Reagent contamination human feces

We evaluated DNA extraction method, initial sample biomass and reagent contamination on the assessment of the human gut microbiota. We found significant differences in the total number of reads among samples from different kits and dilutions, but not between donors. The number of reads from technical controls was negligible. DNA extraction kits allowed inferring microbial consortia with similar membership but different abundances. Furthermore, we found differences in the taxonomic profile of the microbial community. Unexpectedly, the effect of sample dilution was moderate and did not introduce severe bias into the microbial inference. Our results indicate that the gut microbiota inference is not much affected by contamination with laboratory reagents, even in highly diluted samples, but largely impacted by the protocol to extract DNA.