Roadmap for Microbiota optimisation

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

Understanding how the MB affects AH.
Can we develop prognostic tests for various conditions based on the microbiome?
Appropriate microbiome can replace antibiotic treatment?

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

Developing an understanding of niche ecology.
Relating MB components to health status.
Determining functions of microbiome metabolites (what animal sees).
Identify MB biomarkers that predict disease/health.
Investigating real MB function as compared to predicted one.
Identifying the parameters associated with a healthy microbiome.
Linking taxonomy with function.
Defining cut off values to predict disease/health.
How the changes of the environment influence the genes of host and microorganisms (epigenetics).

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

Using proper study design (which shall include an appropriate sample size).
(Defining appropriate sample size for experiments.)
Meta-analysis of existing datasets.
(Data analysts at functional level and whole animal physiologists).
Deep phenotyping of the population.
Develop prognostic tests to identify individuals predisposed to disease.
Artificial intelligence/machine learning approaches
Prognostic tests

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

Investigating how the microbiota interacts with the host.
Defining what is a dysfunctional microbiome.
Understanding the functional capacity of microbiota (including better annotation and characterisation of the organisms present).
Determine what is shaping the microbiome including the interactions within the microbiome with bacteria, viruses etc… – we don’t have a good understanding how it is interacting with itself.

Existing knowledge including successes and failures