Sep 03, 2021
Pig Microbiota Insight: Part 5 - Unravelling microbiota diversity
Sep 03, 2021
In the previous issue we described metagenomics and DNA sequencing based techniques used to characterise bacterial communities such as amplicon sequencing. Here we will see how these help us to better understand the effects of challenges and dietary intervention on pig microbiota.
Unravelling microbiota diversity
Amplicon sequencing, or barcoding, is a technique based on the sequencing of only very small pieces of a bacteria genome, used as a marker or a sort of ID card of a bacteria.
In practice, barcoding can be applied to study the effects of a challenge, dietary change, or probiotic supplementation on the animal microbiota. Using this method allows the structure of the bacteria community to be obtained by giving relative abundance of the different bacteria (called ‘Operational Taxonomic Unit’ or ‘Amplicon Sequence Variants’ depending on the method used), expressed in relative percentage. Different diversity indexes can also be calculated.
Among the various indexes, the Shannon Index is a parameter used to illustrate the richness of a microbiota sample and the evenness of the organisms’ abundance distribution.
* The higher the Shannon Index, the more diverse and evenly abundant the microbiota.
Achard et al. (2019) have shown the detrimental effect of farrowing on sow microbiota diversity with important heterogeneity between the animals, as shown by the drop in the Shannon Index (red control group). The sows’ diet supplementation with live yeast S. c. boulardii CNCM I-1079 prior to farrowing is able to attenuate this drop in diversity after farrowing. In addition, there is more homogeneity between the sows.
Click on the links below to read the other articles in the Pig microbiota insight series.