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. 2013 Jul 25;8(7):e70222.
doi: 10.1371/journal.pone.0070222. Print 2013.

Exploring the sources of bacterial spoilers in beefsteaks by culture-independent high-throughput sequencing

Francesca De Filippis  1 , Antonietta La Storia, Francesco Villani, Danilo Ercolini
Affiliations

Exploring the sources of bacterial spoilers in beefsteaks by culture-independent high-throughput sequencing

Francesca De Filippis et al. PLoS One. .

Abstract

Microbial growth on meat to unacceptable levels contributes significantly to change meat structure, color and flavor and to cause meat spoilage. The types of microorganisms initially present in meat depend on several factors and multiple sources of contamination can be identified. The aims of this study were to evaluate the microbial diversity in beefsteaks before and after aerobic storage at 4°C and to investigate the sources of microbial contamination by examining the microbiota of carcasses wherefrom the steaks originated and of the processing environment where the beef was handled. Carcass, environmental (processing plant) and meat samples were analyzed by culture-independent high-throughput sequencing of 16S rRNA gene amplicons. The microbiota of carcass swabs was very complex, including more than 600 operational taxonomic units (OTUs) belonging to 15 different phyla. A significant association was found between beef microbiota and specific beef cuts (P<0.01) indicating that different cuts of the same carcass can influence the microbial contamination of beef. Despite the initially high complexity of the carcass microbiota, the steaks after aerobic storage at 4°C showed a dramatic decrease in microbial complexity. Pseudomonas sp. and Brochothrix thermosphacta were the main contaminants, and Acinetobacter, Psychrobacter and Enterobacteriaceae were also found. Comparing the relative abundance of OTUs in the different samples it was shown that abundant OTUs in beefsteaks after storage occurred in the corresponding carcass. However, the abundance of these same OTUs clearly increased in environmental samples taken in the processing plant suggesting that spoilage-associated microbial species originate from carcasses, they are carried to the processing environment where the meat is handled and there they become a resident microbiota. Such microbiota is then further spread on meat when it is handled and it represents the starting microbial association wherefrom the most efficiently growing microbial species take over during storage and can cause spoilage.

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Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Figure 1
Figure 1. Carcass sampling points used in this study; beef cuts: A, brisket; B, chuck; C, thick-flank.
A general scheme of the beefsteaks at time zero (t0) and after one week of aerobic storage at 4°C (t6) analyzed in Experiment 1 and 2 is provided. For Experiment 1, beef steaks were divided in three sub-portions (x, y, z) and analyzed separately.
Figure 2
Figure 2. Abundance of bacterial families in carcass swabs, environmental swabs, beefsteaks at time zero (t0) and after one week of aerobic storage at 4°C (t6) in experiment 1 (panel a) and experiment 2 (panel b).
Beefsteaks samples are labeled according to the beef cut of origin: A, brisket; B, chuck; C, thick-flank. Color key legend shows only bacterial families with >8% abundance.
Figure 3
Figure 3. Distribution of bacterial genera and species in carcass swabs, environmental swabs, beefsteaks at time zero (t0) and after one week of aerobic storage at 4°C (t6) in experiment 1 (panel a) and experiment 2 (panel b).
Beefsteaks samples are labeled according to the beef cut of origin: A, brisket; B, chuck; C, thick-flank. Only OTUs occurring at>4% abundance in at least 2 samples were included. Abundance of OTUs in the 3 sub-portions of beefsteaks from experiment 1 was averaged. Color scale indicates the relative abundance of each OTU within the samples.
Figure 4
Figure 4. Principal Coordinates Analysis of weighted UniFrac distances for 16S rRNA gene sequence data.
Panel a, samples from experiment 1; Panel b, samples from experiment 2. Beef cuts: A, brisket; B, chuck; C, thick-flank. For Experiment 1, beef steaks were divided in three sub-portions (x, y, z) and analyzed separately.
See this image and copyright information in PMC

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