BBSRC EASTBIO DTP - The microbiome of tropical livestock and its effect on health and productivity

The microbiome has been described both as a second genome and a forgotten organ, and it is essential that we study the structure and function of the gut microbiome when we try to understand performance traits in farm animals such as feed efficiency; health; and meat and milk production. It is the gut microbiota that is responsible for extracting energy and nutrition from the diet. We have previously shown in Western cattle breeds that changes in the gut microbiome, after controlling for breed and diet effects, can be associated with feed efficiency and high/low methane emissions (DOI: 10.1186/s12864-015-2032-0, DOI: 10.1371/journal.pgen.1005846)
The Centre for Tropical Livestock Genetics and Health (CTLGH) is a collaborative centre with The Roslin Institute, Scotland’s Rural College (SRUC) and the International Livestock Research Institute (ILRI) as founding partners. With initial funding from the Gates Foundation and matched funding from each partner, CTLGH has an ambitious programme of research to drive farm animal improvement in Africa. Our long-term aim is to understand how animals extract energy from food; and understand the healthy gut microbiome and how perturbations from the healthy state affect productivity. This understanding will be crucial to increasing the amount of food we can produce from animals farmed in Africa.

Local African breeds are better at surviving in the environment and are tolerant/resistant to disease, yet produce less than 10% of the milk compared to Western breeds in well-managed farms. Gains can be achieved through both better management, better diet and cross-breeding local breeds with highly productive western breeds. Pure Western breeds are more susceptible to disease and need a richer diet to achieve the promised increased performance. There is a clear interaction between genetics and the environment which drives this increase in production, and we will generate data on the structure and function of the microbiome in both poultry and dairy animals using local, cross and western breeds fed different diets. Additionally, we will generate a microbial gene catalogue from African cattle which we hope will yield novel enzymes adapted to African grasses and feeds which could be useful as future feed additives.

Specifically, we will
1. Train the student and establish routine, standardised and reproducible protocols for rumen fluid sampling in our African partner countries. We will initially target “experimental” animals where sampling can be controlled and under the requiste local ethics approval. Initial samples from small holder poultry farms have been collected, whilst there is an ongoing programme of work on dairy cattle in ILRI experimental units focussing on the impact of different diets on methane production;
2. Train the student and establish routine, standardised and reproducible protocols for whole-genome-shotgun (WGS) metagenomics
3. Train the student in bioinformatics analysis, including (but not limited to)
a. Phylogenetic analysis of WGS metagenomics data
b. Functional analysis of WGS metagenomics data
c. De novo assembly of metagenomics data
d. Functional annotation of predicted metagenomic genes
e. Analysis and comparison of rumen microbiomes/metagenomes fed different diets and from different genetic backgrounds, and the effects on health and productivity