Fermented Foods as Experimentally Tractable Microbial Ecosystems

Wolfe, Benjamin E.; Dutton, Rachel J.

doi:10.1016/j.cell.2015.02.034

Cited by 320 publications

(251 citation statements)

References 51 publications

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“…These studies provided an in‐depth analysis of the cheese maturation process and allowed to better understand the metabolic activities of the different community members and their possible interactions. Indeed, cheese microbial communities were proposed as simplified model to study both microbial assembly and metabolism (as affected by abiotic factors), providing a possible interesting model for understanding microbial dynamics in more complex environments (Wolfe and Dutton, 2015). In a recent example, the evolution of bacterial activities during manufacturing and ripening of a traditional cheese made with an undefined starter was monitored by metatranscriptomics highlighting how to manipulate microbial gene expression through modifications of the process parameters (De Filippis et al ., 2016a).…”

Section: Exploring Microbial Functions Directly In Foodmentioning

confidence: 99%

Metagenomics insights into food fermentations

Filippis

Parente

2016

Microbial Biotechnology

202

117

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SummaryThis review describes the recent advances in the study of food microbial ecology, with a focus on food fermentations. High‐throughput sequencing (HTS) technologies have been widely applied to the study of food microbial consortia and the different applications of HTS technologies were exploited in order to monitor microbial dynamics in food fermentative processes. Phylobiomics was the most explored application in the past decade. Metagenomics and metatranscriptomics, although still underexploited, promise to uncover the functionality of complex microbial consortia. The new knowledge acquired will help to understand how to make a profitable use of microbial genetic resources and modulate key activities of beneficial microbes in order to ensure process efficiency, product quality and safety.

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Section: Exploring Microbial Functions Directly In Foodmentioning

confidence: 99%

Metagenomics insights into food fermentations

Filippis

Parente

2016

Microbial Biotechnology

202

117

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“…This has yielded exciting results, with B. subtilis biofilm formation and properties (Bais, 2004) being studied in the soil, on plant roots in the lab, naturally induced by the plants' polysaccharides (Beauregard et al, 2013). Similarly, both synthetic communities constructed from known microbial species (Hekstra and Leibler, 2012;van Gestel et al, 2014) and microcosm communities made from environmental samples (Wolfe and Dutton, 2015) have been shown to reveal essential characteristics of microbial ecology (for a review, see Widder et al, 2016).…”

Section: Future Directionsmentioning

confidence: 99%

The ecology and evolution of social behavior in microbes

Tarnita

2017

Journal of Experimental Biology

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Cooperation has been studied extensively across the tree of life, from eusociality in insects to social behavior in humans, but it is only recently that a social dimension has been recognized and extensively explored for microbes. Research into microbial cooperation has accelerated dramatically and microbes have become a favorite system because of their fast evolution, their convenience as lab study systems and the opportunity for molecular investigations. However, the study of microbes also poses significant challenges, such as a lack of knowledge and an inaccessibility of the ecological context (used here to include both the abiotic and the biotic environment) under which the trait deemed cooperative has evolved and is maintained. I review the experimental and theoretical evidence in support of the limitations of the study of social behavior in microbes in the absence of an ecological context. I discuss both the need and the opportunities for experimental investigations that can inform a theoretical framework able to reframe the general questions of social behavior in a clear ecological context and to account for eco-evolutionary feedback.

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“…Preliminary studies have shown that DNA sequencing can answer various food-related applications including distinguishing morphologically similar poisonous and edible mushrooms, detecting the accumulation of pathogenic microbes in meat, tracing the fermentation of cheeses, identifying hidden traces of allergens, and even predicting the ripening time of avocados (Dopico et al 1993;Galimberti et al 2013;Dugat-Bony et al 2015;Wolfe and Dutton 2015). As such, sequencing sensors can be a highly flexible backend to monitor various issues in the food supply chain.…”

Section: Food Industrymentioning

confidence: 99%

A vision for ubiquitous sequencing

Erlich

2015

Genome Res.

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Genomics has recently celebrated reaching the $1000 genome milestone, making affordable DNA sequencing a reality. With this goal successfully completed, the next goal of the sequencing revolution can be sequencing sensors-miniaturized sequencing devices that are manufactured for real-time applications and deployed in large quantities at low costs. The first part of this manuscript envisions applications that will benefit from moving the sequencers to the samples in a range of domains. In the second part, the manuscript outlines the critical barriers that need to be addressed in order to reach the goal of ubiquitous sequencing sensors.

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Fermented Foods as Experimentally Tractable Microbial Ecosystems

Cited by 320 publications

References 51 publications

Metagenomics insights into food fermentations

Metagenomics insights into food fermentations

The ecology and evolution of social behavior in microbes

A vision for ubiquitous sequencing

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