Microbiome sequencing: challenges and opportunities for molecular medicine

ABSTRACT

Introduction: Since the discovery of Polymerase Chain Reaction and pioneering work on 16S ribosomal RNA genes in the 1980’s, the use of molecular techniques to study microbial ecosystems and pathogenic microorganisms has been increasing exponentially. Because microbial communities inhabiting various body sites such as the skin or the intestine can influence our physiology, there has been a massive interest in studying their diversity, functions, and role in the development of acute and chronic diseases.

Area covered: In the present review, we gather knowledge on sequencing approaches to study microbial communities, especially human body microbiota, and give opinions on their potential and limitations, particularly with respect to clinical applications.

Expert commentary: High-throughput sequencing delivered unprecedented views on complex microbial communities, but their popularization is accompanied by substantial technical hurdles that will need to be overcome for efficient implementation in routine clinical procedures.

KEYWORDS:

• Complex microbial communities
• gut microbiome
• sequencing
• metagenomics
• 16S rRNA gene
• clinical microbiology
• molecular diagnostics

Declaration of interests

The authors have no relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript. This includes employment, consultancies, honoraria, stock ownership or options, expert testimony, grants or patents received or pending, or royalties.