices. Moreover, untargeted metabolomics analysis was carried out and subjected to chemometrics analysis. Discrimination of blueberry juice, cranberry juice, and its adulterant apple juice and grape juice was obtained by principal component analysis-discriminant analysis. Eighteen characteristic markers discriminating berry fruit juice and its adulterants were selected by comparison of marker abundances in different juice samples. Identification of characteristic markers was accomplished by elemental formula prediction and online database searches based on accurate MS information. These results suggested that the combination of untargeted and targeted metabolomics approach has great potential for authentication of berry fruit juice.

Rapid authentication of edible bird's nest by FTIR spectroscopy combined with chemometrics.

BACKGROUND: Edible bird's nests (EBNs) have been traditionally regarded as a kind of medicinal and healthy food in China. For economic reasons, they are frequently subjected to adulteration with some cheaper substitutes, such as Tremella fungus, agar, fried pigskin, and egg white. As a kind of precious and functional product, it is necessary to establish a robust method for the rapid authentication of EBNs with small amounts of samples by simple processes. In this study, the Fourier transform infrared spectroscopy (FTIR) system was utilized and its feasibility for identification of EBNs was verified. RESULTS: FTIR spectra data of authentic and adulterated EBNs were analyzed by chemometrics analyses including principal component analysis, linear discriminant analysis (LDA), support vector machine (SVM) and one-class partial least squares (OCPLS). The results showed that the established LDA and SVM models performed well and had satisfactory classification ability, with the former 94.12% and the latter 100%. The OCPLS model was developed with prediction sensitivity of 0.937 and specificity of 0.886. Further detection of commercial EBN samples confirmed these results. CONCLUSION: FTIR is applicable in the scene of rapid authentication of EBNs, especially for quality supervision departments, entry-exit inspection and quarantine, and customs administration. © 2017 Society of Chemical Industry.

A digital PCR method for identifying and quantifying adulteration of meat species in raw and processed food.

Meat adulteration is a worldwide concern. In this paper, a new droplet digital PCR (ddPCR) method was developed for the quantitative determination of the presence of chicken in sheep and goat meat products. Meanwhile, a constant (multiplication factor) was introduced to transform the ratio of copy numbers to the proportion of meats. The presented ddPCR method was also proved to be more accurate (showing bias of less than 9% in the range from 5% to 80%) than real-time PCR, which has been widely used in this determination. The method exhibited good repeatability and stability in different thermal treatments and at ultra-high pressure. The relative standard deviation (RSD) values of 5% chicken content was less than 5.4% for ultra-high pressure or heat treatment. Moreover, we confirmed that different parts of meat had no effect on quantification accuracy of the ddPCR method. In contrast to real-time PCR, we examined the performance of ddPCR as a more precise, sensitive and stable analytical strategy to overcome potential problems of discrepancies in amplification efficiency discrepancy and to obtain the copy numbers directly without standard curves. The method and strategy developed in this study can be applied to quantify the presence and to confirm the absence of adulterants not only to sheep but also to other kinds of meat and meat products.

[PFGE profiles and antimicrobial susceptibilities of Staphylococcus aureus in quick-frozen prepared foods].

OBJECTIVE: To analyze the contamination situation, resistance characteristics and PFGE profiles of Staphylococcus aureus from quick-frozen prepared foods in Beijing. METHODS: Staphylococcus aureus were separated according to GB4789. 10-2010, the identification and drug susceptibility was tested by the phoenixTM-100 automated microbiology system, and PFGE method was used for molecular classification. RESULTS: A total of 92 samples were examined and 31 of which( 33. 70%)were positive for Staphylococcus aureus. All strains were divided into 23 kinds of PFGE type, PFGE patterns were obviously spread. 31 strains were antibiotic resistant, the positive ß-lactams and MRSA were 70. 97%( 22/31) and 12. 90%( 4/31), respectively, and all 4 MRSA isolates carried the mec A gene. Moreover, one strain was erythromy cininduced by clindamycin resistant bacteria strain( STAMLS). Those isolates showed different antibiotic resistance resistant phenotype and multidrug resistantce. Antibiotics resistant phenotype has no apparent consistence with PFGE patterns. CONCLUSION: The contamination and serious antimicrobial resistance phenomenon of the Staphylococcus aureus isolates in quick-frozen prepared foods in Beijing was severe.

[Effect of High Hydrostatic Pressure Combined with Temperature on the Antigenicity and Conformation of Tropomyosin Purified from Shrimp].

Foodborne shrimp allergy events have occurred in recent years. To illustrate the mechanism of high hydrostatic pressure technology to change the allergenicity of shrimp, the major allergen tropomyosin was separated and purified from Litopenaeus vannamei, and indentified with matrix assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF-MS). The effect of temperature factor under high hydrostatic pressure was measured with indirect ELISA method, CD and fluorescence spectrum. The results showed that the antigenicity of TM protein had an increase after being heated at 35 or 45 ℃ when treated at 300 MPa for 15 minutes, while the antigenicity decreased at 55, 65, and 75 ℃. With the increase of heat temperature, the secondary structure of TM also changed. The mutual transformation happened between the alpha-helix and beta-sheet, beta-turn, and the random coil. The tertiary structure of TM was observed dynamic changes from the extended state to the folded state, and then re-extended state to re-folded state. These results suggested that high hydrostatic pressure combined with temperature could influence the antigenicity of TM by the change of conformation which would be useful as theoretical guidance on developing new methods or technologies for producing hypoallergenic shrimp products.

Bagging treatment influences production of C6 aldehydes and biosynthesis-related gene expression in peach fruit skin.

Bagging is a useful method to improve fruit quality by altering its exposure to light, whereas its effect on fruit volatiles production is inconsistent, and the genes responsible for the observed changes remain unknown. In the present study, single-layer yellow paper bags were used to study the effects of bagging treatment on the formation of C6 aldehydes in peach fruit (Prunus persica L. Batsch, cv. Yulu) over two succeeding seasons. Higher concentrations of n-hexanal and (E)-2-hexenal, which are characteristic aroma volatiles of peach fruit, were induced by bagging treatment. After bagging treatment, peach fruit had significantly higher LOX and HPL enzyme activities, accompanying increased contents of C6 aldehydes. The gene expression data obtained through real-time PCR showed that no consistent significant differences in transcript levels of LOX genes were observed over the two seasons, but significantly up-regulated expression was found for PpHPL1 after bagging treatment In addition, bagging-treated fruit produced more (E)-2-hexenal and had higher expression levels of PpHPL1 during postharvest ripening at room temperature. The regulatory role of the LOX-HPL pathway on the biosynthesis of n-hexanal and (E)-2-hexenal in response to bagging treatment during peach fruit development is discussed in the text.

Analysis of the interaction between tropomyosin allergens and antibodies using a biosensor based on imaging ellipsometry.

A biosensor based on high spatial resolution imaging ellipsometry has been studied to examine its role in the rapid detection and analysis of the tropomyosin allergen existing in crustaceans. This methodology has been established for detection of the tropomyosin allergen and includes ligand screening, the determination of sensitivity, and a comparison with traditional detection methods. Three kinds of monoclonal antibodies (2F9, 4C7, and 2H6) known to have a high bioactivity against the tropomyosin allergen were screened and separately immobilized as ligands on a silicon wafer surface, thus allowing them to capture the tropomyosin allergen. Resulting changes on the wafer surface were visualized in gray scale variation on an ellipsometry image. Images showed that these antibodies are able to recognize the presence of the tropomyosin allergen in shrimp and crab with sensitivity of 1 mg L(-1), and at a detecting time of approximately 30 min for an extracted sample. This preliminary study has shown that the detection of the tropomyosin allergen is rapid and specific when using this type of assay on products containing shrimp and crab. When compared with the enzyme-linked immunosorbent assay, the biosensor based on imaging ellipsometry is able to perform a fast label-free analysis.

Species-specific identification of seven vegetable oils based on suspension bead array.

Species adulteration of vegetable oils has become a main form of adulteration in vegetable oils, severely violating consumer rights and causing disorder in the market. A reliable method of species authentication of vegetable oils is desirable. This paper reports a novel method for identification of seven species of vegetable oils based on suspension bead array. One pair of universal primers and seven species-specific probes were designed targeting rbcl gene of the chloroplast. Each probe was coupled to a unique color-coded microsphere. Biotinylated PCR amplicons of seven oils were hybridized to the complementary probes on microsphere sets. Bound amplicons were detected fluorometrically using a reporter dye, streptavidin-R-phycoeryt hrin (SA-PE). A sample could be analyzed less than 1 h after PCR amplification. With the exception of olive probe, all probes showed no cross-reactivity with other species. Absolute detection limit of the seven probes ranged from 0.01 ng/µL to 0.0001 ng/µL. Detection limit in DNA mixture was from 10% to 5%. Detection of vegetable oils validated the effectiveness of the method. The suspension bead array as a rapid, sensitive, and high-throughput technology has potential to identify more species of vegetable oils with increased species of probes.

Simultaneous detection of eight food allergens using optical thin-film biosensor chips.

Food allergies are important food safety issues nowadays. To maintain the safety of people who experience allergic reactions, labeling is required in many countries and efficient and reliable detection methods are necessary. This paper reports a novel method for the rapid identification of food allergens through the use of a silicon-based optical thin-film biosensor chip with which color change results can be perceived by the naked eye without any extra equipment. The whole system can detect eight food allergens including soybean, wheat, peanut, cashew, shrimp, fish, beef, and chicken simultaneously. Sensitive and specific detection of the absolute detection limit of this method was 0.5 pg of cashew DNA, and the practical detection limit of 0.001%. The biosensor chip detection time was about 30 min after PCR amplification. The assay is proposed as a sensitive, specific, high-throughput, and ready-to-use analytical tool to detect the presence or confirm the absence of eight food allergens.

Degradation behavior and products of malathion and chlorpyrifos spiked in apple juice by ultrasonic treatment.

Apple juice (13 degrees Brix) spiked with malathion and chlorpyrifos (2-3 mg l(-1) of each compound) was treated under different ultrasonic irradiations. Results showed that ultrasonic treatment was effective for the degradation of malathion and chlorpyrifos in apple juice, and the output power and treatment time significantly influenced the degradation of both pesticides (p<0.05). The maximum degradations were achieved for malathion (41.7%) and chlorpyrifos (82.0%) after the ultrasonic treatment at 500 W for 120 min. The degradation kinetics of both pesticides were fitted to the first-order kinetics model well (R(2)>or=0.90). The kinetics parameters indicated that chlorpyrifos was much more labile to ultrasonic treatment than malathion. Furthermore, malaoxon and chlorpyrifos oxon were identified as the degradation products of malathion and chlorpyrifos by gas chromatography-mass spectrometry (GC-MS), respectively. The oxidation pathway through the hydroxyl radical attack on the P=S bond of pesticide molecules was proposed.

Degradation of endogenous and exogenous genes of roundup-ready soybean during food processing.

Roundup-Ready soybeans have been genetically modified to resist the effects of the herbicidal glyphosate and have become the most prevalent transgenic crop in the world. In this work, Roundup-Ready soybeans were used as raw material to study the effects of critical processing procedures such as grinding, cooking, blending, homogenization, sterilization, and spray-drying on the length of DNA fragments of an endogenous gene (lectin) and an exogenous gene (epsps) examined in material from three soybean foods of bean curd, soy milk, and soy powder and from samples taken during their processing. The results showed that various processing procedures caused degradations of both the endogenous and exogenous genes to different degrees. In the grinding procedure, endogenous gene DNA was degraded from 1883 to approximately 836 bp, and exogenous gene DNA was degraded from 1512 to approximately 408 bp. In the blending and squeeze-molding procedures, exogenous gene DNA was also degraded from about 408 to 190 bp, but there was no obvious action on the endogenous gene. After the endogenous and exogenous genes had been degraded to some degree, such as 836 and 408 bp, respectively, they were not evidently affected by cooking procedure at 100 degrees C for 15 min. However, the endogenous gene was further considerably degraded from around 836 to 162 bp in the sterilization procedure at 121 degrees C for 30 s. The effect of the homogenization step on endogenous and exogenous genes was similar to that of the cooking procedure. The coagulation procedure, principally a biochemical reaction, did not greatly affect the exogenous gene but did affect endogenous gene, reducing DNA size from about 836 to 407 bp. Furthermore, the spray-drying procedure, a process of physical shearing, high temperature, and sudden high pressure, distinctly caused degradation of both the lectin and epsps genes, rapidly decreasing the sizes from about 836 to 162 bp for the endogenous gene and from about 408 to 190 bp for the exogenous gene.

Extraction of natural vitamin E from wheat germ by supercritical carbon dioxide.

An efficient supercritical fluid extraction (SFE) process with carbon dioxide (SFE-CO(2)) was developed for the extraction of natural vitamin E (V(E)) from wheat germ. Both the pretreatment of extracted wheat germ and extraction conditions were optimized to ensure maximal V(E) yield. The extraction was undertaken at the extracting pressure of 4000-5000 psi, the extracting temperature of 40-45 degrees C, and the carbon dioxide flow rate of 2.0 mL/min for 90 min. An optimized pretreatment of wheat germ was usually necessary with a particle size of 30 mesh and a moisture content of 5.1%. A yield comparison of V(E) and its isomers extracted by supercritical CO(2) with those by conventional solvent extraction suggested that this SFE process was a practical process prospectively superior to conventional solvent extraction to prepare V(E) from wheat germ.