Exploring the Sources of Bacterial Spoilers in Beefsteaks by Culture-Independent High-Throughput Sequencing

Filippis, Francesca De; Storia, Antonietta La; Villani, Francesco; Ercolini, Danilo

doi:10.1371/journal.pone.0070222

Cited by 180 publications

(130 citation statements)

References 42 publications

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“…However, recent advances in massively parallel, short-amplicon sequencing technologies have launched a breakthrough in microbial ecology studies of wine-and foodfermentation systems (14,(21)(22)(23)(24)(25)(26)(27), putting hitherto untenable ecological questions within reach.…”

Section: Significancementioning

confidence: 99%

Microbial biogeography of wine grapes is conditioned by cultivar, vintage, and climate

Bokulich

Thorngate²,

Richardson³

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

797

758

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Wine grapes present a unique biogeography model, wherein microbial biodiversity patterns across viticultural zones not only answer questions of dispersal and community maintenance, they are also an inherent component of the quality, consumer acceptance, and economic appreciation of a culturally important food product. On their journey from the vineyard to the wine bottle, grapes are transformed to wine through microbial activity, with indisputable consequences for wine quality parameters. Wine grapes harbor a wide range of microbes originating from the surrounding environment, many of which are recognized for their role in grapevine health and wine quality. However, determinants of regional wine characteristics have not been identified, but are frequently assumed to stem from viticultural or geological factors alone. This study used a high-throughput, short-amplicon sequencing approach to demonstrate that regional, site-specific, and grapevariety factors shape the fungal and bacterial consortia inhabiting wine-grape surfaces. Furthermore, these microbial assemblages are correlated to specific climatic features, suggesting a link between vineyard environmental conditions and microbial inhabitation patterns. Taken together, these factors shape the unique microbial inputs to regional wine fermentations, posing the existence of nonrandom "microbial terroir" as a determining factor in regional variation among wine grapes.viticulture | agriculture | metagenomics | next-generation sequencing

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Section: Significancementioning

confidence: 99%

Microbial biogeography of wine grapes is conditioned by cultivar, vintage, and climate

Bokulich

Thorngate²,

Richardson³

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

797

758

View full text Add to dashboard Cite

show abstract

“…S2) in which each node represented either a sample or a bacterial OTU. Connections were drawn between samples and OTUs, with edge weights defined as the number of sequences from each OTU that occurred in each sample (De Filippis et al 2013). Networks were visualized using Cytoscape 3.0.…”

Section: Comparison Of the Bacterial Microflora Of Btana From The Varmentioning

confidence: 99%

Metagenomic analysis of the bacterial microbiota linked to the traditional Algerian date product “Btana”

et al. 2015

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In this study, using high throughput Bpyrosequencing,ŵ e highlighted the bacterial diversity of the traditional Algerian date product BBtana^that is produced in southern Algeria using both direct (DBM) and indirect (UBM) methods. Metagenomic analysis yielded a total of 103,379 reads, with a 606 total operational taxonomic units (OTUs) detected. Firmicutes represented 84.79 % of the total pyrosequencing reads. Phylogenetic analysis revealed that the Bacillales represented 90.20 % ± 15.12 % of the total reads. Among the phylotypes detected, Bacillus was the dominant genus (39.53 %). While Bacillus megaterium was shared among all of the samples, its distribution varied widely. Non-metric multidimensional scaling (nMDS) analysis showed that UBM samples clustered together, and three main OTUs were found in these UBM samples: Paenibacillus polymyxa, Paenibacillus xylanexedens, and Planomicrobium JN082684. Correlation analysis showed no association between parameters of the samples (age, pH, water activity) and the specific microbiota.

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“…From pork slaughtering to final packaging, their manufacture requires several steps (meat cutting, blending, and stuffing), with each a potential source of bacterial contamination (1)(2)(3). Raw pork sausages are thus very sensitive to spoilage unless specific treatments are applied to prevent their rapid sensory degradation.…”

mentioning

confidence: 99%

Reducing Salt in Raw Pork Sausages Increases Spoilage and Correlates with Reduced Bacterial Diversity

Fougy

Desmonts²,

Coeuret

et al. 2016

Appl Environ Microbiol

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Raw sausages are perishable foodstuffs; reducing their salt content raises questions about a possible increased spoilage of these products. In this study, we evaluated the influence of salt reduction (from 2.0% to 1.5% [wt/wt]), in combination with two types of packaging (modified atmosphere [50% mix of CO 2 -N 2 ] and vacuum packaging), on the onset of spoilage and on the diversity of spoilage-associated bacteria. After 21 days of storage at 8°C, spoilage was easily observed, characterized by noticeable graying of the products and the production of gas and off-odors defined as rancid, sulfurous, or sour. At least one of these types of spoilage occurred in each sample, and the global spoilage intensity was more pronounced in samples stored under modified atmosphere than under vacuum packaging and in samples with the lower salt content. Metagenetic 16S rRNA pyrosequencing revealed that vacuum-packaged samples contained a higher total bacterial richness (n ‫؍‬ 69 operational taxonomic units [OTUs]) than samples under the other packaging condition (n ‫؍‬ 46 OTUs). The core community was composed of 6 OTUs (Lactobacillus sakei, Lactococcus piscium, Carnobacterium divergens, Carnobacterium maltaromaticum, Serratia proteamaculans, and Brochothrix thermosphacta), whereas 13 OTUs taxonomically assigned to the Enterobacteriaceae, Enterococcaceae, and Leuconostocaceae families comprised a less-abundant subpopulation. This subdominant community was significantly more abundant when 2.0% salt and vacuum packaging were used, and this correlated with a lower degree of spoilage. Our results demonstrate that salt reduction, particularly when it is combined with CO 2 -enriched packaging, promotes faster spoilage of raw sausages by lowering the overall bacterial diversity (both richness and evenness). IMPORTANCEOur study takes place in the context of raw meat product manufacturing and is linked to a requirement for salt reduction. Health guidelines are calling for a reduction in dietary salt intake. However, salt has been used for a very long time as a hurdle technology, and salt reduction in meat products raises the question of spoilage and waste of food. The study was conceived to assess the role of sodium chloride reduction in meat products, both at the level of spoilage development and at the level of bacterial diversity, using 16S rRNA amplicon sequencing and raw pork sausage as a meat model.

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Exploring the Sources of Bacterial Spoilers in Beefsteaks by Culture-Independent High-Throughput Sequencing

Cited by 180 publications

References 42 publications

Microbial biogeography of wine grapes is conditioned by cultivar, vintage, and climate

Microbial biogeography of wine grapes is conditioned by cultivar, vintage, and climate

Metagenomic analysis of the bacterial microbiota linked to the traditional Algerian date product “Btana”

Reducing Salt in Raw Pork Sausages Increases Spoilage and Correlates with Reduced Bacterial Diversity

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