Roadmap for Microbiota optimisation

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

Need to define a healthy/dysfunctional microbiome.

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

Definition of what dysbiosis means is contentious -are we talking about, e.g., loss of keystone taxa, loss of diversity, shifts in metabolic capacity, or blooms of pathogen.
Defining what is dysfunctional needs to be set in the context of variation for a specific situation.
Understanding what mechanisms are important to develop and maintain gut microbiome homeostasis.
Identifying what is a “good” microbiota in different species and situations.
Establish standard sampling techniques (small animals, pigs.) for respiratory tract.

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

Combination of readouts/tools to measure the microbiome:

• DNA, RNA, metabolomics…- combine compositional resolution with functional tools
• Case controlled studies that delineate the real from spurious disease associations.
• Move beyond statistical associations and define causal relationships

Interventional study designs.

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

Baseline composition of healthy respiratory microbiota.
Understanding of anaerobic/aerobic condition.
Culturomics (Standard process for cultivating anaerobic/unculturable bacteria, fungus, protozoa, archaea).

Existing knowledge including successes and failures