Characterization of the microbiota of commercially traded finfish fillets

Transcriptome Analysis Reveals the Molecular Mechanism of Pseudomonas with Different Adhesion Abilities on Tilapia Decay

This study aimed to investigate the molecular mechanism of Pseudomonas with varying adhesion capabilities to Tilapia's intestinal mucus influence the spoilage potential of Tilapia. Sodium chloride(NaCl) was used as an environmental factor to regulate Pseudomonas' adhesion ability. After being exposed to 3.5% NaCl stress, the PS01 strain with low adhesion showed an enhancement in adhesion ability, while the LP-3 strain with high adhesion exhibited a decrease. Correspondingly, the expression of critical adhesion genes, such as flgC, fliC, and cheB, was found to be altered. LP-3, with high adhesion ability, was observed to promote a relative increase in Nocardioides and Cloacibacterium in fish intestines. This led to the production of more volatile compounds, including 2-octen-1-ol Z, 2,3-Octanedione, and Eicosane, thus deepening the spoilage of tilapia. LP-3, with reduced adhesion ability after NaCl regulation, showed a diminished capacity to cause fish spoilage. Transcriptomics analysis was used to examine two Pseudomonas strains that exhibited different adhesion abilities, leading to the identification of an adhesion regulatory network involving flagellar assembly regulation, bacterial chemotaxis, quorum sensing, two-component systems, biofilm formation, and bacterial secretion systems. This study identified the Pseudomonas adhesion regulatory pathway and determined 10 key adhesion-related genes.

Bacterial Community Structures in Raw Pork from Supermarkets and Farmers' Markets Determined by High-Throughput Sequencing Analysis

Pork contaminated with bacteria can shorten the shelf life and cause foodborne diseases. Bacterial community analysis of raw pork in sale process can help identify bacteria associated with food quality and safety. In this study, 52 pork samples were collected from various supermarkets and farmers' markets in Qingdao, China. And the bacterial community structures in pork were analyzed by high-throughput sequencing of 16S rDNA. Both the α-diversity and β-diversity of bacterial communities in pork samples from farmers' market were higher than those from supermarkets (ANOSIM test, R2 = 0.049, p = 0.016). Proteobacteria (88.8%) was the most dominant phylum, and Photobacterium (44.5%) and Acinetobacter (23.9%) were the top two dominant genera in all pork samples. The abundance of most dominant bacterial genera was higher in pork samples from farmers' markets than those from supermarkets, But Photobacterium (ranking first) was just the opposite (p = 0.003). The bacterial communities in pork hadn't obvious clustering characteristics between the two sale locations, while Photobacterium was considered as the biomarker in pork samples from supermarkets according to LefSe analysis (linear discriminant analysis score >4.0). A strong correlation was observed between some samples (R >0.7) collected from different stalls within the same sampling location, indicating cross-contamination possibility in sale process. The findings may have implications for the quality and safety control of pork, particularly for microbial prevention and control during selling and consumption.

A Microbial Phenomics Approach to Determine Metabolic Signatures to Enhance Seabream Sparus aurata Traceability, Differentiating between Wild-Caught and Farmed

BACKGROUND

The need for efficient and simplified techniques for seafood traceability is growing. This study proposes the Biolog EcoPlate assay as an innovative method for assessing wild and farmed Sparus aurata traceability, offering advantages over other molecular techniques in terms of technical simplicity.

METHODS

The Biolog EcoPlate assay, known for its high-throughput capabilities in microbial ecology, was utilized to evaluate the functional diversity of microbial communities from various organs of S. aurata (seabream) from the Mediterranean area. Samples were taken from the anterior and posterior gut, cloaca swabs and gills to distinguish between farmed and wild-caught individuals. The analysis focused on color development in OmniLog Units for specific carbon sources at 48 h.

RESULTS

Gills provided the most accurate clusterization of sample origin. The assay monitored the development of color for carbon sources such as α-cyclodextrin, D-cellobiose, glycogen, α-D-lactose, L-threonine and L-phenylalanine. A mock experiment using principal component analysis (PCA) successfully identified the origin of a blind sample. Shannon and Simpson indexes were used to statistically assess the diversity, reflecting the clusterization of different organ samples; Conclusions: The Biolog EcoPlate assay proves to be a quick, cost-effective method for discriminate S. aurata traceability (wild vs. farmed), demonstrating reliable reproducibility and effective differentiation between farmed and wild-caught seabream.

Enhancing seafood traceability: tracking the origin of seabass and seabream from the tuscan coast area by the analysis of the gill bacterial communities

BACKGROUND

The seafood consumption and trade have increased over the years, and along its expected expansion pose major challenges to the seafood industry and government institutions. In particular, the global trade in fish products and the consequent consumption are linked to reliable authentication, necessary to guarantee lawful trade and healthy consumption. Alterations or errors in this process can lead to commercial fraud and/or health threats. Consequently, the development of new investigative tools became crucial in ensuring unwanted scenarios. Here we used NGS techniques through targeted metagenomics approach on the V3-V4 region of the 16S rRNA genes to characterize the gill bacterial communities in wild-caught seabream (Sparus aurata) and seabass (Dicentrarchus labrax) within different fisheries areas of the "Costa degli Etruschi'' area in the Tuscan coast. Our challenge involved the possibility of discriminating between the microbiota of both fish species collected from three different fishing sites very close to each other (all within 100 km) in important areas from a commercial and tourist point of view.

RESULTS

Our results showed a significant difference in the assembly of gill bacterial communities in terms of diversity (alpha and beta diversity) of both seabass and seabream in accordance with the three fishing areas. These differences were represented by a unique site -related bacterial signature, more evident in seabream compared to the seabass. Accordingly, the core membership of seabream specimens within the three different sites was minimal compared to the seabass which showed a greater number of sequence variants shared among the different fishing sites. Therefore, the LRT analysis highlighted the possibility of obtaining specific fish bacterial signatures associated with each site; it is noteworthy that specific taxa showed a unique association with the fishing site regardless of the fish species. This study demonstrates the effectiveness of target-metagenomic sequencing of gills in discriminating bacterial signatures of specimens collected from fishing areas located at a limited distance to each other.

CONCLUSIONS

This study provides new information relating the structure of the gill microbiota of seabass and seabream in a fishing area with a crucial commercial and tourist interest, namely "Costa degli Etruschi". This study demonstrated that microbiome-based approaches can represent an important tool for validating the seafood origins with a central applicative perspective in the seafood traceability system.

Exploring the Feasibility of 16S rRNA Short Amplicon Sequencing-Based Microbiota Analysis for Microbiological Safety Assessment of Raw Oyster

16S rRNA short amplicon sequencing-based microbiota profiling has been thought of and suggested as a feasible method to assess food safety. However, even if a comprehensive microbial information can be obtained by microbiota profiling, it would not be necessarily sufficient for all circumstances. To prove this, the feasibility of the most widely used V3-V4 amplicon sequencing method for food safety assessment was examined here. We designed a pathogen (Vibrio parahaemolyticus) contamination and/or V. parahaemolyticus-specific phage treatment model of raw oysters under improper storage temperature and monitored their microbial structure changes. The samples stored at refrigerator temperature (negative control, NC) and those that were stored at room temperature without any treatment (no treatment, NT) were included as control groups. The profiling results revealed that no statistical difference exists between the NT group and the pathogen spiked- and/or phage treated-groups even when the bacterial composition was compared at the possible lowest-rank taxa, family/genus level. In the beta-diversity analysis, all the samples except the NC group formed one distinct cluster. Notably, the samples with pathogen and/or phage addition did not form each cluster even though the enumerated number of V. parahaemolyticus in those samples were extremely different. These discrepant results indicate that the feasibility of 16S rRNA short amplicon sequencing should not be overgeneralized in microbiological safety assessment of food samples, such as raw oyster.

The power of DNA based methods in probiotic authentication

Introduction

The global probiotic market is growing rapidly, and strict quality control measures are required to ensure probiotic product efficacy and safety. Quality assurance of probiotic products involve confirming the presence of specific probiotic strains, determining the viable cell counts, and confirming the absence of contaminant strains. Third-party evaluation of probiotic quality and label accuracy is recommended for probiotic manufacturers. Following this recommendation, multiple batches of a top selling multi-strain probiotic product were evaluated for label accuracy.

Methods

A total of 55 samples (five multi-strain finished products and 50 single-strain raw ingredients) containing a total of 100 probiotic strains were evaluated using a combination of molecular methods including targeted PCR, non-targeted amplicon-based High Throughput Sequencing (HTS), and non-targeted Shotgun Metagenomic Sequencing (SMS).

Results

Targeted testing using species-specific or strain-specific PCR methods confirmed the identity of all strains/species. While 40 strains were identified to strain level, 60 strains were identified to species level only due to lack of strain-specific identification methods. In amplicon based HTS, two variable regions of 16S rRNA gene were targeted. Based on V5-V8 region data, ~99% of total reads per sample corresponded to target species, and no undeclared species were detected. Based on V3-V4 region data, ~95%-97% of total reads per sample corresponded to target species, while ~2%-3% of reads matched undeclared species (Proteus species), however, attempts to culture Proteus confirmed that all batches were free from viable Proteus species. Reads from SMS assembled to the genomes of all 10 target strains in all five batches of the finished product.

Discussion

While targeted methods enable quick and accurate identification of target taxa in probiotic products, non-targeted methods enable the identification of all species in a product including undeclared species, with the caveats of complexity, high cost, and long time to result.

Host-associated and Environmental Microbiomes in an Open-Sea Mediterranean Gilthead Sea Bream Fish Farm

Gilthead seabream is among the most important farmed fish species in the Mediterranean Sea. Several approaches are currently applied to assure a lower impact of diseases and higher productivity, including the exploration of the fish microbiome and its manipulation as a sustainable alternative to improve aquaculture practices. Here, using 16S rRNA gene high-throughput sequencing, we explored the microbiome of farmed seabream to assess similarities and differences among microbial assemblages associated to different tissues and compare them with those in the surrounding environment. Seabream had distinct associated microbiomes according to the tissue and compared to the marine environment. The gut hosted the most diverse microbiome; different sets of dominant ASVs characterized the environmental and fish samples. The similarity between fish and environmental microbiomes was higher in seawater than sediment (up to 7.8 times), and the highest similarity (3.9%) was observed between gill and seawater, suggesting that gills are more closely interacting with the environment. We finally analyzed the potential connections occurring among microbiomes. These connections were relatively low among the host's tissues and, in particular, between the gut and the others fish-related microbiomes; other tissues, including skin and gills, were found to be the most connected microbiomes. Our results suggest that, in mariculture, seabream microbiomes reflect only partially those in their surrounding environment and that the host is the primary driver shaping the seabream microbiome. These data provide a step forward to understand the role of the microbiome in farmed fish and farming environments, useful to enhance disease control, fish health, and environmental sustainability.

Exposure to Oxy-Tetracycline Changes Gut Bacterial Community Composition in Rainbow Trout: A Preliminary Study

The extensive use of antibiotics is evident in most of the livestock and aquaculture management for inhibiting pathogen infection. Korean aquaculture depends on the usage of oxy-tetracycline for growing rainbow trout. Hence, this study was conducted to evaluate the changes in gut bacterial community profiles of rainbow trout exposed to oxy-tetracycline and predict the metabolic functioning of the bacterial community. The gut bacterial community composition of oxy-tetracycline treated fish was assessed by amplicon sequencing targeting the 16S rRNA gene of bacteria and comparing with the control group that did not receive any antibiotic. The principle coordinate analysis and non-metric multidimensional scaling analysis had shown two distinct clusters that implies the changes in community composition. In phyla level, the relative abundances of Tenericutes and Firmicutes were observed to be significantly higher in oxy-tetracycline treated fish compared to the control. Furthermore, the prediction based metabolic profiling revealed the processes that are affected due to the shift in community profiles. For example, metabolic functioning of membrane efflux system, amino acid metabolism and glycolysis were significantly higher in oxy-tetracycline treated fish compared to the control. This study describes alteration in gut bacterial community composition and potential metabolic profiles of the community that might be responsible for surviving in antibiotic rich environment.

No evidence for a relationship between farm or transformation process locations and antibiotic resistance patterns of Pseudomonas population associated with rainbow trout (Oncorhynchus mykiss)

AIMS

Study the relationship between antibiotic resistance patterns of Pseudomonas isolated from farmed rainbow trout fillets and farm or transformation process locations.

METHODS AND RESULTS

Pseudomonas strains were isolated from rainbow trout sampled in two differently located farms and filleted in laboratory or in a processing factory. One hundred and twenty-five isolates were confirmed as belonging to Pseudomonas using CFC selective media, Gram staining, oxidase test and quantitative polymerase chain reaction methods. Fifty-one isolates from separate fish fillets were further identified using MALDI-TOF mass spectrometry, and the minimal inhibitory concentrations (MIC) of 11 antibiotics were also determined by microdilution method. Most of the isolates belonged to the Pseudomonas fluorescens group (94.1%), and no relationship was established between antibiotic resistance patterns and sampling locations (farms or filleting areas). Multiple resistance isolates with high MIC values (from 64 µg ml^-1 to more than 1024 µg ml^-1 ) were identified.

CONCLUSIONS

Antibiotic resistance patterns found in Pseudomonas isolates were not influenced by farms or transformation process locations. Seven isolates were found highly resistant to four different antibiotic classes.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study does not provide evidence of a relationship between farm or transformation process locations on antibiotic resistance patterns of Pseudomonas population.

Assessment of quality characteristics and bacterial community of modified atmosphere packaged chilled pork loins using 16S rRNA amplicon sequencing analysis

Modified atmosphere packaging (MAP) is widely applied in packaging meat and meat products. While most studies had employed culture-dependent microbiological analyses or polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE), the recent application of high-throughput sequencing (HTS) has been effective and reliable in detecting the microbial consortium associated with food spoilage. Since MAP application is limited in China, applying HTS in assessing the microbial consortium of meat and meat products in the country becomes imperative. In this study, quality indexes and bacterial enumeration often used as spoilage indicators were employed to assess MAP fresh pork under chilled (4 °C) storage for 21 d. The results indicated that 70%O₂/30%CO₂ (Group A) retained more redness (a*) content, while 70%N₂/30%CO₂ (Group B) markedly reduced spoilage indicators compared to the control group. Notably, high-throughput sequencing indicated that Group B and 20%O₂/60%N₂/20%CO₂ (Group C) inhibited the growth of abundant spoilers, Pseudomonas spp. and Brochothrix spp. Thus, MAP (Group B and C) has promising potential in inhibiting predominant meat spoilers during chilled storage. This study provides valuable information to food industries on the potential application of MAP to control meat spoilage in Chinese markets.