The gut of humans and animals comprises a high number of microorganisms, which exert important functions during food digestion and defense of infections. Some of the microorganisms can cause diseases. The gut flora is comprised of bacteria, fungi and protozoa, but a large number of viruses is also present in the gut. Viruses can also be agents of disease. In addition, the viruses of bacteria – the bacteriophages – can regulate the growth of bacteria and transfer genes. The composition of the bacterial gut flora has recently been analysed using metagenomic methods. In contrast, only little is known about the composition of viruses (the so-called virome) in the gut. This is mainly due to methodological problems to identify the large variety of viruses present in a sample. However, the development of high-throughput sequencing techniques – summarized as Next Generation Sequencing (NGS) – has simplified the metagenome analyses during the last years and enables the analysis of viromes. Although first data on human viromes are available now, the viromes of animals have been only scarcely analysed. The aim of the investigations presented here is therefore the analysis of viromes from animals. As the enteric flora is complex and many pathogenic viruses are transmitted by faeces, the metagenomic analyses was conducted using faecal samples. By this, the general composition of the faecal viromes was assessed, but also the possible influence of factors like age and diet was considered. To this end, an NGS-based method for the reliable and reproducible analysis of the faecal virome was developed first. Thereafter, the method was applied to two animal species. Pigs were selected as this animal species represents an important farm animal in Germany and its gut health has a high economic impact. The composition of the viruses in the faeces of pigs should be analysed first. The influence of feeding probiotic bacteria und the age of pigs was investigated. The second selected animal species were wild rats, because these animals are known as reservoirs for pathogens for humans. The viruses detected in these faeces should be mainly analysed regarding their potential for zoonotic transmission to humans. The developed analytic method is based on filtrations and centrifugations to purify and concentrate all virus particles from the faeces. Whole nucleic acid was extracted from the virus particles, amplified and sequenced using NGS. Bioinformatic analyses were used to determine the composition of viruses in the sample based of the sequence data. A control system, which consisted of three bacteriophages added to the samples, was developed and used for optimization of the method and as quality control. In total, 205 different virus species from 36 different virus families were detected in eight pooled faecal sample each derived from six piglets or six young pigs. The main virus groups were pig viruses and bacteriophages. Plant viruses, which are frequently detected in human faecal viromes and which presumably originate from spices of the diet, comprised only a very small fraction in the pig samples. Using the metagenome analysis, a so far unknown pig virus (designated PigSCV) was also identified. In comparative investigations of faecal viromes from a feeding trail of sows and their piglets with the probiotic bacterium Enterococcus faecium NCIMB 10415 a large variability of their composition could generally be identified. However, the faecal virome was nearly not influenced by the probiotic feeding, but strongly by the age of the animals. In contrast to the youngest piglets, which showed a high proportion of pig viruses and a lower proportion of bacteriophages, the sows showed the opposite picture. In addition, the diversity of viral communities increased significantly with the age. Despite bacteriophages, the faecal viromes of 20 wild rats, which originated from the city of Berlin, mainly consisted of known rat viruses from the virus families Parvoviridae and Picobirnaviridae. However, so far unkown picorna-, bocaparvo- and sapoviruses as well as novel circular DNA viruses were also identified. Group A rotaviruses were detected for the first time in rats. Rotaviruses are known as pathogens causing gastroenteritis in animals and humans. The analysis of the whole genome of the rat rotavirus showed that it is closely related to rotaviruses from humans and animals and therefore it may possibly transmissible to them. In conclusion, the investigations show that the developed method is well suited for the analysis of faecal viromes. The application of the method shows the high variability of the virome, which is mainly dependent on the age of the animals. Using the method, we were able to describe viral communities and to detect pathogenic viruses as well as novel viruses identified. Further investigations should simplify the method in order to enable the analysis of higher sample numbers. In addition, the bioinformatic analysis of sequence data should be further developed in order to determine the viromes in more broadness and detail and to enable the analysis of interactions with other microorganisms and the host.