Application of a High-Throughput Amplicon Sequencing Method to Chart the Bacterial Communities that Are Associated with European Fermented Meats from Different Origins
Abstract
:1. Introduction
2. Materials and Methods
2.1. Sampling and Experimental Set-Up
2.2. Extraction of Bacterial Genomic DNA
2.3. PCR Assay and Sequencing
2.4. Bioinformatic Analysis
2.5. Volatile Organic Compound Profiling
2.6. Statistics
3. Results
3.1. Bacterial Communities in Fermented Meat Products from Different Origins
3.2. Volatile Organic Compound Profiling
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Conflicts of Interest
Data Availability
References
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Primer | Primer Sequence | Amplicon Size (bp) |
---|---|---|
Tuf387 | 5’-YCCAATGCCWCAAACKCGTGA-3’ | 379 |
Tuf765 | 5’-RAYTTGHCCACGTTCAACAC-3’ |
Sample | MSA Counts [log(CFU/g)] | MRS Agar Counts [log(CFU/g)] | pH | Salt Content [g/100g] | ||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|
Individual | Average | SD | Individual | Average | SD | Individual | Average | SD | Individual | Average | SD | |
BE1 | 5.40 | 6.75 | 5.12 | 4.10 | ||||||||
BE2 | 5.13 | 5.18 | 0.20 | 8.27 | 7.76 | 0.87 | 5.00 | 5.27 | 0.37 | 4.60 | 4.30 | 0.26 |
BE3 | 5.02 | 8.25 | 5.70 | 4.20 | ||||||||
DE1 | 5.57 | 7.14 | 4.78 | 3.80 | ||||||||
DE2 | 5.00 | 5.17 | 0.35 | 7.91 | 7.64 | 0.43 | 4.57 | 4.66 | 0.11 | 3.25 | 3.43 | 0.32 |
DE3 | 4.94 | 7.88 | 4.63 | 3.25 | ||||||||
ES1 | 5.72 | 6.53 | 5.82 | 3.00 | ||||||||
ES2 | 5.80 | 5.83 | 0.12 | 5.60 | 6.83 | 1.41 | 6.04 | 5.85 | 0.18 | 3.00 | 3.27 | 0.46 |
ES3 | 5.95 | 8.37 | 5.69 | 3.80 | ||||||||
FR1 | 8.16 | 7.70 | 5.70 | 5.70 | ||||||||
FR2 | 6.52 | 7.31 | 0.82 | 8.26 | 8.16 | 0.42 | 5.51 | 5.59 | 0.10 | 4.60 | 4.83 | 0.78 |
FR3 | 7.26 | 8.52 | 5.56 | 4.20 | ||||||||
IT1 | 8.63 | 8.44 | 5.66 | 3.40 | ||||||||
IT2 | 6.68 | 7.34 | 1.12 | 8.56 | 8.34 | 0.30 | 5.26 | 5.57 | 0.28 | 3.30 | 3.67 | 0.55 |
IT3 | 6.70 | 8.00 | 5.80 | 4.30 |
Sample | Culture-Dependent Method (Total Number of Isolates) | Amplicon-Based HTS Method |
---|---|---|
BE1 | S. carnosus (18) | S. carnosus, S. vitulinus, S. xylosus |
BE2 | S. carnosus (29) | S. carnosus, S. saprophyticus, S. xylosus |
BE3 | n.a. 1 | S. carnosus, S. pasteuri, S. saprophyticus, S. sciuri, S. xylosus |
DE1 | S. carnosus, S. xylosus (13) | S. carnosus, S. gallinarum, S. sciuri, S. xylosus |
DE2 | S. carnosus (20) | S. carnosus, S. equorum, S. xylosus |
DE3 | S. carnosus (15) | S. carnosus, S. xylosus |
ES1 | S. equorum, S. saprophyticus (21) | S. arlettae, S. carnosus, S. equorum, S. gallinarum, S. lentus, S. saprophyticus, S. sciuri, S. xylosus |
ES2 | S. carnosus, S. equorum, S. xylosus (15) | S. carnosus, S. equorum, S. gallinarum, S. saprophyticus, S. sciuri, S. succinus, S. xylosus |
ES3 | S. equorum (14) | S. carnosus, S. equorum, S. gallinarum, S. saprophyticus, S. sciuri, S. vitulinus, S. xylosus |
FR1 | S. equorum, S. xylosus (23) | S. carnosus, S. equorum, S. saprophyticus, S. xylosus |
FR2 | S. equorum, S. xylosus (13) | S. carnosus, S. vitulinus, S. xylosus |
FR3 | S. equorum, S. xylosus (10) | S. carnosus, S. equorum, S. saprophyticus, S. xylosus |
IT1 | S. equorum, S. xylosus (12) | S. equorum, S. succinus, S. xylosus |
IT2 | S. xylosus (13) | S. carnosus, S. equorum, S. gallinarum, S. kloosii, S. saprophyticus, S. sciuri, S. xylosus |
IT3 | S. xylosus (20) | S. equorum, S. saprophyticus, S. vitulinus, S. xylosus |
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Van Reckem, E.; Charmpi, C.; Van der Veken, D.; Borremans, W.; De Vuyst, L.; Weckx, S.; Leroy, F. Application of a High-Throughput Amplicon Sequencing Method to Chart the Bacterial Communities that Are Associated with European Fermented Meats from Different Origins. Foods 2020, 9, 1247. https://doi.org/10.3390/foods9091247
Van Reckem E, Charmpi C, Van der Veken D, Borremans W, De Vuyst L, Weckx S, Leroy F. Application of a High-Throughput Amplicon Sequencing Method to Chart the Bacterial Communities that Are Associated with European Fermented Meats from Different Origins. Foods. 2020; 9(9):1247. https://doi.org/10.3390/foods9091247
Chicago/Turabian StyleVan Reckem, Emiel, Christina Charmpi, David Van der Veken, Wim Borremans, Luc De Vuyst, Stefan Weckx, and Frédéric Leroy. 2020. "Application of a High-Throughput Amplicon Sequencing Method to Chart the Bacterial Communities that Are Associated with European Fermented Meats from Different Origins" Foods 9, no. 9: 1247. https://doi.org/10.3390/foods9091247