Comparison of targeted and shotgun animal gut metagenomics

The understanding of the composition and functions of the intestinal environment is particularly useful to evaluate and improve productivity and health of farmed animals, such as chickens. By sequencing the metagenome, that represents the genetic material recovered directly from enviromental samples such as gut sections, scientists attempt to retrieve the abundances of microorganisms that inhabit the gut of animals, in order to access information about the interaction with the host. Our purpose is to compare, with a statistical approach, the reliability of two sequencing techniques, called metataxonomics and metagenomics, that can both provide a solid approach to investigate the populations of bacteria in gut microbiome. Although metagenomics, based on shotgun sequencing of the full metagenome, is usually known as the best suited option to recover abundance profiles of bacteria, recent studies have highlighted remarkable results using amplicon sequencing, that targets and recognizes particular regions of 16S rRNA gene. In our study, we take advantage of a well-structured dataset of 78 samples collected from caeca and crops of 40 chickens, at different days of life(1,14,35) and fed (or not) with a probiotic supplemented to drinking water. The study of abundance profiles retrieved by metagenomics and metataxonomics separately, highlights several differences between the two techniques, in terms of detection of rare genera and connection to biological markers. Shotgun sequencing detects around five times more genera than those commonly detected by both techniques, even if several shotgun sets have low coverage. Furthermore, using silhouette scores to evaluate the space segmentation of abundance profiles in a 2-dimensional PCoA space according to biological metadata, we observe that low-abundance bacteria detected only by shotgun contain important biologic information, hidden to 16S sequencing.