Apr 07, 2021
Poultry Microbiota Insight: Part 4 - How to study the microbiome?
Apr 07, 2021
The poultry gut microbiota is a complex ecosystem, housing billions of bacteria whose role is essential in the bird’s digestion, natural defenses, well-being and overall health maintenance. Recently advances in DNA sequencing has allowed to get a better understanding of the poultry microbiome.
What is metagenomics?
Microbiologists used to apply cultural techniques and microscopy to identify and characterize microorganisms. These techniques are time consuming and provide a limited vision of a microbial community. Lately, thanks to the progress of high-throughput sequencing technologies, microbiologists have made a giant leap with the development of metagenomics.
Metagenomics applies a suite of sequencing technologies and bioinformatics tools to directly access the genetic content of entire communities of microorganisms (Thomas et al., 2012). Cultural and metagenomics approaches are complementary.
What characterises metagenomics techniques:
- They allow us to detect rare bacteria species and ones that cannot be cultivated
- They enable the analysis of a large number of microbial samples at the same time
- They give a snapshot of population diversity within a sample
These techniques require very specific expertise in biostatistics and key bioinformatics resources in order to translate the millions of DNA sequences generated into microbial population composition. They also rely on a specific database of known bacteria sequences, while a large proportion of bacteria sequences remain unknown. Depending on the level of detail needed and the complexity of the experimental design, it can take between one week to several months to analyse a sequencing dataset.
From metagenomics to barcoding
To describe the microbial composition of gut microbiota using sequencing strategy it is not necessary to sequence the full metagenome. A common practice is to target a fragment of the bacterial genome, which is used as a marker or a sort of ID card for a bacteria. This approach, called amplicon sequencing or barcoding, drastically reduces the cost and the time taken for analysis. The 16S ribosomal RNA subunit gene (16S rRNA gene) is the most used marker gene to describe bacteria composition.