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Project Microbiome: Bacterial Happiness and Health

A short article tucked in the New York Times health blog “Well” reported on a Cornell University study published in Microbiome, an obscure medical journal whose circulation is likely in the upper two digits. To my mind, it’s an important piece of research and I’d guess that years from now as we understand more and more about why we’re susceptible to so many chronic illnesses, this pioneering study will be referred to frequently.

To start, let’s clarify the terminology.

Microbiome is defined as a collection of microorganisms (bacteria, fungi, viruses) living in a defined environment, creating a sort of mini-ecosystem. In our bodies, the largest microbiome lives in our intestines and is called the gut microbiome. However, we have others on our skin and in our mouths, vaginas, and eyes.

The microorganisms in any microbiome are divided into three groups:

  • Symbiotic (we help them survive, they help us survive).
  • Commensal (a neutral relationship, they’re just along for a free ride).
  • Pathogenic (disease causing). This is the smallest group.

Your gut microbiome is housed in your large intestine and weighs about five pounds. It contains tens of trillions of microorganisms of more than 1,000 different species. One third of your personal microbiome is just like everyone else’s on the planet, but the remaining two thirds is unique to you. In other words, your gut microbiome is like an individual identity card. It started developing with your first gulp of breast milk or formula, and over the years underwent all sorts of changes depending on what you ate, whose hand you shook, whether you had a family doctor who prescribed a lot of antibiotics, and if you liked making mud pies when you were three years old.

Serious interest in the gut microbiome is a relatively recent phenomenon, probably stemming from our overuse of antibiotics (in people and in livestock) and the various health issues this has caused. Picture your gut microbiome, happily doing its many jobs when, all of a sudden, it’s confronted with a broad-spectrum antibiotic that you probably don’t need. Antibiotics kill bacteria indiscriminately, and yes, it’s sort of like an ecological catastrophe: a forest fire or earthquake. Fortunately, as in the case of most catastrophes, big or small, your personal microbiome eventually recovers.

Your gut’s daily work
Some of the tasks we now attribute to the gut microbiome include:

  • Digesting foods that have not been fully processed and absorbed by your stomach and small intestine.
  • Manufacturing certain vitamins (some of the B vitamins and K).
  • Keeping the bad guys (disease-causing bacteria, fungi, and parasites) in check.
  • Strengthening your immune system.
  • Producing brain chemicals that are intimately involved in your emotional well-being. This is the gut-brain connection you’ve read about. I’ve written a couple of Health Tips on this exciting topic (here and here), which links the microbiome to such issues as susceptibility to depression, ADD, learning disabilities, obesity, type 2 diabetes, chronic intestinal inflammation, and even susceptibility to chronic Lyme Disease.

So what did the NYT blog, quoting the obscure journal Microbiome, have to say?
Essentially, how the puzzling fibromyalgia-chronic fatigue syndrome (FM-CFS) finally has a distinct marker, an actual test that may be useful in diagnosis. FM-CFS affects tens of millions of people around the world and was notorious for having no positive test results to help with diagnosis.

Researchers found that the gut microbiome in FM-CFS patients is markedly different from the microbiome of healthy individuals.

Here’s what happened.

The research team recruited 48 people with CFS along with 39 healthy control subjects. Since FM-CFS is a clinical diagnosis (meaning it’s a diagnosis made in the absence of positive test results), the affected patients had to fulfill the clinical criteria to confirm they had CFS, the so-called Fukuda Criteria. Main symptoms were fatigue, unrefreshing sleep, and widespread muscle pain. Many also had chronic irritable bowel symptoms. On the other hand, the control population felt fine.

When the gut microbiome of these 87 individuals (48 + 39) was examined, those with FM-CFS showed different bacteria and also a lower diversity of bacterial species than did the controls. By examining the group’s gut microbiomes alone, the researchers were 83% correct in identifying who had FM-CFS and who did not.

Their conclusion was understandable excitement about finally finding a valid diagnostic test for FM-CFS that would finally quiet the singularly annoying doctors who have badgered FM-CFS sufferers over the years with the notion that they have a psychiatric disorder.

A truly notable development
What I personally find even more exciting about the study is this: Consider all the patients who lie on one end of that broad spectrum between feeling tired and achy and those on the other who feel perfectly well. You have to wonder how many undiagnosed people are plagued by chronic symptoms and persistently negative tests all because of issues with their gut microbiome.

These are the tens of millions of people who visit their primary care physicians reporting that they’re tired all the time, sadly shaking their heads as they describe how their get-up-and-go-just-got-up-and-went. They don’t fulfill the criteria for FM-CFS. They just feel crummy, struggling through their work days, too tired to do anything in the evening, falling asleep at 8 pm, up in the morning just as tired as when they began.

Gut microbiome problems? Something off with that five pounds of good/bad bacteria deep inside their large intestine? Why not?

A DIY gut fix
Before you start frantically calling a gastroenterologist who is (I hate to say it) probably clueless about this research and will reflexively schedule you for a colonoscopy, take matters into your own hands.

What you eat  Your diet is by far (light years by far!) the most important factor for a healthy gut microbiome. Here’s a nice picture of what to eat and what not to eat. This is not rocket science. High in fiber, fresh fruits and veggies, whole grains, fish. Low in sugar and refined carbs (bread, cookies, desserts, sugary drinks), meat, and processed foods. With a healthy dose of fermented foods–yogurt, kimchi, sauerkraut, and other pickled veggies. Remember, living foods don’t sit in jars on grocery shelves and they’re easy to make yourself.

I highly recommend two books. First, The Microbiome Solution, by Robynne Chutkan, MD. Next, if you have kids or are thinking of becoming a parent, get The Dirt Cure, by Maya Shetreat-Klein, MD. What you’ll learn in this book is that the apparently kid-friendly food found in any grocery store (processed, sugary), recognizable by being placed on kid-high shelves, packaged in blindingly bright colors, and decorated with creepy animal cartoons, are gut microbiome destroyers. Yes, those Girl Scout cookies you’re helping your troop hawk at the mall are very much involved in our current epidemic of childhood obesity, food allergies, learning disabilities, asthma, and the like.

Counseling  If you need some help with this, please schedule a visit with one of our nutritionists–Marla Feingold, Seanna Tully, or Marcy Kirshenbaum. You can get a good idea of the status of your gut microbiome with a test the nutritionists can order called GI Effects (by Genova Labs).

Supplements  You really need just two: a super high-potency broad spectrum probiotic and a prebiotic to speed growth of the good guys in your gut. People who lack the will to eat enough veggies and whole grains (or who are just getting started) can add a fiber supplement. This one is gluten/dairy/egg-free and provides 8.4 grams of fiber per serving. Of course, you could just eat a mango (200 calories, 5 grams of fiber) and you’re almost there.

Mindfulness  Most important is for you to be mindful of your gut microbiome, something you probably haven’t given much thought to over the years. Gut mindfulness is easy once you get the knack of it. When grocery shopping, select good-for-the gut food over the bad. If you like lists, here’s a tidy, gut-pleasing one.

Better yet, next time you’re in some upscale restaurant and the waiter arrives with the dessert menu, just smile and say, “What do you recommend that would be really good for my intestinal bacteria?” (Answer: fruit.)

Be well,
David Edelberg, MD

Leave a Comment

  1. calle says:


    Need to get that article as so many women suffer.

    Wonder if a history of UTI’s could have a tie-in as so many RX are written for them with no regard for gut health.

  2. Bronwyn says:

    For 3rd party validated good probiotics try the Natren brand.

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Far and away, the commonest phone call/e mail I receive asks about COVID-19 diagnosis.
Just print this out, tape it on your refrigerator door, and stay calm.


• Runny nose
• Sneezing
• Red, swollen eyes
• Itchy eyes and nose
• Tickly throat
• No fever

• Runny nose
• Sneezing
• Sore throat
• Mild muscle aches
• Mild dry cough
• Rarely a low fever

• Painful sore throat
• Hurts to swallow
• Swollen glands in neck
• Fever

FLU (Standard seasonal flu)
• Fever
• Dry cough (no mucus)
• Sudden onset over few hours
• Headache
• Sore throat
• Fatigue, sometimes quite severe
• Muscle aches, sometimes quite severe
• Rarely, diarrhea

• Shortness of breath
• Fever (usually above 100 degrees)
• Dry cough (no mucus)
• Slow onset (2-14 days)
• Mild muscle aches
• Mild fatigue
• Mild sneezing

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