- Yaqub MO, Jain A, Joseph CE, Edison LK. Microbiome-Driven Therapeutics: From Gut Health to Precision Medicine. Gastrointestinal Disorders. 2025; 7(1):7. https://doi.org/10.3390/gidisord7010007
Various diseases are closely linked to an imbalance in the intestinal flora: irritable bowel syndrome (IBS), for example, is associated with a significantly reduced diversity of beneficial intestinal bacteria. In chronic inflammatory bowel disease (IBD), the intestinal flora shifts in favour of pro-inflammatory germs (e.g. E. coli) with a simultaneous decrease in protective, anti-inflammatory bacteria (such as Faecalibacterium prausnitzii). Characteristic microbiome changes have also been identified in metabolic diseases such as obesity and diabetes, suggesting that the gut flora plays a role.
The brain and psyche are also influenced by the gut flora via the gut-brain axis – evidence of this can be found in autism and Parkinson's disease, for example. The microbiome is also important for the immune system: dysbiosis is discussed as a possible influencing factor in autoimmune diseases (e.g. rheumatoid arthritis). The gut flora is even involved in the development of cancer – for example, some bacteria can promote DNA damage in colon cancer through chronic inflammation.
In view of these connections, therapeutic interventions in the microbiome are increasingly becoming the focus of research and clinical application. One established method is faecal microbiota transplantation (FMT), in which intestinal bacteria from a healthy donor are transferred to a patient in order to restore balance to their microbiome. FMT has a success rate of over 90%, particularly in cases of recurrent Clostridioides difficile infections; studies have also shown significant improvements in some IBD patients. Another pillar is probiotics – live, beneficial microorganisms that are intended to strengthen the intestinal flora. In combination with prebiotics (nutritional substrate for desirable bacteria), they are used as synbiotics.
The administration of beneficial microbial metabolites (such as short-chain fatty acids) is also being researched as a therapeutic option. The short-chain fatty acid butyrate, for example, has neuroprotective and immunomodulatory effects – with potential therapeutic benefits in neurodegenerative diseases such as Alzheimer's and Parkinson's.
Beyond these approaches, novel strategies are being developed to intervene specifically in the microbiome. Researchers are working on synthetic microbiota – artificially assembled microbial communities – that are designed to perform specific functions and modulate disease processes. In addition, the targeted genetic modification of individual intestinal bacterial strains using CRISPR is coming into focus, for example to eliminate pathogenic germs. In contrast to transplants, which alter the entire microbiome, this microbiome editing preserves the remaining microbial balance.
Another approach is to use the microbiome as a therapeutic target in drug development – particularly for combating infections and antibiotic resistance. However, these methods are still in their early stages. Questions regarding the stable establishment of the modified germs, their safe application and the control of possible risks must be clarified before clinical use.
Despite all the progress that has been made, microbiome-based therapies face various hurdles before they can be routinely used in clinical practice. A key problem is the high degree of interindividual variability in the microbiome – every person has a unique gut flora, meaning that the same treatment can have different effects. As long as the exact mechanisms of action of microbiome interventions remain unclear, targeted further development will also be difficult.
There are also still many gaps in our understanding of microbiome research in general. In addition, there is a lack of uniform protocol standards to make findings from different studies comparable. Furthermore, there are still no clear regulatory guidelines for the approval and application of these novel therapies, which slows down their implementation in practice.
Recent developments highlight the enormous potential of microbiome-driven therapies. In the future, it will be important to close remaining gaps in knowledge and overcome existing hurdles. If this is achieved, microbiome therapies could become a cornerstone of personalised medicine and serve as tailored, effective and sustainable treatment options for numerous diseases.