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

Dynamics of microbiome and resistome in a poultry burger processing line

Traditionally, surveillance programs for food products and food processing environments have focused on targeted pathogens and resistance genes. Recent advances in high throughput sequencing allow for more comprehensive and untargeted monitoring. This study assessed the microbiome and resistome in a poultry burger processing line using culturing techniques and whole metagenomic sequencing (WMS). Samples included meat, burgers, and expired burgers, and different work surfaces. Microbiome analysis revealed spoilage microorganisms as the main microbiota, with substantial shifts observed during the shelf-life period. Core microbiota of meat and burgers included Pseudomonas spp., Psychrobacter spp., Shewanella spp. and Brochothrix spp., while expired burgers were dominated by Latilactobacillus spp. and Leuconostoc spp. Cleaning and disinfection (C&D) procedures altered the microbial composition of work surfaces, which still harbored Hafnia spp. and Acinetobacter spp. after C&D. Resistome analysis showed a low overall abundance of resistance genes, suggesting that effective interventions during processing may mitigate their transmission. However, biocide resistance genes were frequently found, indicating potential biofilm formation or inefficient C&D protocols. This study demonstrates the utility of combining culturing techniques and WMS for comprehensive of the microbiome and resistome characterization in food processing lines.

Draft genome sequence of multidrug-resistant Kurthia gibsonii strain Hakim RU_BHWE isolated from sewage water in Bangladesh

We have sequenced the genome of Kurthia gibsonii strain Hakim RU_BHWE, isolated from sewage water. The assembled genome consists of 2.891 Mb with 58.6883× coverage, presenting an average GC content of 36.60%. This genome includes 8 CRISPR arrays, 3 prophages, 3 antibiotic resistance genes, and 12 virulence factor genes.

Isolation and Identification of the Antibacterial Compounds Produced by Maillard Reaction of Xylose with Phenylalanine or Proline

Maillard reaction products (MRPs) of xylose with phenylalanine and xylose with proline exhibit high antibacterial activity. However, the active antibacterial compounds in MRPs have not yet been identified or isolated. This study aimed to isolate the active compounds in the two antibacterial MRPs. The organic layer of the MRP solution was separated and purified using silica gel chromatography and high-performance liquid chromatography. The chemical structures of the isolated compounds were determined by mass spectrometry and nuclear magnetic resonance spectroscopy. The compounds inhibited the growth of Bacillus cereus and Salmonella Typhimurium at 25 °C for 7 days at a concentration of 0.25 mM. Furthermore, the isolated compounds inhibited the growth of naturally occurring microflora of lettuce and chicken thighs at 25 °C for 2 days at a concentration of 0.5-1.0 mM. The antibacterial compounds found in MRPs demonstrated a wide range of effectiveness and indicated their potential as alternative preservatives.

Quantitative characterization and dynamics of bacterial communities in ready-to-eat chicken using high-throughput sequencing combined with internal standard-based absolute quantification

Ready-to-eat (RTE) chicken products are prone to bacterial contamination, posing foodborne illness risks. High-throughput sequencing (HTS) has been widely used to study the distribution of pathogenic and spoilage bacteria in RTE chicken products but lacks quantitative data on taxa abundances. In this study, we employed a method combining HTS with absolute quantification, using Edwardsiella tarda as an internal standard strain, to achieve the relative and absolute abundances of microbiota in RTE chicken products stored at 4 and 25 °C. The results showed that the addition of appropriate concentration of internal standard strains exhibited no significant impact on the structure composition, relative abundance, and absolute abundance of bacterial communities in chicken meat, achieving comprehensive absolute quantification in RTE chicken products. Furthermore, the absolute abundance of bacterial genera at the end of storage followed a log-normal distribution, with most genera having an absolute abundance between 103 and 105 CFU/g. This study provides insights into the quantification of bacterial communities in RTE chicken products, laying a foundation for the development of strategies to extend the shelf life of RTE products.

Changes in the Microbiota from Fresh to Spoiled Meat, Determined by Culture and 16S rRNA Analysis

Growth of meat microbiota usually results in spoilage of meat that can be perceived by consumers due to sensory changes. However, a high bacterial load does not necessarily result in sensory deviation of meat; nevertheless, this meat is considered unfit for human consumption. Therefore, the aims of this study were to investigate changes in the microbiota from fresh to spoiled meat and whether the proportions of certain bacteria can probably be used to indicate the hygiene status of meat. For this purpose, 12 fresh pork samples were divided into two groups, and simultaneously aerobically stored at 4°C and 22°C. At each time-temperature point (fresh meat, days 6, 13, and 20 at 4°C, and days 1, 2, 3, and 6 at 22°C), 12 meat subsamples were investigated. Sequences obtained from next-generation sequencing (NGS) were further analyzed down to species level. Plate counting of six bacterial groups and NGS results showed that Pseudomonas spp. and lactic acid bacteria (LAB) were found in a high proportion in all stored meat samples and can therefore be considered as important "spoilage indicator bacteria". On the contrary, sequences belonging to Staphylococcus epidermidis were found in a relatively high proportion in almost all fresh meat samples but were less common in stored meat. In this context, they can be considered as "hygiene indicator bacteria" of meat. Based on these findings, the proportion of the "hygiene indicator bacteria" in relation to the "spoilage indicator bacteria" was calculated to determine a "hygiene index" of meat. This index has a moderate to strong correlation to bacterial loads obtained from culture (p < 0.05), specifically to Pseudomonas spp., LAB and total viable counts (TVCs). Knowledge of the proportions of hygiene and spoilage indicator bacteria obtained by NGS could help to determine the hygiene status even of (heat-) processed composite meat products for the first time, thus enhancing food quality assurance and consumer protection.

Next-Generation Sequencing for the Detection of Microbial Agents in Avian Clinical Samples

Direct-targeted next-generation sequencing (tNGS), with its undoubtedly superior diagnostic capacity over real-time PCR (RT-PCR), and direct-non-targeted NGS (ntNGS), with its higher capacity to identify and characterize multiple agents, are both likely to become diagnostic methods of choice in the future. tNGS is a rapid and sensitive method for precise characterization of suspected agents. ntNGS, also known as agnostic diagnosis, does not require a hypothesis and has been used to identify unsuspected infections in clinical samples. Implemented in the form of multiplexed total DNA metagenomics or as total RNA sequencing, the approach produces comprehensive and actionable reports that allow semi-quantitative identification of most of the agents present in respiratory, cloacal, and tissue samples. The diagnostic benefits of the use of direct tNGS and ntNGS are high specificity, compatibility with different types of clinical samples (fresh, frozen, FTA cards, and paraffin-embedded), production of nearly complete infection profiles (viruses, bacteria, fungus, and parasites), production of "semi-quantitative" information, direct agent genotyping, and infectious agent mutational information. The achievements of NGS in terms of diagnosing poultry problems are described here, along with future applications. Multiplexing, development of standard operating procedures, robotics, sequencing kits, automated bioinformatics, cloud computing, and artificial intelligence (AI) are disciplines converging toward the use of this technology for active surveillance in poultry farms. Other advances in human and veterinary NGS sequencing are likely to be adaptable to avian species in the future.

The Effect of Temperature and Storage Duration on the Quality and Attributes of the Breast Meat of Hens after Their Laying Periods

The purpose of this study was to evaluate the effect of temperature (2 °C and 6 °C) and storage duration on the quality and attributes of hens' breast meat after their laying periods. The study included physicochemical characteristics (pH, drip loss, colour, shear force), microbiological quality (total Enterobacteriaceae family and Pseudomonas count), and sensory quality. Bacterial identification was performed using matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry. The increased meat pH and drip loss was greater at 6 than 2 °C (p < 0.05). An increase in the tenderness of the meat stored at 6 °C was found as early as day 4, as well as at 2 °C on day 8 of storage (p < 0.05). On day 4 of storage, the meat was characterised by a darker colour than on the first day, but the darkening was greater at 6 °C than at 2 °C (p < 0.05). At 6 °C, on day 4 of storage, there was an increase in yellow saturation (b*) of the meat, which was higher at 6 °C than at 2 °C (p < 0.05). At 2 °C, the total bacterial count and number of Pseudomonas spp. in the meat gradually increased along with increasing storage duration, reaching 4.64 log cfu/g and 4.48 log cfu/g, respectively, on the 8th day of storage. At 6 °C, on the sixth day of storage, the total bacterial count in the meat exceeded 7 log cfu/g, considered the limit of microbiological safety. The meat stored at 2 °C had an acceptable sensory quality until the 8th day of storage. The study shows that storage at 2 °C preserves the sensory characteristics and microbiological safety of the hen meat longer at an acceptable level after the laying period. Extended storage life may be of importance to consumers and the meat industry.

The efficiency of UV light-emitting diodes (UV-LED) in decontaminating Campylobacter and Salmonella and natural microbiota in chicken breast, compared to a UV pilot-plant scale device

This study investigated the combined effect of Ultraviolet (UV) light-emitting diode (LED) technology treatment with refrigerated storage of chicken breast meat over 7 days on Campylobacter jejuni, Salmonella enterica serovar Typhimurium, total viable counts (TVC) and total Enterobacteriaceae counts (TEC). An optimised UV-LED treatment at 280 nm for 6 min decreased inoculated S. Typhimurium and C. jejuni populations by 0.6-0.64 log CFU/g, and TVC and TEC population by 1-1.2 log CFU/g in chicken samples. During a 7-day storage at 4 °C, a 0.73 log reduction in C. jejuni was achieved compared with non-treated samples. Moreover, the UV-LED effectiveness to reduce TVC and TEC during refrigerated storage was compared with a conventional UV lamp and a similar efficiency was observed. The impact of UV-LED and UV lamp devices on the microbial community composition of chicken meat during storage was further examined using 16 S rRNA gene amplicon sequencing. Although similar bacterial reductions were observed for both technologies, the microbial communities were impacted differently. Treatment with the UV conventional lamp increased the proportion of Brochothrix spp. In meat samples, whilst Photobacterium spp. Levels were reduced.

Microbial trace investigation throughout the entire chicken supply chain based on metagenomic high-throughput sequencing

As poultry possesses a high risk of contamination by various pathogens and has repeatedly been linked to foodborne outbreaks, ensuring microbiological safety throughout the chicken production chain is essential. In this study, bacterial communities in chickens and associated environments (n = 72), including feces, floors, gloves, and worktables, were trace investigated from the broiler farm, slaughterhouse, meat processing plant, and the market by amplicon sequencing of the V4 region of the 16S rRNA. The bacterial composition in live chickens along the production chain significantly changed across the stages, with distinct microbiota noted at each step. Pseudomonas, Shewanella, Acinetobacter, and Psychrobacter were dominant in the final products. Staphylococcus was abundant in live birds originally (36.83 %) but dramatically decreased after slaughter (3.07 %, 0.06 %, and 0.42 % in slaughtered, processed, and market carcasses, respectively), which may be attributed to defeathering. The proportion of Enterobacteriaceae, Acinetobacter, and Pseudomonas increased from 0.95 %, 0.03 %, and 0.04 % before slaughter to 13.57 %, 34.19 %, and 21.90 %, respectively, after slaughter, highlighting the importance of hygiene management in the succeeding steps. Diversity analysis revealed the possibility of bacterial transmission between samples from the processing plant and the market. Source tracking was performed to identify microbial contamination routes in the chicken microbiome; the major bacterial sources in the final products were the samples from the processing plant (such as processed carcasses, gloves, and worktables), accounting for 93.53 % of the total microbial sources. These results suggest that in-depth knowledge of microbial transmission between chickens and their surroundings can facilitate a precise understanding of microbiological concerns across the poultry production system and help establish safety management measures for the poultry industry.

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.

A probabilistic approach to model bisphenol A (BPA) migration from packaging to meat products

Bisphenol A (BPA), a synthetic chemical which has raised concerns due to its potential toxicological effects on humans, has been widely detected in canned and non-canned meat and meat products. This study estimated BPA migration from packaging to non-canned and canned meat products by developing two probabilistic models. BPA concentration data in packaging materials were collated, including polyethylene terephthalate, polyvinyl chloride, epoxy-based coatings, and polyester-based coatings. Migration ratios were calculated from migration tests of BPA molecules moving from packaging to food simulants. The predictive model revealed that the BPA migration concentration from packaging ranges from 0.017 to 0.13 (5th-95th percentile) μg kg-1 with a simulated mean of 0.056 μg kg-1 in non-canned meat products. This is in stark contrast to the simulated mean of 134.57 (5th-95th percentile: 59.17-223.25) μg kg-1 for canned meat products. Nevertheless, plastic packaging was estimated to contribute only 3 % of BPA levels in non-canned meat products. The sensitivity analysis showed that the contact area of meat products with films is the most sensitive parameter of the plastic packaging migration model. It is concluded that plastic packaging may not be the only or dominant source of BPA in non-canned meat products.

In Vitro and In Situ Characterization of Psychrotrophic Spoilage Bacteria Recovered from Chilled Chicken

Spoilage bacteria play a remarkable role in the spoilage of chilled chicken. In this paper, a total of 42 isolates belonging to 16 species of four genera were isolated from chilled chicken and displayed different characterizations of psychrotrophic spoilage. Six isolates of J7, J8, Q20, Q23, R1, and R9 with differences in proteolytic capabilities were further characterized for in situ spoilage potential evaluation. Pseudomonas lundensis J8 exhibited the strongest spoilage potential in situ, displaying a fast growth rate, increased pH velocity, high total volatile basic nitrogen, and high peptide content in the chicken samples. The volatile flavor analysis of chicken samples via electronic nose indicated that the content of characteristic odors representing spoilage, including sulfides, organic sulfide, and hydride, increased during storage. Additionally, the principle component and correlation analyses revealed that the spoilage odors produced by different species of bacteria were significantly different and positively correlated with the results of protease activity in vitro. The characteristics of spoilage bacteria in chilled chicken provided a comprehensive insight into microbial assessment during storage.

Effects of Different Storage Temperatures on Bacterial Communities and Functional Potential in Pork Meat

Storage temperature is considered one of the most important factors that affect the microbial spoilage of fresh meat. Chilling and superchilling are the most popular storage techniques on the market, but during transportation, the temperature may reach 10 °C and may even reach room temperature during local retail storage. In the present study, we stored fresh pork meat at different temperatures, -2 °C, 4 °C, 10 °C, and 25 °C. The composition and functional potential of fresh or spoiled meat resident microbes were analyzed based on 16S rRNA gene amplicon sequencing. The microbial composition exhibited high similarity between pork meat stored at -2 °C and 4 °C, with Pseudomonads and Brochothrix being the dominant taxa. Acinetobacter sp., Myroides sp., and Kurthia sp. were markers for spoiled pork meat stored at 25 °C. Both psychrophilic and mesophilic bacteria were observed to grow under a storage temperature of 10 °C, but the overall composition and functional potential based on Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were found to be similar to that of meat stored at room temperature. Our results broaden the knowledge of possible microbial changes in pork meat during storage, transportation, or retail.

Development and validation of a mathematical model for pseudomonads growth as a basis for predicting spoilage of fresh poultry breast and thigh fillets

The growth of naturally contaminated pseudomonads on fresh breast and thigh poultry fillets during aerobic storage was studied and modeled as a function of temperature (0–30°C). A statistical comparison of the models for breast and thigh fillets showed that muscle type does not significantly affect the temperature dependence of pseudomonads growth kinetics. A unified model for breast and thigh was developed and validated against pseudomonads growth rate data under isothermal conditions extracted from literature and experimental data under dynamic temperature conditions. The validation results showed a satisfactory performance of the model with the bias and accuracy factors ranging from 0.85 to 1.09 and 1.02 to 1.21, respectively. The model was further used to predict the shelf life of fresh poultry as the time required by pseudomonads to reach the spoilage level for various scenarios of temperature, initial contamination level, and physiological state of pseudomonads demonstrating its application in a risk-based shelf-life assessment of fresh poultry products.

Community Composition of Bacteria Isolated from Swiss Banknotes Varies Depending on Collection Environment

Humans interact constantly with surfaces and associated microbial communities in the environment. The factors shaping the composition of these communities are poorly understood: some proposed explanations emphasize the influence of local habitat conditions (niche-based explanations), while others point to geographic structure and the distance among sampled locations (dispersal-based explanations). However, the relative roles of these different drivers for microbial community assembly on human-associated surfaces are not clear. Here, we used a combination of sampling, sequencing (16S rRNA) and culturing to show that the composition of banknote-associated bacterial communities varies depending on the local collection environment. Using banknotes collected from various locations and types of shops across Switzerland, we found taxonomic diversity dominated by families such as Pseudomonadaceae and Staphylococcaceae, but with banknote samples from particular types of shops (especially butcher shops) having distinct community structure. By contrast, we found no evidence of geographic structure: similarity of community composition did not decrease with increasing distance among sampled locations. These results show that microbial communities associated with banknotes, one of the most commonly encountered and exchanged human-associated surfaces, can reflect the local environmental conditions (in this case, the type of shop), and the signal for this type of variation was stronger than that for geographic structure among the locations sampled here.

Improved microbial and sensory quality of chicken meat by treatment with lactic acid, organic acid salts and modified atmosphere packaging

Microbial contamination and growth play important roles in spoilage and quality loss of raw poultry products. We evaluated the suitability of three commercially available organic acid based antimicrobial compounds, Purac FCC80 (l-lactic acid), Verdad N6 (buffered vinegar fermentate) and Provian K (blend of potassium acetate and diacetate) to prevent growth of the innate microbiota, reduce spoilage and enhance the sensory quality of raw chicken under vacuum, high CO₂ (60/40% CO₂/N₂), and high O₂ (75/25% O₂/CO₂) modified atmosphere (MA) storage conditions. Solutions were applied warm (50 °C) or cold (4 °C) to reflect treatments prior to (Prechill) or after (Postchill) cooling of chicken carcasses, respectively. Single postchill treatments of raw chicken wings with 5% Verdad N6 or Provian K solutions and MA storage enabled complete growth inhibition during the first seven days of storage before growth resumed. Enhanced bacterial control was obtained by combining Prechill lactic acid and Postchill Verdad N6 or Provian K treatments which indicated initial reductions up to 1.1 log and where total bacterial increase after 20 days storage was limited to 1.8-2.1 log. Antibacterial effects were dependent on the concentration of the inhibiting salts used, pH and the storage conditions. Bacterial community analyses showed increased relative levels of Gram-positive bacteria and with reductions of potential spoilage organisms in samples treated with the organic acid salts Verdad N6 and Provian K. Sensory analyses of raw, treated wings showed prominent lower scores in several spoilage associated odour attributes when compared with untreated chicken wings after 13 days storage. For heat-treated chicken, only minor differences for 22 tested attributes were detected between seven antimicrobial treatments and untreated control chicken. Immersion in commercially available organic acid/salt solutions combined with MA storage can reduce bacterial levels, improve microbial and sensory quality, and potentially improve shelf life and reduce food waste of chicken products.

The Clash of Microbiomes: From the Food Matrix to the Host Gut

Food fermentation has led to the improvement of the safety characteristics of raw materials and the production of new foodstuffs with elevated organoleptic characteristics. The empirical observation that these products could have a potential health benefit has garnered the attention of the scientific community. Therefore, several studies have been conducted in animal and human hosts to decipher which of these products may have a beneficial outcome against specific ailments. However, despite the accumulating literature, a relatively small number of products have been authorized as ‘functional foods’ by regulatory bodies. Data inconsistency and lack of in-depth preclinical characterization of functional products could heavily contribute to this issue. Today, the increased availability of omics platforms and bioinformatic algorithms for comprehensive data analysis can aid in the systematic characterization of microbe–microbe, microbe–matrix, and microbe–host interactions, providing useful insights about the maximization of their beneficial effects. The incorporation of these platforms in food science remains a challenge; however, coordinated efforts and interdisciplinary collaboration could push the field toward the dawn of a new era.

Kurthia gibsonii, a novel opportunistic pathogen in poultry

Kurthia gibsonii (H. Kurth, 1883) was isolated on 10 unrelated laying hen farms over a period of 15 months. Farmers reported elevated morbidity and mortality rates, and suspected of colibacillosis based on the necropsy findings. The most frequently found lesions were perihepatitis, fibrinous peritonitis, salpingitis and oophoritis. Necropsy findings and bacteriological results allowed the diagnosis of colibacillosis. In addition, K. gibsonii was isolated from the ovarian follicles (44.44 %), liver (22.22%), peritoneum (16.67%), bone marrow (5.56%), spleen (5.56%), and duodenum (5.56%). On all farms, coinfection with E. coli was detected, while on some farms other common avian pathogens were found as well. In total, 18 K. gibsonii strains were identified and phylogenetically analysed based on the 16S rRNA gene sequences. The results showed some variability of the strains originating from the same farm, although the overall phylogenetic diversity was low, regardless of the geographical location of the farm, age of the flock or date of collection. Embryo lethality assay showed K. gibsonii is not able to cause a primary infection. We conclude that Kurthia gibsonii may play a role as an opportunistic pathogen for poultry. This is the first report of coinfection of Kurthia gibsonii and E. coli in laying hens.