Roadmap for Microbiota optimisation

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

Defining the effect of pro/prebiotics, diet, etc on MB.
Understanding mode of action of effective probiotics.
Establishing analytical methods to standardise the pro/prebiotics used.
Disease prevention.
How probiotics can be used to enhance response to vaccination (like an adjuvant effect).

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

Controlled clinical trials involving pro/prebiotics, antibiotics, diet, MB transplants, etc.
Determine sufficient level of depth required to measure positive responses.
Impact on gut wall.
Impact on bacteria in gut – protecting gut epithelia. How the gut environment affects expression of bacterial beneficial antigens, some might be expressed in vitro but not in vivo.
Availability of what we consider as controls (identify controls)
Develop challenge models.
Establishing the mix of organisms in probiotics (probiotics cocktail).
Need to standardise how (functional) probiotics are grown, stored and delivered as this can affect surface molecules presented.
Establishing standards for trials so as to allow comparisons.
Need to study the purity and absolute structures of prebiotics in order to define mechanisms. There is often a difference in the purity of prebiotics (I.e. a treatment may contain many different carbohydrates).

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

Establishing what is the expected effect (functional effect) of the pre/probiotic to be used (what are the expected outcomes?).
Establishing what aspects need to be considered to assess effectiveness (e.g., daily gain, uniformity, challenge models).
Therapeutic use vs disease prevention vs growth promotion.
Defining microbial functionality affecting uniformity.
Is there a microbial basis to the differences in uniformity.

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

Understanding mode of action of effective probiotics.
Establishing analytical methods to standardise the pro/prebiotics used.

Existing knowledge including successes and failures