Resident gut biome

Of the anaerobic bacteria, 25% consist of Bacteroides species. These have a beneficial effect on their host in the intestine. Numerically, they form the largest group of bacteria and are therefore an important part of colonization resistance. This means that pathogens do not get a chance to attach to the intestinal wall, because it is protected by resident bacteria, including Bacteroides species.

In particular, indigestible carbohydrates are converted by them into short-chain fatty acids and hydrogen. This makes this group of bacteria important in supporting Bifidobacteria. A good Bifidus intestinal microbiota is particularly dependent on a good Bacteroides intestinal microbiota. To support both groups of bacteria, there are no probiotics, but there are prebiotics, such as inulin.

Outside the intestine, however, Bacteroides species are important clinical pathogens. They are found in most anaerobic infections, with or without abscess formation. The Bacteroides species contain the most antibiotic-resistant mechanisms of all anaerobic bacteria. They can adapt very well to new circumstances:

• They can adapt to the available nutrition
• They have multiple pumping systems to pump away substances toxic to them
• They can influence the host's immune system so that it tackles other competing pathogens.

Some antibiotics to which Bacteroides are resistant include cefotaxime, clindamycin, metronidazole, carbapenems, and fluoroquinolones (e.g., gatifloxacin, levofloxacin, and moxifloxacin). Bifidobacterium species, like Bacteroides species, form a large part of the resident intestinal microbiota. They convert carbohydrates into short-chain fatty acids such as acetic acid, formic acid, succinate, and ethanol. This achieves a lower acidity of the intestinal environment, which counteracts putrefaction processes. Through the production of short-chain fatty acids, they work synergistically with Lactobacilli and Enterococci. Furthermore, they can split bile acids and inhibit the multiplication of transient bacteria. However, the amount of Bifidobacterium species decreases after the age of 50, which can lead to putrefaction processes and the intestinal microbiota becoming more susceptible to dysbiosis.

Escherichia coli contributes to colonization resistance by producing antimicrobial substances. Furthermore, this bacterium stimulates the immune system of the intestines and contributes to the stabilization of the intestinal barrier. Therapeutically, this bacterium is used to improve mucosal immunity (sIgA, beta-defensin 2). It also removes oxygen from the food bolus and from the intestinal wall to ensure a stable anaerobic environment in the intestine, allowing for a balanced anaerobic intestinal microbiota with Bifidobacterium and Bacteroides species.

Enterococcus species can convert carbohydrates into short-chain fatty acids that acidify the intestinal environment and inhibit the growth of transient bacteria. To support colonization resistance, they produce important bacteriostatic and bactericidal substances. They can also convert proteins. They are used therapeutically to improve mucosal immunity. They also remove oxygen from the food bolus and from the intestinal wall to maintain an anaerobic intestinal environment.