Abstract
16S rRNA gene analysis is the most convenient and robust method for microbiome studies. Inaccurate taxonomic assignment of bacterial strains could have deleterious effects as all downstream analyses rely heavily on the accurate assessment of microbial taxonomy. The use of mock communities to check the reliability of the results has been suggested. However, often the mock communities used in most of the studies represent only a small fraction of taxa and are used mostly as validation of sequencing run to estimate sequencing artifacts. Moreover, a large number of databases and tools available for classification and taxonomic assignment of the 16S rRNA gene make it challenging to select the best-suited method for a particular dataset. In the present study, we used authentic and validly published 16S rRNA gene type strain sequences (full length, V3-V4 region) and analyzed them using a widely used QIIME pipeline along with different parameters of OTU clustering and QIIME compatible databases. Data Analysis Measures (DAM) revealed a high discrepancy in ratifying the taxonomy at different taxonomic hierarchies. Beta diversity analysis showed clear segregation of different DAMs. Limited differences were observed in reference data set analysis using partial (V3-V4) and full-length 16S rRNA gene sequences, which signify the reliability of partial 16S rRNA gene sequences in microbiome studies. Our analysis also highlights common discrepancies observed at varioustaxonomic levels using various methods and databases.
Highlights
Inflammation, including fatty liver diseases such as alcoholic liver disease (ALD) and non-alcoholic fatty liver disease (NAFLD), is an integral component of both all-acute and chronic liver disorder
It is of interest to report the molecular docking analysis of stachydrine and sakuranetin with IL-6 and TNF-α in the context of inflammation
Molecular docking means that the drug is correctly absorbed and The binding force, the number of hydrogen bond interactions and binds with the receptor
Summary
Inflammation, including fatty liver diseases such as alcoholic liver disease (ALD) and non-alcoholic fatty liver disease (NAFLD), is an integral component of both all-acute and chronic liver disorder. It has been convincingly shown that immune mediators, especially pro-inflammatory cytokines, have been able to regulate many of the main characteristics of liver diseases, including acute liver failure, acute phase response, steatosis, cholestasis, hypergammaglobulinemia, and production of fibrosis [1,2]. It points out that classic signalling regulates interleukin-6 regenerative or anti-inflammatory actions, whereas interleukin-6 pro-inflammatory responses are more mediated by trans-signaling. This is relevant because the neutralising anti-interleukin-6 receptor monoclonal antibody tocilizumab has recently been licenced for therapeutic blockade of interleukin-6 in the therapy of inflammatory diseases [4]. Other chronic autoimmune disorders, such as systemic lupus erythematosus (SLE) [8], have a therapeutic benefit by blocking pro-inflammatory cytokines [8]. It is of interest to report the molecular docking analysis of stachydrine and sakuranetin with IL-6 and TNF-α in the context of inflammation
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