[Q&A] Know Your Microbiome: Your Questions, Our answers

Q&A

We celebrated World Microbiome Day 2020 over the weekend by hosting a webinar “Gut feeling is real science: Know your gut microbiome!” with our expert speakers from Malaysia and Singapore who provided insights on the connection of gut microbiome to our health and mental state; how our diet shapes the microbiome; and the latest research on fecal transplant to help grow healthy gut bacteria. 

They were Associate Professor Dr Jeremy Lim who is the founder of Asian Microbiome Library (AMiLi), Southeast Asia’s first and only stool bank serving as a hub for gut microbiome innovation and therapy based in Singapore, and Dr Chong Chun Wie, Senior Lecturer at School of Pharmacy, Monash University Malaysia who has done extensive research in the Antarctic microbial ecology and human gut microbiome.

During the live session, moderated by Dr Mahaletchumy Arujanan, co-founder of Science Media Centre Malaysia, we received many questions from viewers but did not have time to get to everyone. So as promised, here are answers to some of the questions we did not get a chance to answer. 

Question: Prebiotics and probiotics how do they affect our gut microbiomes?

Dr Chong: Probiotics are live “beneficial bacteria” given usually in the form of supplement, food and drinks. Common Probiotics include Lactobacillus and bifidobacterium. They are given to improve the balance of good and bad bacteria. Some studies had shown that probiotics alleviate intestinal bowel diseases and improve nutrient absorption. Prebiotics are nutrients that induce the growth of beneficial gut microorganisms. Prebiotics are usually polysaccharide found in vegetables and fruits such as inulin, glycan and pectin. 

Question: How often should we consume probiotics in order to benefit from the beneficial effect of presumably good bacteria?

Dr Chong: We consume natural probiotics from fermented food such as yogurt, cheese, tempoyak and pickles. There are also commercially available probiotics. The duration and frequency of probiotics intake can be affected by a number of factors, such as the type of probiotics, the dose of probiotics and the purpose for taking them. Nonetheless, there is currently no fixed recommendation for the frequency of probiotics consumption. It is best for you to consult your doctor to evaluate the needs for probiotics supplement.

Dr Jeremy: It might be useful to understand what one’s gut microbiome profile looks like before spending large sums of money on probiotics that may not be useful to one’s health. In many health matters, there is a threshold effect, meaning that the human body needs a minimum amount for proper functioning but more than that does not lead to benefit and may even cause harm. For example, taking excessive Vitamin D supplements can lead to dangerously high levels of calcium in the blood, leading to nausea and vomiting, weakness and eventually kidney stones and damage to the kidneys.

Question: Diet can manipulate gut microbes. How does this affect health?

Dr Chong: The food we eat can affect the composition of microbiota in our gut. For example, frequent consumption of processed food is associated with low gut health as most of the nutrient is directly absorbed in the small intestine resulting in reduced microbial diversity in the colon. In contrast, a diet rich in fibre supports a more healthy microbiota as fibre will be fermented in the colon to produce Short Chain Fatty Acids (SCFAs) that are essential for the growth of other beneficial bacteria. Separately, studies also showed that diets rich in fat may promote pro-inflammatory microbiota, which in turn increase the risk for diabetes and obesity. 

Dr Jeremy: I would add that a vegetarian or vegan diet certainly leads to profound changes in one’s gut microbiome and this based on current science appears to be beneficial to human health. This is a helpful review. But I must caution that it’s early days and many who eat omnivorous diets live perfectly healthy lives also. But the basic point is that what we eat does influence our gut microbiome a lot and this in turn does impact our health.

Question: Those with a heavy meat diet, especially raw or undercooked meat, are they more prone to have unhealthy gut microbiome diversity? Like parasites, etc.

Dr Chong: The impact of a heavy meat diet to the human microbiome is not clear, although changes in the rat’s microbiota was seen after a short period of high protein diet. There is also no evidence to suggest that raw or undercooked meat are “bad” for the gut microorganism. Nonetheless, the consumption of raw meat is always associated with the risk of infection through food-borne pathogens such as Escherichia coli, Salmonella spp. and Listeria spp. etc. Other parasites including tapeworms, toxoplasma gondii and roundworms may also be transmitted with raw meat.

Question: Are there enough evidence to say that the types of cooking utensils affects the microbiome?

Dr Chong: There is little knowledge regarding how the materials of the cooking utensils affect the microbiome. It might be a good research topic for future study.

Dr Jeremy: Agree that this is a very interesting topic which merits study. Related to his would be the role of food additives, artificial sweeteners etc which may adversely affect one’s gut microbiome. The science is controversial and evolving but this review article is typical.

Question: How does the brain-gut axis interaction affect one’s mood? 

Dr Chong: As discussed during the webinar, the interaction between gut and brain takes place via exchange of hormones and neurotransmitters. A number of these such as gamma-aminobutyric acid (GABA), dopamine, serotonin and short-chain fatty acids (SCFAs) are made by gut microbiota. A reduction in GABA may induce stress, while dopamine and serotonin deficiency can cause anxiety and depression. As such, it is important to maintain the number of neurotransmitters producing microorganisms in the gut. 

Question: There have been a few studies that related gut microbiome and mental health. Could analysing fecal microbiome be used as a diagnostic tool for mental health issues?

Dr Chong: Indeed, a number of studies were conducted and many had found strong connections between gut microbiome and mental health. However, we are still not at the stage to replace the current mental health assessment methods using faecal testing.

Dr Jeremy: Agreed and gut microbiome profiling can be a useful adjunct but does not replace standard methods.

Question: There are brain-gut axis interactions (Parkinson’s, Autism, etc.), does the gut microbiome affect motor-degenerative diseases too?

Dr Chong: Yes, gut microbiome was implicated in several of the studies on motor neuron diseases.

Dr Jeremy: This is the Cell paper from May last year that I had mentioned in the webinar. Briefly, the Caltech researchers found that autism-like symptoms could be induced in mice by transplanting stool from children with ASD and this could be ameliorated with administration of 5AV or taurine, which are specific metabolites involved in the neural pathways.

Question: Does having pets or exposure to animals at a very young age change the diversity of gut microbiome?

Dr Chong: Consistent evidence suggested that exposure to pets influence the diversity of gut microbiota, regardless of the age. However, it is still debatable whether such influence is beneficial or potentially posing health risk. 

Question: Are there significant differences in the gut microbiome between healthy people VS those who suffer from a certain disease? ie: can we study poop microbiome to predict/look at an onset of a disease?

Dr Chong: Yes, various studies had shown that healthy and sick individuals harboured different sets of microbiota. For example, an obese person usually carries a higher abundance of Staphyloccocus aureus and lower abundance of Faecalibacterium prausnitzii than a non-obese person. There is a lot of promise for the development of faecal microbiome as a diagnostic tool and to facilitate personalised treatment based on the unique microbiome signatures each of us carries. However, faecal microbiota is not part of the routine clinical diagnostic tools used in the hospital.

Dr Jeremy: One example is in Ulcerative Colitis. Have a look at this paper. In brief, the Stanford researchers found that ulcerative colitis patients had lower amounts of a bacteria called Ruminococcaceae compared to healthy individuals and this led to a depletion of secondary bile acids which are important for metabolism. In other studies, researchers treated mice with ulcerative colitis using enemas containing secondary bile acids with promising results.

Question: Does AMILI store microbiome data for a single individual of different age stages?

Dr Jeremy: Assuming the individual is healthy when they donated their first sample. At AMILI, we are committed to collecting and storing a range of different data points from microbiome donors across diet, lifestyle habits, demographics, and even wearable data. As a library to advance the science of gut microbiome applications for human health, we are keen to collect microbiome donor data across time to track the impact of diet, lifestyle, and age. Please follow us on our website poopsaveslives.com to become a microbiome data donor and follow our Instagram page for regular updates on AMILI.

Question: [To Dr Jeremy] You mentioned that eating leafy vegetables improves the microbiome – did you mean improving the diversity of gut bacteria? Or did you mean that this type of diet favours the growth of “good bacteria” in our gut?

Dr Jeremy: Let’s talk a little about feeding one’s microbiome and the types of foods that are good for the microbes living inside us. Firstly, prebiotics. Prebiotics are a type of fibre or carbohydrate (mainly polysaccharides) found in many different foods, especially leafy vegetables that have lots of fibre. While indigestible by our bodies, this fibre acts as a kind of fertiliser or food for the good bacteria in our guts, encouraging them to thrive. On the other hand, probiotics are live bacteria (or yeasts) that can be found in certain foods or supplements. Probiotics introduce good bacteria (the species of bacteria depends on the food) to the microbiome to encourage a healthy microbiome composition. Good sources of probiotics include fermented foods like kimchi, tempeh, and miso. Remember to consume both pre- and probiotics to make sure your gut is full of good bacteria that are well-fed and happy!

How does one optimize one’s gut microbiome? In general terms, we recommend that you get 6-7 hours of sleep and consume a wide range of healthy ingredients such as green leafy vegetables. Do avoid processed foods, aerated drinks, among others. Vegetables promote a diverse gut microbiome, which in turn can keep you healthy. It is interesting to note that sleep and nutrition are also impacted by the diversity of the gut microbiome and poor sleep and dietary habits can hurt your microbiome. However, your microbiome is unique, so it is generally more difficult to assess the response to generic recommendations. For more personalised recommendations, we recommend that you get your gut microbiome sequenced to identify strains of bacteria and relevant nutritional recommendations.