Q&A With Dr. Chutkan On The COVID-19 Pandemic

Can you talk about your slogan – Live Dirty, Eat Clean – and how it relates to immune health and/or Covid-19?

Live dirty is all about avoiding super-sanitizing our bodies with harmful medications like excessive antibiotics and chemical-filled, self-care products, such as antibacterial soaps, that disturb the microbiome – the trillions of organisms that live in and on our bodies. These microbes are the worker bees that carry out all the tasks that make us who we are. They have the ability to alter our genetic code – for the good… or bad! – depending on the lifestyle choices we make.

Eat Clean means eating unprocessed food, grown in soil, without the use of harmful pesticides – and focusing on consuming those foods that benefit a balanced microbiome; lots and lots of vegetables, fermented foods, and foods high in indigestible plant fiber.

Living by my Live Dirty, Eat Clean motto promotes a balanced microbiome, one that’s rich in beneficial gut bacteria, as well as diverse – a marker consistently associated with good health in the scientific literature. Microbial health is very closely tied to immune health since the majority of our immune system is located in our gut.

When we consider immune health, it’s really about how healthy the host (ie, us) is that determines who gets really sick and who doesn’t. While the virulence of the pathogen is important, the health of the host is also really important. If the host terrain is strong and rooted, the pathogen has little chance to take over; if the terrain is weak and imbalanced, the pathogen can pose a serious threat. What I’m describing is what’s referred to as Terrain theory – the concept that a rich and balanced gut microbiome can protect us against harmful pathogens and prevent us from getting really sick; versus Pasteur’s germ theory  – the conventional idea that the virulence of the pathogen is what determines whether or not we get really sick. Where our health is concerned, so much is in our power, and the power comes in the form of the lifestyle choices we make – Live Dirty, Eat Clean!

Can you tell us more about how COVID-19 impacts the GI tract?

GI symptoms associated with COVID-19 originate from two things that happen during coronavirus infection. First, the SARS-CoV-2 binding sites – angiotensin converting enzyme-2 (ACE2) receptors – are located in the gastrointestinal tract. And second, an inflammatory response to viral shedding triggers direct damage to the gastrointestinal tract. We think the viral replication can lead to increased permeability and diminished barrier function, causing diarrhea, easier invasion by pathogens, and nutrient malabsorption. ACE2 receptors are more plentiful in the GI tract than the lungs. About half of the patients studied in Wuhan had GI complaints (mostly diarrhea) as well as respiratory symptoms, and a few had GI symptoms alone. We also know that the virus is present in stool and can potentially be transmitted through stool, so this is definitely a good time to remember to wash your hands after you use the bathroom! In fact, researchers in China found that 53.4% of patients had SARS-CoV-2 RNA in their stool, and 23% of patients tested positive in their stool despite testing negative for the virus in respiratory samples.

If I already have GI issues, does that make me more susceptible to contracting the disease, or at a greater risk of death?

Your risk for contracting the disease or experiencing complications from the disease really depends on what type of GI symptoms you have. If you have irritable bowel syndrome (IBS) – which is one of the most common GI disorders affecting about 20% of the American population, and you have symptoms of diarrhea, or constipation, or both, accompanied by some abdominal discomfort – you’re not at any increased risk.

If you have inflammatory bowel disease (IBD, consisting of Crohn’s or ulcerative colitis) – which is an autoimmune disease, you may be at an increased risk if you fall into one of two categories: 1). you’re taking an immunosuppressive drug like steroids, or a biologic, or 2). you have poorly controlled disease with a lot of active inflammation. And of course, both of these factors are compounded if you’re over 65. For more on this, check out my webinar on IBD and the coronavirus.

What, if any, are the risks of using antibiotics during the Covid-19 crisis?

When we talk about our immune system, a lot of what we’re talking about is the healthy balance of microbes in the gut. The role of the gut isn’t just to make smelly gas and stool – it plays a critical role in keeping us healthy:

• Protection against pathogens (barrier function)
• Synthesis of vitamins
• Immune system development
• Modulation of the central nervous system (CNS)
• Production of short chain fatty acids (SCFA) produced by dietary fermentation

Antibiotics create something called dysbiosis: disruption of the delicate balance of commensal bacteria, leading to decreased diversity, a less stable microbiome, and increased opportunistic pathogens. When antibiotics are introduced to your gut, the following happens:

• Step 1: reduction in the amount of normal gut flora
• Step 2: greater decrease in normal microflora and COLONIZATION with more pathogenic microflora (PATHOBIONTS – any potentially pathological organism which, under normal circumstances, lives as a non-harming symbiont)
• Step 3: continued decrease in normal, and now ACTIVE REPRODUCTION of fungal organisms and other pathobionts
• Step 4: dramatic decrease in healthy species and ongoing active reproduction of fungal organisms, etc. Ability to crowd out pathogens is significantly affected

When antibiotic-induced dysbiosis occurs, the normal balance of our gut bacteria is thrown off and our ability to recognize and fight off pathogens is hindered, resulting in a weaker immune system. I highly recommend avoiding antibiotics whenever possible, and especially amidst a pandemic where a strong immune system is your best protection. 

How can I rebuild my microbiome if I am on an antibiotic protocol?

First, it’s important to ask your doctor how absolutely necessary the antibiotics are. Are they being used preventively, which in most cases means they can be stopped; are they being used for inflammation, rather than infection, which again means they can likely be stopped; or are they being used for actual active infection? If at all possible, stopping the antibiotics is critical, even if you’re taking a probiotic along with the antibiotics. Otherwise, you’re basically trying to fill up a bathtub with the drain open. So first and foremost, I recommend removing any offending agents to the gut microbiome – antibiotics, acid blocking drugs, steroids, etc.

If your antibiotic protocol is absolutely necessary, the most critical factor for rebuilding the microbiome is food: what you feed your microbes determines which kinds of organisms will grow. And what organisms grow determines your immune health and disease risk.

A study that looked at how diet affects the gut microbiome brings this point to life. Italian researchers compared children in Florence, Italy, eating a typical Western diet (high-fat/high-sugar) with a rural group in Burkina Faso eating fiber-rich legumes and vegetables. Gut bacteria were similar in the children when they were breast-fed babies, but as soon as they started to eat their local diet, significant differences emerged. The European group eating the high-fat/high-sugar diet had less microbial diversity and more species associated with diarrhea, allergy, and obesity. The African children had lots of species associated with leanness and also much higher levels of beneficial short-chain fatty acids that protect against inflammation. This study highlights the intimate connection between what you eat and how it affects your microbial make-up and in turn, your disease risk. Seen through this lens, encouraging our kids (and ourselves) to eat more plants takes on epic importance. Food is powerful medicine!

What about biologics, corticosteroids, or other immunosuppressants – could these increase my risk of disease contraction?

Yes. For steroids, the dose and length of treatment are important determinants of risk. Over 20 mg is considered a high dose and puts you at greater risk for contracting COVID-19 and having more serious complications. Steroids negatively alter the microbiome, leading to overgrowth of fungal organisms and other potential pathogens, and also suppress your ability to fight infection. One of the simple things you can do is talk to your doctor about trying to decrease your dose below 20mg, even if it’s not possible for you to taper off completely.

Biologics suppress inflammation but unfortunately, a side effect for all biologics includes increased risk of infection – including viral infections. In fact, the risk of cancer and serious infection are the main reasons why I work so hard to keep my IBD patients off these drugs. They have good efficacy, meaning they can help control the inflammation, but that comes at a high price.

As of March 25, 2020, there were 87 reports of patients with IBD and COVID-19 in the international Surveillance Epidemiology of Coronavirus Under Research Exclusion database – SECURE-IBD. Of those, 50 had Crohn’s disease, 36 UC, and one unknown IBD. Overall, 19 (21.8%) were hospitalized, 2 (2.3%) placed on ventilators and 5 (5.7%) died. These rates are higher than the general population rates, but we don’t know the details about disease severity, medications, etc. What we do know is that almost half of Crohn’s patients and about one sixth of UC patients take biologics and a recent report identified excessive steroid use in 15% of IBD patients included in the study. So the higher rats of hospitalization and death could be partly due to medication use.

A study last year from Spain looked at stool samples from about 1800 people, some healthy and some with inflammatory bowel disease (IBD), and assessed the impact of single drug use as well as multiple drug use on the gut microbiome. Out of 40 drug categories analyzed, almost half were associated with significant alterations in the microbiome. These alterations varied depending on the medication, and included microbial changes such as bacterial overgrowth in the upper GI tract, alterations in fatty acid production, increased levels of E. coli and problematic species, and heightened antibiotic resistance within the microbiome. Steroids were linked to high levels of methanogenic bacteria, which is associated with an increased BMI and obesity. Proton pump inhibitors (PPIs), antibiotics, laxatives, and metformin (an oral diabetes medication) resulted in the most significant and concerning microbial alterations.  

Every time you take a pill, you’re potentially causing disruption somewhere in your body, so you need to think about the risk-benefit ratio and what other possibilities exist for remediating the problem. The easiest path – take a pill – is sometimes the most dangerous in terms of downstream effects. For more on medication use and COVID-19, check out my webinar on the topic.

What other information are you providing your patients that have autoimmune disorders during Covid-19?

Judicious use of medication is key – taper steroids down to lowest possible dose, increase the interval between biologic doses, and work with your healthcare provider to find out whether you may be a candidiate for terminating use of your medication/s if your condition has been stable and you have well-controlled symptoms.

My medical practice is different than most GI practices – our focus is on treating IBD without biologics or steroids, so most of our patinets aren’t on these drugs. The Crohn’s & Colitis Foundation of America (CCFA) recommends continuing medication regimens during the pandemic, which I think needs to be taken on a case by case basis. We work very closely with our patients when we take them off biologics to keep them stable – spending lots of time on diet, lifestyle (specifically adequate sleep and stress management), and a high dose prescription probiotic. I’m not recommending that anyone reading this should decide on their own to just stop their medication. Tapering/ending prescription medication needs to be a coordinated effort between you and your doctor.

Other important factors for staying healthy during this time (and any time!) are diet, stress reduction, sleep and exercise. But above all is diet. Eating a nutritious diet is probably the number one way to stay healthy. That’s because our immune system relies on a steady supply of nutrients to do its job. For a starter dose of immune-boosting vitamins, minerals and antioxidants, fill half of your plate with vegetables and fruits every time you eat.

Here are some key nutrients that play a role in immunity, and food sources that contain them:

• Beta-carotene (carrots and apricots) – helps antibodies respond to toxins and foreign substances
• Vitamin C (citrus, strawberries) – increases blood-levels of antibodies
• Vitamin D (eggs, fatty fish, tofu and mushrooms) – affects white blood cells, specifically T cells involved in the immune response. There is no evidence to prove that vitamin D supplements will protect you from coronavirus. However, it’s wise to consider a vitamin D supplement if you have low levels.
• Zinc (beans, nuts, cereal and seafood) – encourages cells in your immune system to grow and differentiate
• Prebiotics (bananas, beans, and fibrous veggies) – feed beneficial gut bacteria
• Fermented foods (kimchi, kefir, and sauerkraut) – they include prebiotic and probiotic bacteria that encourage the growth of beneficial gut bacteria and microbial balance
• Any other thoughts on how people with autoimmune disorders balance using medications and increased risk of contracting Covid-19?

Again, weighing risk of infection with COVID-19 with risk of disease flaring is very important. If you have a history of poorly controlled disease, or experience frequent flare-ups, you might not be a good candidate for discontinuing your medications at this time. But even if you can’t stop your medication, you may be able to decrease the dose – there is a wide range of therapeutic doses that may be effective. Or, if you’re on more than one medication, you may be able to stop one, which could be beneficial. An example of this is what we call “combination therapy” for IBD: biologics plus a class of drugs called thiopurines. The risk of cancer and infection for each is well established, but there’s a significantly increased risk when you use both in combination. Now is a great time to talk to your doctor about the possibility of stopping one.

Beyond my meds, are there lifestyle modifications that I, as an immunocompromised person, could be doing right now to improve my overall state of health?

First, as I discussed earlier, watch your diet. Here are more specifics about why and how to do this:

• Most of your immune system is in the gut, so when your gut is healthy, you tend to be able to fight off infections faster and better. When your gut isn’t healthy (or your microbiome is in a state of dysbiosis), your immune system is weaker and more susceptible
• The Mediterranean style of eating, which means a diet rich in fruits, vegetables, whole grains and healthy fats, found in foods such as fatty fish, nuts and olive oil, has proven beneficial in promoting a healthy gut and a strong immune system. This eating pattern is high in nutrients such as vitamin C, zinc and other antioxidants that have been shown to help reduce inflammation and fight infection. People who followed a Mediterranean type of diet, showed increases in disease-fighting cells such as T cells, according to a 2018 study published in the journal Frontiers in Physiology.
• Limit processed foods, excessive animal protein, and fried foods – all of which are more inflammatory. Instead, focus on a whole food diet.
• Include fermented foods in your daily diet, which help increase the good bacteria in your gut, which, in turn, supports a healthy gut and immune system.

Second, stay active.

• Exercise boosts your immune system by mobilizing your body’s white blood cells and antibodies and lowering your stress hormones.
• A British Journal of Sports Medicine study included 1,002 participants who exercised 5 days/week. When compared to a control group the exercise group had a 50% lower risk for contracting a cold and when they did get sick their symptoms were less severe.

Third, reduce your stress

• There’s a strong link between your immune health and your mental health; when you’re under chronic stress or anxiety, your body produces stress hormones that suppress your immune system.
• Research performed at Carnegie Mellon University found that people who are stressed are more susceptible to developing the common cold.
• In a study published in Proceedings of the National Academy of Sciences, 276 healthy adults were exposed to the cold virus, and then monitored in quarantine for five days. Those who were stressed were more likely to produce cytokines, molecules that trigger inflammation, and were about twice as likely to get sick.
• In addition, people who are stressed are less likely to pay attention to other healthy habits, like eating right and getting enough sleep, which can affect immunity.
• Although you can’t avoid stress in your life, you can adopt strategies to help you manage it better. A 2012 study, published in Annals of Internal Medicine, looked at adults 50 and older and found that those who either did a daily exercise routine or performed mindfulness meditation were less likely to get sick with a respiratory infection than subjects in a control group, and if they did get sick, they missed fewer days of work.

And last but definitely not least, get enough sleep:

• Sleep is another natural immune system booster. Your immune system is like your computer — it needs moments of rest so it doesn’t become overheated. Sleep reboots the system.
• When you’re sleep-deprived your body churns out stress hormones like cortisol to keep you awake and alert, which can suppress your immune system.
• People who get 8 hours of sleep had higher levels of T cells than those who slept less, according to a 2019 study.
• A 2015 study, published in the journal Sleep, found that people who got at least 7 hours of sleep were four times less likely to come down with a cold than those who clocked less than six.

What questions should I ask my doctor if I’m taking an immune suppressing drug?

Some of the most important questions include:

• Is this medication I’m taking absolutely necessary?
• What would happen if I stopped this medication?
• When would I expect worsening of my symptoms – days, weeks, months?
• If I stopped it and had a flare, could I restart it and expect a good result?
• Could I lower the dose?
• Can you give me a tapering schedule for lowering the dose or discontinuing?
• Is there a safer alternative?

Are there any autoimmune conditions that are particularly concerning as they relate to COVID-19?

Some autoimmune diseases are mild by nature and don’t pose any additional risk – Raynaud’s, eczema, etc. Some are typically more severe and have more systemic manifestations, meaning they can affect the whole body, like lupus, or muliple sclerosis. Even within one type, there can be mild disease that’s localized to one organ, or more severe disease with manifestations throughout the body (lupus affecting just skin versus kidneys). People with autoimmune diseases where multiple organs are affected – especially major organs like heart, lungs, and kidneys, are more at risk. In general, whether or not your COVID-19 risk is elevated depends on a series of factors, including but not limited to your disease activity, your medical regimen, your age, and any co-morbidities.

And what about NSAIDs? I have seen a lot on this subject, but I’m not too clear what to think.

FDA is aware of news reports stating that the use of non-steroidal anti-inflammatory drugs (NSAIDs), such as ibuprofen, could worsen coronavirus disease (COVID-19). These news reports followed a March 11, 2020 letter in The Lancet medical journal, which hypothesized that an enzyme (a molecule that aids a biochemical reaction in the body) is increased by NSAIDs and could aggravate COVID-19 symptoms.

At this time, FDA is not aware of scientific evidence connecting the use of NSAIDs, like ibuprofen, with worsening COVID-19 symptoms. The agency is investigating this issue further and will communicate publicly when more information is available. However, all prescription NSAID labels warn: “the pharmacological activity of NSAIDs in reducing inflammation, and possibly fever, may diminish the utility of diagnostic signs in detecting infections.”

Are you recommending people to take probiotics in increased dosages now?

No, because we don’t have convincing scientific evidence yet that high dose probiotics are helpful, and we don’t want to distract people from the scientific evidence supporting what we do know – which is the incredible importance of a plant-centric, healthy diet.

However, there are some exciting studies being conducted in Italy where researchers are using a very high dose prescription strength probiotic (3,000 billion CFU, multiple strains) in hospitalized COVID-19 infected patients to see if they do better in terms of not needing a ventilator, etc. But right now, for the average perosn, focus on diet – fibrous veggies, a wide array of colors in terms of your produce, and some fermented foods like sauerkraut – which is really easy to make at home just using cabbage, water and salt. And don’t forget the easy, go-to staples – one organic apple has about 100 million bacteria!

You had a fascinating blog post last month on how open air and outdoor exposure could help combat the disease. Tell us more about that, and any updates there.

Past studies have highlighted the phenomenon called the “open-air factor” (OAF), defined as the “germicidal constituent in outdoor air that reduces the survival and infectivity of pathogens”, which has been proven to reduce the survival and infectivity of harmful bacteria such as Escherichia coli, Staphylococcus epidermidis, group C streptococcus, and the influenza virus. In fact, open-air therapy was the standard treatment for infectious diseases before antibiotics were introduced. Sunlight levels also provide some protection against pathogens: A 2019 study showed that sunlight levels are inversely correlated with influenza transmission.

Not only does spending time outside protect against viral transmission and reduce the survival of pathogenic microbes, but it also helps support the immune system. Sunlight is our main source of vitamin-D, a vitamin that plays a key role in optimizing our immunity. Additionally, a 2016 study found that separate from its vitamin-D-making capabilities, sunlight actually “energizes” T-cells, the immune cells that fight infection; the low levels of blue light present in the sun’s rays speed up T-cell movement, optimizing their response to pathogens. 

The moral of the story is what we already know – spend time outside everyday!

What are the top foods you would recommend everyone includes in their diet to strengthen their immune system?

My top three tips are:

• Eat a variety of brightly colored fruits and vegetables – eat the rainbow!
• Eat lots of unprocessed fiber from plants and green leafy veggies
• Eat fermented foods daily

General COVID Questions

How are healthcare workers, yourself included, educating themselves on procedure right now?

It’s like being in medical school again. I’m probably reading 10-20 scientific articles a day, plus participating in live webinars to get updates about procedures and policy, looking at guidleines from the various advocacy organizations, CDC updates, getting emails with data from colleagues in other parts of the world. It’s exciting to be learning so much at such a fast pace, but also overwhelming and sometimes I have to disconnect and play a little pickleball (my new obsession since I can’t play squash right now), or go for a hike in the woods, or of course take a break altogether and watch Netflix. Dr Mark Pochaipin in New York – the president of the American College of Gastroenterology (ACG) – is doing an amazing job keeping the gastroenterology community up to date.

How are you cleaning your produce right now?

I rinse my produce with water. Thus far there is no evidence for coronavirus transmission by food. I wash my hands carefully when I come home from the supermarket or farmer’s market. Stomach acid also helps to inactivate pathogens like bacteria and viruses that you may swallow. I’m much more concerned at this point about people who are bleaching their produce or using harmful chemicals that they could be ingesting.

Is there an effective homemade version of sanitizers if I can’t buy one at a store?

Yes! We have a recipe for a simple and effective one on our website here.

Closing Questions

How do you think we could better prepare for the next time?

Focusing more on prevention in terms of making Americans healthy, is definitely where we can do better. Focusing more on diet, weight management through exercise and nutrition, and less on pharmaceutical remedies for things that can be prevented through diet and lifestyle. We are incredibly over-medicated. We need to address that.

And of course, investing in our public health system and realizing that access to basic health care should be a right, not a privilege, especially in a wealthy developed country like ours. With this pandemic we really see the interconnections between all of us. We can’t hide in our comfortable homes and ignore what’s happening in our country – with so many people unable to get adequate food, health care, and education. Inequities in our society affect us all, even those of us who are privileged and powerful.

Now, I don’t want to ask you to predict the future, but what factors do you think we should be paying attention to to appreciate how long this may go on for?

Unfortnately I think this could be a very long haul. We will likely see some very carefully orchestrated reopening by early summer, in pockets around the country, but there is certainly going to be a new normal. Schools might do shifts, or alternate days of on-site and virtual learning. We’ll continue to see advances in telehealth, which is good, but also challenging, and we’re fortunate to have distance learning as an option for our kids. Things are not going to go back to how they were before anytime soon, if ever.

What sources do you suggest folks follow for quality information and recommendations about COVID-19?

My go-to resources are Johns Hopkins, NPR, and the CDC

This Q&A accompanies Dr. Chutkan’s webinar with Our Health Talks, Managing Disease in the COVID-19 Age.