Gut bacterial nutrient preferences quantified in vivo.

Area of Science:

• Microbiome research
• Metabolic pathways
• Nutritional science

Background:

• Gut microbiome's role in health and disease is increasingly understood.
• Focus has primarily been on microbial products, with less attention on microbial inputs.
• Understanding nutrient utilization by gut bacteria is crucial for microbiome modulation.

Purpose of the Study:

• To quantitatively examine the inputs and outputs of the mouse gut microbiome.
• To identify specific nutrient preferences of different bacterial genera.
• To correlate nutrient preferences with microbiome composition changes in response to diet.

Main Methods:

• Utilized isotope tracing techniques to track nutrient flow within the mouse gut microbiome.
• Analyzed genus-specific bacterial protein sequences to determine nutrient utilization patterns.
• Investigated the contribution of dietary components (fiber, protein) and host-derived molecules (lactate, 3-hydroxybutyrate, urea) as microbial inputs.

Main Results:

• Dietary fiber is the primary input for microbial carbohydrate fermentation.
• Dietary protein is the main input for branched-chain fatty acids and aromatic metabolites.
• Host-derived lactate, 3-hydroxybutyrate, and urea serve as significant microbial nutrients, unlike glucose or amino acids.
• Distinct nutrient preferences were observed: Firmicutes favor dietary protein, Bacteroides favor dietary fiber, and Akkermansia favor host lactate.
• These bacterial nutrient preferences correlate with observed microbiome composition shifts following dietary changes.

Conclusions:

• Diet composition fundamentally shapes the gut microbiome by selectively promoting bacteria that utilize specific ingested nutrients.
• Understanding nutrient preferences provides a mechanistic link between diet and microbiome structure.
• This study highlights the importance of considering both dietary and host-derived inputs for a comprehensive view of gut microbiome function.