PhD project : “Network analyses of the impact of a quick dietary shift in the gut microbiome of the lizard species, Podarcis sicula”

Most lizards are insectivorous. Yet, several species and populations of lacertid lizards have evolved toward an omnivorous or even herbivorous diet. Our model system, Podarcis sicula, a lizard species has shown rapid evolution of feeding and digestive tract morphology in manipulated populations.

In 1970, five breeding pairs of the insectivorous P. sicula were transferred from the islet of Pod Kopište to the islet of Pod Mraru, Croatia. 36 years later (representing about 30 P. sicula generations), the transplanted P. sicula on Pod Mraru had become mostly herbivorous.

This dietary shift resulted in changes in head size and bite force among the populations on the two islands, and most striking changes in the lizards guts, since the herbivorous Pod Mraru lizards had developed an elaborate hindgut chamber with cecal valves, which had not been seen in any other population of P. sicula. These valves facilitate plant digestion by the gut microbial community of the lizard hosts. With the advances of next generation sequencing, this system offers a unique opportunity to investigate the impact of this dietary change at the level of the microbiome using metagenomic and metranscriptomic data. We will take advantage of the inclusive powerful comparative framework offered by sequence similarity networks, and exploit concepts of graph theory, to analyze the functioning and the evolution of genetic diversity of the lizard gut microbiomes in such massive datasets. In short, we will address the following questions through a comparison of the gut microbiomes of insular herbivorous lizards and of their insectivorous relatives:

1) Does the taxonomy of the microbiome correlates with the diet?

2) What changes in gene content and functions did the dietary shift produce? In particular, what gene families were acquired/lost during this transition?

3) What role did the gut mobilome play in these functional changes?

4) Overall, were the changes mostly functional (and through lateral gene transfer) or taxonomical (through a deep change of the microbial populations).

Supervised by : Anthony Herrel & Eric Bapteste