In an article titled “Microbiome science needs a healthy dose of scepticism” by W. P. Hanage, the author discussed five key questions we should always remember when interpreting scientific literature.
Can experiments detect differences that matter?
Hanage discussed how it is often hard to distinguish functional differences in the world of microorganisms when we don’t already know what to look for or have characterized the network well already. Hanage discusses that until we can identify differences from gene sequences alone, we need to realize that any similarities we might notice may actually be hiding important differences that we haven’t realized yet.
Does the study show causation or correlation?
This question is important to take into consideration because often times a microbiome we see in correlation with a disease may actually just be a bystander in the diverse microbiota of our body. While explanations may fit the data, research often times doesn’t explore the reverse causality, so it is important to pay close attention to other factors that may be affecting the microbiome.
What is the mechanism?
Although we all know that correlation does not always equal causation, Hanage discusses how correlation usually implies some sort of causal relationship. Therefore, Hanage advises that the use of careful experiments to determine the mechanism and understand biochemical activity is crucial to understanding the true causes microbial influences may have.
How do experiments differ from reality?
Often times, microbial studies try to isolate only what is being examined to show more causation and understand the specific effects of a specific microbe – which is why the use of germ free mice is so popular. However, it doesn’t accurately represent an animal’s natural state or the responses an animal normally might have with their diverse microbiome.
Could anything else explain the results?
Because current experimental procedures are not always the most developed or sophisticated due to the nature of exploring microbiotas, there are often many other factors that can influence results such as diet or other environmental factors. Hanage also stresses that findings tend to be exaggerated in the media and thus individuals may make decisions without knowing everything. Therefore, it is always important to consider other contributors.
Out of these five questions, I think the most helpful in discussing controversy is what is the mechanism. A lot of the uncertainty and questions about other potential factors comes from not knowing the specifics of what is happening because there are so many contributors. Therefore, knowing the exact mechanisms that are occurring and the roles they play in the larger microbiome will help provide clarity and a deeper understanding of microbial science and influences on diseases.
