Amplicon of food spoilage microbiota.
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Project description:A prototype oligonucleotide microarray was designed to detect and identify viable bacterial species with the potential to grow of common beer spoilage microorganisms from the genera Lactobacillus, Megasphaera, Pediococcus and Pectinatus. Probes targeted the intergenic spacer regions (ISR) between 16S and 23S rRNA, which were amplified in a combination of reverse transcriptase (RT) and polymerase chain reaction (PCR) prior to hybridization. This method allows the detection and discrimination of single bacterial species in a complex sample. Furthermore, microarrays using oligonucleotide probes targeting the ISR allow the distinction between viable bacteria with the potential to grow and non-growing bacteria. The results demonstrate the feasibility of oligonucleotide microarrays as a contamination control in food industry for the detection and identification of spoilage microorganisms within mixed population. Keywords: microarray, oligonucleotide, species-specific, detection, beer spoilage bacteria
2007-05-23 | GSE7840 | GEO
Project description:Microbiota in spoilage pork meat Metagenome
| PRJNA823539 | ENA
Project description:Early detection of spoilage microorganisms and food pathogens is of major importance in preventing food recalls and foodborne outbreaks. Although constant effort is invested in developing sensitive methods for rapid microbial detection, none of the current methods enables the detection of food pathogens within a few hours; therefore, development of innovative early-warning food-testing strategies are needed. Herein, we assessed a novel strategy that harnesses the microbiome signature of a food product to determine deviations in the abundance of particular community members and detect production defects. Employing the production process of barbecued (BarBQ) pastrami as a model, we characterized the microbiome profiles of the product along the production line using next-generation sequencing of the 16S rRNA gene, concentrating on the live microbiota. Following the establishment of a microbiome dataset representing a properly produced product, we were able to identify shifts in the microbiome profile of a defective batch produced under potassium lactate deficiency. With the identification of Vibrio and Lactobacillus as potential indicator bacteria for potassium lactate deficiency, rapid qPCR assays were designed for their quantification. Aligned with the microbiome profiling results, these qPCR assays were effective for rapid identification of a defective production event. This implies the use of rapid quantification targeting microbiome profile-derived indicator bacteria for in-house detection of defective batches and identification of food-safety and quality events with results obtained on the same day. The suggested strategy should pave the way toward safer and more efficient food-production systems.
2024-08-27 | GSE255249 | GEO
Project description:Mostly, lactic acid bacteria (LAB), including food-spoilage-associated, grow in communities consisting of several microbial species. The interspecies interactions eventually shape the structure and global activity of a given microbial community. Generally, the knowledge on system level responses of LAB (especially food-spoilage-associated) during such interactions is very limited. To study transcriptome responses during interactions between three MAP meat-spoilage-associated LAB (Leuconostoc gelidum subsp. gasicomitatum LMG 18811T, Lactococcus piscium MKFS47 and Lactobacillus oligofermentans LMG 22743T) we grew them separately in individual cultures and in mixed cultures pairwise (three combinations) and all together (triple culture) in three replicates on a glucose-containing growth medium (MRS) under microaerobic conditions at 25 C, samples were taken at three time points (3, 5 and 11 h) and extracted RNA were sequenced. The experiments were performed in two batches. At first (batch 1), co-cultivation of Le. gelidum and Lc. piscium accompanied with their individual cultures was performed and processed. The raw RNA-seq data for the individual culture of Lc. piscium from the batch 1 were uploaded earlier and are available in the ArrayExpress database under accession number E-MTAB-3245. Later (batch 2), two other pairwise cultures (Le. gelidum + Lb. oligofermentans and Lc. piscium + Lb. oligofermentans) and the triple culture were grown together with the individual cultures of all three LAB. Designations used for the sample names: G: Le. gelidum; P: Lc. piscium; O: Lb. oligofermentans; GO, PO, PG: pairwise cultures of the corresponding species; OPG: triple culture; b1: batch 1; b2: batch 2. Example: 3G2_b1: 3 h, Le. gelidum, 2nd replicate, batch 1; 11PO3_b2: 11 h, pairwise culture of Lc. piscium and Lb. oligofermentans, 3d replicate, batch 2. One sample (5PO3_b2) had very low number of reads ~ 9000, and, therefore, was not uploaded under this project. RNA extraction and library construction were done analogously as in the study (Andreevskaya M et al., 2015. Appl. Environ. Microbiol. 81:38003811, doi: 10.1128/AEM.00320-15). Ribosomal RNA was omitted. Libraries were sequenced in five lanes using SOLiD 5500XL (Life technologies, Foster City, Ca, USA) to produce 75 bp single-end reads. For the data submission, xsq files obtained from SOLiD 5500XL machine, were converted into fastq files. Adapter sequences were removed using cutadapt 1.4.1.
2018-04-27 | E-MTAB-5499 | biostudies-arrayexpress
Project description:BackgroundSpoilage of food products is frequently caused by bacterial spores and lactic acid bacteria. Identification of these organisms by classic cultivation methods is limited by their ability to form colonies on nutrient agar plates. In this study, we adapted and optimized 16S rRNA amplicon sequencing for quantification of bacterial spores in a canned food matrix and for monitoring the outgrowth of spoilage microbiota in a ready-to-eat food matrix.ResultsThe detection limit of bar-coded 16S rRNA amplicon sequencing was determined for the number of bacterial spores in a canned food matrix. Analysis of samples from a canned food matrix spiked with a mixture of equinumerous spores from the thermophiles, Geobacillus stearothermophilus and Geobacillus thermoglucosidans, and the mesophiles, Bacillus sporothermodurans, Bacillus cereus, and Bacillus subtilis, led to the detection of these spores with an average limit of 2 × 10(2) spores ml(-1). The data were normalized by setting the number of sequences resulting from DNA of an inactivated bacterial species, present in the matrix at the same concentration in all samples, to a fixed value for quantitative sample-to-sample comparisons. The 16S rRNA amplicon sequencing method was also employed to monitor population dynamics in a ready-to-eat rice meal, incubated over a period of 12 days at 7 °C. The most predominant outgrowth was observed by the genera Leuconostoc, Bacillus, and Paenibacillus. Analysis of meals pre-treated with weak acids showed inhibition of outgrowth of these three genera. The specificity of the amplicon synthesis was improved by the design of oligonucleotides that minimize the amplification of 16S rRNA genes from chloroplasts originating from plant-based material present in the food.ConclusionThis study shows that the composition of complex spoilage populations, including bacterial spores, can be monitored in complex food matrices by bar-coded amplicon sequencing in a quantitative manner. In order to allow sample-to-sample comparisons, normalizations based on background DNA are described. This method offers a solution for the identification and quantification of spoilage microbiota, which cannot be cultivated under standard laboratory conditions. The study indicates variable detection limits among species of bacterial spores resulting from differences in DNA extraction efficiencies.
| S-EPMC4515881 | biostudies-literature
Project description:Origin and ecological selection of core and food-specific bacterial communities associated with meat and seafood spoilage.
| PRJEB4975 | ENA
Project description:Role of salt and storage packaging conditions defining the spoilage microbial diversity of raw pork sausages
| PRJEB9493 | ENA
Project description:Reducing food losses by microbial spoilage prediction (raw sequences data from amplicon analyses)
| PRJNA522361 | ENA
Project description:Proteomic strategy to define therapeutically relevant targets in cell lines that contain the 11q13 amplicon compared to those that do not and to ascertain which genes are amplified at the protein level and, concomitantly, are key drivers for tumor growth and/or maintenance. Furthermore, so called passenger genes that are amplified with driver genes and a manifest on the cell surface can be attractive targets for an antibody – drug conjugate approach (ADC).
2015-08-04 | PXD002486 | Pride
Project description:Meat and seafood spoilage ecosystems harbor extensive bacterial genomic diversity that is mainly found within a small number of species but within a large number of strains with different spoilage metabolic potential. To decipher the intraspecies diversity of such microbiota, traditional metagenetic analysis using the 16S rRNA gene is inadequate. We therefore assessed the potential benefit of an alternative genetic marker, gyrB, which encodes the subunit B of DNA gyrase, a type II DNA topoisomerase. A comparison between 16S rDNA-based (V3-V4) amplicon sequencing and gyrB-based amplicon sequencing was carried out in five types of meat and seafood products, with five mock communities serving as quality controls. Our results revealed that bacterial richness in these mock communities and food samples was estimated with higher accuracy using gyrB than using16S rDNA. However, for Firmicutes species, 35% of putative gyrB reads were actually identified as sequences of a gyrB paralog, parE, which encodes subunit B of topoisomerase IV; we therefore constructed a reference database of published sequences of both gyrB and pare for use in all subsequent analyses. Despite this co-amplification, the deviation between relative sequencing quantification and absolute qPCR quantification was comparable to that observed for 16S rDNA for all the tested species. This confirms that gyrB can be used successfully alongside 16S rDNA to determine the species composition (richness and evenness) of food microbiota. The major benefit of gyrB sequencing is its potential for improving taxonomic assignment and for further investigating OTU richness at the subspecies level, thus allowing more accurate discrimination of samples. Indeed, 80% of the reads of the 16S rDNA dataset were represented by thirteen 16S rDNA-based OTUs that could not be assigned at the species-level. Instead, these same clades corresponded to 44 gyrB-based OTUs, which differentiated various lineages down to the subspecies level. The increased ability of gyrB-based analyses to track and trace phylogenetically different groups of strains will generate improved resolution and more reliable results for studies of the strains implicated in food processes.
| S-EPMC6155546 | biostudies-literature