Microbiomes in Animal Ecology: Advances, Assumptions, and Opportunities

Area of Science:

• Microbiome research
• Host-microbe interactions
• Ecological immunology

Background:

• Animal microbiome studies have advanced understanding of host physiology and ecology.
• Current research often identifies correlations, lacking causal links between microbial dynamics and host outcomes.
• There's a need for methods connecting microbial communities to ecological and fitness-relevant results.

Purpose of the Study:

• To highlight integrative approaches for studying microbe-host interactions in ecologically relevant contexts.
• To emphasize the utility of multi-omics and stable isotope probing for tracking microbial functions.
• To advocate for a shift towards understanding microbiome roles in wild populations' life-history traits.

Main Methods:

• Utilizing longitudinal studies and controlled physiological comparisons.
• Integrating multi-omics approaches (genomics, transcriptomics, etc.) with stable isotope probing (SIP).
• Applying these methods to diverse wild populations (e.g., African herbivores, amphibians) and experimental models.

Main Results:

• Longitudinal sampling and isotopic labeling reveal microbiome plasticity in response to environmental changes.
• Multi-omics combined with microbiome manipulation disentangles host-microbe interactions in various experimental systems.
• Stable isotope probing tracks microbial metabolites and their effects on host physiology.

Conclusions:

• Integrating multi-omics and SIP in field studies provides powerful insights into microbiome functional effects.
• This approach is crucial for understanding microbiome contributions to host resilience and fitness in wild populations.
• Moving beyond lab models to wild systems is key for advancing microbiome research.