Question: Bioinformatic tools for MyCOBIOME analysis.
gravatar for lugonauta
4 months ago by
lugonauta10 wrote:

Hi friends! I'm interested in perfoming an analysis of the fungal community from a set of faecal samples. I have some skills about 16S rDNA amplicon approach for Microbiome analysis, using QIIME2, but I'm completely neofyte in the Mycobiome world. Could anyone explain me how to perform such kind of analysis? I mean, pipelines, bioinformatic tools, etcetera. My starting point are ITS amplicon reads sequenced in a Miseq platform. Thanks a lot!!!

ADD COMMENTlink modified 4 months ago by ashishbansal123000 • written 4 months ago by lugonauta10

I think you can use everything you know about QIIME2 pipeline. You just use a different starting point and database.

ADD REPLYlink written 4 months ago by h.mon24k
gravatar for Daniel
4 months ago by
Cardiff University
Daniel3.7k wrote:

There are ITS databases that are used with qiime2 and several tutorials and pipelines that people have written up:

As long as you're using the correct database it should all be fine to follow most of the standard 16S steps.

ADD COMMENTlink written 4 months ago by Daniel3.7k
gravatar for ashishbansal12300
4 months ago by
ashishbansal123000 wrote:

The human microbiome substantially affects many aspects of human physiology, including metabolism, drug interactions and numerous diseases. This realization, coupled with ever-improving nucleotide sequencing technology, has precipitated the collection of diverse data sets that profile the microbiome. In the past 2 years, studies have begun to include sufficient numbers of subjects to provide the power to associate these microbiome features with clinical states using advanced algorithms, increasing the use of microbiome studies both individually and collectively. Here we discuss tools and strategies for microbiome studies, from primer selection to bioinformatics analysis. Key points New sequencing technologies and open-source computational tools have enabled rapid progress in research into the human microbiota and the human microbiome. Most recent studies use 16S rDNA gene profiling to assess the organisms that are present in a sample or shotgun metagenomics to get a complete profile of gene content in a given habitat. Bacterial and archaeal communities are currently easy to profile using the 16S rDNA gene sequence: techniques for profiling eukaryotes and viruses are more challenging but are intense areas of interest. Both taxonomic and functional profiling are crucial for obtaining a full picture of the microbiota, although error rates both in sequencing and in functional and taxonomic assignment need to be considered when drawing conclusions. Time series studies are proving to be especially useful for understanding variation in the microbiome, as individuals can vary considerably in their microbiome composition. Thus far, developmental trajectories have only been studied in the gut, although it will be fascinating to extend these studies to other body habitats and to developmental disorders. Clustering sequences into taxonomic groups remains challenging, although the quality of current techniques is sufficient to observe clinically relevant differences among subjects. Public resources for functional annotation of metagenomic data are expanding rapidly; they are providing key enabling technology for large-scale projects, such as the Human Microbiome Project and the Earth Microbiome Project. Studies of the microbiome are rapidly moving from preliminary studies that observe differences among groups to mechanistic and longitudinal studies that allow us to see how and why these differences develop. Personalized culture collections will be especially important in this respect.

ADD COMMENTlink written 4 months ago by ashishbansal123000

Can you explain how this answers the question?

ADD REPLYlink written 4 months ago by jrj.healey12k
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