Bacteria have a bad reputation amongst the general populace because the media and health networks report on the diseases they cause. Whooping cough, salmonella, tuberculosis, and Lyme disease are a few bacteria-caused diseases heard in the news and feared. However, despite this negative reputation, bacteria have given humans many benefits and, in turn, we have provided benefits to them.

Within every human gut is an ecosystem of bacteria and other microbes known as the microbiome. The bacteria that live within the gut have been a hot topic of research for the last few decades, and researchers have discovered their benefits. First, the gut bacteria assist in the digestion of complex sugars like starches, along with vitamins and other nutrients we need. Second, the gut bacteria train our immune systems. They teach the immune system to respond to the bad bacteria that enter the body, and the good bacteria also produce chemicals that prevent the immune system from overreacting to the wrong things. Finally, the good bacteria can prevent the bad bacteria from taking hold in the gut and causing problems.

These gut bacteria live in a balanced ecosystem to keep the human host healthy. If something disturbs this balance, then sickness occurs. Inflammatory bowel disease (IBD) is a prime example of how a disrupted microbiome causes major problems.

IBD is an umbrella term used for Crohn’s disease and ulcerative colitis. These diseases differ, but their symptoms, causes, and even the microbiomes involved are similar. The symptoms of IBD include abdominal pain, diarrhea (sometimes with blood), weight loss, malnutrition, and weight loss. Although IBD is classified as an autoimmune disorder, meaning that the person’s own immune system is attacking their gut, researchers found that the gut microbiome is also involved in the disease. Researchers compared the gut microbiomes of IBD patients with healthy patients and found the microbiomes of IBD patients were not as diverse as their healthy counterparts. The ecosystem became imbalanced.

IBD creates a toxic environment within the gut that the microbiome must adapt to. This means that the bacteria that cannot survive die off or hide in areas of the gut that are better for them. The bacteria that can survive then dominate the new ecosystem and tip the scales in their favor. In recent experiments, researchers discovered new strains of bacteria that have gone unrecognized in microbiome research but have adapted and dominated the gut ecosystem in IBD.

Their work, published in Cell Host & Microbe, scoured thousands of genetic samples of the microbiome of IBD and healthy patients. They discovered that the strains of IBD-related bacteria were separate and diverse from the bacteria associated with healthy individuals. Even more interesting, the IBD-related bacteria are present in the guts of healthy individuals but do not cause issues or IBD directly. When the researchers tracked a patient as they developed IBD, the IBD-related bacteria took the opportunity and began to dominate the gut ecosystem.

The researchers confirmed that the IBD-related bacteria were built for the toxic gut by checking their abundance when patients had inflammation and when they had remissions. During inflammation periods, the IBD bacteria were more abundant than the health-associated bacteria. However, when the patient went into remission, and the inflammation subsided, the health-associated bacteria recovered, but the IBD bacteria population did not decrease. When checking the patients’ history, they found that the IBD bacteria could persist for months after remission.

More work needs to be done to determine if the IBD bacteria are involved in maintaining IBD and leading to relapses in inflammation or just a consequence of the disease. However, the change in bacteria populations during the development of IBD offers a new method for tracking the progression and severity of IBD. It also highlights how diseases that involve the microbiome will create two distinct bacterial ecosystems based on ‘‘diseased’’ or ‘‘healthy’’, expanding our knowledge of the relationship between the microbiome and human health.