Conceptual Exchanges for Understanding Free-Living and Host-Associated Microbiomes.

Area of Science:

• Microbial Ecology
• Biogeochemistry
• Environmental Microbiology

Background:

• Microbial existence, whether free-living or host-associated, relies on essential elements and redox processes.
• Historically, distinct research traditions, 'environment first' and 'microbe first', have studied microbial life using different methodologies.
• The 'environment first' approach uses thermodynamics and biogeochemistry to infer microbial activity, while the 'microbe first' approach uses culturing and sequencing to identify microbes and their functions.

Purpose of the Study:

• To illustrate the combined application of 'environment first' and 'microbe first' research approaches in microbiome studies.
• To demonstrate how integrating these approaches enhances understanding of microbial metabolism selection across diverse environments.
• To highlight the utility of these integrated approaches in predicting microbiome alterations in host health and in response to climate change.

Main Methods:

• Review and synthesis of the 'environment first' approach, emphasizing thermodynamics, redox environments, and elemental stoichiometry.
• Review and synthesis of the 'microbe first' approach, highlighting culturing and DNA sequencing for microbial identification and metabolic function analysis.
• Illustrative examples showcasing the integration of both approaches in microbiome research.

Main Results:

• Both 'environment first' and 'microbe first' approaches, when used independently or combined, provide valuable insights into microbial life.
• Integrated approaches reveal the selection of microbial metabolisms in response to specific environmental conditions.
• The study demonstrates how these integrated methods can anticipate microbiome changes related to host health and climate shifts.

Conclusions:

• A comprehensive understanding of microbial ecosystems necessitates the integration of both environmental and microbial perspectives.
• Combining these approaches offers a powerful framework for studying microbiome dynamics in various contexts, from host health to global environmental change.
• This integrated strategy is crucial for predicting and managing microbial functions in a changing world.