The Beginner’s Guide to the Microbiome

These days you can’t escape fermented health foods. Kombucha is on tap at your local café, artisanal sauerkraut is sold in mason jars at the farmers’ market, there are kimchi how-to videos on your Instagram, and kefir muffins at the Thanksgiving potluck.

What’s the deal with this new trend? Are fermented foods really that good for us? I wanted to get the scoop on this new food fad.

My gut was telling me there may be more to it than drinking a cold glass of ‘booch every morning…

Read on or head straight to the verdict.

The basics of the microbiome

We’ll begin at the source: the gut microbiome: the ecosystem of single-cell organisms that live in our gut. The microbiome has become an enormously popular topic in recent years.

As more and more evidence emerges, we are beginning to understand that the composition of our microbiome can influence all sorts of aspects of our health, including vital digestive functions like:

• Helping us process nutrients
• Warding off infection-causing germs
• Regulating metabolism

It turns out that the gut microbiome is the most diverse, dynamic, and highly structured part of our body and it isn’t even made of our own cells! One research paper I read referred to the microbiome as a consortium of bacteria, yeast, and archaea (which is another type of single celled organism). I love that analogy! I looked up the Wikipedia definition of consortium, and it fits the microbiome perfectly:

“An association of two or more individuals, companies, organizations or governments (or any combination of these entities) with the objective of participating in a common activity or pooling their resources for achieving a common goal.”

As consortiums go, our gut microbiome is a ginormous powerhouse. With more than a trillion individual organisms belonging to more than 500 different species it could eat Time Warner and Exxon for lunch.

Our microbiome consortium is actually a diverse network of different types of living cells that reproduce, communicate with each other and break down foods. And, like many corporate conglomerates, the microbiome is protectionist. When hostile bacteria that can make us sick (these are called pathogens) get close, the cells in the microbiome play a big role in fighting them off.

In return for their efforts, the cells in our microbiome earn a tidy profit: a cozy home and the nutrients they need to flourish.

The microbiome consortium is also always changing depending on market conditions like what we eat, where and how we live, and how old we are. The entire ecosystem changes depending on our needs and behaviours! That’s pretty fricken cool if you ask me.

Diversity makes us stronger

Just as every giant multinational has a different business model (you may argue otherwise, but I’m an aspiring scientist not a business student, so just go with it), the consortium of bugs in our gut varies greatly from person to person. Each of us has a unique corporate structure in our intestine!

This makes it really hard for researchers to figure out what constitutes a healthy microbiome. What we do know that diversity is key to cornering the market on good health, and we are starting to pin down some key species of the microbiome that play essential roles in our gut.

There is also strong evidence to show that some things, like stress and antibiotic use seem to deplete our stores of good bacteria and open the door to corporate raiders. But we all experience stress and most of us occasionally require antibiotics for infections. Instead of focusing on the negative, it’s more realistic for us to do all that we can to keep our gut healthy in other ways.

Fermentation: Ingredients for a healthy microbiome

So, researchers have not found a secret formula for making the perfect diverse consortium of beneficial bacteria that help us maintain a healthy gut. But there is one process that is a key player in facilitating happy gut growth: fermentation.

Fermentation is a way for cells to produce energy without using oxygen.

When we breath, we take in oxygen and sugar and turn it into carbon dioxide and water and energy. But this isn’t the only way for our cells—or bacteria or yeast cells—to make energy. Fermentation is a way for cells to produce energy without using oxygen.

Fermentation is a very common way of producing energy—even our own cells can do it! But there are lots of different types of fermentation, depending on the type of organism that’s doing the fermenting and the starting materials that go into the process. In terms of our gut health, there are two really big categories of fermentation that we care about—fermentation that happens inside our gut, and fermentation that happens in food before we eat it.

Internal Factories

1. Prebiotics

Our gut consortium runs its own in-house fermentation factory in our large intestine. The factory (a bunch of beneficial bacteria) ferments prebiotics, which are actually a subcategory of indigestible fibres. These fibres (present in whole grains, vegetables, fruits, and legumes) encourage selective stimulation for growth, which means these foods preferentially feed the good bacteria in our gut!

Our own cells can’t break the prebiotic (fibrous) elements of food into small enough pieces to use as an energy source on it’s own. Instead of squandering these valuable nutrients, they become the main course for the bacteria living inside us. (I go more in depth into the importance of fibre in my post about juice cleanses).

In short: prebiotics feed good bacteria, good bacteria use prebiotics as starting material to create vitamins and small molecules called short chain fatty acids (SCFAs). We use vitamins and SCFAs to keep our bodies healthy and happy (they regulate energy production and consumption of our cells). It’s a pretty great system. The molecules that some of these bacteria produce are used as neurotransmitters in our brain, too!

If you eat lots of fresh whole grains, whole fruits and vegetables and legumes, you are likely getting plenty of prebiotics in your diet.

Importing fermented products into the gut

In addition to in-house fermentation, our gut consortium increases its productivity when foods that have already been fermented are imported. Humans have been fermenting their food for more than 6,000 years.

Back in the day, fermentation was kind of a happy accident—people would leave their fresh food out, and it would start to ferment on its own. They realized quickly that not only did fermented food taste good, but it also preserved food better than any other technology available at the time.

In the past hundred years or so, humans have found other ways to keep food fresh—we us fridges, nitrates, and other processing techniques. It also means that we eat far fewer fermented foods than our ancestors. As a result, we’re missing out on the extra benefits these foods may provide.

Broadly speaking, there are two types of fermented foods we can eat: probiotics, which are foods that have been fermented but still contain the bacteria that did the hard work, and fermented foods with no living organisms. The probiotics are the ones that we really care about.

2. Probiotics

Probiotics can play an important role in maintaining a happy consortium of our resident microbiome. Foods like yogurt, kefir, kimchi, kombucha, sauerkraut and some cheeses all have their own mini colonies of bacteria. The most well studied type of bacteria in probiotics are a very broad class of bacteria in the lactobacillus genus that produce lactic acid. These are the bacteria present in most yogurts, kimchi, and sauerkraut.

We still have a lot to learn about how these bacteria help improve our overall health, but we do understand how they help out our microbiome. When we eat these bacteria, very few of them hang around in the gut and come on board the consortium, and most of them get pooped out.  However, even the ones we poop help our bottom line with some positive benefits.

The bacteria in probiotics release chemicals called bacteriocins that are toxic to some bad bacteria, they release molecules that our good bacteria can use as energy sources, and they take up space so that bad bacteria have less opportunity to grow in our intestines.

When we use antibiotics, many of the good bacteria get wiped out in the process of killing the bad guys in our gut. To replenish the void of the consortium, doctors and scientists have proposed supplementing dietary probiotics with antibiotics. There is evidence that shows that by taking probiotics you reduce your chance of contracting antibiotic-related diarrhea. However, since the probiotics are made up of a different consortium of bacteria then your natural microbiome, a group of scientists in Tel Aviv recently found that when you take probiotics after taking antibiotics, it actually slows the recovery time to get back to your normal, or indigenous microbiome. That’s not to say it’s a bad idea to take probiotics while you’re on antibiotics—it just shows how there are so many more aspects to the use of probiotics that we still don’t fully understand!

While these effects all seem to have a net positive impact on our gut bacteria, everyone’s microbiome is so unique that even probiotics effects are different for everyone. For some, probiotic foods may have a much larger impact than others!

While probiotics are established to have positive (if small) health benefits in otherwise healthy individuals, you probably don’t need to be spending big bucks on probiotic supplements. These fancy probiotic supplements don’t contain anything more special than probiotic foods, and they can be very pricey. Eating probiotic foods seems to be the way to go. Go ahead, spice up your salad with some tempeh!

Fermented n dead

You know what else fermented? Wine! And beer! And bread!  It’s all about the yeast.

But maybe take a breath before you run to the local bar or bakery. Unfortunately, these tempting products don’t contain living organisms in their final product.

The yeast in wine is removed in processing; most of it in dies off in beer before we drink it; and the hot temperatures of the oven kill ‘em in bread.

Not all is lost on these foods, though. Even though the living organisms are long gone, the yeast and bacteria that did the fermenting leave their finished product behind. Some of the molecules they produce may have beneficial properties. For example, the fermentation process of grapes lets out more polyphenols into the wine, which have been shown to have (very small) positive effects on human health. These benefits are specific to the food that is fermented, and they definitely aren’t essential to consume in order to be healthy.

The Verdict

My biggest takeaway from this mini investigation is that everyone’s microbiome is extremely individualized. There is no overarching solution to a happy gut, so try to listen to your body and see what works for you. Eating healthy, whole foods with plenty of fibre, staying active, and minimizing stress is the best way to curate your happiest gut consortium (groundbreaking, I know).

Adding some foods with live probiotics won’t hurt either–next week I will go into more details about some specific fermented foods and whether they live up to the test of probiotic status, so stay tuned!