Bacterial diversity in typical Italian salami at different ripening stages as revealed by high-throughput sequencing of 16S rRNA amplicons

Polka, Justyna Urszula; Rebecchi, Annalisa; Pisacane, Vincenza; Morelli, Lorenzo; Puglisi, Edoardo

doi:10.1016/j.fm.2014.08.023

Cited by 199 publications

(129 citation statements)

References 43 publications

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“…that our study was based on Illumina sequencing technology, while the ones here cited on 454 pyrosequencing technology, which has a lower throughput. The high coverage values that we obtained, together with an assignment at the species level of 94.3% of all analysed sequences, prove that Illumina NGS of 16S amplicons is a reliable approach for a thorough analyses of cheese bacterial communities, as already demonstrated for fermented meats (Połka et al, 2015) and beverages (Bokulich et al, 2012). It must also be stressed out that, among all the OTUs retrieved, just a fraction of maximum 26 OTUs covers the 99.9% of the total bacterial community.…”

Section: Discussionsupporting

confidence: 73%

“…The new methodologies based on 16S rDNA amplification together with Next-Generation Sequencing technology (NGS) have the advantage to determine, with a high resolution power, the bacterial communities present in food environments: published examples include cheese (De Filippis et al, 2014;Ercolini et al, 2012;Masoud et al, 2011Masoud et al, , 2012, seafood (Kiyohara et al, 2012;Koyanagi et al, 2011;Roh et al, 2010) and dry fermented sausages (Połka et al, 2015). The recent development in Illumina technology, coupled with multiplexing approaches, allows analysing up two 16S rRNA hypervariable regions in thousands sequences per sample, an approach that was shown to gain an almost complete coverage of the bacterial communities of fermented foods, with correct taxonomical assignment at the species level for more than 95% of the analysed reads (Połka et al, 2015). However, these approaches have not yet been applied for the study of microbial communities involved in late blowing spoilage of hard cheese.…”

Section: Introductionmentioning

confidence: 99%

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Understanding the bacterial communities of hard cheese with blowing defect

2015

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Section: Discussionsupporting

confidence: 73%

Section: Introductionmentioning

confidence: 99%

Understanding the bacterial communities of hard cheese with blowing defect

2015

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“…In a recent study (Połka et al, 2015) on typical Italian dry fermented sausages reported the presence of 32 different Staphylococcaceae and 33 Lactobacillaceae identified by using DNA based HTS coupled with DGGE technique. Our evidence showed that only few species belonging to those genera may be metabolically active and can really contribute to determine the final characteristics of the products.…”

Section: Discussionmentioning

confidence: 99%

“…They are produced using the same main ingredients (pork meat, pork fat, sugars and salts) but with important differences in the type and quantities of spices (Cocolin et al, 2009). Microbiota development during ripening of these products has been largely studied (Aquilanti et al, 2007;Cocolin et al, 2009;Połka et al, 2015;Villani et al, 2007).…”

Section: Introductionmentioning

confidence: 99%

Monitoring of the microbiota of fermented sausages by culture independent rRNA-based approaches

Greppi

Ferrocino

Storia

et al. 2015

International Journal of Food Microbiology

103

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In Italy, fermented sausages (called "salami") are consumed in large quantities. Salami samples from a local meat factory in the area of Torino were analysed at 0, 3, 7, 30 and 45 days of ripening. Swab samples from the production environment were collected as well at the beginning of the experiment. The diversity of metabolically active microbiota occurring during the natural fermentation of salami was evaluated by using RT-PCR-DGGE coupled with RNA-based pyrosequencing of the 16S rRNA gene. A culture-dependent approach was also applied to identify and characterize isolated Staphylococcaceae and LAB populations.Staphylococcus succinus, S. xylosus and Lactobacillus sakei were the species more frequently isolated during the maturation time. Rep-PCR analysis showed that S. succinus and S. xylosus isolated from swabs and salami samples clustered together suggesting a possible contamination during the production process. RT-PCR-DGGE and rRNA based pyrosequencing showed that the metabolically active populations were dominated by S. succinus, Lb. sakei and Leuconostoc carnosum. In this specific case study, only few species belonging to Staphylococcaceae, Lactobacillaceae and Leuconostocaceae may be metabolically active and contribute to determine the final characteristics of the products.

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“…NGS has been applied extensively to a variety of environments, including the sea (11) and soil (12) as well as the gut (13). More recently, NGS of bacterial 16S rRNA amplicons has been used to characterize the microbial communities of a variety of fermented foods and beverages (14)(15)(16)(17)(18)(19)(20) as well as of raw milk and raw milk cheeses (21)(22)(23)(24)(25)(26). Indeed, this approach has led to identification of a number of genera previously not associated with cheese ecosystems (Prevotella and Helcococcus) or with particular cheese types (Arthrobacter in goat's milk cheese).…”

mentioning

confidence: 99%

Temporal and Spatial Differences in Microbial Composition during the Manufacture of a Continental-Type Cheese

O’Sullivan

Cotter

O’Sullivan

et al. 2015

Appl Environ Microbiol

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We sought to determine if the time, within a production day, that a cheese is manufactured has an influence on the microbial community present within that cheese. To facilitate this, 16S rRNA amplicon sequencing was used to elucidate the microbial community dynamics of brine-salted continental-type cheese in cheeses produced early and late in the production day. Differences in the microbial composition of the core and rind of the cheese were also investigated. Throughout ripening, it was apparent that cheeses produced late in the day had a more diverse microbial population than their early equivalents. Spatial variation between the cheese core and rind was also noted in that cheese rinds were initially found to have a more diverse microbial population but thereafter the opposite was the case. Interestingly, the genera Thermus, Pseudoalteromonas, and Bifidobacterium, not routinely associated with a continental-type cheese produced from pasteurized milk, were detected. The significance, if any, of the presence of these genera will require further attention. Ultimately, the use of high-throughput sequencing has facilitated a novel and detailed analysis of the temporal and spatial distribution of microbes in this complex cheese system and established that the period during a production cycle at which a cheese is manufactured can influence its microbial composition.

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Bacterial diversity in typical Italian salami at different ripening stages as revealed by high-throughput sequencing of 16S rRNA amplicons

Cited by 199 publications

References 43 publications

Understanding the bacterial communities of hard cheese with blowing defect

Understanding the bacterial communities of hard cheese with blowing defect

Monitoring of the microbiota of fermented sausages by culture independent rRNA-based approaches

Temporal and Spatial Differences in Microbial Composition during the Manufacture of a Continental-Type Cheese

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