The worldwide prevalence of obesity more than doubled between 1980 and 2014. The most frequent cause, which leads to the obesity development, is an imbalance between energy intake and expenditure. In this complex process, genetic susceptibility, environmental and lifestyle factors are involved. The gut microbiota is a part of a complex network. Numerous studies have shown that the gut microbiota interacts with the host metabolism and plays an important role in various processes. The core gut microbial profile mainly embodies bacteria, belonging to the Gram-positive Firmicutes and the Gram-negative Bacteroidetes. An increase in gut Firmicutes/Bacteroidetes ratio is detected in obese patients and during high-fat diet consumption in human and animal studies. Strains belonging to the genera Lactobacillus and Bifidobacterium are commonly used as probiotics and are most studied for the treatment and prevention of obesity-associated disorders. Moreover, several potential bacterial candidates, such as Akkermansia muciniphila, Faecalibacterium prausnitzii, Prevotella copri, Roseburia or Ruminococcus, have been identified and novel mechanisms of action intervening their positive effects for obesity have been elucidated. Consequently, the gut microbiota is gaining significant research interest in relation to obesity and associated metabolic disorders in an attempt to better understand the etiology of obesity and potentially new methods of its prevention and treatment. However, traditional culture methods are very limited for identifying microbes. With the application of molecular biologic technologies, especially metagenomic next-generation sequencing, progress has been made in the study of the human intestinal microbiome.