Category: Featured

Exercise Helps a Healthy Microbiome!

We all know that exercise is great for our health, strengthening both the muscles and the heart. Now new research sheds light on another reason why exercise is so beneficial. The benefit of exercise goes beyond just our muscles and cardiovascular system. Exercise also has dramatic impacts of the gut microbiome which, in turn, has a dramatic impact on overall health.

Exercise Impacts the Microbiome

It is amazing to see the myriad of ways of our bodies and our gut and our lifestyle interconnect. Recent research found that the gut microbiome of people who exercise have a much more diverse and dense population of gut bacteria which is ideal compared to their sedentary counterparts. (1) Research from earlier this year explored the impact of exercise with a variety of diets on the gut microbiome. Both lean and obese exercisers displayed a decreased COX-2, an enzyme that promotes inflammation, as well as increased gut integrity. (2) Exercise plays a powerful role in the health of the gut and its microbiome.

Exercise is Best Early

Exercise at an early age also has a profound impact on the gut microbiome. Researchers found that exercise in early life can alter the gut microbiome for the better, supporting healthier brain and metabolic activity. (3) They weren’t able to pinpoint a certain age but the research showed that the microbiome was more plastic when young and exercise has the most long term beneficial impact on the microbiome during this time. This study seems to show the younger the better when it comes to exercise benefitting the gut microbiome over a lifetime.

Let’s look at what exercise is doing to the gut microbiome. 

Bile acids- One of the factors by which exercise causes changes in gut microbiota is the modification of bile acids. Bile acids help break down fats so the body can absorb the necessary lipids from our diets. They also act as anti-microbial agents inhibiting the growth of some bacteria while favoring the growth of others. Several studies have found an inverse relation between the amount of fecal bile acids and physical activity, with the more exercise you get, the less bile acids you have. (4) Rats whose diets were supplemented with bile acid had a change in the microbiota in both diversity and composition. The diet high in bile acids resulted in an increase of the Firmicutes phylum of bacteria that is associated with obesity and decrease of the Bacteroidetes phylum associated with lean metabolic function. (5) This beneficial modification of the bile acids by exercise has a powerful impact on our microbiome for the better.

Short-chain fatty acids- In animal models, it has been observed that exercise increases fecal butyrate levels as well as increasing butyrate-producing bacteria groups (6). More recent research has also found an increase in short chain fatty acids from exercise. (7) Researchers found that moderate exercise increased short chain fatty acids in the gut as much as fiber intake did. This increase in short chain fatty acids fuels the microbiome and shifts the ratio of harmful/beneficial fiber in a positive direction. 

Ig-A-mediated mucosal immunity- IgA is a mucousal immunoglobulin that helps fend off pathogens as well keep the gut inflammation in check. An increase of immunoglobulin A (IgA) production and a reduced number of B and CD4 + T cells have been observed in the gut of animals that performed long-term moderate exercise compared to sedentary mice. (8) The increased levels of intestinal IgA caused by exercise may augment the resistance of exercised mice to intestinal pathogen infections, as well as the resistance to colonization by commensal microbiota, ultimately influencing the composition of the microbiota (9). This increased IgA from exercise positively impacts the gut microbiome. 

Gut transit time- Moderate exercise reduces intestinal transit time which can impact the microbiome. (10) We know that there are microbiota differences between constipated individuals and those that had regular bowel movements. Normalizing transit time is just another way that exercise can impact the gut microbiome for the better.

Exercise is has powerful actions throughout the body and as we’ve seen, powerful actions on the gut microbiome. Exercise positively influences the diversity and density of the gut microbiome as well as increasing the integrity of the gut and decreasing gut inflammation. Exercise early in life even has the power to influence the make-up of the gut microbiota, influencing health throughout a lifetime. So get those little ones exercising early and often and do yourself a favor and exercise with them!

– Dr. Catherine Clinton



(3) early life

(4) Physical activity as a determinant of fecal bile acid levels. Wertheim BC, Martínez ME, Ashbeck EL, Roe DJ, Jacobs ET, Alberts DS, Thompson PA Cancer Epidemiol Biomarkers Prev. 2009 May; 18(5):1591-8.

(5) Bile acid is a host factor that regulates the composition of the cecal microbiota in rats. Islam KB, Fukiya S, Hagio M, Fujii N, Ishizuka S, Ooka T, Ogura Y, Hayashi T, Yokota A Gastroenterology. 2011 Nov; 141(5):1773-81.

(6) Voluntary running exercise alters microbiota composition and increases n-butyrate concentration in the rat cecum. Matsumoto M, Inoue R, Tsukahara T, Ushida K, Chiji H, Matsubara N, Hara H Biosci Biotechnol Biochem. 2008 Feb; 72(2):572-6.


(8) Effect of moderate exercise on IgA levels and lymphocyte count in mouse intestine. Viloria M, Lara-Padilla E, Campos-Rodríguez R, Jarillo-Luna A, Reyna-Garfias H, López-Sánchez P, Rivera-Aguilar V, Salas-Casas A, Berral de la Rosa FJ, García-Latorre E Immunol Invest. 2011; 40(6):640-56.

(9) The bilateral responsiveness between intestinal microbes and IgA. Macpherson AJ, Köller Y, McCoy KD Trends Immunol. 2015 Aug; 36(8):460-70.

(10) Effect of moderate exercise on bowel habit. Oettlé GJ Gut. 1991 Aug; 32(8):941-4.

Viruses Can Keep Us Healthy and Here’s How to Get Yours Working for You!

Did you know that not all viruses are harmful? In fact, many are necessary for our health! We’ve heard a lot in recent years about the importance of a healthy microbiome. I’ve lectured and written many times about the impact that the balance of bacteria in the gut microbiome has on our health. Research has shown the positive influences of good bacteria in the gut on the cardiovascular, immune, neurological, gastrointestinal, and metabolic systems as well as the development in utero and early life. Much of the talk about the microbiome focuses on the bacteria that line the digestive tract but today we’re going to explore a fascinating subset of the microbiome- the virome. The study of viruses and how they impact our health is vital for understanding our own viromes. Let’s delve deeper!

What is the Virome?

Viruses are actually the most abundant biological entity on earth. The number of viruses is staggering and there is much we still don’t know about the virome. While we are still exploring the role of the virome in health, there are some valuable tools that we can take away today to improve our health and the health of our children. When we talk about viruses, we are talking about a few different things. First, there are what we commonly think of as viruses, the RNA and DNA classified viruses that infect our cells and cause the viral symptoms we are familiar with. With common symptoms of a runny nose or cough from an upper respiratory virus or the digestive upset from a stomach virus, these viruses are familiar to all of us. Then there are the more obscure viruses like the viral elements that are embedded in our own DNA and the bacteriophages that infect the bacteria in our microbiome. (1) Recent research into the virome illustrates why these different classes of viruses are important to our overall health. 

How Viruses Make Us Healthy

We are starting to realize the importance that bacteriophages play in our immune systems. Bacteriophages are viruses that infect and kill the bacteria in our individual microbiomes. They do not infect us, but do a wonderful job fighting the bacterial infections that plague us. Each bacteriophage is specific to a certain bacteria, making them a precise antibiotic agent without any of the myriad of side effects that modern day antibiotics cause. (2) Bacteriophage therapy is common in Eastern Europe and is just starting to be used with success in the US. I’ve seen success with some patients using bacteriophages to balance the microbiome in IBD or inflammatory bowel disease like Crohn’s or colitis. Research has consistently shown that bacteriophages play a role in the regulation of the gut microbiome and IBD is characterized as having deranged gut microbiomes. (3) This is an exciting new approach to balancing the microbiome in a time when antibiotic resistance and inflammatory bowel disease continue to rise.

Bacteriophages are not the only virus to help balance the gut microbiome and positively influence our health. In one 2014 study mice were infected with a certain strain of the norovirus after completing a course of antibiotics. (4) Amazingly, the norovirus helped to rebalance the gut microbiome, both the viral and bacterial components of the biome. This balancing influence has never been observed with viruses and it is an exciting discovery. This has been replicated in other studies that show the same balancing of the microbiome by adding a virus to the gut of mice. (5) Recent research has also shown that viruses present in saliva can target harmful bacteria, acting as a line of defense in the immune system. (6) The research is absolutely showing that viruses can have a positive impact on our health.

So How Can We Keep Our Virome Healthy?
Diversity in exposure to microbes is really the key to a healthy virome. Diversity in diet is a cornerstone of maintaining a beneficial virome. (7) We want to eat a large variety of food to get the fiber and phytonutrients needed to maintain the balance of the virome. If you look at traditional diets and look at a food category like tubers, for example, you see these diets included as many as 120 different kinds of tubers. This type of variety is important and while the tuber section at the farm stand or grocery store might not have 120 varieties, we can always find a variety of whole foods to introduce in our diet. Diversity in our environment is also important for exposing yourself to a diversity of microbes that keeps the microbiome well. We need to be getting outside daily as nature is the ultimate source of microbes for a healthy virome. Even opening the windows in your house and getting houseplants in every room can help support a balanced virome.

Dr. Lim from Washington University School of Medicine has done some interesting research with infant twins showing that the development of the infant virome parallels the development of the bacterial microbiome in the gut. (8) This research coupled with the recent studies showing that early introduction of allergenic food and exposure to microbes lowers asthma and allergies can all be seen as another argument for diversity in exposure, especially in early life.

Avoiding things that derange a healthy virome is also an important step in maintaining health. Medications like antibiotics and proton pump inhibitors used to treat excess stomach acid in GERD (PPIs) negatively impact the balance of the virome. Avoiding processed foods and overly sanitized environments is also very important for maintaining wellness. (9) Avoiding these things that disrupt the gut ecology will positively impact the balance of microbes in the digestive tract. We still have a lot to learn about the virome and the microbiome in general, but recent research promises exciting new avenues in medicine and real tools we can use today to improve our health.

– Dr. Catherine Clinton


Alternatives to Antibiotics

First thing, let me say that the advent of antibiotics is one of the biggest miracles of modern medicine. They are an invaluable tool to combat bacterial infections. But… while antibiotics have their spot in our toolbox, we are experiencing an epidemic of antibiotic resistant bugs and chronic diseases associated with their use/overuse. Diet, lifestyle, supplements, and herbs are also valuable tools for fending off bacterial infections without the risks that antibiotics can pose. Be sure to talk to your doctor about whether alternatives to antibiotics are right you and your family.

Why We Should Exercise Caution When Deciding To Use Antibiotics

Antibiotics have been heavily overused. Often, patients with infections which are viral (antibiotics are only effective against bacteria) or would resolve on their own are given antibiotics as a matter of course. One Harvard study published in 2013 determined that 60% of sore throat patients and 73% of acute bronchitis patients were prescribed antibiotics. This even though the textbook answer is that only about 10% of sore throat cases are bacterial and acute bronchitis almost never is. (1) This happens for a number of reasons but it’s usually a combination of the patient’s expectations/demands and a “better safe than sorry” attitude from the doctor. This unnecessary and inappropriate prescription of antibiotics has given rise to the worrisome, drug-resistant superbugs that occasionally make the news. Each year as many as 2 million people in the US become infected with antibiotic resistant bacteria resulting in at least 23,000 deaths and the numbers are rising worldwide. A recent UN meeting about global health in 2016 called for prioritization of this worldwide epidemic of antibiotic resistance. The CDC started a Get Smart campaign to raise awareness about unnecessary and inappropriate antibiotic prescriptions. (2)

Antibiotics also negatively impact the gut microbiome and have been associated with many chronic diseases. The gut microbiome is crucial for immune regulation, digestive health, metabolic maintenance, cardiovascular and neurological health. Many studies have found a connection between antibiotic use in early life and chronic disease in later life. A study out of the University of Minnesota in 2015 found that antibiotic use in infancy increases the risk for certain diseases later in life. (2) The study highlights how the use of antibiotics may eradicate key gut bacteria that help immune cells in the prevention of allergies and how antibiotic-induced changes in the gut microbiota resulted in increased levels of short-chain fatty acids that affect metabolism, increasing obesity risk. This was also a key finding in a recent study out of the University of British Columbia in 2014 where researchers found that different antibiotics killed different strains of gut flora which in turn, resulted in different diseases because of the lost strain. (3) These studies show the importance of a robust and diverse microbiome. Remove or decrease just one strain and the body suffers. Interesting research from the University of Helsinki in 2016 looked at 142 Finnish children, aged 2 to 7 years. Researchers investigated how many courses of antibiotics the children had received in their lifetime and how the use of antibiotics impacted their intestinal microbiota. They found that the more rounds of antibiotics, particularly the class of antibiotics called macrolides such as azithromycin or clarithromycin, a child has in the first two years of life the greater the risk for asthma, obesity and metabolic diseases. (4)

What Are The Other Options?

Keeping the immune system balanced to prevent or prepare for a bacterial infection is the first step to avoiding antibiotics. Plenty of exercise and movement balanced with enough rest and down time are vital for keeping the immune system healthy. A diet rich in fresh fruits and vegetables that includes a rainbow of colors ensures that you are getting the phytonutrients and antioxidants necessary for a strong immune system. Protein is an essential building block for the production of immune cells so getting enough in your diet is crucial. Research has shown that adequate vitamin D3, zinc and probiotics in the diet or through supplements is also a great way to keep immunity up. (5,6,7) Our first line of defense against bacterial infections are the mucous membranes in our nose and mouth/airway and keeping them moist is important so they can effectively defend against germs. Hydration is key to maintaining moisture in those tissues so drinking enough water is essential. It’s also important to incorporate time in nature and stress management tools. Both have been shown to dramatically regulate the immune system. Even with the best intentions and practices we’re bound to get a bacterial infection sometime and then what? Below are six alternatives to antibiotics that are safe for both adults and children:

Propolis– Propolis is a substance that honey bees make with a resin exudate gathered from tree buds or other plant sources. Research has demonstrated its powerful antibiotic properties. (8,9,10,11) Propolis is rich in flavonoids which makes it a powerful antimicrobial agent. Propolis is great for fighting bacteria, viruses, fungi and helping wounds heal. 

Echinacea- Echinacea is a North American cone flower that has been used medicinally for hundreds of years. Echinacea has long been used to fight infections and held a special place in medicine until the advent of modern day antibiotics. Research has confirmed the important antibiotic nature of Echinacea. (12,13)

Garlic- Garlic is a wonderful antibiotic that fends off the harmful bacteria while leaving the beneficial bacteria unharmed. Metabolites are released when the cell wall of garlic is broken that act as a defense against bacteria and viruses. (14, 15)

Elderberry- Elderberry has powerful antimicrobial properties making it a great choice for both bacterial and viral infections. (16) The berries also contain vitamins A and C, and the flavonoids quercetin, anthocyanin and rutin, all of which boost immune function. Elderberry comes in a great tasting liquid syrup form making it an easy option for kids. We put a teaspoon or so in seltzer water and the kids think elderberry sodas are a perfect treat! 

Ginger- Ginger is another plant that has been shown effective against several multidrug resistant bacteria. It comes in a variety of forms from fresh, dried tea, syrups, tinctures and even fermented sodas from ginger bugs which makes it an easy option to find something that works for you. (17)

Usnea- Usnea is a lichen that grows from tree branches in wet climates. The common name for Usnea is Old Man’s Beard because its light green strands resemble a beard. It is hard to pull the immune properties of out of Usnea with tea or capsules so an alcohol extract works best. A recent study from 2016 showed that Usnea was effective for treating several strains of multidrug resistant bacteria. (18)

I love using these natural medicines to treat bacterial as well as viral infections. Nature offers an abundance of medicines without the side effects of prescription antibiotics. While antibiotics may be necessary in certain cases, it is good to have these alternatives to antibiotics on hand. If you suspect you or your child is suffering from a bacterial infection make sure to work with a qualified healthcare practitioner to see if any alternative treatments might be right for you. 

– Dr. Catherine Clinton

1. Michael L. Barnett. Antibiotic Prescribing to Adults With Sore Throat in the United States, 1997-2010. JAMA Internal Medicine, 2013; DOI:10.1001/jamainternmed.2013.11673 


3. Pajau Vangay, Tonya Ward, Jeffrey S. Gerber, Dan Knights. Antibiotics, Pediatric Dysbiosis, and Disease. Cell Host & Microbe, 2015

4. Shannon L. Russell, Matthew J. Gold, Lisa A. Reynolds, Benjamin P. Willing, Pedro Dimitriu, Lisa Thorson, Stephen A. Redpath, Georgia Perona-Wright, Marie-Renée Blanchet, William W. Mohn, B. Brett Finlay, Kelly M. McNagny. Perinatal antibiotic-induced shifts in gut microbiota have differential effects on inflammatory lung diseases. Journal of Allergy and Clinical Immunology, 2014

5. Katri Korpela, Anne Salonen, Lauri J. Virta, Riina A. Kekkonen, Kristoffer Forslund, Peer Bork, Willem M. de Vos. Intestinal microbiome is related to lifetime antibiotic use in Finnish pre-school children. Nature Communications, 2016

6. Anna-Carin Norlin, Susanne Hansen, Emilie Wahren-Borgström, Carl Granert, Linda Björkhem-Bergman, and Peter Bergman Vitamin D3 Supplementation and Antibiotic Consumption – Results from a Prospective, Observational Study at an Immune-Deficiency Unit in Sweden. PLoS One. 2016; 11(9): e0163451.

7. John K Crane, Jackie E Broome, Ryan M Reddinger, and Benjamin B Werth. Zinc protects against shiga-toxigenic Escherichia coli by acting on host tissues as well as on bacteria. BMC Microbiol. 2014; 14: 145.

8. Gregor Reid, BSc (Hons) PhD MBA. Probiotics to Prevent the Need For, and Augment the Use Of, Antibiotics Can J Infect Dis Med Microbiol. 2006 Sep-Oct; 17(5): 291–295.

9. Al-Waili N, Al-Ghamdi A, Ansari MJ, Al-Attal Y, Salom K. Synergistic effects of honey and propolis toward drug multi-resistant Staphylococcus aureus, Escherichia coli and Candida albicans isolates in single and polymicrobial cultures. Int J Med Sci. 2012;9(9):793-800. doi: 10.7150/ijms.4722. 

10. Cushnie TP, Lamb AJ. Antimicrobial activity of flavonoids. Int J Antimicrob Agents.Int J Antimicrob Agents. 2005 Nov;26(5):343-56.

11. Qiao Z, Chen R. Isolation and identification of antibiotic constituents of propolis from Henan. Zhongguo Zhong Yao Za Zhi. 1991 Aug;16(8):481-2, 512.

12. Grange, J. M. and Davey, R. W. “Antibacterial properties of propolis (bee glue).” J R.Soc Med 1990;83:159-160.

13. Sharma SM, Anderson M, Schoop SR, Hudson JB. Bactericidal and anti-inflammatory properties of a standardized Echinacea extract (Echinaforce): dual actions against respiratory bacteria. Phytomedicine. 2010 Jul;17(8-9):563-8.

14. Sullivan AM1, Laba JG, Moore JA, Lee TD. Echinacea-induced macrophage activation. Immunopharmacol Immunotoxicol. 2008;30(3):553-74. 

15. Saha SK, Saha S, Hossain MA, Paul SK. In vitro assessment of antibacterial effect of garlic (allium sativum) extracts on pseudomonas aeruginosa. Mymensingh Med J. 2015 Apr;24(2):222-32.

16. Saha S, Saha SK, Hossain MA, Paul SK, Gomes RR, Imtiaz M, Islam MM, Nahar H, Begum SA, Mirza TT. Anti-Bacterial effect of Aqueous Garlic Extract (AGE) determined by Disc Diffusion Method against Escherichia coli. Mymensingh Med J. 2016 Jan;25(1):23-6.

17. Salehzadeh A, Asadpour L, Naeemi AS, Houshmand E. Antimicrobial activity of methanolic extracts of Sambucus ebulus and Urtica dioica against clinical isolates of methicillin resistant Staphylococcus aureus. Afr J Tradit Complement Altern Med. 2014 Aug 23;11(5):38-40. 

18. Revati S, Bipin C, Chitra PB, Minakshi B. In vitro antibacterial activity of seven Indian spices against high level gentamicin resistant strains of enterococci. Arch Med Sci. 2015 Aug 12;11(4):863-8. 

19. Tozatti MG, Ferreira DS, Flauzino LG, Moraes Tda S, Martins CH, Groppo M, Andrade e Silva ML, Januário AH, Pauletti PM, Cunhaa WR. Activity of the Lichen Usnea steineri and its Major Metabolites against Gram-positive, Multidrug-resistant Bacteria. Nat Prod Commun. 2016 Apr;11(4):493-6.