16S rRNA gene sequencing is commonly used for identification, classification and quantitation of microbes within complex biological mixtures such as environmental samples and gut samples. Many studies [1][2] are trying to establish the link between the intestinal microbiota with different neurodevelopment, neurogical disorders etc. In these studies the BioInformatic analysis of the data coming from gut samples plays a very important role. So, in our brainhack project we will work on the publicly available data from one of these article[1]. So, this project is aimed for those who are interested in the BioInformatic analysis of Gut Microbiota and are also interested in the different pipelines and analysis tools like QIIME2[4] , cutadapt[5] , Kraken2[6] etc.
In this project, we propose:
To go through this [1] article to understand their method of analyzing the gut microbiota
To download their 16s sequencing data from NCBI (submitted by the authors)
To extract and filter the data
For advaced users, We also propose:
To write( Python ) few tools for filtering the sequencing data
To try to create an Anaconda environment or a Singularity image with the 16s analysis pipeline QIIME2[4]
To try to implement some of the methods of analysis with QIIME2 (as described in the article)
To understand the importance of reproducibility of the results
References:
[1] The microbial metabolite p-Cresol induces autistic-like behaviors in mice by remodeling the gut microbiota. Patricia Bermudez-Martin et al.
[2] Gut Microbiota Regulate Motor Deficits and Neuroinflammation in a Model of Parkinson's Disease. Timothy R Sampson et al.
[3] 16S rRNA Gene Sequencing for identification, classification and quantitation of microbes
[4] Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Evan Bolye et al.
[5] Cutadapt
[6] Kraken 2