Abstract
The combined effect of environment and diet in shaping the gut microbiota remains largely unknown. This knowledge, however, is important for animal welfare and safe food production. For these reasons, we determined the effect of experimental units on the chicken cecum microbiota for a full factorial experiment where we tested the combined effect of room, diet, and antimicrobial treatment. By Illumina Deep sequencing of the 16S rRNA gene, we found that diet mainly affected the dominant microbiota, while the room as a proxy for environment had major effects on the non-dominant microbiota (p = 0.006, Kruskal–Wallis test). We, therefore, propose that the dominant and non-dominant microbiotas are shaped by different experimental units. These findings have implications both for our general understanding of the host-associated microbiota and for setting up experiments related to specific targeting of pathogens.
Highlights
The gut microbiota plays a crucial role for the host health through providing essential metabolites and vitamins, in addition to immune/gut maturation and protection toward pathogen colonization [1]
We evaluated the effect of different experimental units in a full factorial experimental design, where both the microbiota composition and the level of Clostridium perfringens were determined for the chicken cecum microbiota
Our main finding was the presence of a diverse but low-abundant microbiota associated with the experimental unit room, while diet mainly affected the high-abundant microbiota
Summary
The gut microbiota plays a crucial role for the host health through providing essential metabolites and vitamins, in addition to immune/gut maturation and protection toward pathogen colonization [1]. Despite this crucial role, our knowledge about the ecological driving forces shaping the gut microbiota is limited. It is well known that diet and antimicrobial compounds can affect the gut microbiota, the influence of the environment is still largely unknown [2]. This represents a major challenge when setting up experiments involving antimicrobial and/or dietary perturbations of the gut microbiota. We used Illumina deep sequencing of the 16S rRNA gene [3], while the level of C. perfringens was determined by real-time PCR [4]
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