Metagenomic analysis in a mouse model of steatohepatitis

Published: 10 July 2019| Version 1 | DOI: 10.17632/pmpb5khx48.1
Contributors:
Adriana Carino,
Silvia Marchianò,
Stefano Fiorucci

Description

It is previously established that the ratio of Bacteroidetes and Firmicutes, the two dominant phyla that make up over 90% of bacterial phylogenetic types in the human distal gut, is modulated by the diet; in particular a diet enriched in fat causes a modulation of the intestinal microbiota composition that results in a decreased proportion of Bacteroidetes which is compensated by a robust increase in the proportion of Firmicutes. The goals of this study are to confirme these findings analyzing the composition of microbiota in mice fed a High Fat diet and fructose (HFD-F), and to evaluate the effects of two bile acid receptors ligands, Ursodeoxycholic acid (UDCA) and Obeticholic acid (OCA), on intestinal flora in this mouse model of NASH. Here we report the information obtained from metagenomics workflow for each sample.

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The microbial DNA was purified from mouse stool samples, using the PureLink Microbiome DNA Purification Kit (Thermo Fisher Scientific), according the manufacturer’s instructions. 16S rRNA sequencing was performed using Ion 16S Metagenomics Kit (Thermo Fisher Scientific) on the Ion Torrent S5 platform. Automated analysis, annotation, and taxonomical assignment were generated using Ion Reporter Software - Metagenomics Workflow (Ion Reporter 5.10.2.0). The Ion Reporter Software enables the rapid identification (at genus or species level) of microbes present each sample, using both curated Greengenes and premium curated MicroSEQ ID 16S rRNA reference databases. Here we report the information obtained from metagenomics workflow, in particular the reads analysis per consensus for each sample.