Intestinal Microbiota, the Advantages and Disadvantages of Different Methods Established for Assessing the Resident Bacterial Populations

Abstract

At the level of the gastrointestinal (GI) tract exists a consortium of living microorganisms like bacteria, fungi, protozoa and viruses, which represent the intestinal microbiota. This term, microbiota, comes from Greek, where ‘bios’ means ‘life’ and nowadays this is the right word to use, even if in the older literature the authors used the term microflora with the same meaning (Suchodolski, 2 016). In order to describe the intestinal microbiota, there are more methods available, each of them having advantages and disadvantages. The aim of this literature study was to compare the data available regarding each method used for assessing the intestinal microbiota. Among the five methods available in the present to assess the intestinal microbiota, none of them is considered a gold standard. There are available cultural and non-cultural methods, each of them having the purpose to describe the intestinal resident bacterial populations. The most commonly used methods for characterization of the intestinal microbiota are represented by FISH- Fluorescence in situ hybridization, qPCR- quantitative real-time PCR, NGS- next-generation sequencing (e.g. 454- pyrosequencing, Illumine) and Metagenomics (shotgun sequencing of genomic DNA). In this review we made a comparison between the methods available for assessing the intestinal microbiota, showing that in the present there is not a golden standard for this and that the methods used have advantages and disadvantages.