Roadmap for Microbiota optimisation

What are we trying to achieve and why? What is the problem we are trying to solve?

Investigating how the microbiota interacts with the host.
Investigating capacity of MB in accelerating immunity development (adaptive and innate).
Investigate implications of early-life modification
Understanding mode of action of effective probiotics

What are the scientific and technological challenges (knowledge gaps needing to be addressed)?

Determine which GIT section is the most predictive of the host response under investigation e.g., microbiota in the small intestine may have a greater impact on the immune response while microbes in the large intestine may have a greater impact on feed efficiency.
Improve understanding of the host’s response to microbial metabolites.
Determine how early-life microbiota and subsequent succession affect host performance.
Investigating what is shaping MB (including nonbacterial factors)
Correlating the composition of the microbiota with its activity and link that with the host response – very different organisms may be affecting the host in the same way so it is their functionality that is important but also the same microbe might be having a different function under different circumstances.
Improving understanding of different compartments (interactions between different physiological compartments of the host and barriers e.g. blood udder barrier, gut-brain barrier).
Understand to what extent and how gut microbiota communicates with the brain, and which fraction of the microbiota plays an important role in this communication.
How to integrate all knowledge especially from murine models where there is the ability to disrupt function.
Study the transfer of plasmids and the blocking of their transfer.

What approaches could/should be taken to address the research question?

For field studies, considering animal in cohorts, as to reduce external confounding factors (e.g., antibiotic treatments, diet) and then see the differences in responses to the common stressors.
Using suitable approaches to investigate the host-pathogen-interaction-HPI (including, but not limited to, -omics techniques) to perform the studies including looking at how it interacts with the immune system – glycomics is often ignored but it is the surface of the microbe and the host as this could be where the interactions are taking place.
Functional models
Integrating the results of functional models, with studies utilising the diversity in the livestock host population.

What else needs to be done before we can solve this need?

Investigating animal genomic and impact on microbiome.
Studying systems biology.
Investigating capacity of MB in accelerating immunity development (adaptive and innate).
Investigate implications of early-life modification.

Existing knowledge including successes and failures