In vitro modelling of chicken caecal microbiota ecology and metabolism using the PolyFermS platform. Chicken in vitro caecal model

Continuous in vitro fermentation models provide a useful tool for a fast, reproducible and direct assessment of treatment-related changes in microbiota metabolism and composition independent of the host. Here we investigated a novel continuous in vitro chicken intestinal fermentation model inoculated with immobilized caecal microbiota (PolyFermS platform). We first set the composition of the fermentation media to reach metabolitic profile and bacterial ecology akin to the caecum inoculum using three independent fermentations operated for 70 to 82 days. Our final model, fed with mVL-3 medium , is composed of a first-stage inoculum reactor (IR) containing the ceacal microbiota immobilized in gel beads, that continuously inoculate a set of parallel second-stage reactors and operated in conditions of the chicken caecum. The mVL-3 fermentation medium increased the total metabolite production (174.5 ± 10.5 mM) and total carbon (512.1 ± 24.5 C-mM) in the model. The continuous inoculation provided by the IR, generated reproducible microbial ecosystems and metabolic profiles in all second-stage reactors comparable to the chicken caecum, allowing for the simultaneous investigation and direct comparison of different treatments with a control. Illumina MiSeq sequencing ,however, showed a decreased bacterial diversity and compositional differences compared to caecal inoculum microbiota. Most of the caecal bacterial were represented in vitro, however, taxa of the Lactobacillus and Faecalibacterium were not maintained. An independent repetition of the final model parameters showed a comparable and stable metabolite production and microbial composition and diversity over 82 days. Conserved metabolic and functional KEGG pathways were observed between in vitro microbiota and caecal inoculum microbiota as predicted by functional metagenomics analysis. The chicken caecal microbiota in vitro can be used to investigate ex vivo the effects of nutritional and environmental factors on the composition and activity of the caecal microbiota prior to in vivo studies.