The Microbiome Contributes to Irritable Bowel Disease (Crohn’s Disease, Ulcerative Colitis)

Inflammatory Bowel Disease (IBD) (both Crohn’s disease and ulcerative colitis) is associated with debilitating inflammation in the gastrointestinal tract. Affecting millions worldwide, IBD disorders have complex origins. Recent research has shone a light on the role of the gut microbiome, the community of microorganisms residing in our intestines, in the pathogenesis of IBD. Understanding how microbiome dysfunction contributes to these conditions is pivotal for developing more effective treatments. In this post, I touch on the important relationship between IBD and the microbiome.

As a basis for this post, I’m using both peer reviewed research as well as my own clinical experience. What I suspected from my own experience was verified in the literature. Research has shown dysbiosis is common in IBD, with microbiome composition greatly affecting disease pathogenesis. Overall, with both Crohn’s disease and ulcerative colitis there is a decrease in diversity within the microbiome while there is an overgrowth of inflammatory species. The severity of this lack of diversity and/or bacteria overgrowth corresponds directly to the severity of IBD.

Microbiome Species Implicated in IBD

Here is a list of microbes that are either deficent or overgrown in IBD. I’m certain the list isn’t exhaustive, as the microbiome is more complex than we know.

Decrease Bacteria Species
Alistipes shahii
Pseudosulfovibrio aespoeensis
Porphyromonus asaccharalytica
Akkermansia muciniphilla
Bifidobacteria species
Faecalibacterium prasnitzii
Bacteroides species
Lachnospiraceae species

Overgrown Bacteria Species
Polynucleobacter wianus
Pantoea candidatus
Ruminococcus gnavus
Escherichia coli

It is notable that many of the species on the “decreased” list are overall anti-inflammatory, and species on the “overgrown” list are inflammatory.

There are certain bellweather species that I look at when assessing the health of the microbiome. I generally look at the whole set of data. However, I give extra attention to Desulfovibrio piger, Methanobacter smithii, and Akkermansia muciniphilla.

Dysbiosis and Mucosal Membrane/Gut Permeability

Crohn’s disease and ulcerative colitis progress through the deterioration of the mucosal membrane. This is a mucus rich region that acts as a defensive barrier, protecting against unwanted substances and microbes. When intact, it is a haven for beneficial bacteria. In this region, various antimicrobial compounds are made, such as antimicrobial peptides (APMs), and immunoglobulins (Ig). The deterioration of this layer allows for greater overgrowth of bacteria and infectious agents, providing for ever greater inflammation as the disease progresses.

Akkermansia muciniphilla is the major bacteria that has been identified in research and in practice that maintains the mucosal barrier. It upregulates production of goblet cells, which are responsible fro production of the mucus entrained in the layer. Generally, if I see this species is low in a stool sample, I’m more concerned about intestinal permeability and increased gut inflammation.

Treatment Approach

Not all bacterial species presented in the research are commonly used in a functional stool test. However, it’s not necessary to know the status of every species. Treatment of the microbiome works best when we zoom out to look at the whole community. Each of these species support each other when in balance. Therefore, your functional medicine doctor will be looking for indications of dysbiosis as a whole.

Generally, there are three actions that need to be taken to create a healthy microbiome. First, we remove bacterial overgrowth and infectious species. Second, we grow the healthy bacteria that have diminished, effectively increasing microbiome diversity. Third, we heal the gut lining and mucosal membrane.

The specifics of how this is done varies with each individual case. However, I have a few notes to add here. First, for the elimination of pathogens and bacterial overgrowth, it’s necessary to use strong antimicrobial agents to ensure this is done properly. For increasing microbial diversity and repairing the mucosal membrane, we often use herbs and supplements. However, this works best in combination with a healthy diet high in fiber, fruits, and vegetables. We need to feed the good bacteria the right foods to make sure it grows strong. Research has shown that the composition of the microbiome can change rapidly under these optimal diet conditions.

Treatment at My Clinic

I’ve been treating digestive orders such as Crohn’s and ulcerative colitis for many years. It requires a comprehensive approach of microbiome management, intestinal barrier repair, and inflammation reduction. If you’re ready to take the steps to lasting health, click on the link below to book an appointment.