• Biotechnological applications of functional metagenomics in the food and pharmaceutical industries

      Coughlan, Laura M.; Cotter, Paul D.; Hill, Colin; Alvarez-Ordonez, Avelino; Science Foundation Ireland; 13/SIRG/2157 (Frontiers Media S. A., 30/06/2015)
      Microorganisms are found throughout nature, thriving in a vast range of environmental conditions. The majority of them are unculturable or difficult to culture by traditional methods. Metagenomics enables the study of all microorganisms, regardless of whether they can be cultured or not, through the analysis of genomic data obtained directly from an environmental sample, providing knowledge of the species present, and allowing the extraction of information regarding the functionality of microbial communities in their natural habitat. Function-based screenings, following the cloning and expression of metagenomic DNA in a heterologous host, can be applied to the discovery of novel proteins of industrial interest encoded by the genes of previously inaccessible microorganisms. Functional metagenomics has considerable potential in the food and pharmaceutical industries, where it can, for instance, aid (i) the identification of enzymes with desirable technological properties, capable of catalyzing novel reactions or replacing existing chemically synthesized catalysts which may be difficult or expensive to produce, and able to work under a wide range of environmental conditions encountered in food and pharmaceutical processing cycles including extreme conditions of temperature, pH, osmolarity, etc; (ii) the discovery of novel bioactives including antimicrobials active against microorganisms of concern both in food and medical settings; (iii) the investigation of industrial and societal issues such as antibiotic resistance development. This review article summarizes the state-of-the-art functional metagenomic methods available and discusses the potential of functional metagenomic approaches to mine as yet unexplored environments to discover novel genes with biotechnological application in the food and pharmaceutical industries.
    • Effect of milk centrifugation and incorporation of high heat-treated centrifugate on the microbial composition and levels of volatile organic compounds of Maasdam cheese

      Lamichhane, Prabin; Pietrzyk, Anna; Feehily, Conor; Cotter, Paul D.; Mannion, David T.; Kilcawley, Kieran; Kelly, Alan L.; Sheehan, Diarmuid (JJ); Dairy Levy Trust; Teagasc Walsh Fellowship Programme; et al. (Elsevier, 2018-03-15)
      Centrifugation is a common milk pretreatment method for removal of Clostridium spores which, on germination, can produce high levels of butyric acid and gas, resulting in rancid, gassy cheese. The aim of this study was to determine the effect of centrifugation of milk, as well as incorporation of high heat-treated centrifugate into cheese milk, on the microbial and volatile profile of Maasdam cheese. To facilitate this, 16S rRNA amplicon sequencing in combination with a selective media-based approach were used to study the microbial composition of cheese during maturation, and volatile organic compounds within the cheese matrix were analyzed by HPLC and solid-phase microextraction coupled with gas chromatography–mass spectrometry. Both culture-based and molecular approaches revealed major differences in microbial populations within the cheese matrix before and after warm room ripening. During warm room ripening, an increase in counts of propionic acid bacteria (by ∼101.5 cfu) and nonstarter lactic acid bacteria (by ∼108 cfu) and a decrease in the counts of Lactobacillus helveticus (by ∼102.5 cfu) were observed. Lactococcus species dominated the curd population throughout ripening, followed by Lactobacillus, Propionibacterium, and Leuconostoc, and the relative abundance of these accounted for more than 99% of the total genera, as revealed by high-throughput sequencing. Among subdominant microflora, the overall relative abundance of Clostridium sensu stricto was lower in cheeses made from centrifuged milk than control cheeses, which coincided with lower levels of butyric acid. Centrifugation as well as incorporation of high heat-treated centrifugate into cheese milk seemed to have little effect on the volatile profile of Maasdam cheese, except for butyric acid levels. Overall, this study suggests that centrifugation of milk before cheesemaking is a suitable method for controlling undesirable butyric acid fermentation without significantly altering the levels of other volatile organic compounds of Maasdam cheese.
    • Health Benefits of Lactic Acid Bacteria (LAB) Fermentates

      Mathur, Harsh; Beresford, Tom P.; Cotter, Paul D.; Food for Health Ireland; TC/2018/0025 (MDPI AG, 2020-06-04)
      Consuming fermented foods has been reported to result in improvements in a range of health parameters. These positive effects can be exerted by a combination of the live microorganisms that the fermented foods contain, as well as the bioactive components released into the foods as by-products of the fermentation process. In many instances, and particularly in dairy fermented foods, the microorganisms involved in the fermentation process belong to the lactic acid group of bacteria (LAB). An alternative approach to making some of the health benefits that have been attributed to fermented foods available is through the production of ‘fermentates’. The term ‘fermentate’ generally relates to a powdered preparation, derived from a fermented product and which can contain the fermenting microorganisms, components of these microorganisms, culture supernatants, fermented substrates, and a range of metabolites and bioactive components with potential health benefits. Here, we provide a brief overview of a selection of in vitro and in vivo studies and patents exclusively reporting the health benefits of LAB ‘fermentates’. Typically, in such studies, the potential health benefits have been attributed to the bioactive metabolites present in the crude fermentates and/or culture supernatants rather than the direct effects of the LAB strain(s) involved.
    • Irish research response to dairy quality in an era of change

      O'Brien, Bernadette J.; Beresford, Tom; Cotter, Paul D.; Gleeson, D.; Kelly, A.; Kilcawley, Kieran; Magan, J.; McParland, Sinead; Murphy, E.; O’Callaghan, Tom; et al. (Teagasc, 2022-02-26)
      The Irish dairy sector is recognised for its very significant contribution to the national economic status; it is now worth ∼€5 billion annually and represents the largest food and drink export category, which, in turn, represents one of the four largest manufacturing industries in the country. Given anticipated further growth in global demand for dairy products and the positive attributes and capabilities that Ireland has to meet that demand, in terms of pasture-based production and cost competitiveness, it is incumbent for the sector to attain the highest quality milk and dairy products. The combined collaborative approach between research and industry has ensured significant progress and enabled Ireland to remain at the forefront globally in terms of production of quality milk and dairy products. This paper highlights some specific scientific platforms and technologies currently shaping the industry in this regard and discusses current research activity as well as anticipating key requirements for future progress. While research, and farm and processing plant management have accomplished very significant advances in milk and dairy product quality, some overarching emerging challenges include product substitution and sustainability. Some key pillars for the future have been identified on which a strong, efficient dairy sector can be maintained and progressed. Specifically, the use of evidence-based information and real-time measures in prediction and decision-making will be a crucial pillar for the dairy sector of the future. This can promote an approach of proactive maintenance and optimisation of production through improved predictability and control of manufacturing processes.
    • New Weapons to Fight Old Enemies: Novel Strategies for the (Bio)control of Bacterial Biofilms in the Food Industry

      Coughlan, Laura M.; Cotter, Paul D.; Hill, Colin; Alvarez-Ordonez, Avelino; Science Foundation Ireland; 13/SIRG/2157 (Frontiers, 18/10/2016)
      Biofilms are microbial communities characterized by their adhesion to solid surfaces and the production of a matrix of exopolymeric substances, consisting of polysaccharides, proteins, DNA and lipids, which surround the microorganisms lending structural integrity and a unique biochemical profile to the biofilm. Biofilm formation enhances the ability of the producer/s to persist in a given environment. Pathogenic and spoilage bacterial species capable of forming biofilms are a significant problem for the healthcare and food industries, as their biofilm-forming ability protects them from common cleaning processes and allows them to remain in the environment post-sanitation. In the food industry, persistent bacteria colonize the inside of mixing tanks, vats and tubing, compromising food safety and quality. Strategies to overcome bacterial persistence through inhibition of biofilm formation or removal of mature biofilms are therefore necessary. Current biofilm control strategies employed in the food industry (cleaning and disinfection, material selection and surface preconditioning, plasma treatment, ultrasonication, etc.), although effective to a certain point, fall short of biofilm control. Efforts have been explored, mainly with a view to their application in pharmaceutical and healthcare settings, which focus on targeting molecular determinants regulating biofilm formation. Their application to the food industry would greatly aid efforts to eradicate undesirable bacteria from food processing environments and, ultimately, from food products. These approaches, in contrast to bactericidal approaches, exert less selective pressure which in turn would reduce the likelihood of resistance development. A particularly interesting strategy targets quorum sensing systems, which regulate gene expression in response to fluctuations in cell-population density governing essential cellular processes including biofilm formation. This review article discusses the problems associated with bacterial biofilms in the food industry and summarizes the recent strategies explored to inhibit biofilm formation, with special focus on those targeting quorum sensing.