PeerJ:Food Science and Technologyhttps://peerj.com/articles/index.atom?journal=peerj&subject=1600Food Science and Technology articles published in PeerJAnalysis of the differences in physicochemical properties, volatile compounds, and microbial community structure of pit mud in different time spaceshttps://peerj.com/articles/170002024-02-292024-02-29Baolin HanHucheng GongXiaohu RenShulin TianYu WangShufan ZhangJiaxu ZhangJing Luo
Pit mud (PM) is among the key factors determining the quality of Nongxiangxing baijiu, a Chinese liquor. Microorganisms present inside PM are crucial for the unique taste and flavor of this liquor. In this study, headspace solid-phase microextraction was used in combination with gas chromatography and high-throughput sequencing to determine the volatile compounds and microbial community structure of 10- and 40-year PM samples from different spaces. The basic physicochemical properties of the PM were also determined. LEfSe and RDA were used to systematically study the PM in different time spaces. The physicochemical properties and ester content of the 40-year PM were higher than those of the 10-year PM, but the spatial distribution of the two years PM samples exhibited no consistency, except in terms of pH, available phosphorus content, and ester content. In all samples, 29 phyla, 276 families, and 540 genera of bacteria, including four dominant phyla and 20 dominant genera, as well as eight phyla, 24 families, and 34 genera of archaea, including four dominant phyla and seven dominant genera, were identified. The LEfSe analysis yielded 18 differential bacteria and five differential archaea. According to the RDA, the physicochemical properties and ethyl caproate, ethyl octanoate, hexanoic acid, and octanoic acid positively correlated with the differential microorganisms of the 40-year PM, whereas negatively correlated with the differential microorganisms of the 10-year PM. Thus, we inferred that Caproiciproducens, norank_f__Caloramatoraceae, and Methanobrevibacter play a dominant and indispensable role in the PM. This study systematically unveils the differences that affect the quality of PM in different time spaces and offers a theoretical basis for improving the declining PM, promoting PM aging, maintaining cellars, and cultivating an artificial PM at a later stage.
Pit mud (PM) is among the key factors determining the quality of Nongxiangxing baijiu, a Chinese liquor. Microorganisms present inside PM are crucial for the unique taste and flavor of this liquor. In this study, headspace solid-phase microextraction was used in combination with gas chromatography and high-throughput sequencing to determine the volatile compounds and microbial community structure of 10- and 40-year PM samples from different spaces. The basic physicochemical properties of the PM were also determined. LEfSe and RDA were used to systematically study the PM in different time spaces. The physicochemical properties and ester content of the 40-year PM were higher than those of the 10-year PM, but the spatial distribution of the two years PM samples exhibited no consistency, except in terms of pH, available phosphorus content, and ester content. In all samples, 29 phyla, 276 families, and 540 genera of bacteria, including four dominant phyla and 20 dominant genera, as well as eight phyla, 24 families, and 34 genera of archaea, including four dominant phyla and seven dominant genera, were identified. The LEfSe analysis yielded 18 differential bacteria and five differential archaea. According to the RDA, the physicochemical properties and ethyl caproate, ethyl octanoate, hexanoic acid, and octanoic acid positively correlated with the differential microorganisms of the 40-year PM, whereas negatively correlated with the differential microorganisms of the 10-year PM. Thus, we inferred that Caproiciproducens, norank_f__Caloramatoraceae, and Methanobrevibacter play a dominant and indispensable role in the PM. This study systematically unveils the differences that affect the quality of PM in different time spaces and offers a theoretical basis for improving the declining PM, promoting PM aging, maintaining cellars, and cultivating an artificial PM at a later stage.DNA mini-barcoding reveals the mislabeling rate of canned cat food in Taiwanhttps://peerj.com/articles/168332024-02-212024-02-21Yu-Chun WangShih-Hui LiuHsuan Ching HoHsiao-Yin SuChia-Hao Chang
Background
Domestic cats are important companion animals in modern society that live closely with their owners. Mislabeling of pet food can not only harm pets but also cause issues in areas such as religious beliefs and natural resource management. Currently, the cat food market is booming. However, despite the risk that mislabeling poses to cats and humans, few studies have focused on species misrepresentation in cat food products.
Methods
To address this issue, we used DNA barcoding, a highly effective identification methodology that can be applied to even highly processed products. We targeted a short segment (~85 basepairs) of the mitochondrial 16S rRNA (16S) gene as a barcode and employed Sanger or next generation sequencing (NGS) to inspect 138 canned cat food products in the Taiwanese market.
Results
We discovered that the majority of mislabeling incidents were related to replacement of tuna with other species. Moreover, our metabarcoding revealed that numerous undeclared ingredients were present in all examined canned products. One product contained CITES Appendix II-listed shortfin mako shark (Isurus oxyrinchus). Overall, we uncovered a mislabeling rate of at least 28.99%. To verify cases of mislabeling, an official standardized list of vernacular names, along with the corresponding scientific species names, as well as a dependable barcoding reference sequence database are necessary.
Background
Domestic cats are important companion animals in modern society that live closely with their owners. Mislabeling of pet food can not only harm pets but also cause issues in areas such as religious beliefs and natural resource management. Currently, the cat food market is booming. However, despite the risk that mislabeling poses to cats and humans, few studies have focused on species misrepresentation in cat food products.
Methods
To address this issue, we used DNA barcoding, a highly effective identification methodology that can be applied to even highly processed products. We targeted a short segment (~85 basepairs) of the mitochondrial 16S rRNA (16S) gene as a barcode and employed Sanger or next generation sequencing (NGS) to inspect 138 canned cat food products in the Taiwanese market.
Results
We discovered that the majority of mislabeling incidents were related to replacement of tuna with other species. Moreover, our metabarcoding revealed that numerous undeclared ingredients were present in all examined canned products. One product contained CITES Appendix II-listed shortfin mako shark (Isurus oxyrinchus). Overall, we uncovered a mislabeling rate of at least 28.99%. To verify cases of mislabeling, an official standardized list of vernacular names, along with the corresponding scientific species names, as well as a dependable barcoding reference sequence database are necessary.Biochemical, anatomical, and histochemical characterization of cachichín (Oecopetalum mexicanum Greenm. & C.H. Thomps: Metteniusaceae) seeds exposed to different thermal treatmentshttps://peerj.com/articles/166632024-01-152024-01-15Alejandro Esli Hernández-MoraLibia Iris Trejo-TéllezHilda Araceli Zavaleta-ManceraJosé Andrés Herrera-CorredorMaría Magdalena Crosby-GalvánFernando Carlos Gómez-Merino
Background
Cachichín (Oecopetalum mexicanum Greenm. & C.H. Thomps: Metteniusaceae) is an arboreal species native to the Misantla mountain range, Veracruz, Mexico, whose fruit contains an edible seed with potential nutraceutical properties. Basic biochemical analyses have been performed, though the effects of thermal treatments on the concentration of vital molecules, the seed structure and the histochemistry have yet to be elicited. Herewith we determined the effect of different thermal treatments on the concentrations of total sugars; glucose and fructose; proteins; and amino acids; as well as the impact of such treatments on the anatomy and histochemistry of seeds.
Methods
Biochemical, anatomical, and histochemical characterizations of the cachichín seed were carried out in raw form (T1) and under three thermal treatments: boiled (T2), commercial toasting (T3), and controlled toasting (T4). The biochemical variables evaluated were total and reducing sugars, total proteins, and total amino acids. Observations of the seed structure were performed by scanning electron microscopy (SEM), while histochemical staining was carried out to identify starch, lipids, tannins, polysaccharides and proteins under compound light microscopy.
Results
Concentration of total sugars was reduced in boiled (T2) and commercial toasting (T3) seeds as compared to raw (T1) and controlled toasting (T4) seeds; boiled seeds (T3) displayed the lowest concentration of total sugars. An increase in the concentrations of glucose and fructose was observed in T4. As compared to T1, all other treatments did not change protein concentrations in the seed; the only significant difference observed was between T2 and T3, with commercial toasting displaying the highest mean for this variable. Amino acid concentrations decreased in T3 and T4 compared to T1, while in T2 the concentration of these molecules increased. The anatomic analysis of (T1) revealed a well-organized structure, compared to applied thermal treatments, where degradation of anatomical structures was observed. In general, the thermal treatments tested modified the concentrations and distribution of starch, lipids, tannins, polysaccharides and proteins as compared to raw seeds. The raw cachichín seed has a well-defined anatomical and cellular compartmental organization, while the application of the thermal treatments caused a loss of its structural organization and degradation of vital biomolecules.
Conclusion
The cachichín seed can be considered a good source of proteins and lipids. Thermal treatments can improve its organoleptic properties, though they negatively impact its nutritional value and anatomical structure. Among thermal treatments tested, the controlled toasting can maintain or even improve some nutraceutical properties with a few structural and biochemical modifications.
Background
Cachichín (Oecopetalum mexicanum Greenm. & C.H. Thomps: Metteniusaceae) is an arboreal species native to the Misantla mountain range, Veracruz, Mexico, whose fruit contains an edible seed with potential nutraceutical properties. Basic biochemical analyses have been performed, though the effects of thermal treatments on the concentration of vital molecules, the seed structure and the histochemistry have yet to be elicited. Herewith we determined the effect of different thermal treatments on the concentrations of total sugars; glucose and fructose; proteins; and amino acids; as well as the impact of such treatments on the anatomy and histochemistry of seeds.
Methods
Biochemical, anatomical, and histochemical characterizations of the cachichín seed were carried out in raw form (T1) and under three thermal treatments: boiled (T2), commercial toasting (T3), and controlled toasting (T4). The biochemical variables evaluated were total and reducing sugars, total proteins, and total amino acids. Observations of the seed structure were performed by scanning electron microscopy (SEM), while histochemical staining was carried out to identify starch, lipids, tannins, polysaccharides and proteins under compound light microscopy.
Results
Concentration of total sugars was reduced in boiled (T2) and commercial toasting (T3) seeds as compared to raw (T1) and controlled toasting (T4) seeds; boiled seeds (T3) displayed the lowest concentration of total sugars. An increase in the concentrations of glucose and fructose was observed in T4. As compared to T1, all other treatments did not change protein concentrations in the seed; the only significant difference observed was between T2 and T3, with commercial toasting displaying the highest mean for this variable. Amino acid concentrations decreased in T3 and T4 compared to T1, while in T2 the concentration of these molecules increased. The anatomic analysis of (T1) revealed a well-organized structure, compared to applied thermal treatments, where degradation of anatomical structures was observed. In general, the thermal treatments tested modified the concentrations and distribution of starch, lipids, tannins, polysaccharides and proteins as compared to raw seeds. The raw cachichín seed has a well-defined anatomical and cellular compartmental organization, while the application of the thermal treatments caused a loss of its structural organization and degradation of vital biomolecules.
Conclusion
The cachichín seed can be considered a good source of proteins and lipids. Thermal treatments can improve its organoleptic properties, though they negatively impact its nutritional value and anatomical structure. Among thermal treatments tested, the controlled toasting can maintain or even improve some nutraceutical properties with a few structural and biochemical modifications.Classification and selection of the main features for the identification of toxicity in Agaricus and Lepiota with machine learning algorithmshttps://peerj.com/articles/165012024-01-092024-01-09Jacqueline S. Ortiz-LetechipiaCarlos E. Galvan-TejadaJorge I. Galván-TejadaManuel A. Soto-MurilloErika Acosta-CruzHamurabi Gamboa-RosalesJosé María Celaya PadillaHuizilopoztli Luna-García
The occurrence of fungi is cosmopolitan, and while some mushroom species are beneficial to human health, others can be toxic and cause illness problems. This study aimed to analyze the organoleptic, ecological, and morphological characteristics of a group of fungal specimens and identify the most significant features to develop models for fungal toxicity classification using genetic algorithms and LASSO regression. The results of the study indicated that odor, spore print color, and habitat were the most significant characteristics identified by the genetic algorithm GALGO. Meanwhile, odor, gill size, stalk shape, and twelve other features were the relevant characteristics identified by LASSO regression. The importance score of the odor variable was 99.99%, gill size obtained 73.7%, stalk shape scored 39.9%, and the remaining variables did not score higher than 18%. Logistic regression, k-nearest neighbor (KNN), and XG-Boost classification algorithms were used to develop models using the features selected by both GALGO and LASSO. The models were evaluated using sensitivity, specificity, and accuracy metrics. The models with the highest AUC values were XGBoost, with a maximum value of 0.99 using the features selected by LASSO, followed by KNN with a maximum value of 0.99. The GALGO selection resulted in a maximum AUC of 0.98 in KNN and XGBoost. The models developed in this study have the potential to aid in the accurate identification of toxic fungi, which can prevent health problems caused by their consumption.
The occurrence of fungi is cosmopolitan, and while some mushroom species are beneficial to human health, others can be toxic and cause illness problems. This study aimed to analyze the organoleptic, ecological, and morphological characteristics of a group of fungal specimens and identify the most significant features to develop models for fungal toxicity classification using genetic algorithms and LASSO regression. The results of the study indicated that odor, spore print color, and habitat were the most significant characteristics identified by the genetic algorithm GALGO. Meanwhile, odor, gill size, stalk shape, and twelve other features were the relevant characteristics identified by LASSO regression. The importance score of the odor variable was 99.99%, gill size obtained 73.7%, stalk shape scored 39.9%, and the remaining variables did not score higher than 18%. Logistic regression, k-nearest neighbor (KNN), and XG-Boost classification algorithms were used to develop models using the features selected by both GALGO and LASSO. The models were evaluated using sensitivity, specificity, and accuracy metrics. The models with the highest AUC values were XGBoost, with a maximum value of 0.99 using the features selected by LASSO, followed by KNN with a maximum value of 0.99. The GALGO selection resulted in a maximum AUC of 0.98 in KNN and XGBoost. The models developed in this study have the potential to aid in the accurate identification of toxic fungi, which can prevent health problems caused by their consumption.Biocontrol potential of endophytic bacterium Bacillus altitudinis GS-16 against tea anthracnose caused by Colletotrichum gloeosporioideshttps://peerj.com/articles/167612024-01-092024-01-09Youzhen WuYumei TanQiuju PengYang XiaoJiaofu XieZhu LiHaixia DingHang PanLongfeng Wei
Background
As one of the main pathogens causing tea anthracnose disease, Colletotrichum gloeosporioides has brought immeasurable impact on the sustainable development of agriculture. Given the adverse effects of chemical pesticides to the environment and human health, biological control has been a focus of the research on this pathogen. Bacillus altitudinis GS-16, which was isolated from healthy tea leaves, had exhibited strong antagonistic activity against tea anthracnose disease.
Methods
The antifungal mechanism of the endophytic bacterium GS-16 against C. gloeosporioides 1-F was determined by dual-culture assays, pot experiments, cell membrane permeability, cellular contents, cell metabolism, and the activities of the key defense enzymes.
Results
We investigated the possible mechanism of strain GS-16 inhibiting 1-F. In vitro, the dual-culture assays revealed that strain GS-16 had significant antagonistic activity (92.03%) against 1-F and broad-spectrum antifungal activity in all tested plant pathogens. In pot experiments, the disease index decreased to 6.12 after treatment with GS-16, indicating that strain GS-16 had a good biocontrol effect against tea anthracnose disease (89.06%). When the PE extract of GS-16 treated mycelial of 1-F, the mycelial appeared deformities, distortions, and swelling by SEM observations. Besides that, compared with the negative control, the contents of nucleic acids, protein, and total soluble sugar of GS-16 group were increased significantly, indicating that the PE extract of GS-16 could cause damage to integrity of 1-F. We also found that GS-16 obviously destroyed cellular metabolism and the normal synthesis of cellular contents. Additionally, treatment with GS-16 induced plant resistance by increasing the activities of the key defense enzymes PPO, SOD, CAT, PAL, and POD.
Conclusions
We concluded that GS-16 could damage cell permeability and integrity, destroy the normal synthesis of cellular contents, and induce plant resistance, which contributed to its antagonistic activity. These findings indicated that strain GS-16 could be used as an efficient microorganism for tea anthracnose disease caused by C. gloeosporioides.
Background
As one of the main pathogens causing tea anthracnose disease, Colletotrichum gloeosporioides has brought immeasurable impact on the sustainable development of agriculture. Given the adverse effects of chemical pesticides to the environment and human health, biological control has been a focus of the research on this pathogen. Bacillus altitudinis GS-16, which was isolated from healthy tea leaves, had exhibited strong antagonistic activity against tea anthracnose disease.
Methods
The antifungal mechanism of the endophytic bacterium GS-16 against C. gloeosporioides 1-F was determined by dual-culture assays, pot experiments, cell membrane permeability, cellular contents, cell metabolism, and the activities of the key defense enzymes.
Results
We investigated the possible mechanism of strain GS-16 inhibiting 1-F. In vitro, the dual-culture assays revealed that strain GS-16 had significant antagonistic activity (92.03%) against 1-F and broad-spectrum antifungal activity in all tested plant pathogens. In pot experiments, the disease index decreased to 6.12 after treatment with GS-16, indicating that strain GS-16 had a good biocontrol effect against tea anthracnose disease (89.06%). When the PE extract of GS-16 treated mycelial of 1-F, the mycelial appeared deformities, distortions, and swelling by SEM observations. Besides that, compared with the negative control, the contents of nucleic acids, protein, and total soluble sugar of GS-16 group were increased significantly, indicating that the PE extract of GS-16 could cause damage to integrity of 1-F. We also found that GS-16 obviously destroyed cellular metabolism and the normal synthesis of cellular contents. Additionally, treatment with GS-16 induced plant resistance by increasing the activities of the key defense enzymes PPO, SOD, CAT, PAL, and POD.
Conclusions
We concluded that GS-16 could damage cell permeability and integrity, destroy the normal synthesis of cellular contents, and induce plant resistance, which contributed to its antagonistic activity. These findings indicated that strain GS-16 could be used as an efficient microorganism for tea anthracnose disease caused by C. gloeosporioides.The effects of different rootstocks on aroma components, activities and genes expression of aroma-related enzymes in oriental melon fruithttps://peerj.com/articles/167042024-01-052024-01-05Kedong GuoJiateng ZhaoSiyu FangQian ZhangLanchun NieWensheng Zhao
Grafting is widely applied in the cultivation of melon. In this study, ‘Qinmi No.1’ (Cucumis melo L.(QG)) and ‘Ribenxuesong’ (Cucurbita maxima Duch. (RG)) were used as rootstocks for ‘Qingxin Yangjiaocui’ (Cucumis melo L.). The results showed that grafting with muskmelon rootstocks had no significant effect on fruit aroma, but grafting with pumpkin rootstocks significantly reduced the odor intensity and odor preference scores of melon fruits. Compared with the fruits from self-grafted plants (SG), four new aromatic volatiles with a sweet smell were detected, the alcohol dehydrogenase (ADH) activity was significantly decreased at 30 DAP, but unaffected at 42 DAP in QG fruits. There was no difference for alcohol acetyltransferase (AAT) activity between QG and SG fruits. The expression level of CmADH2 was significantly higher at 30 DAP and 42 DAP, but CmAAT2 was significantly lower at 42 DAP in QG fruits compared with SG fruits. In RG fruits, the main aroma compounds including butanoic acid ethyl ester, 2-methyl-2-butene-1-al, and 2-methylheptan-1-al were absent, while the volatile compounds with unpleasant odor characteristics including trans, cis-2,6-nonadien-1-ol, (E,E)-2,4-heptadienal, octanoic acid, and styrene were detected. Compared with SG fruits, 1-nonanol and 1-heptanol with green odor characteristics were significantly increased, but eucalyptol and farnesene with fruity aroma characteristics were significantly decreased in RG fruits. The ADH activity of RG fruits was significantly lower than that of SG fruits at 30 DAP and the AAT activity was significantly lower than that of SG fruits at 42 DAP. In addition, the expression levels of CmADH and CmAAT homologs in RG fruits were significantly lower than those in SG or QG fruits. These results show that grafting with pumpkin rootstocks affected the main aroma components, reduced ADH and AAT activities, and down-regulated the expression levels of CmADHs and CmAATs in the melon fruits. This study reveals the mechanism of different rootstocks on melon fruit aroma quality, and lays a theoretical foundation for the selection of rootstocks in melon production. Future studies using overexpression or CRISPR/CAS system to obtain stable transgenic lines of genes encoding key aromatic volatiles, would be promising to effectively improve the flavor quality of melon.
Grafting is widely applied in the cultivation of melon. In this study, ‘Qinmi No.1’ (Cucumis melo L.(QG)) and ‘Ribenxuesong’ (Cucurbita maxima Duch. (RG)) were used as rootstocks for ‘Qingxin Yangjiaocui’ (Cucumis melo L.). The results showed that grafting with muskmelon rootstocks had no significant effect on fruit aroma, but grafting with pumpkin rootstocks significantly reduced the odor intensity and odor preference scores of melon fruits. Compared with the fruits from self-grafted plants (SG), four new aromatic volatiles with a sweet smell were detected, the alcohol dehydrogenase (ADH) activity was significantly decreased at 30 DAP, but unaffected at 42 DAP in QG fruits. There was no difference for alcohol acetyltransferase (AAT) activity between QG and SG fruits. The expression level of CmADH2 was significantly higher at 30 DAP and 42 DAP, but CmAAT2 was significantly lower at 42 DAP in QG fruits compared with SG fruits. In RG fruits, the main aroma compounds including butanoic acid ethyl ester, 2-methyl-2-butene-1-al, and 2-methylheptan-1-al were absent, while the volatile compounds with unpleasant odor characteristics including trans, cis-2,6-nonadien-1-ol, (E,E)-2,4-heptadienal, octanoic acid, and styrene were detected. Compared with SG fruits, 1-nonanol and 1-heptanol with green odor characteristics were significantly increased, but eucalyptol and farnesene with fruity aroma characteristics were significantly decreased in RG fruits. The ADH activity of RG fruits was significantly lower than that of SG fruits at 30 DAP and the AAT activity was significantly lower than that of SG fruits at 42 DAP. In addition, the expression levels of CmADH and CmAAT homologs in RG fruits were significantly lower than those in SG or QG fruits. These results show that grafting with pumpkin rootstocks affected the main aroma components, reduced ADH and AAT activities, and down-regulated the expression levels of CmADHs and CmAATs in the melon fruits. This study reveals the mechanism of different rootstocks on melon fruit aroma quality, and lays a theoretical foundation for the selection of rootstocks in melon production. Future studies using overexpression or CRISPR/CAS system to obtain stable transgenic lines of genes encoding key aromatic volatiles, would be promising to effectively improve the flavor quality of melon.End-point rapid detection of total and pathogenic Vibrio parahaemolyticus (tdh+ and/or trh1+ and/or trh2+) in raw seafood using a colorimetric loop-mediated isothermal amplification-xylenol orange techniquehttps://peerj.com/articles/164222024-01-032024-01-03Aekarin LamaleeSoithong SaiyudthongChartchai ChangsenWansika KiatpathomchaiJitra LimthongkulChanita NaparswadCharanyarut SukphattanaudomchokeJarinya ChaopreechaSaengchan SenapinWansadaj JaroenramSureemas Buates
Background
Vibrio parahaemolyticus is the leading cause of bacterial seafood-borne gastroenteritis in humans worldwide. To ensure seafood safety and to minimize the occurrence of seafood-borne diseases, early detection of total V. parahaemolyticus (pathogenic and non-pathogenic strains) and pathogenic V. parahaemolyticus (tdh+ and/or trh1+ and/or trh2+) is required. This study further improved a loop-mediated isothermal amplification (LAMP) assay using xylenol orange (XO), a pH sensitive dye, to transform conventional LAMP into a one-step colorimetric assay giving visible results to the naked eye. LAMP-XO targeted rpoD for species specificity and tdh, trh1, and trh2 for pathogenic strains. Multiple hybrid inner primers (MHP) of LAMP primers for rpoD detection to complement the main primer set previously reported were designed by our group to maximize sensitivity and speed.
Methods
Following the standard LAMP protocol, LAMP reaction temperature for rpoD, tdh, trh1, and trh2 detection was first determined using a turbidimeter. The acquired optimal temperature was subjected to optimize six parameters including dNTP mix, betaine, MgSO4, Bst 2.0 WarmStart DNA polymerase, reaction time and XO dye. The last parameter was done using a heat block. The color change of the LAMP-XO result from purple (negative) to yellow (positive) was monitored visually. The detection limits (DLs) of LAMP-XO using a 10-fold serial dilution of gDNA and spiked seafood samples were determined and compared with standard LAMP, PCR, and quantitative PCR (qPCR) assays. Subsequently, the LAMP-XO assay was validated with 102 raw seafood samples and the results were compared with PCR and qPCR assays.
Results
Under optimal conditions (65 °C for 75 min), rpoD-LAMP-XO and tdh-LAMP-XO showed detection sensitivity at 102 copies of gDNA/reaction, or 10 folds greater than trh1-LAMP-XO and trh2-LAMP-XO. This level of sensitivity was similar to that of standard LAMP, comparable to that of the gold standard qPCR, and 10-100 times higher than that of PCR. In spiked samples, rpoD-LAMP-XO, tdh-LAMP-XO, and trh2-LAMP-XO could detect V. parahaemolyticus at 1 CFU/2.5 g spiked shrimp. Of 102 seafood samples, LAMP-XO was significantly more sensitive than PCR (P < 0.05) for tdh and trh2 detection and not significantly different from qPCR for all genes determined. The reliability of tdh-LAMP-XO and trh2-LAMP-XO to detect pathogenic V. parahaemolyticus was at 94.4% and 100%, respectively.
Conclusions
To detect total and pathogenic V. parahaemolyticus, at least rpoD-LAMP-XO and trh2-LAMP-XO should be used, as both showed 100% sensitivity, specificity, and accuracy. With short turnaround time, ease, and reliability, LAMP-XO serves as a better alternative to PCR and qPCR for routine detection of V. parahaemolyticus in seafood. The concept of using a one-step LAMP-XO and MHP-LAMP to enhance efficiency of diagnostic performance of LAMP-based assays can be generally applied for detecting any gene of interest.
Background
Vibrio parahaemolyticus is the leading cause of bacterial seafood-borne gastroenteritis in humans worldwide. To ensure seafood safety and to minimize the occurrence of seafood-borne diseases, early detection of total V. parahaemolyticus (pathogenic and non-pathogenic strains) and pathogenic V. parahaemolyticus (tdh+ and/or trh1+ and/or trh2+) is required. This study further improved a loop-mediated isothermal amplification (LAMP) assay using xylenol orange (XO), a pH sensitive dye, to transform conventional LAMP into a one-step colorimetric assay giving visible results to the naked eye. LAMP-XO targeted rpoD for species specificity and tdh, trh1, and trh2 for pathogenic strains. Multiple hybrid inner primers (MHP) of LAMP primers for rpoD detection to complement the main primer set previously reported were designed by our group to maximize sensitivity and speed.
Methods
Following the standard LAMP protocol, LAMP reaction temperature for rpoD, tdh, trh1, and trh2 detection was first determined using a turbidimeter. The acquired optimal temperature was subjected to optimize six parameters including dNTP mix, betaine, MgSO4, Bst 2.0 WarmStart DNA polymerase, reaction time and XO dye. The last parameter was done using a heat block. The color change of the LAMP-XO result from purple (negative) to yellow (positive) was monitored visually. The detection limits (DLs) of LAMP-XO using a 10-fold serial dilution of gDNA and spiked seafood samples were determined and compared with standard LAMP, PCR, and quantitative PCR (qPCR) assays. Subsequently, the LAMP-XO assay was validated with 102 raw seafood samples and the results were compared with PCR and qPCR assays.
Results
Under optimal conditions (65 °C for 75 min), rpoD-LAMP-XO and tdh-LAMP-XO showed detection sensitivity at 102 copies of gDNA/reaction, or 10 folds greater than trh1-LAMP-XO and trh2-LAMP-XO. This level of sensitivity was similar to that of standard LAMP, comparable to that of the gold standard qPCR, and 10-100 times higher than that of PCR. In spiked samples, rpoD-LAMP-XO, tdh-LAMP-XO, and trh2-LAMP-XO could detect V. parahaemolyticus at 1 CFU/2.5 g spiked shrimp. Of 102 seafood samples, LAMP-XO was significantly more sensitive than PCR (P < 0.05) for tdh and trh2 detection and not significantly different from qPCR for all genes determined. The reliability of tdh-LAMP-XO and trh2-LAMP-XO to detect pathogenic V. parahaemolyticus was at 94.4% and 100%, respectively.
Conclusions
To detect total and pathogenic V. parahaemolyticus, at least rpoD-LAMP-XO and trh2-LAMP-XO should be used, as both showed 100% sensitivity, specificity, and accuracy. With short turnaround time, ease, and reliability, LAMP-XO serves as a better alternative to PCR and qPCR for routine detection of V. parahaemolyticus in seafood. The concept of using a one-step LAMP-XO and MHP-LAMP to enhance efficiency of diagnostic performance of LAMP-based assays can be generally applied for detecting any gene of interest.Combined microbiome and metabolomics analysis of Taorong-type baijiu high-temperature Daqu and medium-temperature Daquhttps://peerj.com/articles/166212024-01-032024-01-03Yanbo LiuJunyi WuHaideng LiWenxi LiuZhenke ZhangSuna HanJianguang HouChunmei Pan
Background
Daqu is an essential starter for baijiu brewing in China. However, the microbial enrichment and metabolic characteristics of Daqu formed at different fermentation temperatures are still unclear.
Methods
High-throughput sequencing technology and the non-targeted metabolomics were used to compare the microbial communities and metabolites of Taorong-type high-temperature Daqu and middle-temperature Daqu. In this study, the relationship between microorganisms and metabolites was established.
Results
The study found that the composition and metabolites of the microbial community differed due to the difference in Daqu-making temperature. The bacterial diversity of Taorong-type high-temperature Daqu was higher than that of middle-temperature Daqu, while the fungal community diversity of Taorong-type middle-temperature Daqu was higher than that of high temperature Daqu. A total of 1,034 differential metabolites were screened from the two types of Daqu, and 76 metabolites with significant differences were detected (P < 0.001 and variable importance in projection (VIP) > 1.15). Tetraacetylethylenediamine is the metabolite with the largest differential fold among the 76 differential metabolites, which can be used as a potential marker metabolite of high-temperature Daqu.
Conclusion
This study helps elucidate the microbial assembly mechanisms and functional expression under different processing conditions through a further understanding of the composition and metabolic profile differences of different types of Daqu microflora in Taorong-type baijiu.
Background
Daqu is an essential starter for baijiu brewing in China. However, the microbial enrichment and metabolic characteristics of Daqu formed at different fermentation temperatures are still unclear.
Methods
High-throughput sequencing technology and the non-targeted metabolomics were used to compare the microbial communities and metabolites of Taorong-type high-temperature Daqu and middle-temperature Daqu. In this study, the relationship between microorganisms and metabolites was established.
Results
The study found that the composition and metabolites of the microbial community differed due to the difference in Daqu-making temperature. The bacterial diversity of Taorong-type high-temperature Daqu was higher than that of middle-temperature Daqu, while the fungal community diversity of Taorong-type middle-temperature Daqu was higher than that of high temperature Daqu. A total of 1,034 differential metabolites were screened from the two types of Daqu, and 76 metabolites with significant differences were detected (P < 0.001 and variable importance in projection (VIP) > 1.15). Tetraacetylethylenediamine is the metabolite with the largest differential fold among the 76 differential metabolites, which can be used as a potential marker metabolite of high-temperature Daqu.
Conclusion
This study helps elucidate the microbial assembly mechanisms and functional expression under different processing conditions through a further understanding of the composition and metabolic profile differences of different types of Daqu microflora in Taorong-type baijiu.Polymethoxylated flavonoids in citrus fruits: absorption, metabolism, and anticancer mechanisms against breast cancerhttps://peerj.com/articles/167112024-01-032024-01-03Yiyu WangYuan MouSenlin LuYuhua XiaBo Cheng
Polymethoxylated flavonoids (PMFs) are a subclass of flavonoids found in citrus fruits that have shown multifunctional biological activities and potential anticancer effects against breast cancer. We studied the absorption, metabolism, species source, toxicity, anti-cancer mechanisms, and molecular targets of PMFs to better utilize their anticancer activity against breast cancer. We discuss the absorption and metabolism of PMFs in the body, including the methylation, demethylation, and hydroxylation processes. The anticancer mechanisms of PMFs against breast cancer were also reviewed, including the estrogen activity, cytochrome P-450 enzyme system, and arylhydrocarbon receptor (AhR) inhibition, along with various molecular targets and potential anticancer effects. Although PMFs may be advantageous in the prevention and treatment for breast cancer, there is a lack of clinical evidence and data to support their efficacy. Despite their promise, there is still a long way to go before PMFs can be applied clinically.
Polymethoxylated flavonoids (PMFs) are a subclass of flavonoids found in citrus fruits that have shown multifunctional biological activities and potential anticancer effects against breast cancer. We studied the absorption, metabolism, species source, toxicity, anti-cancer mechanisms, and molecular targets of PMFs to better utilize their anticancer activity against breast cancer. We discuss the absorption and metabolism of PMFs in the body, including the methylation, demethylation, and hydroxylation processes. The anticancer mechanisms of PMFs against breast cancer were also reviewed, including the estrogen activity, cytochrome P-450 enzyme system, and arylhydrocarbon receptor (AhR) inhibition, along with various molecular targets and potential anticancer effects. Although PMFs may be advantageous in the prevention and treatment for breast cancer, there is a lack of clinical evidence and data to support their efficacy. Despite their promise, there is still a long way to go before PMFs can be applied clinically.Replacement of milk fat by rapeseed oil stabilised emulsion in commercial yogurthttps://peerj.com/articles/164412023-12-112023-12-11Mirosław M. KasprzakMarek SadyJoanna KrukSimona BartkovaImmanuel SankaOtt SchelerEwelina JamrózWiktor BerskiSylwia Onacik-GürRafał SzramCharles Odilichukwu R. OkpalaJoanna TkaczewskaMarzena ZającJacek DomagałaStanisław Ptasznik
The incorporation of lipid droplets and further characterization of matrices within dairy products may be possible using such adjacent particles as protein complexes/lipids. Among the range of varied emulsions and their functionalities, great attention has recently focused on the fabrication of high internal phase types. Feasibly, stable alternatives structured with health-beneficial lipids like those derived from plants could replace saturated fatty acids. As a fat replacement strategy, the fate of incorporated HIPE would require some adjustments either with storage stability and/or structural feat for the food matrix. Therefore, the replacement of milk fat by rapeseed oil stabilised emulsion in commercial yogurt was investigated. This involved 25%, 50% and 75% rapeseed oil respectively assigned as low (LIPE), medium (MIPE), and high internal phase emulsion (HIPE). Specifically, emulsions were examined by droplet size, encapsulation, pH, zeta potential, phase separation, and rheology. The fat free yogurt supplemented by HIPE were examined by droplet size, zeta potential, pH, color, sensory, texture and microbiological aspects against positive (regular milk fat) and negative (fat free) yogurt controls. Results showed increasing rapeseed oil contents would form smaller droplet-like emulsions. Within the yogurt matrix however, incorporating HIPE would seemingly reduce oil droplet size without much compromise to bacterial viability, sensory, or texture. Overall, this simple method of lipid alternation shows promise in dairy products.
The incorporation of lipid droplets and further characterization of matrices within dairy products may be possible using such adjacent particles as protein complexes/lipids. Among the range of varied emulsions and their functionalities, great attention has recently focused on the fabrication of high internal phase types. Feasibly, stable alternatives structured with health-beneficial lipids like those derived from plants could replace saturated fatty acids. As a fat replacement strategy, the fate of incorporated HIPE would require some adjustments either with storage stability and/or structural feat for the food matrix. Therefore, the replacement of milk fat by rapeseed oil stabilised emulsion in commercial yogurt was investigated. This involved 25%, 50% and 75% rapeseed oil respectively assigned as low (LIPE), medium (MIPE), and high internal phase emulsion (HIPE). Specifically, emulsions were examined by droplet size, encapsulation, pH, zeta potential, phase separation, and rheology. The fat free yogurt supplemented by HIPE were examined by droplet size, zeta potential, pH, color, sensory, texture and microbiological aspects against positive (regular milk fat) and negative (fat free) yogurt controls. Results showed increasing rapeseed oil contents would form smaller droplet-like emulsions. Within the yogurt matrix however, incorporating HIPE would seemingly reduce oil droplet size without much compromise to bacterial viability, sensory, or texture. Overall, this simple method of lipid alternation shows promise in dairy products.