Good and Bad Bacteria - Is There No Such Thing?

Good and Bad Bacteria – Are We Oversimplifying?

Good and Bad Bacteria - Is There No Such Thing?

Do You REALLY Need Probiotics?

“There’s no need to buy fancy sourdough: White bread DOESN’T make you fat (as long as your body doesn’t react to It).” (1) So blared Stephen Matthew’s headline for a February 2017 Daily Mail article.

Oprah and the legions of I-love-bread people certainly loved this headline, clearly meant to rile healthcare professionals who recommend gluten-free, low-carbohydrate whole foods.

In the study Matthew references, eventually published in Cell Metabolism, Israeli researchers gave participants either traditionally made sourdough-leavened whole-grain bread or industrially made white bread and monitored their blood sugar every five minutes over several weeks.

Sourdough bread is fermented by using lactobacillus cultures, so it lands squarely among probiotic foods. You would think it clearly would prove healthier cheap-o factory-made white bread.

For the record, sourdough bread is not on my list of best probiotics for weight loss (or best probiotic period.) But I’m jumping ahead here.

Among the benefits of foods with probiotics – those healthy gut flora that according to Dr. Vincent Pedre in Happy Gut “compete against unfavorable flora for bacterial binding sites on the inside lining of our intestines [to] protect us from harmful pathogens” – include maintaining the correct gut bacterial balance.

But back to our study.

“All of the participants in the study normally consumed about 10% of their calories from bread,” says a synopsis in Science Daily. “Half were assigned to consume an increased amount of processed, packaged white bread for a week — around 25% of their calories — and half to consume an increased amount of whole wheat sourdough, which was baked especially for the study and delivered fresh to the participants. After a 2-week period without bread, the diets for the two groups were reversed.”

Researchers measured participants’ glucose, nutrient, fat, and cholesterol levels as well as kidney and liver enzymes before and during the study. More importantly, they tracked their microbiomes before, during, and after the study. (2)


According to a riveting article several years ago by famed author Michael Pollan in the New York Times, gut microbiome are

“the genes… of the several hundred microbial species with whom I share this body. These bacteria, which number around 100 trillion, are living (and dying) right now on the surface of my skin, on my tongue and deep in the coils of my intestines, where the largest contingent of them will be found, a pound or two of microbes together forming a vast, largely uncharted interior wilderness that scientists are just beginning to map.” (3)

Here’s what researchers found in that bread study: Blood sugar levels spiked in both groups and participants’ weight gain was about equal. In other words, probiotic-rich sourdough bread didn’t perform any better than white bread.

What does that have to do with your gut microbiome? Well, from these statistics, researchers argued “the gut microbiome is responsible for weight gain.” The bread didn’t make participants fat; their gut flora did.

More specifically, Dr Evan Elinav and his team at the Weizmann Institute of Science in Israel concluded the “type of bread that induces the lower glycemic response in each person can be predicted based solely on microbiome data prior to the intervention.” (4)

Put simply, it doesn’t so much matter what you eat so much as the kind of bacteria or microbiota your gut houses. Want to lose weight, reduce your disease risk, and create glowing health? Optimize your gut flora. It’s really that simple… and that complicated.

Bacteria in the Human Body

“When you hear the word bacteria, it isn’t uncommon to imagine creeping hordes of microscopic germs threatening to get you and everyone you love horribly sick,” writes John Staughton. “We live in a world full of antibacterial soaps, germophobes, and parents who rush to administer antibiotics at the slightest sign of an infection.” (5)

Bacteria are simply single-celled organisms, and they aren’t all intended to make us sick. In fact, calling them good or bad might vastly simplify bacteria, but more on that in a minute.

Bacteria linger nearly everywhere on your body and in some cases, can be harmful (such as in your lungs). Most aren’t, and they hang out primarily in three places: Your mouth, skin, and gut. Let’s briefly look at each.

1. Bacteria in Mouth.

Oral bacteria depend on what you eat and what lingers between your teeth. Too much bad bacteria can lead to gingivitis, plaque, oral disease, and other things your dentist will identify. Good bacteria support oral health, and too little could be just as harmful as too much bad bacteria. (5)

2. Skin Bacteria.

You have about 1,000 species of bacteria on your skin and hair follicles, most of them harmless or mutually beneficial. Good bacteria can help prevent bacterial infections by protecting your skin’s surface area. Those healthy bacteria secrete chemicals to prevent pathogenic organisms from colonizing your skin. They might also stimulate your skin’s immune response against potential invaders. Fair trade: You house your skin bacteria and they in turn protect you. Healthy skin bacteria also lower your risk for skin infections like dermatitis, acne, and rosacea. (5)

3. Gut Bacteria.

“Gut microbiota (formerly called gut flora) is the name given today to the microbe population living in our intestine,” says Gut Microbiota for Health, created by the Gut Microbiota and Health Section of the European Society for Neurogastroenterology & Motility (ESNM). “One third of our gut microbiota is common to most people, while two thirds are specific to each one of us. In other words, the microbiota in your intestine is like an individual identity card.” (6)

That brings us back to the aforementioned bread study. What you eat is important (despite what that study might imply), but how your individualized gut bacteria react might be equally important.

Stomach Bacteria – The Trillions of Organisms Your Gut Houses (and Other Stats)

Gut health has become a hot 21st-century topic. Why is gut health and, by extension, consuming probiotic foods, so important? Here’s why.

  • Your gastrointestinal microbiota has about 300 – 500 bacterial species, comprising nearly two million genes (your microbiome) (7)
  • About 30 – 40 species represent about 99 percent of your gut flora
  • You have about one hundred trillion bacteria living within you (or maybe you don’t… More on that in a minute)
  • All those bacteria weight about two to three pounds (Pollan estimated less, and I’ve read studies that say it clocks in more like four or five pounds)
  • Your stomach has few bacteria due to its acidic environment. Most of your bacteria live in your colon, which has a much lower acidity where they thrive (8)
  • When you hear the phrase “human microbiota,” that includes bacteria, fungi, archaea (organisms with no cell nucleus or any other membrane-bound organelles in their cells), and viruses. “Human microbiome” refers to their genomes or genetic material. (9)

When you hear stats like those, keep in mind gut flora understanding is still in its infancy. We’re still learning.

Don’t believe me? Whereas experts once believed bacteria outnumber human cells by a ratio of at least 10:1, in 2014 the American Academy of Microbiology argued we “only” have 37.2 trillion (rather than 100 trillion) bacterial cells is correct, making it closer to a 3:1 ratio. (10) Even more recent research finds the ratio much closer to 1:1. (11)

Regardless of these and other statistics, two factors stand out:

  1. You have a unique microbiome depending on numerous factors including age, diet, environment, genes, and medications (especially antibiotics). (12)
  2. Gut health is really, really important.

“When I say it all starts in your gut, I mean almost everything!” says Pedre in Happy Gut. “Headaches, migraines, allergies, autoimmunity, weight gain, acne, skin rashes, yeast infections, hormonal imbalances, fatigue, immune challenges, even the way you sense pain—they all relate to the condition and health of your gut.”

Let’s take cancer. We can talk about nearly any disease with gut health, but let’s focus on cancer.

Studies show gut flora can influence carcinogenesis (cancer formation) via several factors: Altering the balance of tumor cell proliferation and death, regulating immune system function, and influencing metabolism of host-produced factors, foods, and pharmaceuticals. (13)

In other words, your gut influences cancer – and really, pretty much any disease including obesity – more than you might suspect.

Your Good Gut Flora are Real Workhorses

Why do so many bacteria decide to colonize in your gut, which decidedly seems like a turbulent environment to reside?

“Millions of microbes enter your body at every meal. Indeed, after your skin, the digestive system is the main place where your body comes in contact with microbes,” says the American Museum of Natural History.  “But unlike your skin, your digestive system is a warm, sheltered space—and it’s filled with food, making it the perfect spot for microbes. So it’s no surprise that the vast majority of your body’s microbiome is inside your digestive tract.” (14)

A healthy gut maintains the right balance of good and bad bacteria.

“A healthy person has about 85% good and 15% bad bacteria,” says the American Nutrition Association. “The word eubiosis means balanced while dysbiosis means unbalanced. Antibiotics, non-steroidal anti-inflammatory medications, etc., geographic location, race, diet, aging, or illness can upset this balance.”  (8)

Without that good bacteria, you “would be unable to digest our food, synthesize certain essential vitamins, absorb water, and fend off the dangerous bacteria that often tries to attack our gut,” writes Staughton.

If you have any doubt your gut flora are workhorses that keep you healthy, Pollan describes some of their many roles.

“Our gut bacteria also play a role in the manufacture of substances like neurotransmitters (including serotonin); enzymes and vitamins (notably Bs and K) and other essential nutrients (including important amino acid and short-chain fatty acids); and a suite of other signaling molecules that talk to, and influence, the immune and the metabolic systems,” he says in that aforementioned article. (3)

Back up there. Pollan mentions serotonin. About 95 percent of this feel-good neurotransmitter gets produced in your gut. (15) And about 70 percent of your immune system lies in… You guessed it, your gut. (16)

Based on the many roles healthy bacteria play, you theoretically want to keep as many good bugs around and zap or downsize the bad ones, right? Like most things, the answer isn’t so clear-cut.

Good Bacteria Usually Keep Bad Bacteria in Check

Let’s start with the good.

“Some of the most important good gut bacteria include Lactobacilli, Bifidobacterium and Caulobacter.  In the stomach and digestive tracts, the most populous pathogenic bacteria include Salmonella, Clostridium, and E. coli,” says Staughton. “Food poisoning is probably the most common symptom of a bad gut bacteria taking control, but if you have enough beneficial bacteria in your stomach, you should be able to recover quickly.” (5)

Our everything-phobic culture today creates many opportunities to imbalance that bacteria and potentially let the bad guys take over.

Hand sanitizers, compulsive hygiene, chemical cleaning products, chronic stress, a terrible diet, and antibiotics overuse are among the enemies for a diverse, balanced gut ecosystem. (5)

“When your gut ecosystem shifts from a predominance of friendly to a preponderance of unfriendly bacteria, yeast, or parasites, the resulting microbial imbalances can wreak havoc in your digestive tract, including dysbiosis, small intestine bacterial overgrowth, and yeast overgrowth,” says Pedre.

Symptoms of dysbiosis include fatigue, poor memory, mood disorders like anxiety or depression, insomnia, frequent colds, gas and bloating, and skin problems like rashes, eczema, and psoriasis. Dysbiosis also manifests with other gut issues including inflammation and candida. (8)

It sounds like a horror movie. Good bacteria thrive and exist peacefully when suddenly something wrecks that harmony and the bad guys usurp everything, creating chaos. But does that description dumb down a far more complicated scenario?

Good Bacteria, Bad Bacteria… Are We Oversimplifying Things?

“There’s really no such thing as a ‘good microbe’ or a ‘bad microbe’,” writes Ed Yong, author of I Contain Multitudes: The Microbes Within Us and a Grander View of Life. “These broad-brush terms belong in children’s stories. They are ill-suited for describing the messy, fractious, contextual relationships of the natural world.”

Yong really, really doesn’t like the over-simplification some experts have created about good and bad bacteria, and he vents his frustration in almost-poetic rants.

“We like our black-and-white narratives, with clear heroes and villains,” he says. “The very term symbiosis has been twisted so that its original, neutral meaning – ‘living together’ – has been infused with positive spin, and almost flaky connotations of cooperation and blissful harmony. But evolution doesn’t work that way. It doesn’t necessarily favour cooperation, even if that’s in everyone’s interests. And it saddles even the most harmonious relationships with conflict.”

Yong provides several blurred-line bacterial scenarios:

  1. Some microbes can become friendly or unfriendly depending on the strain and host.
  2. Others can simultaneously be pathogen and friendly.
  3. Some microbes can be friendly in your gut but dangerous when they cross over into your bloodstream. They can thrive in one organ and wreak havoc in another. In other words, they can be friendly or not depending on where they live.

“The stomach bacterium Helicobacter pylori is well known as a cause of ulcers and stomach cancer,” he says. “Less famously, it also protects against oesophageal cancer – and it’s the same strains that account for both these pros and cons. H. pylori is neither a good nor a bad microbe; it’s both.”

Yong says some get negative names like “virulence factors” because they were initially discovered with disease, yet realistically they are neutral. (They were just at the wrong place at the wrong time.)

“They are just tools, like computers, pens and knives: they can be used to do wonderful things and terrible things,” he says.

Put another way, bacteria are very much like humans: They behave differently based on factors like environment. Think about how you might act with a close friend, at a cocktail hour where you don’t know anyone, and in a meeting with colleagues who don’t agree with anything you’re doing in a work project. You would behave differently in every situation, right?

To further complicate that scenario, let’s say you met your close friend when you were starving, tired, or in a bad mood. You’re probably going to act differently than if you slept well and ate recently, right?

Same with bacteria: They can behave good or bad depending on multiple variables.

“These terms are more like states of being, like hungry or awake or alive, or behaviours like cooperating or fighting,” says Yong. “They are adjectives and verbs rather than nouns. They describe how two partners relate to one another at a given time and place.” (17)

From that perspective, you can understand why classifying bacteria can be difficult.

“It would be great if we could identify 10 or so bacteria and say these are the ones you need most, but it doesn’t work that way, and there is no magic bullet,” says Dr. Elizabeth Hohmann of the infectious diseases division at Harvard-affiliated Massachusetts General Hospital. “There may be a community dynamic at play as well as good mixtures of communities.” (12)

Some microbiota that colonize humans co-exist without harming you. Others have a mutualistic relationship with their human hosts. (18) (Mutualism is the way two organisms of different species exist in a relationship where each benefit from the other’s activity.)

Some non-pathogenic microbiota can harm human hosts via the metabolites they produce such as trimethylamine (TMA), a microbiota-generated metabolite linked to atherosclerosis development. (19)

You’re absolutely correct if this all sounds complicated, and as I keep emphasizing, we’re still learning. Most likely, five or 10 years down the road we’ll have a radically different understanding about gut bacteria.

Balance Becomes Key with Probiotics (and Nearly Everything)

“There is no such thing as ‘good’ bacteria—just bacteria that harm you less and outcompete the bacteria that harm you more,” writes Liam Springer. “It’s not simply the presence of ‘good’ bacteria, but rather a healthy balance of intestinal bacteria that’s most important when it comes to your health.” (20)

That all steers back to that initial study about bread, where researchers concluded “understanding dietary effects requires integration of person-specific factors.” (21) While I agree bacteria can impact things like weight gain and disease risk, what you eat has a dramatic impact on your gut flora.

Sugar makes a great example: Researchers show it can adversely impact your gut, creating dysbiosis (22) and feeding bad bacteria with small intestinal bacterial overgrowth (SIBO). (23)

So yes, your bacterial balance can determine things like weight gain and disease risk, but the food you eat can powerfully shape that bacterial balance.

Testing to Predict Your Good and Bad Bacteria?

Wouldn’t it be great if you can determine what types of flora your gut house? You can… Maybe.

Some companies now provide at-home microbiome testing.

“SmartGut™ is the world’s first sequencing-based clinical microbiome screening test, providing detailed and accurate information to help you understand your gut health,” says uBiome. (24)

The process sounds fairly simple.

“Customers receive test tubes in the mail and send them back with fecal swabs to be analyzed in a lab,” writes Emily Mullin in MIT Technology Review. “The companies say they can do things like make diet recommendations and predict risk for certain diseases based on a person’s unique microbial makeup.” (25)

They can be pricey: Thryve, a startup offering a monthly microbiome testing subscription service this year, starts at $59.95 a month. (Insurance companies will cover some or all of some testing like uBiome.)  (25)

The bigger question is, do they work? Some critics remain skeptical about the efficacy of at-home microbiome testing.

“These people are usually let down when they get the results of the analysis and realise that there’s really only so much one can learn about one’s microbiome from conducting a fecal microbiome analysis,” writes Eirik Garnas in Darwinian Medicine. (26)

He continues:

“A microbiome analysis will give you an overview of the bugs that are living in your bowels, as well as an indication of how diverse your gut microbiome is; however, it won’t give you a conclusive answer to [whether you have healthy gut flora]. It won’t tell you everything you want to know about your microbiome.” (26)

Garnas believe you can learn a lot about your microbiome by paying attention to everyday things like your energy levels, gut issues, bowel movements, and overall mood.

I agree, and find that a more practical way to understand gut flora rather than potentially expensive, flawed testing. If you frequently feel sluggish, depressed, running to the bathroom after meals, and don’t have frequent bowel movements (at least once a day), those typically serve as signs of gut imbalances.

If you do suspect dysbiosis, I strongly work with an integrative physician who specializes in gut health. Guessing what problems you have and spending a fortune on supplements or other therapies to optimize gut health can cost more than visiting a professional, and in some cases it can create more harm than good.

Prebiotics, Probiotics + Other Strategies to Optimize Gut Health

Biochemical individuality underlies functional nutrition. That simply means everyone is unique.

Over the next decade, scientists will find novel ways to optimize gut flora. We’ll find new ways to test microbiome health. I’m sure new supplements will come out that supposedly heal gut imbalances or otherwise contribute to gut health.

I look forward to these findings. At the same time, you can implement these seven tried-and-true ways right now – they will still be relevant in 10 years, despite what new discoveries experts make – that can optimize gut flora to help you lose weight, reduce disease risk, have more energy, and overall improve your health.

1. Eat foods that support gut health.

Nutrient-dense, probiotic foods, especially those high in fiber, might be the most effective way to optimize gut flora. Good gut health goes beyond probiotic foods (though those are important!). Buy organic (produce), go grass-fed (meat), get wild (seafood), and focus on anti-inflammatory foods that optimize gut health like wild salmon and leafy greens. Your body converts dietary fiber into short chain fatty acids (SCFAs), which fuel your colon and help maintain optimal gut flora. (27)

2. Sleep well.

Aiming for eight hours of solid, uninterrupted sleep every night provides numerous benefits including optimizing gut health.

“Scientists investigating the relationship between sleep and the microbiome are finding that this microbial ecosystem may affect sleep and sleep-related physiological functions in a number of different ways: shifting circadian rhythms, altering the body’s sleep-wake cycle, affecting hormones that regulate sleep and wakefulness,” writes Dr. Michael J. Breus in The Huffington Post. “Sleep, in turn, may affect the health and diversity of the human microbiome.” (28)

3. Control stress levels.

Like with subpar sleep, chronic stress adversely impacts gut health. Researchers find modulating gut microflora could become a novel strategy to manage complex stress-related central nervous system disorders. (29) You know the drill: Yoga, deep breathing, meditation, and walking your dog make great de-stressors.

4. Exercise regularly.

You need another reason to exercise? No, you don’t, but here are three: Recent studies show exercise can enhance the number of beneficial microbial species, enrich the microflora diversity, and improve the development of commensal bacteria. (30) Burst training or weight lifting is perfect, but so are yoga, spin classes, and even brisk walking. Whatever gets you moving regularly!

5. Eat more probiotic foods.

Sauerkraut, kimchi, non-genetically modified (GMO) fermented soy, and no-sugar-added yogurt (if you aren’t dairy intolerant) are among the foods rich in good probiotics or friendly gut flora. You’re probably not eating enough of these foods, but they add variety to your meals while optimizing gut flora. I recommend them daily if possible. All apologies to that aforementioned bread-study team: While theoretically sourdough bread is a probiotic food, high carbohydrates and nearly-empty nutrients mean it didn’t make this list.

6. Feed your gut flora.

Prebiotics are the food your good gut bacteria (probiotics) feed on.

“Most prebiotics, including fructooligosaccharides and inulin, are digested by bifidobacteria and stimulate the growth of their colonies,” write Ji Youn Yoo and Sung Soo Kim in the journal Nutrients. “These bacteria influence homeostasis of intestinal cells and inhibit the growth of pathogenic bacteria.” (31)

According to Pedre, raw chicory root, raw Jerusalem artichoke, and raw dandelion greens are your best prebiotic sources. You might opt for inulin powder (which has a mildly sweet taste) or Bob’s Red Mill Unmodified Potato Starch.

7. Take the best probiotic.

A systematic review of 25 animal and 15 human randomized controlled trials found certain strains of probiotic bacteria from the Bifidobacterium and Lactobacillus genera for one to two months could benefit anxiety, depression, autism spectrum disorder, obsessive–compulsive disorder (OCD), and memory. (32) Those are among the many benefits of a probiotic supplement. Quality matters here. Look for a professional-quality supplement with billions (not millions) of microorganisms. Pedre, a Manhattan-based medical doctor who specializes in gut health, says the best probiotic is a professionally quality supplement with “at least 15 billion CFUs each of Lactobacillus and Bifidobacterium (a total of 30 billion CFUs) guaranteed by the manufacturer through the expiration date.” Remember these are living bugs, so shelf life matters. The best probiotic also needs to survive through your acidic stomach. I’ll say this again: Quality matters to get the benefits of probiotics.

Good and Bad Bacteria - Is There No Such Thing?

Dr. B.J. Hardick

About Dr. B.J. Hardick

Dr. B.J. Hardick is a Doctor of Chiropractic and internationally-recognized natural health author and speaker. His health journey began as a child — alternative medicine is the only medicine he has ever known. In 2009, he authored his first book, Maximized Living Nutrition Plans. In 2018, he authored his second book, Align Your Health. An energizing and passionate speaker, Dr. Hardick shares his lifestyle methods to numerous professional and public audiences every year in the United States and Canada. His teachings encompass the principles of ancestral nutrition, detoxification, functional fitness, mindfulness, and green living. Learn More