Scientists investigate links between cancer and the gut microbiome on several fronts. Certain gut bacteria are associated with cancer and can be used to diagnose the disease – this is the case for colorectal cancer as an EMBL study shows. The gut microbiome can influence the effectiveness of cancer medication, and researchers are looking at ways to modify the microbiome of individuals to improve treatment. Scientists know that some bacteria or viruses themselves cause cancer, and are looking whether other species living in our body may cause or prevent the disease.

Databases such as Mgnify, hosted by EMBL’s European Bioinformatics Institute (EMBL-EBI), hold the genetic information from thousands of entire human gut microbiomes. Metagenomics allows us to sequence the genomes of all species in an ecosystem at the same time in a single sample. In addition, information on the approximately 5,000 species, as well as the hundreds of strains found for each species are available within this database. Combining and analysing such large datasets leads to better understanding of the diverse microbial communities that live in our body, as well as paving the paths for diagnosis and treatments of disease.

Antibiotics directly affect the bacteria living in our gut. Although used to treat bacterial infections, antibiotics can also kill harmless bacteria, compromising our gut microbiota. EMBL scientists look for ways to mitigate this collateral damage of antibiotics. At the same time, bacteria with natural resistance to the antibiotics can multiply during treatment and take the place of those wiped out. This encourages the propagation of bacteria with antibiotic resistance. Bacteria can also evolve resistance by exchanging stretches of DNA that confer antibiotic resistance. So unfortunately, antibiotics select for resistant microbes and can imbalance our microbiota composition, hence should be only used when necessary. 

Variations in each person’s gut microbiome mean that even genetically identical twins process food in different ways. This may be one reason why some of us have a higher chance of being obese or diabetic. The gut microbiome is linked to many diseases, from irritable bowel syndrome to cancer, and from depression to psychiatric disorders. As scientists begin to understand better the bacterial species in our microbiomes and their genes, this may lead to personalised treatments for diseases and targeted ways of improving overall health.