Culture independent methods to assess the diversity and dynamics of microbiota during food fermentation

Cocolin, Luca Simone; Alessandria, Valentina; Dolci, Paola; Gorra, Roberta; Rantsiou, Kalliopi

doi:10.1016/j.ijfoodmicro.2013.05.008

Cited by 200 publications

(115 citation statements)

References 175 publications

(22 reference statements)

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“…Recent advances in bacterial detection methods, most notably culture-independent molecular-based technologies, have resulted in a deeper understanding of the structure and function of the human intestinal microbiota (Cocolin et al, 2013;Hiergeist et al, 2015). Historically, culture-based plating techniques were the primary method of examining the intestinal microbiota.…”

Section: The Intestinal Microbiota Microbiota Conceptsmentioning

confidence: 99%

An overview of the bacterial contribution to Crohn disease pathogenesis

Alhagamhmad

Day

Lemberg

et al. 2016

Journal of Medical Microbiology

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Section: The Intestinal Microbiota Microbiota Conceptsmentioning

confidence: 99%

An overview of the bacterial contribution to Crohn disease pathogenesis

Alhagamhmad

Day

Lemberg

et al. 2016

Journal of Medical Microbiology

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“…PCR-based molecular profiling techniques targeting either particular populations or select taxonomic communities are also routinely used and have been extensively reviewed (8)(9)(10). PCR-based methods cannot, however, provide comprehensive coverage of total microbial populations.…”

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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“…Culture-independent methods are the preferred, since they are neither affected by the viability of the microorganism nor by low populations of less abundant species [46]. Some of the preferred techniques are highthroughput or next generation sequencing (HTS or NGS, respectively), denaturing gradient gel electrophoresis (DGGE), and quantitative PCR (qPCR), as it is summarized in Table 1 [47][48][49].…”

Section: Determination Of Yeast Diversitymentioning

confidence: 99%

Growth Kinetics for the Selection of Yeast Strains for Fermented Beverages

Miranda-Castilleja¹,

Tapia²,

Arvizu-Medrano³

et al. 2017

Yeast - Industrial Applications

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Criteria to select autochthonous yeast strains for their use in fermented beverages include their ability to dominate the media and to enhance desired sensorial characteristics and their inability to produce undesired compounds such as biogenic amines or off-odors. One of the key features in yeast selection is its Implantation, surpassing different stresses, and its fermentation performance, which requires setting up the process and monitoring it, involving important amount of resources. Methods to evaluate the tolerance of yeast strains are usually based in the qualitative measure of the growth of the microorganism in a medium containing the limiting compound after a specific time of incubation. However, studying strain growth through optical density measurements permits to estimate quantitative and comparable parameters providing an insight into the fitness of the cell to certain environment, lag phase duration, growth rate, and maximum population, among others. In the last decades, cultureindependent methods have been used to evaluate the dynamic of microbial populations during fermentative process. In this chapter, a review of recent advances in the selection of fermentative yeasts as well as the utilization of kinetic evaluation and molecular strategies in conditions associated with fermented beverage for selecting yeast strains is presented.

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Culture independent methods to assess the diversity and dynamics of microbiota during food fermentation

Cited by 200 publications

References 175 publications

An overview of the bacterial contribution to Crohn disease pathogenesis

An overview of the bacterial contribution to Crohn disease pathogenesis

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

Growth Kinetics for the Selection of Yeast Strains for Fermented Beverages

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