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

Frontiers in Oncology
Sidney P WalkerMarcus J Claesson

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.

References

Feb 5, 2000·Advances in Experimental Medicine and Biology·R D Berg
Mar 30, 2007·Journal of Microbiological Methods·Soumitesh ChakravortyDavid Alland
Apr 17, 2008·Cancer Research·Kathrin WestphalSiegfried Weiss
Jan 29, 2010·Human Gene Therapy·Jan Peter van PijkerenMark Tangney
Apr 13, 2010·Nature Methods·J Gregory CaporasoRob Knight
Apr 15, 2010·Molecular Therapy : the Journal of the American Society of Gene Therapy·Michelle CroninMark Tangney
Jun 28, 2011·Bioinformatics·Robert C EdgarRob Knight
Jul 19, 2011·Nature Methods·Dan KnightsScott T Kelley
Nov 25, 2011·Cancer Biomarkers : Section a of Disease Markers·William E GrizzleKatherine C Sexton
Sep 22, 2012·Cancer Gene Therapy·M CroninM Tangney
Mar 30, 2013·Infectious Agents and Cancer·Joanne Cummins, Mark Tangney
Jan 15, 2014·PloS One·Caiyun XuanDelphine J Lee
Feb 27, 2014·Molecular Therapy : the Journal of the American Society of Gene Therapy·Michelle CroninMark Tangney
Mar 13, 2014·Applied and Environmental Microbiology·Camilla UrbaniakGregor Reid
Nov 26, 2014·Clinical Chemistry·Hongdo Do, Alexander Dobrovic
Dec 4, 2014·Journal of Controlled Release : Official Journal of the Controlled Release Society·W L ByrneM Tangney
Mar 5, 2015·Proceedings of the National Academy of Sciences of the United States of America·Charles A SwoffordNeil S Forbes
May 29, 2015·Science Translational Medicine·Tal DaninoSangeeta N Bhatia
Sep 30, 2015·Scientific Reports·Panos LehouritisMark Tangney
Dec 15, 2015·Journal of Controlled Release : Official Journal of the Controlled Release Society·Panos LehouritisMark Tangney
Jan 1, 2016·Biochemical and Biophysical Research Communications·Ravi RanjanDavid L Perkins
Jun 28, 2016·Applied and Environmental Microbiology·Camilla UrbaniakGregor Reid
Jul 21, 2016·Nature·M Omar DinJeff Hasty
Apr 15, 2017·Oncotarget·Sagarika BanerjeeErle S Robertson
Apr 25, 2017·European Urology·Ilaria CavarrettaAndrea Salonia
Jul 1, 2017·PloS One·Carola MurphyMark Tangney
Jul 22, 2017·The ISME Journal·Benjamin J CallahanSusan P Holmes
Jan 16, 2018·Annals of Gastroenterology : Quarterly Publication of the Hellenic Society of Gastroenterology·Stergios A PolyzosJannis Kountouras
Feb 6, 2018·Nature Reviews. Microbiology·David T Riglar, Pamela A Silver
Feb 13, 2018·Nature Biotechnology·Miten JainMatthew Loose
Feb 27, 2018·Journal of Controlled Release : Official Journal of the Controlled Release Society·Yensi Flores BuesoMark Tangney
Feb 28, 2018·Microbiome·Clarisse A MarotzKarsten Zengler
Mar 23, 2018·World Journal of Gastrointestinal Oncology·Fu-Mei Shang, Hong-Li Liu
Jul 27, 2018·Nature Microbiology·Marcus C de GoffauJulian Parkhill
Dec 1, 2018·Trends in Microbiology·Raphael EisenhoferLaura S Weyrich

❮ Previous
Next ❯

Citations

Aug 12, 2020·Journal of Biomolecular Structure & Dynamics·Zina RavnikPremnath Dhanaraj
Mar 14, 2021·Cancer Discovery·Diego Salas-BenitoIgnacio Melero
Jun 18, 2021·Frontiers in Microbiology·Holger BrüggemannRolf Lood
Jul 11, 2020·Cancer Cell·K Leigh GreathouseCurtis C Harris
Sep 19, 2021·Scientific Reports·Glenn HoganMark Tangney

❮ Previous
Next ❯

Methods Mentioned

BETA
PCR
Illumina sequencing
amplicon sequencing
biopsy

Software Mentioned

UCHIME
MolYsis
Decontam
QIIME
lyPMA
Chimera Slayer
Usearch
SourceTracker

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.