Tools for stools: the challenge of assessing human intestinal microbiota using molecular diagnostics

Abstract

The human GI tract is inhabited by an incredibly complex and abundant microbiota, whose composition is dependent on a variety of factors. The gut microbiota has an influence in the morphological, immunological and nutritional functions of the digestive tract and may be involved in many diseases. This article proposes the rationale behind conducting in vitro diagnostics (IVDs) of the human microbiota, as well as outlining the conceptual and technical difficulties involved in IVD testing. The molecular methods that can be used according to whether the IVD tools are employed to study one individual constituent species or to determine the microbiota as a whole will also be described. In the latter case, these technologies include high-throughput sequencing for metagenomics and DNA microarrays, which can now be efficiently used to study gut ecology and are believed to represent the future of standardized diagnostics.

Keywords::

• colorectal cancer
• DNA microarray
• GI tract
• gut microbiota
• in vitro diagnostic
• inflammatory bowel disease
• metagenomic

Acknowledgements

The authors acknowledge the reviewers for their contributions with their expert comments.

Financial & competing interests disclosure

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.

No writing assistance was utilized in the production of this manuscript.