Next-generation sequencing: The future of molecular genetics in poultry production and food safety

Abstract

The era of molecular biology and automation of the Sanger chain-terminator sequencing method has led to discovery and advances in diagnostics and biotechnology. The Sanger methodology dominated research for over 2 decades, leading to significant accomplishments and technological improvements in DNA sequencing. Next-generation high-throughput sequencing (HT-NGS) technologies were developed subsequently to overcome the limitations of this first generation technology that include higher speed, less labor, and lowered cost. Various platforms developed include sequencing-by-synthesis 454 Life Sciences, Illumina (Solexa) sequencing, SOLiD sequencing (among others), and the Ion Torrent semiconductor sequencing technologies that use different detection principles. As technology advances, progress made toward third generation sequencing technologies are being reported, which include Nanopore Sequencing and real-time monitoring of PCR activity through fluorescent resonant energy transfer. The advantages of these technologies include scalability, simplicity, with increasing DNA polymerase performance and yields, being less error prone, and even more economically feasible with the eventual goal of obtaining real-time results. These technologies can be directly applied to improve poultry production and enhance food safety. For example, sequence-based (determination of the gut microbial community, genes for metabolic pathways, or presence of plasmids) and function-based (screening for function such as antibiotic resistance, or vitamin production) metagenomic analysis can be carried out. Gut microbialflora/communities of poultry can be sequenced to determine the changes that affect health and disease along with efficacy of methods to control pathogenic growth. Thus, the purpose of this review is to provide an overview of the principles of these current technologies and their potential application to improve poultry production and food safety as well as public health.

Comparison of Typing Methods with a New Procedure Based on Sequence Characterization for Salmonella Serovar Prediction

“…This might favor the implementation of PCRand sequencing-based methods in some laboratories, particularly as advances in sequencing technology might make these methods more attractive. Sequencing-based approaches for serovar determination can also be easily integrated into whole-genome sequencing-based approaches for Salmonella characterization, which are emerging as a viable alternative to other subtyping methods (58,59). Sequence data for fliC, fljB, genes in the rfb cluster, and genes targeted by MLST can be rapidly extracted from full-genome sequence data and used for serovar identification.…”

Изменение Микробиоты Кишечника Кур В Онтогенезе

“…Отметим, что полученные результаты в целом соответствуют современным представлениям о микробиоте кишечника птицы (Diaz-Sanchez et al, 2013). Сравнительный анализ бактериального сообщества содержимого слепых отростков кишечника птицы позволил установить статистически значимые различия в составе микробиоты, связанные с периодом онтогенеза.…”

Scientific Opinion on the evaluation of molecular typing methods for major food‐borne microbiological hazards and their use for attribution modelling, outbreak investigation and scanning surveillance: Part 1 (evaluation of methods and applications)

“…LOS and CPS are also involved in the interaction between Campylobacter and the human innate and acquired immune system. Full definition of the genetic basis of the pathogenicity of Campylobacter has been limited by the lack of suitable in vivo models, but information is growing and linkage of extensive gene array and sequencing data with epidemiological and metagenomic features should facilitate identification of more definitive gene targets for risk assessment (Diaz-Sanchez et al, 2013;Marotta et al, 2013;Melo et al, 2013;Szymanski et al, 2012). The use of gene association studies comparing organisms with different phenotypes is likely to be influential in this area (Sheppard, et al, 2013b).…”