Comparison of maximum specific growth rates and lag times estimated from absorbance and viable count data by different mathematical models

Induction into viable but non culturable state and outgrowth heterogeneity of Listeria monocytogenes is affected by stress history and type of growth

Exposure to sublethal stresses related to food-processing may induce a heterogenous mixture of cells that co-exist, comprising healthy, sublethally injured, dormant and dead cells. Heterogeneity in survival capacity and dormancy of single cells may impede the detection of foodborne pathogens. In this study, we exposed Listeria monocytogenes Scott A strain, to peracetic acid (PAA; 20-40 ppm) and to acidic conditions (hydrochloric (HCl) and acetic (AA) acid, adjusted to pH 2.7-3.0, to evaluate the resuscitation capacity and outgrowth kinetics of metabolically active cells in two different media. Injury and the viable-but-non-culturable (VBNC) status of cells were assessed by flow cytometry using CFDA (metabolically active) and PI (dead) staining. Stressed CFDA+PI- cells were sorted on Tryptic Soy (TS) Agar or in TS broth, both supplemented with 0.6 % Yeast Extract (TSAYE or TSBYE), to evaluate culturability. Resuscitation capacity of CFDA+PI-sorted cells (10 events/well) was monitored by visual inspection on TSAYE and by optical density measurement in TSBYE for 5 days. Sorting of L. monocytogenes viable cells (CFDA+PI-) in Ringer's solution on TSAYE and TSBYE showed 100 % recovery in both media (control condition), while the mean lag time in TSBYE was 9.6 h. Treatment with 20 ppm PAA for 90 and 180 min resulted in 74.79 % and 85.82 % of non-culturable cells in TSBYE and increased the average lag time to 41.7 h and 43.8 h, respectively, compared to the control (9.6 h). The longest average lag time (79.5 h) was detected after treatment with 30 ppm PAA for 90 min, while at the same condition sorting of CFDA+PI- cells resulted in 95.05 % and 93.94 % non-culturable cells on TSAYE and TSBYE, respectively. The highest percentage of wells with non-culturable cells (96.17 %) was detected on TSAYE after treatment with 40 ppm PAA for 30 min. Fractions of VBNC cells were detected in TSBYE after treatment with HCl pH 3.0 for 60 and 240 min, and in TSAYE and TSBYE after exposure to AA pH 2.7. Treatment with AA pH 2.7 for 150-300 min increased the range of recorded lag time values compared to 60 min, from 8.6 h up to 13.3 h, as well as the mean lag times in TSBYE. Modelling of the outgrowth kinetics comparing the two types of stress (oxidative vs acid) and the two systems of growth (colonial vs planktonic) revealed that low starting concentrations hindered the detection of viable L. monocytogenes cells, either due to VBNC induction or cell heterogeneity.

Exploring Rhodospirillum rubrum response to high doses of carbon monoxide under light and dark conditions

Environmental concerns about residues and the traditional disposal methods are driving the search for more environmentally conscious processes, such as pyrolysis and gasification. Their main final product is synthesis gas (syngas) composed of CO, CO2, H2, and methane. Syngas can be converted into various products using CO-tolerant microorganisms. Among them, Rhodospirillum rubrum is highlighted for its biotechnological potential. However, the extent to which high doses of CO affect its physiology is still opaque. For this reason, we have studied R. rubrum behavior under high levels of this gas (up to 2.5 bar), revealing a profound dependence on the presence or absence of light. In darkness, the key variable affected was the lag phase, where the highest levels of CO retarded growth to more than 20 days. Under light, R. rubrum ability to convert CO into CO2 and H2 depended on the presence of an additional carbon source, such as acetate. In those conditions where CO was completely exhausted, CO2 fixation was unblocked, leading to a diauxic growth. To enhance R. rubrum tolerance to CO in darkness, a UV-accelerated adaptive laboratory evolution (UVa-ALE) trial was conducted to isolate clones with shorter lag phases, resulting in the isolation of clones 1.4-2B and 1.7-2A. The adaptation of 1.4-2B was mainly based on mutated enzymes with a metabolic function, while 1.7-3A was mostly affected at regulatory genes, including the anti-repressor PpaA/AerR. Despite these mutations having slight effects on biomass and pigment levels, they successfully provoked a significant reduction in the lag phase (-50%). KEYPOINTS: • CO affects principally R. rubrum lag phase (darkness) and growth rate (light) • CO is converted to CO2/H2 during acetate uptake and inhibits CO2 fixation (light) • UVa-ALE clones showed a 50% reduction in the lag phase (darkness).

Assessment of the biochemical methane potential of in-house and outdoor stored pig and dairy cow manure by evaluating chemical composition and storage conditions

Biogas production is a suitable option for producing energy from dairy and pig manure types. During manure storage, organic matter degradation results in methane emissions decreasing the potential biogas yield. The present research advances the understanding of the biochemical methane potential (BMP) and the chemical characteristics of manure collected year-round from sequential stages of the liquid manure management chain of commercial dairy cow and pig farms. To this end, manure samples from six livestock farms in Germany were analyzed. The results showed that changes in chemical composition during storage led to a 20.5% decrease in the BMP of dairy manure from the barn to outdoor storage. For fattening pig manure samples, there was a 39.5% decrease in the BMP from intermediate to outdoor storage. An analysis of BMP according to manure age showed that pig manure degrades faster than dairy manure; the importance of promptly feeding manure to the biogas plant in order to avoid significant CH4 emission losses and reduction in energy producing capacity was highlighted. The best BMP predictors for dairy manure were the contents of dry matter, volatile solids and lignin, whereas best BMP predictors for pig manure were dry matter and volatile fatty acid (VFA) content. Prediction models performed well for samples from outdoor storages; refinements for predicting BMP of less aged samples presenting lower chemical variability would be necessary.

Prediction of Pseudomonas spp. Population in Food Products and Culture Media Using Machine Learning-Based Regression Methods

Machine learning approaches are alternative modelling techniques to traditional modelling equations used in predictive food microbiology and utilise algorithms to analyse large datasets that contain information about microbial growth or survival in various food matrices. These approaches leverage the power of algorithms to extract insights from the data and make predictions regarding the behaviour of microorganisms in different food environments. The objective of this study was to apply various machine learning-based regression methods, including support vector regression (SVR), Gaussian process regression (GPR), decision tree regression (DTR), and random forest regression (RFR), to estimate bacterial populations. In order to achieve this, a total of 5618 data points for Pseudomonas spp. present in food products (beef, pork, and poultry) and culture media were gathered from the ComBase database. The machine learning algorithms were applied to predict the growth or survival behaviour of Pseudomonas spp. in food products and culture media by considering predictor variables such as temperature, salt concentration, water activity, and acidity. The suitability of the algorithms was assessed using statistical measures such as coefficient of determination (R²), root mean square error (RMSE), bias factor (Bf), and accuracy (A_f). Each of the regression algorithms showed appropriate estimation capabilities with R² ranging from 0.886 to 0.913, RMSE from 0.724 to 0.899, B_f from 1.012 to 1.020, and A_f from 1.086 to 1.101 for each food product and culture medium. Since the predictive capability of RFR was the best among the algorithms, externally collected data from the literature were used for RFR. The external validation process showed statistical indices of B_f ranging from 0.951 to 1.040 and A_f ranging from 1.091 to 1.130, indicating that RFR can be used for predicting the survival and growth of microorganisms in food products. Therefore, machine learning approaches can be considered as an alternative to conventional modelling methods in predictive microbiology. However, it is important to highlight that the prediction power of the machine learning regression method directly depends on the dataset size, and it requires a large dataset to be employed for modelling. Therefore, the modelling work of this study can only be used for the prediction of Pseudomonas spp. in specific food products (beef, pork, and poultry) and culture medium with certain conditions where a large dataset is available.

Cardinal models to describe the effect of temperature and pH on the growth of Anoxybacillus flavithermus & Bacillus licheniformis

Anoxybacillus flavithermus and Bacillus licheniformis are among the predominant spore-formers of heat-processed foods. To our knowledge, no systematic analysis of growth kinetic data of A. flavithermus or B. licheniformis is currently available. In the present study, the growth kinetics of A. flavithermus and B. licheniformis in broth at various temperature and pH conditions were studied. Cardinal models were used to model the effect of the above-mentioned factors on the growth rates. The estimated values for the cardinal parameters T_min,T_opt,T_max,pH_min and pH_1/2 for A. flavithermus were 28.70 ± 0.26, 61.23 ± 0.16 and 71.52 ± 0.32 °C, 5.52 ± 0.01 and 5.73 ± 0.01, respectively, while for B. licheniformis they were 11.68 ± 0.03, 48.05 ± 0.15, 57.14 ± 0.01 °C, 4.71 ± 0.01 and 5.670 ± 0.08, respectively. The growth behaviour of these spoilers was also investigated in a pea beverage at 62 and 49 °C, respectively, to adjust the models to this product. The adjusted models were further validated at static and dynamic conditions and demonstrated good performance with 85.7 and 97.4% of predicted populations for A. flavithermus and B. licheniformis, respectively, being within the -10%-10% relative error (RE) zone. The developed models can be useful tools in assessing the potential of spoilage of heat-processed foods including plant-based milk alternatives.

Lactobacillus plantarum strains show diversity in biofilm formation under flow conditions

In many natural and technological applications, microbial biofilms grow under fluid flow. In this project, we investigated the influence of flow on the formation and growth of biofilms produced by gram-positive Lactobacillus plantarum strains WCFS1 and CIP104448. We used an in-house designed device based on a 48-well plate with culture volumes of 0.8 ml, and quantified total biofilm formation under static and flow conditions with flow rates 0.8, 1.6, 3.2 and 4.8 ml/h (with 1, 2, 4 and 6 volume changes per hour) using crystal violet (CV) staining, and determined the number of viable biofilm cells based on plate counts. The amount of total biofilm under flow conditions increased in the CIP 104448 strain, with significantly increased staining at the wall of the wells. However, in the WCFS1 strain, no significant difference in the amount of biofilm formed under flow and static conditions was observed. Plate counts showed that flow caused an increase in the number of viable biofilm cells for both strains. In addition, using enzyme treatment experiments, we found that for WCFS1 in the static condition, the amount of mature biofilm was declined after DNase I and Proteinase K treatment, while for flow conditions, the decline was only observed for DNase I treatment. The CIP104448 biofilms formed under both static and flow conditions only showed a decline in the CV staining after adding Proteinase K, indicating different contributions of extracellular DNA (eDNA) and proteinaceous matrix components to biofilm formation in the tested strains.

Deciphering longitudinal optical-density measurements to guide clinical dosing regimen design: A model-based approach

BACKGROUND

Model-based analysis of longitudinal optical density measurements from a bacterial suspension exposed to antibiotics has been proposed as a potentially efficient and effective method for extracting useful information to improve the individualized design of treatments for bacterial infections. To that end, the authors developed in previous work a mathematical modeling framework that can use such measurements for design of effective dosing regimens.

OBJECTIVES

Here we further explore ways to extract information from longitudinal optical density measurements to predict bactericidal efficacy of clinically relevant antibiotic exposures.

METHODS

Longitudinal optical density measurements were collected in an automated instrument where Acinetobacter baumannii, ATCC BAA747, was exposed to ceftazidime concentrations of 1, 4, 16, 64, and 256 mg/L and to ceftazidime/amikacin concentrations of 1/0.5, 4/2, 16/8, 64/32, and 256/128 (mg/L)/(mg/L) over 20 h. Calibrated conversion of measurements produced total (both live and dead) bacterial cell concentration data (CFU/mL equivalent) over time. Model-based data analysis predicted the bactericidal efficacy of ceftazidime and of ceftazidime/amikacin (at ratio 2:1) for periodic injection every 8 h and subsequent exponential decline with half-life of 2.5 h. Predictions were experimentally tested in an in vitro hollow-fiber infection model, using peak concentrations of 60 and 150 mg/L for injected ceftazidime and of 40/20 (mg/L)/(mg/L) for injected ceftazidime/amikacin.

RESULTS

Model-based analysis predicted low (<62%) confidence in clinically relevant suppression of the bacterial population by periodic injections of ceftazidime alone, even at high peak concentrations. Conversely, analysis predicted high (>95%) confidence in bacterial suppression by periodic injections of ceftazidime/amikacin combinations at a wide range of peak concentrations ratioed at 2:1. Both predictions were experimentally confirmed in an in vitro hollow fiber infection model, where ceftazidime was periodically injected at peak concentrations 60 and 150 mg/L (with predicted suppression confidence 38% and 59%, respectively) and a combination of ceftazidime/amikacin was periodically injected at peak concentrations 40/20 (mg/L)/(mg/L) (with predicted suppression confidence 98%).

CONCLUSIONS

The paper highlights the potential of clinicians using the proposed mathematical framework to determine the utility of different antibiotics to suppress a patient-specific isolate. Additional studies will be needed to consolidate and expand the utility of the proposed method.

From degrader to producer: reversing the gallic acid metabolism of Pseudomonas putida KT2440

Gallic acid is a powerful antioxidant with multiple therapeutic applications, usually obtained from the acidic hydrolysis of tannins produced by many plants. As this process generates a considerable amount of toxic waste, the use of tannases or tannase-producing microorganisms has become a greener alternative over the last years. However, their high costs still impose some barriers for industrial scalability, requiring solutions that could be both greener and cost-effective. Since Pseudomonas putida KT2440 is a powerful degrader of gallic acid, its metabolism offers pathways that can be engineered to produce it from cheap and renewable carbon sources, such as the crude glycerol generated in biodiesel units. In this study, a synthetic operon with the heterologous genes aroG4, quiC and pobA* was developed and expressed in P. putida, based on an in silico analysis of possible metabolic routes, resulting in no production. Then, the sequences pcaHG and galTAPR were deleted from the genome of this strain to avoid the degradation of gallic acid and its main intermediate, the protocatechuic acid. This mutant was transformed with the vector containing the synthetic operon and was finally able to convert glycerol into gallic acid. Production assays in shaker showed a final concentration of 346.7 ± 0.004 mg L^-1 gallic acid after 72 h.

Inflammation-associated nitrate facilitates ectopic colonization of oral bacterium Veillonella parvula in the intestine

Colonization of the intestine by oral microbes has been linked to multiple diseases such as inflammatory bowel disease and colon cancer, yet mechanisms allowing expansion in this niche remain largely unknown. Veillonella parvula, an asaccharolytic, anaerobic, oral microbe that derives energy from organic acids, increases in abundance in the intestine of patients with inflammatory bowel disease. Here we show that nitrate, a signature metabolite of inflammation, allows V. parvula to transition from fermentation to anaerobic respiration. Nitrate respiration, through the narGHJI operon, boosted Veillonella growth on organic acids and also modulated its metabolic repertoire, allowing it to use amino acids and peptides as carbon sources. This metabolic shift was accompanied by changes in carbon metabolism and ATP production pathways. Nitrate respiration was fundamental for ectopic colonization in a mouse model of colitis, because a V. parvula narG deletion mutant colonized significantly less than a wild-type strain during inflammation. These results suggest that V. parvula harness conditions present during inflammation to colonize in the intestine.

Effects of Different Nutritional Zinc Forms on the Proliferation of Beneficial Commensal Microorganisms

This study compared the minimal inhibition concentrations (MICs) and their effects on the growth kinetics of seven different types of zinc (Zn) compounds and Na2EDTA in the case of three typical commensal beneficial microorganisms (Bacillus subtilis, Lactococcus lactis, and Saccharomyces cerevisiae). The seven Zn compounds included ZnSO4, four Zn–amino acid chelates, and two Zn–EDTA complexes. Both MICs and growth kinetic parameters indicated that different microorganisms show different sensitivities; for example, B. subtilis, L. lactis, and S. cerevisiae were most sensitive to ZnSO4, Na2EDTA, and Zn(NH3)2(Gly)2, respectively. Both ZnEDTA and Zn(NH3)2(Lys)2 improved the growth rate of all beneficial commensal intestinal microorganisms at low concentrations (5–10 mg/L) and showed low toxicity towards all tested strains. At higher concentrations (100–500 mg/L), all compounds decreased the growth rate and increased the lag phase. In conclusion, both growth kinetic parameters and MICs tested effectively measured the inhibitory effects of the test materials; however, growth kinetics provides a more detailed picture of the concentration-dependent effects and those on the mechanisms of microbial growth inhibition.

The possibility of a halal mix probiotic medium for the cultivation of Lactobacillus plantarum N16 and Saccharomyces cerevisiae

This study aimed to determine the effects of interaction between media type (halal mix preparation) and culture mixtures of Lactobacillus plantarum N16 and Saccharomyces cerevisiae (probiotics). A completely randomised factorial design (CRFD) consisting of 2 factors and three replications was used, where factor A was a mixture of Lactobacillus plantarum N16 and Saccharomyces cerevisiae at a ratio of 1:1 (A1); 1:2 (A2) and 2:1 (A3) and factor B was the type of growth media, that is, control (B1), whey tofu, molasses, and fish waste flour (B2), and coconut water, onggok flour and shrimp waste flour (B3). The variables measured were viability, cell biomass, and pH. The results showed interactions between factors A and B, which were significantly different (p <0.05) in terms of viability, cell biomass, and pH. Based on the results of the study, it can be concluded that the mixture of Lactobacillus plantarum N16 and Saccharomyces cerevisiae at a ratio of 2:1 (A3), using coconut water, onggok flour, and shrimp waste flour (B3) as medium and incubated at 36 °C for 24 hours was the best medium. It had a 2.37 viability, 42.33 mg/ml biomass cell, and a pH of 2.37.

Tryptone in Growth Media Enhances Pseudomonas putida Biofilm

Extracellular factors and growth conditions can affect the formation and development of bacterial biofilms. The biofilm of Pseudomonas putida has been studied for decades, but so far, little attention has been paid to the components of the medium that may affect the biofilm development in a closed system. It is known that Fis strongly enhances biofilm in complete LB medium. However, this is not the case in the defined M9 medium, which led us to question why the bacterium behaves differently in these two media. Detailed analysis of the individual medium components revealed that tryptone as the LB proteinaceous component maintains biofilm in its older stages. Although the growth parameters of planktonic cells were similar in the media containing tryptone or an equivalent concentration of amino acids, only the tryptone had a positive effect on the mature biofilm of the wild type strain of P. putida. Thus, the peptides in the environment may influence mature biofilm as a structural factor and not only as an energy source. Testing the effect of other biopolymers on biofilm formation showed variable results even for polymers with a similar charge, indicating that biopolymers can affect P. putida biofilm through a number of bacterial factors.

Strain Variability in Growth and Thermal Inactivation Characteristics of Listeria monocytogenes Strains after Acid Adaptation

ABSTRACT

Given the importance of strain variability to predictive microbiology and risk assessment, this study aimed to quantify the magnitude of strain variability in growth and thermal inactivation kinetics behaviors after acid adaptation. Thirty-three Listeria monocytogenes strains were exposed to acid-adapted tryptic soy broth supplemented with yeast extract (TSBYE; pH 5.5) and non-acid-adapted TSBYE (pH 7.0) for 20 h. Next, the growth parameters of these adapted and nonadapted strains that grew in nonbuffered TSBYE at 25°C were estimated. The tested strains were inactivated at 60°C in nonbuffered broth to obtain the heat resistance parameters. The results revealed that strain variability was present in the growth and thermal inactivation characteristics. The maximum specific growth rate ranged from 0.21 to 0.44 h-1 and from 0.20 to 0.45 h-1 after acid and nonacid adaptation, respectively. The lag times were from 0.69 to 2.56 h and from 0.24 to 3.36 h for acid-adapted and non-acid-adapted cells, respectively. The apparent D-values at 60°C of the pathogen ranged between 0.56 and 3.93 min and between 0.52 and 3.63 min for the presence and absence of acid adaptation condition, respectively. Acid adaptation significantly (P < 0.05) increased the magnitude of strain variability in the thermal inactivation characteristics of L. monocytogenes, with the coefficient of variation increasing to 0.17, whereas acid adaptation did not significantly (P ≥ 0.05) influence the variabilities in the growth parameters of the tested strains. Furthermore, the subsequent growth behaviors of all strains did not exhibit significant (P > 0.05) changes after exposure to acidic broth. However, the thermal resistance of most (25 of 33) of the tested strains increased (P < 0.05) after growing in acid-adapted broth. The relevant data generated in the present study can be used to describe the strain variability in predictive microbiology and to deeply understand the behavioral responses of different strains to acid adaptation.

HIGHLIGHTS

Development and validation of a predictive model for the effect of temperature, pH and water activity on the growth kinetics of Bacillus coagulans in non-refrigerated ready-to-eat food products

A cardinal model (CM) for the effects of temperature (range: 32-59 °C), pH (range: 5.0-8.5) and water activity (a_w) (range: 0.980-0.995) on Bacillus coagulans DSM 1 growth rate was developed in brain heart infusion broth (BHI), using the Bioscreen C method and further validated in selected food products. The estimated values for the cardinal parameters T_min, T_opt, T_max, pH_min, pH_opt, pH_max, [Formula: see text] and [Formula: see text] were 23.77 ± 0.19 °C, 52.89 ± 0.01 °C, 59.37 ± 0.07 °C, 4.70 ± 0.02, 6.43 ± 0.02, 8.56 ± 0.01, 0.969 ± 0.0007 and 0.998 ± 0.0011, respectively. The growth behaviour of B. coagulans was studied in five commercial non-refrigerated ready-to-eat food products under static conditions at 53 °C in order to estimate the optimum specific growth rate for each tested food product. The developed models were validated in the five selected food products under four different dynamic temperature profiles by comparing predicted and observed growth behaviour of B. coagulans. The validation results indicated a good performance of the model for all tested products with the overall Bias factor (B_f) and Accuracy factor (A_f) estimated at 1.00 and 1.12, respectively. The developed model can be considered an effective tool in predicting B. coagulans growth and spoilage risks of non-refrigerated ready-to-eat food products during distribution and storage.

Development and validation of an extended predictive model for the effect of pH and water activity on the growth kinetics of Geobacillus stearothermophilus in plant-based milk alternatives

The cardinal model for the effect of temperature on Geobacillus stearothermophilus ATCC 7953 growth developed by Kakagianni, Gougouli, & Koutsoumanis, 2016 was expanded for the effect of pH and water activity (a_w). The effect of pH (range: 5.7-8.5) and a_w (range: 0.985-0.999) on G. stearothermophilus growth rate was studied in tryptone soy broth (TSB) using the Bioscreen C method and further modelled using a Cardinal Model (CM). The estimated values for the cardinal parameters [Formula: see text] , and [Formula: see text] were 5.65 ± 0.14, 6.74 ± 0.03, 8.71 ± 0.03, 0.984 ± 0.007 and 0.998 ± 0.001, respectively. The growth behaviour of G. stearothermophilus was investigated in 7 commercial non-refrigerated plant-based milk alternatives under static conditions (62 °C) and the estimated maximum specific growth rates were used to determine the optimum growth rate for each product. The developed model was validated against observed growth of G. stearothermophilus in the 7 products during storage at non-isothermal conditions (testing 4 different temperature profiles). The validation results showed a good performance of the model with overall Bias factor (B_f) = 1.06 and Accuracy factor (A_f) = 1.12. The developed model can be used as an effective tool by the food industry in predicting spoilage of plant-based milk alternatives during distribution and storage at retail and domestic levels.

Evaluation of Scenarios for Improving the Collection System for a Milk Factory in Ethiopia

The milk for a factory in Sululta (Ethiopia) is currently collected at ambient temperature. To increase milk production, the sourcing must be extended. This requires the collection of not only the morning milk but also the evening milk from smallholder farms. To accomplish this, the collection of milk from small farmers has to be improved, whereby the milk quality has to be assured with reasonable cost and environmental impact. A model predicting milk rejection was developed based on initial contamination and time and temperature profiles. With this model, different cooling scenarios we reevaluated regarding the expected effectiveness of reducing the rejection rate during collection. Second, cost estimations were made to implement the scenarios to collect morning and evening milk from smallholder farms. A third criterion was greenhouse gas (GHG) emissions per litre of collected milk. Finally, the feasibility of the scenarios was assessed in terms of technical, practical, and economic aspects. Including both quality and economics, the best scenario can be expected from a cooling centre where farmers bring their milk twice a day, except there are signals that the farmers would not be willing to deliver the evening milk to the centre at night. In that case, an additional collecting system would be needed to increase the milk supply. This would result in higher collection costs and an increased risk of milk rejection at the factory gate. Furthermore, this would reduce the value of the chilling centre, as in that case it would be better to deliver the milk directly to the factory. Both scenarios would increase GHG emissions compared with the current situation. Only the use of an off-grid solar power-driven cooling system at the farms would reduce the GHG emissions. However, this solution is less feasible economically. The applied combination of a simple model, economic analysis and the effect on GHG emissions gives valuable information on the effectiveness and limitations of different cooling scenarios for the milk factory. It can help to successfully apply a scenario for increasing the milk supply.

Behavior of Vibrio spp. in Table Olives

The presence of Vibrio species in table olive fermentations has been confirmed by molecular biology techniques in recent studies. However, there has been no report of any foodborne outbreak caused by Vibrio due to the consumption of table olives, and their role as well as the environmental conditions allowing their survival in table olives has not been elucidated so far. The aims of this work were to model the behavior of an inoculated Vibrio cocktail in diverse table olive environments and study the possible behavior of an inoculated Vibrio cocktail in table olives. First, an in vitro study has been performed where the microbial behavior of a Vibrio cocktail was evaluated in a laboratory medium and in olive brines using predictive models at different NaCl concentrations (2-12%) and pH levels (4.0-9.0). Afterward, a challenge testing was done in lye-treated olives inoculated at the beginning of fermentation with the Vibrio cocktail for 22 days. The Vibrio cocktail inoculated in table olives has not been detected in olive brines during fermentation at different pH levels. However, it was observed that this microorganism in a laboratory medium could reach an optimal growth at pH 9 and 2% salt, without time of constant absorbance (t _A), and the maximum absorbance value (y _end) observed was at pH 8 and 2% salt conditions. The statistical analysis demonstrated that the effect of salt concentration was higher than pH for the kinetic growth parameters (μ_max, t _A, and y _end). On the other hand, it was confirmed that no growth of the Vibrio cocktail on any sample was noticed in lye-treated olive fermentations. Thus, it was concluded that the presence of olive compounds (unknown) did not allow the development of Vibrio strains, so it is a very safety product as it has a natural antimicrobial compound, but the possibility that a native Vibrio sp. is able to acquire the capacity to adapt to this compound should be considered in further studies.

Growth Optimisation and Kinetic Profiling of Diesel Biodegradation by a Cold-Adapted Microbial Consortium Isolated from Trinity Peninsula, Antarctica

Simple Summary

Diesel fuel is very crucial for anthropogenic activities in Antarctica and the surges in annual demand mean higher likelihood of spillages from improper handling during transportation, storage and disposal processes. The impacts can be very extensive or well-contained depending on the scale of the spills as well as the terrain involved. Nevertheless, the freezing temperature and prolonged solar irradiance in the south pole greatly hampered the natural attenuation and photovolatilisation of petrogenic hydrocarbons, contributing to their persistency. The most susceptible groups are the soil microorganisms, mosses, seabirds and pinnipeds as they are easily found near the shore where hydrocarbons spillage is very common. Microbial bioremediation is a well-established approach in restoring many hydrocarbons-polluted areas, thus the current study focused on the optimisation and application of locally isolated microbial consortium to simulate the in situ diesel clean-up process in aqueous medium. This study highlights the ability of the selected consortium to degrade diesel almost completely at moderately low temperature, suggesting its potential application in Antarctic settings.

Abstract

Pollution associated with petrogenic hydrocarbons is increasing in Antarctica due to a combination of increasing human activity and the continent’s unforgiving environmental conditions. The current study focuses on the ability of a cold-adapted crude microbial consortium (BS24), isolated from soil on the north-west Antarctic Peninsula, to metabolise diesel fuel as the sole carbon source in a shake-flask setting. Factors expected to influence the efficiency of diesel biodegradation, namely temperature, initial diesel concentration, nitrogen source type and concentration, salinity and pH were studied. Consortium BS24 displayed optimal cell growth and diesel degradation activity at 1.0% NaCl, pH 7.5, 0.5 g/L NH₄Cl and 2.0% v/v initial diesel concentration during one-factor-at-a-time (OFAT) analyses. The consortium was psychrotolerant based on the optimum growth temperature of 10‒15 °C. In conventionally optimised media, the highest total petroleum hydrocarbons (TPH) mineralisation was 85% over a 7-day incubation. Further optimisation of conditions predicted through statistical response-surface methodology (RSM) (1.0% NaCl, pH 7.25, 0.75 g/L NH₄Cl, 12.5 °C and 1.75% v/v initial diesel concentration) boosted mineralisation to 95% over a 7-day incubation. A Tessier secondary model best described the growth pattern of BS24 in diesel-enriched medium, with maximum specific growth rate, μ_max, substrate inhibition constant, K_i and half saturation constant, K_s, being 0.9996 h⁻¹, 1.356% v/v and 1.238% v/v, respectively. The data obtained suggest the potential of microbial consortia such as BS24 in bioremediation applications in low-temperature diesel-polluted soils.

Emergence of two AcrB substitutions conferring multidrug resistance to Salmonella spp

AcrAB-TolC is a major tripartite multidrug efflux pump conferring resistance to a wide variety of compounds in Gram-negative pathogens. Many AcrB mutants have been constructed through site-directed mutagenesis to probe the mechanism of AcrB function in antibiotic resistance. However, much less is known about the actual drug resistance related mutants that naturally occur in clinically isolated pathogens. Here, we report two novel AcrB substitutions, M78I and P319L, in clinically isolated Salmonella strains with high-level ciprofloxacin resistance. Plasmids expressing the detected acrB mutations were constructed and introduced into SL1344△acrB Antimicrobial susceptibility assay showed that all AcrB M78I, AcrB P319L and AcrB M78I/319L conferred reduced susceptibilities to multiple substrates, including fluoroquinolones, erythromycin, tetracyclines, bile salts and dyes. Site-directed mutagenesis and MIC results revealed that increased hydrophobicity of M78I was one of the reasons why AcrB M78I had lower susceptibility to fluoroquinolones. Fluorescence labeling experiments suggested that the AcrB M78I substitution enhanced the binding of substrates to certain amino acid sites in the efflux pathway (e.g., site Q89, E673 and F617) and weakened the binding to other amino acids (e.g., S134 and N274). Structural modeling disclosed the increased flexibility of Leu was favorable for the functional rotation of AcrB compared to the original Pro. AcrA 319L makes the functional rotation of AcrB more flexible, this enables substrate efflux more efficiently. In order to understand the mechanism of AcrAB-TolC drug efflux well, interaction between AcrA and AcrB in the role of substrate efflux of AcrAB-TolC should be further investigated.

Cardinal parameter growth and growth boundary model for non-proteolytic Clostridium botulinum - Effect of eight environmental factors

A new cardinal parameter growth and growth boundary model for non-proteolytic C. botulinum was developed and validated for fresh and lightly preserved seafood and poultry products. 523 growth rates in broth were used to determine cardinal parameter values and terms for temperature, pH, NaCl/water activity, acetic, benzoic, citric, lactic and sorbic acids. The new growth and growth boundary model included the inhibiting interactive effect between these factors and it was calibrated using growth curves from 10 challenge tests with unprocessed seafood. For model evaluation, 40 challenge tests with well characterized fresh and lightly preserved seafood were performed. Comparison of these observed growth curves and growth rates (μ_max-values) predicted by the new model resulted in a bias factor (B_f) of 1.12 and an accuracy factor (A_f) of 1.40. Furthermore, the new model was evaluated with 94 growth rates and 432 time to toxin formation data extracted from the scientific literature for seafood, poultry, meat, pasta and prepared meals. These data included responses for 36 different toxigenic strains of non-proteolytic C. botulinum. The obtained B_f-/A_f-values were 0.97/2.04 for μ_max-values and 0.96/1.80 for time to toxin formation. The model correctly predicted 93.8% of the growth responses with 5.6% being fail-safe and <1% fail-dangerous. A cocktail of four non-toxin producing Clostridium spp. isolates was used to develop the new model and these isolates had more than 99.8% 16S rRNA gene similarity to non-proteolytic C. botulinum (Group II). The high number of environmental factors included in the new model makes it a flexible tool to facilitate development or reformulation of seafood and poultry products that do not support the growth of non-proteolytic C. botulinum. Further, evaluation of the new model with well characterized products is desirable particularly for meat, vegetables, pasta and prepared meals as well as for dairy products that was not included in the present study.

Coordination of primary metabolism and virulence factors expression mediates the virulence of Vibrio parahaemolyticus towards cultured shrimp (Penaeus vannamei)

AIMS

Acute hepatopancreatic necrosis disease (AHPND) caused by Vibrio parahaemolyticus has emerged as a severe bacterial disease of cultured shrimp. To identify the key virulence factors, two AHPND-causing V. parahaemolyticus (Vp_AHPND ) strains (123 and 137) and two non-Vp_AHPND strains (HZ56 and ATCC 17082) were selected.

METHODS AND RESULTS

Challenge tests showed that the four strains exhibited different virulence towards shrimp with cumulative mortalities at 48 h postinfection (hpi) ranging from 10 to 92%. The expression of pirAB^VP in strain 123 and 137 was not significantly different. Genomic analysis revealed that the two Vp_AHPND strains contain a plasmid with the PirAB^VP toxins (pirAB^VP ) flanked by the insertion sequence (ISVal1) that has been identified in various locations of chromosomes in Vp_AHPND strains. The two Vp_AHPND strains possessed almost identical virulence factors, while ISVal1 disrupted three genes related to flagellar motility in strain 137. Phenotype assay showed that strain 123 possessed the highest growth rate and swimming motility, followed by strain 137, suggesting that the disruption of essential genes mediated by ISVal1 significantly affected the virulence level. Transcriptome analysis of two Vp_AHPND strains (123 and 137) further suggested that virulence genes related to the capsule, flagella and primary metabolism were highly expressed in strain 123.

CONCLUSIONS

Here for the first time, it is demonstrated that the virulence of Vp_AHPND is not only determined by the expression of pirAB^VP , but also is mediated by ISVal1 which affects the genes involved in flagellar motility and primary metabolism.

SIGNIFICANCE AND IMPACT OF THE STUDY

The genomic and transcriptomic analysis of Vp_AHPND strains provides valuable information on the virulence factors affecting the pathogenicity of Vp_AHPND.

Antimicrobial effect of nisin in processed cheese - Quantification of residual nisin by LC-MS/MS and development of new growth and growth boundary model for Listeria monocytogenes

This study tested the hypothesis that growth of Listeria monocytogenes in processed cheese with added nisin can be predicted from residual nisin A concentrations in the final product after processing. A LC-MS/MS method and a bioassay were studied to quantify residual nisin A concentrations and a growth and growth boundary model was developed to predict the antilisterial effect in processed cheese. 278 growth rates were determined in broth for 11 L. monocytogenes isolates and used to determine 13 minimum inhibitory concentration (MIC) values for nisin between pH 5.5 and 6.5. To supplement these data, 67 MIC-values at different pH-values were collected from the scientific literature. A MIC-term was developed to describe the effect of pH on nisin MIC-values. An available growth and growth boundary model (doi: https://doi.org/10.1016/j.fm.2019.103255) was expanded with the new MIC-term for nisin to predict growth in processed cheese. To generate data for model evaluation and further model development, challenge tests with a total of 45 growth curves, were performed using processed cheese. Cheeses were formulated with 11.2 or 12.0 ppm of nisin A and heat treated to obtain residual nisin A concentrations ranging from 0.56 to 5.28 ppm. Below 15 °C, nisin resulted in extended lag times. A global regression approach was used to fit all growth curves determined in challenge tests. This was obtained by combining the secondary growth and growth boundary model including the new term for the inhibiting effect of nisin on μ_max with the primary logistic growth model with delay. This model appropriately described the growth inhibiting effect of residual nisin A and showed that relative lag times depended on storage temperatures. With residual nisin A concentrations, other product characteristics and storage temperature as input the new model correctly predicted all observed growth and no-growth responses for L. monocytogenes. This model can support development of nisin A containing recipes for processed cheese that prevent growth of L. monocytogenes. Residual nisin A concentrations in processed cheese were accurately quantified by the developed LC-MS/MS method with recoveries of 83 to 110% and limits of detection and quantification being 0.04 and 0.13 ppm, respectively. The tested bioassay was less precise and nisin A recoveries varied for 53% to 94%.

Effect of Pulsed Electric Fields on the Growth and Acidification Kinetics of Lactobacillus delbrueckii Subsp. bulgaricus

The aim of this work was to investigate the effect of pulsed electric fields (PEF) on the growth and acidification kinetics of Lactobacillus delbrueckii subsp. bulgaricus CFL1 during fermentation. The PEF treatments were applied during the fermentation process using a recirculation pump and a PEF treatment chamber coupled with a PEF generator. The medium flow rate through the chamber was first optimized to obtain the same growth and acidification kinetics than the control fermentation without medium recirculation. Different PEF intensities (60-428 V cm-1) were then applied to the culture medium to study the impact of PEF on the cells' behavior. The growth and acidification kinetics were recorded during the fermentation and the specific growth rates µ, pH, and acidification rate (dpH/dt) were assessed. The results obtained showed a biphasic growth by applying high PEF intensities (beyond 285 V cm-1) with the presence of two maximal specific growth rates and a decrease in the acidification activities. It was demonstrated that the cells were stressed during the PEF treatment, but presented an accelerated growth after stopping it, leading thereby to similar absorbance and pH at the end of the fermentation. These results show the great potential of PEF technology to be applied to generate low acidified products by performing PEF-assisted fermentations.

Bacteriological and histopathological analysis of Penaeus vannamei experimentally infected with Vibrio parahaemolyticus-AHPND strains

Vibrio parahaemolyticus strains have been identified as the causative agent of acute hepatopancreas necrosis disease (Vp AHPND+) in shrimp. In the present work, a highly virulent (M0904) and less virulent (M0607) strain of Vp AHPND+ were used in experimental infections of Penaeus vannamei. Throughout the experiment, histopathological analyses were conducted on shrimp tissues, and samples from the bottom (B) and water column (WC) of each aquarium were taken to estimate bacterial growth. The first deaths of shrimp challenged with Vp M0904 occurred 4 h post-infection (hpi), reached 50% mortality at 17 hpi, and showed more acute pathological progression associated with AHPND despite both strains having similar bacterial densities from 0-4 hpi. The first deaths of shrimp inoculated with Vp M0607 occurred at 13 hpi, a difference of 9 h. These shrimps displayed reduction of reserve vacuoles in R and B cells of the hepatopancreas, and reached 50% mortality at 27 hpi. As bacterial growth in the WC and B in the first hours was similar for both strains, bacterial density was not a significant factor in Vp virulence. Since pirAB toxin is the causative agent of AHPND, it is possible that there is a threshold level at which the toxin damages hepatopancreatic tissues, so production or secretion of the toxin can be dependent of the Vp strain. We propose new AHPND stage: remission with 3 main routes for the disease outcome after the remission stage (re-infection, chronic effect and recuperation). Hepatopancreatic embryonic cells can be used as a biological indicator of this stage.

Efficacy of Acacia nilotica aqueous extract in treating biofilm-forming and multidrug resistant uropathogens isolated from patients with UTI syndrome

Escherichia coli is the dominant bacterial cause of UTI among the uropathogens in both developed and developing countries. This study is to investigate the effect of Acacia nilotica aqueous extract on the survival and biofilm of isolated pathogens to reduce UTIs diseases. A total of 170 urine samples were collected from Luxor general hospital and private medical analysis laboratories in Luxor providence, Egypt. Samples were screened for the incidence of uropathogens by biochemical tests, antibiotics susceptibility, detection of virulence, and antibiotic-resistant genes by multiplex PCR, biofilm formation, and time-killing assay. Escherichia coli is by far the most prevalent causative agent with the percentage of 73.7% followed by Klebsiella pneumoniae, Proteus mirabilis, Pseudomonas aeuroginosa, and Acinetobacter baumanii. Isolates were multidrug-resistant containing blaTEM, blaSHV, blaCTX, qnrs, and aac(3)-Ia resistant genes. All isolates were sensitive to 15-16.7 mg ml-1 of Acacia nilotica aqueous extract. Time killing assay confirmed the bactericidal effect of the extract over time (20-24 h). A high percentage of 3-Cyclohexane-1-Carboxaldehyde, 2,6,6-trimethyl (23.5%); á-Selinene (15.12%); Oleic Acid (14.52%); Globulol (11.35%) were detected among 19 bioactive phytochemical compounds in the aqueous extract of A. nilotica over the GC-mass spectra analysis. The plant extract reduced significantly the biofilm activity of E. coli, K. pneumoniae, P. mirabilis, and P. aeuroginosa by 62.6, 59. 03, 48.9 and 39.2%, respectively. The challenge to improve the production of A. nilotica phytochemicals is considered a very low price for the return.

Enhancement of Production of D-Glucosamine in Escherichia coli by Blocking Three Pathways Involved in the Consumption of GlcN and GlcNAc

D-Glucosamine is a commonly used dietary supplement that promotes cartilage health in humans. Metabolic flux analysis showed that D-glucosamine production could be increased by blocking three pathways involved in the consumption of glucosamine-6-phosphate and acetylglucosamine-6-phosphate. By homologous single-exchange, two key genes (nanE and murQ) of Escherichia coli BL21 were knocked out, respectively. The D-glucosamine yields of the engineered strains E. coli BL21ΔmurQ and E. coli BL21ΔnanE represented increases by factors of 2.14 and 1.79, respectively. Meanwhile, for bifunctional gene glmU, we only knocked out its glucosamine-1-phosphate acetyltransferase domain by 3D structural analysis to keep the engineered strain E. coli BL21glmU-Δgpa survival, which resulted in an increase in the production of D-glucosamine by a factor of 2.16. Moreover, for further increasing D-glucosamine production, two genes encoding rate-limiting enzymes, named glmS and gna1, were coexpressed by an RBS sequence in those engineered strains. The total concentrations of D-glucosamine in E. coli BL21 glmU-Δgpa', E. coli BL21ΔmurQ', and E. coli BL21ΔnanE' were 2.65 g/L, 1.73 g/L, and 1.38 g/L, which represented increases by factors of 8.83, 5.76, and 3.3, respectively.

New Insights into Modelling Bacterial Growth with Reference to the Fish Pathogen Flavobacterium psychrophilum

Simple Summary

Flavobacteriumpsychrophilum is a cold-water bacterium responsible for cold water disease and rainbow trout fry syndrome which has significant impacts on fish health and, by extension, negative economic impacts on aquaculture operations. Models can be applied to bacterial growth curves yielding parameter estimates describing rates of bacterial growth and the time it takes for a bacterium to reach its exponential phase of growth (lag time). These parameter estimates can be used to establish the relationship between microbial growth and environmental variables such as pH, temperature and effect of anti-microbial treatments. Two novel models are derived and their potential to describe bacterial growth assessed through their ability to mimic the growth of Flavobacteriumpsychrophilum on liquid media. Due to their mechanistic derivation, the proposed models result in flexible and robust growth functions that can be expressed as equations with biologically meaningful parameters. Based upon statistical measures of goodness-of-fit and cross-validation, the purposed models were able to describe satisfactorily the growth of Flavobacteriumpsychrophilum on various media. Furthermore, the proposed models also provide insight into underlying mechanisms that are driving microbial growth and how the current environment affects bacterial rate of growth.

Abstract

Two new models, based upon the principles promulgated by Baranyi and co-workers are presented and resulting growth functions evaluated based upon their ability to mimic bacterial growth of the fish pathogen Flavobacterium psychrophilum. These growth functions make use of a dampening function to suppress potential growth, represented by a logistic, and are derived from rate:state differential equations. Dampening effects are represented by a rectangular hyperbola or a simple exponential, incorporated into a logistic differential equation and solved analytically resulting in two newly derived growth equations, viz. logistic × hyperbola (log × hyp) and logistic × exponential (log × exp). These characteristics result in flexible and robust growth functions that can be expressed as equations with biologically meaningful parameters. The newly derived functions (log × hyp and log × exp), along with the Baranyi (BAR), simple logistic (LOG) and its modified form (MLOG) were evaluated based upon examination of residuals and measures of goodness-of-fit and cross-validation. Using these criteria, log × hyp, log × exp and BAR performed better than, or at least equally well as, LOG and MLOG. In contrast with log × exp and BAR, log × hyp can be easily manipulated mathematically allowing for simple algebraic expressions for time and microbial biomass at inflexion point, in addition to maximum and scaled maximum growth rates.

Strain Variability of Listeria monocytogenes under NaCl Stress Elucidated by a High-Throughput Microbial Growth Data Assembly and Analysis Protocol

Listeria monocytogenes causes the severe foodborne illness listeriosis and survives in food-associated environments due to its high stress tolerance. A data assembly and analysis protocol for microbial growth experiments was compiled to elucidate the strain variability of L. monocytogenes stress tolerance. The protocol includes measurement of growth ability under stress (step 1), selection of a suitable method for growth parameter calculation (step 2), comparison of growth patterns between strains (step 3), and biological interpretation of the discovered differences (step 4). In step 1, L. monocytogenes strains (n = 388) of various serovars and origins grown on media with 9.0% NaCl were measured using a Bioscreen C microbiology reader. Technical variability of the growth measurements was assessed and eliminated. In step 2, the growth parameters determined by Gompertz, modified-Gompertz, logistic, and Richards models and model-free splines were compared, illustrating differences in the suitability of these methods to describe the experimental data. In step 3, hierarchical clustering was used to describe the NaCl tolerance of L. monocytogenes measured by strain-specific variation in growth ability; tolerant strains had higher growth rates and maximum optical densities and shorter lag phases than susceptible strains. The spline parameter area under the curve best classified "poor," "average," and "good" growers. In step 4, the tested L. monocytogenes lineage I strains (serovars 4b and 1/2b) proved to be significantly more tolerant toward 9.0% NaCl than lineage II strains (serovars 1/2a, 1/2c, and 3a). Our protocol provides systematic tools to gain comparable data for investigating strain-specific variation of bacterial growth under stress.IMPORTANCE The pathogen Listeria monocytogenes causes the foodborne disease listeriosis, which can be fatal in immunocompromised individuals. L. monocytogenes tolerates several environmental stressors and can persist in food-processing environments and grow in foodstuffs despite traditional control measures such as high salt content. Nonetheless, L. monocytogenes strains differ in their ability to withstand stressors. Elucidating the intraspecies strain variability of L. monocytogenes stress tolerance is crucial for the identification of particularly tolerant strains. To enhance reliable identification of variability in bacterial stress tolerance phenotypes, we compiled a large-scale protocol for the entire data assembly and analysis of microbial growth experiments, providing a systematic approach and checklist for experiments on strain-specific growth ability. Our study illustrated the diversity and strain-specific variation of L. monocytogenes stress tolerance with an unprecedented scope and discovered biologically relevant serovar- and lineage-dependent phenotypes of NaCl tolerance.

Microbial synergy between Pichia kudriazevii YS201 and Bacillus subtilis BS38 improves pulp degradation and aroma production in cocoa pulp simulation medium

Interactions between two major microorganisms from Ivorian cocoa fermentation, namely Bacillus subtilis BS38 and Pichia kudriazevii YS201, were investigated during fermentation in cocoa pulp simulation medium. The strains were mutually inhibitory, with Bacillus being more susceptible to this antagonistic effect than Pichia. However, both strains yielded different pulp-degrading enzymes, namely polygalacturonase (PG) from Pichia and pectate lyase (Pel) from Bacillus, that cooperate to efficiently breakdown pectin and vegetable pulp. The quantification of aromas from microbial cultures using Gas Chromatography-Mass Spectroscopy (GC-MS) coupled with headspace microextration (SPME) method, showed that P. kudriazevii produce mainly alcohols such as ethanol (63.165 g/L), phenylethanol (1.005 g/L), methylbutanol (0.138 g/L) and esters, notably ethyl acetate (0.037 g/L) and isoamyl acetate (0.032 g/L). The volatile fraction produced by Bacillus was dominated by butanediol (5.707 g/L), acetoin (1.933 g/L), phenylethanol (0.035 g/L) and acetic acid (0.034 g/L). In co-culture, Bacillus produced low levels of aroma compounds whereas a moderate decrease in the production of these compounds was observed in the yeasts strain. Thus, the dominant aromas present in the co-culture were mainly those from the yeasts strain; however, a 1.37 fold increase of ethanol production was observed in co-culture indicating a synergy between the strains. This study showed that cooperation between B. subtilis BS38 and P. kudriazevii YS201 leads principally to increasing pulp degradation and ethanol production, known as desirable properties for a well processing of cocoa fermentation.

Growth and growth boundary model with terms for melting salts to predict growth responses of Listeria monocytogenes in spreadable processed cheese

The aim of this study was to develop and validate a growth and growth boundary model with terms for melting salts to predict growth of Listeria monocytogenes in spreadable processed cheese. Cardinal parameter terms for phosphate salts and citric acid were developed in broth studies and used to expand an available growth and growth boundary model. The expanded model includes the effect of nine environmental factors (temperature, pH, a_w, lactic acid, acetic acid, citric acid, orthophosphate, di-phosphate and tri-phosphate). To generate growth data for model evaluation challenge tests with inoculated commercial (n = 10) and customized (n = 10) spreadable processed cheeses were performed. Evaluation of the new model by comparison of observed and predicted μ_max-values resulted in a bias factor of 1.12 and an accuracy factor of 1.33 (n = 42). Prediction of growth and no-growth responses in processed cheese (n = 60) were 89% correct with 11% fail-safe and 0% fail-dangerous predictions. The developed model can be used to support product development, reformulation or risk assessment for spreadable processed cheese.

Characterization of Listeria monocytogenes enhanced cold-tolerance variants isolated during prolonged cold storage

In this study, we show that growth and prolonged storage of Listeria monocytogenes at 4 °C can promote the selection of variants with enhanced cold and heat tolerance. Enhanced cold-tolerance (ECT) variants (n = 12) were successfully isolated from a strain with impaired cold growth abilities following 84 days of storage at 4 °C in brain heart infusion broth (BHIB). Whole genome sequencing, membrane fatty acid analysis, and stress tolerance profiling were performed on the parent strain and two ECT variants: one displaying regular-sized colonies and the other displaying small colonies when grown at 37 °C on BHI agar. Under cold stress conditions, the parent strain exhibited an impaired ability to produce branched-chain fatty acids which are known to be important for cold adaptation in L.monocytogenes. The ECT variants were able to overcome this limitation, a finding which is hypothesized to be associated with the identification of two independent single-nucleotide polymorphisms in genes encoding subunits of acetyl-coA carboxylase, an enzyme critical for fatty acid biosynthesis. While the ECT phenotype was not found to be associated with improved salt (BHIB + 6% NaCl, 25 °C), acid (BHIB pH 5, 25 °C) or desiccation (33% RH, 20 °C) tolerance, the small-colony variant exhibited significantly (p < 0.05) enhanced heat tolerance at 52 °C in buffered peptone water compared to the parent strain and the other variant. The results from this study demonstrate that the continuous use of refrigeration along the food-supply chain has the potential to select for L.monocytogenes variants with enhanced cold and heat tolerance, highlighting the impact that microbial intervention strategies can have on the evolution of bacterial strains and likewise, food safety.

New Term to Quantify the Effect of Temperature on pH min -Values Used in Cardinal Parameter Growth Models for Listeria monocytogenes

The aim of this study was to quantify the influence of temperature on pH min -values of Listeria monocytogenes as used in cardinal parameter growth models and thereby improve the prediction of growth for this pathogen in food with low pH. Experimental data for L. monocytogenes growth in broth at different pH-values and at different constant temperatures were generated and used to determined pH min -values. Additionally, pH min -values for L. monocytogenes available from literature were collected. A new pH min -function was developed to describe the effect of temperatures on pH min -values obtained experimentally and from literature data. A growth and growth boundary model was developed by substituting the constant pH min -value present in the Mejlholm and Dalgaard (2009) model (J. Food. Prot. 72, 2132-2143) by the new pH min -function. To obtain data for low pH food, challenge tests were performed with L. monocytogenes in commercial and laboratory-produced chemically acidified cheese including glucono-delta-lactone (GDL) and in commercial cream cheese. Furthermore, literature data for growth of L. monocytogenes in products with or without GDL were collected. Evaluation of the new and expanded model by comparison of observed and predicted μ max -values resulted in a bias factor of 1.01 and an accuracy factor of 1.48 for a total of 1,129 growth responses from challenge tests and literature data. Growth and no-growth responses of L. monocytogenes in seafood, meat, non-fermented dairy products, and fermented cream cheese were 90.3% correctly predicted with incorrect predictions being 5.3% fail-safe and 4.4% fail-dangerous. The new pH min -function markedly extended the range of applicability of the Mejlholm and Dalgaard (2009) model from pH 5.4 to pH 4.6 and therefore the model can now support product development, reformulation or risk assessment of food with low pH including chemically acidified cheese and cream cheese.

Characterization and Control of Erwinia spp. and Pluralibacter sp. in Tuna Salad Preparations

HIGHLIGHTS

Modeling Growth of Listeria and Lactic Acid Bacteria in Food Environments

Predictive food microbiology models can facilitate the assessment and management of microbial food safety. Importantly, the combined effect of storage conditions and product characteristics can be predicted by successfully validated models. This makes it easier and faster to develop or reformulation safe food recipes and predictions can be used to documents safety of available foods. The effect of various product characteristics and storage conditions must be taken into account and extensive mathematical models including the effect of these environmental factors are needed. Here the development, evaluation and application of an extensive growth and growth boundary model for Listeria monocytogenes including the effect of 12 environmental factors as well as the growth dampening effect of lactic acid bacteria is described. The Food Spoilage and Safety Predictor software is used to illustrate how predictions can be applied.

The importance of lag time extension in determining bacterial resistance to antibiotics

It is widely appreciated that widespread antibiotic resistance has significantly reduced the utility of today's antibiotics. Many antibiotics now fail to cure infectious diseases, although they are classified as effective bactericidal agents based on antibiotic susceptibility tests. Here, via kinetic growth assays, we evaluated the effects of 12 commonly used antibiotics on the lag phase of a range of pure environmental isolates and of sludge bacterial communities with a high diversity. We show that an extended lag phase offers bacteria survival advantages and promotes regrowth upon the removal of antibiotics. By utilizing both lag phase extension and IC50, the killing efficiency of an antibiotic on a strain or a community can be easily revealed. Interestingly, for several strains of relevance to endemic nosocomial infections (e.g. Acinetobacter sp. and Pseudomonas aeruginosa) and the diverse sludge communities, tetracycline and quinolone antibiotics are most likely to be resisted via extended lag phase. This discovery is significant from a clinical point view since underestimation of bacteria resistance can lead to the recurrence of diseases.

Methods of determing biokinetics of arsenate accumulation and release in Microcystis aeruginosa regulated by common environmental factors: Practical implications for enhanced bioremediation

Only little information is available on combined effects of abiotic environmental factors on algal arsenate (As^V ) metabolic biokinetics. Herein, we demonstrated the methods of using the Taguchi statistical method to investigate four environmental factors including As^V , nitrate (N), orthophosphate (P) and pH for their combined effects on algal growth and arsenic (As) uptake but also extracellular adsorption of Microcystis aeruginosa, as well as As release from dead algal cells. Results showed that an increase of N facilitated M. aeruginosa growth and thus was the principal factor for the algal maximum specific growth rate (  μmax ). P was vital to As^V bioconcentration factor (BCF) and As partition coefficients (LogK_d ) released from deal algal cells. As^V impacted the extracellular As adsorption onto the algal cells, which thereby increased with increasing initial As^V level. The initial pH had an imperative effect on the As^V uptake (k_u ) and release rate (K_e ) from the dead cells. Collectively, the condition of low P, high N and alkaline pH level was favorable to As accumulation rate of living cells and restrictive to As release rate from dead cells of M. aeruginosa. The obtained information can pave a road for extensive understanding on efficient utilization of As bioremediation of algae in practical environment. •Principal factors were identified on As^V metabolic biokinetics by Taguchi method.•High N and pH but low P fasten As^V uptake and reduce As efflux from dead cells.•As^V only as the main factor impacted As extracellular adsorption on algal cells.

Antimicrobial and Antibiofilm Activities of Citrus Water-Extracts Obtained by Microwave-Assisted and Conventional Methods

Citrus pomace is a huge agro-food industrial waste mostly composed of peels and traditionally used as compost or animal feed. Owing to its high content of compounds beneficial to humans (e.g., flavonoids, phenol-like acids, and terpenoids), citrus waste is increasingly used to produce valuable supplements, fragrance, or antimicrobials. However, such processes require sustainable and efficient extraction strategies by solvent-free techniques for environmentally-friendly good practices. In this work, we evaluated the antimicrobial and antibiofilm activity of water extracts of three citrus peels (orange, lemon, and citron) against ten different sanitary relevant bacteria. Both conventional extraction methods using hot water (HWE) and microwave-assisted extraction (MAE) were used. Even though no extract fully inhibited the growth of the target bacteria, these latter (mostly pseudomonads) showed a significant reduction in biofilm biomass. The most active extracts were obtained from orange and lemon peel by using MAE at 100 °C for 8 min. These results showed that citrus peel water infusions by MAE may reduce biofilm formation possibly enhancing the susceptibility of sanitary-related bacteria to disinfection procedures.

Computational modeling of immune system of the fish for a more effective vaccination in aquaculture

Motivation

A computational model equipped with the main immunological features of the sea bass (Dicentrarchus labrax L.) immune system was used to predict more effective vaccination in fish. The performance of the model was evaluated by using the results of two in vivo vaccinations trials against L. anguillarum and P. damselae.

Results

Tests were performed to select the appropriate doses of vaccine and infectious bacteria to set up the model. Simulation outputs were compared with the specific antibody production and the expression of BcR and TcR gene transcripts in spleen. The model has shown a good ability to be used in sea bass and could be implemented for different routes of vaccine administration even with more than two pathogens. The model confirms the suitability of in silico methods to optimize vaccine doses and the immune response to them. This model could be applied to other species to optimize the design of new vaccination treatments of fish in aquaculture.

Availability and implementation

The method is available at http://www.iac.cnr.it/∼filippo/c-immsim/.

Contact

nromano@unitus.it.

Supplementary information

Supplementary data are available at Bioinformatics online.

Robust, linear correlations between growth rates and β-lactam-mediated lysis rates

It is widely acknowledged that faster-growing bacteria are killed faster by β-lactam antibiotics. This notion serves as the foundation for the concept of bacterial persistence: dormant bacterial cells that do not grow are phenotypically tolerant against β-lactam treatment. Such correlation has often been invoked in the mathematical modeling of bacterial responses to antibiotics. Due to the lack of thorough quantification, however, it is unclear whether and to what extent the bacterial growth rate can predict the lysis rate upon β-lactam treatment under diverse conditions. Enabled by experimental automation, here we measured >1,000 growth/killing curves for eight combinations of antibiotics and bacterial species and strains, including clinical isolates of bacterial pathogens. We found that the lysis rate of a bacterial population linearly depends on the instantaneous growth rate of the population, regardless of how the latter is modulated. We further demonstrate that this predictive power at the population level can be explained by accounting for bacterial responses to the antibiotic treatment by single cells. This linear dependence of the lysis rate on the growth rate represents a dynamic signature associated with each bacterium-antibiotic pair and serves as the quantitative foundation for designing combination antibiotic therapy and predicting the population-structure change in a population with mixed phenotypes.

Characterization of Condensed Tannins from Purple Prairie Clover (Dalea purpurea Vent.) Conserved as either Freeze-Dried Forage, Sun-Cured Hay or Silage

Conservation methods have been shown to affect forage nutrient composition and value, but little information is available about the effect of forage conservation on plant condensed tannins (CT). The objective of this study was to assess the effects of conservation method on the concentration, chemical composition and biological activity of CT. Whole-plant purple prairie clover (PPC, Dalea purpurea Vent.) was harvested at full flower and conserved as freeze-dried forage (FD), hay (HAY) or silage (SIL). Concentration of CT in conserved PPC was determined by the butanol-HCl-acetone method. Structural composition, protein-precipitation capacity and anti-bacterial activity of CT isolated from conserved forage were determined by in situ thiolytic degradation followed by HPLC-MS analysis, a protein precipitation assay using bovine serum albumin and ribulose 1,5-disphosphate carboxylase as model proteins and by an Escherichia coli (E. coli) growth test, respectively. Conservation method had no effect on concentration of total CT, but ensiling decreased (p < 0.001) extractable CT and increased (p < 0.001) protein- and fiber-bound CT. In contrast, hay-making only increased (p < 0.01) protein-bound CT. Regardless of conservation method, epigallocatechin (EGC), catechin (C) and epicatechin (EC) were the major flavan-3-ol units, and gallocatechin (GC) was absent from both terminal and extension units of PPC CT. The SIL CT had the lowest (p < 0.001) EGC, but the highest (p < 0.01) EC in the extension units. Similarly, SIL CT exhibited a lower (p < 0.001) mean degree of polymerization (mDP), but higher (p < 0.001) procyanidins (PC) than FD or HAY CT. The protein-precipitating capacity of CT in conserved PPC ranked (p < 0.001) as FD > HAY > SIL. E. coli growth n M9 medium was inhibited by 25-100 µg/mL of CT isolated from FD, HAY and SIL (p < 0.05), but preservation method had no effect on the ability of CT to inhibit bacterial growth. The results demonstrated that ensiling decreased the extractability and protein-precipitating capacity of CT by increasing the proportions of PC. Purple prairie clover conserved as hay retained more biologically active CT than if it was conserved as silage.

Development and validation of predictive models for the effect of storage temperature and pH on the growth boundaries and kinetics of Alicyclobacillus acidoterrestris ATCC 49025 in fruit drinks

This study was undertaken to provide quantitative tools for predicting the behavior of the spoilage bacterium Alicyclobacillus acidoterrestris ATCC 49025 in fruit drinks. In the first part of the study, a growth/no growth interface model was developed, predicting the probability of growth as a function of temperature and pH. For this purpose, the growth ability of A. acidoterrestris was studied at different combinations of temperature (15-45 °C) and pH (2.02-5.05). The minimum pH and temperature where growth was observed was 2.52 (at 35 and 45 °C) and 25 °C (at pH ≥ 3.32), respectively. Then a logistic polynomial regression model was fitted to the binary data (0: no growth, 1: growth) and, based on the concordance index (98.8%) and the Hosmer-Lemeshow statistic (6.226, P = 0.622), a satisfactory goodness of fit was demonstrated. In the second part of the study, the effects of temperature (25-55 °C) and pH (3.03-5.53) on A. acidoterrestris growth rate were investigated and quantitatively described using the cardinal temperature model with inflection and the cardinal pH model, respectively. The estimated values for the cardinal parameters T_min, T_max, T_opt and pH_min, pH_max, pH_opt were 18.11, 55.68, 48.60 °C and 2.93, 5.90, 4.22, respectively. The developed models were validated against growth data of A. acidoterrestris obtained in eight commercial pasteurized fruit drinks. The validation results showed a good performance of both models. In all cases where the growth/no growth interface model predicted a probability lower than 0.5, A. acidoterrestris was, indeed, not able to grow in the tested fruit drinks; similarly, when the model predicted a probability above 0.9, growth was observed in all cases. A good agreement was also observed between growth predicted by the kinetic model and the observed kinetics of A. acidoterrestris in fruit drinks at both static and dynamic temperature conditions.

Soft, adhesive (+) alpha tocopherol phosphate planar bilayers that control oral biofilm growth through a substantive antimicrobial effect

'Soft' nanomaterials have the potential to produce substantive antibiofilm effects. The aim of this study was to understand the oral antimicrobial activity of soft nanomaterials generated from alpha-tocopherol (α-T) and alpha-tocopherol phosphate (α-TP). (+) α-TP formed planar bilayer islands (175 ± 21 nm, -14.9 ± 3.5 mV) in a Trizma® buffer, whereas (+) α-T formed spherical liposomes (563 ± 1 nm, -10.5 ± 0.2 mV). The (+) α-TP bilayers displayed superior Streptococcus oralis biofilm growth retardation, a more substantive action, generated a superior adsorption to hydroxyapatite and showed an enhanced inhibition of multi-species bacterial saliva biofilm growth (38 ± 7μm vs 58 ± 18 μm, P ˂ 0.05) compared to (+) α-T. Atomic force microscopy data indicated that the ability of the 'soft' α-TP nanomaterials to transition into planar bilayer structures upon contact with interfaces facilitated their adhesive properties and substantive antimicrobial effects.

Influence of culture media, pH and temperature on growth and bacteriocin production of bacteriocinogenic lactic acid bacteria

There has been continued interest in bacteriocins research from an applied perspective as bacteriocins have potential to be used as natural preservative. Four bacteriocinogenic lactic acid bacteria (LAB) strains of Lactobacillus curvatus (Arla-10), Enterococcus faecium (JFR-1), Lactobacillus paracasei subsp. paracasei (JFR-5) and Streptococcus thermophilus (TSB-8) were previously isolated and identified in our lab. The objective of this study was to determine the optimal growth conditions for both LAB growth and bacteriocins production. In this study, various growth conditions including culture media (MRS and BHI), initial pH of culture media (4.5, 5.5, 6.2, 7.4 and 8.5), and incubation temperatures (20, 37 and 44 °C) were investigated for LAB growth measured as optical density (OD), bacteriocin activity determined as arbitrary unit and viability of LAB expressed as log CFU ml-1. Growth curves of the bacteriocinogenic LAB were generated using a Bioscreen C. Our results indicated that Arla-10, JFR-1, and JFR-5 strains grew well on both MRS and BHI media at growth temperature tested whereas TSB-8 strain, unable to grow at 20 °C. LAB growth was significantly affected by the initial pH of culture media (p < 0.001) and the optimal pH was found ranging from 6.2 to 8.5. Bacteriocin activity was significantly different in MRS versus BHI (p < 0.001), and the optimal condition for LAB to produce bacteriocins was determined in MRS broth, pH 6.2 at 37 °C. This study provides useful information on potential application of bacteriocinogenic LAB in food fermentation processes.