Chicken microbiota (bioinformatics)

At the Host-Microbe Interactomics (HMI) group at the Department of Animal Sciences (ASG), we currently have a project for a student to combine 16S amplicon sequencing results to metabolites and physiological data of broilers. In this project, the student will learn how to use R (R-studio) to analyse sequencing data, integrate this using integration techniques such as MOFA2, and Canoco to link explanatory variables measured in the broilers to differential abundance of microbiota genera.

Study background:

In this study, the researchers aimed to evaluate the effect of protein fermentation on gut health by developing a model that creates a contrast in protein fermentation by increasing the pre-caecal flow of protein within ingredients. They achieved this by using additional toasting of protein sources and evaluated the effect on pre-caecal nitrogen and amino acid flows. The study was started with one-day-old Ross 308 male broilers; the broiler group was divided upon which each subgroup received one of six dietary treatments containing different protein sources, regular soybean meal (SBM), high protein sunflower seed meal (SFM), and dehulled rapeseed meal (dRSM), with or without additional toasting (t). The results showed that additional toasting increased the flow of histidine, lysine, and aspartate through the distal ileum and excretion in SBM but had no effect on SFM. Toasting dRSM increased the pre-caecal flows and excretion of nitrogen and amino acids. Therefore, toasting dRSM is a suitable model to increase protein flows into the hind-gut, permitting the assessment of effects of protein fermentation. However, additional toasting increased the feed conversion ratio only in birds fed dRSM, indicating that further research is required to optimize the toasting process to prevent adverse effects on feed efficiency.

https://doi.org/10.1016/j.psj.2022.101910

The thesis:

From these animals, caecal and faecal material was processed for 16S ribosomal gene analysis and bacterial taxonomy. The samples have been processed in the lab of microbiology (MIB), sequenced, and preliminary analysed. The student will take this data and integrate this with other available data and write a report on their findings. The student will also prepare a short literature survey during their thesis to accommodate their report. Students with bioinformatic creativity are well-needed, and we are looking forward to your application.