Microbiome Contributes to Inflammatory Bowel Disease and Depression

In 2012, Jeroen Raes of KU Leuven launched the Flemish Gut Flora Project. Sequencing fecal samples of over 3,000 healthy volunteers, Raes and his team defined the boundaries of a normal, health-associated gut microbiota. Next, the team turned to patient groups to identify microbiome alterations associated with diseases. In a study published today in Nature Microbiology, they describe the so-called B2 enterotype, which is deficient in anti-inflammatory bacteria.

According to Raes, many research groups have attempted to investigate alterations in microbiota associated with diseases, especially inflammatory bowel disease IBD. But the team’s new approach differs from previous attempts in three ways:

“First, we compared the microbiota of patients with profiles from healthy volunteers from our Flemish Gut Flora Project catalog of over 3,000 microbiomes. Second, in our analyses, we did not only look at the percentages of different bacteria present in the stool samples but also used a new technique to quantify their abundances. Third, we corrected our results for factors such as loose stools, often symptomatic in the diseases studied, but affecting the outcome of microbiome analyses,” Raes says.

The researchers identified an altered microbiome configuration—also known as an enterotype—with high prevalence among patient groups. It was observed in 13% of healthy volunteers, but it was found in 38–78% of patients with IBD and primary sclerosing cholangitis.

“This aberrant microbiome configuration, which we call the B2 enterotype, is characterized by low bacterial abundances and biodiversity,” explains coauthor Séverine Vermeire of KU Leuven. “It is notably deficient in some anti-inflammatory bacteria such as Faecalibacterium. In fact, we detect higher levels of intestinal inflammation in patients with the B2 enterotype. Even among healthy individuals, carriers of this enterotype have slightly higher levels of overall low-grade inflammation.”

Surprisingly, the researchers found a similar microbiota alteration to be associated with lower quality of life and even depression. “There appears to be a large overlap in microbiome alterations observed across different patient groups,” Raes says.

And although some healthy individuals do carry the B2 enterotype, the researchers claim that this should not be a reason for concern.

“At this point, we cannot make any prediction on disease susceptibility or risk based on a person’s enterotype,” Raes notes. “Moreover, enterotypes are not fixed and can be altered by, for example, changing your diet.”