Abstract

The human microbiome in terms of the number of bacteria exceeds the number of cells in the human body. It is defined as an additional “forgotten organ” and plays a key role in maintaining a high health status, which is conditioned by the maintenance of certain proportions and natural relations between bacteria and cells of the host organism. New diagnostic methods can enable profiling not only the human microbiome, but also livestock. An innovative analytical method, which is next generation sequencing (NGS), is increasingly used in the study of the microbiome. Many bacteria are referred to as “uncultivated” or “non-culturable” and metagenomics has played an important role in detecting these bacteria and has contributed to the development of new media for their cultivation. The main application of NGS in microbiology is to replace the conventional characterization of pathogens based on the assessment of morphology, staining properties and metabolic traits with their genome related characteristics. There are several platforms, i.e. “diagnostic tools”, that use a variety of DNA sequencing technologies, among others Ion Torrent Personal Genome Machine (PGM), Pacific Biosciences (PacBio) and Illumina MiSeq. In the case of swine microbiome, studies of the microbiome with the use of modern sequencing technologies seem to be particularly interesting in the aspect of the upcoming, inevitable changes in preventive and therapeutic procedures in animals. Analyses of this type integrate with the concept of the shared human and animal health and enable an in-depth assessment of the impact of specific factors on the population of intestinal microbes and learning how to “form” the composition of the microbiome in order to improve the quality of husbandry and to maintain the pig’s proper health status.

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