Would someone like to tell me that while constructing a metagenomic library from human source samples, such as Skin, Mucus, intestine and whatever else, do we keep in mind about the contaminants?
As humans' contains more than 10 times bacterial cells of their own, and one of the main reason of this is our continuous contact with the surrounding environment. So let suppose if one wants to construct a metagenomic library of Mouth flora, how will he consider the contaminating bacteria coming through food, air or water? If there is no mean of considering contaminants, then i think we are providing 50% or more false data to coming and present generations.
Hello Raees,
You pose a very interesting question, which i'm sure has passed through a lot of minds.
Of course there will be contamination in most of the samples we're looking at which will confound the underlying signal. (we'll call it "reality"). The important thing is that these extra random signals don't drown out the real one.
Based on some playing around with the HMP (human microbiome project) data as well as a series of publications on the matter, it would say that we're certainly reading out some of the real signal. I say this because the distance (choose your way of measuring this) between samples taken from the same individual is smaller than between individuals. Which means that we're getting a glimpse of a "stable" community. I think this is mostly a numbers game. So, the microbes that are randomly ingested or float around are usually going to be a lot fewer than the comensals which have evolved to inhabit the host. Obviously, some pathogens will not follow this rule.
A lot more if left to be understood about all of this.
Thanks Xarrin B. Sindhu and Paul Costea.
Hello Paul,
Your answers helped me a lot, and now I have even a more better understanding regarding the matter in question.
Importantly, Genomic Standards Consortium has made and published recommendations about contextual information
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