What’s the Microbiome? The Pathobiome?

I was talking to a friend today who loves all things gut-related, including poo.

He’s highly educated, very smart, and on top of the news.

“Microbiome,” he laughed. “I’m a gut guy. But I had to look it up. I still don’t really know what it is. That word confuses me. What’s the microbiome?”

So what’s the microbiome?

We think of ourselves as humans.

We believe we are a distinct, highly intelligent species apart from other animals.

And as humans, we value cleanliness and hygiene.

At the same time, we know that non-human microorganisms as unintelligent, unclean, and unsafe.

And we do absolutely everything we can to stop them. We are at war with microbes. We defeat them by using:

Antibacterial soap
Antibiotics for infections
Antibacterial hand sanitizer

We want to stop the microbes because—in this old-school worldview—microbes are bad.

“Germs make us sick.”

Right?

Except none of that is correct.

We aren’t actually humans.

We’re walking colonies of many different species, including something like 37 trillion bacteria as well as fungi, protists, and viruses.

These microorganisms live on our skin, in our mouths, in our reproductive organs, in our guts, and elsewhere.

Voilà the answer to the question what’s the microbiome?:

The microbiome is the non-human microscopic life that lives in us and on us.

Our bodies’ microscopic cohabitators aren’t just freeloaders.

These microscopic organisms help us with digestion, circulation, and healthy immune response to diseases. They also play a role in detoxification, and possibly much more.

Why does the microbiome matter?

New science about the microbiome and its role in human health and human disease is emerging all the time.

In one small but fascinating study of 19 healthy volunteers, scientists found that people who use anti-bacterial mouthwash had increased high blood pressure.

The team of researchers at Queen Mary University in London hypothesized that antiseptic mouthwash may kill beneficial bacteria. These are bacteria that help the blood vessels relax.

The scientists conclude:

Our data further suggest that disturbances in nitrite homeostasis (herein achieved via interruption of nitrate reduction in the oral cavity by commercial mouthwash use) have small, yet potentially important, implications for cardiovascular health.

Apart from vasodilator actions, nitrite-derived nitric oxide has a number of other potentially beneficial effects in humans, including inhibition of platelet aggregation, preservation of endothelial function, and improvement of mitochondrial efficiency.

In other words, some “germs” make us sick (a slogan that was popular in the 1970s when I was growing up). But other “germs” help keep us well.

In another study, scientists gave lab animals antibiotics when they were fighting a viral infection. After doing so, they discovered that you can severely compromise the immune system, making it much more likely that sick animals will die of viral infections.

Is the one germ causes one disease model out of date?

As we discover more about the microbes living in us and on us, the answer to the question, “What’s the microbiome?” becomes more nuanced

Scientists have understood there is some kind of microbiome for more than a decade. Despite this, scientists are just beginning to understand the beneficial role bacteria and other organisms play in human health.

Writing in Trends in Ecology & Evolution, a team of five scientists from the University of Exeter and The Centre for Environment, Fisheries and Aquaculture Science (Cefas) posits that our understanding of how humans get sick must fundamentally change. Firstly, we need to understand how the microbiome helps keep us well.

Read the highlights here.

The one pathogen one disease model, these scientists argue, may be an outdated and inaccurate concept.

Instead of believing that one “germ” causes one disease, it may be that diseases are caused by a “pathobiome.” That is, a complicated interaction between microbes and their hosts. It’s this complicated interaction that leads to disease in plants, animals, and humans.

Does your head hurt from all these new ideas?

Now that you know what the microbiome is, what’s the take-away?

Channel your inner evolutionary biologist (aka be like my mom, Lynn Margulis) and embrace the microbial world.

It’s time to understand that microbes have been around longer than we have. Moreover, they may well be smarter than we are.

Bacteria and other microorganisms are small but they’re mighty. And they’re helping us humans survive and thrive.

What’s the Microbiome? Related articles:

Make these lifestyle changes and never take antibiotics again
Treat your sinus infection without antibiotics
Don’t wash your hands before you eat?
Lynn Margulis, Science Teacher Extraordinaire 
Beneficial Bacteria May Make You More Social

Published: September 12, 2019
Last update: July 1, 2021

About Jennifer Margulis, Ph.D.

Jennifer Margulis, Ph.D., is an investigative journalist, book author, and Fulbright awardee. She is the author of Your Baby, Your Way: Taking Charge of Your Pregnancy, Childbirth, and Parenting Decisions for a Happier, Healthier Family, co-author (with Paul Thomas, M.D.) of The Vaccine-Friendly Plan, and The Addiction Spectrum: A Compassionate, Holistic Approach to Recovery. Follow her on Facebook, Twitter, and Pinterest.