Gut microbes are suggested to play an essential role in maintaining humanhealth, and unfavorable alterations in gut microbiota have been associated with several human diseases and disorders. Despite the significant advancements in analysis tools, several sources of uncertainty still exist in the gut microbiota composition analyses, limiting the reproducibility and comparability of the results from distinct gut microbiota studies. 

The first main aim of this study was to set up a functional high-throughput pipeline for 16S rRNA gene sequencing -based gut microbiota composition analysis. This was achieved by evaluating the effects of fecal sample processing, i.e. two sample storage conditions and five DNA extraction kits, along with two different 16S rRNA gene sequencing protocols. The second main aim of this study was to explore the role of gut microbiota in the onset of obesity-related metabolic disorders such as non-alcoholic fatty liver disease. This was done by studying the effects of intragastric administration of two distinct gut microbes, Faecalibacterium prausnitzii and Enterobacter cloacae, on host health and metabolism of high fat diet -fed C57BL/6N mice. 

The results of this study showed that the 16S rRNA gene sequencing protocol had a significant effect on the analysis results. Meanwhile, the effect of sample pre-processing was more modest, yet still potentially important. These results indicate that careful design and adequate method optimization are required in order to produce reliable 16S rRNA gene sequencing results. Moreover, the results of this study revealed that the intragastric F. prausnitzii administration appeared to protect the C57BL/6N mice from liver steatosis, whereas the intragastric administration of E. cloacae seemed to induce liver damage. Further studies are needed in order to clarify the underlying mechanisms and to fully 
elucidate the possible therapeutic potential of F. prausnitzii.