 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Aug 27, 2024 |
| Title |
Early detection of food safety and spoilage incidents based on live microbiome profiling and qPCR-based monitoring of indicators |
| Organism |
food metagenome |
| Experiment type |
Other
|
| Summary |
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.
|
| |
|
| Overall design |
Samples of 16S V3 and V4 region DNA from pastrami production process were sequenced using the Illumina MiSeq platform
|
| |
|
| Contributor(s) |
Cohen Hakmon M, Buhnik-Rosenblau K, Hanani H, Korach-Rechtmana H, Mor D, Etkin E, Kashi Y |
| Citation(s) |
39123650 |
| |
| Submission date |
Feb 07, 2024 |
| Last update date |
Aug 27, 2024 |
| Contact name |
May Cohen Hakmon |
| Organization name |
Technion
|
| Street address |
Shikago
|
| City |
Haifa |
| ZIP/Postal code |
3200005 |
| Country |
Israel |
| |
|
| Platforms (1) |
| GPL34170 |
Illumina MiSeq (food metagenome) |
|
| Samples (145)
|
| GSM8067421 |
BarBQ pastrami, batch A, rep 4 |
| GSM8067422 |
BarBQ pastrami, batch A, rep 5 |
| GSM8067423 |
BarBQ pastrami, batch B, rep 1 |
| GSM8067424 |
BarBQ pastrami, batch B, rep 2 |
| GSM8067425 |
BarBQ pastrami, batch B, rep 3 |
| GSM8067426 |
BarBQ pastrami, batch B, rep 4 |
| GSM8067427 |
BarBQ pastrami, batch B, rep 5 |
| GSM8067428 |
BarBQ pastrami, batch C, rep 1 |
| GSM8067429 |
BarBQ pastrami, batch C, rep 2 |
| GSM8067430 |
BarBQ pastrami, batch C, rep 3 |
| GSM8067431 |
BarBQ pastrami, batch C, rep 4 |
| GSM8067432 |
sausage, batch A, rep 1 |
| GSM8067433 |
sausage, batch A, rep 2 |
| GSM8067434 |
sausage, batch A, rep 3 |
| GSM8067435 |
sausage, batch A, rep 4 |
| GSM8067436 |
sausage, batch A, rep 5 |
| GSM8067437 |
sausage, batch B, rep 1 |
| GSM8067438 |
sausage, batch B, rep 2 |
| GSM8067439 |
sausage, batch B, rep 3 |
| GSM8067440 |
sausage, batch B, rep 4 |
| GSM8067441 |
sausage, batch B, rep 5 |
| GSM8067442 |
sausage, batch C, rep 1 |
| GSM8067443 |
sausage, batch C, rep 2 |
| GSM8067444 |
sausage, batch C, rep 3 |
| GSM8067445 |
sausage, batch C, rep 4 |
| GSM8067446 |
sausage, batch C, rep 5 |
| GSM8067447 |
kabanos, batch A, rep 1 |
| GSM8067448 |
kabanos, batch A, rep 2 |
| GSM8067449 |
kabanos, batch A, rep 3 |
| GSM8067450 |
kabanos, batch A, rep 4 |
| GSM8067451 |
kabanos, batch A, rep 5 |
| GSM8067452 |
kabanos, batch B, rep 1 |
| GSM8067453 |
kabanos, batch B, rep 2 |
| GSM8067454 |
kabanos, batch B, rep 3 |
| GSM8067455 |
kabanos, batch B, rep 4 |
| GSM8067456 |
kabanos, batch B, rep 5 |
| GSM8067457 |
kabanos, batch C, rep 1 |
| GSM8067458 |
kabanos, batch C, rep 2 |
| GSM8067459 |
kabanos, batch C, rep 3 |
| GSM8067460 |
kabanos, batch C, rep 4 |
| GSM8067461 |
smoked pastrami, rep 1 |
| GSM8067462 |
smoked pastrami, rep 2 |
| GSM8067463 |
smoked pastrami, rep 3 |
| GSM8067464 |
smoked pastrami, rep 4 |
| GSM8067465 |
smoked pastrami, rep 5 |
| GSM8067466 |
BarBQ pastrami, former batch, rep 1 |
| GSM8067467 |
BarBQ pastrami, former batch, rep 2 |
| GSM8067468 |
BarBQ pastrami, former batch, rep 3 |
| GSM8067469 |
BarBQ pastrami, former batch, rep 4 |
| GSM8067470 |
BarBQ pastrami, former batch, rep 5 |
| GSM8067471 |
BarBQ pastrami production chain, raw material, with lactate, rep 1 |
| GSM8067472 |
BarBQ pastrami production chain, raw material, with lactate, rep 2 |
| GSM8067473 |
BarBQ pastrami production chain, raw material, with lactate, rep 3 |
| GSM8067474 |
BarBQ pastrami production chain, raw material, with lactate, rep 4 |
| GSM8067475 |
BarBQ pastrami production chain, raw material, with lactate, rep 5 |
| GSM8067476 |
BarBQ pastrami production chain, brine, with lactate, rep 1 |
| GSM8067477 |
BarBQ pastrami production chain, brine, with lactate, rep 2 |
| GSM8067478 |
BarBQ pastrami production chain, brine, with lactate, rep 3 |
| GSM8067479 |
BarBQ pastrami production chain, brine, with lactate, rep 4 |
| GSM8067480 |
BarBQ pastrami production chain, brine, with lactate, rep 5 |
| GSM8067481 |
BarBQ pastrami production chain, mixture, with lactate, rep 1 |
| GSM8067482 |
BarBQ pastrami production chain, mixture, with lactate, rep 2 |
| GSM8067483 |
BarBQ pastrami production chain, mixture, with lactate, rep 3 |
| GSM8067484 |
BarBQ pastrami production chain, mixture, with lactate, rep 4 |
| GSM8067485 |
BarBQ pastrami production chain, mixture, with lactate, rep 5 |
| GSM8067486 |
BarBQ pastrami production chain, after cooking, with lactate, rep 1 |
| GSM8067487 |
BarBQ pastrami production chain, after cooking, with lactate, rep 2 |
| GSM8067488 |
BarBQ pastrami production chain, after cooking, with lactate, rep 3 |
| GSM8067489 |
BarBQ pastrami production chain, after cooking, with lactate, rep 4 |
| GSM8067490 |
BarBQ pastrami production chain, after cooking, with lactate, rep 5 |
| GSM8067491 |
BarBQ pastrami production chain, after slicing, with lactate, rep 1 |
| GSM8067492 |
BarBQ pastrami production chain, after slicing, with lactate, rep 2 |
| GSM8067493 |
BarBQ pastrami production chain, after slicing, with lactate, rep 3 |
| GSM8067494 |
BarBQ pastrami production chain, after slicing, with lactate, rep 4 |
| GSM8067495 |
BarBQ pastrami production chain, after slicing, with lactate, rep 5 |
| GSM8067496 |
BarBQ pastrami production chain, brine, without lactate, rep 1 |
| GSM8067497 |
BarBQ pastrami production chain, brine, without lactate, rep 2 |
| GSM8067498 |
BarBQ pastrami production chain, brine, without lactate, rep 3 |
| GSM8067499 |
BarBQ pastrami production chain, brine, without lactate, rep 4 |
| GSM8067500 |
BarBQ pastrami production chain, brine, without lactate, rep 5 |
| GSM8067501 |
BarBQ pastrami production chain, mixture, without lactate, rep 1 |
| GSM8067502 |
BarBQ pastrami production chain, mixture, without lactate, rep 2 |
| GSM8067503 |
BarBQ pastrami production chain, mixture, without lactate, rep 3 |
| GSM8067504 |
BarBQ pastrami production chain, mixture, without lactate, rep 4 |
| GSM8067505 |
BarBQ pastrami production chain, mixture, without lactate, rep 5 |
| GSM8067506 |
BarBQ pastrami production chain, after cooking, without lactate, rep 1 |
| GSM8067507 |
BarBQ pastrami production chain, after cooking, without lactate, rep 2 |
| GSM8067508 |
BarBQ pastrami production chain, after cooking, without lactate, rep 3 |
| GSM8067509 |
BarBQ pastrami production chain, after cooking, without lactate, rep 4 |
| GSM8067510 |
BarBQ pastrami production chain, after cooking, without lactate, rep 5 |
| GSM8067511 |
BarBQ pastrami production chain, after slicing, without lactate, rep 1 |
| GSM8067512 |
BarBQ pastrami production chain, after slicing, without lactate, rep 2 |
| GSM8067513 |
BarBQ pastrami production chain, after slicing, without lactate, rep 3 |
| GSM8067514 |
BarBQ pastrami production chain, after slicing, without lactate, rep 4 |
| GSM8067515 |
BarBQ pastrami production chain, after slicing, without lactate, rep 5 |
| GSM8067516 |
BarBQ pastrami production chain, after one week in storage, with lactate, rep 1 |
| GSM8067517 |
BarBQ pastrami production chain, after one week in storage, with lactate, rep 2 |
| GSM8067518 |
BarBQ pastrami production chain, after one week in storage, with lactate, rep 3 |
| GSM8067519 |
BarBQ pastrami production chain, after one week in storage, with lactate, rep 4 |
| GSM8067520 |
BarBQ pastrami production chain, after one week in storage, with lactate, rep 5 |
| GSM8067521 |
BarBQ pastrami production chain, after one week in storage, without lactate, rep 1 |
| GSM8067522 |
BarBQ pastrami production chain, after one week in storage, without lactate, rep 2 |
| GSM8067523 |
BarBQ pastrami production chain, after one week in storage, without lactate, rep 3 |
| GSM8067524 |
BarBQ pastrami production chain, after one week in storage, without lactate, rep 4 |
| GSM8067525 |
BarBQ pastrami production chain, after one week in storage, without lactate, rep 5 |
| GSM8067526 |
BarBQ pastrami production chain, after two weeks in storage, with lactate, rep 1 |
| GSM8067527 |
BarBQ pastrami production chain, after two weeks in storage, with lactate, rep 2 |
| GSM8067528 |
BarBQ pastrami production chain, after two weeks in storage, with lactate, rep 3 |
| GSM8067529 |
BarBQ pastrami production chain, after two weeks in storage, with lactate, rep 4 |
| GSM8067530 |
BarBQ pastrami production chain, after two weeks in storage, with lactate, rep 5 |
| GSM8067531 |
BarBQ pastrami production chain, after two weeks in storage, without lactate, rep 1 |
| GSM8067532 |
BarBQ pastrami production chain, after two weeks in storage, without lactate, rep 2 |
| GSM8067533 |
BarBQ pastrami production chain, after two weeks in storage, without lactate, rep 3 |
| GSM8067534 |
BarBQ pastrami production chain, after two weeks in storage, without lactate, rep 4 |
| GSM8067535 |
BarBQ pastrami production chain, after two weeks in storage, without lactate, rep 5 |
| GSM8067536 |
BarBQ pastrami production chain, after six weeks in storage, with lactate, rep 1 |
| GSM8067537 |
BarBQ pastrami production chain, after six weeks in storage, with lactate, rep 2 |
| GSM8067538 |
BarBQ pastrami production chain, after six weeks in storage, with lactate, rep 3 |
| GSM8067539 |
BarBQ pastrami production chain, after six weeks in storage, with lactate, rep 4 |
| GSM8067540 |
BarBQ pastrami production chain, after six weeks in storage, with lactate, rep 5 |
| GSM8067541 |
BarBQ pastrami production chain, after six weeks in storage, without lactate, rep 1 |
| GSM8067542 |
BarBQ pastrami production chain, after six weeks in storage, without lactate, rep 2 |
| GSM8067543 |
BarBQ pastrami production chain, after six weeks in storage, without lactate, rep 3 |
| GSM8067544 |
BarBQ pastrami production chain, after six weeks in storage, without lactate, rep 4 |
| GSM8067545 |
BarBQ pastrami production chain, after six weeks in storage, without lactate, rep 5 |
| GSM8067546 |
BarBQ pastrami production chain, after three months in storage, with lactate, rep 1 |
| GSM8067547 |
BarBQ pastrami production chain, after three months in storage, with lactate, rep 2 |
| GSM8067548 |
BarBQ pastrami production chain, after three months in storage, with lactate, rep 3 |
| GSM8067549 |
BarBQ pastrami production chain, after three months in storage, with lactate, rep 4 |
| GSM8067550 |
BarBQ pastrami production chain, after three months in storage, with lactate, rep 5 |
| GSM8067551 |
BarBQ pastrami production chain, after three months in storage, without lactate, rep 1 |
| GSM8067552 |
BarBQ pastrami production chain, after three months in storage, without lactate, rep 2 |
| GSM8067553 |
BarBQ pastrami production chain, after three months in storage, without lactate, rep 3 |
| GSM8067554 |
BarBQ pastrami production chain, after three months in storage, without lactate, rep 4 |
| GSM8067555 |
BarBQ pastrami production chain, after three months in storage, without lactate, rep 5 |
| GSM8067556 |
BarBQ pastrami production chain, mixture, live bacteria, rep 1 |
| GSM8067557 |
BarBQ pastrami production chain, mixture, live bacteria, rep 2 |
| GSM8067558 |
BarBQ pastrami production chain, mixture, live bacteria, rep 3 |
| GSM8067559 |
BarBQ pastrami production chain, mixture, all bacteria, rep 1 |
| GSM8067560 |
BarBQ pastrami production chain, mixture, all bacteria, rep 2 |
| GSM8067561 |
BarBQ pastrami production chain, mixture, all bacteria, rep 3 |
| GSM8067562 |
BarBQ pastrami production chain, mixture, all bacteria, rep 4 |
|
| Relations |
| BioProject |
PRJNA1074259 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE255249_figure_1_quantified_microorganisms.csv.gz |
31.3 Kb |
(ftp)(http) |
CSV |
| GSE255249_figure_2_quantified_microorganisms.csv.gz |
14.1 Kb |
(ftp)(http) |
CSV |
| GSE255249_figure_3_quantified_microorganisms.csv.gz |
28.5 Kb |
(ftp)(http) |
CSV |
| GSE255249_processed.tar.gz |
8.9 Mb |
(ftp)(http) |
TAR |
| GSE255249_supplametary_quantified_microorganisms.csv.gz |
9.2 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
|
|
|
|
 |
Less...
More...