Aromatherapy: More than meets the Nose?

Keypoints: This post will review the basic science of smell and summarize research supporting that certain aromas may trigger specific neurotransmitters that effect positive moods and reduce the sensation of pain.

Language is colored with idiomatic expressions that refer to the senses, including the sense of smell.  We commonly use our senses when we are conveying a higher level of understanding, and smell is no exception.  A sample paragraph with no reference to actual events is below:  

The politician came out smelling like a rose, even though he was involved in a scandal.  I am not convinced and still think something smells fishy.  I can smell a rat.  Well, I will review the hearing and see if it passes my smell test.  It is getting late.  Tomorrow, I will wake up early and smell the coffee (real coffee and about this whole situation)

smell like a rose:  to come out successful in the end or escape ill-repute

smell fishy: suspicious

smell a rat: to sense something suspicious about a person or thing

smell test: to test the credibility of something usually using common sense.

smell the coffee: face reality and stop fooling oneself.


Our world is experienced through our senses.  We learn early that we have five senses, but never imagine the amount of overlap there is.  It is only when we get sick that we realize that our senses enhance our entire experience, including having your favorite food while you have a “stuffy nose,” leading to chemotactic responses – drawing us closer with a pleasant scent or repelling us with a noisome scent.  Indeed smell is one of the most primitive of our senses.

The reaction to smell is dichotomous, as personal as it is universal. Though, I imagine that most people walking into a French bakery might begin to smell the aroma of freshly baked bread and instantly know why they are there or even think of happy thoughts.  Food that is putrid can repel someone away from a possibly dangerous situation.  Our instinctual curiosity drives us to check the odors of milk before we drink it, day old food before we eat it, and half-worn socks to see if they can be used another time when the clothes need to be laundered and you are tired and don’t want to (and other crazy things that you have done).

I remember a friend told me a story about being on a train and smelling a passenger with whom he shared a train cabin, while backpacking through Europe.  He occasionally noted whiffs of a putrid body odor coming from the passenger – only to realize the dreaded reality that it was actually coming from him! 

Aroma can also evoke specific memories. I remember when I traveled to Africa for the first time. I wanted to bring an oil to use that smelled fresh. I was recommended Egyptian musk.  Africa was an incredible time and each day I used the oil. After that experience, every time I either wear Egyptian musk or smell it on someone else, those memories of Africa pour out.

An odor can trigger memories and feelings. But how does our body detect an odor and how does it interact with our brain to induce memories. Are there any positive therapeutic effects from the use of essential oils ?  Is there any scientific validity to the claims of aromatherapy – or is it all pseudoscience?

Essential oils have been used for thousands of years, either as topical applications or for their aromas. An essential oil, as defined by the International Standards Organization (ISO) is a product obtained from a plant source, either by a process of distillation or by mechanical measures.

The Neurobiology of Smell

Our brain processes smells in a way not so different from other organisms, demonstrative of the fact that olfactory sense is a tool for survival.  Smell can draw us toward a safe source or repel us away from a dangerous one.  Our prefrontal cortex stores memories of smells, which can affect our emotional response and direct a behavior.   

Even a primitive form of smell can be seen in bacteria and other single-celled organisms and how they register various chemical gradients in their habitats, known as chemotaxis.   And even bacteria show some degree of “learning” or memory from the experience.   The overarching principal is that an organism decides from how it interacts with environment through its various senses whether something is safe or harmful.

What happens when someone smells something?  The nose comes across odorant molecules (not usually one type of molecule – e,g, smell of chocolate is a blend of 600 chemicals).  Our brains signal to us what it is smelling usually cued in by the eyes, as it recalls the memories of the expected odor when triggered by sight and other cues.  That is to say, that smells are usually referenced from prior experiences.  The response to odorant molecules are affected by timing, whether they are mixed with other odors and wind currents.  Certainly, if someone has rhinitis (nasal membrane inflammation) from allergies or a viral infection, the scent may be blunted.

A sniff from the nose directs the air and various molecules carried in, or odorants, to come into exposure with olfactory sensing neurons (OSN).  The circulation of air can be retronasal (from the mouth) or orthonasal (directly from air to nose).  Each neuron expresses a specific gene (1000 types in rodents, 350 in humans, 100 in fish) and are scattered in the olfactory epithelial tissue.


Source:  Patrick J. Lynch, medical illustrator

Aromatherapy: The Research Base

Let’s start with the fact that research on odors is fraught with study design problems and challenges in drawing conclusions. It sounds appealing and intuitive to think that one’s mood can suddenly improve or that one can benefit simply by smelling a unique essential oil for an occasion. However, what differentiates a substance with anecdotal or individual benefits to one that has measured and observed benefits is the gold standard study design, the double-blind, randomized, placebo-controlled trial. As of 2017, there were a total of 549 original and review articles on aromatherapy published in 287 peer-reviewed journals with a steady increase in submissions yearly. A search on pubmed as of October 16, 2019 revealed 1,366 published studies with the key word “aromatherapy”.  Most of the research on aromatherapy hasn’t met and may never be able to meet the rigors of scientific studies – and maybe we actually need less aromatherapy research.

There are several inherent problems as well as entry points for bias with a study design in aromatherapy research. First, essential oils are not easy to conceal – the odor declares itself (unlike a white, odorless pill). Many people are aware of common aromas; an odorless oil may not be the best placebo either. Therefore, it would be difficult to separate out how much the patient’s knowledge of the essential oil is affecting the result. Second is the research dilemma of determining the extent the odor of an essential oil triggers a response, such as calmer state or livelier mood, and what extent is it from the person’s reaction and memory recall to that odor. The active chemical ingredient is producing an effect by being sensed – physiologically – but the brain’s reaction is inherently tied in with it. Third, along this same direction, is many of the tools to assess activity are qualitative measures (trying to be quantitative) of improved state, such as Likert scales, which makes it challenging to draw conclusions on reproduceable results; objective measures of effect may also be more challenging to rely on. This is in contradistinction to a glucose lowering medication, in which a response is assessed by measurable levels (glucose or HbA1c) compared with an inert substance.

Another question is does it even matter whether the effect originates in our brain, since the brain has an active and powerful control of our physical responses anyways and most certainly exerts an effect on other organs (take the example of Takotsubo Cardiomyopathy).  Thus, a positive response to a pleasant odor in one’s repertoire may lessen cortisol, epinephrine and norepinephrine release to produce a more relaxed state.  Sensations such as pain require both the sensory trigger and the brain’s neurotransmitter response to modulate the severity — so a direction toward greater relaxation could conceivably reduce the pain experience.  Though, this mind over matter stunt is purely natural and authentic not greater (though great enough!).

Aromatherapy for Pain, Happy Thoughts and Cognitive function

There are multiple studies in this area. One randomized controlled study by Soden et al. looked at four weeks of aromatherapy plus massage compared to massage alone in a hospice setting. Forty-two patients were randomly assigned to these two groups: one with lavender essential oil and massage and another with inert carrier oil and massage and other groups with inert oil or no intervention. The results did not show any benefit in pain, anxiety and depression scores (multiple used) in either aromatherapy or massage, though sleep scores were significant improved in the massage groups. This was a negative study (no benefit) for lavender oil.

A recent study by Kouzuki et al. published in October 2, 2019 in Psychogeriatrics evaluated the effect of aroma oil (blend of lavender and sweet orange) on cognitive function. This was a small study with only 35 patients (10 with Alzheimer’s disease and 25 with mild cognitive impairment) enrolled and analyzed. Furthermore, the groups were divided into 0.1%, 0.5% and 1% aroma bath salts. The study was conducted over 24 weeks and various dementia scales were checked 4 weeks before and 4 weeks after the intervention. There were no significant differences – another negative study.

There was a positive (slight) study with the use of essential oils to improve sleep for patients in cardiac rehabilitation in a recent article out of Journal of Alternative Complementary Medicine. Forty-two participants were studied, using cotton balls infused with lavender, bergamot and ylang ylang compared to placebo. There was a crossover after five days. There was no difference in duration of sleep or sleep efficiency, though sleep quality was reported as improved by those given the essential oils.

On the basic science side, Komiya et al. in 2006 measured the serotonin and dopamine activities in mice after exposing them to lemon oil, rose and lavender. Lemon oil was found to have the strongest anti-stress effect. With various medications, they deduced that the anti-stress effect of lemon oil was related to the suppression of dopamine activity related to enhanced serotonergic neurons. In a nutshell, the lemon oil caused the mice to have less stress through a pathway that has been shown in humans to relate to stress-reduction.

Karan,NB. studied the influence of lavender oil inhalation on vital signs and anxiety in a recent article published in September 2019. One hundred twenty-six patients undergoing wisdom tooth removal were assigned to lavender oil or control. Various tests for anxiety were assessed and vital signs were noted before, during, and after the operation. There were changes in blood pressure observed in the lavender oil group post-operatively (p<0.05). Pre-operative anxiety levels were comparable in both groups. There was patient satisfaction with the lavender oils but there was no mention in improved anxiety scores.

Aromatherapy for Perennial allergic rhinitis (PAR)

A 2016 study from Evidence Based Complementary Alternative Medicine by Seo Choi and Kyungsook Park investigated whether the use of inhaled aromatherapy containing sandalwood, geranium, and almond oil would help allergic rhinitis symptoms. This was a randomized, double-blinded study. In the experimental group after an intervention of 7 days, the Total Nasal Symptom Score (TNSS) suggested significant improvement, especially in obstruction (“stuffiness”) symptoms, where a significant p-value was reached (p=0.031). After review of this article, I wouldn’t say that this was a profound practice-changing result, though definitely fulfills an alternative option.

Aromatherapy for labor pain

An August 2019 article by Chen SF et al. in Women Birth entitled Labour pain control by aromatherapy: A meta-analysis of randomized controlled trials reviewed a total of 17 trials on this very question. Specifically, aromatherapy reduced pain during labor into the active phases, with a trend of reducing the time in the second stage (or active pushing). As a metanalysis, there was some variability in the blinding, but most were single-blinded or unclear. These studies were performed worldwide, including countries such as Thailand, Iran, Egypt, Pakistan, India, Korea and Italy. Some of the oils used were jasmine, lavender, salvia, rose, sweet almond and mixed essential oils. I am not sure in the United States whether most women in labor would favor this over an epidural or other pain regimen. But why not add some essential oil to the experience?

Source: Metanalysis **see transition phase where studies favor aromatherapy.

Phytoncides on natural killer cell function
Phytoncides are released by conifers and have added benefit to the practice of “Forest Bathing” or Shinrin-yoku.  Q Li and other researchers demonstrated an increased NK cell, an important cell in our innate immunity with anti-cancer activity, lasting for several days, when 12 male subjects experienced a day in a forest park.  They walked for approximately 4 hours and had their blood and urine assessed for levels of NK and its products to show activity (perforin, granulysin and granzymes) T cells, and adrenaline concentrations.  The researchers confirmed that phytoncides were present in the air of the forest.  There were increased levels of NK cells and decreased CD4(+) T cells, which lasted even 7 days after the trip, when reassessed.   Q Li and others did an interesting article to see if this benefit could be “bottled up”. They assessed natural killer (NK) cell activity after twelve healthy male (not sure if same) subjects stayed in an urban hotel for 3 nights and were subjected to vaporized aromatic volatile substances (phytonsides) compared to controls.  Afterwards, their blood samples were checked for NK activity.  In his book, Into the Forest, Q Li wrote of an increase in NK activity from 17% to 26.5% and NK cell number from 440 to 661, both of these approximately a 50% increase after subjects went on a three day, two night hike in the forest.

But the question that remains is whether the process of escaping the stressors of the city or the benefits of a relaxing scent was responsible for these changes or whether it was a signature effect of these phytoncides. This is an inherent challenge in trying to discern from where the response came – internal or external.  We can all agree that a calming walk hike in the park with healthy, conditioning exercise, comes with many health benefits.  In fact, similar findings of increased NK activity have been seen with exercise as well.


Aromatherapy is an exciting area to gain an understanding of the neurophysiology of the olfactory sense and how neurotransmitters are actuated by odors. At this time, there is no conclusive evidence that aromatherapy offers a significant advantage in improving health and treating depression. But anyone who uses essential oils would declare that “it works for me”.  And maybe that’s good enough. If someone could avoid taking an anxiety or pain pill and use their aroma kit instead, that is a good thing. Likely, big pharma will never attempt to mass-market essential oil combinations, because of lack of research and significant clinical effect. People will order their essential oil kits from a aroma therapy dealer and diffuse or apply these for various issues – and no harm will likely be done. If I could bottle up fresh bread, I would probably be very relaxed from it*.
*I would avoid vaping any essential oil, given the spate of lipoid pneumonia cases, and then it would be more hazardous than helpful.


For further reading:  Learning to Smell, Olfactory Perception from Neurobiology to Behavior.  Donald Wilson and Richard Stevenson.



COVID-19: Tips to Understanding the (Next) Pandemic

An Infectious Diseases Specialist Perspective for Planning for the Next Pandemic


The Emergence of the novel Coronavirus 

The caseload of those infected with COVID-19 continues to ascend in an exponential manner in China; with spread mainly with those traveling from the outbreak zone to multiple neighboring and more distant countries, including Germany, France, Italy, Iran, Canada and the United States.

What began in an animal marketplace in the bustling city of 11 million in Wuhan, China, has developed into 75,129 cases predominantly in Wuhan and other parts of Hubei province. Public transportation in 17 populous cities in China has been suspended, as the Chinese government grapples with trying to contain the illness.

The first case of COVID-19 was reported on December 31st, after a person developed symptoms three weeks earlier (December 8th), along with 27 other cases (suspected) over the course of a few weeks.  COVID-19 has now approached pandemic proportions.   All of this is happening during one of the busiest times in China, the Lunar New Year.



Infection Characteristics: A Review of Epidemiology

In order to understand the gravity of the novel coronavirus, it is important to define some epidemiology terms:  attack rate and mortality rate.  The attack rate represents the number of people who acquire an illness divided by the number of those at risk.  The mortality rate is the number of those that have died from the infection divided by the amount of those infected.

Even when a disease has a lower mortality rate, if it has a high attack rate, it can make a severe impact.  The seasonal flu has an estimated attack rate of 10-20%.  This means about one-fifth of the US population may contract influenza during the season!  During the current flu season, the CDC estimates that there have been up to 21 million flu illnesses in the United States, with up to 10 million flu medical visits, 250,000 flu hospitalizations and up to 20,000 deaths related to the flu.

With the amount of cases of seasonal influenza, the mortality rate is around 0.1% (9 cases/100,000).  Thusfar, with the 75,129 cases reported of the COVID-19, there were 2,007 reported deaths (mostly in Wuhan) making the estimated mortality rate 2.6%. This is expected to change, as more cases are identified.  If the attack rate of COVID-19 is similar to influenza, it will have a significant impact across the globe if it is not contained. Diseases with menacingly high mortality rates, such as SARS (10%), Avian flu (59%), and Ebola (50-90%), have lower attack rates, meaning they were not able to affect as many.

What’s particularly more concerning is the amount of severe cases reported, which, if the number is accurate, a rate of 21% of those infected with COVID-19 have a more severe infection.  Though, most likely these cases are among the highest risk populations for severe disease, the very old and those with chronic diseases.

Another thing to keep in mind: When epidemiologists determine the above rates, they must ensure an accurate numerator and denominator.  Oftentimes, the first cases that are identified are the more severe cases – making the estimated mortality rate higher than it may actually be.   When you tally up the cases of milder diseases, your denominator increases, and the mortality rate consequently decreases.

An illness that can cause mortality and be spread easily requires preparation and containment strategies.


Was the rapidity of this process predictable?

The first case of COVID-19 was believed to have been acquired at a market in Wuhan – and was reported as a novel infection on December 28th.  There were 27 other people that were being evaluated for viral pneumonia during that time.  One day following, a report of a family cluster of six patients who flew from Shenzhen to Wuhan on December 29, 2019, started presenting with influenza like symptoms on January 1, 2020.  None of the family members had contact with markets or animals in Wuhan.  This suggests that they were exposed to secondary cases (i.e. person-to-person) by the time that the primary case was identified as having the novel coronavirus.

Given that this disease emerged during the flu season, it is not unusual that it took some time to differentiate this from the usual viral infections. The usual “shotgun” gene sequencing tests were used including respiratory viral panels.  Samples were sent for further methods to identify it as a novel coronavirus, similar to those of bat origin.

The epidemic was already well into phase 4 sustained human transmission by the time it was identified.  Given that respiratory viruses, such as influenza, respiratory syncytial virus (RSV) and coronaviruses are transmitted by respiratory droplets as little as 10 microns (micrometers), the diseases can be easily transmitted with casual contact, shaking hands, or touching contaminated surfaces or objects (fomites).  Remember these droplets can get passed not only from the secretions from sneezing or coughing, but also saliva from talking.

Any respiratory disease has the capabilities of exponential spread over a short period.  


What can one do to protect themselves from this scourge?

A simple surgical mask, when worn correctly (sealed well around the nose), is probably sufficient to prevent particles larger than 5 microns from entering the mask.  Since respiratory droplets are larger than this size, risk of transmission is expected to be low.  Although an N95 mask offers greater protection for very small particles (0.3 microns), it is likely unnecessary to prevent transmission of COVID-19. Nevertheless, until the dynamics of transmission are understood better, the CDC recommends healthcare workers to use N95 masks. As with SARS, an important risk group for acquiring the disease is healthcare workers.

The average amount of people infected per person is a little higher than influenza (estimated 1.5-4 vs. 1.5-2.5), suggesting there may be some airborne droplet spread. Though, in contradistinction with measles, which is associated with airborne droplet transmission and can be as high as 20 people, it is likely that COVID-19 is mostly transmitted by larger respiratory droplets.

Another important recommendation is that someone who suspects or is suspected of having the infection should comply with using a mask and washing hands after touching his/her face.

Do we need to stock up and “hunker down”?

Preparation for an apocalypse is a common theme in many popular movies and streaming series.  While COVID-19 is expected to make a significant wave of disease throughout the world – which is what I gather when I see the case reports double in a day – it is unlikely that it is going to have a major impact on most of our lives. It is always sad to hear of people who develop complications or die from this infection – and one excess death from this infection is one too many. Rather than the infection, fear and panic is likely to have a greater impact on order and stability.

The containment measures seem to have made some progress on reducing new cases spread outside of Wuhan and Hubei province. Though, from what we learned with with the recent infections in South Korea, Italy and Iran, it can change in a day.

There is always a possibility that the virus may transform as it is spreads from human to human – potentially becoming more virulent.  If that were to occur, the dynamics of the attack rate would likely change.  I don’t expect that we will see this with COVID-19.

As for now, my recommendation would be to keep informed of the disease rates while reading the news or listening to the radio.  These rates are constantly being updated throughout the day.  Staying glued to this information is likely not beneficial and may be hazardous to your mental health – increasing fear and panic.

Seasonal influenza has made a greater impact and your likelihood of getting it is much greater too. So if you still haven’t been vaccinated, it is never too late.


Wuhan Coronavirus: An Emerging Global Pandemic?

I was recently featured on KGW regarding risk factors for Coronavirus, after a Portland women and her family were quarantines aboard a cruise ship for 2 weeks. She was essentially asymptomatic.

Patient Education: Making Sleep a Health Priority

Get the best out of your sleep

Good sleep is a necessity for the healthy functioning of the mind and body.  It is also one of the things that we can forcibly deprive ourselves.  Ideally, we spend one-third of our lives asleep.  Improving your sleep quality can be the first step toward stress resilience and  healthy decisions.

Could you imagine sleeping for 4 hours, then waking up to go to the gym to exercise, then going to work, and taking an extra cup of coffee to stay up?! If this happens to you, wouldn’t you skip the gym and maybe skip preparing a healthy meal? Without sleep, the brain has a lower threshold to develop stress, anger and impatience.  Driving a car after not sleeping well the night before is equivalent to driving under the influence of alcohol.  The system doesn’t just recalibrate the sleep deficit by sleeping in on a Saturday morning.

Sleep affects more than just the neurologic system.  Many first-time parents probably remember getting up at night because of a crying baby.  Most people recognize that sleep reduces memory and concentration and impairs judgement, but sleep also reduces the immune system, leads to weight gain and increases the risk of high blood pressure and stroke.  The endocrine, immunologic and vascular systems are regulated by sleep.

Here is a list of tips to ensure ideal sleep:

  1. Tone down technology: Silence your cellphones and other technology and put them in a different room at a set time each evening, preferably at least 2 hours before bedtime.  The screen lights can inhibit the production of melatonin, which would otherwise prepare you for sleep.
  2. Preparation: Provide yourself a 30-60 minute of winding down before lights out. Limit reading time to 20-30 minutes.
  3. Make sleep a routine: Go to bed and wake up at consistent times.  Most of the time, you will sleep for 6-8 hours naturally.  With a natural routine, you will very likely not need an alarm clock.  If you do use it, stop it and get up – don’t hit snooze 5 times.
  4. Your bed, the slumber throne. Limit activities to sex and sleep.  Watching TV, eating, working on the computer may affect your body’s ability to rest in bed.
  5. Avoid medicating to sleep: Medications to sleep should be avoided or limited to a low dose of melatonin (2-4mg nightly).  Although the medications may sometimes “work”, they come with side effects and, moreover, are not addressing the source of the problem.  The last thing you want to do is develop dependence on alcohol, benzodiazepines or ambien, etc.  and then can’t sleep without it.  As for the other side of things, avoid any intake of caffeine after noon hours.  Avoid any stimulant medications, e.g. albuterol inhalers, immediately prior to sleeping.  One interesting association of sleep apnea is the patient who drinks high levels of caffeine during the day and then takes a sleeping medication at night.
  6. Environment: Keep sleeping area dimly lit or dark.  Ambient noise should be at a minute, though white noise is acceptable.  Temperature should be on the lower side, between 60-67 degrees F.
  7. Trouble-shoot for the future: If you are having problems sleeping at night and find yourself tossing and turning, thinking too much or waiting until that magic click to start, limit time in bed to about 15-20 minutes. There is usually a reason that this has happened and it is up to you to brainstorm it.  You can sit in your chair to begin to rest, meditate and then return to your bed to sleep.  The next day, think why this happened:  It could have been that maybe you exercised too close to bedtime, took too warm of a shower before sleeping, saw a stimulating program on TV, or tried to squeeze some work on the computer too close to bedtime.

If you still have trouble sleeping after following this checklist, you should consider being evaluated for sleep apnea or other conditions (parasomnias) associated with sleeping, such as restless legs, etc.

sleep man on desk

COVID-19: Can a novel coronavirus epidemic be contained?

A wave of influenza-like illness caused by a novel Coronavirus, now referred to as COVID-19 by the WHO, has swept through a populous area of China. Since December 31, 2019, there have been more than 830 people infected with at least 26 deaths (as of January 23rd, 2020).  Chinese authorities have placed Wuhan, a city of 11 million in the Hubei province, on lock down, or quarantine, canceling flights and not allowing public transportation into or out of the region.  This comes amid the busiest travel season in China, the Chinese New Year on January 25th.  During this time, it is projected that there will be 2.5 billion trips by land, 356 million by rail, 58 million by plane and another 43 million by sea.

The current caseload is 75,129 cases with 2,007 deaths. The majority of cases are confined to Wuhan. Singapore has reported 77 cases, Thailand has confirmed 35 cases, and an unfortunate cruise ship Diamond Princess has 454 cases confirmed. Now how’s that for spoiling vacation plans!

Expect that anytime respiratory viruses (more easily transmissible) emerge in a populous city, there will be a high caseload.  Cases have already been confirmed in other parts of China, including Beijing, Shanghai, Macau and Hong Kong and now 26 countries in all. In the month. countries outside of China, including Japan, South Korea, Thailand and Tawain, Singapore and Vietnam have confirmed cases. On January 21st, the first case of COVID-19 was confirmed in Everett, Washington, after a traveler to Wuhan arrived in Seattle-Tacoma airport on January 17th and presented a few days later.  As of Thursday, a second and third case were being evaluated in Los Angeles and Texas. As of February 18, after a cruise ship carrying passengers with disease was quarantined off in a Japanese harbor, 14 US passengers became infected, and adding to 15 US cases makes 29 US cases.

Wuhan virus map 11.1579841262468

What are Coronaviruses?

Coronaviruses (CoV) are zoonotic RNA viruses which cause infections in a variety of animals including pigs, cows, chickens, cows, bats and humans.  It is the virus’s infection of bats from which likely was the source of severe acute respiratory syndrome (SARS-CoV) and Middle Eastern Respiratory Syndrome (MERS-CoV).  Viruses are typically host and tissue specific.  Though, a favorable mutation can cause a virus to be able to jump from animal to human and be transmitted from human to human.

While CoV generally causes mild respiratory infections overlapping the flu season, their usual behavior diverged with SARS-CoV.  From the outbreak of 2002-2003, there were a total of 8098 cases with 774 deaths, amounting to a mortality rate of 9% – even towards 50% in those older than 60.  Fortunately SARS wasn’t as easily transmissible as other respiratory viruses.

How did such a disease severity occur?  It likely relates to the effects of two types of damage: the damage caused directly by the virus infecting cells within the lining of the lungs and the damage caused by components of the immune system, such as cytokines. Some viruses can induce a greater inflammatory response and lead to a more severe presentation.

MERS-CoV was likely transmitted from its natural host camels, functioning as an intermediate host between bats and humans.  In one report in 2017, of the 660 cases of MERS in Saudi Arabia, 42% had contact with camels.  The mortality rate of this infection is approximately 30%, with the elderly and those with pre-existing illnesses at the highest risk.

The COVID-19 has had the greatest impact on the elderly (>60) and those with comorbid conditions, similar to the other emerged coronaviruses.  In a case series of 99 initial Wuhan cases, the average age was closer to 58, >60% were men and the calculated mortality rate was 4%. There are some unanswered questions about why the calculated mortality rate was higher than what it now appears to be – around 2.6%, much lower than SARS and MERS.  Whether there were unknown pre-existing conditions or whether the air pollution of Wuhan could have increases risk for more severe disease remains unanswered. For instance, in Wuhan the levels of particular matter 2.5 (very small particles 2.5 microns) are sometimes several times greater than the cutoff of what is considered a harmful level. Studies have indicated an increase risk of more severe presentations of viral infections in the setting of pollution.

Although there are no treatments or recognized vaccinations for this emerging coronavirus, Wuhan-based scientists have already determined the genetic sequence of 2019-nCoV, and Chinese health officials have released this information to the public.  Scientists are beginning to work toward determining a feasible future vaccine.

What is being done to prevent cases in the United States?

As a method of containing the outbreak, the CDC is screening passengers entering into the United States from Wuhan for signs of respiratory illness.  Also, the flights from Wuhan have been routed to several U.S. airports for screening, including Los Angeles’s and San Francisco’s International Airports, New York’s JFK airport,  Chicago’s O’Hare, and Atlanta’s Hartsfield-Jackson airport. Multiple quarantine centers for those returning from China have been approved and are in operation.

Presently, the CDC has defined those at highest risk for COVID-19 as Patients Under Investigation (PUI) to have these criteria:

How much should the general US population worry?

The disease has been traced to animal markets in Wuhan and has spread over the course of three weeks to include imported cases in neighboring and distant countries.  So far, there has been no local spread in the United States.  With heightened awareness and screening, it is with hope that the disease will not be as heavily transmitted to the general population.  Combined with a lower mortality rate than the other emerged coronavirus infections, I think the general population should not need to worry about this infection.  At this point, those with higher risk, including the elderly and those with health problems, are much more likely to be infected by influenza than COVID-19.

Do masks protect from this infection?

Respiratory droplets from sneezing or coughing are well contained by masks.  Given that coronaviruses are transmitted this way, it is likely that anyone infected with COVID-19 would prevent spread by wearing a mask.  I don’t think that everyone should get a mask at this point.  It is also important to mention that respiratory droplets containing virus can contaminate objects and the hands and then simply be ingested and cause infection.  As with any viral infection, good hand-washing and social distancing an are important part of prevention.

It is certainly too early to tell how many people will be affected by this virus – and what impact it will have.  Fortunately disease is still mostly contained within the outbreak area. As the caseload increased in other countries, a tipping point may be reached, where local spread occurs.

Sometimes mortality rates can change during an epidemic, if subsequent mutations confer greater virulence (potency).  It is possible that this virus spread at a low rate not to re-emerge, if enough are infected. It is no coincidence that the virus emerged from a populous area where livestock and human meet – an animal market in Wuhan, a city in China of 11 million.

Wuhan Coronavirus:  Tips to Understanding the (Next) Pandemic



Ahmed, Anwar E. 2017.   The Predictors of 3- and 30-day Mortality in MERS-CoV patients. BMC Infec Dis. 2017; 17:615.

Fehr A, Perlman S. 2015.  Coronaviruses: An Overview of Their Replication and Pathogenesis.  Methods Mol Biol. 2017; 1282: 1-23



Summary: The 2019-2020 influenza season is off to an early start. Interestingly, the majority of cases have been associated with influenza B. With an increase in influenza-like illness identified in these last few weeks, it is possible that this season could be similar or worse than the 2017-2018 season.  Brace yourselves for an active season.


Welcome to the new year 2020.  As expected, at around the 46-48 week of 2019, we exceed the baseline of 2.5% of influenza-like illness (ILI).  The percentage of ILI has soared in the last few weeks compared to what it was last season.   Presently in United States, the seasonal influenza epidemic is widespread.  This season has been unique from others in the percentage of cases attributable to influenza B followed by H1N1.  The Centers of Disease Control (CDC) estimates approximately 64% of the flu cases are from influenza B.  Usually, influenza B cases pick up towards the second half of the season.




From the FLUVIEW CDC site (above), there has been a very high level of influenza-like activity.  Influenza has a high attack rate, affecting 5-10% of the adult population and 20-30% of the population of children.  High ILI activity suggests that there will be a high rate of transmission in those affected areas.  

The current activity in this flu season is already trending toward a higher caseload than 2017, with a steeper and earlier curve than in 2017-2018 (see red line in the graph below).  That season was the most severe season in recent years. By April 2018, more than 34 million people had the flu, about 1 million were hospitalized, and approximately 54,000 people died.    These deaths are usually from a secondary bacterial infection, complications of respiratory distress, or a cardiovascular complication attributable to influenza.  Although we have yet to see the peak of this season, should the percentage of ILI exceed those of 2017-2018, it is possible that this season will see a record number of influenza-attributable hospitalizations and deaths. 

ili curve.gif

Update 1/12/2019:

The curve has come down from its peak at about week 52.  It is not clear yet and it is still fairly early in the season for the possibility of another increase.  What also is important to mention is that the rate of laboratory-confirmed influenza hospitalizations is less than where cases were for 2017-18 at the similar time.  Though, it is still too early to tell.

The good news is that if you have received the vaccine, you are likely to either be protected from the disease or get a milder case.  The CDC estimates the average efficacy of influenza vaccination ranges from 40 and 60%.  Other than getting a milder infection, the vaccine reduced the risk of the influenza-associated diseases, such as heart failure, respiratory failure, and secondary pneumonia.  Predictions for the 2019-2020 influenza vaccination are forthcoming.  The components for the H1N1 vaccine and usually for influenza B are more effective than the H3N2 (H1N1 (75-80%), H3N2 (20-25%)). Last season, the estimated vaccine efficacy was 47%, approximating 61% in ages 7 months to 18 years, and lower in the over 50 age group.  

As a general estimate, around 5-15% of the total US population gets the flu yearly. The hospitalization rate is 1 in 100 (1%) and the death rate is 1 in 1000 (0.1%). The highest risk of mortality is seen in the 65 and older age group, but almost 60% of reported hospitalization are ages of 18-64 years. Sure, most people will get a mild case of influenza and many people will get a classic case – with rapid onset of tiredness, body aches, chills and fever with cough, fewer will need to be hospitalized and a small percentage will die. Given the sheer magnitude of those affected, this means a lot of peopleInfluenza is NOT a mild illness.

The vaccinations consist of two type of influenza viruses, influenza A and B. Type A viruses are named after cell membrane (the outer layer of a virus) components – called hemagglutinin (H) and neuraminidase (N). The 2019-2020 vaccines are quadrivalent,  consisting of 2 types of A viruses (H1N1 pandemic 2009 and H3N2) and 2 The type B viruses named after lineages B/Yamagata and B/Victoria.  The influenza B cases for 2019-2020 are from the B/Victoria lineage. 

Unfortunately, unlike the measles or other childhood viruses, there is more virus differentiation — changes known as antigenic drift, when gradual, or antigenic shift, when sudden. A new vaccine has to be decided upon each year. An extensive vetting occurs involving input from multiple centers, where the most common strains are selected. Occasionally, the vaccinations do not match the years prominent strains. This year, the majority of cases have been caused by the H1N1 pdm 09. Why not 100% effective — there are enough differences from the vaccine strains and the seasonal strains (yes – it changes/re-assorts that fast) that make an immune response from the vaccination not as effective.


Below are some general questions and answers regarding influenza:

  1. Is it too late to get the vaccine if I missed earlier?  No. It is not too late to get vaccinated. The flu season usually tapers off after April. Getting a flu vaccination now would provide some protection for the remaining 2+ months. If you don’t want to make an appointment with your doctor, you can get it at many pharmacies. I would recommend the recombinant vaccination (quadrivalent) and the high-dose if you are older than 64.
  2. How is the flu spread? What are the signs and symptoms of the flu and how do these differ from the common cold.

The influenza virus can be transmitted fairly easily in both coarse/large and fine respiratory droplets – the greater density of virus is on the smaller droplets. You can breathe these droplets in or put them in your mouth. How does this happen?  1) the droplets can land on a surface and you can touch it and then put your fingers in your mouth or touch food you then eat; 2) Person-to-person a person could cover their cough and sneeze and shake your hands 3) Fomite, a person can contaminate an inanimate object, such as a doorknob, keys and a cell phone, and you can touch it and…

Unlike the common cold (rhinovirus), the symptoms for the flu come on abruptly.  There will be fatigue and muscle aches, though cough is the most common symptom.  The reason is that influenza causes varying degrees of infection in the  lungs, known as pneumonitis. Those with advanced age may have confusion or delirium along with a non-focal fever and cough. Anyone coming in with any exacerbation of chronic disease, e.g. lung disease or heart disease or even a heart attack, should be screened for seasonal influenza, given its association as an illness trigger.

3. How can I protect myself from getting the flu?

  • The influenza vaccine – Get it sooner than later.
  • Hand-washing : think about doing this more often during this time of the year -particularly when you touch a public surface or object (e.g. pen, doorknob). It might be a good time to do the fist-bump, air handshake, bowing ? or maybe just remembering to use alcohol rub if you shake someone’s hand – and wash your hands before eating.
  • Quit smoking :  Smokers have a greater risk of more severe sequellae. It may be a good time to consider quitting or seriously reducing.
  • Limit alcohol : For multiple reasons, excessive alcohol intake can affect the immune system and increase the risk of aspiration which is likely a risk factor to secondary bacterial infections in influenza. My recommendation would to limit alcohol to no more than 1 or 2 drinks a day or less.
  • Eat a healthy diet, maintain a healthy weight : Eating a variety of vegetables rife with minerals and vitamins is a great way to bolster the body’s immune system. Various vitamins such as vitamin A, D and to a lesser extent C and E have been shown to affect the immune system in deficiency states. (complexity alert) For instance Vitamin A deficiency was found in mice to impair respiratory epithelium (layer) regeneration and antibody response to influenza A. Vitamin D has been touted to be beneficial from a meta-analysis to reduce risk of infection, but there is some conflicting evidence from other studies. Nevertheless there is some biologic plausibility that Vitamin D plays a role in both adaptive (T- and B-cell) and innate (Natural killer, macrophages,etc) immunity. A prospective controlled study of 463 students 18 to 30 years old showed a benefit in the use of mega-doses of vitamin C, with a reduction in symptoms and severity (85% reduction) if taken before or after the appearance of cold or flu symptoms. A study on vitamin E in mice showed a reduction in influenza viral titer (amount), possibly linked to enhanced T helper 1 (TH1) cytokines.
  • Get plenty of sleep:   I will explore the topic of sleep and immunity on another post. Suffice it to stay, the many effector signals are involved in keeping our immune system robust and sleep is an important piece of the puzzle of why some people get more severe infections than other.
  • Exercises and keep a stress-free lifestyle
  • Obesity has come out as a new risk factor since the 2009 H1N1 pandemic flu season. One study looking at the cases of influenza showed an increase risk of hospitalization for a respiratory illness. In a person with class I obesity (BMI 30-35) the odds ratio was 1.45 and class II (BMI 35-40) and III (BMI 40-45) obesity, the odds ratio was 2.12 — for pneumonia and influenza. This fits similarly the association of more severe presentation of influenza and chronic diseases including diabetes, lung and heart disease and advanced age (impaired immunity).

4. Do omega-3 fish oils help influenza?   NO, I was asked this question recently. From my review online, fish oils may impair immune reactivity from the influenza virus (lower IgG and IgA levels) but may not have clinical impact. In one study in 1999, fish oils had anti-inflammatory properties and led to less viral clearance and some increase symptoms in mice but did not change the outcome. The possiblity of worsening the severity of influenza was suggested in another mice study

At this point, I am going with the likelihood that fish oils do not enhance one’s recovery from influenza.

5.  Are there any treatment options available for influenza YES!  

  1.  Oseltamivir.  Oseltamivir (Tamiflu) is given twice daily over five days and is a neuraminidase inhibitor, which blocks an important step of viral progeny (new virions) leaving an infected cell to go on to infect other cells.  It likely reduces the severity and shortens the course by a few days.  Take the therapy within a day of onset.
  2.  Baloxavir is a single-dose option recently approved for this flu season (Oct 2018) and has a novel mechanism – an endonuclease inhibitor, which blocks a step needed in viral replication (“making copies”).  The important thing about these medications is that they have to be taken within 24-48 hours of the onset of flu symptoms to experience the maximal benefits, which amount to a reduction of severity and duration by a few days.

Not everyone requires treatment other than supportive care, particularly in those with mild disease.  I would recommend that anyone with an age over 60 or BMI >30 and/or with conditions such as diabetes, cirrhosis, cardiovascular or pulmonary diseases consider taking this medication to reduce the risk of severity and duration.  Patient with lymphoma and leukemia or solid organ cancer are also at higher risk of complications.  In all of these patients, I would suggest if they present with disease within 24-72 hours or are hospitalized even after this period, that they receive the therapy.

Conclusion.  Happy New Year 2020!  I hope that you have an uneventful 2019-2020 flu season.  If you are unfortunate to get it this year, I hope it is as mild for you as the common cold. There are things you can do to ensure that it is. Remember influenza can be a significant disease.  Thank you for reading this post and please share this to your friends and contacts.  If you want to stay up-to-date with future Your Health Forum posts, register your email on the the side panel.

        Share the Post but don’t share this (Cover your cough with an arm)

Patient Information: Make a Home for Your Microbiome

Your microbiome/microbiota refers to the trillions of microbes that reside inside and outside your body.  Human cells are outnumbered by the bacterial cell population.  The highest source of bacteria in the body is within the large intestines.  The status of resident bacteria has been associated with health and illness, with greater diversity being more protective.  Bacteria perform a number of functions including 1) production of certain vitamins such as Vitamin B12, B9, B2 and Vitamin K, 2) protection from infections by competing with more harmful bacteria, and 3) maintain a healthy immune system response.

Protecting your bacteria is not difficult, can occur quickly with dietary changes, and will likely benefit your body as a whole.  Here are some tips to maintaining a healthy microbiome:

  1. Eat mostly a plant-based, high fiber diet with low processed carbohydrates.  Limit the amount of processed carbohydrates that you consume during the meal and with snacks.  Raw plant matter may be more beneficial over cooked.  Plain yoghurt or kefir contains a healthy dose of normal gut bacteria.


  1. Avoid a significant amount of alcohol, milk, juice or sugary drinks.  Favor the fruit itself, since it will have less sugar and more fiber.  More of these substances high in alcohol and/or sugar lead to less gut diversity, GI side effects, and increased inflammation.


  1. Limit the consumption of sugar and use of sugar substitutes. Sugar, processed carbohydrates (bread, pasta, white rice) in the diet has been associated with increased inflammation.  Even sugar substitutes like saccharin, sucralose and stevia have been associated with changes in the gut microbiome.


  1. Judicious Use of Antibiotics, Steroids and Proton pump inhibitors (PPI’s). Antibiotics can cause a shift in healthy gut flora and increase the risk of Clostridium difficile (a bacteria that causes diarrhea and colitis), yeast, Methicillin-resistant Staphylococcus aureus (MRSA).  It takes a team effort in coordination with your doctor, because antibiotics are often prescribed unnecessarily.  Prednisone can affect the immune system and cause a shift in gut flora, including increasing the risk of yeast.  PPI’s reduce acid and increase risk of more harmful bacteria populating.
  2.  Take Care of Your Health. Good sleep hygiene, exercise and low stress have all        been associated with more diverse gut microbiota.


If you have any of the following conditions, consider making a dietary adjustment to see if there is improvement, since a shift in gut microbiome, known as dysbiosis with less diversity, has been correlated either directly with these conditions or flare-ups:

  1. Gastroenterologic conditions: Peptic ulcer disease, reflux, Irritable Bowel Syndrome, Crohn’s, Small intestine bacterial overgrowth (SIBO), celiac disease
  2. Connective tissue diseases: Rheumatoid arthritis, lupus, psoriasis
  3. Skin: Atopic eczema, Rosacea, Acne
  4. Endocrine: Diabetes mellitus, Obesity
  5. Neurologic: Parkinsonism, Multiple sclerosis, other neurologic
  6. Cardiac: Coronary Artery Disease, Atherosclerosis
  7. Mental Health: Depression, Anxiety, other conditions


Get to Know Your Gut Bacteria.  The following are general overview of the most common bacteria in the gut.  Though, an imbalance of even these bacteria could cause host effects.

Bifidobacterium and Lactobacillus help to protect the gut from harmful bacteria Plant-based foods which contain polyphenols, found in nuts, seeds, vegetables, teas, cocoa, wine and berries, feed these beneficial bacteria.  There may be a benefit in reducing inflammation in the cardiovascular system.  Bifidobacterium is associated with butyrate production, which has a protective role in the gut and anti-inflammatory effect.

Bacteroides and Firmicutes are found in a healthy gut.  Consumption of a plant-based diet with no animal fat or protein has been associated with greater populations of these bacteria.  Plant starch can also lead to a greater population of Bacteroides, also tied to obesity prevention/treatment.

Prevotella, also may favor a setting of a high fiber, plant-based diet.

Ruminococcus is more associated with a higher amount of fruit and vegetables.  These bacteria are associated with breaking down complex plant carbohydrates and producing butyrates.

Bilophila and Faecalibacterium are found in increased populations in a high saturated fat diet and may be associated with increased inflammation.



Ruiz-Ojeda FJ et al.  Effects of Sweeteners on the Gut Microbiota: A Review of Experimental Studies and Clinical Trials.  Adv Nutr.  2019 1;10(suppl1): S31-S48.

Tomova et al. The Effects of Vegetarian and Vegan Diets on Gut Microbiota.  Front Nutr. 2019; 6: 47

Other relevant content on the YHF blog:

The Human Microbiome: Unlocking the Key to Health at YHF blog.

Wellness and Infection Prevention: 10 Tips to Steer Clear of Infections

Guidelines for Antibiotic Decision-making

Respiratory Infections and Antibiotic Decision-making

The Human Microbiome: Unlocking the Key to Health

What is the microbiome?

The word microbiome  describes the trillions of viruses, fungi, and bacteria that live on or within the human body in various habitats such as the skin, mouth, colon and vagina.  Each site has characteristics, including pH, water and oxygen content, temperature, and chemical metabolites, that favor certain bacteria over others.  Our normal flora can cause disease particularly if they are introduced into a different environment, such as from aspiration, surgery  or trauma.  Among these conditions represent the most common cases seen by an infectious diseases physician, such as pneumonia, surgical site infection, diverticular abscess, dental abscess, and urinary tract infections.  However, most of the times, our microbiome is either harmless, a state known as commensalism (+ for bacteria, 0 for host)  or even beneficial and important to human health, a relationship known as mutualism (+ for both).

Our bodies are actually a hybrid of human cells and bacterial cells.  In fact, we are more bacteria than human: 40 trillion bacterial cells compared to 30 trillion human cells, greater than 80% are red blood cells. Bacterial genes probably outnumber our human genes by 150 times.  Together our microbiome weighs between two and six pounds – about as much as an organ like the brain. 

Now that you have gotten a grasp of the scale of the microbiome, it is not a big leap to speculate that likely humans have evolved to accommodate this microbial relationship.  Microbes undoubtedly existed in the environment way before larger animals.  Our usual microbiome, although by no means static, is acquired from our first contacts with the environment, including the birth canal, the skin of the breast/hands of our mother, and later food.  The microbes in our gut may have been the key to the development of our gut immune system, which in an infant is at first impaired. since the gut is an entry point of the environment in the food ingested and is one of the immune system’s most active sites (70-80% of immune cells).  Stepping back a little, I will provide a broad summary of the gut microbiome.


What is the gut microbiome?  How do gut bacteria affect the digestive tract?

The  “gut microbiome” describes those microorganisms that live mostly within the large intestine, or colon.  It is the environment that is the most populous of bacteria within our bodies.  Within the gut, there may be more than 1,000 different species of bacteria (even closer to 35,000! species).  The majority of bacteria thrive without oxygen, and are known as obligate anaerobes.  Scientists are only able to isolate 10-25% of the microbiota with culture techniques.  Instead they rely on more specific DNA testing (e.g. 16S ribosome).  Bacteria represent 55% of the dry mass of stool, an estimated 4×10 exp 11 bacteria per gram of stool.

Gut bacteria begin to affect the human from at least the moment of birth – if not before. Babies are exposed to bacteria as they pass through the birth canal – but there’s some evidence that the fetus may pick up bacteria while still in utero (in the womb).  Researchers can determine this by culturing from the amniotic fluid the meconium, or the first movement of feces (Walker et. al, 2017).  Even how an infant is delivered affects the first bacteria that they will acquire:  with normal vaginal delivery, common vaginal flora, such as Prevotella and Lactobacillus; with a c-section, skin flora mainly Staphylococcus. Within the infant gut, Bifidobacteria are among the first bacteria to be found. These bacteria, along with factors such as antibiotic exposure, hygiene, geography and nutrition, will influence the development of the gut microbiome and the immune system.

As a child grows, the gut microbiome expands to include numerous microbial species, the top being Firmicutes and Bacteroides (both accounting for 3/4 of gut flora), Bifidobacteria and E. coli.  Near adolescence, a child’s microbiome reaches a peak of diversity before it reduces to what is seen in a normal, healthy adult (Heiman M, Greenway F, 2016).  Greater gut diversity has been associated with health and wellness, and less diversity is associated with disease states. Diet is the principle driver of microbiome diversity (discussed below). 

The bacteria housed in the gut can fulfill several benefits in the human host.  Certain bacteria, such as Bacteroides activate the gut immunity, causing the intestinal mucosa to express a gut antibody (secretory IgA).  Other bacteria, such as Bifidobacteria and Lactobacillus, provide competitive inhibition, keeping harmful bacteria from adhering to the intestinal wall and potentially causing an infection.  These bacteria reduce the risk of microbial or toxin translocation, or “leaky gut syndrome” (I will refer to it as microbial translocation).  In microbial translocation, bacteria and/or toxins (e.g. lipopolysaccharide from E. coli) gain entry into deeper tissues or even the portal bloodstream (which drains into the liver) through weaknesses in the intestinal cell barrier.  Microbial translocation may contribute to disease manifestations, such as liver abscess, local processes like diverticulitis and appendicitis, irritable bowel syndrome (IBS) and even endocarditis (There is a certain pathogen Streptococcus bovis that is associated with colon cancer). Some chronic diseases increase the risk of microbial translocation, including Crohn’s disease, celiac disease, lupus, cirrhosis, HIV, and diabetes.


Slide showing colonic architecture.  This patient was found to have local tuberculosis infection of the colon.


Taking probiotics that contain Lactobacilli and Bifidobacteria may relieve the symptoms of IBS in some people, but for many a diet replete in plant fiber and with reduced simple sugars and processed foods is often useful.  Fiber provides a number of benefits, including regulation of stools and some benefit in preventing weight gain and reducing the risk of diabetes, cancer, and heart disease.  Some gut bacteria produce fatty-chain acids, which benefit gut health, by digesting fiber. 

What are some of the other effects of the gut microbiome?

An important function of the gut microbiome is the production of several vitamins, such as B vitamins (e.g. cobalamin (Vitamin b12) and Vitamin K, a clotting factor.  For this reason, people who are taking blood thinners like warfarin, may need to have their dose adjusted if they need to go on antibiotics (antibiotics kill bacteria – lead to less vitamin K and less clotting protection).

The gut microbiome can also affect the central nervous system and autonomic nervous system, sometimes referred to as the gut-brain axis. For example, some gut bacteria produce metabolites which are similar to neurotransmitters, chemicals that are used by our nervous system. One of these serotonin is produced almost entirely within the gut and exerts a positive effect on the mood.  Millions of nerves connect the gut to the brain, so the gut microbiome may also regulate the messages that those nerves send to the brain. Some researchers have found differences between the gut microbiomes of healthy people and those of people with psychological disorders. Such differences suggest that the gut microbiome may affect mental health. It is still unclear if diet and other lifestyle choices affected those differences.

The gut microbiome helps control how the body responds to an infection by communicating with the immune system, and those communications keep the immune system from attacking beneficial bacteria. As Vitamin A strengthens the immune system, the gut bacteria control the amount of active Vitamin A in the system to keep the immune system from becoming overactive. In 2018, researchers at Brown University found that inflammatory bowel disease was caused by disrupted communications between the gut microbiome and the immune system.

How does the gut microbiome affect the heart and circulatory system?
The gut microbiome may also affect the health of the heart. A 2015 study involving 1500 people found that gut bacteria affected cholesterol levels. More specifically, they affected the production of triglycerides and HDL, “good” cholesterol. The researchers also found that certain bacterial families were less common in people who were overweight or obese.

Some harmful bacteria can increase the risk of heart disease by producing a chemical called trimethylamine N-oxide (TMAO) that can cause blocked arteries and can thus lead to a stroke or heart attack. TMAO causes blocked arteries by increasing coagulation. Some bacteria produce TMAO by converting L-carnitine and choline, which are nutrients found in animal products like red meat, into TMAO.

Gut bacteria can also affect blood sugar levels. In 2015, researchers worked with 33 infants who were genetically predisposed to developing Type 1 diabetes. The scientists noted marked changes in the infants’ gut microbiomes right before they developed diabetes: The diversity of their gut microbiomes declined, and the number of harmful bacterial species increased.

Another 2015 study found that people who followed the exact same diets could have different blood sugar levels. The researchers speculated that the differences were due to variations within their gut microbiomes.

What is gut dysbiosis or bacterial overgrowth?
Gut dysbiosis, or bacterial overgrowth, represents an imbalance between beneficial and harmful bacteria, where selection pressures favor the growth of more harmful bacteria and less microbial diversity.  The multiple causes include behavior (alcohol, hygiene, etc), certain medications, some chronic disease, antibiotics, and significant stress.

Behavior.  Diet has a strong effect on microbiome.  In the infant, breast milk provides an advantage for the growth of Bifidobacterium, which is not as prevalent in infants fed formula.  In adults, an intake of higher fruit and vegetable fiber, even if done for a short period of time, results in greater diversity of gut bacteria.  A western diet, high in animal protein, sugar and starch and low in fibers leads to a predominance of Bacteroides. 

Unprotected sex, particularly anal-oral sex, can lead to gut dysbiosis simply by exposing the participants to harmful bacteria.  Other than sexually-transmitted diseases, transmission of Salmonella and Shigella has been associated with higher risk practices. 

Additionally, poor dental and oral hygiene causes an increase in numbers of certain bacteria to that grow in the mouth, such as Streptococci and Prevotella and with this can cause imbalance in the entire population.  

Medications.  The main medications involved that can lead to dysbiosis includes antibiotics, proton pump inhibitors, steroids and chemotherapy.  Antibiotics can selectively wipe out certain bacteria or have a more generalized action, depending on the spectrum of the effect.  The more broad-spectrum an antibiotic, the greater the risk for significant gut dysbiosis.  Antibiotics such as fluoroquinolones, clindamycin and cephalosporins are among the greatest risk factors for Clostridium difficile (C. diff), known for toxin-associated diarrhea and more severe colitis.  The resulting infection causes symptoms like abdominal pain, watery diarrhea, nausea, and fever.  Proton pump inhibitors, and to a lesser extent H2 blockers (zantac, pepcid, etc) reduce the acid that is produced by the parietal cells of the stomach.  Acid is an important defense to bacterial populations ingested in food or drink.  This type of medication has been associated with an increased risk of C. diff, traveler’s disease, and gut dysbiosis or bacterial overgrowth.  Prednisone and other anti-inflammatory modulate the immune system.  There is also an impairment of glucose synthesis, referred to as a diabetogenic effect.  This can lead to an increase in populations of yeast and other microbes.  Some chemotherapies affect white blood cell lines temporarily, the greatest immune being the gut, and can be a source of gut translocation and fever. 

Disease conditions.  Gut dysbiosis has co-associated with a variety of conditions including irritable bowel syndrome, diabetes, inflammatory bowel disease, obesity, Type 2 diabetes, rheumatoid arthritis, psoriasis and atopic eczema.  Whether a particular microbiome signature is found in a specific disease state (e.g. cancer) is the subject of research efforts.

Stress states.  Various states of stress increase the production of hormones such as epinephrine, norepinephrine and cortisol.  For instance, surgery leads to excess norepinephrine release, which has been associated with overgrowth of Pseudomonas aeruginosa in one study.  Psychological stressors, even short disruptions, could alter microbial populations as well, likely related to stress hormones.


Get to Know Your Gut Bacteria.  The following is a general overview of the most common bacteria in the colon.  Although, given the situation (mainly diet), the overgrowth any type of bacteria could cause host effects and increase inflammation.

Bifidobacterium and Lactobacillus help to protect the gut from harmful bacteria Plant-based foods which contain polyphenols, found in nuts, seeds, vegetables, teas, cocoa, wine and berries, feed these beneficial bacteria.  There may be a benefit in reducing inflammation in the cardiovascular system.  Bifidobacterium is also associated with butyrate production, which has a protective role in the gut and anti-inflammatory effect.

Bacteroides and Firmicutes are found in a healthy gut.  Consumption of a plant-based diet with no animal fat or protein has been associated with greater populations of these bacteria.  Plant starch can also lead to a greater population of Bacteroides, also tied to obesity prevention/treatment.

Prevotella, also may favor a setting of a high fiber, plant-based diet.

Ruminococcus is more associated with a diet higher in fruit and vegetables.  These bacteria are associated with breaking down complex plant carbohydrates and producing butyrates.

Bilophila and Faecalibacterium are found in increased populations in a high saturated fat diet and may be associated with increased inflammation.


How can you improve your gut microbiome?

  • Healthy, Diverse diet:  For example, eating fruits and vegetables, replete with fiber, will increase the diversity of the gut microbiome.  Consuming less simple sugars and processed carbohydrates will also help to maintain gut bacterial diversity.  Eating fiber-rich foods like fruit, beans, whole grains, and legumes can stimulate the growth of Bifidobacteria. Whole grains are also a good source of beneficial carbohydrates that can help control weight and reduce the risk of cancer and diabetes. Prebiotics are a type of fiber that stimulate the growth of beneficial bacteria. Good sources of prebiotics include apples, artichokes, asparagus, bananas, and oats.Fermented foods like yogurt and sauerkraut contain beneficial bacteria like Lactobacilli and can decrease the number of harmful bacteria in the gut.

          By contrast, people should avoid diets that are high in simple sugars, such as with              processed foods, sweets and sweet drinks.  Even using artificial sweeteners like                  aspartame can stimulate the growth of harmful bacteria like Enterobacteriaceae                that can raise blood sugar levels.

  • Take antibiotics judiciously, when you really have no other choice.  Remember that probably 50% of antibiotics that are prescribed in the outpatient setting are unnecessary.  In my experience, this mostly occurs in the setting of a viral syndrome (upper respiratory tract infection), rhinosinusitis, or a miscellaneous skin condition.  The shift in microbe flora can lead to yeast infections and other dysbiosis, including a risk of C. diff.
  • Good sleep, regular exercise and good coping are likely also help.

Summary:  The gut microbiome should be considered an important “organ” in your body.  The greatest effects of our microbiome are in modulating the immune system and aiding in nutrition and digestion.  Studies have suggested a healthy, diverse state of microbiome is necessary for health and lack of complexity has been co-associated with disease states.  When you eat – you eat for your microbes too!


If you enjoyed this, pass it on to your friends and contacts.  Be sure to register your email for the latest posts and updates!



Heiman ML, Greenway FL.  A healthy gastrointestinal microbiome is dependent on dietary diversity.  Molecular Metabolism.  2016.  5(5): 317-320.
Jandhyala SM, et al.  Role of the normal gut microbiota.  World J Gastroenterol.  2015 Aug 7; 21(29): 8787-8803.

Ruiz-Ojeda FJ et al.  Effects of Sweeteners on the Gut Microbiota: A Review of Experimental Studies and Clinical Trials.  Adv Nutr.  2019 1;10(suppl1): S31-S48.

Tomova et al. The Effects of Vegetarian and Vegan Diets on Gut Microbiota.  Front Nutr. 2019; 6: 47

Web resources:




Happy New Years 2020 from YHF!

Breaking Habits

The first theme of YHF Community Discussion Page is regarding the process of breaking a habit. If you have had a habit that is detrimental to your health, what were some ways that you were able to liberate yourself from it? For more information on behavior change theory, refer to the recent post on Understanding Your Readiness for Behavior Change.

Describe the habit and then outline some ways that you were able to overcome it…

We are looking for actionable tips for the members, so that we can all benefit from your success.

I will start:

When I get home, I have a tendency to run to the cupboards and start snacking on reasonably healthy foods like nuts – but to the point where I lose control of the amount. I notice when I get too much, that I will have stomach cramps at night. Meanwhile, I am coming home very hungry – so not filling myself with the best foods. If I can grab a snack, like a small piece of fruit and have that in between lunch and home, I usually do not have the same cravings. I also have to make a salad and eat it pretty soon after coming home from work to try to overcome the drive to the cupboards.

At this time, the tendency to the habit is still there but not as strong. I am working on the Maintenance phase.

Please provide your behavior change success stories in the comment section and I will have them available for those involved.


Understanding your readiness for behavior change

Understanding your readiness for behavior change: I have included a revised post to refer to when thinking about the YHF discussion community board.

I found out very early in parenting that even if you point out an unhealthy behavior in your child, the only way that they are going to change is when you partner with them or convince them that it is their own idea.  This example applies to anyone that has developed a consistent behavior through time.  Emotional reactions and behaviors are more reflexive in our brain’s neural circuitry than we may realize.  Although the most egregious example is substance abuse, any other behavior can be an almost instinctual or subconscious automation.  Fortunately, positive behaviors can also become that way.  Anyone exercising daily can recall the feeling of absence or loss when they skip a day or two.

The Transtheoretical model (TTM), or the Stages of Change Model was developed by Prochaska and DiClemente in the 1970s. It is a useful tool in understanding the process by which one may overcome a behavior cycle.  We are approaching a greater understanding of how these changes relate to the neurotransmitter and brain functional changes involved. As our understanding of neuroplasticity increases, we may be able to develop optimal strategies.

The steps to behavior change are described below. It is important when reviewing this that a behavior, by definition, represents a circuit that has fired many times before. Therefore, the wiring is well-established and entails action, thoughts, statements, senses (e.g. phantom odors, visual awareness, etc) and dreams. Although I use smoking to illustrate these behavior steps, any behavior could apply:

Precontemplation is the time before one begins to realize that their behavior is potentially harmful or associated with negative consequences.  There is often a degree of rationalization to support the behavior, with an emphasis on the disadvantages of discontinuing the behavior.  Some responses that I have heard from smokers that are precontemplative of quitting are “I smoke so I don’t get thrown in prison,” or “I smoke so my wife doesn’t kill me” or “it is one of the last pleasures in my life,” or “I don’t want to talk about it.”   These responses are often seem completely reasonable to those who smoke, as they grapple with how stressors affect their lives and the behavior is well integrated in words and thoughts – denial, rationalization are reflexive.  If I determine that a person is in this stage, I usually don’t bring up the point of quitting as much as I encourage them to look for healthier methods of coping and managing stress.  I will usually bring up some of the benefits of not smoking and discuss resilience-building techniques without the price tag, literally and figuratively, that smoking has.

Contemplation is the stage when a person realizes that a behavior is more harmful than helpful and is considering the risks and benefits of changing that behavior.  They may even have a goal in the next several months toward this direction.  Sometimes, it follows an adverse outcome directly related to the behavior.  When a person who smokes comes in with consequences related to smoking, e.g. a myocardial infarction, pneumonia or an asthma exacerbation, they will be at a heightened awareness of the behavior’s risks.  This is a good opportunity to bring up the benefits of completely changing the behavior.     

Preparation is the time when someone is ready to make a behavior change within the next few weeks to month.  They may plan a quit date for abrupt withdrawal, work toward building other coping strategies or taper off.  More recently, smokers have shifted to other nicotine delivery systems (e-cigarettes or juul) as a transitional phase – though have found themselves at risk of gaining a new nicotine delivery habit.  It is at this stage that encouragement and providing resources is most useful.  The national smoking quit-line offers a resource where a person can call for information and tips at 1-800-QUIT-NOW. They can register and be appointed a tobacco cessation coach.  There are other resources online for smoking, substance abuse and behaviors.   

Action is the stage when a person enacts the behavior change. S/he is motivated to make decisions that support the change and protect them from relapse.  This is where the rubber hits the road.  A smoker may decide to buy their “last pack” and divide the cigarettes out in plastic bags to smoke daily, maybe 4 cigarettes a day for 5 days or a taper of cigarettes.  They may have contemplated this stage and mentally visualized it for many months before acting on it.  It is at this step, where a person attempts to transcend the cycle of behavior. Tied to behavior are strong cyclical phases of dopamine, serotonin and norepinephrine that reinforce the behavior in emotional and memory centers in the brain.

A person may experience withdrawal symptoms, both physical and psychological during this phase.  Mental images of smoking cigarettes in the morning, after a meal or sex, or during a work break spill into conscious thought from memory centers.  Sometimes one may even hallucinate the sensory memory of the behavior, including odor of cigarette smoke, dream relapses, etc. There are also external cues that triggers memories include smelling smoke, performing co-behaviors (like drinking alcohol) or seeing someone smoking.  These memories are likely related to dopamine receptor activity (D2/D3) in corticostriatal-limbic pathways in the brains, which cue into behaviors, motivation and action.  After a period of time, the strength of the cravings diminish.  Studies suggest that stress and trauma may strengthen the craving pathway and lead to relapse.  Hence, the importance of having a context of stress management, resilience training and mindfulness before the action phase. 

Maintenance is the stage where one develops a protective mesh around the new behavior to sustain the behavior and prevent a relapse of an old behavior.  This usually takes several weeks of adjustment.  Some may have small relapses, for instances smoking a cigarette, and at that point, either go back to repeat the behavior at the prior level of activity or reset their action plan.  This is one of the reasons that relapses of opiates are at a high risk of overdose and death (More than 30,000 people die from opiate overdose yearly – many from relapse).  In many cases, after a successful withdrawal, forced or planned, the effective and lethal dose are reduced.  When the person relapses and uses the prior usual dose, they are supra-therapeutic in dose and may develop respiratory failure and anoxic brain injury and a chance of dying.      

After many years of maintaining this new behavior, it becomes automatic enough to prevent someone from having a craving to return to the prior behavior, at least in theory.  This is known as the Termination stage.  Most people who have had experience with quitting smoking, alcohol or drugs are aware that significant stressors can sometimes bring them back to thinking about returning to their unhealthy life. I would consider the maintenance stage of the healthy behavior to be a life-long journey.

Shortcomings and Strategies

Although this model is useful, there are some shortcomings. It doesn’t take into account various factors, such as socioeconomic status and other influences on sustainable behavior change.  People with higher socioeconomic status may have more resources to protect them from relapse or provide a greater support system.  In my care of patients with opiate addiction and an infection, many are in a marginalized state, such as homelessness and have mental health diagnoses and post-traumatic stress disorder.  To try to maintain a drug-free behavior is often approaching futility.   

Another important thing not described in this model is that if someone fails to maintain a behavior by relapsing, they are not necessarily back to the beginning.   They may have stopped a behavior with some tools, such as smoking but they relapsed.   They are setting up a framework to make a future attempt more successful.  I remind this to the patients I see who use drugs.  They may have come in with an infection and were unprepared to learn other coping techniques required to maintain the behavior change after acute withdrawal.  Or very commonly, they may have no resources to provide them socioeconomic stability.  Relapse is all too common.  I encourage them that they are starting a path to behavior change that may be circuitous but not a failure as they are still working toward that goal perhaps with new social support or rehabilitation contacts (e.g. social worker, quitting resources).  The shame of failure is often a power inhibitor to future behavior change.

In the clinic setting, I often address wellness and substance issues toward encouraging behavior change even at a new patient visit.  During this visit, we discuss health behaviors and habits, as well as review their medical diagnoses and medications.  If during this visit, I come across some consistent behaviors that could be contributing to the patient’s health issues, I will start to lay the foundation toward future discussion.  A discussion of this approach is often tailored to the patient’s readiness to change their behavior.  A patient may be unmotivated to change, or exhibit amotivation, a state when he/she may lack intention to make a change (source, Vallerand).  Yet, a visit with a clinician could be viewed as a health-seeking behavior.

Strategies to motivating the unmotivated with motivation interviewing have been posited.  Unraveling this barrier to change often begin with determining the factors that are involved in the behaviors, the pros and the cons of maintaining the behavior and stopping the behavior, and learning of cues to the behavior.  Other forces may be involved in derailing one’s willingness to change.  These include low self-efficacy, value and effort beliefs and outcome expectancies.  If an individual has challenges with self-esteem or confidence, he/she may not be able to envision a change of an unhealthy behavior because of this barrier.  They may not have yet developed reliable approaches or coping strategies to persevere through a behavior change.   Value and effort beliefs relate to a patient’s perception.  The patient may not perceive the behavior change outcome as worthwhile enough to pursue.  The patient may not feel that they are capable of applying sufficient effort toward this new behavior or stopping the harmful behavior.   

Counseling toward behavior change

The following section will describe the harmful behavior of drug addiction. However, this can be applied to changing any behavior. The approach to coaching a person who is in the beginning of making a behavior change should be toward identifying positive skills and attributes a person has. A person who is in the grips of a behavioral cycle often has poor alternate coping skills – given that a destructive behavior can consume all of their conscious and subconscious faculties and wipe away any other support network. In this way, homelessness can be the face of a severe addiction, such as heroin.

There also can be a lot of shame associated with destructive behaviors, such as IV drug use, smoking or alcohol. A person may be distrustful or lukewarm when they are approaching counseling, often concealing or lying about facts. I like to approach it as objectively as possible. I counsel them about the difference between the “brain” and the “mind”, even if it may be a semantic distinction. I mention that the brain is stuck in a behavioral loop that has caused them harm and has prevented them from being free, almost as if they are caught in an orbit. This means that the brain will call up all its resources, including thoughts, perceptions, words and actions to complete the circuit and repeat the behavior. The brain has received supra-normal neurotransmitter cues and has reshaped the brain for the addiction, causing other parts to atrophy.

The brain is causing harm to the rest of the body. The mind is conscious that the behavior is harmful and enslaving it. I urge them not to listen to the brain cues to relapse. I ask them to Identify another activity – a hobby like art or writing, walking, or even listening to music — even if for just the next several minutes. They can also call a support friend to talk it through. Usually the wave craving will pass after that. Eventually, the cues and cravings will diminish – and a person will build a new life – free of the grasp of addiction – though the brain will always remember the experience- gone but not forgotten. I counsel them to remember the harm that the behavior has caused – and never let their brain convince them that the “grass is greener” on the side of the harmful behavior.

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