Probabilistic Invasion Underlies Natural Gut Microbiome Stability

Area of Science:

• Microbiology
• Ecology
• Genetics

Background:

• Gut microbiome species composition significantly impacts host health.
• The processes governing gut microbiome establishment and stability remain largely unknown.
• Individual gut microbiomes exhibit wide variation between hosts but temporal stability within hosts.

Purpose of the Study:

• To quantify and model the dose response, dynamics, and stability of bacterial colonization in the fruit fly gut.
• To investigate the mechanisms underlying alternative stable states in gut microbial communities.
• To understand the role of stochasticity in maintaining gut microbiome stability.

Main Methods:

• Utilized a precise, high-throughput technique to study bacterial colonization in germ-free Drosophila melanogaster.
• Administered natural commensals, including Lactobacillus plantarum, to assess colonization.
• Modeled dose response, colonization dynamics, and stability.

Main Results:

• Demonstrated stable between-host variation in colonization, with some flies remaining germ-free despite high bacterial doses.
• Confirmed the existence of alternative stable states (colonized vs. germ-free) in a low-complexity model.
• Identified spatial localization and population bottlenecks as key drivers of stochastic effects and alternative stable states.
• Showed that prior colonization reduces subsequent colonization, enhancing gut stability.

Conclusions:

• Alternative stable states in gut microbial communities are driven by stochastic processes, including spatial localization and population bottlenecks.
• These findings have significant implications for understanding host-microbe interactions, combating infectious diseases, and the stable establishment of probiotics.
• Gut microbiome stability may be fundamentally linked to inherent stochasticity in microbial community assembly.