Project Summary/Abstract
The intestinal microbiota plays a major role in human health and is therefore the focus of significant interest as
a target for therapeutic interventions. However, our understanding at the mechanistic level of the ecological
and evolutionary forces shaping this diverse and densely colonized ecosystem is still tenuous. Notably,
although we know that horizontal gene transfer is pervasive in the gut community, we understand only
superficially the different roles of the majority of these exchanged genes and how this repertoire affects
community dynamics. Similarly, little is known about the mechanisms underlying community resiliency. This
question is particularly intriguing for the Bacteroidales, the most abundant Gram-negative gut microbiome
members, which can stably colonize for decades. This proposal will investigate the importance of biofilm
formation by the Bacteroidales for community ecology and resilience, focusing on the conjugative
megaplasmid pMMCAT which enables biofilm formation in the strains that acquire it. This plasmid is
exceptional because of the high frequency of intrapersonal transfer to multiple Bacteroidales species and its
ubiquity, with conserved architecture, across global human populations. Some studies suggest that mucosal
biofilms in healthy humans are rare, but there is little information about other locations or unattached biofilms. I
hypothesize that this megaplasmid, shared among many species in a community, enables the formation of
multi-species biofilms and plays a role in community cooperation, notably through increasing community
resilience. To test this hypothesis, or otherwise understand alternative roles of pMMCAT, I will systematically
characterize the phenotypes conferred by this plasmid in culture and in gnotobiotic mice in a single strain (aim
1) or in different Bacteroidales consortia where some strains carry it (aim 2). To understand the ecological role
of pMMCAT, I will evaluate if its conferred phenotypes are synergized or inhibited by the co-resident strains
and whether all, only some, or none of the other strains benefit. To visualize biofilms in the colon prior to and
following a stress pulse, I will use two different methods to preserve the spatial structure of the gut community
and use a biofilm matrix-specific stain. I will subsequently examine the evolutionary dynamics of pMMCAT
transfer in these consortia (aim 3). To this end, I will directly quantify and visualize plasmid transfer in culture
and in a gnotobiotic mouse. I will also quantify the cost of carrying pMMCAT and expressing biofilm formation
genes. I will evaluate the impact of the introduction of a cheater strain that doesn’t pay this fitness cost of
producing the biofilm matrix public good. Finally, I will track the evolution of pMMCAT over the course of twelve
years in four human volunteers previously found to have pMMCAT-harboring strains. This dissection of the
dynamics and mechanisms underlying plasmid-encoded biofilm formation in the gut will improve our current
understanding of intestinal ecology and its recent changes in human populations, and will provide one more
stepping stone towards targeted microbiome interventions for health benefits.