Identification and characterization of psychrotolerant sporeformers associated with fluid milk production and processing

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.

Effects of ohmic heating with different voltages on the quality and microbial diversity of cow milk during thermal treatment and subsequent cold storage

Ohmic heating (OH), an innovative heating technology, presents potential applications in the pasteurization of liquid foods. Therefore, the study was conducted to evaluate the effect of OH at various voltage gradients (10 V/cm, 12.5 V/cm, and 15 V/cm) and water bath (WB) on microbial inactivation, physicochemical and sensory properties and microbial flora of pasteurized milk. Results indicated that OH with higher voltage could effectively inactivate microorganisms in milk, requiring less heating time and energy. Moreover, OH treatment at higher voltages could decelerate lipid oxidation and better maintain the sensory quality and essential amino acids content of milk. Additionally, all treatments significantly altered the microbial community, and during storage, the microbial community in milk treated with 10 V/cm and 12.5 V/cm OH remained relatively stable. OH treatments with voltage gradients exceeding 12.5 V/cm could effectively inactive microorganisms and maintain the quality attributes of milk.

Microbacterium represents an emerging microorganism of concern in microfiltered extended shelf-life milk products

Growing interest in the manufacture of extended shelf-life (ESL) milk, which is typically achieved by a high-temperature treatment called ultra-pasteurization (UP), is driven by distribution challenges, efforts to reduce food waste, and more. Even though high-temperature, short-time (HTST) pasteurized milk has a substantially shorter shelf life than UP milk, HTST milk is preferred in the United States because consumers tend to perceive UP milk as less desirable due to the "cooked" flavor associated with high-temperature processing. While ESL beyond 21 d may be possible for HTST, the survival and outgrowth of psychrotolerant aerobic spore-forming bacteria can still be a limitation to extending shelf life of HTST milk. Microfiltration (MF) is effective for reducing vegetative microorganisms and spores in raw milk, but it is unclear what the effects of membrane pore size, storage temperature, and milk type (i.e., skim vs. whole) are on the microbial shelf life of milk processed by both MF and HTST pasteurization. To investigate these factors, raw skim milk was MF using different pore sizes (0.8 or 1.2 μm), and then MF skim milk and standardized whole milk (MF skim with heat-treated [85°C for 20 s] cream) were HTST pasteurized at 75°C for 20 s. Subsequently, milk was stored at 3°C, 6.5°C, or 10°C and total bacteria counts were measured for up to 63 d. An ANOVA indicated that mean bacterial concentrations between storage temperatures were significantly different from each other, with mean maximum observed concentrations of 3.67, 5.33, and 8.08 log10 cfu/mL for storage temperatures 3°C, 6.5°C, and 10°C, respectively. Additionally, a smaller difference in mean maximum bacterial concentrations throughout shelf life was identified between pore sizes (<1 log cfu/mL), but no significant difference was attributed to milk type. An unexpected outcome of this study was the identification of Microbacterium as a major contributor to the bacterial population in MF ESL milk. Microbacterium is a psychrotolerant, thermoduric gram-positive, non-spore-forming rod with a small cell size (∼0.9 μm length and ∼0.3 μm width), which our data suggest was able to permeate the membranes used in this study, survive HTST pasteurization, and then grow at refrigeration temperatures. While spores continue to be a key concern for the manufacture of MF, ESL milk, our study demonstrates the importance of other psychrotolerant, thermoduric bacteria such as Microbacterium to these products.

An improved DNA extraction method for detecting Bacillus subtilis spores in spiked foods and beverages

Bacillus and Paenibacillus spp. are essential aerobic spoilage bacteria in various food industry sectors. Spoilage from microorganisms occurs at many points throughout food production systems. Due to their complex wall structures, spores can resist heat, radiation, chemical agents, and enzymatic treatments. An alkaline lysis and mechanical disruption combination method was developed and evaluated to counter this. This combination method effectively improved DNA extraction from B. subtilis spore cells spiked into food (solid) and beverages (liquid milk and coffee) at concentrations down to 10² CFU/mL or g when spiked into food matrices and drinks. Released DNA recoveries were 27 % and 25 % for potato salad and 38 % and 36 % for whole corn spiked at 10⁶ and 10³ CFU/mL concentrations. Conversely, there was a low recovery for wheat flour (10 % and 8.8 %) and milk powders (12 % and 25 %) at 10⁶ and 10³ CFU/mL spiked concentrations. The combination method provides rapid, specific, reliable, and accurate signature sequences identification for the detection and presence confirmation of psychrophilic and psychrotolerant spoilage spore cells, improving food spoilage assessments and food control applications.

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.

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.

Efficient degradation of rice straw through a novel psychrotolerant Bacillus cereus at low temperature

BACKGROUND

Rice straw (RS) is one of the largest sources of lignocellulosic, which is an abundant raw material for biofuels and chemicals. However, the natural degradation of RS under a low temperature environment is the biggest obstacle to returning straw to the field.

RESULTS

In the present study, one bacillus strain W118 was isolated. Strain W118 was identified as Bacillus cereus through morphological and physiological characterization and 16S rDNA sequencing. The optimum growth temperature and pH of strain W118 were 20 °C and 6.5, respectively. Simultaneously, it was found that the strain W118 grew well at low temperature, even at a temperature of 4 °C (OD₆₀₀  = 1.40 ± 0.01). The decrease of various compositions of RS after the fermentation process at a temperature of 20 °C and 4 °C for 14 days was 27.00 ± 0.02% and 23.70 ± 0.04%, respectively. The composition of RS decreased to 50.71 ± 0.02% after being fermented at 4 °C for 25 days. The results of scanning electron microscopy, Fourier transform infrared spectroscopy and X-ray diffraction of RS showed that the compositions of RS were significant decreased.

CONCLUSION

This test suggests that the strain W118 is efficient for degrading RS at low temperature, which has great application potential for straw degradation in a low temperature area. © 2022 Society of Chemical Industry.

Simultaneous Discrimination of Cereulide-Producing Bacillus cereus and Psychrotolerant B. cereus Group by Matrix-Assisted Laser Desorption Ionization-Time-of-Flight Mass Spectrometry

ABSTRACT

Cereulide-producing Bacillus cereus, which causes foodborne illnesses with vomiting, and psychrotolerant B. cereus group strains such as Bacillus mycoides, which can grow at ≥7°C and cause spoilage of refrigerated foods, are significant concerns for the food industry. Rapid and simple methods to discriminate the cereulide-producing B. cereus and psychrotolerant B. cereus group strains from other B. cereus group strains are needed. We developed a novel, rapid, and simple method with matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS) analysis for simultaneous discrimination of these two groups from other B. cereus group strains. A potassium adduct of cereulide was used to detect cereulide-producing B. cereus, and three ribosomal subunit proteins (L30, S16, and S20) were used to detect psychrotolerant B. cereus group. A total of 51 B. cereus group strains were analyzed by MALDI-TOF MS. The biomarkers allowed successful discrimination of 16 cereulide-producing B. cereus and 15 psychrotolerant B. cereus group strains from other B. cereus group strains. The results showed that this MALDI-TOF MS analysis allows simultaneous discrimination of cereulide-producing B. cereus and psychrotolerant B. cereus group strains from other B. cereus group strains. This efficient method has the potential to be a valuable tool for ensuring food safety.

HIGHLIGHTS

Strains Associated with Two 2020 Welder Anthrax Cases in the United States Belong to Separate Lineages within Bacillus cereus sensu lato

Anthrax-causing members of Bacillus cereus sensu lato (s.l.) pose a serious threat to public health. While most anthrax-causing strains resemble B. anthracis phenotypically, rare cases of anthrax-like illness caused by strains resembling “B. cereus” have been reported. Here, whole-genome sequencing was used to characterize three B. cereus s.l. isolates associated with two 2020 welder anthrax cases in the United States, which resembled “B. cereus” phenotypically. Comparison of the three genomes sequenced here to all publicly available, high-quality B. cereus s.l. genomes (n = 2890 total genomes) demonstrated that genomes associated with each case effectively belonged to separate species at the conventional 95% average nucleotide identity prokaryotic species threshold. Two PubMLST sequence type 78 (ST78) genomes affiliated with a case in Louisiana were most closely related to B. tropicus and possessed genes encoding the Bps exopolysaccharide capsule, as well as hemolysin BL (Hbl) and cytotoxin K (CytK). Comparatively, a ST108 genome associated with a case in Texas was most closely related to B. anthracis; however, like other anthrax-causing strains most closely related to B. anthracis, this genome did not possess Bps-, Hbl-, or CytK-encoding genes. Overall, results presented here provide insights into the evolution of anthrax-causing B. cereus s.l.

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.

The Potential Benefits of N2 Gas Flushing Technology for Various Dairy Products: A Sustainable Approach That Proved to Be Multiadvantageous for Preserving the Quality and Safety of Raw Milk During Its Storage

Worldwide, food production systems are confronted with multifaceted challenges. In the context of global climate change, the necessity to feed an expanding population while addressing food insecurity and reducing the tremendous losses and wastage of food places all production steps under considerable pressure. In this context, dairies also face extensive pressure to reduce greenhouse gas emissions, wastewater, and sludge; here, as elsewhere, innovative technological solutions must meet sustainable criteria. To preserve the quality and safety of raw milk during its storage, N2 gas flushing technology was devised and implemented at laboratory and pilot plant scales: the treatment proved to be multiadvantageous considering microbiological, biochemical, and technological aspects. The proposed study aims to reconsider the benefits of the patented N2 flushing technology, applied at the “raw milk stage” and evaluate the potential advantages that the treatment would confer, in terms of quality and safety aspects, to various dairy products such as liquid milk products, butters, creams, ice creams, and cheeses, including local and traditional dairy products.

Characterization of Vegetative Bacillus cereus and Bacillus subtilis Strains Isolated from Processed Cheese Products in an Italian Dairy Plant

Processed cheese is a commercial product characterized by high microbiological stability and extended shelf life obtained through the application of severe heat treatment. However, spore-forming bacteria can survive through thermal processes. Among them, microorganisms belonging to Bacillus genus have been reported. In this study, we examined the microbiological population of the first hours' production of processed cheeses in an Italian dairy plant during two seasons, between June and October 2020. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) was used to identify bacteria colonies, allowing the isolation of Bacillus cereus and Bacillussubtilis strains. These results were further confirmed by amplification and sequencing of 16 rRNA bacterial region. A multi-locus sequence type (MLST) analysis was performed to assess the genetic similarity among a selection of isolates. The fourteen B. cereus strains showed two sequence types: ST-32 was observed in only one strain and the ST-371 in the remaining thirteen isolates. On the contrary, all twenty-one B. subtlis strains, included in the study, showed a new allelic profile for the pycA gene, resulting in a new sequence type: ST-249. For B. cereus strains, analysis of toxin genes was performed. All isolates were positive for nheABC, entFM, and cytK, while hblABCD, bceT, and ces were not detected. Moreover, the biofilm-forming ability of B. cereus and B. subtilis strains was assessed, and all selected isolates proved to be biofilm formers (most of them were stronger producers). Considering the genetical similarity between isolates, jointly with the capacity to produce biofilm, the presence of a recurring Bacillus population could be hypothesized.

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.

Microbiological Contamination of Ready-to-Eat Algae and Evaluation of Bacillus cereus Behavior by Microbiological Challenge Test

ABSTRACT

Consumption of seaweeds (forms of algae), often categorized as a superfood, is becoming popular in western countries. Algae can be marketed fresh, but are usually sold dehydrated to ensure longer shelf life. Their consumption, often as ready-to-eat, opens up possible risks for public health because of foodborne pathogens that can contaminate the raw material during harvesting or manipulation. In this study, 14 ready-to-eat foods based on dehydrated algae, representative of the most consumed species, were considered. The microbial content, with a focus on Listeria monocytogenes and Bacillus cereus, was investigated by plate counts, and B. cereus strains were isolated and identified by 16S rRNA gene sequencing. The microbiological quality was heterogeneous among the samples and, in particular, marine bacteria, Listeria spp., B. cereus, and coliforms were detected. To contribute to related risk assessment, the ability of B. cereus to grow during refrigerated storage was evaluated, to our knowledge for the first time, by a microbiological challenge test on two ready-to-eat foods based on Undaria pinnatifida and Palmaria palmata. Despite this study demonstrating the inability of B. cereus to proliferate in seaweed-based food, its presence in dehydrated foodstuffs cannot rule out replication after rehydration before consumption, making it necessary to elucidate the possible risks for consumers.

HIGHLIGHTS

Morphological Features and Cold-Response Gene Expression in Mesophilic Bacillus cereus Group and Psychrotolerant Bacillus cereus Group under Low Temperature

At low temperatures, psychrotolerant B. cereus group strains exhibit a higher growth rate than mesophilic strains do. However, the different survival responses of the psychrotolerant strain (BCG³⁴) and the mesophilic strain (BCG^T) at low temperatures are unclear. We investigated the morphological and genomic features of BCG^T and BCG³⁴ to characterize their growth strategies at low temperatures. At low temperatures, morphological changes were observed only in BCG^T. These morphological changes included the elongation of rod-shaped cells, whereas the cell shape in BCG³⁴ was unchanged at the low temperature. A transcriptomic analysis revealed that both species exhibited different growth-related traits during low-temperature growth. The BCG^T strain induces fatty acid biosynthesis, sulfur assimilation, and methionine and cysteine biosynthesis as a survival mechanism in cold systems. Increases in energy metabolism and fatty acid biosynthesis in the mesophilic B. cereus group strain might explain its ability to grow at low temperatures. Several pathways involved in carbohydrate mechanisms were downregulated to conserve the energy required for growth. Peptidoglycan biosynthesis was upregulated, implying that a change of gene expression in both RNA-Seq and RT-qPCR contributed to sustaining its growth and rod shape at low temperatures. These results improve our understanding of the growth response of the B. cereus group, including psychrotolerant B. cereus group strains, at low temperatures and provide information for improving bacterial inhibition strategies in the food industry.

Keeping up with the Bacillus cereus group: taxonomy through the genomics era and beyond

The Bacillus cereus group, also known as B. cereus sensu lato (s.l.), is a species complex that contains numerous closely related lineages, which vary in their ability to cause illness in humans and animals. The classification of B. cereus s.l. isolates into species-level taxonomic units is thus essential for informing public health and food safety efforts. However, taxonomic classification of these organisms is challenging. Numerous-often conflicting-taxonomic changes to the group have been proposed over the past two decades, making it difficult to remain up to date. In this review, we discuss the major nomenclatural changes that have accumulated in the B. cereus s.l. taxonomic space prior to 2020, particularly in the genomic sequencing era, and outline the resulting problems. We discuss several contemporary taxonomic frameworks as applied to B. cereus s.l., including (i) phenotypic, (ii) genomic, and (iii) hybrid nomenclatural frameworks, and we discuss the advantages and disadvantages of each. We offer suggestions as to how readers can avoid B. cereus s.l. taxonomic ambiguities, regardless of the nomenclatural framework(s) they choose to employ. Finally, we discuss future directions and open problems in the B. cereus s.l. taxonomic realm, including those that cannot be solved by genomic approaches alone.

Growth interferences between bacterial strains from raw cow's milk and their impact on growth of Listeria monocytogenes and Staphylococcus aureus

AIMS

The purpose of this study was to detect growth enhancing or inhibiting activity between bacterial populations from raw milk under different conditions (temperature, medium).

METHODS AND RESULTS

The interference of 24 raw milk isolates on growth of each other and on Listeria monocytogenes, Staphylococcus aureus, Bacillus subtilis and Micrococcus luteus was screened by drop assay and for selected pairs in co-cultivation experiments. By drop assay, antibacterial activity was observed for 40% of the strains. About 30% of the strains showed growth-enhancing activity on other strains. Most of the isolates were well adapted to cold temperatures and showed consistent or even increased inhibiting or enhancing effects on growth of other strains at 10°C. The growth of L. monocytogenes DSM 20600^T and S. aureus DSM 1104^T was significantly (P < 0·05) reduced in co-cultivation with Pseudomonas protegens JZ R-192.

CONCLUSIONS

Growth interferences between bacterial populations have an impact on the structure of raw milk microbiota, especially when it develops under cold storage, and it may have an effect on the prevalence of certain foodborne pathogens.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study demonstrates growth-inhibiting and also growth-enhancing interactions between raw milk bacteria, which must be considered when predicting bacterial growth and spoilage in food. A Ps. protegens strain isolated from raw milk showed an antagonistic effect on growth of L. monocytogenes in refrigerated raw milk.

Bacillus weihenstephanensis can readily evolve for increased endospore heat resistance without compromising its thermotype

Proper elimination of bacterial endospores in foods and food processing environment is challenging because of their extreme resistance to various stresses. Often, sporicidal treatments prove insufficient to eradicate the contaminating endospore population as a whole, and might therefore serve as a selection pressure for enhanced endospore resistance. In the sporeforming Bacillus cereus group, Bacillus weihenstephanensis is an important food spoilage organism and potential cereulide producing pathogen, due to its psychrotolerant growth ability at 7 °C. Although the endospores of B. weihenstephanensis are generally less heat resistant compared to their mesophilic or thermotolerant relatives, our data now show that non-emetic B. weihenstephanensis strain LMG 18989^T can readily and reproducibly evolve to acquire much enhanced endospore heat resistance. In fact, one of the B. weihenstephanensis mutants from directed evolution by wet heat in this study yielded endospores displaying a > 4-fold increase in D-value at 91 °C compared to the parental strain. Moreover, these mutant endospores retained their superior heat resistance even when sporulation was performed at 10 °C. Interestingly, increased endospore heat resistance did not negatively affect the vegetative growth capacities of the evolved mutants at lower (7 °C) and upper (37 °C) growth temperature boundaries, indicating that the correlation between cardinal growth temperatures and endospore heat resistance which is observed among bacterial sporeformers is not necessarily causal.

Spoilage potential of Bacillus subtilis in a neutral-pH dairy dessert

The objective of this study was the characterization of the microbiota associated with spoilage of vanilla cream pudding during storage at different temperatures. Commercial cream samples were stored aerobically at 4, 8, 12 and 15 °C for a maximum time period of 40 days. At appropriate time intervals, cream samples were subjected to: (i) microbiological analyses, and (ii) high-performance liquid chromatography (HPLC). Furthermore, the spoilage microbiota was identified through repetitive extragenic palindrome-PCR, while selected isolates were further characterized based on sequencing of the V1-V3 region of the 16S rRNA gene. Microbial growth was observed only during storage of cream samples at 12 and 15 °C, with the applied genotypic analysis demonstrating that Bacillus subtilis subsp. subtilis was the dominant spoilage microorganism of this product. Based on the HPLC analysis results, citric acid and sucrose were the most abundant organic acid and sugar, respectively throughout storage of cream pudding, whereas notable changes mainly included: (i) increase in the concentration of lactic acid and to a lesser extent of formic and acetic acids, and (ii) increase in the concentration of glucose and fructose at the expense of sucrose and lactose. The results of this study should be useful for the dairy industry in detecting and controlling microbiological spoilage in cream pudding and other chilled, neutral-pH dairy desserts.

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

Microbial community analysis with a specific statistical approach after a record breaking snowfall in Southern Italy

Purpose

Snow and ice ecosystems present unexpectedly high microbial abundance and diversity. Although arctic and alpine snow environments have been intensively investigated from a microbiological point of view, few studies have been conducted in the Apennines. Accordingly, the main purpose of this research was to analyze the microbial communities of the snow collected in two different locations of Capracotta municipality (Southern Italy) after a snowfall record occurred on March 2015 (256 cm of snow in less than 24 h).

Methods

Bacterial communities were analyzed by the Next-Generation Sequencing techniques. Furthermore, a specific statistical approach for taxonomic hierarchy data was introduced, both for the assessment of diversity within microbial communities and the comparison between different microbiotas. In general, diversity and similarity indices are more informative when computed at the lowest level of the taxonomic hierarchy, the species level. This is not the case with microbial data, for which the species level is not necessarily the most informative. Indeed, the possibility to detect a large number of unclassified records at every level of the hierarchy (even at the top) is very realistic due to both the partial knowledge about the cultivable fraction of microbial communities and limitations to taxonomic assignment connected to the quality and completeness of the 16S rRNA gene reference databases. Thus, a global approach considering information from the whole taxonomic hierarchy was adopted in order to obtain a more consistent assessment of the biodiversity.

Result

The main phyla retrieved in the investigated snow samples were Proteobacteria, Actinobacteria, Bacteroidetes, and Firmicutes. Interestingly, DNA from bacteria adapted to thrive at low temperatures, but also from microorganisms normally associated with other habitats, whose presence in the snow could be justified by wind-transport, was found. Biomolecular investigations and statistical data analysis showed relevant differences in terms of biodiversity, composition, and distribution of bacterial species between the studied snow samples.

Conclusion

The relevance of this research lies in the expansion of knowledge about microorganisms associated with cold environments in contexts poorly investigated such as the Italian Apennines, and in the development of a global statistical approach for the assessment of biological diversity and similarity of microbial communities as an additional tool to be usefully combined with the barcoding methods.

No Assembly Required: Using BTyper3 to Assess the Congruency of a Proposed Taxonomic Framework for the Bacillus cereus Group With Historical Typing Methods

The Bacillus cereus group, also known as B. cereus sensu lato (s.l.), is a species complex comprising numerous closely related lineages, which vary in their ability to cause illness in humans and animals. The classification of B. cereus s.l. isolates into species-level taxonomic units is essential for facilitating communication between and among microbiologists, clinicians, public health officials, and industry professionals, but is not always straightforward. A recently proposed genomospecies-subspecies-biovar taxonomic framework aims to provide a standardized nomenclature for this species complex but relies heavily on whole-genome sequencing (WGS). It thus is unclear whether popular, low-cost typing methods (e.g., single- and multi-locus sequence typing) remain congruent with the proposed taxonomy. Here, we characterize 2,231 B. cereus s.l. genomes using a combination of in silico (i) average-nucleotide identity (ANI)-based genomospecies assignment, (ii) ANI-based subspecies assignment, (iii) seven-gene multi-locus sequence typing (MLST), (iv) single-locus panC group assignment, (v) rpoB allelic typing, and (vi) virulence factor detection. We show that sequence types (STs) assigned using MLST can be used for genomospecies assignment, and we provide a comprehensive list of ST/genomospecies associations. For panC group assignment, we show that an adjusted, eight-group framework is largely, albeit not perfectly, congruent with the proposed eight-genomospecies taxonomy, as panC alone may not distinguish (i) B. luti from Group II B. mosaicus and (ii) B. paramycoides from Group VI B. mycoides. We additionally provide a list of loci that capture the topology of the whole-genome B. cereus s.l. phylogeny that may be used in future sequence typing efforts. For researchers with access to WGS, MLST, and/or panC data, we showcase how our recently released software, BTyper3 (https://github.com/lmc297/BTyper3), can be used to assign B. cereus s.l. isolates to taxonomic units within this proposed framework with little-to-no user intervention or domain-specific knowledge of B. cereus s.l. taxonomy. We additionally outline a novel method for assigning B. cereus s.l. genomes to pseudo-gene flow units within proposed genomospecies. The results presented here highlight the backward-compatibility and accessibility of the recently proposed genomospecies-subspecies-biovar taxonomic framework and illustrate that WGS is not a necessity for microbiologists who want to use the proposed nomenclature effectively.

Draft Genome Sequences of Five Paenibacillus Species of Dairy Origin

Paenibacillus species are important spoilage organisms in the dairy industry. The genomes of five Paenibacillus species which were isolated from dairy products in Canada were sequenced using the Illumina MiSeq platform. Draft genomes ranging from 5.1 to 7.1 Mb with GC contents of 49 to 53% were generated.

Paenibacillus species are important spoilage organisms in the dairy industry. The genomes of five Paenibacillus species which were isolated from dairy products in Canada were sequenced using the Illumina MiSeq platform. Draft genomes ranging from 5.1 to 7.1 Mb with GC contents of 49 to 53% were generated.

Detection of spore forming Paenibacillus macerans in raw milk

Paenibacillus macerans can cause spoilage of milk during extended storage. However, the natural milk microbiota interferes with the enumeration of Paenibacillus species in raw milk. In this study, a qualitative SYBR Green real-time PCR assay based on the groEL gene was developed for detecting P. macerans (PMassay) in raw milk and compared with one designed for total Paenibacillus detection (TPassay). The specificity of the PMassay was confirmed against a panel of dairy-related spore forming isolates. In the presence of background DNA substituted up to 95%, P. macerans DNA could still be detected by the PMassay although interference occurred as non-target DNA substitution increased. The PMassay was sensitive (detection limit of 2 log CFU/ml in milk) and specific as non-P. macerans isolates gave a Ct > 30. After enrichment of raw milk for 7 days at 37 °C in Reinforced Clostridial Medium with D-cycloserine (RCM-D) under anaerobiosis, Paenibacillus was detected in 10 of the 16 raw milk samples tested. Enrichment in RCM-D yielded about 0.5 to 5.8 log CFU/ml total Paenibacillus and 0.3 to 4.6 log CFU/ml P. macerans in the samples. The assay could be useful in commercial settings, allowing a sensitive detection of P. macerans.

Characterization of Bacillus cereus sensu lato isolates from milk for consumption; phylogenetic identity, potential for spoilage and disease

This study addresses the biodiversity of Bacillus cereus group population present along the value chain of milk for consumption. The B. cereus population did not grow and remained mainly unaltered during storage of milk at 4 °C while storage at a suboptimal temperature at 8 °C (representative of a broken cold chain) caused a major shift in its composition. Mesophilic strains dominated the B. cereus population in raw milk and after storage at 4 °C, while psycrotrophic strains dominated after storage at 8 °C. All psycrotrophic and mesophilic isolates (n = 368) demonstrated high spoilage potentials of the milk components. Fifteen out of 20 mesophilic isolates but only two out of 40 psychrotrophic isolates, exhibited vero cell toxicity. No genes encoding the emetic toxin cereulide were detected in the genomes of 100 milk isolates while 14 of them harbored the enterotoxin genes cytK1/cytK2. Both psycrotrophic and mesophilic isolates carried the enterotoxin genes nheA and hblA. Together, the results provide insight into the composition and properties, of the B. cereus population present in milk along the value chain and during storage at optimal refrigerated temperature and at suboptimal temperature. This knowledge is useful in the dairy industry's work to assure high quality products and for risk assessment.

Mitigating Milk-Associated Bacteria through Inducing Zinc Ions Antibiofilm Activity

Dairy products are a sector heavily impacted by food loss, often due to bacterial contaminations. A major source of contamination is associated with the formation of biofilms by bacterial species adopted to proliferate in milk production environment and onto the surfaces of milk processing equipment. Bacterial cells within the biofilm are characterized by increased resistance to unfavorable environmental conditions and antimicrobial agents. Members of the Bacillus genus are the most commonly found spoilage microorganisms in the dairy environment. It appears that physiological behavior of these species is somehow depended on the availability of bivalent cations in the environment. One of the important cations that may affect the bacterial physiology as well as survivability are Zn²⁺ ions. Thus, the aim of this study was to examine the antimicrobial effect of Zn²⁺ ions, intending to elucidate the potential of a zinc-based antibacterial treatment suitable for the dairy industry. The antimicrobial effect of different doses of ZnCl₂ was assessed microscopically. In addition, expression of biofilm related genes was evaluated using RT-PCR. Analysis of survival rates following heat treatment was conducted in order to exemplify a possible applicative use of Zn²⁺ ions. Addition of zinc efficiently inhibited biofilm formation by B. subtilis and further disrupted the biofilm bundles. Expression of matrix related genes was found to be notably downregulated. Microscopic evaluation showed that cell elongation was withheld when cells were grown in the presence of zinc. Finally, B. cereus and B. subtilis cells were more susceptible to heat treatment after being exposed to Zn²⁺ ions. It is believed that an anti-biofilm activity, expressed in downregulation of genes involved in construction of the extracellular matrix, would account for the higher sensitivity of bacteria during heat pasteurization. Consequently, we suggest that Zn²⁺ ions can be of used as an effective antimicrobial treatment in various applications in the dairy industry, targeting both biofilms and vegetative bacterial cells.

Potential of N2 Gas Flushing to Hinder Dairy-Associated Biofilm Formation and Extension

Worldwide, the dairy sector remains of vital importance for food production despite severe environmental constraints. The production and handling conditions of milk, a rich medium, promote inevitably the entrance of microbial contaminants, with notable impact on the quality and safety of raw milk and dairy products. Moreover, the persistence of high concentrations of microorganisms (especially bacteria and bacterial spores) in biofilms (BFs) present on dairy equipment or environments constitutes an additional major source of milk contamination from pre- to post-processing stages: in dairies, BFs represent a major concern regarding the risks of disease outbreaks and are often associated with significant economic losses. One consumption trend toward "raw or low-processed foods" combined with current trends in food production systems, which tend to have more automation and longer processing runs with simultaneously more stringent microbiological requirements, necessitate the implementation of new and obligatory sustainable strategies to respond to new challenges regarding food safety. Here, in light of studies, performed mainly with raw milk, that considered dominant "planktonic" conditions, we reexamine the changes triggered by cold storage alone or combined with nitrogen gas (N2) flushing on bacterial populations and discuss how the observed benefits of the treatment could also contribute to limiting BF formation in dairies.

Discrimination of psychrotolerant Bacillus cereus group based on MALDI-TOF MS analysis of ribosomal subunit proteins

Psychrotolerant species of the Bacillus cereus group, Bacillus mycoides and Bacillus weihenstephanensis, can grow at ≥ 7 °C and are significant concerns for the food industry due to their ability to cause spoilage of refrigerated food. In addition to that, some strains of B. weihenstephanensis can produce emetic toxin, namely cereulide, which is known to cause vomiting. Therefore, rapid and simple methods to discriminate psychrotolerant B. cereus group species are crucial. Here, matrix assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF MS) and the S10-spc-alpha operon gene encoded ribosomal protein mass spectrum (S10-GERMS) method were used to discriminate psychrotolerant species of the B. cereus group based on a set of four ribosomal subunit proteins (S10, S16, S20 and L30). A total of 36 strains of B. cereus group were cultured on LB agar, and analyzed by MALDI-TOF MS. The four biomarkers successfully discriminated 12 strains of psychrotolerant species from mesophilic species of the B. cereus group. Furthermore, the four biomarkers also classified some Bacillus thuringiensis strains. MALDI-TOF MS analysis using the S10-GERMS method allowed simple and rapid discrimination of psychrotolerant species of the B. cereus group from other mesophilic species. This method has a possibility to enable manufacturers and distributors of refrigerated foods to control psychrotolerant species of the B. cereus group effectively.

Role of Bacillus species in biofilm persistence and emerging antibiofilm strategies in the dairy industry

Biofilm-forming Bacillus species are often involved in persistent contamination and spoilage of dairy products. They therefore present a major microbiological challenge in the field of dairy food quality and safety. Due to their substantial physiological versatility, Bacillus species can survive in various parts of dairy manufacturing plants, leading to a high risk of product spoilage and potential dissemination of foodborne diseases. Furthermore, biofilm and heat-resistant spore formation make these bacteria challenging to eliminate. Thus, some strategies have been employed to remove, prevent, or delay the formation of Bacillus biofilms in the dairy industry, but with limited success. Lack of understanding of the Bacillus biofilm structure and behavior in conditions relevant to dairy-associated environments could partially account for this situation. The current paper reviews dairy-associated biofilm formation by Bacillus species, with particular attention to the role of biofilm in Bacillus species adaptation and survival in a dairy processing environment. Relevant model systems are discussed for the development of novel antimicrobial approaches to improve the quality of dairy food. © 2020 Society of Chemical Industry.

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.

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.

The ability of spore formers to degrade milk proteins, fat, phospholipids, common stabilizers, and exopolysaccharides

Spore formers are common spoilage-causing microorganisms in dairy products; however, their modes of spoilage (proteolysis, lipolysis, etc.) have not been described in detail for cultured dairy products such as sour cream and yogurt. The objective of the present study was to test the ability of spore-forming strains isolated from dairy environments for their spoilage-causing activities at typical sour cream (24°C) and yogurt (42°C) fermentation temperatures. A total of 25 spore-forming strains were isolated from different sources, including raw milk, pasteurizer balance tank, biofilms formed on heat exchangers, and milk powder. These strains were tested for proteolytic and lipolytic activities and for their ability to degrade phospholipids, common stabilizers (starch, gelatin, xanthan gum, pectin), and exopolysaccharides (EPS) at sour cream and yogurt fermentation temperatures. A higher percentage of positive strains was observed for selected activities at yogurt fermentation temperature compared with sour cream fermentation temperature. Identified proteolytic spore-forming strains, based on a skim milk agar method, were subsequently quantified for their level of proteolysis using non-casein nitrogen (NCN) content and sodium dodecyl sulfate-PAGE (SDS-PAGE). The proteolytic strains that showed the highest levels of proteolysis (highest percentages of NCN content) at 24°C were Bacillus mojavensis BC, Bacillus cereus DBC, Bacillus subtilis DBC, B. mojavensis DBC1, and Paenibacillus polymyxa DBC1. At 42°C the strains with the highest levels of proteolysis (highest percentages of NCN content) were B. subtilis DBC, B. mojavensis BC, B. mojavensis DBC1, B. cereus DBC, and Bacillus licheniformis DBC6. Results of SDS-PAGE demonstrated that proteolytic strains had primarily hydrolyzed β- and κ-CN. A viscometric method was used to evaluate the susceptibility of exopolysaccharides (EPS) to degradation by selected spore formers. This method helped to determine that EPS produced by commercial yogurt and sour cream cultures is susceptible to degradation by spore formers present in dairy environments.

Dairy farm management practices and the risk of contamination of tank milk from Clostridium spp. and Paenibacillus spp. spores in silage, total mixed ration, dairy cow feces, and raw milk

The occurrence of Paenibacillus and Clostridium spores in silage is of great concern for dairy producers because their spores can contaminate milk and damage processed milk and semi-hard cheeses. Spoiled silage is considered to be the main contamination source of the total mixed ration (TMR), feces of dairy cows, and consequently bulk tank milk via the contamination of cow teats by dirt during milking. The presence of an anaerobic and facultative anaerobic sporeformer population in different matrices (soil, corn silage, other feeds, TMR, feces, and milk) and its transmission pathway has been studied on 49 dairy farms by coupling plate count data with 16S-DNA identification. The different matrices have shown a high variability in the anaerobic and facultative anaerobic spore count, with the highest values being found in the aerobically deteriorated areas of corn silages. Clostridium tyrobutyricum, Paenibacillus macerans, and Paenibacillus thermophilus were detected in all the matrices. The TMR spore count was influenced by the amount of spoiled corn silage in the TMR and by the care taken when cleaning the spoiled silage before feed-out. Most of the farms that prevent the presence of visible moldy silage in the silo and carefully clean to remove molded spots were able to maintain their TMR spore counts below 4.0 log spores/g. When a level of 4.5 log spores/g of TMR was exceeded, the feces presented a greater contamination than 3.0 log spores/g. Moreover, the higher the number of spores in the feces was, the higher the number of spores in the milk. Most of the farms that presented a feces contamination greater than 5.0 log spores/g had a higher milk spore contamination than 1,000 spores/L. Careful animal cleaning and good milking practices have been found to be essential to maintain low levels of contamination in bulk tank milk, but it has emerged that only by coupling these practices with a correct silage management and cleaning during TMR preparation can the contamination of milk by spores be kept at a low level. It has been found that aerobically deteriorated silage has a great capacity to contaminate TMR and consequently to increase the risk of milk spore contamination, even when routine milking practices are adopted correctly.

Bedding and bedding management practices are associated with mesophilic and thermophilic spore levels in bulk tank raw milk

Mesophilic and thermophilic spore-forming bacteria represent a challenge to the dairy industry, as these bacteria are capable of surviving adverse conditions associated with processing and sanitation and eventually spoil dairy products. The dairy farm environment, including soil, manure, silage, and bedding, has been implicated as a source for spores in raw milk. High levels of spores have previously been isolated from bedding, and different bedding materials have been associated with spore levels in bulk tank (BT) raw milk; however, the effect of different bedding types, bedding management practices, and bedding spore levels on the variance of spore levels in BT raw milk has not been investigated. To this end, farm and bedding management surveys were administered and unused bedding, used bedding, and BT raw milk samples were collected from dairy farms (1 or 2 times per farm) across the United States over 1 yr; the final data set included 182 dairy farms in 18 states. Bedding suspensions and BT raw milk were spore pasteurized (80°C for 12 min), and mesophilic and thermophilic spores were enumerated. Piecewise structural equation modeling analysis was used to determine direct and indirect pathways of association among farm and bedding practices, levels of spores in unused and used bedding, and levels of spores in BT raw milk. Separate models were constructed for mesophilic and thermophilic spore levels. The analyses showed that bedding material had a direct influence on levels of spores in unused and used bedding as well as an indirect association with spore levels in BT raw milk through used bedding spore levels. Specific bedding and farm management practices as well as cow hygiene in the housing area were associated with mesophilic and thermophilic spore levels in unused bedding, used bedding, and BT raw milk. Notably, levels of spores in used bedding were positively related to those in unused bedding, and used bedding spore levels were positively related to those in BT raw milk. The results of this study increase the understanding of the levels and ecology of mesophilic and thermophilic spores in raw milk, emphasize the possible role of bedding as a source of spores on-farm, and present opportunities for dairy producers to reduce spore levels in BT raw milk.

Robust Biofilm-Forming Bacillus Isolates from the Dairy Environment Demonstrate an Enhanced Resistance to Cleaning-in-Place Procedures

One of the main strategies for maintaining the optimal hygiene level in dairy processing facilities is regular cleaning and disinfection, which is incorporated in the cleaning-in-place (CIP) regimes. However, a frail point of the CIP procedures is their variable efficiency in eliminating biofilm bacteria. In the present study, we evaluated the susceptibility of strong biofilm-forming dairy Bacillus isolates to industrial cleaning procedures using two differently designed model systems. According to our results, the dairy-associated Bacillus isolates demonstrate a higher resistance to CIP procedures, compared to the non-dairy strain of B. subtilis. Notably, the tested dairy isolates are highly persistent to different parameters of the CIP operations, including the turbulent flow of liquid (up to 1 log), as well as the cleaning and disinfecting effects of commercial detergents (up to 2.3 log). Moreover, our observations indicate an enhanced resistance of poly-γ-glutamic acid (PGA)-overproducing B. subtilis, which produces high amounts of proteinaceous extracellular matrix, to the CIP procedures (about 0.7 log, compared to the wild-type non-dairy strain of B. subtilis). We therefore suggest that the enhanced resistance to the CIP procedures by the dairy Bacillus isolates can be attributed to robust biofilm formation. In addition, this study underlines the importance of evaluating the efficiency of commercial cleaning agents in relation to strong biofilm-forming bacteria, which are relevant to industrial conditions. Consequently, we believe that the findings of this study can facilitate the assessment and refining of the industrial CIP procedures.

Genes Associated With Psychrotolerant Bacillus cereus Group Isolates

The Bacillus cereus group comprises 18 different species, including human pathogens as well as psychrotolerant strains that are an important cause of fluid milk spoilage. To enhance our understanding of the genetic markers associated with psychrotolerance (defined here as > 1 log₁₀ increase in cfu/mL after 21 days incubation at 6°C) among dairy-associated B. cereus group isolates, we used genetic (whole genome sequencing) and phenotypic methods [growth in Skim Milk Broth (SMB) and Brain Heart Infusion (BHI) broth] to characterize 23 genetically-distinct representative isolates from a collection of 503 dairy-associated isolates. Quality threshold clustering identified three categories of psychrotolerance: (i) 14 isolates that were not psychrotolerant in BHI or SMB, (ii) 6 isolates that were psychrotolerant in BHI but not in SMB, and (iii) 2 isolates that were psychrotolerant in BHI and SMB. One isolate, which was psychrotolerant in BHI broth but was just below the cut-off of >1 log₁₀ cfu/mL increase in SMB was not assigned to a cluster. A maximum likelihood phylogeny constructed with core genome single nucleotide polymorphisms classified all psychrotolerant isolates (i.e., psychrotolerant in BHI) into clade VI (representing B. mycoides/weihenstephanensis). Analysis of correlations between gene ortholog presence or absence patterns and psychrotolerance identified 206 orthologous gene clusters that were significantly overrepresented among psychrotolerant strains, including two clusters of cold shock proteins, which were identified in 8/9 and 7/9 psychrotolerant isolates. Gene ontology analyses revealed 36 gene ontology terms that were overrepresented in psychrotolerant isolates, including putrescine catabolic processes and putrescine transmembrane transporter activity. Lastly, Hidden Markov Model searches identified three protein family motifs, including cold shock domain proteins and fatty acid hydroxylases that were significantly associated with psychrotolerance in BHI broth. Analyses of CspA sequences revealed a positive association between psychrotolerant strains and a previously identified “psychrotolerant” CspA sequence. Overall, our data highlight genetic and phenotypic differences in psychrotolerance among B. cereus group dairy-associated isolates and show that psychrotolerance is dependent on the growth medium. We also identified a number of gene targets that could be used for specific detection or control of psychrotolerant B. cereus group isolates.

Characterization of Emetic and Diarrheal Bacillus cereus Strains From a 2016 Foodborne Outbreak Using Whole-Genome Sequencing: Addressing the Microbiological, Epidemiological, and Bioinformatic Challenges

The Bacillus cereus group comprises multiple species capable of causing emetic or diarrheal foodborne illness. Despite being responsible for tens of thousands of illnesses each year in the U.S. alone, whole-genome sequencing (WGS) is not yet routinely employed to characterize B. cereus group isolates from foodborne outbreaks. Here, we describe the first WGS-based characterization of isolates linked to an outbreak caused by members of the B. cereus group. In conjunction with a 2016 outbreak traced to a supplier of refried beans served by a fast food restaurant chain in upstate New York, a total of 33 B. cereus group isolates were obtained from human cases (n = 7) and food samples (n = 26). Emetic (n = 30) and diarrheal (n = 3) isolates were most closely related to B. paranthracis (group III) and B. cereus sensu stricto (group IV), respectively. WGS indicated that the 30 emetic isolates (24 and 6 from food and humans, respectively) were closely related and formed a well-supported clade distinct from publicly available emetic group III genomes with an identical sequence type (ST 26). The 30 emetic group III isolates from this outbreak differed from each other by a mean of 8.3 to 11.9 core single nucleotide polymorphisms (SNPs), while differing from publicly available emetic group III ST 26 B. cereus group genomes by a mean of 301.7-528.0 core SNPs, depending on the SNP calling methodology used. Using a WST-1 cell proliferation assay, the strains isolated from this outbreak had only mild detrimental effects on HeLa cell metabolic activity compared to reference diarrheal strain B. cereus ATCC 14579. We hypothesize that the outbreak was a single source outbreak caused by emetic group III B. cereus belonging to the B. paranthracis species, although food samples were not tested for presence of the emetic toxin cereulide. In addition to showcasing how WGS can be used to characterize B. cereus group strains linked to a foodborne outbreak, we also discuss potential microbiological and epidemiological challenges presented by B. cereus group outbreaks, and we offer recommendations for analyzing WGS data from the isolates associated with them.