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Apr 20, 2021

Poultry Microbiota Insight: Part 5 - Unraveling microbiota diversity

Apr 20, 2021

In our last article we described metagenomics and DNA sequencing based techniques used to characterise bacterial communities such as amplicon sequencing. Let’s see how these help better understand the effects of challenges and probiotic intervention on poultry microbiota.

Unraveling 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 for bacteria.  Amplicon sequencing generates thousands of data from a single microbiota sample, but how do we make sense of these?

Scientists use several indicators to analyze the diversity and richness of a microbial population and to evaluate the effect of an intervention on microbiota diversity.

  • Alpha-diversity represents the diversity within one microbiota sample. Shannon index is one of the most used criteria to describe alpha-diversity. It considers both the total number of different taxa found in the sample, called the richness, and the abundance or predominance of some taxa among the sample. The higher the Shannon Index, the more diverse and evenly abundant the microbiota.
  • Beta diversity represents the similarity (or dissimilarity) between two samples. The beta diversity between groups of samples is evaluated using powerful software and specific statistical techniques (ordination). It applies a set of multiple variables to distinguish samples from each other. The shorter the distance between two samples, the lower the difference between the microbiota, the lower the beta-diversity.

Microbiota modulation

Recent metagenomic studies (Massacci et al., 2019) have enabled us to show how probiotic yeast interacts with broiler intestinal microbiota under challenging situations (Campylobacter jejuni experimental challenge), showing that the C. jujeni challenge:

  • Lowers the richness and alpha-diversity of the birds’ gut microbiota (control group).
  • Increases the beta-diversity between different birds of the same group: the microbiota composition become more disparate and is more heterogeneous in the control group.
  • Microbiota richness and diversity (Shannon Index, figure 1) is less impacted. There is a higher number of different species and less predominance of certain species in the gut microbiota.
  • The beta-diversity is reduced within the group: microbiota is more homogenous after the challenge when compared to the control.


Read the full series here … 

Massacci, F. R., Lovito, C., Tofani, S., Tentellini, M., Genovese, D. A., De Leo, A. A. P., … & Moscati, L. (2019). Dietary Saccharomyces cerevisiae boulardii CNCM I-1079 Positively Affects Performance and Intestinal Ecosystem in Broilers during a Campylobacter jejuni Infection. Microorganisms7(12), 596.