Frontiers in Oncology (Feb 2020)

Sequence-Based Characterization of Intratumoral Bacteria—A Guide to Best Practice

  • Sidney P. Walker,
  • Sidney P. Walker,
  • Sidney P. Walker,
  • Sidney P. Walker,
  • Mark Tangney,
  • Mark Tangney,
  • Mark Tangney,
  • Marcus J. Claesson,
  • Marcus J. Claesson

DOI
https://doi.org/10.3389/fonc.2020.00179
Journal volume & issue
Vol. 10

Abstract

Read online

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.

Keywords