Abstract
Tumors are hospitable environments to bacteria and several recent studies on cancer patient samples have introduced the concept of an endogenous tumor microbiome. For a variety of reasons, this putative tumor microbiome is particularly challenging to investigate, and a failure to account for the various potential pitfalls will result in erroneous results and claims. Before this potentially extremely medically-significant habitat can be accurately characterized, a clear understanding of all potential confounding factors is required, and a best-practice approach should be developed and adopted. This review summarizes all of the potential issues confounding accurate bacterial DNA sequence analysis of the putative tumor microbiome, and offers solutions based on related research with the hope of assisting in the progression of research in this field.
Highlights
Amplicon sequencing in bacterial microbiota studies typically targets the 16S rRNA gene subunit
16S rRNA gene sequencing is still affected by the low ratio of bacterial DNA, but to a lesser extent than whole genome sequencing methods
The presence of damaged DNA could make methods reliant on amplicon sequence variants (ASV) generation unsuitable, as an example, SNPs arising as artifacts of the FFPE process would erroneously be recorded as different strains
Summary
The recent work characterizing the microbiomes of solid tumors is outlined in Table 1 below. Due to the challenges posed in characterizing the tumor microbiome, it is likely that some or all of the studies referenced have been negatively impacted in some way, reducing their accuracy. This caveat must be kept in mind when assessing the results, and reinforces the need for the introduction of a best practice methodology to make future research more reliable
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