Unraveling strain-level variation in the induction of anti-inflammatory responses in the intestine

PROJECT SUMMARY: Inflammatory bowel disease (IBD) is an increasingly prevalent disease that currently
affects ~1.3% of adults in the US. IBD is characterized by chronic inflammatory immune responses directed
against the gut microbiota, and severely impedes the health of its sufferers. Current therapeutic approaches
involve neutralization of pathogenic inflammatory pathways. However, many patients are non-responsive or
become refractory to treatment, and the requirement for sustained administration of these agents can enhance
susceptibility to infection. A major unmet clinical need entails development of improved therapeutic regimens
that quell ongoing inflammation while sparing protective immunity. Strategies that seek to restore host immune-
gut microbiota homeostasis through introduction of health-promoting immunomodulatory microbes (probiotics),
represent an attractive alternative to blockade of immune function. To date, these approaches have demon-
strated limited efficacy. Our incomplete understanding of the mechanisms through which microbes induce anti-
inflammatory responses, and how transplanted microbes survive the hostile environment of the inflamed intes-
tine to establish a niche have severely hampered these efforts. An approach where the optimal features from
different microbes are combined, so-called designer probiotics, represents an improved treatment strategy.
Knowledge gap: The identity of the bacterial pathways that actively promote intestinal anti-inflammatory im-
mune responses and allow probiotic strains to colonize the inflamed intestine have remained enigmatic due to
microbiota complexity and difficulties associated with the genetic manipulation of gut microbes. Hypothesis:
Strain-specific differences impact the probiotic potential of gut bacterial species. Preliminary studies: Through
the study of distinct strains of the genetically tractable gut symbiont Bacteroides thetaiotaomicron, we have (i)
identified extensive strain-level variation in the ability of B. thetaiotaomicron strains to induce accumulation of
colonic Tregs in monocolonized gnotobiotic mice, (ii) revealed significant strain-level variation in the biofilm-
forming capacity of different strains of B. thetaiotaomicron, and (iii) uncovered the existence of a novel, B. the-
taiotaomicron-derived, immunomodulatory factor that promotes production of the anti-inflammatory cytokine IL-
10. Our systems provide an opportunity to leverage the relatedness of strains within a species that impart dif-
ferential phenotypes to provide insight into pathways related to the optimal function of probiotics. Project ob-
jective: To leverage the strain-level variation and genetic tractability of B. thetaiotaomicron to define the bacte-
rial genes and molecules that most potently confer anti-inflammatory capacity to gut microbes. Impact: Results
of these studies will advance efforts to develop designer probiotic therapeutics that provide durable remission
from disease for IBD patients. Aim 1: Define the molecular basis for strain-level variation in bacterial driven
colonic Treg induction. Aim 2: Define the B. thetaiotaomicron-derived immunomodulatory factor(s) that limit
colitis. Aim 3: Define the genetic determinants mediating bacterial strain-level fitness in the inflamed intestine.

Grant Number: 5R01DK126772-05
NIH Institute/Center: NIH
Principal Investigator: Philip Ahern