The pig gut microbiota analysis techniques, a comparison

Abstract

Abstract The gastrointestinal tract microbiota composition can be radically different among pigs with regards to their health, age, feed intake, breed, and local conditions making its investigation into an important and multifaceted tool for evaluating the effects of new breeding and feeding schemes and animal welfare. For a long time, scientists have relied upon classical microbiology techniques to identify the makeup of bacterial populations from the gastrointestinal tract. Since their conceptions, high throughput sequencing and other molecular techniques contributed immensely in better understanding the pig gut microbiota and its makeup. Since many techniques to identify and quantify the microbiota are based on bacterial gene targets, they can, be used to determine the relation between different bacterial taxons and developmental processes, how it influences the host metabolism or diseases impact. In our review, we offer an overview of the different methods employed in the assay of the gut microbiota of pigs along with differences and pitfalls.