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Journal ArticleDOI

Nucleic acid-based approaches to investigate microbial-related cheese quality defects

21 Jan 2013-Frontiers in Microbiology (Frontiers Media SA)-Vol. 4, pp 1-1
TL;DR: The DNA-based methods that are available to detect/quantify spoilage bacteria, and relevant metabolic pathways in cheeses are reviewed and it is highlighted how these strategies can be employed to improve cheese quality and reduce the associated economic burden on cheese processors.
Abstract: The microbial profile of cheese is a primary determinant of cheese quality. Microorganisms can contribute to aroma and taste defects, form biogenic amines, cause gas and secondary fermentation defects, and can contribute to cheese pinking and mineral deposition issues. These defects may be as a result of seasonality and the variability in the composition of the milk supplied, variations in cheese processing parameters, as well as the nature and number of the non-starter microorganisms which come from the milk or other environmental sources. Such defects can be responsible for production and product recall costs and thus represent a significant economic burden for the dairy industry worldwide. Traditional non-molecular approaches are often considered biased and have inherently slow turnaround times. Molecular techniques can provide early and rapid detection of defects that result from the presence of specific spoilage microbes and, ultimately, assist in enhancing cheese quality and reducing costs. Here we review the DNA-based methods that are available to detect/quantify spoilage bacteria, and relevant metabolic pathways in cheeses and, in the process, highlight how these strategies can be employed to improve cheese quality and reduce the associated economic burden on cheese processors.

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Citations
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Journal ArticleDOI
TL;DR: The evolution of CRE is discussed, with a focus on the epidemiology of the CPE pandemic; risk factors for colonization and infection with the most common transmissible CPE worldwide, Klebsiella pneumoniae carbapenemase-producing K. pneumoniae are reviewed; and strategies used to halt the striking spread of these deadly pathogens are presented.
Abstract: Carbapenem-resistant Enterobacteriaceae (CRE) are a serious public health threat. Infections due to these organisms are associated with significant morbidity and mortality. Mechanisms of drug resistance in gram-negative bacteria (GNB) are numerous; β-lactamase genes carried on mobile genetic elements are a key mechanism for the rapid spread of antibiotic-resistant GNB worldwide. Transmissible carbapenem-resistance in Enterobacteriaceae has been recognized for the last 2 decades, but global dissemination of carbapenemase-producing Enterobacteriaceae (CPE) is a more recent problem that, once initiated, has been occurring at an alarming pace. In this article, we discuss the evolution of CRE, with a focus on the epidemiology of the CPE pandemic; review risk factors for colonization and infection with the most common transmissible CPE worldwide, Klebsiella pneumoniae carbapenemase-producing K. pneumoniae; and present strategies used to halt the striking spread of these deadly pathogens.

944 citations

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TL;DR: The major microbially mediated and abiotic reactions in the biogeochemical Fe cycle are discussed and an integrated overview of biotic and chemically mediated redox transformations is provided.
Abstract: Many iron (Fe) redox processes that were previously assumed to be purely abiotic, such as photochemical Fe reactions, are now known to also be microbially mediated. Owing to this overlap, discerning whether biotic or abiotic processes control Fe redox chemistry is a major challenge for geomicrobiologists and biogeochemists alike. Therefore, to understand the network of reactions within the biogeochemical Fe cycle, it is necessary to determine which abiotic or microbially mediated reactions are dominant under various environmental conditions. In this Review, we discuss the major microbially mediated and abiotic reactions in the biogeochemical Fe cycle and provide an integrated overview of biotic and chemically mediated redox transformations.

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Journal ArticleDOI
TL;DR: This review paper attempts to develop the first comprehensive single source of existing information on pathogen contamination in multiple types of water resources, and describes the challenges associated with using indicator organisms.
Abstract: Water-borne pathogen contamination in water resources and related diseases are a major water quality concern throughout the world. Increasing interest in controlling water-borne pathogens in water resources evidenced by a large number of recent publications clearly attests to the need for studies that synthesize knowledge from multiple fields covering comparative aspects of pathogen contamination, and unify them in a single place in order to present and address the problem as a whole. Providing a broader perceptive of pathogen contamination in freshwater (rivers, lakes, reservoirs, groundwater) and saline water (estuaries and coastal waters) resources, this review paper attempts to develop the first comprehensive single source of existing information on pathogen contamination in multiple types of water resources. In addition, a comprehensive discussion describes the challenges associated with using indicator organisms. Potential impacts of water resources development on pathogen contamination as well as challenges that lie ahead for addressing pathogen contamination are also discussed.

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Journal ArticleDOI
TL;DR: In the future, the use of meta-omics methods should help to decipher how traditional cheese ecosystems form and function, opening the way to new methods of risk-benefit management from farm to ripened cheese.

469 citations


Cites background from "Nucleic acid-based approaches to in..."

  • ...Acidifying starters selected for a given traditional cheese variety are composed of a few strains, compared to traditional starters (§ traditional starters); they are increasingly used to limit major taste and aroma defects by normalizing acidification kinetics (O'Sullivan et al., 2013)....

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Journal ArticleDOI
TL;DR: In this article, the abundance and community structure of functional genes involved in the biogeochemical cycling of N in forest soils offers an approach to directly link microbial groups to soil characteristics and ecosystem processes.
Abstract: The understanding of nitrogen (N) cycling in forest ecosystems has undergone a major shift in the past decade as molecular methods are being used to link microorganisms to key processes in soil. The analysis of the abundance and community structure of functional genes involved in the biogeochemical cycling of N in forest soils offers an approach to directly link microbial groups to soil characteristics and ecosystem processes. The majority of N entering ecosystems is biologically-derived from fixation of atmospheric N2. Molecular studies of N-fixation use the nitrogenase reductase (nifH) marker gene, and can be used to link N-fixation to other N- and C-cycling processes. Inorganic N entering soil via N-fixation, fertilization and deposition can have several fates, depending on the soil environment and the microbial community. The loss of N from forests stands subject to fertilization and atmospheric deposition is of increasing interest as the outputs of nitrate (NO3−) and nitrous oxide (N2O) are implicated in ground water pollution and climate change, respectively. Ammonia-oxidizing bacteria (AOB) and archaea (AOA) oxidize ammonia (NH3) to NO3− as the first step of nitrification and are studied using the ammonium monooxygenase (amoA) marker. The abundance and community structure of ammonia-oxidizers is largely dependent on pH and availability of reactive N forms, and can change rapidly following N addition or after fire. These organisms can also release N2O during nitrifier denitrification or through linked nitrification–denitrification. In some forest soils, N2O emissions are correlated with genes in the denitrification pathway (napA, narG, nirK, nirS, nosZ) making these genes useful indicators of greenhouse gas (GHG) flux potential. A review of this topic is timely as there is currently much concern regarding the effect of N fertilization and deposition on North American and European forests due to the potential alteration of dissimilative N-cycling processes and the potential for increased N2O emissions in forest stands.

441 citations

References
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Journal ArticleDOI
TL;DR: An astounding potential exists for next-generation DNA sequencing technologies to bring enormous change in genetic and biological research and to enhance the authors' fundamental biological knowledge.
Abstract: Recent scientific discoveries that resulted from the application of nextgeneration DNA sequencing technologies highlight the striking impact of these massively parallel platforms on genetics. These new methods have expanded previously focused readouts from a variety of DNA preparation protocols to a genome-wide scale and have fine-tuned their resolution to single base precision. The sequencing of RNA also has transitioned and now includes full-length cDNA analyses, serial analysis of gene expression (SAGE)-based methods, and noncoding RNA discovery. Next-generation sequencing has also enabled novel applications such as the sequencing of ancient DNA samples, and has substantially widened the scope of metagenomic analysis of environmentally derived samples. Taken together, an astounding potential exists for these technologies to bring enormous change in genetic and biological research and to enhance our fundamental biological knowledge.

2,354 citations


"Nucleic acid-based approaches to in..." refers background or methods in this paper

  • ...Therefore, each cluster is sequenced by the color associated with the nucleotide added (Mardis, 2008; Morozova and Marra, 2008; Zhang et al., 2011)....

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  • ...For these instruments single stranded DNA fragments are attached to a flow cell, a solid, multichannel single molecule array (Mardis, 2008)....

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  • ...This process is termed paired end sequencing (Mardis, 2008, 2011)....

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  • ...Less common systems include the Helicos Heliscope, Pacific Biosciences SMRT, Life Technologies Ion Torrent PGM and Oxford NanoPore Technologies (Mardis, 2008, 2011)....

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  • ...These beads carry oligonucleotide sequences that complement adaptor sequences ligated to the DNA fragments of interest (Mardis, 2008)....

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Journal ArticleDOI
TL;DR: A future challenge is to translate information from 16S rRNA gene sequencing into convenient biochemical testing schemes, making the accuracy of the genotypic identification available to the smaller and routine clinical microbiology laboratories.
Abstract: The traditional identification of bacteria on the basis of phenotypic characteristics is generally not as accurate as identification based on genotypic methods. Comparison of the bacterial 16S rRNA gene sequence has emerged as a preferred genetic technique. 16S rRNA gene sequence analysis can better identify poorly described, rarely isolated, or phenotypically aberrant strains, can be routinely used for identification of mycobacteria, and can lead to the recognition of novel pathogens and noncultured bacteria. Problems remain in that the sequences in some databases are not accurate, there is no consensus quantitative definition of genus or species based on 16S rRNA gene sequence data, the proliferation of species names based on minimal genetic and phenotypic differences raises communication difficulties, and microheterogeneity in 16S rRNA gene sequence within a species is common. Despite its accuracy, 16S rRNA gene sequence analysis lacks widespread use beyond the large and reference laboratories because of technical and cost considerations. Thus, a future challenge is to translate information from 16S rRNA gene sequencing into convenient biochemical testing schemes, making the accuracy of the genotypic identification available to the smaller and routine clinical microbiology laboratories.

1,683 citations


"Nucleic acid-based approaches to in..." refers methods in this paper

  • ...Frequently the target region within bacterial genomes is the 16S rRNA gene or the 16S/23S spacer region, either using species/genera specific primers or universal primers (Clarridge, 2004; Randazzo et al., 2009; Ndoye et al., 2011)....

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Journal ArticleDOI
TL;DR: New starter cultures of lactic acid bacteria with an industrially important functionality are being developed that can contribute to the microbial safety or offer one or more organoleptic, technological, nutritional, or health advantages.
Abstract: The production of fermented foods is based on the use of starter cultures, for instance lactic acid bacteria that initiate rapid acidification of the raw material. Recently, new starter cultures of lactic acid bacteria with an industrially important functionality are being developed. The latter can contribute to the microbial safety or offer one or more organoleptic, technological, nutritional, or health advantages. Examples are lactic acid bacteria that produce antimicrobial substances, sugar polymers, sweeteners, aromatic compounds, vitamins, or useful enzymes, or that have probiotic properties.

1,567 citations

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TL;DR: The scientific, medical, and diagnostic communities have been presented the most powerful tool for quantitative nucleic acids analysis: real-time PCR, a refinement of the original Polymerase Chain Reaction (PCR) developed by Kary Mullis and coworkers in the mid 80:ies.

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Journal ArticleDOI
TL;DR: A better knowledge of the factors controlling the formation of amines is necessary in order to improve the quality and safety of food as discussed by the authors, which can be found in both raw and processed foods.

1,283 citations

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