Identification, enzymatic spoilage characterization and proteolytic activity quantification of Pseudomonas spp. isolated from different foods

Discovery of a temperature-dependent protease spoiling meat from Pseudomonas fragi: Target to myofibrillar and sarcoplasmic proteins rather than collagen

Chilled meat frequently suffered microbial spoilage because bacteria can secrete various proteases that break down the proteins. In this study, Pseudomonas fragi NMC 206 exhibited a temperature-dependent secretion pattern, with the ability to release the specific protease only below 25 °C. It was identified as alkaline protease AprA by LC-MS/MS, with the molecular weight of 50.4 kDa, belonging to the Serralysin family metalloprotease. Its significant potential for meat spoilage in situ resulted in alterations in meat color and sensory evaluation, as well as elevated pH, total volatile basic nitrogen (TVB-N) and the formation of volatile organic compounds (VOCs). The hydrolysis of meat proteins in vitro showed that AprA possessed a considerable proteolysis activity and degradation preferences on meat proteins, especially its ability to degrade myofibrillar and sarcoplasmic proteins, rather than collagen. These observations demonstrated temperatures regulated the secretion of AprA, which was closely related to chilled chicken spoilage caused by bacteria. These will provide a new basis for the preservation of meat products at low temperatures.

Effects of community ecological network construction on physicochemical, microbial, and quality characteristics of inoculated northeast sauerkraut: A new insight in food fermentation processes

The enhancement of the quality of northeast sauerkraut can be achieved by inoculation with lactic acid bacteria. However, a comprehensive ecological understanding of the intricate dynamic processes involved is currently lacking, which could yield valuable insights for regulating sauerkraut fermentation. This study compares spontaneously sauerkrauts with the sauerkrauts inoculated with autochthonous Lactiplantibacillus plantarum SC-MDJ and commercial L. plantarum, respectively. We examine their physicochemical properties, quality characteristics, bacterial community dynamics, and ecological network interactions. Inoculation with L. plantarum leads to reduced bacterial community richness and niche breadth, but an increase in robustness, interactions, and assembly processes. Notably, there appears to be a potential correlation between bacterial community structure and quality characteristics. Particularly, sauerkraut inoculated with L. plantarum SC-MDJ may produce a sourness more quickly, possibly attributed to the enhanced ecological role of L. plantarum SC-MDJ. This study establishes a foundation for the targeted regulation of sauerkraut fermentation.

Improving the bacterial community, flavor, and safety properties of northeastern sauerkraut by inoculating autochthonous Levilactobacillus brevis

The effect of Levilactobacillus brevis as a starter in northeastern sauerkraut fermentation is still unknown, and further evaluation is worthwhile. Hence, this study aimed to evaluate the effect of autochthonous L. brevis inoculation on the bacterial community succession and formation of flavor and harmful substances in sauerkrauts. Inoculation with L. brevis lowered the pH and increased the total acid content of sauerkrauts (P < 0.05). The nitrite content of the inoculated sauerkraut was significantly lower than that of control (P < 0.05). Moreover, the spoilage bacteria of the inoculated sauerkraut were decreased and nitrogen metabolism was improved. The contents of aldehydes, alcohols, esters, acids, and alkanes increased significantly (P < 0.05), and the sensory attributes such as aroma, sourness, and gloss were also improved. L. brevis was positively and negatively correlated with flavor metabolites and nitrite, respectively, which proved to be a potential starter culture to manufacture sauerkraut.

An inhibitor of the adaptability of Pseudomonas fluorescens in a high-salt environment. Phenomenon and mechanism of inhibition

Pseudomonas fluorescens is a spoilage bacterium in food that has the ability to maintain growth and reproduction in high-salt environments. It acts as a defence mechanism through the exclusion of ions and the formation of biofilms. Hence, disrupting this defence mechanism may be a good way to control food spoilage. In this study, a specific flavonoid small molecule baicalin was found, which was able to dismantle the defence mechanism of the bacteria at a lower concentration (400 μM) of treatment. In synergy with salt, baicalin showed a significant inhibitory effect on the growth, c-di-gmp synthetics and biofilm formation of Pseudomonas fluorescens Pf08. Through transcriptomics, we also found that baicalein interfered with bacterial transport and polysaccharide production functions. Through molecular docking and QPCR, we found that baicalin is able to binding with the RpoS protein through hydrogen bonding and thus interfere with its function.

Metabarcoding approach to identify bacterial community profiling related to nosocomial infection and bacterial trafficking-routes in hospital environments

Nosocomial infections (NIs) appear in patients under medical care in the hospital. The surveillance of the bacterial communities employing high-resolution 16S rRNA profiling, known as metabarcoding, represents a reliable method to establish factors that may influence the composition of the bacterial population during NIs. The present study aimed to utilize high-resolution 16S rRNA profiling to identify high bacterial diversity by analyzing 11 inside and 10 outside environments from the General Hospital of Ribeirão Preto Medical School, Brazil. Our results identified a high bacterial diversity, and among these, the most abundant bacterial genera linked to NIs were Cutibacterium, Streptococcus, Staphylococcus, and Corynebacterium. A Acinetobacter was detected in cafeterias, bus stops, and adult and pediatric intensive care units (ICUs). Data suggest an association between transport and alimentation areas proximal to the hospital ICU environment. Interestingly, the correlation and clusterization analysis showed the potential of the external areas to directly influence the ICU pediatric department microbial community, including the outpatient's clinic, visitor halls, patient reception, and the closest cafeterias. Our results demonstrate that high-resolution 16S rRNA profiling is a robust and reliable tool for bacterial genomic surveillance. In addition, the metabarcoding approach might help elaborate decontamination policies, and consequently reduce NIs.

Identification, proteolytic activity quantification and biofilm-forming characterization of Gram-positive, proteolytic, psychrotrophic bacteria isolated from cold raw milk

Psychrotrophic bacteria of raw milk face the dairy industry with significant spoilage and technological problems due to their ability to produce heat-resistant enzymes and biofilms. Despite extensive information about Gram-negative psychrotrophic bacteria in milk, little is known about Gram-positive psychrotrophic bacteria in milk, and their proteolytic activity and biofilm-forming characteristics. In the present study, Gram-positive, proteolytic, psychrotrophic bacteria of cold raw milk were identified, and their proteolytic activity and biofilm-forming capacity were quantified. In total, 12 genera and 22 species were represented among the bacterial isolates, however 50% belonged to three genera, namely Staphylococcus (19.4%), Bacillus (16.7%), and Enterococcus (13.9%). Different levels of proteolytic activity were detected in the identified isolates, even among the strains belonging to the same species. In addition, proteolytic activity was significantly higher at 25°C than at 7°C for all isolates. The crystal violet staining assay in polystyrene microtitre plates revealed a high level of variation in the biofilm-forming capacity at 7°C. After 72 hours of incubation, 11.1% of the strains did not produce a biofilm, while 27.8%, 52.8%, and 8.3% produced low, moderate, and high amounts of biofilm on polystyrene, respectively. The psychrotrophic bacteria were also able to produce biofilms on the surface of stainless steel coupons in ultra-high temperature milk after 72 h of incubation at 7°C; the number of attached cells ranged from 1.34 to 5.11 log cfu/cm2. These results expand the knowledge related to the proteolytic activity and biofilm-forming capacity of Gram-positive psychrotrophic milk bacteria.

Bacterial Changes in Boiled Crayfish between Different Storage Periods and Characterizations of the Specific Spoilage Bacteria

This study investigated changes in the microbial compositions of crayfish tails during storage at 4 °C (for 0-12 days) as measured using high-throughput sequencing (HTS). The specific spoilage organisms (SSOs) in the crayfish tails were isolated using culture-dependent cultivation methods, and they were identified by 16S rRNA and characterized for their enzymatic spoilage potentials (e.g., protease, lipase, phospholipase, and amylase). The spoilage abilities of the selected strains in the crayfish tails were assessed by inoculating them into real food. Moreover, the microbial growth and the volatile basic nitrogen (TVB-N) changes were monitored during the storage period. The results from the HTS showed that the dominant genus of shrimp tails evolved from Streptococcus (D0) to Pseudomonas (D4) and, finally, to Paenisporosarcina (D12) during storage. Seven bacterial species (Acinetobacter lwoffii, Aeromonas veronii, Kurthia gibsonii, Pseudomonas sp., Exiguobacterium aurantiacum, Lelliottia amnigena, and Citrobacter freundii) were screened from the spoiled shrimp tails by the culture-dependent method, among which Aeromonas veronii had the strongest spoilage ability.

Proteolytic activity and heat resistance of the protease AprX from Pseudomonas in relation to genotypic characteristics

AprX is an alkaline metalloprotease produced by Pseudomonas spp. and encoded by its initial gene of the aprX-lipA operon. The intrinsic diversity among Pseudomonas spp. regarding their proteolytic activity is the main challenge for the development of accurate methods for spoilage prediction of ultra-high temperature (UHT) treated milk in the dairy industry. In the present study, 56 Pseudomonas strains were characterized by assessing their proteolytic activity in milk before and after lab-scale UHT treatment. From these, 24 strains were selected based on their proteolytic activity for whole genome sequencing (WGS) to identify common genotypic characteristics that correlated with the observed variations in proteolytic activity. Four groups (A1, A2, B and N) were determined based on operon aprX-lipA sequence similarities. These alignment groups were observed to significantly influence the proteolytic activity of the strains, with an average proteolytic activity of A1 > A2 > B > N. The lab-scale UHT treatment did not significantly influence their proteolytic activity, indicating a high thermal stability of proteases among strains. Amino acid sequence variation of biologically-relevant motifs in the AprX sequence, namely the Zn²⁺-binding motif at the catalytic domain and the C-terminal type I secretion signaling mechanism, were found to be highly conserved within alignment groups. These motifs could serve as future potential genetic biomarkers for determination of alignment groups and thereby strain spoilage potential.

High biofilm-forming Pseudomonas strains isolated from poultry slaughterhouse surfaces: Their importance in the persistence of Salmonella enteritidis in slaughterhouses

The surfaces of poultry slaughterhouse equipment are significant sources of contamination with Pseudomonas strains, which leads to spoilage of poultry meat during subsequent refrigerated storage. In this study, Pseudomonas strains with high biofilm-forming ability were isolated from different surfaces of the poultry slaughterhouse equipment, identified based on molecular data, and characterized their biofilm-forming ability. After 24 h of incubation at 25 °C, 54 out of 58 Pseudomonas strains produced biofilm in vitro on polystyrene microplates. Seven isolates with high-ability to produce biofilm were identified as P. fragi (three strains), P. fluorescens (two strains), P. lundensis and P. cedrina. Despite their differences, these strains produced high amounts of biofilm in pure- and dual-species cultures with S. enteritidis on stainless steel surfaces. However, their ability to produce dual-species biofilms with S. enteritidis depends on whether S. enteritidis form the biofilm simultaneously with the Pseudomonas strains or whether Pseudomonas strains have already formed a biofilm. In concurrent inoculation, S. enteritidis participated in biofilm formation with all seven Pseudomonas strains with varying percent contributions. However, in delayed inoculation, S. enteritidis did not contribute in the biofilm formed by P. lundensis R26, P. fragi R39, and P. fluorescens R47. In addition to highlighting the complexity of bacterial interactions associated with Pseudomonas strains, these results showed that Pseudomonas strains can be implicated in Salmonella persistence in poultry slaughterhouses.

Virulence factors of Gram-negative bacteria from free-ranging Amazon river dolphins (Inia geoffrensis)

Freshwater cetaceans play a significant role as sentinel animals, providing important data on animal species and aquatic ecosystem health. They also may serve as potential reservoirs of emerging pathogens and host virulence genes in their microbiota. In this study, we evaluated virulence factors produced by Gram-negative bacteria recovered from individuals belonging to two populations of free-ranging Amazon river dolphins (Inia geoffrensis). A total of 132 isolates recovered from the oral cavity, blowhole, genital opening and rectum of 21 river dolphins, 13 from Negro River and 8 from Tapajós River, Brazil, were evaluated for the production of virulence factors, such as biofilms and exoproducts (proteases, hemolysins and siderophores), in planktonic and biofilm forms. In planktonic form, 81.1% (107/132) of the tested bacteria of free-ranging Amazon river dolphins were able to produce virulence factors, with 44/132 (33.4%), 65/132 (49,2%) and 54/132 (40,9%) positive for protease, hemolysin and siderophore production, respectively. Overall, 57/132 (43.2%) of the isolates produced biofilms and, under this form of growth, 66/132 (50%), 88/132 (66.7%) and 80/132 (60.6%) of the isolates were positive for protease, hemolysin and siderophore production. In general, the isolates showed a higher release of exoproducts in biofilm than in planktonic form (P < 0.001). The present findings show that Amazon river dolphins harbor potentially pathogenic bacteria in their microbiota, highlighting the importance of monitoring the micro-organisms from wild animals, as they may emerge as pathogens for humans and other animals.

Prevalence and Antibiotic Resistance Phenotypes of Pseudomonas spp. in Fresh Fish Fillets

In fresh fish products, excessive loads of Pseudomonas can lead to their rapid spoilage. It is wise for Food Business Operators (FBOs) to consider its presence both in whole and prepared fish products. With the current study, we aimed to quantify Pseudomonas spp. in fresh fillets of Salmo salar, Gadus morhua and Pleuronectes platessa. For all three fish species, we detected loads of presumptive Pseudomonas no lower than 10⁴-10⁵ cfu/g in more than 50% of the samples. We isolated 55 strains of presumptive Pseudomonas and carried out their biochemical identification; 67.27% of the isolates were actually Pseudomonas. These data confirm that fresh fish fillets are normally contaminated with Pseudomonas spp. and the FBOs should add it as a "process hygiene criterion" according to EC Regulation n.2073/2005. Furthermore, in food hygiene, it is worth evaluating the prevalence of antimicrobial resistance. A total of 37 Pseudomonas strains were tested against 15 antimicrobials, and they all were identified as being resistant to at least one antimicrobial, mainly penicillin G, ampicillin, amoxicillin, tetracycline, erythromycin, vancomycin, clindamycin and trimethoprim. As many as 76.47% of Pseudomonas fluorescens isolates were multi-drug resistant. Our results confirm that Pseudomonas is becoming increasingly resistant to antimicrobials and thus should be continuously monitored in foods.

Quality and Microbiological Safety of Poultry Meat Marinated with the Use of Apple and Lemon Juice

The aim of the study was to evaluate the use of apple juice for the marinating of poultry meat and its effect on the technological as well as sensory characteristics and microbiological safety of the raw product after heat treatment. Broiler chicken breast muscles were marinated for 12 h in apple juice (n = 30), a mixture of apple and lemon juice (n = 30) and compared with those in lemon juice (n = 30). The control group (n = 30) consisted of unmarinated breast muscles. Following the evaluation of the technological parameters (pH, L*, a*, b* colour, cutting force, cooking losses) quantitative and qualitative microbiological evaluations were performed on the raw and roasted products. The microbiological parameters were determined as total Mesophilic aerobic microorganisms, Enterobacteriaceae family, and Pseudomonas count. The bacterial identification was performed using a matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry. The marinating resulted in lower pH value, but increased tenderness of raw and roasted products. Marinating chicken meat in both apple and lemon juices, including their mixtures and in the control sample, resulted in increased yellow saturation (b*). The highest flavour desirability and overall desirability were obtained in products marinated using a mixture of apple and lemon juice, while the most desirable aroma was obtained from products marinated with apple juice. A significant antimicrobial effect was observed in marinated meat products compared to unmarinated, irrespective of the type of marinade used. The lowest microbial reduction was observed in the roasted products. Apple juice can be used as a meat marinade because it promotes interesting sensory properties and improves the microbiological stability of poultry meat while maintaining the product's good technological characteristics. It makes a good combination with the addition of lemon juice.

Development of a real-time loop-mediated isothermal amplification method for monitoring Pseudomonas lurida in raw milk throughout the year of pasture

Introduction

The psychrophilic bacterium Pseudomonas lurida (P. lurida) and its thermostable alkaline proteases can seriously damage raw milk quality.

Methods

In this study, specific primers were designed for P. lurida's gyrB and aprX genes, and a real-time loop-mediated isothermal amplification (RealAmp) rapid detection method was developed for the early monitoring of P. lurida and its proteases in raw milk. A phylogenetic tree of the gyrB and aprX genes of P. lurida was constructed to analyze the homology of the design sequence of the RealAmp primer. The DNA of 2 strains of P. lurida and 44 strains of non-P. lurida were detected via RealAmp to analyze the specificity of the primer.

Results

It was found that aprX-positive proteases were produced by P. lurida-positive strains only when Pseudomonas fluorescens was negative. The dissociation temperatures of gyrB and aprX in the RealAmp-amplified products were approximately 85.0°C and 90.0°C, respectively. Moreover, DNA was detected through a 10-fold dilution of P. lurida in a pure bacterial solution and artificially contaminated skimmed milk. The limit of detection of P. lurida DNA copy number in the pure bacterial solution was 8.6 copies/μL and that in the 10% skimmed milk was 5.5 copies/μL. Further, 144 raw milk samples throughout the year from three farms in Hebei province were analyzed using RealAmp. The highest detection rate of P. lurida was 56% in the first and third quarters, and that of proteases was 36% in the second quarter. The detection rates of P. lurida and its proteases were the highest in samples collected from pasture 2 (52 and 46%, respectively), and the ability of P. lurida to produce proteases reached 88%.

Discussion

In conclusion, RealAmp established an early and rapid method for the detection of P. lurida and its proteases in raw milk samples, allowing the identification and control of contamination sources in a timely manner to ensure the quality of milk and dairy products.

Preparation, Characterization, In Vitro Release, and Antibacterial Activity of Oregano Essential Oil Chitosan Nanoparticles

Essential oils have unique functional properties, but their environmental sensitivity and poor water solubility limit their applications. Therefore, we encapsulated oregano essential oil (OEO) in chitosan nanoparticles (CSNPs) and used tripolyphosphate (TPP) as a cross-linking agent to produce oregano essential oil chitosan nanoparticles (OEO-CSNPs). The optimized conditions obtained using the Box-Behnken design were: a chitosan concentration of 1.63 mg/mL, TPP concentration of 1.27 mg/mL, and OEO concentration of 0.30%. The OEO-CSNPs had a particle size of 182.77 ± 4.83 nm, a polydispersity index (PDI) of 0.26 ± 0.01, a zeta potential of 40.53 ± 0.86 mV, and an encapsulation efficiency of 92.90%. The success of OEO encapsulation was confirmed by Fourier transform infrared spectroscopy (FT-IR) and thermogravimetric analysis (TGA). The scanning electron microscope (SEM) analysis showed that the OEO-CSNPs had a regular distribution and spherical shape. The in vitro release profile at pH = 7.4 showed an initial burst release followed by a sustained release of OEO. The antibacterial activity of OEO before and after encapsulation was measured using the agar disk diffusion method. In conclusion, OEO can be used as an antibacterial agent in future food processing and packaging applications because of its high biological activity and excellent stability when encapsulated.

Diversity and proteolytic activity of Pseudomonas species isolated from raw cow milk samples across China

Pseudomonas spp. are common microorganisms from cold-storage raw milk, and protease secreted by Pseudomonas spp. can cause the deterioration of stored milk. However, analyses of Pseudomonas spp. diversity and proteolytic activity in raw milk from different regions of China have not been extensively examined. With this aim, the diversity and proteolytic activity of Pseudomonas isolated from 25 raw cow milk samples from Inner Mongolia, Heilongjiang, Gansu, Henan, Anhui, Jiangsu, Chongqing and Hunan of China in different seasons were evaluated by PCR targeting 16S rDNA and rpoD, as well as TNBS method, respectively. A total of 116 Pseudomonas isolates from 25 raw cow milk samples were identified at the species level, including P. fluorescens, P. veronii, P. psychrophila, P. lundensis, P. lactis, P. azotoformans, P. granadensis, P. lurida, P. rhizosphaerae, P. rhodesiae and P. extremorientalis. P. fluorescens accounted for 75.8% of the total. Of all 116 Pseudomonas isolates, 68.9% of them displayed proteolytic activity at 4 °C, 81.9% at 10 °C and 85.3% at 25 °C, respectively. The aprX gene encoded a secreted and heat-resistant metalloprotease that was present in 60.3% of the Pseudomonas isolates tested. The proteases showed residual activity ranged from 73 ± 4% to 84 ± 7% residual activity after the heat treatment at 72 °C for 15 s and 62 ± 3% to 74 ± 2% after the heat treatment at 132 °C for 4 s. This is the first report to compare Pseudomonas spp. diversity and proteolytic activity at species levels in raw milk from different regions of China. The results of this study provide valuable data about the diversity and spoilage potential of Pseudomonas species in raw milk and the thermal resistance of the proteases. Therefore, these findings provide a reference for the importance to prevent Pseudomonas spp. contamination of raw cow milk to ensure the quality and safety of milk and dairy products.

Phytochemical Profile and Antioxidant, Antiproliferative, and Antimicrobial Properties of Rubus idaeus Seed Powder

In the context of the contemporary research on sustainable development and circular economy, the quest for effective strategies aimed at revaluation of waste and by-products generated in industrial and agricultural production becomes important. In this work, an ethanolic extract from red raspberry (Rubus idaeus) seed waste (WRSP) was evaluated for its phytochemical composition and functional properties in term of antioxidative, antiproliferative, and antimicrobial activities. Chemical composition of the extract was determined by both HPLC-ESI-MS/MS and spectrophotometric methods. Phytochemical analysis revealed that flavan-3-ols and flavonols were the major phenolic compounds contained in WRSP. The extract demonstrated very high radical-scavenging (4.86 ± 0.06 µmol TE/DW) and antioxidant activity in a cell-based model (0.178 ± 0.03 mg DW/mL cell medium). The WRSP extract also exhibited antiproliferative activity against three different epithelial cancer cell lines (MCF-7, HepG2, and HeLa cells) in a dose-dependent manner. Finally, microbiological assays showed the absence of colonies of bacteria and microscopic fungi (yeasts and molds) and revealed that the WRSP extract has a large inhibition spectrum against spoilage and pathogenic bacteria, without inhibitory activity against pro-technological bacteria. In conclusion, the obtained results show that WRSP is a rich source of phytochemical compounds exerting interesting biological activities. For these reasons WRSP could find applications in the nutritional, nutraceutical, and pharmacological fields.

Pseudomonas species prevalence, protein analysis, and antibiotic resistance: an evolving public health challenge

Psychrotrophic Pseudomonas is one of the significant microbes that lead to putrefaction in chilled meat. One of the biggest problems in the detection of Pseudomonas is that several species are seemingly identical. Currently, antibiotic resistance is one of the most significant challenges facing the world's health and food security. Therefore, this study was designed to apply an accurate technique for eliminating the identification discrepancy of Pseudomonas species and to study their resistance against various antimicrobials. A total of 320 chicken meat specimens were cultivated, and the isolated bacteria’ were phenotypically recognized. Protein analysis was carried out for cultured isolates via Microflex LT. The resistance of Pseudomonas isolates was recorded through Vitek® 2 AST-GN83 cards. Overall, 69 samples were identified as Pseudomonas spp. and included 18 Pseudomonas lundensis (P. lundensis), 16 Pseudomonas fragi (P. fragi), 13 Pseudomonas oryzihabitans (P. oryzihabitans), 10 Pseudomonas stutzeri (P. stutzeri), 5 Pseudomonas fluorescens (P. fluorescens), 4 Pseudomonas putida (P. putida), and 3 Pseudomonas aeruginosa (P. aeruginosa) isolates. Microflex LT identified all Pseudomonas isolates (100%) correctly with a score value ≥ 2.00. PCA positively discriminated the identified isolates into various groups. The antimicrobial resistance levels against Pseudomonas isolates were 81.16% for nitrofurantoin, 71% for ampicillin and ampicillin/sulbactam, 65.22% for cefuroxime and ceftriaxone, 55% for aztreonam, and 49.28% for ciprofloxacin. The susceptibilities were 100% for cefotaxime, 98.55% for ceftazidime, 94.20% for each piperacillin/tazobactam and cefepime, 91.3% for cefazolin. In conclusion, chicken meat was found to be contaminated with different Pseudomonas spp., with high incidence rates of P. lundensis. Microflex LT is a potent tool for distinguishing Pseudomonads at the species level.

Single Molecule Real-Time Sequencing and Traditional Cultivation Techniques Reveal Complex Community Structures and Regional Variations of Psychrotrophic Bacteria in Raw Milk

In this study, we investigated the species composition and diversity of psychrotrophic bacteria in raw milk from Heilongjiang, Inner Mongolia, Gansu, Henan, Anhui, Jiangsu, Chongqing, and Hunan provinces in China using traditional cultivation and PacBio Single Molecule Real-Time sequencing methods. The isolated psychrotrophic bacteria were highly diverse, which composed of 21 genera and 59 species. Pseudomonas accounted for 58.9% of the total genera while Stenotrophomonas and Enterococcus were also highly represented (above 5.0%). In particular, P. azotoformans occurred at a level of 16.9% and P. paralactis, P. lactis, E. faecalis, and P. marginalis were present in relatively high proportions (above 4.0%). Regional differences were found significantly among the test regions except samples from Heilongjiang and Inner Mongolia were similar. Additionally, differences were observed between days in Henan, Anhui, and Jiangsu samples. Therefore, control strategies must be implemented on regional and season basis.

Enhanced antibacterial efficacy and mechanism of octyl gallate/beta-cyclodextrins against Pseudomonas fluorescens and Vibrio parahaemolyticus and incorporated electrospun nanofibers for Chinese giant salamander fillets preservation

A series of alkyl gallates were evaluated for the antibacterial activity against two common Gram-negative foodborne bacteria (Pseudomonas fluorescens and Vibrio parahaemolyticus) associated with seafood. The length of the alkyl chain plays a pivotal role in eliciting their antibacterial activities and octyl gallate (OG) exerted an excellent inhibitory efficacy. To extend the aqueous solubility, stability, and bactericidal properties of octyl gallate (OG), an inclusion complex between OG and β-cyclodextrin (βCD), OG/βCD, was prepared and identified with various methods including X-ray diffraction (XRD), differential scanning calorimeter (DSC) and Fourier transform infrared spectroscopy (FTIR). Furthermore, the enhanced inhibitory effect and potential antibacterial mechanism of OG/βCD against two Gram-negative and Gram-positive foodborne bacteria were comprehensively investigated. The results show that OG/βCD could function against bacteria through effectively damaging the membrane, permeating into cells, and then disturbing the activity of the respiratory electron transport chain to cause the production of high-level intracellular hydroxyl radicals. Moreover, the reinforced OG/βCD-incorporated polylactic acid (PLA) nanofibers were fabricated using the electrospinning technique as food packaging to extend the Chinese giant salamander fillet's shelf life at 4 °C. This research highlights the antibacterial effectiveness of OG/βCD in aqueous media, which can be used as a safe multi-functionalized food additive combined with the benefits of electrospun nanofibers to extend the Chinese giant salamander fillets shelf life by 15 d at 4 °C.

The response of bacterial communities to carbon dioxide in high-oxygen modified atmosphere packaged beef steaks during chilled storage

The objective of this study was to establish the effect of CO₂ on the bacterial community in beef steaks held under both high-oxygen modified atmosphere packaging (HiOx-MAP) types (CO₂ treated MAP: 50% O₂/40% CO₂/10% N₂; control MAP: 50% O₂/50% N₂). Steaks were stored at 2 °C for 20 days. Gas composition, meat color, pH values, total volatile basic nitrogen values, total viable counts (TVC) and microbial community dynamics were monitored. Compared to the control MAP, the high level of CO₂ in the contrast MAP significantly delayed bacterial growth, resulting in a bright red color as well as extending the shelf-life to over 20 days. The microbial diversity decreased with prolonged storage in both MAP types, but it was more complex in high-CO₂ treated MAP steaks. When TVC values approached the shelf-life threshold for the control MAP, Pseudomonas and Brochothrix were the predominant bacteria, while Pseudomonas and Serratia under the CO₂ containing MAP were at a lower abundance than under the control MAP. The dominant Pseudomonas species causing spoilage in the control MAP steaks was P. fragi, and this species was inhibited significantly by CO₂, followed by P. weihenstephanensis. Inversely, P. versuta instead of P. fragi became the dominant Pseudomonas species under the CO₂ treated MAP. Overall, the application of CO₂ in HiOx-MAP influenced microbiota succession, which played an important role in retaining beef quality.

Recent Advances in the Mechanisms and Regulation of QS in Dairy Spoilage by Pseudomonas spp

Food spoilage is a serious issue dramatically impacting the worldwide need to counteract food insecurity. Despite the very expensive application of low temperatures, the proper conservation of fresh dairy products is continuously threatened at different stages of production and commercialization by psychrotrophic populations mainly belonging to the Pseudomonas genus. These bacteria cause discolouration, loss of structure, and off-flavours, with fatal implications on the quality and shelf-life of products. While the effects of pseudomonad decay have been widely reported, the mechanisms responsible for the activation and regulation of spoilage pathways are still poorly explored. Recently, molecule signals and regulators involved in quorum sensing (QS), such as homoserine lactones, the luxR/luxI system, hdtS, and psoR, have been detected in spoiled products and bacterial spoiler species; this evidence suggests the role of bacterial cross talk in dairy spoilage and paves the way towards the search for novel preservation strategies based on QS inhibition. The aim of this review was to investigate the advancements achieved by the application of omic approaches in deciphering the molecular mechanisms controlled by QS systems in pseudomonads, by focusing on the regulators and metabolic pathways responsible for spoilage of fresh dairy products. In addition, due the ability of pseudomonads to quickly spread in the environment as biofilm communities, which may also include pathogenic and multidrug-resistant (MDR) species, the risk derived from the gaps in clearly defined and regulated sanitization actions is underlined.

Ultra-efficient antimicrobial photodynamic inactivation system based on blue light and octyl gallate for ablation of planktonic bacteria and biofilms of Pseudomonas fluorescens

Pseudomonas fluorescens is a Gram-negative spoilage bacterium and dense biofilm producer, causing food spoilage and persistent contamination. Here, we report an ultra-efficient photodynamic inactivation (PDI) system based on blue light (BL) and octyl gallate (OG) to eradicate bacteria and biofilms of P. fluorescens. OG-mediated PDI could lead to a > 5-Log reduction of viable cell counts within 15 min for P. fluorescens. The activity is exerted through rapid penetration of OG towards the cells with the generation of a high-level toxic reactive oxygen species triggered by BL irradiation. Moreover, OG plus BL irradiation can efficiently not only prevent the formation of biofilms but also scavenge the existing biofilms. Additionally, it was shown that the combination of OG/poly(lactic acid) electrospun nanofibers and BL have great potential as antimicrobial packagings for maintaining the freshness of the salamander storge. These prove that OG-mediated PDI can provide a superior platform for eradicating bacteria and biofilm.

Effect of grape pomace from red cultivar 'Nero d'Avola' on the microbiological, physicochemical, phenolic profile and sensory aspects of ovine Vastedda-like stretched cheese

AIMS

The purpose of this study was to functionalize an ovine stretched cheese belonging to 'Vastedda' typology with red grape pomace powder (GPP) of Nero d'Avola cultivar and to characterize the microbiological, physicochemical, phenolic profile and sensory characteristics of the final cheeses.

METHODS AND RESULTS

Before cheeses production, GPP was characterized for its microbiological profile, antibacterial activity and polyphenolic content. No colonies of bacteria and yeasts were detected in the GPP. GPP showed a large inhibition spectrum against spoilage and pathogenic bacteria. Three classes of polyphenolic compounds belonging to flavan-3-ols, flavonol and phenolic acids were identified. Two cheeses [0 and 1% (w w^-1 ) of GPP] were produced with pasteurized ewe's milk and commercial starter cultures. Plate counts and randomly amplified polymorphic DNA analysis demonstrated the ability of the starter strains to drive the fermentation process in the presence of GPP. GPP enrichment resulted in an increase of protein, phenolic compounds, sensory traits and reduced fat.

CONCLUSIONS

GPP addition to cheese represents an optimal strategy for the valorization of winemaking by-products and to obtain polyphenol-enriched cheese.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study allowed to achieve an ovine cheese with specific physicochemical, nutraceutical and sensorial characteristics able to enlarge the functional dairy product portfolio.

Heterogeneity in biofilm formation and identification of biomarkers of strong biofilm formation among field isolates of Pseudomonas spp

The biofilm formation ability of a collection of thirty-three Pseudomonas spp. isolates from food processing facilities was investigated in order to find biomarkers of strong biofilm production, a characteristic that can determine persistence in food processing environments. The strains were classified according to the colony pigmentation on solid media as green, brown or not pigmented. The biofilm production on stainless steel and polystyrene was assessed by spectrometric determination of the fixed crystal violet, and the biofilm formed on glass, through confocal laser scanning microscopy. Besides, pyoverdine production, catalase activity, RpoS status and cellular hydrophobicity were also monitored. A significantly higher biofilm production level on stainless steel and polystyrene was observed for green-pigmented strains as compared to brown or not pigmented strains. The influence of iron availability on biofilm formation on stainless steel was studied through the addition of the iron scavenger 2,2-bipyridine resulting in a decrease of 40 % in biofilm formation for the not pigmented strains. For most of the potential biomarkers studied (i.e., pyoverdine production, catalase activity, cellular hydrophobicity), the phenotypic heterogeneity observed among strains was mainly dependent on the Pseudomonas species and no strong associations with the biofilm formation capacity were detected. However, the green colony pigmentation on solid media showed good potential as a biomarker of strong biofilm formation on stainless steel and polystyrene both in P. aeruginosa and Pseudomonas spp.

Together Is Better: The Rumen Microbial Community as Biological Toolbox for Degradation of Synthetic Polyesters

Identfication of plastics degradation and microbial community analysis of Rumen.

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Microbiota of Chicken Breast and Thigh Fillets Stored under Different Refrigeration Temperatures Assessed by Next-Generation Sequencing

Chicken is one of the most widely consumed meats worldwide. The exploration of the bacterial diversity of chicken meat may provide new insights into the chicken-associated microbiome that will lead to moderation of food spoilage or safety. This study was undertaken to explore the bacterial communities of chicken breast and thigh fillets stored at refrigeration (0 °C and 5 °C) and slightly abuse (10 °C) temperatures for 5 days through conventional cultural methods along with next-generation sequencing (NGS) analysis. Total viable counts (TVC), Brochothrix thermosphacta, Pseudomonas spp., and lactic acid bacteria (LAB) were enumerated, while the bacterial communities were mapped through 16S rRNA gene amplicon sequencing. Chicken breast and thigh fillets possessed a complex bacterial structure that incorporated a total of >200 Operational Taxonomic Units (OTUs) at the genus level. The core microbiota of fresh samples consisted of Acinetobacter, Brochothrix, Flavobacterium, Pseudomonas, Psychrobacter, and Vibrionaceae (family). These genera persisted until the end of storage in >80% of samples, except Psychrobacter and Flavobacterium, while Photobacterium was also identified. Hierarchical clustering showed a distinction of samples based on storage time and chicken part. Conventional plate counting with growth media commonly used in spoilage studies did not always correspond to the microbial community profiles derived from NGS analysis, especially in Pseudomonas, Acinetobacter, Photobacterium, and Vibrionaceae. Results of the present study highlight Photobacterium and Vibrionaceae, in general, as potent chicken meat spoilers and suggest the necessity to combine classical microbiological methods along with NGS technologies to characterize chicken meat spoilage microbiota.

Effect of honeycomb, granular, and powder activated carbon additives on continuous lactic acid fermentation of complex food waste with mixed inoculation

To accelerate and stabilize lactic acid fermentation from food waste, three types of activated carbon, including honeycomb activated carbon, granular activated carbon, and powder activated carbon, were tested as additives in continuous food waste fermentation processes. The results showed that carbohydrate was the primary substrate for lactic acid production, but its conversion reached a high, stable level after a long period of microbial acclimation in the control system. Activated carbon, especially honeycomb activated carbon accelerated the stabilization of lactic acid fermentation and enhanced the tolerance of fermentation systems to a hostile and fluctuating environment. The addition of activated carbon increased the oxidation-reduction potential to approximately 100 mV and altered the microbial communities. Homolactic fermentation bacteria were dominant in all the systems, and the honeycomb activated carbon addition stimulated the growth of unclassified Lactobacillus and immobilized Lactobacillus panis with strong carbohydrate metabolism. In addition, powder activated carbon enhanced the degradation of protein due to the multiplying Pseudomonas. At the stable stage, the organic conversion rates were close in the control system and the systems with the activated carbon addition, and the lactic acid concentrations in these systems remained at 8000-10,000 mg/L. Considering the cost of the additives, honeycomb activated carbon is a good choice to stabilize lactic acid production from food waste.

Breast milk contains probiotics with anti-infantile diarrhoea effects that may protect infants as they change to solid foods

Infants often experience complementary food-induced diarrhoea (CFID), which occurs when infants switch from breast milk to solid foods. The relative abundances of Prevotella and Rothia were higher in stools of infants with CFID, while the relative abundances of Enterococcus and Escherichia were higher in healthy infants. The abundance of Lactobacillus spp. normally found in breast milk fed to infants with CFID was significantly reduced, and Enterococcus spp. were less abundant when diarrhoea occurred. Furthermore, Lactobacillus and Enterococcus were present as shared bacteria in both mother and infant, and they were considered potential anti-CFID probiotics as their relative abundances in breast milk were negatively correlated to infant CFID. Kyoto encyclopedia of genes and genomes (KEGG) functional analysis showed that the function of amino acid metabolism differed between infants with CFID and healthy infants. Therefore, CFID might be related to the decomposition of proteins in food supplements. The screening revealed seven hydrolytic casein and five hydrolytic casein and rice protein isolates from 320 suspected Lactobacillus and Enterococcus isolates. The animal experiments demonstrated that a mixture of five isolates effectively hydrolysed the casein and rice protein and prevented diarrhoea in young rats. Thus, the occurrence of CFID was found to be closely related to the intestinal and breast milk microbiota, and bacteria that could assist in the digestion of cereal proteins were involved in CFID.

Pseudomonas kielensis sp. nov. and Pseudomonas baltica sp. nov., isolated from raw milk in Germany

In this study, nine Gram-negative, motile and rod-shaped bacteria were isolated during a Germany-wide investigation of raw milk microbiota. The strains could be differentiated from their closest relatives by phenotypic and chemotaxonomic characterization and average nucleotide identity (ANIb) values calculated from draft genome assemblies. Strains MBT-1^T, MBT-8, MBT-9, MBT-10, MBT-11 and MBT-12 were related to the Pseudomonas chlororaphis subgroup. Isolates MBT-2^T, MBT-13 and MBT-14 were closely related to Pseudomonas rhizosphaerae DSM 16299^T with an ANIb of 88.2 % and a genome-to-genome distance result of 36.0 %. The G+C content of the DNA of strains MBT-1^T and MBT-2^T was 60.84 and 62.48 mol%, respectively. The major fatty acids were C_16 : 1 ω7c (summed feature 3), C_16 : 0 and C_18 : 1 ω7c (summed feature 8). The strains were catalase-positive, while production of urease, β-galactosidase and indole were negative. Growth occurred at 4-30 °C and at pH values of pH 6.0-8.0. Based on these results, we conclude that the strains belong to two novel species, for which the names Pseudomonas kielensis sp. nov. and Pseudomonas baltica sp. nov. are proposed. The type strains are MBT-1^T (=DSM 111668^T= LMG 31954^T) and MBT-2^T (=DSM 111761^T=LMG 31955^T).

Simultaneous quantification of the most common and proteolytic Pseudomonas species in raw milk by multiplex qPCR

Abstract

The heat-stable peptidase AprX, secreted by psychrotolerant Pseudomonas species in raw milk, is a major cause of destabilization and premature spoilage of ultra-high temperature (UHT) milk and milk products. To enable rapid detection and quantification of seven frequent and proteolytic Pseudomonas species (P. proteolytica, P. gessardii, P. lactis, P. fluorescens, P. protegens, P. lundensis, and P. fragi) in raw milk, we developed two triplex qPCR assays taking into account species-dependent differences in AprX activity. Besides five species-specific hydrolysis probes, targeting the aprX gene, a universal rpoB probe was included in the assay to determine the total Pseudomonas counts. For all six probes, linear regression lines between C_q value and target DNA concentration were obtained in singleplex as well as in multiplex approaches, yielding R² values of > 0.975 and amplification efficiencies of 85–97%. Moreover, high specificity was determined using genomic DNA of 75 Pseudomonas strains, assigned to 57 species, and 40 other bacterial species as templates in the qPCR. Quantification of the target species and total Pseudomonas counts resulted in linear detection ranges of approx. 10³–10⁷ cfu/ml, which correspond well to common Pseudomonas counts in raw milk. Application of the assay using 60 raw milk samples from different dairies showed good agreement of total Pseudomonas counts calculated by qPCR with cell counts derived from cultivation. Furthermore, a remarkably high variability regarding the species composition was observed for each milk sample, whereby P. lundensis and P. proteolytica/P. gessardii were the predominant species detected.

Key points

• Multiplex qPCR for quantification of seven proteolytic Pseudomonas species and total Pseudomonas counts in raw milk

• High specificity and sensitivity via hydrolysis probes against aprX and rpoB

• Rapid method to determine Pseudomonas contamination in raw milk and predict spoilage potential

Supplementary Information

The online version contains supplementary material available at 10.1007/s00253-021-11109-0.

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.

Quantification of Extracellular Proteases and Chitinases from Marine Bacteria

A total of 92 marine bacteria belonging to Pseudomonas, Pseudoalteromonas, Psychrobacter, and Shewanella were first screened for their proteolytic activity. In total, four Pseudomonas strains belonging to Ps. fluorescens, Ps. fragi, Ps. gessardii, and Ps. marginalis; 14 Pseudoalteromonas strains belonging to Psa. arctica, Psa. carrageenovora, Psa. elyakovii, Psa. issachenkonii, Psa. rubra, Psa. translucida, and Psa. tunicata; and two Shewanella strains belonging to S. baltica and S. putrefaciens were identified to have a weak to high proteolytic activity (from 478 to 4445 mU/mg trypsin equivalent) against skim milk casein as protein source. Further chitinolytic activity screening based on these 20 proteolytic strains using colloidal chitin yielded five positive strains which were tested against three different chitin substrates in order to determine the various types of chitinases. Among the strains that can produce both proteases and chitinases, Psa. rubra DSM 6842^T expressed not only the highest proteolytic activity (2558 mU/mg trypsin equivalent) but also the highest activity of exochitinases, specifically, β-N-acetylglucosaminidase (6.33 mU/10⁷ cfu) as well. We anticipate that this strain can be innovatively applied to the valorization of marine crustaceans side streams.

Identification of Pseudomonas jessenii and Pseudomonas gessardii as the most proteolytic Pseudomonas isolates in Iranian raw milk and their impact on stability of sterilized milk during storage

Identification of the most proteolytic Pseudomonas strains that can produce heat-resistant proteases and contribute to the Ultra High Temperature (UHT) milk destabilization is of great interest. In the present study, among the 146 Pseudomonas isolates that encoded the aprX gene, five isolates with the highest proteolytic activity were selected and identified based on 16S rRNA, rpoD and gyrB gene sequences data. The identification results were confirmed by phylogenetic analysis based on multilocus sequence analysis and identified the representative isolates as P. jessenii (two isolates) and P. gessardii (three isolates). Casein zymography demonstrated the ability of these species to produce heat-resistant enzymes, AprX, with molecular mass of about 48 kDa during storage at 7° C for 72 h. In sterilized milk samples, the residual activity of AprX caused a considerable enhancement in the degree of protein hydrolysis, non-protein nitrogen and non-casein nitrogen contents of the samples during a two-month storage. This enhancement was slightly higher in samples containing enzyme produced by P. jessenii compared to P. gessardii ones, resulting in earlier onset of sterilized milk destabilization. Hence, this study revealed that P. jessenii and P. gessardii can play a considerable role in deterioration of Iranian commercial long-life milk.

Targeting fish spoilers Pseudomonas and Shewanella with oregano and nettle extracts

To control Pseudomonas and Shewanella as important psychrotrophic spoilage bacteria in fish meat, we used ethanolic extracts of oregano (Origanum vulgare subsp. vulgare) and nettle (Urtica dioica), with phytochemical characterisation of the extracts and their bioactive compounds. Liquid chromatography coupled with photodiode array detection and electrospray ionisation-mass spectrometry was used for qualitative compositional determination of the extracts. Four main compounds were identified in the oregano extract, with rosmarinic acid the most abundant, followed by three glycosylated phenolics, one of which is reported for the first time in O. vulgare: 4'-O-β-d-glucopyranosyl-3',4'-dihydroxybenzyl-4-hydroxybenzoate. Six main compounds were identified in the nettle extract, as caffeoylmalic acid and five flavonoid glycosides. These oregano and nettle ethanolic extracts showed in-vitro antimicrobial activities against selected Pseudomonas and Shewanella strains in broth and fish meat homogenate when evaluated at two inoculum concentrations. The antimicrobial activities were more pronounced for the nettle extract at the lower inoculum concentration, and for both the Shewanella strains. Growth inhibition in the fish meat homogenate was evaluated at 3.13 mg/mL and 1.56 mg/mL at 5 °C. Again, the nettle extract showed greater antimicrobial activity, which was seen as the lowest maximum growth rate, followed by the oregano extract, which was inhibitory only at 3.13 mg/mL. Finally, the extracts were applied to fish meat that was then stored at 5 °C for 9 days. Evaluation here was for the counts of the mesophilic, psychrotrophic, Pseudomonas and H2S producers. These confirmed the better antimicrobial effects of the nettle extract, especially against the H2S-producing bacteria, which included Shewanella. Both of the extracts were rich in glycosides of flavonoids and phenolic acids. The enzymatic activities of the Pseudomonas and Shewanella spoilage bacteria and their actions on the phenolic glycosides from natural sources will be further investigated.