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Approaches to Microbiome Analysis
NGS Leaders
Posted: Friday, May 4, 2012 8:29 AM
Joined: 7/30/2015
Posts: 20

We had a great webinar the other day with infomative presentations on microbiome analysis. We didn't have time to address audience questions during the session so we will post some here with with replies from the panelists! 



Q: How much homology is there between different species or genera in a broader context? 

Laura Wegener Parfrey: The level of sequence similarity found within species and genera is variable within eukaryotes (PMID:19592529) 

Q: Can single-cell sequencing have any impact in metagenomics? 

Laura Wegener Parfrey: Yes, any approach that expands the catalog of genomic sequences for known organisms will improve metagenomic annotation.

Q: How reliable is to annotate data from Illumina (~50-100bp) reads? 

Laura Wegener Parfrey: Illumina data works great in general, the biggest caveat is that the level of taxonomic resolution is often limited to family level. (PMID: 22402401, 20534432)  

NGS Leaders
Posted: Friday, May 18, 2012 1:26 PM
Joined: 7/30/2015
Posts: 20

And more...


Q: What is your minority detection in % that you can detect at the microbiome and is there not a limitation regarding the accuracy? 

Laura Wegener Parfrey: This really depends on the level of sequencing you do. With millions of sequences per sample in illumina sequencing rare members can be detected. There is always a caveat that it can be difficult to distinguish rare members from sequencing noise.


Q: Do journals now require uploading of metagenomic data on publication? 

Laura Wegener Parfrey: Yes, all sequence data must be made public.  We are also pushing hard for metadata that conforms to the Genomic Standards Consortium (MIxS) to also be made available for every study.  


Q: IQ vs. paracyte correlation, is it really causal, or just reflects lower level of education in less developed countries? 

Laura Wegener Parfrey: This is a correlation, see this paper for their methods and more detail: PMID: 20591860 


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