Interspecies interaction controls Escherichia coli growth in human gut microbiome samples

Area of Science:

• Microbiology
• Ecology
• Systems Biology

Background:

• Gut microbial community composition is highly variable between individuals.
• This variation suggests that ecological interactions within the gut may differ significantly among people.
• Directly testing these interactions and identifying ecological drivers in human microbiomes is challenging.

Purpose of the Study:

• To quantify the variability in population growth of a key commensal species across different human gut microbiome samples.
• To identify the intra- and interspecific ecological interactions influencing this growth variability.
• To investigate how specific microbial interactions shape the gut environment and impact other species.

Main Methods:

• Utilized replicated anaerobic microcosms to simulate gut environments.
• Conducted reciprocal transplant experiments with different Escherichia coli strains across various human microbiome samples.
• Employed targeted microbial identification and measurement of environmental factors like pH and fermentation products.

Main Results:

• Escherichia coli growth performance varied significantly among different gut microbiome samples, influenced by both absolute and relative growth.
• Intraspecific competition was a factor, with E. coli growth associated with the displacement of resident conspecifics.
• In one sample, acidification by resident microbes, driven by Clostridium butyricum, impaired E. coli growth, altering pH and fermentation profiles.

Conclusions:

• Natural interindividual variation in gut microbiomes leads to distinct ecological interactions for incoming bacteria.
• Specific interspecies interactions, like those involving Clostridium butyricum, can predictably alter gut environmental conditions (pH, metabolites).
• These microbial dynamics can be manipulated, offering potential avenues for modulating gut microbiome composition and function.