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How Your Microbiome May Help Fight Viruses

National Geographic just published an article regarding the study of how our microbiome may help fight viruses, even Covid-19, National_Geographic. “Some preliminary studies have shown unusual microbiomes in hospitalized Covid-19 patients”.


The article mentions that there are 3 possible mechanisms where the microbiome may help combat a virus:


1) The lining of one’s stomach and intestines prevents viruses from getting to organs other than the stomach and lungs. In other words, “leaky gut” may allow access to other organs. The virus has been detected in “the liver, kidney, heart, and brain”.
2) The microbiome could also produce chemicals that interfere with the viral life cycle.
3) The microbiome supports one’s immune system.


The article goes on to discuss some ideas on possible treatments based on these theories, but emphasizes that there has not been enough studies prove the impact of the microbiome on viruses.


The only advice, for now, is to support your microbiome through diet (and even exercise) to give yourself the best possible chances for good health. Look out for more developments in this area over the next few years.

Traveling: Use the Happy Cow App

Whether you are traveling to foreign countries or searching for a local restaurant the HappyCow App and website are the single best resource to use.

The app does cost $3.99 but the cost is justified.  We have used it in Europe and found great restaurants not listed in guidebooks or blogs.

One can search by Vegan, Vegetarian, or Veg Options (meaning has both veg/vegan and meat/dairy).  There are clear ratings and descriptions with business hours that seem to be up to date.

There are free apps, as well, but I would go straight to HappyCow.  It is well worth it!

Useful Websites for a Healthy Lifestyle & Plant Based Diets:

Like any topic now, there are an overwhelming number of online resources somehow related to health and plant based diets.  We have found the following sources useful.

We have looked on Facebook, Twitter and Instagram as well.  All the organizations below have a presence on these forums too.  I find there is too much on social media to wade through to get to useful information.  Especially if you follow groups, you end up seeing hundreds of posts a day that, while nice, do not really provide any information. 

Medical and Technical Information:

Nutritionfacts.org is Dr. Michael Greger’s site.  Dr. Greger is the author of How Not to Die and How Not to Diet and now, How to Survive a Pandemic.  His books are packed with great reviews of scientific research on what is good for you and what is not.

This site has his free videos and articles.  This is really a great place to start any research.  If you only look at one site for scientific evidence-based guidance, I’d recommend this site.

Center_for_Nutrition_Studies is T. Colin Campbell’s site.  Dr. Campbell, from Cornell,  is the author of The China Study, the largest study on the effect of diet on health.  In addition to technical articles there is a great Guide for Living a Plant Based life The_Guide.  There is also a Cornell run Plant Based Nutrition certificate program, if you want to get deep into the topic.  If you don’t want to endure the scientific, technical aspects, just jump to The Guide (link above).

Plant Based Websites:

Of the general, plant based websites, Forks Over Knives may be the best.  Their Beginner’s Guide at Beginners_Guide is a great starting resource.  Lots of current information, recipes and hints.

Vegan.com is another comprehensive source of information at Vegan.com.

The site has a lot of basic vegan information.  Instead of one guide for going plant based, they have several guides on various topics.

Lastly, “Veg News” at  Veg_News has all sorts of news and recipes.  They have a hard copy magazine, as well.

Psychobiotics: A new application for microbes and your gut

Psychobiotics are microbes (probiotics) that can affect (improve) your mood or depression and possibly more.  There is a growing understanding that your gut health can affect your mental state.

Psychology_Today describes a link between “leaky gut” where one’s natural system breaks down and allows toxins and bacteria to enter the blood system potentially increasing depression, anxiety and other issues. 

Several articles on the topic refer to the “gut-brain axis”, meaning there is a relationship between your gut and how you think and feel.  The effects go both ways, meaning your gut health can impact your mood and your mood can impact your gut health.

Their recommendation is essentially to “consume more fibers and fermented foods and avoid refined sugars and junk foods”.  The objective is to nourish your gut lining.

Researchers have identified certain probiotics that seem to help with stress and other mental health issues and it seems prebiotics also can help.  This, being a new area of research, will undoubtedly have more developments in the near future.  It is pretty exciting to read that you can improve your mental state by improving your gut health!

If your have severe mental health issues consult medical professionals.  Many of them will know little nothing of this gut-brain link, so you may need to search for someone who has followed this research.  Also, be aware that the studies so far have been limited.

It will sound a little odd to hear the main side effect of a, in this case, psychobiotic protocol is an improvement in one’s digestive health.  

For anyone who wants to go (way) deeper into this, the National Institute of Health’s Library has a wealth of scientific papers, at Psychobiotics_NIH . 

Probiotics & Prebiotics:

Both probiotics and prebiotics are hot topics now, but many people may not be familiar with the differences or how to incorporate them into a healthy, plant based diet. This post will give you some things you need to know to improve your microbiome or “gut health”.

A recurring theme here at Plants Be With You is that your microbiome is critical to your health and well being and that your diet has a huge impact on how you feel. There has been a saying for longer than I have been alive that “You are what you eat” and more true today “You are what your microbiome eats”.  It certainly applies here.

Probiotics are better known, probably due to the many supplements we’ve all seen in health stores for years. They are live bacteria that add to the healthy microbes already working in your digestive system. This is a case where more good bacteria is always better.

Probiotics can be obtained through supplements, but is more effective found in:

  • Yogurt
  • Kefir, and plant based, fermented foods such as
  • Sauerkraut
  • Kimchi
  • Kombucha
  • Tempeh and Miso (fermented soy products), and
  • Pickles (watch the added sugar).

Probiotic supplements contain live organisms and there is an overwhelming array of options, some marketed for specific conditions. If you have a medical condition that warrants considering supplements, consider consulting with a registered dietician.

Prebiotics are plant based fibers that help the healthy bacteria in your stomach to grow. The good news here is that while there are supplements, there is a long list of fruits and vegetables that contain these complex carbohydrates. They are not digested so they pass through to become food for microbes and bacteria.

A very partial list of foods with prebiotics is:

  • Dandelion greens
  • Jerusalem Artichoke
  • Garlic
  • Onions
  • Leeks
  • Asparagus
  • Bananas
  • Barley & Oats
  • Apples
  • Cocoa
  • Flaxseeds (needs to be ground up)
  • Wheat bran (the outer shell of the whole wheat grain)
  • Seaweed
  • Walnuts
  • Lentils
  • Yams.

There is something for everyone on this list and there are more options.

We hope this summary of Probiotics and Prebiotics has been helpful and given you a list of this to incorporate into meals without adding a lot of complexity in you life. Again, if you have a serious medical condition, please consider working with a registered dietician or other medical professional.

The State of Dairy Alternatives

There are more plant based milk, cheese, butter and yogurt alternatives every month. Oh and don’t forget other dairy options, such as cream cheese, ice cream, whipped cream, etc. One thing to note is that plant based alternatives are still more expensive. Some very rough (California) grocery store pricing is given below, just to give you an idea of the difference.


Milk has been easy to replace with many almond, soy, oat, rice and combination alternatives. Just keep trying brands until you find what you like. Oat “milk” is much thinner as is soy or rice than an almond or cashew based beverage. If in doubt, try the Califia (Califia) brand almond (in Costco and many other stores) or oat beverage. Trader Joe’s has a nice almond, cashew & macadamia nut beverage as well. Again, the options are almost limitless now. Remember that a lot of these drinks are sweetened! Organic milk is around $4.99 for 64 oz., while Califia Almondmilk is $3.99 for 48 oz.

Cheeses have been a little harder to duplicate. Both the range of tastes and melting capability have been hard to replicate. Miyoko’s Creamery has some sliced options that are very good, as well as some cream cheese alternatives (Miyoko’s). There are many options, so this may take some trial and error before you settle on brands you like. You are not going to match some of the exotic cheeses from Europe and if you are partial to Velveeta, we can’t help you here.


Butter alternatives have increased rapidly, as well. If in doubt, try Miyoko’s. Costco has 2 packs. Some of the bigger companies are getting into plant-based spreads. I recommend trying the smaller brands first. Miyoko’s 8oz butter spread is $6.99 vs organic butter around $5.99-$6.99 for 16 oz. Earth Balance ($4.99 for 15 oz.) and Kite Hill have some great options, as well.
Forager yogurt ($4.94 for 24 oz vs $3.99-5.49 for 32 oz organic whole milk yogurt). I often see the Forager brand at Costco.

Sales of plant based dairy and egg alternatives is expect to be $5.2Billion, up from $4.3B in 2020 according to Packaged_Facts, a market research firm. Just the dairy market, not including eggs, in 2024 is expected to be around $1Trillion worldwide, so we have a long, long way to go.

What is the Microbiome?

The National Institute of Health (NIH) defines the microbiome this way:

“The microbiome is the collection of all microbes, such as bacteria, fungi, viruses, and their genes, that naturally live on our bodies and inside us. Although microbes require a microscope to see them, they contribute to human health and wellness in many ways. They protect us against pathogens, help our immune system develop, and enable us to digest food to produce energy. Some microbes alter environmental chemicals in ways that make them more toxic, while others act as a buffer and make environmental chemicals less toxic.

The critical role of the microbiome is not surprising when considering that there are as many microbes as there are human cells in the body.  The human microbiome is diverse and each body site – for example, the gut, skin, and oral and nasal cavities – is home to a unique community of microbes.  A person’s core microbiome is formed in the first few years of life, but can change over time in response to different factors including diet, medications, and a variety of environmental exposures.

Differences in the microbiome may lead to different health effects from environmental exposures and may also help determine individual susceptibility to certain illnesses. Environmental exposures can also disrupt a person’s microbiome in ways that could increase the likelihood of developing conditions such as diabetes, obesity, cardiovascular diseases, allergies, and inflammatory bowel disease.”

The microbiome, which I’d never heard of until a few years ago, is now getting a lot of attention as doctors and scientists learn that it not only affects stomach issues such as acid reflux, irritable bowel and other digestive disorders, related only to what one eats and drinks.  It is being shown that stress and anxiety (stress leads to more stomach issues and stomach issues lead to more stress) and a variety of environmental issues are inter-related, as well.

Of course, what we eat and drink has a huge affect on our microbiome or “gut health” and a whole new medical and naturopath industry has been created as a result of the health issues people are having.  Fortunately, we are hearing that many people have been able to switch their diets, weaning themselves off of highly processed foods and in many cases moving to a plant based diet.

If you have a serious stomach health issue, please see a medical professional to help you sort through the myriad of information, but don’t think you have to accept a lifetime of taking traditional pills.

I was suffering from frequent bouts with acid reflux, to the point of having an endoscopy to check the damage to my esophagus and starting a prescription for a common acid reflux drug.  I was concerned with the long-term affects of the drug and didn’t really want to take any meds anyway, so I am fortunate to have (easily) weaned myself off of the drugs and endoscopies, through a plant based diet.  I didn’t eat too much in the way of processed foods, except those darn deserts, but I did eat a bit too much on occasion and sometimes snacked too late at night.  It seemed I got the acid reflux after the “best” meals.  It was probably the great sauces and the 3rd helpings of meat that got me.  I have not had to become a ‘hard core vegan’ to kick acid reflux, meaning we still eat meat or dairy when we travel or eat at a friend’s house, but then I can’t say I miss meat or cheese either.  There are too many great plant based alternatives out there.

There are a couple of things that can give you some temporary relief:

  1. Try not to eat to close to bedtime.  This is what got me in trouble.
  2. If you have reflux now or have a rich meal coming up, instead of pills, drink a Kombucha.  Kombucha is a fermented tea so, if you don’t like caffeine, try GT’s ( GTs ) Kombucha.  We love it.
  3. Other fermented foods such as sauerkraut, kimchi may help

It pains me to mention this, but the experts always recommend cutting out alcohol.  Since I have not done this, I guess I can’t tell you how well that works.

The science of the microbiome, or gut health, is very extensive and complex.  We will bring you more information as we learn more.

The State of the Meat Alternative Industry

This article will give you an update on the latest news regarding meat alternatives.  There are 2 broad categories of alternatives to traditional meat production.  There are many plant-based alternatives to beef, chicken, sausages and even attempts at bacon and then there are “cell cultured meats”.  I’ll briefly touch on the latter group, just so you know it exists.

Cell cultured meats take cells from animals and then grow them in a lab.  There are a few companies, most notably Eat Just, Inc. (Eat Just) and Memphis Meats (Memphis), pursuing this.  Their idea is to create a “cleaner, safer” (but real) meat.  Eat Just has been a plant based producer so far, with egg substitutes and plant based sauces.  The company just received approval in Singapore to sell their cell cultured chicken this past December.  This is the first approval to sell a cell cultured meat in the world.  Until this point, cost and volume production capability have kept these options in the background.

There are many plant-based alternatives to ground beef, chicken and sausage, but the alternative meat industry seems to have taken off since Beyond Meat (Beyond) and Impossible Foods (Impossible) entered.  Both took a scientific approach to simulate the taste and look of real meat and both are sold at numerous grocery, specialty and fast food outlets.  Costco now has Beyond patties and sausage as well as Impossible burger in warehouses.  Trader Joes is now selling a 12 ounce Impossible burger for $5.99, down from $7.99!

These meat-like alternatives are frequently found in the meat aisle, depending on the store, rather than the vegan section.  The meat industry is understandably trying to keep them out of the meat section.  The cost is still slightly higher than meat, but is getting closer.  The other detractor is that the calories and fat content are very similar to meat.  Beyond Meat just announced that early this year they plan to ship a new version of the burger with 35% less saturated fat than beef.  Both taste great in our opinion, but we are slightly partial to Impossible burgers.  We’ll need to do some more investigation to be able to comment on the sausage comparison.  We have only tried the Beyond sausage and like it.

There still are the traditional vege-burger patties made of soy/tofu or beans, as well, but those options don’t taste like meat.  There are more of these options, as well, too many to review.

The Impact of Meat and Dairy

You probably heard or read some of this information.  There are some great resources in documentaries, books and articles regarding the impact of livestock (meat and dairy) production on the earth.  Some are listed at the end of this.  All this information is readily available, so don’t hesitate to check my work.

I’ll save the impact of meat and dairy consumption on you for another day.

The (negative) impact of meat and dairy production is in a few general areas:

  1. Greenhouse gas emissions
  2. Water use
  3. Land use
    1. Deforestation – clear cutting more land to convert it to use for livestock
    2. Wildlife habitat is lost among other impacts

From “Meat and Dairy Production” by Ritchie and Rosner in 2017, 14.5% of all greenhouse gases are produced by livestock production.  That’s roughly equal to emissions from all cars, trucks, airplanes and ships.  That’s alot! Source:  Meat&Dairy

A (very) large study of 40,000 farms in 119 countries in the journal, Science, confirmed several eye opening facts.  All meat and dairy provides 18% of all calories in the world and 37% of all protein but utilizes 83% of all farmland and produces 60% of all of agriculture’s greenhouse gas emissions.  The authors concluded that if the entire world went plant based, land use for agriculture could be reduced by 75% and still feed the entire world, returning much land to its natural state.  One of the study authors, Joseph Poore of the University of Oxford in the UK, stated  “A vegan diet is probably the biggest way to reduce your impact on the planet.  It is bigger than cutting down on your flights or buying electric cars”.  Source:  Reducing_Your_Impact

Lastly, water use is another impact.  According to Professor Arjen Hoekstra, agriculture in total uses 85% of the world’s fresh water, with only 5% used for domestic consumption (our showers, cooking, watering lawns, washing our cars or driveways, etc.).  Good luck saving the world by taking shorter showers.  Most of the water use for livestock is in production of the feed for livestock.  In the US, 68% of all grain production is for livestock feed, so meat and dairy use a very sizable portion of the world’s water.  Source: Water_Use

I’ll stop here.  There is a lot more information out there and I will leave the deforestation and animal cruelty topics to others.

Some more resources:

Forks Over Knives is a good starting point.  It is a classic, more concerned with the health benefits of a plant based diet.

In Defense of Food is based on Michael Pollan’s best-selling book, discussing how traditional diets have been “making us sick”.

Cowspirac:  The Sustainability Secret has been around a while.  This one does focus on the environment.

Taking Your First Steps to a Healthier Lifestyle

While we’re in those peak earning years and, for some, raising kids at the same time our own physical and mental health take a (way) back seat to other priorities.  I mean who wants to be cooking some healthy dinner after picking up kids at their after school activity, while on the phone with a business partner in Asia.  Why not hit a fast food place on the way home, get the family fed quickly and then make the first of the night time work calls … or do the invoices … or pay the bills … or _______________ (insert your choice of extra work).   Maybe you once had a few hobbies that went by the wayside when kids activities and work travel took over.

Well now you are retired or thinking of retiring and you want to make a few changes or maybe you feel like you are stepping off a cliff from the grind to unknown territory.  It may be easy to make the transition, especially if you were able to hang on to a hobby or two and if you were able to resist the convenience food some of the time, or it may be harder if your working life left no time for personal pursuits and activities.

A good first step is to move towards a healthier diet.  There is no reason, unless your health is compromised, to take extreme steps.  Small steps in a new direction are more likely to lead to long-term changes.  Improved diet can help other aspects of your life, which may help your energy and motivation levels which, in turn, may help (your energy level) in resuming many hobbies.

Please note:  If you are suffering significant health issues, it is best to consult a medical professional.  Some medical professionals just want to prescribe pharmaceuticals and/or surgery, but there are more and more who are interested in more natural solutions.  It is important to have a medical expert helping you navigate the alternatives.

So what are some simple steps to take to ease your self into a healthier diet?

If you frequently eat convenience food (frozen meals, fast food, etc.), try 1 or 2 more dinners a week that are home cooked.  Stick to relatively simple recipes, without really long ingredient lists.  Every recipe site on the internet has healthy, vegetarian or vegan recipes.  We’ve done full vegan holiday meals, without feeling like we missed anything.  Again, look at the ingredients lists.  Skip the ones with lots of spices, exotic ingredients and complicated prep.  Keep the recipes that are hits and toss those that weren’t a success.  We don’t think one needs to take on extreme changes in lifestyle to be healthier.  Some incremental changes will make a difference.

If you don’t want to spend lots of time in the kitchen, look for 1-pot, crockpot types of recipes.  An Instant Pot, crockpot or Dutch oven that you throw everything in and wait are invaluable.  Another time saver is pre-cut produce, pre-diced garlic and similar pre-prepped foods.  Some say the pre-processed foods are less healthy the whole produce, but any of these options are better than processed food.

Start reading food labels.  Work towards reducing/eliminating refined sugars, unpronounceable additives, and highly processed foods.  You would not believe how many foods and recipes have (a lot of) added sugars.  Recipes still taste good with ½ or ¼ of the sugar.  You might need something to thicken a sauce instead of the sugar, but generally you can just reduce or eliminate the sugar.

Some good foods are the so-called “super foods”.  Every list is different but most lists include the following):

            Dark leafy greens (Kale, spinach, chard, etc)

            Berries (Blueberries, raspberries, etc)

            Green tea

            Legumes (beans including soy, lentils, peas, peanuts)

            Nuts and seeds

            Kefir and yoghurt (can be made from non-dairy bases)

            Garlic

            Olive oil

            Ginger

            Turmeric

            Avocado

            Sweet potato

            Mushrooms

            Fish, Seaweed, other vegetables such as broccoli, Brussels sprouts, radishes/turnips, etc are often listed

Most of the super foods, above, are high in fiber.  When you are reading labels of breads and cereals, look for a ratio of total carbohydrates (in grams) to dietary fiber content (also in grams). The lowest ratio possible ratio, in the range of 5 carbs to fiber is desirable, but hard to find.    Grab the most processed looking loaf of bread and compare it to a more nutty/seedy loaf and it will be an eye opener.

For those who like their meat and dairy, try 1 plant based meal a week.  You can try a vegan recipe or simply substitute meat and dairy alternatives in one of your existing recipes.  We’ll cover some of the great plant based alternatives in subsequent articles.

In the future, we’ll also cover other health related topics, related resources that we’ve come across, plant based diets, products, restaurants and services.  If this seems of interest bookmark this site for future reference.