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

Greppi, Anna; Ferrocino, Ilario; Storia, Antonietta La; Rantsiou, Kalliopi; Ercolini, Danilo; Cocolin, Luca Simone

doi:10.1016/j.ijfoodmicro.2015.01.016

Cited by 103 publications

(78 citation statements)

References 31 publications

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“…Moreover, RT-PCR-DGGE and RNA-based pyrosequencing of the 16S rRNA gene have also been used to monitor the microbiota of fermented sausages [102].…”

Section: Competitiveness Of Starter Culturesmentioning

confidence: 99%

The Use of Starter Cultures in Traditional Meat Products

Laranjo

Elías

Fraqueza

2017

Journal of Food Quality

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Starter cultures could play an essential role in the manufacture of traditional cured meat products. In order to achieve objectives related to meat products' quality and safety improvement, the selection of particular strains constituting a starter culture should be carried out in the context of its application, since its functionality will depend on the type of sausage and process conditions. Also, strain selection should comply with particular requirements to warrant safety. The aim of the current review is to update the knowledge on the use of starter cultures in traditional meat products, with focus on dry-fermented products. In this manuscript, we will try to give answers to some relevant questions: Which starter cultures are used and why? Why are LAB used? What are their role and their specific mode of action? Which other groups of microorganisms (bacteria and fungi) are used as starter cultures and how do they act? A particular revision of omics approach regarding starter cultures is made since the use of these techniques allows rapid screening of promising wild strains with desirable functional characteristics, enabling the development of starter cultures better adapted to the meat matrix.

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“…Moreover, RT-PCR-DGGE and RNA-based pyrosequencing of the 16S rRNA gene have also been used to monitor the microbiota of fermented sausages [102].…”

Section: Competitiveness Of Starter Culturesmentioning

confidence: 99%

The Use of Starter Cultures in Traditional Meat Products

Laranjo

Elías

Fraqueza

2017

Journal of Food Quality

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“…16S rRNA data were analyzed by using QIIME 1.9.0 software (25) and a previously described pipeline (26). Operational taxonomic units (OTUs) were picked at 99% similarity by the UCLUST clustering methods (27), and representative sequences of each cluster were used to assign taxonomy using the Greengenes 16S rRNA gene database version 2013 by the RDP classifier (28).…”

Section: Samplingmentioning

confidence: 99%

Microbiota of an Italian Grana-Like Cheese during Manufacture and Ripening, Unraveled by 16S rRNA-Based Approaches

Alessandria

Ferrocino

Filippis

et al. 2016

Appl Environ Microbiol

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The microbial ecology of cheese involves a rich and complex interaction between starter lactic acid bacteria and nonstarter lactic acid bacteria (NSLAB), mainly originating from raw milk and/or from the environment, that can contribute to the final characteristics of cheese. The aim of the present research was the exploration of the active microbiota by RNA-based approaches during the manufacturing and ripening of a Grana-like cheese. Reverse transcriptase PCR (RT-PCR)-denaturing gradient gel electrophoresis (DGGE) and RNA-based high-throughput sequencing were applied to profile microbial populations, while the enumeration of active bacteria was carried out by using quantitative PCR (qPCR). Three different cheese productions (named D, E, and F) collected in the same month from the same dairy plant were analyzed. The application of the qPCR protocol revealed the presence of 7 log CFU/ml of bacterial load in raw milk, while, during ripening, active bacterial populations ranged from <4 to 8 log CFU/ml. The natural whey starters used in the three productions showed the same microbiota composition, characterized by the presence of Lactobacillus helveticus and Lactobacillus delbrueckii. Nevertheless, beta-diversity analysis of the 16S rRNA sequencing data and RT-PCR-DGGE showed a clear clustering of the samples according to the three productions, probably driven by the different milks used. Milk samples were found to be characterized by the presence of several contaminants, such as Propionibacterium acnes, Acidovorax, Acinetobacter, Pseudomonas, and NSLAB. The core genera of the starter tended to limit the development of the spoilage bacteria only in two of the three batches. This study underlines the influence of different factors that can affect the final microbiota composition of the artisanal cheese. IMPORTANCEThis study highlights the importance of the quality of the raw milk in the production of a hard cheese. Independent from the use of a starter culture, raw milk with low microbiological quality can negatively affect the populations of lactic acid bacteria and, as a consequence, impact the quality of the final product due to metabolic processes associated with spoilage bacteria. G rana-like hard cheese is a typical raw cow's milk cheese produced in the Piedmont region in northwest Italy. Curd fermentation is carried out by natural thermophilic whey cultures obtained from the manufacturing of the previous day, after heating at 53 to 55°C, and the ripening is commonly carried out for 12 months.Natural whey starters (NWS) are used for several protected designation of origin (PDO) cheeses. They are usually dominated by thermophilic lactic acid bacteria (LAB), but subdominant species, including mesophilic LAB, may also occur. NWS have a complex microbial association of various species as well as a large number of biotypes (1).Temperature is the main factor associated with the variability of the microbiota composition of the NWS. Cooking treatment and whey cooling lead to the selection of a characteristic mi...

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“…Another series of 324 burgers in 12 bags were packed as described above using nonactivated bags and strips and were used as a control. From each control (C) and treated (T) sample, 1 ml of the first 10-fold serial dilution was used to determine: (i) total aerobic bacteria, (ii) lactic acid bacteria (LAB), (iii) Staphylococcaceae, (iv) Enterobacteriaceae, (v) yeasts, and (vi) molds by using selective media and conditions previously described (19). Results were expressed as means of log CFU for three independent determinations on each batch.…”

Section: Preparation Of Antimicrobial Bags and Filmsmentioning

confidence: 99%

“…The V3 region of the 16S rRNA gene was amplified with the primers 338f-GC/518r, as previously described (21). PCR products were analyzed by denaturing gradient gel electrophoresis (DGGE) at 30% to 60% by using a Bio-Rad Dcode, as suggested elsewhere (19).…”

Section: Preparation Of Antimicrobial Bags and Filmsmentioning

confidence: 99%

Impact of Nisin-Activated Packaging on Microbiota of Beef Burgers during Storage

Ferrocino

Greppi

Storia

et al. 2016

Appl Environ Microbiol

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bBeef burgers were stored at 4°C in a vacuum in nisin-activated antimicrobial packaging. Microbial ecology analyses were performed on samples collected between days 0 and 21 of storage to discover the population diversity. Two batches were analyzed using RNA-based denaturing gradient gel electrophoresis (DGGE) and pyrosequencing. The active packaging retarded the growth of the total viable bacteria and lactic acid bacteria. Culture-independent analysis by pyrosequencing of RNA extracted directly from meat showed that Photobacterium phosphoreum, Lactococcus piscium, Lactobacillus sakei, and Leuconostoc carnosum were the major operational taxonomic units (OTUs) shared between control and treated samples. Beta diversity analysis of the 16S rRNA sequence data and RNA-DGGE showed a clear separation between two batches based on the microbiota. Control samples from batch B showed a significant high abundance of some taxa sensitive to nisin, such as Kocuria rhizophila, Staphylococcus xylosus, Leuconostoc carnosum, and Carnobacterium divergens, compared to control samples from batch A. However, only from batch B was it possible to find a significant difference between controls and treated samples during storage due to the active packaging. Predicted metagenomes confirmed differences between the two batches and indicated that the use of nisinbased antimicrobial packaging can determine a reduction in the abundance of specific metabolic pathways related to spoilage. The present study aimed to assess the viable bacterial communities in beef burgers stored in nisin-based antimicrobial packaging, and it highlights the efficacy of this strategy to prolong beef burger shelf life. Spoilage of meat or meat products is caused by uncontrolled growth and various metabolic activities of the dominant microbiota found on these foods (1, 2). It is commonly assumed that microbiota of meat can originate from the processed animal's skin or intestines and that contamination may occur during the successive steps of processing and distribution (3-6). Undesired microbial development in meat could also appear during storage. In particular, different storage conditions of meat products can influence the development of different microbial groups and their ability to produce spoilage-associated compounds, such as esters, ketones, aldehydes, sulfur compounds, amines, and volatile fatty acids (2, 7). In recent decades, numerous methods had been applied for storage of meat to control the spoilage process, extending the shelf life of raw meat and meat products. Among them, refrigerated storage conditions, addition of natural preservatives, vacuum pack (VP), and modified atmosphere packaging (MAP) could influence the development and activities of the ephemeral spoilage microorganisms and, consequently, the spoilage process (3). Antimicrobial nisin-based active packaging has also been recently developed as a powerful tool for meat storage (8-11). Depending on the storage conditions and other extrinsic factors, only a few species are able to sufficiently ...

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

Cited by 103 publications

References 31 publications

The Use of Starter Cultures in Traditional Meat Products

The Use of Starter Cultures in Traditional Meat Products

Microbiota of an Italian Grana-Like Cheese during Manufacture and Ripening, Unraveled by 16S rRNA-Based Approaches

Impact of Nisin-Activated Packaging on Microbiota of Beef Burgers during Storage

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