Interspecies competitions in the microbiota


The dynamic balance of the intestinal microbiota, regarding its composition and relative abundance of its constituents, not only depends on the interactions with the host but also on the interactions that occur between co-habiting microbes. How do they coexist in this ecosystem? An American team invites us to discover the interactions within the microbiota and describes potent and unique antimicrobial activities.


The microbiota is usually colonized simultaneously by several strains of the same species. These closely-related bacteria have developed properties that allow them to either coexist in this ecosystem (by using different nutrients, occupying different spatial niches, and cooperating), or to antagonize or compete with their co-residents. While studying one of the strains of the species Bacteroides fragilis, which is particularly abundant, the researchers discovered it interacts with its co-residents through a new and unique type of microbial antagonism.

Eukaryotic ubiquitin-like toxin

Most strains of B. fragilis secrete antimicrobial molecules. However, until now, only one had been identified: the protein BSAP-1*, a toxin able to lyse bacteria.  This study uncovered a novel secreted protein produced by B. fragilis strain 638R that mediates interspecies antagonism.  It is an eukaryotic ubiquitin-like protein (BfUbb**). Although it is 84% similar to human ubiquitin, BfUbb is a distinct protein: it has an N-terminal signaling peptide, which will be cleaved from the mature protein. Whether it was secreted by the original strain (638R) or produced synthetically, the mature 76-amino-acid protein had an antimicrobial activity against many strains of B. fragilis. Together, toxins BSAP-1 and BfUbb target 75% of the 40 B. fragilis strains tested.

Selective advantage

How this gene is acquired is still unclear according to the authors, although the underlying mechanism is likely horizontal gene transfer. The strains that have acquired this gene have a selective advantage compared to other B. fragilis strains. It allows them to more efficiently colonize the intestinal ecosystem. By understanding the microbial antagonistic mechanisms between the strains and identifying the molecules that provide a competitive advantage to better colonize the intestinal ecosystem, we will be able to develop probiotic strains capable of durably colonizing the intestine and releasing their therapeutic benefits.


*Bacteroidales secreted antimicrobial protein 1

**B. fragilis eukaryotic ubiquitin-like protein



1.Chatzidaki-Livanis, M. et al. Gut Symbiont Bacteroides fragilis Secretes a Eukaryotic-Like Ubiquitin Protein That Mediates Intraspecies Antagonism. MBio 8, (2017)