Pseudomonas fluorescens group bacterial strains are responsible for repeat and sporadic postpasteurization contamination and reduced fluid milk shelf life

Strain-specific Growth Parameters are Important to Accurately Model Bacterial Growth on Baby Spinach in Simulation Models

Digital tools to predict produce shelf life have the potential to reduce food waste and improve consumer satisfaction. To address this need, we (i) performed an observational study on the microbial quality of baby spinach, (ii) completed growth experiments of bacteria that are representative of the baby spinach microbiota, and (iii) developed an initial simulation model of bacterial growth on baby spinach. Our observational data showed that the predominant genera found on baby spinach were Pseudomonas, Pantoea and Exiguobacterium. Rifampicin-resistant mutants (rifR mutants) of representative bacterial subtypes were subsequently generated to obtain strain-specific growth parameters on baby spinach. These experiments showed that: (i) it is difficult to select rifR mutants that do not have fitness costs affecting growth (9 of 15 rifR mutants showed substantial differences in growth, compared to their corresponding wild-type strain) and (ii) based on estimates from primary growth models, the mean (geometric) maximum population of rifR mutants on baby spinach (7.6 log10 CFU/g, at 6°C) appears lower than that of the spinach microbiota (9.6 log10 CFU/g, at 6°C), even if rifR mutants did not have substantial growth-related fitness costs. Thus, a simulation model, parameterized with the data obtained here as well as literature data on home refrigeration temperatures, underestimated bacterial growth on baby spinach. The root mean square error of the simulation's output, compared against data from the observational study, was 1.11 log10 CFU/g. Sensitivity analysis was used to identify key parameters (e.g., strain maximum population) that impact the simulation model's output, allowing for prioritization of future data collection to improve the simulation model. Overall, this study provides a roadmap for the development of models to predict bacterial growth on leafy vegetables with strain-specific parameters and suggests that additional data are required to improve these models.

Time and temperature abuse of milk in conditions representing a school cafeteria share table does not meaningfully reduce microbial quality

Share tables (ST) are tables or stations in school cafeterias where students can return unopened foods and beverages, providing an opportunity to access these items at no cost. Currently, research suggests that milk is among the most wasted items in breakfast and lunch programs in the United States. Share tables present a simple solution for reducing milk waste, but research is needed to understand the microbial spoilage potential of milk in ST. To this end, uninoculated milk cartons and milk cartons inoculated with 2 to 3 log10(cfu/mL) Pseudomonas poae, a fast-growing psychrotroph, was exposed to ambient temperature during winter (mean temperature = 20.3°C) and summer (23.1°C) for 125 min, repeated over 5 d (the length of a school week). Microbial counts in the inoculated milk cartons increased linearly, exceeding the spoilage threshold of 6.0 log10(cfu/mL) after d 3 and after d 4 in the winter and summer season trials, respectively. In the winter trial, the microbial counts for uninoculated milk cartons never exceeded the lower limit of detection, 2.31 log10(cfu/mL), and in the summer trials, microbial counts never reached the spoilage threshold, indicating that initial contamination is a driving factor of microbial milk spoilage. Regardless of sharing status or seasonality, the greatest changes in counts for inoculated milk cartons occurred during overnight refrigeration, ranging from 0.56 to 1.4 log10(cfu/mL), while during the share table ranged from no observable change up to 0.29 log10(cfu/mL), emphasizing that school nutrition personnel should focus efforts on tightly controlling refrigeration temperatures and returning milk to refrigeration as soon as possible. A previously developed model for school cafeteria share tables was adapted to understand the typical residence time of milk in a simulated cafeteria with an ambient temperature share table for the summer and winter seasons over 1,000 wk. Milk was predicted to have a very short mean residence time (85 min) regardless of sharing status or season, with 99.8% of milk consumed, discarded, or donated within the first 2 d. As a result, only 3 out of 451,410 and 6 out of 451,410 simulated milks spoiled in the winter and summer seasons, respectively. The data generated here can be used to inform science-based decision-making for including milk in share tables, or applied to any system where one might have to accept short-term unrefrigerated storage of milk to meet a waste reduction or food security goal.

Characterizing Spoilage of Coconut-based Creamers: A Multifaceted Approach to Identify Problematic Bacteria and Their Potential Sources in a New Product Category

Beverage innovation is a growing trend with a reliance on comanufacturing relationships to launch products quickly. A recent comanufacturing relationship is the utilization of dairy processing facilities to process plant-based beverages using high-temperature short-time (HTST) pasteurization. While the shelflife of HTST bovine milk is well established at 21 days, retailers are expecting new refrigerated beverages to achieve a 60-day shelflife. Little is known about the microbial stability of these new beverages, particularly those with complex formulations. Our objective was to identify bacterial taxa leading to the spoilage of four coconut-based creamers and their potential sources (raw ingredients or packaging). We used a multifaceted approach including plate counting and 16S rRNA metabarcoding to monitor microbial growth in products throughout shelflife (60 d, 4 °C), and cold enrichment (7 °C, 11 d) of ingredients and packaging. Nearly all product units (25/26) had elevated microbial loads (>4.3 log CFU/mL) prior to the 60-d target, with early spoilage detected at 21 d. Key spoilage taxa included Pseudomonas, Streptococcus, Aerococcus, Paenibacillus, Sphingomonas, and Oceanobacillus. Pseudomonas were responsible for "early" product spoilage (21-32 d), whereas Oceanobacillus were important in products with very "late" spoilage (60-62 d). All key spoilage taxa were identified in cold enrichments of multiple units of waxboard cartons. Paenibacillus was the dominant bacterium in 47% (10/21) of product units. In addition to carton samples, Paenibacillus was also identified in one raw ingredient (mushroom extract). Metabarcoding identified Listeria sensu stricto as a dominant taxon in three individual product units from three distinct production lots. Listeria was also found in 31% (5/16) of cold enrichments of individual cartons. Taxa responsible for spoilage of plant-based beverages were identified as well as demonstrating packaging as an important contamination source.

Calcium-mediated modulation of Pseudomonas fluorescens biofilm formation

Biofilm formation is usually affected by many environmental factors, including divalent cations. The purpose of the current work was to analyze how calcium (Ca2+) affects the biofilm formation of dairy Pseudomonas fluorescens isolates by investigating their growth, swarming motility, biofilm-forming capacity, extracellular polymeric substance production, and biofilm structures. Moreover, the regulation mechanism of Ca2+ involved in its biofilm formation was explored through RNA-sequencing analysis. This work revealed that supplementation of 5, 10, 15, and 20 mM Ca2+ significantly reduced the swarming motility of P. fluorescens strains (P.F2, P.F4, and P.F17), but the biofilm-forming ability and polysaccharide production were increased after the supplementation of 5 and 10 mM Ca2+. By the supplementation of Ca2+, complex structures with more cell clusters glued together in P. fluorescens P.F4 biofilms were confirmed by scanning electron microscopy, and increased biomass and coverage of P. fluorescens P.F4 biofilms were observed by confocal laser scanning microscopy. In addition, RNA-sequencing results showed that P. fluorescens P.F4 showed a transcriptional response to the supplementation of 10 mM Ca2+, and a total of 137 genes were significantly expressed. The differential genes were represented in 4 upregulated Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways (nonribosomal peptide structures, quorum sensing, biosynthesis of siderophore group nonribosomal peptides, and phenylalanine metabolism), and 4 downregulated KEGG pathways (flagellar assembly, amino sugar and nucleotide sugar metabolism, nitrotoluene degradation, and cationic antimicrobial peptide resistance). The results indicate that Ca2+ might serve as an enhancer to substantially trigger the biofilm formation of dairy P. fluorescens isolates in the dairy industry.

Phenotypic and genomic characterizations of Klebsiella pneumoniae ssp. pneumoniae and Rahnella inusitata strains reveal no clear association between genetic content and ropy phenotype

Ropy defect of pasteurized fluid milk is a type of spoilage which manifests itself by an increased viscosity, slimy body, and string-like flow during pouring. This defect has, among other causes, been attributed to the growth, proliferation and exopolysaccharide production by coliform bacteria, which are most commonly introduced in milk as post-pasteurization contaminants. As we identified both Klebsiella pneumoniae ssp. pneumoniae and Rahnella inusitata that were linked to a ropy defect, the goal of this study was to characterize 3 K. pneumoniae ssp. pneumoniae strains and 2 R. inusitata for (1) their ability to grow and cause ropy defect in milk at 6°C and 21°C and to (2) probe the genetic basis for observed ropy phenotype. Although all K. pneumoniae ssp. pneumoniae and R. inusitata strains showed net growth of >4 log10 over 48 h in UHT milk at 21°C, only R. inusitata strains displayed growth during 28-d incubation period at 6°C (>6 log10). Two out of 3 K. pneumoniae ssp. pneumoniae strains were capable of causing the ropy defect in milk at 21°C, as supported by an increase in the viscosity of milk and string-like flow during pouring; these 2 strains were originally isolated from raw milk. Only one R. inusitata strains was able to cause the ropy defect in milk; this strain was able to cause the defect at both 6°C and 21°C, and was originally isolated from a pasteurized milk. These findings suggest that the potential of K. pneumoniae ssp. pneumoniae and R. inusitata to cause ropy defect in milk is a strain-dependent characteristic. Comparative genomics provided no definitive answer on genetic basis for the ropy phenotype. However, for K. pneumoniae ssp. pneumoniae, genes rffG, rffH, rfbD, and rfbC involved in biosynthesis and secretion of enterobacterial common antigen (ECA) could only be found in the 2 strains that produced ropy defect, and for R. inusitata a set of 2 glycosyltransferase- and flippase genes involved in nucleotide sugar biosynthesis and export could only be identified in the ropy strain. Although these results provide some initial information for potential markers for strains that can cause ropy milk, the relationship between genetic content and ropiness in milk remains poorly understood and merits further investigation.

Gram-negative postpasteurization contamination patterns of single-serve fluid milk produced in 4 different processing facilities

An analysis of historic data on high temperature, short time (HTST) fluid milk quality showed higher total bacterial counts and lower sensory defect judging scores at d 14 postprocessing for milk packaged in single-serve containers as compared with milk packaged in half-gallon containers from the same processing facilities. As postpasteurization contamination with gram-negative bacteria is likely a major contributor to an increased spoilage risk associated with milk packaged in single-serve containers, we performed a comprehensive assessment of the microbial quality and shelf life of 265 commingled single-serve HTST fluid milk samples (including white [unflavored] skim, white [unflavored] 1%, chocolate skim, and chocolate 1%) collected over 2 visits to 4 commercial fluid milk processing facilities. Over 2 initial sampling visits, the frequency of gram-negative spoilage ranged from 14 to 79% of the product collected from the 4 facilities, with significant differences of gram-negative spoilage frequency between sampling visits, facilities (sampling visit 1, sampling visit 2, and both sampling visits combined), milk types (sampling visit 2), and filler lanes (sampling visit 2). We found no significant differences in the frequency of gram-negative spoilage between sampling time points (e.g., beginning, middle, and end of production run). Across facilities, single-serve containers of milk with gram-negative contamination showed significantly higher bacterial counts on d 7 and 14 and significantly lower sensory scores as compared with those without gram-negative contamination. Follow-up investigations, based on in-facility surveys that identified carton forming mandrels as filler components that frequently failed quality assurance ATP swab checks, found that bacterial genera, including Pseudomonas and Bacillus, isolated from single-serve milk samples were also frequently isolated from mandrels. Although interventions aimed at improving cleaning and sanitation of mandrels did not lead to significant reduction of gram-negative spoilage frequency in a comparison of 398 control and 400 intervention samples, our data still suggest that the unhygienic design of single-serve fillers is likely a root cause of gram-negative contamination of single-serve milk.

Low-cost, on-farm intervention to reduce spores in bulk tank raw milk benefits producers, processors, and consumers

Bacterial spores, which are found in raw milk, can survive harsh processing conditions encountered in dairy manufacturing, including pasteurization and drying. Low-spore raw milk is desirable for dairy industry stakeholders, especially those who want to extend the shelf life of their product, expand their distribution channels, or reduce product spoilage. A recent previous study showed that an on-farm intervention that included washing towels with chlorine bleach and drying them completely, as well as training milking parlor employees to focus on teat end cleaning, significantly reduced spore levels in bulk tank raw milk. As a follow up to that previous study, here we calculate the costs associated with that previously described intervention as ranging from $9.49 to $13.35 per cow per year, depending on farm size. A Monte Carlo model was used to predict the shelf life of high temperature, short time fluid milk processed from raw milk before and after this low-cost intervention was applied, based on experimental data collected in a previous study. The model predicted that 18.24% of half-gallon containers of fluid milk processed from raw milk receiving no spore intervention would exceed the pasteurized milk ordinance limit of 20,000 cfu/mL by 17 d after pasteurization, while only 16.99% of containers processed from raw milk receiving the spore intervention would reach this level 17 d after pasteurization (a reduction of 1.25 percentage points and a 6.85% reduction). Finally, a survey of consumer milk use was conducted to determine how many consumers regularly consume fluid milk near or past the date printed on the package (i.e., code date), which revealed that over 50% of fluid milk consumers surveyed continue to consume fluid milk after this date, indicating that a considerable proportion of consumers are exposed to fluid milk that is likely to have high levels spore-forming bacterial growth and possibly associated quality defects (e.g., flavor or odor defects). This further highlights the importance of reducing spore levels in raw milk to extend pasteurized fluid milk shelf life and thereby reducing the risk of adverse consumer experiences. Processors who are interested in extending fluid milk shelf life by controlling the levels of spores in the raw milk supply should consider incentivizing low-spore raw milk through premium payments to producers.

Invited review: Redefining raw milk quality-Evaluation of raw milk microbiological parameters to ensure high-quality processed dairy products

Raw milk typically has little bacterial contamination as it leaves the udder of the animal; however, through a variety of pathways, it can become contaminated with bacteria originating from environmental sources, the cow herself, and contact with contaminated equipment. Although the types of bacteria found in raw milk are very diverse, select groups are particularly important from the perspective of finished product quality. In particular, psychrophilic and psychrotolerant bacteria that grow quickly at low temperatures (e.g., species in the genus Pseudomonas and the family Enterobacteriaceae) and produce heat-stable enzymes, and sporeforming bacteria that survive processing hurdles in spore form, are the 2 primary groups of bacteria related to effects on processed dairy products. Understanding factors leading to the presence of these important bacterial groups in raw milk is key to reducing their influence on processed dairy product quality. Here we examine the raw milk microbiological parameters used in the contemporary dairy industry for their utility in identifying raw milk supplies that will perform well in processed dairy products. We further recommend the use of a single microbiological indicator of raw milk quality, namely the total bacteria count, and call for the development of a whole-farm approach to raw milk quality that will use data-driven, risk-based tools integrated across the continuum from production to processing and shelf-life to ensure continuous improvement in dairy product quality.

Extending the Shelf Life of Raw Milk and Pasteurized Milk with Plantaricin FB-2

Raw milk and pasteurized milk are characterized by a short shelf life, and drinking expired raw milk and pasteurized milk causes illness. In the study, Plantaricin FB-2 (extracted from Lactiplantibacillus plantarum FB-2) was added to liquid milk. By evaluating the microbial growth, acidity changes, protein content, and sensory changes in raw milk and pasteurized milk during storage, it was found that when Plantaricin FB-2 was added at 0.4 g/kg, the shelf life of raw milk was extended by 3 days (7 days if not added). The shelf life of pasteurized milk with Plantaricin FB-2 was extended to 31 days (25 days in the control group), and the optimal amount was 0.3 g/kg. This confirmed that Plantaricin FB-2 can effectively prolong the shelf life of raw and pasteurized milk. This study provides valuable information for the application of bacteriocins produced by Lactiplantibacillus plantarum in raw milk and pasteurized milk to improve their shelf life.

Culture-independent bacterial cell extraction from fluid milk and oat-based beverage for basic qualitative microscopy

Butterfat and protein complicate attempts to extract bacterial cells from milk by centrifugation for use in basic microscopy. Some types of bacteria preferentially separate into the butterfat layer upon centrifugation and are lost when this layer is discarded, and the action of bacterial protease enzymes can cause milk proteins to precipitate and partition into the centrifugal pellet. Butterfat and precipitated protein remaining in the centrifugal pellet along with the desired bacterial cells can confound the results of differential staining and microscopy. Oat- and other plant-based beverages, which are often manufactured by dairy processors on shared equipment, present similar hurdles to bacterial extraction and microscopic visualization because of the presence of oils, starch granules, and dietary fiber particles in these products. Herein we describe methods for centrifugal separation of bacterial cells for microscopy from unflavored milk, chocolate milk, and oat-based beverage. Cell suspensions prepared through these methods were used for phase-contrast microscopy, Gram staining, and viability staining. These techniques can be used to provide rapid, culture-independent diagnostic information when bacterial cells are expected to be present in high concentrations, as in the event of sporadic product spoilage or mass product spoilage incidents.

Pseudomonas fluorescens group bacterial strains interact differently with pathogens during dual-species biofilm formation on stainless steel surfaces in milk

In order to develop strategies for preventing biofilm formation in the dairy industry, a deeper understanding of the interaction between different species during biofilm formation is necessary. Bacterial strains of the P. fluorescens group are known as the most important biofilm-formers on the surface of dairy processing equipment that may attract and/or shelter other spoilage or pathogenic bacteria. The present study used different strains of the P. fluorescens group as background microbiota of milk, and evaluated their interaction with Staphylococcus aureus, Bacillus cereus, Escherichia coli O157:H7, and Salmonella Typhimurium during dual-species biofilm formation on stainless steel surfaces. Two separate scenarios for dual-species biofilms were considered: concurrent inoculation of Pseudomonas and pathogen (CI), and delayed inoculation of pathogen to the pre-formed Pseudomonas biofilm (DI). The gram-positive pathogens used in this study did not form dual-species biofilms with P. fluorescens strains unless they were simultaneously inoculated with Pseudomonas strains. E. coli O157:H7 was able to form dual-species biofilms with all seven P. fluorescens group strains, both in concurrent (CI) and delayed (DI) inoculation. However, the percentage of contribution varied depending on the P. fluorescens strains and the inoculation scenario. S. Typhimurium contributed to biofilm formation with all seven P. fluorescens group strains under the CI scenario, with varying degrees of contribution. However, under the DI scenario, S. Typhimurium did not contribute to the biofilm formed by three of the seven P. fluorescens group strains. Overall, these are the first results to illustrate that the strains within the P. fluorescens group have significant differences in the formation of mono-or dual-species biofilms with pathogenic bacteria. Furthermore, the possibility of forming dual-species biofilms with pathogens depends on whether the pathogens form the biofilm simultaneously with the P. fluorescens group strains or whether these strains have already formed a biofilm.

Graduate Student Literature Review: Farm management practices: Potential microbial sources that determine the microbiota of raw bovine milk

Environmental and herd-associated factors such as geographical location, climatic conditions, forage types, bedding, soil, animal genetics, herd size, housing, lactation stage, and udder health are exploited by farmers to dictate specific management strategies that ensure dairy operation profitability and enhance the sustainability of milk production. Along with milking routines, milking systems, and storage conditions, these farming practices greatly influence the microbiota of raw milk, as evidenced by several recent studies. During the past few years, the increased interest in high-throughput sequencing technologies combined with culture-dependent methods to investigate dairy microbial ecology has improved our understanding of raw milk community dynamics throughout storage and processing. However, knowledge is still lacking on the niche-specific communities in the farm environment, and on the factors that determine bacteria transfer to the raw milk. This review summarizes findings from the past 2 decades regarding the effects of farm management practices on the diversity of bacterial species that determine the microbiological quality of raw cow milk.

Effect of gaseous ozone treatment on biofilm of dairy-isolated Pseudomonas spp. strains

Microbial biofilms existing in food industries have been implicated as important contamination sources of spoilage and pathogenic microorganisms in the finished products. Among the innovative strategies proposed to contrast biofilms in food environments, ozone is recognised as an environmentally friendly technology but there are few studies about its effect against bacterial biofilms. The objective of this study was to evaluate the effect of gaseous ozone (50 ppm for 6 h) in inhibition and eradication of biofilm formed by twenty-one dairyisolated Pseudomonas spp. strains. Before ozone treatments, all isolates were screened for biofilm formation according to a previously described method. Strains were then divided in four groups: weak, weak/moderate, moderate/strong, and strong biofilm producers based on the biofilm biomass value of each isolate determined using the optical density (OD - 595 nm). Inhibition treatment was effective on the strain (C1) belonging to the weak producers' group, on all strains classified as weak/moderate producers, on two strains (C8 and C12) belonging to the group of moderate/strong producers and on one strain (C13) classified as strong producer. Conversely, eradication treatments were ineffective on all strains tested, except for the strain C4 which reduced its biofilm-forming abilities after exposure to ozone gas. In conclusion, gaseous ozone may be used to enhance existing sanitation protocols in food processing environments, but its application alone not seems sufficient to contrast Pseudomonas spp. established biofilms.

The Complex Role of Lactic Acid Bacteria in Food Detoxification

Toxic ingredients in food can lead to serious food-related diseases. Such compounds are bacterial toxins (Shiga-toxin, listeriolysin, Botulinum toxin), mycotoxins (aflatoxin, ochratoxin, zearalenone, fumonisin), pesticides of different classes (organochlorine, organophosphate, synthetic pyrethroids), heavy metals, and natural antinutrients such as phytates, oxalates, and cyanide-generating glycosides. The generally regarded safe (GRAS) status and long history of lactic acid bacteria (LAB) as essential ingredients of fermented foods and probiotics make them a major biological tool against a great variety of food-related toxins. This state-of-the-art review aims to summarize and discuss the data revealing the involvement of LAB in the detoxification of foods from hazardous agents of microbial and chemical nature. It is focused on the specific properties that allow LAB to counteract toxins and destroy them, as well as on the mechanisms of microbial antagonism toward toxigenic producers. Toxins of microbial origin are either adsorbed or degraded, toxic chemicals are hydrolyzed and then used as a carbon source, while heavy metals are bound and accumulated. Based on these comprehensive data, the prospects for developing new combinations of probiotic starters for food detoxification are considered.

Evaluating Paenibacillus odorifer for its potential to reduce shelf life in reworked high-temperature, short-time fluid milk products

Rework is a common practice used in the dairy industry as a strategy to help minimize waste from processing steps or errors that might otherwise render the product unsaleable. Dairy processors may rework their high-temperature, short-time (HTST) fluid milk products up to code date (21 d) at a typical dilution rate of ≤20% rework into ≥80% fresh raw milk. Bacterial spores present in raw milk that can survive pasteurization and grow at refrigeration temperatures are often responsible for milk spoilage. However, the potential impact of growth and thermal resistance of organisms in reworked product has not been investigated. Our objective was to characterize growth, sporulation, and thermal resistance of Paenibacillus odorifer under conditions representative of extreme storage conditions (time and temperature) of reduced fat (2%) and chocolate milk to evaluate whether product containing rework would have a reduced shelf life. Commercial UHT-pasteurized 2% milk and chocolate milk were independently inoculated with 4 strains of P. odorifer at 1 to 2 log cfu/mL and stored at 4°C and 7°C for 30 d. Changes in P. odorifer cell densities were determined by standard serial dilution with spread plating on tryptic soy agar with yeast extract and incubation at 25°C for 48 h. Spore counts were determined following thermal treatment at 80°C for 12 min. Thermal resistance of a cocktail of P. odorifer in milk was determined after treatments at 63°C for 30 min and 72°C for 15 s. Strains of P. odorifer grew rapidly at 7°C and reached a maximum cell density of ~8 log cfu/g in both 2% and chocolate milk within 12 d. All strains grew more slowly at 4°C and had not reached maximum cell density by 21 d. With extreme temperature abuse (25°C, 24 h), P. odorifer will sporulate in milk; however, thermally resistant subpopulations, including spores, did not develop in milk at 4°C until after stationary phase was achieved (>24 d). Vegetative cells of P. odorifer were verified to be sensitive to pasteurization (>7 log reduction); therefore, P. odorifer would not be expected to contribute to reduced shelf life of fluid milk products containing rework, even with extended storage before rework.

Development of a Monte Carlo simulation model to predict pasteurized fluid milk spoilage due to post-pasteurization contamination with gram-negative bacteria

Psychrotolerant gram-negative bacteria introduced as post-pasteurization contamination (PPC) are a major cause of spoilage and reduced shelf life of high-temperature, short-time pasteurized fluid milk. To provide improved tools to (1) predict pasteurized fluid milk shelf life as influenced by PPC and (2) assess the effectiveness of different potential interventions that could reduce spoilage due to PPC, we developed a Monte Carlo simulation model that predicts fluid milk spoilage due to psychrotolerant gram-negative bacteria introduced as PPC. As a first step, 17 gram-negative bacterial isolates frequently associated with fluid milk spoilage were selected and used to generate growth data in skim milk broth at 6°C. The resulting growth parameters, frequency of isolation for the 17 different isolates, and initial concentration of bacteria in milk with PPC, were used to develop a Monte Carlo model to predict bacterial number at different days of shelf life based on storage temperature of milk. This model was then validated with data from d 7 and 10 of shelf life, collected from commercial operations. The validated model predicted that the parameters (1) maximum growth rate and (2) storage temperature had the greatest influence on the percentage of containers exceeding 20,000 cfu/mL standard plate count on d 7 and 10 (i.e., spoiling due to PPC), which indicates that accurate data on maximum growth rate and storage temperature are important for accurate predictions. In addition to allowing for prediction of fluid milk shelf life, the model allows for simulation of "what-if" scenarios, which allowed us to predict the effectiveness of different interventions to reduce overall fluid milk spoilage due to PPC through a set of proof-of-concept scenario (e.g., frequency of PPC in containers reduced from 100% to 10%; limiting distribution temperature to a maximum of 6°C). Combined with other models, such as previous models on fluid milk spoilage due to psychrotolerant spore-forming bacteria, the data and tools developed here will allow for rational, digitally enabled, fluid milk shelf life prediction and quality enhancement.

Development of a database and standardized approach for rpoB sequence-based subtyping and identification of aerobic spore-forming Bacillales

Aerobic spore-forming Bacillales are a highly diverse and ubiquitous group that includes organisms that cause foodborne illnesses and food spoilage. Classical microbiological and biochemical identification of members of the order Bacillales represents a challenge due to the diversity of organisms in this group as well as the fact that the phenotypic-based taxonomic assignment of some named species in this group is not consistent with their phylogenomic characteristics. DNA-sequencing-based tools, on the other hand, can be fast and cost-effective, and can provide for a more reliable identification and characterization of Bacillales isolates. In comparison to 16S rDNA, rpoB was shown to better discriminate between Bacillales isolates and to allow for improved taxonomic assignment to the species level. However, the lack of a publicly accessible rpoB database, as well as the lack of standardized protocols for rpoB-based typing and strain identification, is a major challenge. Here, we report (i) the curation of a DNA sequence database for rpoB-based subtype classification of Bacillales isolates; (ii) the development of standardized protocols for generating rpoB sequence data, and a scheme for rpoB-based initial taxonomic identification of Bacillales isolates at the species level; and (iii) the integration of the database in a publicly accessible online platform that allows for the analysis of rpoB sequence data from uncharacterized Bacillales isolates. Specifically, we curated a database of DNA sequences for a 632-nt internal variable region within the rpoB gene from representative Bacillales reference type strains and a large number of isolates that we have previously isolated and characterized through multiple projects. As of May 21, 2021, the rpoB database contained more than 8350 rpoB sequences representing 1902 distinct rpoB allelic types that can be classified into 160 different genera. The database also includes 1129 rpoB sequences for representative Bacillales reference type strains as available on May 21, 2021 in the NCBI database. The rpoB database is integrated into the online Food Microbe Tracker platform (www.foodmicrobetracker.com) and can be queried using the integrated BLAST tool to initially subtype and taxonomically identify aerobic and facultative anaerobic spore-formers. While whole-genome sequencing is increasingly used in bacterial taxonomy, the rpoB sequence-based identification scheme described here provides a valuable tool as it allows for rapid and cost-effective initial isolate characterization, which can help to identify and characterize foodborne pathogens and food spoilage bacteria. In addition, the database and primers described here can also be adopted for metagenomics approaches that include rpoB as a target, improving discriminatory power and identification over what can be achieved using 16S rDNA as a target.

Machine Learning and Advanced Statistical Modeling Can Identify Key Quality Management Practices That Affect Postpasteurization Contamination of Fluid Milk

ABSTRACT

Spoilage of high-temperature, short-time (HTST)- and vat-pasteurized fluid milk due to the introduction of gram-negative bacteria postpasteurization remains a challenge for the dairy industry. Although processing facility-level practices (e.g., sanitation practices) are known to impact the frequency of postpasteurization contamination (PPC), the relative importance of different practices is not well defined, thereby affecting the ability of facilities to select intervention targets that reduce PPC and provide the greatest return on investment. Thus, the goal of this study was to use an existing longitudinal data set of bacterial spoilage indicators obtained for pasteurized fluid milk samples collected from 23 processing facilities between July 2015 and November 2017 (with three to five samplings per facility) and data from a survey on fluid milk quality management practices, to identify factors associated with PPC and rank their relative importance. This ranking was accomplished using two separate approaches: multimodel inference and conditional random forest. Data preprocessing for multimodel inference analysis showed (i) nearly all factors were significantly associated with PPC when assessed individually using univariable logistic regression and (ii) numerous pairs of factors were strongly associated with each other (Cramer's V ≥ 0.80). Multimodel inference and conditional random forest analyses identified similar drivers associated with PPC; factors identified as most important based on these analyses included cleaning and sanitation practices, activities related to good manufacturing practices, container type (a proxy for different filling equipment), in-house finished product testing, and designation of a quality department, indicating potential targets for reducing PPC. In addition, this study illustrates how machine learning approaches can be used with highly correlated and unbalanced data, as typical for food safety and quality, to facilitate improved data analyses and decision making.

HIGHLIGHTS

Optimizing Pasteurized Fluid Milk Shelf-Life Through Microbial Spoilage Reduction

Psychrotolerant spore-forming bacteria, entering raw milk primarily on-farm, represent a major challenge for fluid milk processors due to the ability of these bacteria to survive heat treatments used for milk processing (e.g., pasteurization) and to cause premature spoilage. Importantly, fluid milk processors require tools to identify optimal strategies for reducing spore-forming bacteria, thereby extending product shelf-life by delaying spoilage. Potential strategies include (i) introducing farm-level premium payments (i.e., bonuses) based on spore-forming bacteria counts in raw milk and (ii) investing in spore reduction technologies at the processing level of the fluid milk supply chain. In this study, we apply an optimization methodology to the problem of milk spoilage due to psychrotolerant spore-forming bacteria and propose two novel mixed-integer linear programming models that assess improving milk shelf-life from the dairy processors' perspective. Our first model, imposed to a budgetary constraint, maximizes milk's shelf-life to cater to consumers who prefer milk with a long shelf-life. The second model minimizes the budget required to perform operations to produce milk with a shelf-life of a certain length geared to certain customers. We generate case studies based on real-world data from multiple sources and perform a comprehensive computational study to obtain optimal solutions for different processor sizes. Results demonstrate that optimal combinations of interventions are dependent on dairy processors' production volume and quality of raw milk from different producers. Thus, the developed models provide novel decision support tools that will aid individual processors in identifying the optimal approach to achieving a desired milk shelf-life given their specific production conditions and motivations for shelf-life extension.

A Milk Foodomics Investigation into the Effect of Pseudomonas fluorescens Growth under Cold Chain Conditions

Pseudomonas fluorescens is a psychrotrophic species associated with milk spoilage because of its lipolytic and proteolytic activities. Consequently, monitoring P. fluorescens or its antecedent activity in milk is critical to preventing quality defects of the product and minimizing food waste. Therefore, in this study, untargeted metabolomics and peptidomics were used to identify the changes in milk related to P. fluorescens activity by simulating the low-temperature conditions usually found in milk during the cold chain. Both unsupervised and supervised multivariate statistical approaches showed a clear effect caused by the P. fluorescens inoculation on milk samples. Our results showed that the levels of phosphatidylglycerophosphates and glycerophospholipids were directly related to the level of contamination. In addition, our metabolomic approach allowed us to detect lipid and protein degradation products that were directly correlated with the degradative metabolism of P. fluorescens. Peptidomics corroborated the proteolytic propensity of P. fluorescens-contaminated milk, but with lower sensitivity. The results obtained from this study provide insights into the alterations related to P. fluorescens 39 contamination, both pre and post heat treatment. This approach could represent a potential tool to retrospectively understand the actual quality of milk under cold chain storage conditions, either before or after heat treatments.

Antimicrobial Activity and Proposed Action Mechanism of Linalool Against Pseudomonas fluorescens

In this study, linalool, one of the principal components of essential oils, was used as an antibacterial agent to investigate the antibacterial activity and mechanism of linalool against Pseudomonas fluorescens. The reduction in membrane potential (MP), leakage of alkaline phosphatase (AKP) and the release of macromolecules, including DNA, RNA and protein confirmed that damage to cell wall membrane structure and leakage of cytoplasmic contents were due to the linalool treatment. Furthermore, the decrease of enzyme activity, including the succinate dehydrogenase (SDH), malate dehydrogenase (MDH), pyruvate kinase (PK), and ATPase indicated that linalool could lead to metabolic dysfunction and inhibit energy synthesis. In addition, the activity of respiratory chain dehydrogenase and metabolic activity of respiration indicated that linalool inhibits cellular respiration. These results revealed that linalool had strong antibacterial activity against P. fluorescens via membrane damage, bacterial metabolic and oxidative respiratory perturbations, interfering in cellular functions and even causing cell death. It was suggested that linalool may be a new potential source as food antiseptics in food systems.

Identification, subtyping, and tracking of dairy spoilage-associated Pseudomonas by sequencing the ileS gene

Pseudomonas spp. are important spoilage bacteria that negatively affect the quality of refrigerated fluid milk and uncultured cheese by generating unwanted odors, flavors, and pigments. They are frequently found in dairy plant environments and enter dairy products predominantly as postpasteurization contaminants. Current subtyping and characterization methods for dairy-associated Pseudomonas are often labor-intensive and expensive or provide limited and possibly unreliable classification information (e.g., to the species level). Our goal was to identify a single-copy gene that could be analyzed in dairy spoilage-associated Pseudomonas for preliminary species-level identification, subtyping, and phenotype prediction. We tested 7 genes previously targeted in a Pseudomonas fluorescens multilocus sequence typing scheme for their individual suitability in this application using a set of 113 Pseudomonas spp. isolates representing the diversity of typical pasteurized milk contamination. For each of the 7 candidate genes, we determined the success rate of PCR and sequencing for these 113 isolates as well as the level of discrimination for species identification and subtyping that the sequence data provided. Using these metrics, we selected a single gene, isoleucyl tRNA synthetase (ileS), which had the most suitable traits for simple and affordable single-gene Pseudomonas characterization. This was based on the number of isolates successfully sequenced for ileS (113/113), the number of unique allelic types assigned (83, compared with 50 for 16S rDNA), nucleotide and sequence diversity measures (e.g., number of unique SNP and Simpson index), and tests for genetic recombination. The discriminatory ability of ileS sequencing was confirmed by separation of 99 additional dairy Pseudomonas spp. isolates, which were indistinguishable by 16S rDNA sequencing, into 28 different ileS allelic types. Further, we used whole-genome sequencing data to demonstrate the similarities in ileS-based phylogenetic clustering to whole-genome-based clustering for 27 closely related dairy-associated Pseudomonas spp. isolates and for 178 Pseudomonas type strains. We also found that dairy-associated Pseudomonas within an ileS cluster typically shared the same proteolytic and lipolytic activities. Use of ileS sequencing provides a promising strategy for affordable initial characterization of Pseudomonas isolates, which will help the dairy industry identify, characterize, and track Pseudomonas in their facilities and products.

Invited review: Controlling dairy product spoilage to reduce food loss and waste

Food loss and waste is a major concern in the United States and globally, with dairy foods representing one of the top categories of food lost and wasted. Estimates indicate that in the United States, approximately a quarter of dairy products are lost at the production level or wasted at the retail or consumer level annually. Premature microbial spoilage of dairy products, including fluid milk, cheese, and cultured products, is a primary contributor to dairy food waste. Microbial contamination may occur at various points throughout the production and processing continuum and includes organisms such as gram-negative bacteria (e.g., Pseudomonas), gram-positive bacteria (e.g., Paenibacillus), and a wide range of fungal organisms. These organisms grow at refrigerated storage temperatures, often rapidly, and create various degradative enzymes that result in off-odors, flavors, and body defects (e.g., coagulation), rendering them inedible. Reducing premature dairy food spoilage will in turn reduce waste throughout the dairy continuum. Strategies to reduce premature spoilage include reducing raw material contamination on-farm, physically removing microbial contaminants, employing biocontrol agents to reduce outgrowth of microbial contaminants, tracking and eliminating microbial contaminants using advanced molecular microbiological techniques, and others. This review will address the primary microbial causes of premature dairy product spoilage and methods of controlling this spoilage to reduce loss and waste in dairy products.

Impacts of Milking and Housing Environment on Milk Microbiota

The aim of the present study was to determine the effects of farming environments on microbiota in raw milk and to assess the relationship among microbes by 16S rRNA sequencing methods. Samples of raw milk, cow trough water, teat dip cup, teat, teat liner, dairy hall air, cowshed air, feces, feed, and bedding from two farms were collected. The two highest abundant bacterial groups of Moraxellaceae and Staphylococcaceae were found in milk and teat liner samples, respectively, at Zhengzhou farm, Henan Province. Moreover, the two highest abundant bacterial groups of Enterobacteriaceae and Moraxellaceae were found in milk and teat dip cup samples, respectively, at Qiqihar farm, Heilongjiang Province. Source Tracker analysis revealed that the teat liner and teat dip cup were the most important contributors of microbes in milk samples at Zhengzhou farm and Qiqihar farm, respectively, which could be attributed to the management level of the farm. Therefore, disinfection and cleaning procedures should be developed to improve the quality of raw milk.

Spore-Forming Bacteria Associated with Dairy Powders Can Be Found in Bacteriological Grade Agar-Agar Supply

ABSTRACT

Thermophilic spore-forming bacteria are found ubiquitously in natural environments and, therefore, are present in a number of agricultural food products. Spores produced by these bacteria can survive harsh environmental conditions encountered during food processing and have been implicated in food spoilage. During research efforts to develop a standardized method for enumerating spores in dairy powders, the dairy powder-associated thermophilic sporeformer Anoxybacillus flavithermus was discovered growing in uninoculated control plates of tryptic soy agar (TSA) supplemented with 1% (w/v) starch, after incubation at thermophilic (55°C) growth temperatures. This article reports the investigation into the source of this thermophilic sporeformer in TSA medium components and characterization of the bacterial isolates collected. Aqueous solutions of tryptic soy broth powder from four suppliers and four agar-agar powders (two manufacturing lots from one supplier [agar A_1 and agar A_2] and two from separate suppliers [agar B and agar C]) were subjected to two different autoclave cycle times (121°C for 15 min or 121°C for 30 min) and then prepared as TSA. After incubation at 55°C for 48 h, bacterial growth was observed only in media prepared from both lots of agar A agar-agar powder, and only when they were subjected to a 15-min autoclave cycle, implicating these powders as a source of the sporeformer contamination. Genetic characterization of 49 isolates obtained indicated the presence of five unique rpoB allelic types of the thermophilic sporeformer Geobacillus spp. in agar-agar powder from agar A. These results not only highlight the importance of microbiological controls but also alert researchers to the potential for survival of thermophilic sporeformers such as Anoxybacillus and Geobacillus in microbiological media used for detection and enumeration of these same thermophilic sporeformers in products such as dairy powders.

HIGHLIGHTS

Milking time hygiene interventions on dairy farms reduce spore counts in raw milk

Spore-forming bacteria, such as Paenibacillus spp. and Bacillus spp., can survive HTST pasteurization in spore form and affect the quality of dairy products (e.g., spoilage in fluid milk). With the demand for higher quality finished products that have longer shelf lives and that can be distributed further and to new markets, dairy processors are becoming interested in obtaining low-spore raw milk supplies. One method to reduce spores in the dairy system will require disrupting the transmission of spores from environmental locations, where they are often found at high concentrations (e.g., manure, bedding), into bulk tank raw milk. Previous research has suggested that cow hygiene factors (e.g., udder hygiene, level of spores in milk from individual cows) are important for the transmission of spores into bulk tank raw milk, suggesting that one potential strategy to reduce spores in bulk tank milk should target cow hygiene in the parlor. To that end, we conducted a study on 5 New York dairy farms over a 15-mo period to evaluate the effect of a combination of intervention strategies, applied together, on the levels of aerobic spores in bulk tank raw milk. The combination of interventions included (1) training milking staff to focus on teat-end cleaning during milking preparation, and (2) implementing changes in laundered towel preparation (i.e., use of detergent, chlorine bleach, and drying). Study design involved collecting bulk tank raw milk samples for a week before and a week after initiating the combination of interventions (i.e., training on the importance of teat-end cleaning and towel treatment). Observations on teat-end condition, udder hygiene scores, and number of kickoffs during milking were also collected for 24 h before and after implementation of the interventions. A total of 355 bulk tank raw milk samples were collected with mean mesophilic and thermophilic spore counts of 2.1 and 2.4 cfu/mL, respectively, before interventions were applied, and 1.6 and 1.5 cfu/mL, respectively, after the interventions were applied. These reductions represent decreases of 37 and 40% in bulk tank raw milk mesophilic spores and thermophilic spores, respectively. Importantly, spore reductions were observed during each of the 3 visits once the interventions were applied, and the largest reduction in spores was recorded for the first sampling after training the milking staff. Further, when a higher proportion of very rough teat ends was observed, bulk tank milk thermophilic spore counts were significantly higher. The intervention strategies tested here represent easy-to-execute cleaning strategies (e.g., focusing on teat-end hygiene and towel washing procedures) that can reduce bulk tank raw milk spore levels. Future studies should validate the effect of on-farm interventions for reduced spore raw milk on corresponding processed product quality and will need to verify the effects of these small changes on product shelf life.

Sequenceserver: A Modern Graphical User Interface for Custom BLAST Databases

Comparing newly obtained and previously known nucleotide and amino-acid sequences underpins modern biological research. BLAST is a well-established tool for such comparisons but is challenging to use on new data sets. We combined a user-centric design philosophy with sustainable software development approaches to create Sequenceserver, a tool for running BLAST and visually inspecting BLAST results for biological interpretation. Sequenceserver uses simple algorithms to prevent potential analysis errors and provides flexible text-based and visual outputs to support researcher productivity. Our software can be rapidly installed for use by individuals or on shared servers.

Paenibacillus odorifer, the Predominant Paenibacillus Species Isolated from Milk in the United States, Demonstrates Genetic and Phenotypic Conservation of Psychrotolerance but Clade-Associated Differences in Nitrogen Metabolic Pathways

Although Paenibacillus species isolates are frequently isolated from pasteurized fluid milk, the link between the genetic diversity and phenotypic characteristics of these isolates was not well understood, especially as some Bacillales isolated from milk are unable to grow at refrigeration temperatures. Our data demonstrate that Paenibacillus spp. isolated from fluid milk represent tremendous interspecies diversity, with P. odorifer being the predominant Paenibacillus sp. isolated. Furthermore, genetic and phenotypic data support that P. odorifer is well suited to transition from a soil-dwelling environment, where nitrogen fixation (and other nitrate/nitrite reduction pathways present only in clade A) may facilitate growth, to fluid milk, where its multiple cold shock-associated adaptations enable it to grow at refrigeration temperatures throughout the storage of milk. Therefore, efforts to reduce bacterial contamination of milk will require a systematic approach to reduce P. odorifer contamination of raw milk.

Paenibacillus is a spore-forming bacterial genus that is frequently isolated from fluid milk and is proposed to play a role in spoilage. To characterize the genetic and phenotypic diversity of Paenibacillus spp., we first used rpoB allelic typing data for a preexisting collection of 1,228 Paenibacillus species isolates collected from raw and processed milk, milk products, and dairy environmental sources. Whole-genome sequencing (WGS) and average nucleotide identity by BLAST (ANIb) analyses performed for a subset of 58 isolates representing unique and overrepresented rpoB allelic types in the collection revealed that these isolates represent 21 different Paenibacillus spp., with P. odorifer being the predominant species. Further genomic characterization of P. odorifer isolates identified two distinct phylogenetic clades, clades A and B, which showed significant overrepresentation of 172 and 164 ortholog clusters and 94 and 52 gene ontology (GO) terms, respectively. While nitrogen fixation genes were found in both clades, multiple genes associated with nitrate and nitrite reduction were overrepresented in clade A isolates; additional phenotypic testing demonstrated that nitrate reduction is specific to isolates in clade A. Hidden Markov models detected 9 to 10 different classes of cold shock-associated genetic elements in all P. odorifer isolates. Phenotypic testing revealed that all isolates tested here can grow in skim milk broth at 6°C, suggesting that psychrotolerance is conserved in P. odorifer. Overall, our data suggest that Paenibacillus spp. isolated from milk in the United States represent broad genetic diversity, which may provide challenges for targeted-control strategies aimed at reducing fluid milk spoilage.

IMPORTANCE Although Paenibacillus species isolates are frequently isolated from pasteurized fluid milk, the link between the genetic diversity and phenotypic characteristics of these isolates was not well understood, especially as some Bacillales isolated from milk are unable to grow at refrigeration temperatures. Our data demonstrate that Paenibacillus spp. isolated from fluid milk represent tremendous interspecies diversity, with P. odorifer being the predominant Paenibacillus sp. isolated. Furthermore, genetic and phenotypic data support that P. odorifer is well suited to transition from a soil-dwelling environment, where nitrogen fixation (and other nitrate/nitrite reduction pathways present only in clade A) may facilitate growth, to fluid milk, where its multiple cold shock-associated adaptations enable it to grow at refrigeration temperatures throughout the storage of milk. Therefore, efforts to reduce bacterial contamination of milk will require a systematic approach to reduce P. odorifer contamination of raw milk.

Characterization of Bacterial Microbiota in Tilapia Fillets Under Different Storage Temperatures

This paper investigates the bacterial microbiota in tilapia fillets under cold (4 °C), iced (0 °C), and superchilled (-3 °C) storage conditions. At 4 °C, at least seven species/strains of Pseudomonas were detected in the fillets, five of which were dominant either at a certain stage or throughout the entire storage period. Shewanella was less dominant than Pseudomonas at 4 °C, while Serratia became dominant after 6 days storage at 4 °C. The microbiota in fillets stored at 0 and -3 °C were very similar and rarely changed during storage, yet differed greatly from the microbiota at 4 °C. Only two Pseudomonas species/strains grew at 0 and -3 °C, one of which was the most dominant. A Vibrionimonas sp. not found at 4 °C was found to be the second most dominant species at 0 and -3 °C. Shewanella and Psychrobacter were also present at 0 and -3 °C but were the minor genera. The most dominant strains at -3, 0, and 4 °C were separately isolated and subjected to full length 16S rDNA sequencing, which demonstrated that they were identical and were Pseudomonas fluorescens. The changes of the total bacterial count and TVBN value of the fillets inoculated with the isolated P. fluorescens were very similar to those of fillets with natural microbiota. This implies that P. fluorescens is the most important spoiler of tilapia fillets at -3, 0, or 4 °C. PRACTICAL APPLICATION: This research shows that fewer species of bacteria survive at 0 and -3 °C than those at 4 °C, while among these bacteria, the most important spoiler is P. fluorescens. This may provide some clues to extend the shelf life of tilapia fillets by taking some inhibitory measures targeted at P. fluorescens in the future.