Contamination Issues in Microbiome Sequencing Studies
Sharon Bewick, David Karig and William F. Fagan
from: Microbial Ecology: Current Advances from Genomics, Metagenomics and Other Omics (Edited by: Diana Marco). Caister Academic Press, U.K. (2019) Pages: 13-26.
Contamination in microbiome sequencing studies is a well-known but difficult to address problem. Unlike culture experiments, in which only living cell contamination is of consequence, sequencing analyses can be disrupted by dead cells or even small pieces of non-viable DNA. Although all sequencing studies face contamination issues, these issues are likely to be more or less important, depending on the microbiome under examination. Systems characterized by low input samples, for example the human skin microbiome, may be highly susceptible to contamination. By contrast, systems characterized by high input samples, for example the human gut microbiome, may be less influenced. Here, we use a simulation model to examine when contamination is likely to be problematic, relating the degree to which sequencing results are influenced by contamination to sample characteristics such as DNA input, as well as ecological characteristics such as taxon diversity. We also study how well methods such as thresholding work to differentiate target taxa from contaminants. This work illustrates some of the challenges associated with the collection and interpretation of sequencing studies when used to understand the composition and behaviour of complex microbial communities read more ...