Development of Molecular Typing Methods for Bacillus spp. and Paenibacillus spp. Isolated from Fluid Milk Products

Bacillus spp. and related sporeformers are important food spoilage organisms. While use of molecular subtyping methods has provided important information on the ecology and transmission of foodborne pathogens, the lack of rapid, reliable, and affordable subtyping methods for Bacillus spp. has limited our ability to understand and control their transmission throughout the food chain. We used a previously described collection of Bacillus spp. and Paenibacillus spp. isolated from dairy products to develop a DNA sequencing‐based subtyping approach for these spoilage microorganisms. After optimization of polymerase chain reaction (PCR) parameters, primers targeting the rpoB housekeeping gene allowed for successful amplification in all isolates. rpoB sequencing allowed differentiation of 29 subtypes (that is, sequence types) among the 57 isolates characterized. Phylogenetic analyses of rpoB sequences revealed distinct monophyletic lineages that correlated with bacterial genera (Bacillus and Paenibacillus) as well as with species or species‐like assemblages within each genus. rpoB sequencing provided improved subtype discrimination over 16S rDNA sequencing; therefore, rpoB sequencing allows for both sensitive subtype discrimination as well as for species and genus identification. Analysis of subtypes isolated over time in dairy products revealed the presence of both persistent and transient bacterial subtypes, indicating that application of these methods can improve our understanding of the ecology of these spoilage organisms and can help in identification of bacterial niches that may contribute to the persistence of these spoilage organisms in food systems.     

Microbiological aspects and challenges of whey powders – I thermoduric,thermophilic and spore-forming bacteria

For dairy processors, spoilage and pathogenic spore-forming bacteria are key sources of concern, not only due to their ability to remain dormant in a desiccated state in powders and to survive heat treatments, but also their ability to form biofilms in the vegetative state that lead to contamination of foods. These include members of the genera Bacillus, Geobacillus, Anoxybacillus, Brevibacillus, Paenibacillus and Clostridium, many of which are associated with food poisoning and spoilage. Here, we review the common bacterial species that form spores in whey powders and their sources and provide insights into their risks and strategies to control them.     

Biofilm Formation Characteristics of Pseudomonas lundensis Isolated from Meat

Biofilms formations of spoilage and pathogenic bacteria on food or food contact surfaces have attracted increasing attention. These events may lead to a higher risk of food spoilage and foodborne disease transmission. While Pseudomonas lundensis is one of the most important bacteria that cause spoilage in chilled meat, its capability for biofilm formation has been seldom reported. Here, we investigated biofilm formation characteristics of P. lundensis mainly by using crystal violet staining, and confocal laser scanning microscopy (CLSM). The swarming and swimming motility, biofilm formation in different temperatures (30, 10, and 4 °C) and the protease activity of the target strain were also assessed. The results showed that P. lundensis showed a typical surface‐associated motility and was quite capable of forming biofilms in different temperatures (30, 10, and 4 °C). The strain began to adhere to the contact surfaces and form biofilms early in the 4 to 6 h. The biofilms began to be formed in massive amounts after 12 h at 30 °C, and the extracellular polysaccharides increased as the biofilm structure developed. Compared with at 30 °C, more biofilms were formed at 4 and 10 °C even by a low bacterial density. The protease activity in the biofilm was significantly correlated with the biofilm formation. Moreover, the protease activity in biofilm was significantly higher than that of the corresponding planktonic cultures after cultured 12 h at 30 °C.     

The Predominance of Psychrotrophic Pseudomonads on Aerobically Stored Chilled Red Meat

Microbial spoilage of meat during chilled aerobic storage causes significant financial losses to the industry. Even with modern day preservation techniques, spoilage remains an unsolved problem. Spoilage of meat is a complex process that involves the activity of endogenous enzymes and microorganisms. Psychrotrophic Pseudomonas species are the key microorganisms that cause spoilage in aerobically stored chilled meat. Spoilage pseudomonads are highly robust and able to withstand stressful environmental conditions that would otherwise inhibit the growth of other spoilage organisms. In order to implement efficient control measures, and to minimize spoilage, a thorough understanding of the characteristics of spoilage pseudomonads is essential. This review focuses on the spoilage process and the key metabolic attributes of the main psychrotrophic spoilage Pseudomonas species to explain their predominance on meat over other psychrotrophic bacteria. This review also highlights less studied, but important, characteristics of psychrotrophic pseudomonads such as biofilm formation and quorum sensing in the context of meat spoilage. The importance of the use of model systems that are closely applicable to the food industry is also discussed in detail.     

Tracking heat-resistant, cold-thriving fluid milk spoilage bacteria from farm to packaged product

Control of psychrotolerant endospore-forming spoilage bacteria, particularly Bacillus and Paenibacillus spp., is economically important to the dairy industry. These microbes form endospores that can survive high-temperature, short-time pasteurization; hence, their presence in raw milk represents a major potential cause of milk spoilage. A previously developed culture-dependent selection strategy and an rpoB sequence-based subtyping method were applied to bacterial isolates obtained from environmental samples collected on a New York State dairy farm. A total of 54 different rpoB allelic types putatively identified as Bacillus (75% of isolates), Paenibacillus (24%), and Sporosarcina spp. (1%) were identified among 93 isolates. Assembly of a broader data set, including 93 dairy farm isolates, 57 raw milk tank truck isolates, 138 dairy plant storage silo isolates, and 336 pasteurized milk isolates, identified a total of 154 rpoB allelic types, representing an extensive diversity of Bacillus and Paenibacillus spp. Our molecular subtype data clearly showed that certain endospore-forming bacterial subtypes are present in the dairy farm environment as well as in the processing plant. The potential for entry of these ubiquitous heat-resistant spoilage organisms into milk production and processing systems, from the dairy farm to the processing plant, represents a considerable challenge that will require a comprehensive farm-to-table approach to fluid milk quality.     

Quorum Sensing Inhibitory and Anti-Biofilm Activity of Essential Oils and Their in vivo Efficacy in Food Systems

The present study investigated the effect of the essential oils of Cuminium cymium, Murraya koenigii, Curcuma longa, Zingiber officinale, Myristica fragrans (mace and nutmeg), Trigonella foenum graceum, and Elettaria cardamomum on AHL-mediated quorum sensing and biofilm formation. Inhibition of quorum sensing (QS) regulated phenotypes by the essential oils at subinhibitory concentrations was investigated using the biosensor bacteria Chromobacterium violaceum (C. violaceum 12472 and C. violaceum CV026) and Pseudomonas aeruginosa PA01. Sub-MIC of essential oils was screened for inhibition of quorum-sensing regulated pigment production, motility and biofilm formation in the biosensors. The essential oil of M. koenigii showed the most promising QS inhibitory and anti-biofilm activity at a concentration of 0.02% v/v and hence was used for further studies. Anti-biofilm activity against food spoilage Pseudomonas species was studied by crystal-violet MTP method and fluorescence microscopy. The essential oil of M. koenigii at sub-MICs inhibited biofilm formation in the pseudomonads by inhibiting cell attachment, reducing metabolic activity and EPS production, and preventing biofilm maturation. Further, it was capable of delaying spoilage by psychrotrophic P. psychrophila PSPF19 in refrigerated milk. The major components present in M. koenigii essential oil were caryophyllene, caryophyllene oxide, cinnamaldehyde, α-, and β-phellandrene and eugenol. Application of M. koenigii essential oil and its constituents based on the quorum-sensing inhibitory and anti-biofilm activity would be a novel intervention strategy to enhance shelf life and food safety.     

Beer enemy number one: genetic diversity,physiology and biofilm formation of Lactobacillus brevis

Lactobacillus brevis is the most significant beer spoilage bacteria worldwide. It is found as a contaminant at all stages of brewing, including during primary and secondary fermentation, storage, filtration and the packaging process. In production with flash pasteurisation and subsequent hygienic filling, avoiding and tracing secondary contaminations is the key to a microbiologically stable product. However, L. brevis strains vary in their spoilage potential and can grow in many different beer types. This study presents a physiological test scheme for growth potential and biofilm formation in various media. It was determined that a large number of L. brevis strains can form biofilms as a first coloniser. The identification of the species alone is therefore not enough to be sure of the spoilage risk, which shows the need for a more in depth differentiation. DNA fingerprint techniques are crucial to differentiate isolates of this species at strain level. The rep‐PCR fingerprint system (GTG)₅ was used to differentiate a selected collection of 20 isolates, which were characterised in growth and biofilm formation in various media. The data showed a high variation within the selected isolates. As second step, generated fingerprint clusters of L. brevis were traced back to contamination sources in a German brewery, revealing a high number of isolates with potentially varying growth, spoilage and biofilm potential. L. brevis being the demonstrator species, the PCR system used is a powerful and compatible tracing and troubleshooting tool for all kinds of spoilage bacteria in the brewing industry. © 2019 The Institute of Brewing & Distilling     

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.     

食源性细菌关键小分子信号通路研究进展

食源性细菌引起的食品腐败和生物被膜形成是食品科学领域关注的热点。研究表明这些现象与细菌群体感应（quorum sensing,QS）系统和第二信使环二鸟苷酸（cyclic di-guanosine monophosphate,c-di-GMP）系统密切相关,深入研究发现细菌可通过利用胞外自诱导物和胞内c-di-GMP分别感知细胞密度和外界刺激来调控一系列生理活性。鉴于此,本文主要围绕食品腐败和生物被膜形成关联的QS和c-di-GMP这两个系统,阐述食源性细菌关键小分子信号通路,探讨QS和c-di-GMP信号通路之间的调控网络,旨在更好地理解食品体系中细菌引起的腐败和生物被膜形成现象,提供保障食品品质与安全的控制靶点。     

Quorum Sensing Regulation and Inhibition of Exoenzyme Production and Biofilm Formation in the Food Spoilage Bacteria Pseudomonas psychrophila PSPF19

Gram-negative bacteria use the mechanism of acylated homoserine lactone (AHL) mediated quorum-sensing to regulate gene expression in response to population density. The present work aimed to detect signal molecule production and its influence on the production of food spoilage phenotypes such as exoenzyme (lipases and proteases) synthesis and biofilm formation in Pseudomonas psychrophila PSPF19, isolated from freshwater fish stored in refrigerated conditions. The C4-HSL signaling molecule produced by the isolate induced exoenzyme production by twofold and increased attachment and biofilm formation. Further, studies on the effect of a synthetic quorum sensing inhibitor, furanone C-30 on protease and lipase production and biofilm formation, revealed that it inhibited exoenzyme production and bacterial attachment. This study adds to our understanding that quorum sensing plays a role in the low temperature spoilage of foods by psychrotrophic Pseudomonads and quorum sensing inhibitors such as furanones can be developed as new intervention techniques and food preservatives.     

Growth Characteristics and Biofilm Formation of Various Spoilage Bacteria Isolated from Fresh Produce

This study investigated the characteristics of spoilage bacteria isolated from fresh produce including growth at various temperatures, biofilm formation, cell hydrophobicity, and colony spreading. The number of spoilage bacteria present when stored at 35 °C was significantly greater than when stored at lower temperatures, and maximum population size was achieved after 10 h. However, Bacillus pumilus, Dickeya zeae, Pectobacterium carotovorum subsp. Carotovorum Pcc21, and Bacillus pumilus (RDA‐R) did not grow at the storage temperature of 5 °C. The biofilm formation by Clavibacter michiganensis, Acinetobacter calcoaceticus, and A. calcoaceticus (RDA‐R) are higher than other spoilage bacteria. Biofilm formation showed low correlation between hydrophobicity, and no significant correlation with colony spreading. These results might be used for developing safe storage guidelines for fresh produce at various storage temperatures, and could be basic information on the growth characteristics and biofilm formation properties of spoilage bacteria from fresh produce.     

A mixed-species microarray for identification of food spoilage bacilli

Failure of food preservation is frequently caused by thermostable spores of members of the Bacillaceae family, which show a wide spectrum of resistance to cleaning and preservation treatments. We constructed and validated a mixed-species genotyping array for 6 Bacillus species, including Bacillus subtilis, Bacillus licheniformis, Bacillus pumilus, Bacillus sporothermodurans, Bacillus cereus and Bacillus coagulans, and 4 Geobacillus species, including Geobacillus stearothermophilus, Geobacillus thermocatenulatus, Geobacillus toebii and Geobacillus sp., in order to track food spoilage isolates from ingredient to product. The discriminating power of the array was evaluated with sets of 42 reference and 20 test strains. Bacterial isolates contain a within-species-conserved core genome comprising 68-88% of the entire genome and a non-conserved accessory genome comprising 7-22%. The majority of the core genome markers do not hybridise between species, thus they allow for efficient discrimination at the species level. The accessory genome array markers provide high-resolution discrimination at the level of individual isolates from a single species. In conclusion, the reported mixed-species microarray contains discriminating markers that allow rapid and cost-effective typing of Bacillus food spoilage bacteria in a wide variety of food products.     

Formation and dispersal of biofilms in dairy substrates

The formation and dispersion of biofilms in the dairy industry is a problem because it increases cross‐contamination, affecting the shelf life of the products and their safety. The objective of this study was to evaluate the influence of different dairy substrates (cows’ milk and whey protein) on the formation and dispersion of Enterococcus faecalis, Listeria monocytogenes, Staphylococcus aureus and Bacillus cereus in two biofilm systems (mono‐species and multi‐species) on stainless steel at 25 °C. The dominant behaviour of E. faecalis occurred in most of the tests on mono‐species and multi‐species biofilms. A greater dispersion of biofilm cells was observed in skimmed milk.     

Attachment and biofilm formation of Pseudomonas fluorescens PSD4 isolated from a dairy processing line

The effects of different nutrient sources and temperatures on attachment and biofilm formation of Pseudomonas fluorescens PSD4, a dairy isolate, were studied. Initial adherence and attachment capabilities among different strains were studied using microtitre plate assays. Biofilm development was observed using confocal microscopy. Strongly adherent cells were seen in protein rich media. Citrate as a carbon source enhanced biofilm formation. Glucose did not favor biofilm development. Psychrotrophic P. fluorescens PSD4 formed strongly adherent biofilms having high metabolic activities at low temperatures. P. fluorescens PSD4 with spoilage potential was capable of forming strong biofilms in dairy processing environments. Biofilm formation was influenced by nutrient availability and growth conditions. These factors should be considered for design of effective anti-biofilm strategies.     

Residential Bacteria on Surfaces in the Food Industry and Their Implications for Food Safety and Quality

Surface hygiene is commonly measured as a part of the quality system of food processing plants, but as the bacteria present are commonly not identified, their roles for food quality and safety are not known. Here, we review the identity of residential bacteria and characteristics relevant for survival and growth in the food industry along with potential implications for food safety and quality. Sampling after cleaning and disinfection increases the likelihood of targeting residential bacteria. The increasing use of sequencing technologies to identify bacteria has improved knowledge about the bacteria present in food premises. Overall, nonpathogenic Gram‐negative bacteria, especially Pseudomonas spp., followed by Enterobacteriaceae and Acinetobacter spp. dominate on food processing surfaces. Pseudomonas spp. persistence is likely due to growth at low temperatures, biofilm formation, tolerance to biocides, and low growth requirements. Gram‐positive bacteria are most frequently found in dairies and in dry production environments. The residential bacteria may end up in the final products through cross‐contamination and may affect food quality. Such effects can be negative and lead to spoilage, but the bacteria may also contribute positively, as through spontaneous fermentation. Pathogenic bacteria present in food processing environments may interact with residential bacteria, resulting in both inhibitory and stimulatory effects on pathogens in multispecies biofilms. The residential bacterial population, or bacteriota, does not seem to be an important source for the transfer of antibiotic resistance genes to humans, but more knowledge is needed to verify this. If residential bacteria occur in high numbers, they may influence processes such as membrane filtration and corrosion.     

Biofilm − An unrecognised source of spoilage enzymes in dairy products?

Enzymes play an important role in food processing, where they either increase or decrease the value of food commodities. Within the dairy context, undesirable enzymes include indigenous enzymes originating from the cow and microbial enzymes produced by the natural bacteria associated with the cow and its environment. Some of the heat-stable enzymes can remain active after the heat treatments applied during processing and may eventually reduce the quality of the final product. Biofilms may play a role in promoting enzyme production in microorganisms because of the microenvironments created within the biofilm structure. Many studies have been carried out on indigenous and bacterial enzymes that occur in milk, but few studies have looked at the relationship between spoilage enzymes and biofilms. We suggest that bacterial biofilms in dairy manufacture can be a source of dairy spoilage enzymes.     

Incidence and characterisation of aerobic spore‐forming bacteria originating from dairy milk in Tunisia

The purpose of this study was to evaluate the incidence and characterisation of aerobic spore‐forming bacteria originating from dairy milk in Tunisia. The distribution of Bacillus species in raw milk, pasteurised milk and UHT milk were 47.5%, 27.5% and 25%, respectively. Seven Bacillus species, including Bacillus pumilus (10%), Bacillus subtilis (12.5%), Brevibacillus brevis (10%), Bacillus cereus (22.5%), Bacillus sphaericus (7.5%), Bacillus licheniformis (12.5%) and Bacillus sporothermodurans (25%) were identified in different milk samples. Bacillus cereus was predominant in raw and pasteurised milk. Although B. sporothermodurans was the predominant sporogenous micro‐organism in UHT milk, B. cereus, B. sphaericus and B. licheniformis were also present. This study showed that there is a high degree of diversity, both phenotypic and genotypic, among Bacillus isolates from Tunisian milk and the persistence of spoilage risk in UHT milk.     

Characterization of aerobic spore-forming bacteria associated with industrial dairy processing environments and product spoilage

Due to changes in the design of industrial food processing and increasing international trade, highly thermoresistant spore-forming bacteria are an emerging problem in food production. Minimally processed foods and products with extended shelf life, such as milk products, are at special risk for contamination and subsequent product damages, but information about origin and food quality related properties of highly heat-resistant spore-formers is still limited. Therefore, the aim of this study was to determine the biodiversity, heat resistance, and food quality and safety affecting characteristics of aerobic spore-formers in the dairy sector. Thus, a comprehensive panel of strains (n = 467), which originated from dairy processing environments, raw materials and processed foods, was compiled. The set included isolates associated with recent food spoilage cases and product damages as well as isolates not linked to product spoilage. Identification of the isolates by means of Fourier-transform infrared spectroscopy and molecular methods revealed a large biodiversity of spore-formers, especially among the spoilage associated isolates. These could be assigned to 43 species, representing 11 genera, with Bacillus cereus s.l. and Bacillus licheniformis being predominant. A screening for isolates forming thermoresistant spores (TRS, surviving 100 °C, 20 min) showed that about one third of the tested spore-formers was heat-resistant, with Bacillus subtilis and Geobacillus stearothermophilus being the prevalent species. Strains producing highly thermoresistant spores (HTRS, surviving 125 °C, 30 min) were found among mesophilic as well as among thermophilic species. B. subtilis and Bacillus amyloliquefaciens were dominating the group of mesophilic HTRS, while Bacillus smithii and Geobacillus pallidus were dominating the group of thermophilic HTRS. Analysis of spoilage-related enzymes of the TRS isolates showed that mesophilic strains, belonging to the B. subtilis and B. cereus groups, were strongly proteolytic, whereas thermophilic strains displayed generally a low enzymatic activity and thus spoilage potential. Cytotoxicity was only detected in B. cereus, suggesting that the risk of food poisoning by aerobic, thermoresistant spore-formers outside of the B. cereus group is rather low.     

Stress resistance of biofilm and planktonic Lactobacillus plantarum subsp. plantarum JCM 1149

The purpose of this study was to investigate the change in resistance of biofilm and planktonic food spoilage lactic acid bacteria (LAB) to environmental stresses, which strongly inhibit bacterial growth and are important in food preservation or in disinfection. The stress responses of biofilm and planktonic cells of Lactobacillus plantarum subsp. plantarum JCM 1149, which was used as a model spoilage bacterium, in various organic acids (namely, acetic acid, citric acid, lactic acid, and malic acid), ethanol, and sodium hypochlorite, were investigated using survival tests. The bacterial cells in biofilms showed greater resistance to all treatments than the planktonic bacterial cells in either the stationary or logarithmic phase. The planktonic bacterial cells showed reduced resistance to acetic acid after the cell suspension was diluted; however, intriguingly, the bacterial cells in biofilms maintained their resistance to acetic acid even after they were suspended or the cell suspension was diluted. These findings suggested the risk for food spoilage due to LAB derived from biofilms and suspended or diluted in foods, and demonstrated the importance of controlling biofilms of LAB in the food industry.     

Thermophilic bacilli and their importance in dairy processing

The thermophilic bacilli, such as Anoxybacillus flavithermus and Geobacillus spp., are an important group of contaminants in the dairy industry. Although these bacilli are generally not pathogenic, their presence in dairy products is an indicator of poor hygiene and high numbers are unacceptable to customers. In addition, their growth may result in milk product defects caused by the production of acids or enzymes, potentially leading to off-flavours. Dairy thermophiles are usually selected for by the conditions during dairy manufacture. These bacteria are able to grow in sections of dairy manufacturing plants where temperatures reach 40-65 °C. Furthermore, because they are spore formers, they are difficult to eliminate. In addition, they exhibit a wide temperature growth range, exhibit a fast growth rate (generation time of approximately 15-20 min) and tend to readily form biofilms. Many strategies have been tested to remove, prevent and/or delay the formation of thermophilic bacilli biofilms in dairy manufacture, but with limited success. This is, in part, because little is known about the structure and composition of thermophilic bacilli biofilms in general and, more specifically, in milk processing environments. Therefore, new cleaning regimes often do not target the problem optimally. A greater understanding of the structure of thermophilic biofilms within the context of the milk processing environment and their link with spore formation is needed to develop better control measures. This review discusses the characteristics and food spoilage potential, enumeration and identification methods for the thermophilic bacilli, as well as their importance to dairy manufacture, with an emphasis on biofilm development and spore formation.