In Predicting Disease, Is the Microbiome More Accurate Than Genes?

Is the microbiome more accurate than genes in predicting disease?

Check out this answer from Consensus:

The evidence suggests that the microbiome holds significant promise in disease prediction, often outperforming traditional genetic markers. As research progresses and methodologies improve, the microbiome could become a cornerstone in the predictive landscape of precision medicine.

The quest to predict disease accurately has led researchers to explore various biological markers. Traditionally, genetic markers have been the cornerstone of disease prediction. However, recent studies suggest that the human microbiome might offer superior predictive capabilities. This article delves into the comparative accuracy of the microbiome versus genetic markers in disease prediction, drawing on recent research findings.

The Predictive Power of the Microbiome

Recent studies have highlighted the microbiome’s potential in disease prediction. For instance, a comprehensive study comparing the predictive capabilities of the human microbiome and genetic markers across 13 common diseases found that microbiomic indicators significantly outperformed genetic markers. The study reported an overall Microbiome-Association-Study (MAS) area under the curve (AUC) of 0.79, compared to a Genome-Wide-Association-Study (GWAS) AUC of 0.67, indicating a higher predictive accuracy for the microbiome2.

Microbiome-Based Diagnostic Tools

The development of microbiome-based diagnostic tools has shown promising results. For example, a study on cancer diagnostics revealed that unique microbial signatures in tissue and blood could discriminate between different types of cancer, even in early stages. This suggests that microbiome-based diagnostics could be a valuable tool in oncology6. Another study introduced a machine learning model, the Multimodal Variational Information Bottleneck (MVIB), which effectively combined various data modalities to predict disease based on microbiome data, achieving competitive results5.

Gene-Level Insights from the Microbiome

The microbiome’s predictive power extends to gene-level insights. Research has shown that gene-level metagenomic architectures can yield high-resolution diagnostic indicators for various diseases. For instance, specific gene-level signatures associated with the Streptococcus genus were linked to coronary artery disease, inflammatory bowel diseases, and liver cirrhosis, while type 2 diabetes had a distinct metagenomic signature1.

Challenges and Future Directions

Despite the promising results, there are challenges in microbiome research, such as the lack of standardization in research methods and the need for large-scale population-level microbiome sequencing resources. Addressing these challenges could further enhance the predictive accuracy and clinical utility of microbiome-based diagnostics9.

In predicting disease, is the microbiome more accurate than genes?

Kate Secombe has answered Uncertain

An expert from University of Adelaide in Microbiome, Cancer

With our current levels of understanding about the microbiome and analysis techniques, I do not believe that we can predict disease more accurately than genetic testing. In future, as our knowledge increases, this may become possible, however it would also depend on what disease we were looking at. Some diseases have a very strong genetic basis, and therefore would be best predicted via genetic testing, whereas other diseases with a strong environmental basis may be better predicted by the microbiome in future.

The study linked in the question was retrospective, so we don’t have a lot of information about whether we can prospectively predict disease using the microbiome! In future, I can envisage the use of microbial tests in conjunction with genetic tests.