Changes in the gut microbiome have long been linked with Crohn’s disease and other forms of inflammatory bowel disease (IBD), but the biology behind those links has remained murky.
Researchers at the Broad Institute, Massachusetts General Hospital (MGH), and Harvard Medical School (HMS) have now found that one bacterium, Ruminococcus gnavus, which is associated with Crohn’s disease, releases a certain type of polysaccharide (or a chain of sugar molecules) that triggers an immune response.
This study, published in the Proceedings of the National Academy of Sciences, is one of the first studies to delve into the mechanisms underlying a well-known association between a gut microbe and human disease.
“This is a distinct molecule that represents the potential link between gut microbes and an inflammatory disease,” said first author Matthew Henke, a postdoctoral fellow in the laboratory of study corresponding author and Broad Institute senior associate member Jon Clardy of Harvard Medical School.
“More and more studies on the correlations between the bacteria in the microbiota and disease were coming out,” said Clardy, who is the Hsien Wu and Daisy Yen Wu Professor of Biological Chemistry and Molecular Pharmacology at HMS.
“Some were very strong, some were weak, but it was really all correlations.”
About 2 million Americans suffer from an inflammatory bowel disease (IBD), including Crohn’s.
Previous work from the lab of Broad core institute member and Infectious Disease and Microbiome Program co-director Ramnik Xavier proved that during some flares of Crohn’s disease, the abundance of R. gnavus can jump from less than one percent of the gut microbiota to greater than 50 percent.
“That experiment was a correlation experiment.
A is correlated with B. Now the challenge was to get to causation,” said Xavier, who is also the Kurt Isselbacher Professor of Medicine at HMS, director of the Center for Computational and Integrative Biology and a member of the Department of Molecular Biology at MGH, and co-director of the Center for Microbiome Informatics and Therapeutics at Massachusetts Institute of Technology.
The researchers, including Xavier, Clardy, and Henke, wanted to determine if the link between Crohn’s and R. gnavus was more than a correlation.
Was it simply an association, or were there molecular mechanisms by which the bacteria were contributing to disease flares?
After growing colonies of R. gnavus in the laboratory, they characterized all of the molecules produced by the bacteria, to see if there was anything pro-inflammatory.
One polysaccharide comprised mainly of rhamnose, a sugar not familiar to the human immune system, antagonized the immune system by activating the cytokine TNF-α.
Using a variety of techniques borrowed from chemistry, Henke determined that the polysaccharide was made up of two different sugars: chains of glucose protruding from a spine made up of rhamnose.
After uncovering the structure, they searched the genome of R. gnavus and identified the genes responsible for making the polysaccharide.
Future experiments will study if these genes are overexpressed before a flare of Crohn’s.
“If we can track a single patient and see that the genes for this polysaccharide become expressed before disease symptoms get worse, that’s really powerful,” said Henke.
“That would suggest that maybe the polysaccharide is contributing to disease flares.”
Should this theory prove true, the researchers could be on their way to developing new treatments for Crohn’s and similar inflammatory diseases that target R. gnavus growth or its ability to produce this inflammatory polysaccharide.
The microbiome’s impacts are broad, and these findings have applicability beyond Crohn’s disease.
“Now that we’ve established this methodology, we can rapidly go through the other bacteria and find out how the microbiome plays a role in contributing to the chemistry of disease,” said Xavier.
This study is one of the first to look into the molecular mechanisms behind a correlation between the microbiome and human health.
“There’s a lot of really great work being done on cataloging what bacteria, fungi, and viruses are in us,” said Henke.
“But the health effects of the small molecules and protein products and chemicals that they make hasn’t been fully documented yet.
We thought for a really long time that microbes had just a passive role in our biology, but that’s definitely changing.”
Inflammatory bowel disease (IBD) is a chronic inflammatory disease of gastrointestinal tract with two main clinical manifestations: Crohn’s disease (CD) and ulcerative colitis (UC).
The pathogenesis of IBD in genetically susceptible individuals likely involves an overactive immune response to the gut microbiome [1].
Changes in the intestinal microenvironment may contribute to the altered gut microbial community composition in IBD.
The inflammation of IBD is associated with increased generation of reactive oxygen species (ROS) and reactive nitrogen species (RNS), causing oxidative stress for both host cells and the gut microbiome [2–4].
Additionally, the gut microbiome in IBD shows dysbiosis characterized by increased abundance of functional pathways involved in the microbial response to oxidative stress [5].
However, the species and/or strains of microbes that contribute to this functionality remain unclear.
The increased availability of whole metagenome sequencing, as opposed to 16S rRNA gene sequencing, has provided the opportunity to study the taxonomic composition of microbiomes at unprecedented resolution, allowing strain-level and functional profiling.
In addition, several computational tools for metagenomic sequencing data have recently enabled high-resolution study of specific strain variants within abundant species [6, 7].
It is increasingly clear that strain variability can result in important physiological and functional differences in how microbes interact with the host [8].
For example, different strains of the same species can provoke different host immune responses [8], and in the context of IBD, analysis of Escherichia colishowed a specific enrichment of adherent invasive E. coli (AIEC) strains in IBD vs. healthy individuals [9].
IBD is characterized by relapsing inflammation followed by periods of remission, highlighting the importance of tracking patients and their microbiome over time.
Because the symptoms of IBD vary temporally, it is important to collect multiple samples from each patient to understand the changing landscape of the IBD gut microbiome.
Furthermore, longitudinal studies of healthy individuals have revealed large inter-subject variations within the gut microbiome [10–12], suggesting the importance of understanding IBD disease-specific effects across multiple individuals.
One notable study performed metagenomic sequencing on longitudinal IBD samples [13]. With recently developed tools, it is now possible to analyze large-scale, longitudinal, metagenomic cohorts to study the IBD gut microbiome at the strain level.
In this study, we aim to address two outstanding questions in IBD:
1) How does oxidative stress in IBD shape the composition of the gut microbiome at the species and strain levels?
2) Do IBD-associated strains have specific genomic adaptations that increase their fitness in the IBD gut?
We used metagenomic sequencing of a longitudinal cohort to analyze functionally binned microbial species by their ability to tolerate oxidative stress, and we found increased abundance of facultative anaerobe species in the IBD gut.
We detected dramatic, transient blooms in the relative abundance of Ruminococcus gnavus in IBD, often corresponding with increased disease activity.
We further experimentally characterized aerotolerance of R. gnavus and identified an R. gnavus clade that is enriched in IBD patients and has a distinct functional repertoire including genes exclusively present in this clade.
These genes often involve functions that may improve colonization of the IBD gut, including oxidative stress responses, adhesion, iron acquisition, and mucus utilization. This study highlights the importance of strain-level analysis to reveal IBD-specific taxonomic features and their functionality.
More information: Matthew T. Henke et al. Ruminococcus gnavus, a member of the human gut microbiome associated with Crohn’s disease, produces an inflammatory polysaccharide, Proceedings of the National Academy of Sciences (2019). DOI: 10.1073/pnas.1904099116
Journal information: Proceedings of the National Academy of Sciences
Provided by Broad Institute of MIT and Harvard
