Methods used to study stomach microbiome

Following are methods which are used to Study gastric microbiota.

  1. Culturing based methods:

Culture based methods are used to study the composition of gastric microbiota. This method focusses on easy to culture gastric microbes. This approach is used for the analysis of only 10-15 % gastric microbiota. The culture based have several limitations because it do not give the whole microbiome profile of stomach.

  1. Microbial culturomics:

To study the microbiome population present in stomach new approaches for culturing are introduced. This technique eliminates easy to culture method due to its limitations.New culturing techniques are coupled with matrix-assisted laser desorption/ionization–time of flight mass spectrometry used for study of stomach microbiota.

Culture-independent approaches:

Culture-independent studies use a variety of molecular methods based on 16S rRNA gene sequencing. A multitude of reasons define these methods as far superior to those which are culture-dependent.

16S rRNA is present in almost all bacteria. The function of the 16S rRNA gene has remained unchanged over time, suggesting that random sequence changes are a more accurate measure of time (evolution).The 16S rRNA gene is large enough for computational purposes.

A variety of other methods for the analysis of microbiota including:

1-Fluorescent in situ hybridization (FISH)

2-HTS methods

3- Targeted qPCR

4-Traditional or sequence-aided community fingerprinting

5-bioinformatics tools

6-pyrosequencing

7-Sequencing of cloned 16S rDNA

8-Microarrays (PhyloChip)

9-Next-generation sequencing (NGS)

(Stewart, O. A., et al 2020)

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