Microbiome-based environmental monitoring of a dairy processing facility highlights the challenges associated with low microbial-load samples

Abstract

Efficient and accurate identification of microorganisms throughout the food chain can potentially allow the identification of sources of contamination and the timely implementation of control measures. High throughput DNA sequencing represents a potential means through which microbial monitoring can be enhanced. While Illumina sequencing platforms are most typically used, newer portable platforms, such as the Oxford Nanopore Technologies (ONT) MinION, offer the potential for rapid analysis of food chain microbiomes. Initial assessment of the ability of rapid MinION-based sequencing to identify microbes within a simple mock metagenomic mixture is performed. Subsequently, we compare the performance of both ONT and Illumina sequencing for environmental monitoring of an active food processing facility. Overall, ONT MinION sequencing provides accurate classification to species level, comparable to Illumina-derived outputs. However, while the MinION-based approach provides a means of easy library preparations and portability, the high concentrations of DNA needed is a limiting factor.

Artisanal Household Milk Pasteurization Is Not a Determining Factor in Structuring the Microbial Communities of Labneh Ambaris: A Pilot Study

“…On the other hand, the presence of microorganisms in the samples could be due to contaminations that occurred after heat treatments and that originated from the surrounding production environment [ 8 ]. Various studies have found that the microbial species that colonize production facilities and the air in the manufacturing areas have a significant impact on the microbial compositions of dairy products [ 31 , 32 , 33 ]. A study showed that the same yeast species were detected in cheese and in the environment of its production facility, although at varying abundances [ 34 ].…”

Development of sequencing-based methodologies to distinguish viable from non-viable cells in a bovine milk matrix: A pilot study

“…These factors could account for the numerical difference in species level classification of the Staphylococcus strain, where Illumina sequencing afforded greater taxonomic resolution than ONT sequencing, as S. hominis is specifically classified within the S. haemolyticus group ( Becker et al, 2014 ). Additionally, for shotgun sequencing with ONT, MDA amplification was needed to generate sufficient quantities of DNA required for sequencing, which has been previously found to introduce some biases ( McHugh et al, 2021 ). Despite all these points, as improvements are made to the sequencing technology and analytical tools, coupled with its advantages in portability, time effectiveness and the possibility of real-time analysis, there is great potential for the use of ONT sequencing in characterising microbial communities in food and food-related environments.…”

Biosensors and Microfluidic Biosensors: From Fabrication to Application

“…Biosensors are utilized to increase quality of life in a variety of applications. The quality, safety, and upkeep of food items as well as their processing are difficult in food processing industries, and hence the food sector would benefit from cost-effective technologies for food authentication and monitoring [ 121 , 122 , 123 ]. Potentiometric alternating biosensing devices are also used to detect the changes in pH caused by ammonia, and have been used to identify E. coli [ 124 ]; ingredients were mixed in a sonicator to separate the bacteria from the food [ 125 ].…”