Intestinal flora: These bacterial strains play a special role

Billions of bacteria live in the human intestine. These not only have an impact on digestion, but also on health. Gut bacteria are an important part of our immune system and they help prevent disease. Researchers are now reporting on bacterial strains that play a special role in fighting infections.

Numerous scientific studies have shown that intestinal bacteria have an enormous influence on human health and can, among other things, efficiently protect against infections. However, if the balance of this community, known as the microbiota, is disturbed – for example by antibiotic therapy – pathogens can gain the upper hand – with sometimes serious consequences for those affected. Researchers who deal with the interaction and conflict of intestinal bacteria have recently identified strains of bacteria that play a special role in two studies.

Protection against pathogens

Most of them have already experienced firsthand how important a healthy microbiome (intestinal flora) is when they had to take a broad-spectrum antibiotic. The drug not only destroys the pathogens, it also destroys the “good” bacteria in the intestine, which otherwise occupy the most important niches and help pathogens to refuse entry.

This protective mechanism is called colonization resistance, is explained in a communication from the Helmholtz Center for Infection Research (HZI).

But which types of bacteria are “good” or, in technical jargon, “commensal” and how can they protect against colonization, i.e. colonization by pathogens? Prof. Dr. Till Strowig, head of the “Microbial Immune Regulation” department at the HZI, and Prof. Dr. Bärbel Stecher from the Max von Pettenkofer Institute of the Ludwig Maximilians University (LMU) in Munich have taken on these questions and taken a closer look.

They report on their results on Klebsiella pneumoniae and E. coli bacteria in two independent studies in the specialist magazine “Cell Host & Microbe”.

Increasingly resistant to common antibiotics

As the report states, the intestinal dweller Klebsiella pneumoniae is one of the dreaded hospital germs, as it can cause severe pneumonia, urinary tract infections or even sepsis in weakened patients. The pathogen is increasingly resistant to common antibiotics and can promote further infections.

Till Strowig’s department at the HZI and partners in Magdeburg and Hanover were able to isolate strains of a related bacterium from the intestine that are highly effective against K. pneumoniae. This species, identified as Klebsiella oxytoca, uses the same sugars as the pathogen, but so efficiently that it has too little to survive.

“K. oxytoca can purposefully displace multi-resistant K. pneumoniae bacteria, as it effectively blocks the niche to be occupied by the hospital germ, ”explains Strowig.

In addition, the scientists were able to show in the mouse model that these bacteria help the bacterial composition in the intestine to regenerate faster after antibiotic therapy and to restore protection against infections.

Reduce susceptibility to hospital germs

“We first wanted to find out how susceptible healthy adults and children are to colonization with multi-resistant K. pneumoniae bacteria,” says first author Lisa Osbelt. To do this, the researchers took stool samples from 100 healthy people and incubated them with the germ overnight. The growth of the bacteria was then measured the next day.

According to the experts, there was great variability in the colonization, depending on the individual microbial community in the intestine. In a further step, the team then examined the samples in which the germ had grown poorly, and K. Oxytoca was repeatedly identified here.

They then tested the behavior of the two bacteria in different mouse models and it was shown that the addition of K. Oxytoca can significantly reduce susceptibility to the hospital germ. When germ-free mice were colonized with different groups of bacteria (a total of 12 bacterial species), three other species also showed a protective effect.

The protective effect also depends on the microbial environment in the intestine

As the German Center for Infection Research (DZIF) writes in a press release, Escherichia coli, or E. Coli for short, is one of the best-known bacteria in the human intestine. It often gets into the headlines as a “bad” bacterium because it is considered an indicator of faecal contamination of drinking water and certain variants can cause infections.

But the bacterium has many different strains and, in addition to the pathogenic variants, there are also commensal representatives. However, little is known about their role in human health. Bärbel Stecher, Professor of Medical Microbiology and Hygiene at the Max von Pettenkofer Institute at LMU Munich, and her team discovered some time ago that commensal E.coli protect against Salmonella infection.

Here, too, it is their sugar consumption that puts the salmonella in their place by depriving them of food.

In the current study, the researchers were able to show that this protective effect of E. Coli also depends on the microbial environment in the intestine. In other words, it depends on which microorganisms are still present and whether E. Coli is in good company.

“If there are Lachnospiraceae in our model, which can also metabolize simple sugars, E. Coli can protect – otherwise not,” explains Stecher. She adds: “Overall, we now understand better why probiotics may also work well for some people but not for others. The reason for this is the microbial environment, which varies greatly from person to person. “

Complex interrelationships

With the mouse model they have developed, the scientists can specifically examine the colonization and influence of pathogens. A synthetic cocktail of twelve types of bacteria colonizes germ-free mice stably over several generations and forms an intestinal flora representative of mice.

Both the studies on Klebsiella and E. Coli use this model to probe the interactions in the intestinal flora. But even with the mouse it becomes clear how complex the relationships are. The studies by the microbiota researchers give hope, however, because they show once again that we are on the trail of the processes in the intestine in detail.

“The use of living bacteria, so-called probiotics, for the treatment of patients with an existing colonization and as a preventive administration after antibiotic therapy is generally conceivable,” says Till Strowig. “The utilization of a wide range of sugars plays a major role in the design of such bacterial cocktails, and a protective cocktail must always contain more than one bacterium,” says Bärbel Stecher. (ad)

Author and source information

This text complies with the requirements of specialist medical literature, medical guidelines and current studies and has been checked by medical professionals.


  • Helmholtz Center for Infection Research: In search of bacterial cocktails to fight infections, (accessed: October 11, 2021), Helmholtz Center for Infection Research
  • Claudia Eberl, Anna S. Weiss, Lara M. Jochum, Abilash Chakravarthy Durai Raj, Diana Ring, Saib Hussain, Simone Herp, Chen Meng, Karin Kleigrewe, Michael Gigl, Marijana Basic, Bärbel Stecher: E. coli enhance colonization resistance against Salmonella Typhimurium by competing for galactitol, a context-dependent limiting carbon source; in: Cell Host & Microbe, (veröffentlicht: 04.10.2021), Cell Host & Microbe
  • Lisa Osbelt, Marie Wende, Éva Almási, Elisabeth Derksen, Uthayakumar Muthukumarasamy, Till R. Lesker, Eric JC Galvez, Marina C. Pils, Enrico Schalk, Patrick Chhatwal, Jacqueline Färber, Meina Neumann-Schaal, Thomas Fischer, Dirk Schlüter, Till Strowig: Klebsiella oxytoca causes colonization resistance against multidrug-resistant K. pneumoniae in the gut via cooperative carbohydrate competition; in: Cell Host & Microbe, (published: 04.10.2021), Cell Host & Microbe
  • German Center for Infection Research: In search of bacterial cocktails to fight infections, (accessed: October 11, 2021), German Center for Infection Research

Important NOTE:
This article is for general guidance only and is not intended to be used for self-diagnosis or self-treatment. He can not substitute a visit at the doctor.


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