Metagenome‐based surveillance and diagnostic approaches to studying the microbial ecology of food production and processing environments

Doyle, Conor; O’Toole, Paul W.; Cotter, Paul D.

doi:10.1111/1462-2920.13859

Cited by 44 publications

(15 citation statements)

References 67 publications

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“…The same technology could, in the future, be employed to establish authenticity. However, as these topics, and studies related to microbial dynamics of food ecosystems, processing environments, and production facilities have been reviewed in depth recently (Mayo et al, 2014 ; Galimberti et al, 2015 ; Bokulich et al, 2016 ; De Filippis et al, 2017 ; Doyle et al, 2017b ; Macori and Cotter, 2018 ), we are not addressing those topics here. In this review, we specifically focus on providing an overview of studies in which HTS has been applied to provide insights into the microbiota of different cheeses that are of value from an industrial perspective as well as the factors that modulate these microbes (Table 1 ) and the identity of adventitious and other microbes (Table 2 ).…”

Section: Introductionmentioning

confidence: 99%

Sequencing of the Cheese Microbiome and Its Relevance to Industry

et al. 2018

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The microbiota of cheese plays a key role in determining its organoleptic and other physico-chemical properties. It is essential to understand the various contributions, positive or negative, of these microbial components in order to promote the growth of desirable taxa and, thus, characteristics. The recent application of high throughput DNA sequencing (HTS) facilitates an even more accurate identification of these microbes, and their functional properties, and has the potential to reveal those microbes, and associated pathways, responsible for favorable or unfavorable characteristics. This technology also facilitates a detailed analysis of the composition and functional potential of the microbiota of milk, curd, whey, mixed starters, processing environments, and how these contribute to the final cheese microbiota, and associated characteristics. Ultimately, this information can be harnessed by producers to optimize the quality, safety, and commercial value of their products. In this review we highlight a number of key studies in which HTS was employed to study the cheese microbiota, and pay particular attention to those of greatest relevance to industry.

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Section: Introductionmentioning

confidence: 99%

Sequencing of the Cheese Microbiome and Its Relevance to Industry

et al. 2018

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“…Whole genome sequencing is a potential game changer in providing identification and characterization of pathogenic bacteria for epidemiological investigations [215]. Retrieving data on pathogen genomes directly from metagenomic data provides a possibility to identify unknown or overlooked etiological organisms that cause millions of cases of foodborne illness each year [57,216,217]. Future studies on Aeromonas strains from seafood products should aim to couple systematized and validated data on the distribution of virulence factors with relevant HTS data, in particular whole-genome sequences of highly virulent strains.…”

Section: Discussionmentioning

confidence: 99%

The Significance of Mesophilic Aeromonas spp. in Minimally Processed Ready-to-Eat Seafood

2019

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Minimally processed and ready-to-eat (RTE) seafood products are gaining popularity because of their availability in retail stores and the consumers’ perception of convenience. Products that are subjected to mild processing and products that do not require additional heating prior to consumption are eaten by an increasing proportion of the population, including people that are more susceptible to foodborne disease. Worldwide, seafood is an important source of foodborne outbreaks, but the exact burden is not known. The increased interest in seafood products for raw consumption introduces new food safety issues that must be addressed by all actors in the food chain. Bacteria belonging to genus Aeromonas are ubiquitous in marine environments, and Aeromonas spp. has held the title “emerging foodborne pathogen” for more than a decade. Given its high prevalence in seafood and in vegetables included in many RTE seafood meals, the significance of Aeromonas as a potential foodborne pathogen and a food spoilage organism increases. Some Aeromonas spp. can grow relatively uninhibited in food during refrigeration under a broad range of pH and NaCl concentrations, and in various packaging atmospheres. Strains of several Aeromonas species have shown spoilage potential by the production of spoilage associated metabolites in various seafood products, but the knowledge on spoilage in cold water fish species is scarce. The question about the significance of Aeromonas spp. in RTE seafood products is challenged by the limited knowledge on how to identify the truly virulent strains. The limited information on clinically relevant strains is partly due to few registered outbreaks, and to the disputed role as a true foodborne pathogen. However, it is likely that illness caused by Aeromonas might go on undetected due to unreported cases and a lack of adequate identification schemes. A rather confusing taxonomy and inadequate biochemical tests for species identification has led to a biased focus towards some Aeromonas species. Over the last ten years, several housekeeping genes has replaced the 16S rRNA gene as suitable genetic markers for phylogenetic analysis. The result is a more clear and robust taxonomy and updated knowledge on the currently circulating environmental strains. Nevertheless, more knowledge on which factors that contribute to virulence and how to control the potential pathogenic strains of Aeromonas in perishable RTE seafood products are needed.

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“…By understanding the FPE microbiome, valuable information can be gained regarding persistence or transience of strains. This facilitates source tracking of persistent strains, can identify other microbial species that may provide either a positive or negative effect on the target strain, and can identify strains surviving the disinfection processes ( Dass and Anandappa, 2017 ; Doyle et al, 2017 ). From this information, the appropriate biocontrol method can then be determined.…”

Section: Discussionmentioning

confidence: 99%

Novel Biocontrol Methods for Listeria monocytogenes Biofilms in Food Production Facilities

et al. 2018

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High mortality and hospitalization rates have seen Listeria monocytogenes as a foodborne pathogen of public health importance for many years and of particular concern for high-risk population groups. Food manufactures face an ongoing challenge in preventing the entry of L. monocytogenes into food production environments (FPEs) due to its ubiquitous nature. In addition to this, the capacity of L. monocytogenes strains to colonize FPEs can lead to repeated identification of L. monocytogenes in FPE surveillance. The contamination of food products requiring product recall presents large economic burden to industry and is further exacerbated by damage to the brand. Poor equipment design, facility layout, and worn or damaged equipment can result in Listeria hotspots and biofilms where traditional cleaning and disinfecting procedures may be inadequate. Novel biocontrol methods may offer FPEs effective means to help improve control of L. monocytogenes and decrease cross contamination of food. Bacteriophages have been used as a medical treatment for many years for their ability to infect and lyse specific bacteria. Endolysins, the hydrolytic enzymes of bacteriophages responsible for breaking the cell wall of Gram-positive bacteria, are being explored as a biocontrol method for food preservation and in nanotechnology and medical applications. Antibacterial proteins known as bacteriocins have been used as alternatives to antibiotics for biopreservation and food product shelf life extension. Essential oils are natural antimicrobials formed by plants and have been used as food additives and preservatives for many years and more recently as a method to prevent food spoilage by microorganisms. Competitive exclusion occurs naturally among bacteria in the environment. However, intentionally selecting and applying bacteria to effect competitive exclusion of food borne pathogens has potential as a biocontrol application. This review discusses these novel biocontrol methods and their use in food safety and prevention of spoilage, and examines their potential to control L. monocytogenes within biofilms in food production facilities.

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Metagenome‐based surveillance and diagnostic approaches to studying the microbial ecology of food production and processing environments

Cited by 44 publications

References 67 publications

Sequencing of the Cheese Microbiome and Its Relevance to Industry

Sequencing of the Cheese Microbiome and Its Relevance to Industry

The Significance of Mesophilic Aeromonas spp. in Minimally Processed Ready-to-Eat Seafood

Novel Biocontrol Methods for Listeria monocytogenes Biofilms in Food Production Facilities

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