The Microbiome of Catfish (<i>Ictalurus punctatus</i>) Treated with Natural Preservatives During Refrigerated Storage
Fish is an essential lean protein source worldwide. Unfortunately, fresh fish food products deteriorate rapidly due to microbial spoilage. With consumers’ growing concerns about using chemical preservatives, we propose using natural preservatives as safer alternatives to prevent microbial spoilage....
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MDPI AG
2025-01-01
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| author | Jung-Lim Lee Gregory Yourek |
| author_facet | Jung-Lim Lee Gregory Yourek |
| author_sort | Jung-Lim Lee |
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| description | Fish is an essential lean protein source worldwide. Unfortunately, fresh fish food products deteriorate rapidly due to microbial spoilage. With consumers’ growing concerns about using chemical preservatives, we propose using natural preservatives as safer alternatives to prevent microbial spoilage. In this study, we used Next-Generation Sequencing (NGS) metagenomics to study microbiomes on catfish fillets at early (day one for all samples), middle (day seven for control store-bought and aquaculture-raised samples, day nine for other treatment store-bought samples, and day eleven for other treatment aquaculture-raised samples), and late (day fifteen for all store-bought, day eleven for control aquaculture-raised samples, and day twenty-seven for other treatment aquaculture-raised samples) points. Store-bought and aquaculture-raised catfish were treated individually with natural preservatives (vinegar, lemon, and grapefruit seed [GSE]). We observed bacterial populations and sequenced 16S NGS libraries of catfish microbes. Vinegar treatment showed the greatest suppression of bacterial growth in both groups, and GSE and lemon treatment had similar levels of suppression in the mid and late points (−4 to −5 Log CFU/g vinegar and −0.1 to −4 Log CFU/g other treatments in aquaculture and −1 to −2 Log CFU/g vinegar and −0.2 to −0.5 Log CFU/g other treatments in store-bought). Aquaculture-raised vinegar treatment samples had similar proportional taxonomy abundance values through storage duration. <i>Pseudomonas</i>, <i>Janthinobacterium</i>, and <i>Camobacteriaceae</i> were the dominant bacteria species in the early point for store-bought fish. Still, <i>Pseudomonas</i> was suppressed by vinegar treatment in the middle point, which allowed for less biased relative abundance compared to other treatments. <i>Chryseobacterium</i>, CK-1C4-19, and <i>Cetobacterium</i> were the dominant bacteria species for early point treatments in aquaculture-raised fish. Still, they remained the predominant bacteria for only aquaculture-raised vinegar samples in the middle and late points, which allowed for a similar relative abundance to fresh catfish. Meanwhile, <i>Pseudomonas</i> in most lemon and GSE samples became the dominant species at a later point. This study provides a better understanding of bacterial spoilage of catfish during storage. Additionally, we showed that natural preservative treatments can effectively extend the shelf-life of fishery products. |
| format | Article |
| id | doaj-art-27fb0b8a33de4b55add22ab287c6da7c |
| institution | OA Journals |
| issn | 2076-2607 |
| language | English |
| publishDate | 2025-01-01 |
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| spelling | doaj-art-27fb0b8a33de4b55add22ab287c6da7c2025-08-20T02:04:02ZengMDPI AGMicroorganisms2076-26072025-01-0113224410.3390/microorganisms13020244The Microbiome of Catfish (<i>Ictalurus punctatus</i>) Treated with Natural Preservatives During Refrigerated StorageJung-Lim Lee0Gregory Yourek1Food Science and Biotechnology Program, Food Microbiology Laboratory, College of Agriculture Science and Technology, Delaware State University, Dover, DE 19901, USADelaware Nucleotide Analysis (DNA) Core Center, Delaware State University, Dover, DE 19901, USAFish is an essential lean protein source worldwide. Unfortunately, fresh fish food products deteriorate rapidly due to microbial spoilage. With consumers’ growing concerns about using chemical preservatives, we propose using natural preservatives as safer alternatives to prevent microbial spoilage. In this study, we used Next-Generation Sequencing (NGS) metagenomics to study microbiomes on catfish fillets at early (day one for all samples), middle (day seven for control store-bought and aquaculture-raised samples, day nine for other treatment store-bought samples, and day eleven for other treatment aquaculture-raised samples), and late (day fifteen for all store-bought, day eleven for control aquaculture-raised samples, and day twenty-seven for other treatment aquaculture-raised samples) points. Store-bought and aquaculture-raised catfish were treated individually with natural preservatives (vinegar, lemon, and grapefruit seed [GSE]). We observed bacterial populations and sequenced 16S NGS libraries of catfish microbes. Vinegar treatment showed the greatest suppression of bacterial growth in both groups, and GSE and lemon treatment had similar levels of suppression in the mid and late points (−4 to −5 Log CFU/g vinegar and −0.1 to −4 Log CFU/g other treatments in aquaculture and −1 to −2 Log CFU/g vinegar and −0.2 to −0.5 Log CFU/g other treatments in store-bought). Aquaculture-raised vinegar treatment samples had similar proportional taxonomy abundance values through storage duration. <i>Pseudomonas</i>, <i>Janthinobacterium</i>, and <i>Camobacteriaceae</i> were the dominant bacteria species in the early point for store-bought fish. Still, <i>Pseudomonas</i> was suppressed by vinegar treatment in the middle point, which allowed for less biased relative abundance compared to other treatments. <i>Chryseobacterium</i>, CK-1C4-19, and <i>Cetobacterium</i> were the dominant bacteria species for early point treatments in aquaculture-raised fish. Still, they remained the predominant bacteria for only aquaculture-raised vinegar samples in the middle and late points, which allowed for a similar relative abundance to fresh catfish. Meanwhile, <i>Pseudomonas</i> in most lemon and GSE samples became the dominant species at a later point. This study provides a better understanding of bacterial spoilage of catfish during storage. Additionally, we showed that natural preservative treatments can effectively extend the shelf-life of fishery products.https://www.mdpi.com/2076-2607/13/2/244catfish16S metagenomicsmicrobial spoilagefood qualityvinegarlemon |
| spellingShingle | Jung-Lim Lee Gregory Yourek The Microbiome of Catfish (<i>Ictalurus punctatus</i>) Treated with Natural Preservatives During Refrigerated Storage Microorganisms catfish 16S metagenomics microbial spoilage food quality vinegar lemon |
| title | The Microbiome of Catfish (<i>Ictalurus punctatus</i>) Treated with Natural Preservatives During Refrigerated Storage |
| title_full | The Microbiome of Catfish (<i>Ictalurus punctatus</i>) Treated with Natural Preservatives During Refrigerated Storage |
| title_fullStr | The Microbiome of Catfish (<i>Ictalurus punctatus</i>) Treated with Natural Preservatives During Refrigerated Storage |
| title_full_unstemmed | The Microbiome of Catfish (<i>Ictalurus punctatus</i>) Treated with Natural Preservatives During Refrigerated Storage |
| title_short | The Microbiome of Catfish (<i>Ictalurus punctatus</i>) Treated with Natural Preservatives During Refrigerated Storage |
| title_sort | microbiome of catfish i ictalurus punctatus i treated with natural preservatives during refrigerated storage |
| topic | catfish 16S metagenomics microbial spoilage food quality vinegar lemon |
| url | https://www.mdpi.com/2076-2607/13/2/244 |
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