Using culture 'omics to explore the microbial structure and function in an equid in vitro digestion model

Area of Science:

• Equine nutrition and microbiology
• In vitro fermentation systems
• Ruminant vs. Equid digestive physiology

Background:

• The in vitro gas production system (GPS) is established for ruminant feedstuff analysis.
• Adaptation of the GPS for equine research requires characterization of its microbial and metabolic behavior.
• Understanding equine gut microbiome dynamics is crucial for optimizing nutrition.

Purpose of the Study:

• To characterize the bacterial community and metabolome of equine fecal inoculum within the GPS.
• To compare the microbial and metabolic profiles in the GPS with donor equine feces.
• To assess the suitability of the GPS for equine nutritional studies.

Main Methods:

• Six Welsh ponies on identical diets served as fecal donors.
• Gas production was measured over 156 hours.
• Bacterial community profiling (16S rRNA sequencing) and metabolomics (1H NMR) were performed on fecal and inoculum samples.
• Viability PCR (PMAxx) assessed microbial viability.

Main Results:

• Significant alterations in bacterial community profile and metabolic phenotype were observed over time in the GPS.
• A transient system dysbiosis occurred at 8 hours.
• End-point metabolic profiles in the GPS resembled donor feces, but fiber-degrading bacteria aligned more with rumen than equine literature.
• The GPS accurately estimated dry matter digestibility.

Conclusions:

• The equine GPS provides a similar end-point metabolic profile to donor feces and estimates digestibility accurately.
• The system may favor rumen-associated microbes or exhibit functional redundancy compared to the native equine gut microbiome.
• Further research is needed to fully validate the GPS for equine applications.