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Shanahan addresses "is my microbiome normal?"

Fergus Shanahan, professor and chairman of the Department of Medicine at University of College Cork, recently gave the Presidential Lecture in honor of a decade of success at the Underwood Center for Digestive Disorders at Houston Methodist and saluting the achievements and leadership of his longtime friend and collaborator Eamonn Quigley, Underwood Chair of Medicine in Digestive Disorders. Click here to watch the lecture. Dr. Shanahan welcomed questions in follow-up to his lecture and his most recent work. Questions and answers from Dr. Shanahan follow.
Fergus Shanahan
How do you propose to change language conventions so our answers and data around microbiomics are more comparable and useful in our studies and results? How long do you think it will take to make a language change?
I don't have an easy solution except to say that for my part I will continually call out bad language in microbiome science and have published on the topic to entreat other investigators to be more conscious of their choice of words and to avoid loose language. I also give lectures to young scientists on the topic and highlight it on twitter. My bottom line is that if scientific language is sloppy, then there is a strong likelihood that scientific thoughts, logic and interpretation become sloppy. At times I despair and feel that science journals have abandoned their role in policing good science communications.
Can you propose better probiotics language that we can begin to use right away? How can we change our probiotics language across markets and advertising so that it catches on and is used correctly?
My suggestion is to abandon the word probiotic and always to precisely specify the name of the organism under discussion and to state precisely what beneficial action is being proposed and for what clinical problem is such an action required.
You found studying folks geographically is important and will help broaden study subjects right away so that we are sampling a wider group and have a better than 15 percent variance. How will geographic studies work?
I propose two specific things that can be done: a) to study minority ethnic groups living in the Western world and b) to study people living in developing countries where the risk of “Western” diseases is low because once they become developed, they will encounter such diseases.
Are you prepared to recommend a Mediterranean diet now to improve gut health?
Yes, but not with any rigidity - in other words I favor a Med diet in the main but with considerable flexibility. I favor a lower consumption of red meat, dairy products and saturated fats and increased intake of vegetables, fruits, legumes, fish, olive oil and nuts. Everything allowed but in moderation. (As far as trendy intermittent fasting), I don't believe in regimented food consumption – no need to become neurotic, lots of flexibility.
Do you recommend a more ancestral diet or lifestyle based on your findings?
I would if that were possible, but I don't think it is possible to revert to ancestral lifestyles. Nor do I think we can actually re-invent ancestral diets. The food chain has changed with selective breeding of various foodstuffs. However, I do favor consumption of traditional whole foods and less processed foods if possible. I am realistic and conscious that modern foods have been able to feed a larger population base than would have been possible with ancestral food sources. We need to study and understand the past so that we can learn how to retain some of the most healthful features of the past while benefiting from all that is good about the world today. (In other words, I believe we need to find a way to have our cake and eat it too and I'm optimistic we can do that.)
Where do you see the line drawn for processed food and too processed food?
This is where we need to clean up our language and be precise about what we mean about processed foods and ultra-processed foods. These terms are used loosely and mean different things to different people. Food processing is not per se a bad thing. Nor is it necessarily always bad. Much depends on what chemicals are introduced during the processing, if any. The main point I would emphasize is to state that the less processing the greater the retention of dietary fiber. This is different from stating that processing is bad.
How do we achieve dietary diversity and what spectrum do you recommend? Fruits, vegetables, protein, carbohydrates, etc.
Yes, all of the above – simply try to have variety in the diet but not to the point of becoming neurotic about it.
You indicate there are solutions in microbiome biomarkers and gut health that will impact the growing population of people suffering from cognitive impairment. Do we know some answers yet and what are they?
Dietary diversity and particularly by introducing a variety of dietary fibers such as in a Mediterranean diet has actually been shown to delay cognitive decline with age.
As you say, the goal of your studies is to fulfill the promise of personalized medicine. How far are we away and how do we get there? Any specific actions you’re trying to take in your gut microbiome studies or as a result of your studies?
We are not there yet – but we can stop abusing our microbiome with bad diets.
And the ultimate goal of personalized medicine is to live longer and healthier lives. Do you see any specific anti-aging trends in your research? Do you see any natural or cultural markers that help?
I'm not really interested in longer lives, just healthier lives while we are alive. And I believe the most accessible and simplest ways to promote that are the old reliables: dietary diversity, diet in moderation, exercise (any amount of exercise is better than none), avoidance of unnecessary broad-spectrum antibiotics and good sleep.