geneIQ – Genetics and Diagnostics

This is an edited version of the Human body and microbiome | LinkedIn article.

We all know the old saying, ” You are what you eat.” It may have more truth in it than we ever thought. Our gut microbiome appears to affect many of our health processes. Microbial metabolites have obvious effects on our digestion and all related functions. This in fact can go further than occasional digestive problems. In recent years multiple publications have indicated that certain gut microbes are closely associated with the development of colon cancer.

We are starting to identify the ways microbes can interact with human tissues. This is particularly important for people at high risk of colon cancer:

• patients with inherited mutations in mismatch repair genes in Lynch syndrome, APC or STK11.
• patients with persistent inflammatory states in diseases like ulcerative colitis, or Crohn’s disease.

Studying the mechanisms by which early damage occurs in the intestine reveals important insights. It became clear that dysbiosis of gut microbiota can be one of the big factors driving the changes.

Certain foods have been known for many years to contribute to colon cancer. Now, we are starting to understand the mechanisms and how to prevent this. By making smart choices combined with gut microbiome testing, we can help to keep ourselves healthy. The microbes in our gut do a great job of protecting gut mucosa by reducing inflammation.

The big question is whether we should look at the gut microbiome in addition to hereditary predisposition to colon cancer. Would this provide a better picture of an individual’s risk for developing the disease? In my opinion, the answer is yes. However, microbiome analysis is still not an easily accessible test or giving clear answers. The tools for analysis are just now starting to expand. This is led by the release of APOLLO by the team at the University of Galway. In reality, we are probably still a bit away from a wide adoption of dual testing. However, it can become a standard clinical practice in the future.

Can we challenge the testing even further and use a single sample to do both tests? Can such testing be done only by large central labs or can it be more distributed leading to better accessibility?

References:

1. Heineken, A et al (2025) A genome-scale metabolic reconstruction resource of 247,092 diverse human microbes spanning multiple continents, age groups, and body sites. Cell Systems 16, 101196
2. Piccinno, G et al (2025) Pooled analysis of 3,741 stool metagenomes from 18 cohorts for cross-stage and strain-level reproducible microbial biomarkers of colorectal cancer. Nature Medicine volume 31, pages 2416–2429 (2025)