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

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 var...

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Main Authors:	Sidney P. Walker, Mark Tangney, Marcus J. Claesson
Format:	Article
Language:	English
Published:	Frontiers Media S.A. 2020-02-01
Series:	Frontiers in Oncology
Subjects:	cancer low biomass FFPE sequence analysis microbiome
Online Access:	https://www.frontiersin.org/article/10.3389/fonc.2020.00179/full

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spelling	doaj-ac96e074466a49dfb8fe805ef02db5d62020-11-25T01:33:24ZengFrontiers Media S.A.Frontiers in Oncology2234-943X2020-02-011010.3389/fonc.2020.00179488981Sequence-Based Characterization of Intratumoral Bacteria—A Guide to Best PracticeSidney P. Walker0Sidney P. Walker1Sidney P. Walker2Sidney P. Walker3Mark Tangney4Mark Tangney5Mark Tangney6Marcus J. Claesson7Marcus J. Claesson8Cancer Research at UCC, University College Cork, Cork, IrelandSynBioCentre, University College Cork, Cork, IrelandAPC Microbiome Ireland, University College Cork, Cork, IrelandSchool of Microbiology, University College Cork, Cork, IrelandCancer Research at UCC, University College Cork, Cork, IrelandSynBioCentre, University College Cork, Cork, IrelandAPC Microbiome Ireland, University College Cork, Cork, IrelandAPC Microbiome Ireland, University College Cork, Cork, IrelandSchool of Microbiology, University College Cork, Cork, IrelandTumors 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.https://www.frontiersin.org/article/10.3389/fonc.2020.00179/fullcancerlow biomassFFPEsequence analysismicrobiome
collection	DOAJ
language	English
format	Article
sources	DOAJ
author	Sidney P. Walker Sidney P. Walker Sidney P. Walker Sidney P. Walker Mark Tangney Mark Tangney Mark Tangney Marcus J. Claesson Marcus J. Claesson
spellingShingle	Sidney P. Walker Sidney P. Walker Sidney P. Walker Sidney P. Walker Mark Tangney Mark Tangney Mark Tangney Marcus J. Claesson Marcus J. Claesson Sequence-Based Characterization of Intratumoral Bacteria—A Guide to Best Practice Frontiers in Oncology cancer low biomass FFPE sequence analysis microbiome
author_facet	Sidney P. Walker Sidney P. Walker Sidney P. Walker Sidney P. Walker Mark Tangney Mark Tangney Mark Tangney Marcus J. Claesson Marcus J. Claesson
author_sort	Sidney P. Walker
title	Sequence-Based Characterization of Intratumoral Bacteria—A Guide to Best Practice
title_short	Sequence-Based Characterization of Intratumoral Bacteria—A Guide to Best Practice
title_full	Sequence-Based Characterization of Intratumoral Bacteria—A Guide to Best Practice
title_fullStr	Sequence-Based Characterization of Intratumoral Bacteria—A Guide to Best Practice
title_full_unstemmed	Sequence-Based Characterization of Intratumoral Bacteria—A Guide to Best Practice
title_sort	sequence-based characterization of intratumoral bacteria—a guide to best practice
publisher	Frontiers Media S.A.
series	Frontiers in Oncology
issn	2234-943X
publishDate	2020-02-01
description	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.
topic	cancer low biomass FFPE sequence analysis microbiome
url	https://www.frontiersin.org/article/10.3389/fonc.2020.00179/full
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Sequence-Based Characterization of Intratumoral Bacteria—A Guide to Best Practice

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