The intestinal bacterium Ruminococcus gnavus: friend or foe?

The gut microbiome

Our gut is literally teeming with life. Billions of bacteria, viruses and yeasts live in our intestines and make up the gut microbiome. The composition of the gut microbiome is unique to everyone and consists mainly of hundreds of different types of bacteria. Among other things, gut bacteria help digest our food, such as dietary fiber, and support the immune system. However, certain gut bacteria have been linked to chronic intestinal inflammation (such as Crohn's disease) or type 2 diabetes. What makes these gut bacteria different?

Prime suspect: R. gnavus

Researchers at the Leiden University Center for Infectious diseases (LUCID) analyzed data from more than 10,000 individuals worldwide in search of a possible link between R. gnavus, a common gut bacterium and health, age, residence and lifestyle. The results were published in the prestigious scientific journal Nature Communications.

Researcher and PhD student Sam Nooij: “Our research shows that R. gnavus occurs more often and in higher numbers in chronic intestinal inflammation (Crohn's disease), type 2 diabetes, high blood pressure and arteriosclerosis (= atherosclerosis). This mostly confirms what is already known about R. gnavus but the link to arteriosclerosis is new. If we look at the global distribution of R. gnavus, we find that the bacterium is surprisingly more prevalent in residents of Western countries and is linked to the Western lifestyle.”

Genetic differences

But why is this gut bacteria more prevalent in Crohn's disease? To answer that question, the researchers looked at the DNA of R. gnavus. DNA can be compared to a bar code in which all the genetic information is recorded. By making small changes in their DNA (=mutations), bacteria continuously adapt to their environment. Some mutations work well, others don't. This is how different types of R. gnavus are formed.

The LUCID researchers isolated R. gnavus from the stool of both patients with Crohn's disease and healthy individuals (=isolates). They also received isolates from other research institutes or companies. The bacteria were further cultured in the laboratory. After that, the entire genetic code (=genome) was mapped. “In total, we determined the genome of 45 different isolates. By comparing these, we can see whether or not certain genes are present in R. gnavus from patients with Crohn's disease,” said Quinten Ducarmon.

This is the first time the genome of different R. gnavus isolates has been described on such a large scale. Prior to the LUCID group's research, the complete genome of only one R. gnavus isolate was known. The 45 isolates and their genomes are a treasure trove of information to find out if, why and how R. gnavus is involved in Crohn's disease. Ducarmon: “Our analysis shows that 163 genes of R. gnavus are linked to Crohn's disease. Follow-up research should reveal the exact function of these genes and whether this knowledge can play a role in treatment.”

Open Science: accelerating research by sharing information and materials

To accelerate further research on R. gnavus, the LUCID researchers are making all data and isolates available to other researchers free of charge. Wiep Klaas Smits: “Isolating R. gnavus from stool samples and then growing it further in the laboratory takes a lot of time. The 45 isolates from our study will be included in a biobank. Researchers worldwide can request our isolates through this biobank. This means they do not have to isolate and grow the bacteria themselves. Also, determining the genome is a very time-consuming and costly process. By offering both the isolates and their genome in this way, we accelerate research and hopefully gain insights that can help in the treatment of Crohn's disease faster.”

This study was funded by the Leiden University Fund.