Genomic diversity of Serratia proteamaculans and Serratia liquefaciens predominant in seafood products and spoilage potential analyses

Green Packaging Solutions for Extending the Shelf Life of Fish Fillet: Development and Evaluation of Cinnamon Essential Oil-Infused Cassava Starch and Fish Gelatin Edible Films

Edible, eco-friendly films made from cassava starch, cinnamon essential oil (CEO), and fish gelatin have been shown to extend the shelf life of fish fillets. These biodegradable films offer an environmentally friendly alternative to conventional plastic packaging. This study explores the production of edible films using cassava starch, fish gelatin from processing waste, and CEO nanoemulsion (CEON), focusing on their physical, mechanical, antioxidant, and antibacterial properties. The optimal film blend, consisting of 5% cassava starch and a 1:3 ratio of fish gelatin with 10% CEON (SGCEON3), demonstrated excellent antioxidant and antibacterial properties, extending the fish fillet shelf life to 10 days. These films were light brown with increased thickness (0.19 ± 0.001 mm), tensile strength (20.15 MPa), and elongation at break (270.50%). The TGA analysis showed a consistent mass loss from 30 to 600 °C, and AFM results indicated an average height deviation of 39.925 nm, a roughness of 54.439 nm, a surface symmetry skewness of 0.860, and a kurtosis of 1.77. The FE-SEM images and FTIR spectra confirmed compatibility between fish gelatin and CEON. The migration assay observed a more gradual and constant release of the CEO from the SG films, and the SGCEON3 film is suitable as an antimicrobial packaging material. This study highlights the potential of biopolymer packaging infused with essential oils to extend the shelf life of perishable foods effectively.

Spontaneous nanoemulsification of cinnamon essential oil: Formulation, characterization, and antibacterial and antibiofilm activity against fish spoilage caused by Serratia rubidaea BFMO8

The contemporary food industry's uses of nanoemulsions (NEs) include food processing, effective nutraceutical delivery, the development of functional chemicals, and the synthesis of natural preservatives, such as phytocompounds. Although cinnamon essential oil (CEO) is widely used in the cosmetic, pharmaceutical, and food industries, it is difficult to add to aqueous-based food formulations due to its weak stability and poor water solubility. This study describes the formulation of a CEO nanoemulsion (CEONE) by spontaneous emulsification and evaluates its antibacterial and antibiofilm properties against biofilm-forming Serratia rubidaea BFMO8 isolated from spoiled emperor fish (Lethrinus miniatus). Bacteria causing spoilage in emperor fish were isolated and identified as S. rubidaea using common morphological, cultural, and 16S RNA sequencing methods, and their ability to form biofilms and their susceptibility to CEONE were assessed using biofilm-specific methods. The spontaneous emulsification formulation of CEONE was accomplished using water and Tween 20 surfactant by manipulating organic and aqueous phase interface properties and controlling particle growth by capping surfactant increases. The best emulsification, with highly stable nano-size droplets, was accomplished at 750 rpm and a 1:3 ratio concentration. The stable CEONE droplet size, polydispersity index, and zeta potential values were 204.8 nm, 0.115, and -6.05 mV, respectively. FTIR and high-resolution liquid chromatography-mass spectrometry (HR-LCMS) analyses have revealed carboxyl, carbonyl, and phenol-like primary phytochemical functional groups in CEO and CEONE, which contribute to their antibacterial and antibiofilm properties.

Biological Characterization and Genomic Analysis of Three Novel Serratia- and Enterobacter-Specific Virulent Phages

Due to the high microbiological contamination of raw food materials and the increase in the incidence of multidrug-resistant bacteria, new methods of ensuring microbiological food safety are being sought. One solution may be to use bacteriophages (so-called phages) as natural bacterial enemies. Therefore, the aim of this study was the biological and genomic characterization of three newly isolated Serratia- and Enterobacter-specific virulent bacteriophages as potential candidates for food biocontrol. Serratia phage KKP_3708 (vB_Sli-IAFB_3708), Serratia phage KKP_3709 (vB_Sma-IAFB_3709), and Enterobacter phage KKP_3711 (vB_Ecl-IAFB_3711) were isolated from municipal sewage against Serratia liquefaciens strain KKP 3654, Serratia marcescens strain KKP 3687, and Enterobacter cloacae strain KKP 3684, respectively. The effect of phage addition at different multiplicity of infection (MOI) rates on the growth kinetics of the bacterial hosts was determined using a Bioscreen C Pro growth analyzer. The phages retained high activity in a wide temperature range (from -20 °C to 60 °C) and active acidity values (pH from 3 to 12). Based on transmission electron microscopy (TEM) imaging and whole-genome sequencing (WGS), the isolated bacteriophages belong to the tailed bacteriophages from the Caudoviricetes class. Genomic analysis revealed that the phages have linear double-stranded DNA of size 40,461 bp (Serratia phage KKP_3708), 67,890 bp (Serratia phage KKP_3709), and 113,711 bp (Enterobacter phage KKP_3711). No virulence, toxins, or antibiotic resistance genes were detected in the phage genomes. The lack of lysogenic markers indicates that all three bacteriophages may be potential candidates for food biocontrol.

Correlation investigation between core microbe inoculation and the evolution of flavor characteristics during the storage of sturgeon caviar (Acipenser gueldenstaedtii)

The volatile and non-volatile compounds were monitored to investigate the microbial evolution associated with the characteristic flavors for sturgeon caviar during refrigeration. The results revealed that the composition of volatile compounds changed significantly with prolonged refrigeration time, especially hexanal, nonanal, phenylacetaldehyde, 3-methyl butyraldehyde, and 1-octen-3-ol. The nonvolatile metabolites were mainly represented by the increase of bitter amino acids (Thr. Ser, Gly, Ala, and Pro) and a decrease in polyunsaturated fatty acids, especially an 18.63 % decrease in 5 months of storage. A total of 332 differential metabolites were mainly involved in the biosynthetic metabolic pathways of α-linolenic acid, linoleic acid, and arachidonic acid. The precursors associated with flavor evolution were mainly phospholipids, including oleic, linoleic, arachidonic, eicosapentaenoic (EPA), and docosahexaenoic (DHA) acids. The most abundant at the genus level was Serratia, followed by Arsenophnus, Rhodococcus, and Pseudomonas, as obtained by high-throughput sequencing. Furthermore, seven core microorganisms were isolated and characterized from refrigerated caviar. Among them, inoculation with Mammalian coccus and Bacillus chrysosporium restored the flavor profile of caviar and enhanced the content of nonvolatile precursors, contributing to the characteristic aroma attributes of sturgeon caviar. The study presents a theoretical basis for the exploitation of technologies for quality stabilization and control of sturgeon caviar during storage.

A comparison of Oxford nanopore library strategies for bacterial genomics

BACKGROUND

Oxford nanopore Technologies (ONT) provides three main library preparation strategies to sequence bacterial genomes. These include tagmentation (TAG), ligation (LIG) and amplification (PCR). Despite ONT's recommendations, making an informed decision for preparation choice remains difficult without a side-by-side comparison. Here, we sequenced 12 bacterial strains to examine the overall output of these strategies, including sequencing noise, barcoding efficiency and assembly quality based on mapping to curated genomes established herein.

RESULTS

Average read length ranged closely for TAG and LIG (> 5,000 bp), while being drastically smaller for PCR (< 1,100 bp). LIG produced the largest output with 33.62 Gbp vs. 11.72 Gbp for TAG and 4.79 Gbp for PCR. PCR produced the most sequencing noise with only 22.7% of reads mappable to the curated genomes, vs. 92.9% for LIG and 87.3% for TAG. Output per channel was most homogenous in LIG and most variable in PCR, while intermediate in TAG. Artifactual tandem content was most abundant in PCR (22.5%) and least in LIG and TAG (0.9% and 2.2%). Basecalling and demultiplexing of barcoded libraries resulted in ~ 20% data loss as unclassified reads and 1.5% read leakage.

CONCLUSION

The output of LIG was best (low noise, high read numbers of long lengths), intermediate in TAG (some noise, moderate read numbers of long lengths) and less desirable in PCR (high noise, high read numbers of short lengths). Overall, users should not accept assembly results at face value without careful replicon verification, including the detection of plasmids assembled from leaked reads.

Cryptic Oral Microbiota: What Is Its Role as Obstructive Sleep Apnea-Related Periodontal Pathogens?

Periodontitis has been commonly linked to periodontopathogens categorized in Socransky's microbial complexes; however, there is a lack of knowledge regarding "other microorganisms" or "cryptic microorganisms", which are rarely thought of as significant oral pathogens and have been neither previously categorized nor connected to illnesses in the oral cavity. This study hypothesized that these cryptic microorganisms could contribute to the modulation of oral microbiota present in health or disease (periodontitis and/or obstructive sleep apnea (OSA) patients). For this purpose, the presence and correlation among these cultivable cryptic oral microorganisms were identified, and their possible role in both conditions was determined. Data from oral samples of individuals with or without periodontitis and with or without OSA were obtained from a previous study. Demographic data, clinical oral characteristics, and genera and species of cultivable cryptic oral microorganisms identified by MALDI-TOF were recorded. The data from 75 participants were analyzed to determine the relative frequencies of cultivable cryptic microorganisms' genera and species, and microbial clusters and correlations tests were performed. According to periodontal condition, dental-biofilm-induced gingivitis in reduced periodontium and stage III periodontitis were found to have the highest diversity of cryptic microorganism species. Based on the experimental condition, these findings showed that there are genera related to disease conditions and others related to healthy conditions, with species that could be related to different chronic diseases being highlighted as periodontitis and OSA comorbidities. The cryptic microorganisms within the oral microbiota of patients with periodontitis and OSA are present as potential pathogens, promoting the development of dysbiotic microbiota and the occurrence of chronic diseases, which have been previously proposed to be common risk factors for periodontitis and OSA. Understanding the function of possible pathogens in the oral microbiota will require more research.

Dynamic Changes of Bacterial Communities and Microbial Association Networks in Ready-to-Eat Chicken Meat during Storage

Ready-to-eat (RTE) chicken is a popular food in China, but its lack of food safety due to bacterial contamination remains a concern, and the dynamic changes of microbial association networks during storage are not fully understood. This study investigated the impact of storage time and temperature on bacterial compositions and microbial association networks in RTE chicken using 16S rDNA high-throughput sequencing. The results show that the predominant phyla present in all samples were Proteobacteria and Firmicutes, and the most abundant genera were Weissella, Pseudomonas and Proteus. Increased storage time and temperature decreased the richness and diversity of the microorganisms of the bacterial communities. Higher storage temperatures impacted the bacterial community composition more significantly. Microbial interaction analyses showed 22 positive and 6 negative interactions at 4 °C, 30 positive and 12 negative interactions at 8 °C and 44 positive and 45 negative interactions at 22 °C, indicating an increase in the complexity of interaction networks with an increase in the storage temperature. Enterobacter dominated the interactions during storage at 4 and 22 °C, and Pseudomonas did so at 22 °C. Moreover, interactions between pathogenic and/or spoilage bacteria, such as those between Pseudomonas fragi and Weissella viridescens, Enterobacter unclassified and Proteus unclassified, or those between Enterobacteriaceae unclassified and W.viridescens, were observed. This study provides insight into the process involved in RTE meat spoilage and can aid in improving the quality and safety of RTE meat products to reduce outbreaks of foodborne illness.

Unraveling the effect of the combination of modified atmosphere packaging and ε-polylysine on the physicochemical properties and bacterial community of greater amberjack (Seriola dumerili)

The combined effect of ε-polylysine (PL) and modified atmosphere packaging (MAP; 60% CO2/40% N2) on the bacterial community of greater amberjack filets and their physicochemical properties was evaluated at 4°C. The total viable counts (TVC), psychrotrophic bacterial count, sensory index, texture analysis, and total volatile basic nitrogen (TVB-N) revealed that PL, MAP, and MAP + PL treatment delayed the deterioration of greater amberjack filets. These treatment groups also showed decreased accumulation of biogenic amines. High-throughput 16S rRNA gene sequencing results indicated that these treatments suppressed the growth of Pseudomonas in greater amberjack filets. Furthermore, the MAP + PL treatment group was observed to be more effective than the PL and MAP groups, extending the shelf life of greater amberjack filets by 6 days. This investigation showed that the combination of PL and MAP has the potential to retain the quality and extend the shelf life of greater amberjack.

Microbiota Succession of Whole and Filleted European Sea Bass (Dicentrarchus labrax) during Storage under Aerobic and MAP Conditions via 16S rRNA Gene High-Throughput Sequencing Approach

In the present work, the profiles of bacterial communities of whole and filleted European sea bass (Dicentrarchus labrax), during several storage temperatures (0, 4, 8 and 12 °C) under aerobic and Modified Atmosphere Packaging (MAP) conditions, were examined via the 16S rRNA High-Throughput Sequencing (HTS) approach. Sensorial attributes were also assessed to determine products’ shelf-life. Results indicated that shelf-life was strongly dependent on handling, as well as on temperature and atmosphere conditions. HTS revealed the undisputed dominance of Pseudomonas from the very beginning and throughout storage period in the majority of treatments. However, a slightly different microbiota profile was recorded in MAP-stored fillets at the middle stages of storage, which mainly referred to the sporadic appearance of some bacteria (e.g., Carnobacterium, Shewanella, etc.) that followed the dominance of Pseudomonas. It is noticeable that a major difference was observed at the end of shelf-life of MAP-stored fillets at 12 °C, where the dominant microbiota was constituted by the genus Serratia, while the relative abundance of Pseudomonas and Brochothrix was more limited. Furthermore, at the same temperature under aerobic storage of both whole and filleted fish, Pseudomonas almost co-existed with Acinetobacter, while the presence of both Erwinia and Serratia in whole fish was noteworthy. Overall, the present study provides useful information regarding the storage fate and spoilage status of whole and filleted European sea bass, suggesting that different handling and storage conditions influence the shelf-life of sea bass by favoring or delaying the dominance of Specific Spoilage Organisms (SSOs), affecting in parallel to some extent the formation of their consortium that is responsible for products’ sensorial deterioration. Such findings enrich the current knowledge and should be used as a benchmark to develop specific strategies aiming to delay spoilage and thus increase the products’ added value.