Bacteria cause decay and disease, but they’re also the key to a long and healthy life.

A  fierce wind is blowing over the wide-open fields of Midwoud, a village of farmers and agrarians an hour’s drive north of Amsterdam. Midwoud is home to organic farm De Anna Hoeve, where the Blokker family produces a very special drink: kefir, a creamy buttermilk-type dairy beverage. Farmer Ilse Blokker, a sprightly, friendly woman in boots, is just emerging from the stables into the yard.

Her husband, Paul Blokker, suddenly had this idea eight years ago, she says. “He said, ‘Humanity is going to run into trouble. The quality of our food isn’t good enough anymore. We need to change our way of thinking.’ ” His products were already organically grown, and no chemicals or antibiotics were allowed on his farm. But now he also decided to start producing kefir, which is said to date back thousands of years to the ancient shepherds of the Caucasus Mountains, between Europe and Asia.

The existence of kefir had almost been forgotten. But right now, the recipe is being dusted off all over the world. More and more research shows that we need healthy bacteria—such as the lactic acid bacteria in kefir—for a stronger immune system and better digestion. We call these health-boosting microorganisms “probiotics.” Good bacteria and yeasts are crucial in all types of processes in the body. “Most importantly, they keep the immune system on track,” says Liz Lipski, a clinical nutritionist and academic director of Nutrition and Integrative Health Programs at Maryland University of Integrative Health.

Lipski points out that there is a growing body of scientific work that says probiotics can modulate inflammatory responses in the body. Finding a way to prevent inflammation is one of the major challenges in the medical community today. More and more scientists point to chronic inflammation as the cause of all kinds of Western diseases, such as Alzheimer’s, some types of cancer, heart disease and Parkinson’s.

Over many thousands of years, humanity has co-evolved with healthy bacteria, and our digestive system has been the proving ground. Our intestines are in open communication with the outside world; that’s why they’re sometimes known as “the cradle of the immune system.” Two-thirds of our immune system resides in the digestive tract. But since we have been rooting out too many good microbes—both by eating fewer cultured and fermented foods and obsessively using antibiotics and antibacterial sanitizers—we’ve seen an increase in inflammatory and degenerative diseases. To restore the natural power of the human gut, we need to put down the Purell and take in more kefir, more sauerkraut, more yogurt and kombucha. But what we need even more is the understanding that probiotics are an important part of the future of medicine. 

Every week, Ilse Blokker produces more than 800 liters (210 gallons) of fresh kefir, a time-consuming process that involves letting the kefir culture—a combination of bacteria, yeast and fungi—ferment in raw milk in two enormous tanks. Since the sudden death of her husband last year, Ilse has been continuing his life’s work and mission. Customers come from far and wide to pick up her kefir. They have heard of the healing properties of this drink and take it for their eczema, digestive troubles, psoriasis or chronic fatigue, in the hope that it will alleviate their symptoms.

It’s quaintly interesting that in these times, people with all sorts of ailments and diseases travel to a farm in search of a drink full of bacteria. In the past, conventional wisdom held that people who were sick—for example, those suffering from infectious disease like tuberculosis—had to banish bacteria from their bodies as soon as possible, instead of ingesting a new dose.

Indeed, since the second half of the 19th century, waging war against microorganisms such as bacteria and fungi has saved millions of lives. Clever scientists like Louis Pasteur demonstrated that the bugs in our bodies cause decay and disease. Using pasteurization, disinfection, improved hygiene, antibiotics and other medications, we’ve been able to considerably increase the average human life span. It’s because of this that, in the West at least, cholera, tuberculosis and the plague became diseases of the past.

But nowadays, many of our diseases no longer go away when we take an additional course of antibiotics or create an even cleaner home environment. Those antibiotics you took for a cold as a child could lead to the development of diabetes in your body 40 years later, say scientists like Martin Blaser, professor of microbiology at the New York University School of Medicine. He quite bluntly points out the impact of aggressively fighting symptoms or illnesses with heavy artillery, which eradicates complete bacterial strains from our body. This throws off the natural balance, he says.

And his explanation really isn’t so strange. The microorganisms in our bodies have always worked together ingeniously with the body’s own cells. Take a look at our immune system. If unwanted organisms enter the body, our immune cells induce an inflammatory response to ensure that extra attention is given to the invaders. As Liz Lipski explains it, inflammatory markers “are like the conductor of an orchestra who says, ‘Everybody get really loud now!’ ” All that fuzz is necessary to eliminate the unwanted guests, but the inflammation needs to subside at some point, because it, too, can damage healthy cells.

“We need a balance of inflammation and anti-inflammation, and probiotics help to modulate both these processes,” says Lipski. “We know that probiotics can dampen or modulate those responses.” Since chronic inflammation nowadays is seen as a root cause of all kinds of lifestyle diseases, it’s crucial that the body get its bacteria back, to work together with the immune system. 

Once you know all this, it doesn’t make sense anymore to consider the little bugs in our body the enemy. It is not in the interest of our health to keep washing our hands with disinfectant soap, to clean the house with aggressive agents until it’s almost sterile, and to take antibiotics every time we get a cold. We have been removing these little critters from our bodies for centuries, and now it’s become clear how badly we need them for our health.

The human microbiome—the aggregation of fungi, viruses and, in particular, bacteria in our bodies—has become one of the hottest new fields of medical research in the past decade. In the United States, the giant Human Microbiome Project was completed last year. For the first time ever, this research project mapped out the entire collection of microorganisms that live in the body, also known as microbiota. The scientists wanted to know how our body’s cells interact with these tiny organisms. Their research showed that billions of bacteria are living in our bodies and that there are easily 10 bacteria for each cell in the body. The total weight of the bacteria we each carry with us adds up to—wait for it—around three pounds (1.35 kilograms).

What is becoming clearer and clearer is that our Western lifestyle has disrupted our microbiomes. Slowly but surely, one scientist after another is standing up to alert us to the urgency of this fact. They are still being mocked at times. Martin Blaser knows all about that. He published the book Missing Microbes in 2014, which discussed the hypothesis that excessive use of antibiotics, cesarean sections and disinfectants have changed our microbiomes forever. Blaser argued that this could be a major cause of the increase in modern diseases such as obesity, diabetes and asthma. He received a lot of criticism for it. “What? Now antibiotics cause obesity? And allergies?” was one scientist’s response to an article about Blaser in Time.

Blaser’s studies suggest that the use of antibiotics in early childhood poses a grave risk to health in the long term. Alarmingly enough, American children on average receive 17 courses of antibiotics before they reach the age of 20, particularly for treatment of viral infections that cause ear infections and colds. At the same time, he claims, C-sections are robbing newborns of an important first contact with their mother’s microbiome, since, during natural childbirth, a child gets its first dose of bacteria from the mother’s birth canal.

“There are times when both [antibiotics and C-sections] are needed urgently, but we already know that we are overusing them,” wrote Blaser in an opinion article for CNN. He added: “I predict that in the future we will routinely be giving children back their lost microbes.”

According to Blaser, we humans have already lost 15 to 40 percent of our microbiome diversity. Studies of people who don’t live a Western lifestyle show that they carry far more varied types of microorganisms. This April, a study that appeared in the journal Science Advances showed that Yanomami nomads living in the Amazon region have hugely diverse microbiomes—at least 40 percent more diverse than people living in the industrialized West.

The puzzling thing is this: for millennia we lived together with all these tiny beasties, and now that we are diminishing their populations to fight off disease, we are faced with more allergies and new types of illnesses. According to the well-documented hygiene hypothesis, allergies are on the rise now that our lives are getting cleaner and we are keeping bacteria at a distance (see “Dishwashing as medicine”).

In our food production, too, it is seen as increasingly important to prolong the shelf life of foods by using chemicals, and to produce food in an environment that is as clean as humanly possible. Farmlands all look so tidy nowadays, Ilse Blokker says. “It’s all tidy little rows of the same types of plants, while nature’s way is to grow diverse plants so that the soil remains healthy. All sorts of ‘undesirable’ herbs are being labeled as weeds. Farms are hygienic and regulated. Nature cannot do her work anymore. In today’s world, everything has to be too clean.”

As an organic farmer, Paul Blokker devoted years of work to generating a natural balance in the soil on his farm. “Everything was all about creating balance,” says Ilse. No chemicals are ever used at De Anna Hoeve. Additionally, the manure is not injected into the ground, as is done at most farms, but spread onto the surface, which is better for the quality of the soil. This way, the sunlight kills harmful bacteria and viruses and promotes the growth of healthy plants.

Coincidence or not, whenever the human microbiome is discussed, the word “balance” pops up an awful lot. But what is balance? Gregor Reid finds it too broad a word to apply to the human body, because balance means something different for every person. Reid is a professor of microbiology and immunology at the Schulich School of Medicine of the University of Western Ontario, in Canada. Interviewed remotely from his study in London, Ontario, Reid said, “You’re trying to restore homeostasis.” By this he means that every body has its own unique profile of microorganisms that is able to keep the internal environment in the body in balance. That’s how smart our bodies are.

“The question you should be asking is: Are all the organisms I have doing the right things in terms of energy utilization, deposition of fat and breaking down carbohydrates?” According to Reid, who was born in Scotland (his Twitter bio reads “Aberdeen supporter. Take probiotics daily”), probiotics, the beneficial microorganisms, are constantly supporting these systems. He imagines a future in which we go to the hospital to pick up a pill or potion containing a good bacterial strain that plays a healing or regenerative role for a specific ailment. He is a pioneer in this area and has been doing research into these healthy little beasties for decades now. 

The Human Microbiome Project brought about a huge change in the way scientists think, said Reid. “People suddenly realized, Wait a minute, we need to look at the composition of our microbiota to learn more about disease and health.” Medicine in the future, he said, will be more focused on developing a healthy microbiome and less on destroying microorganisms, as it is now.

Gregor Reid moved from Scotland to Canada in the 1980s. There, he became acquainted with the urologist Andy Bruce, another Scot, and they got along very well. Bruce was interested in the role of microorganisms in the preservation and repair of the body—the microbes that today we call probiotics.

Bruce made an intriguing discovery while conducting a study of vaginal bacteria in a group of women suffering from chronic bladder infections. E. coli bacteria, present in the women’s vaginas, turned out to be the perpetrator. The remarkable thing was that women who had never had a bladder infection had a high rate of Lactobacilli instead of E. coli. It almost seemed as if the Lactobacilli were protecting the vagina and keeping the sickness-inducing E. coli at bay.

Together with Bruce, Reid started researching this further. He remembers telling a colleague about their study and being asked mockingly, “What exactly are you going to do? Put yogurt into their vaginas? Which flavor?”

Reid said he even received the following response to his grant request: “Why are you looking into this? We’ve got antibiotics to treat these women.” His research was viewed with derision for a long time. But things are starting to change now. More and more studies are appearing that show probiotics are playing a positive role in the body, and that administering them has a preventive or healing effect.

The Russian Ilya Mechnikov is often seen as the founder of the science of probiotics. At the end of the 19th century, he was studying a group of nomads in Bulgaria who lived very long lives. You might already be able to guess his discovery: they drank sour milk—fermented dairy products such as kefir. Convinced of the health benefits, Mechnikov began to drink fermented dairy products every day. He made it himself, with the bacterial strain Lactocillus bulgaricus, and also distributed it among his friends. Mechnikov later received the Nobel Prize for the discovery of phagocytosis, the process by which cells—such as white blood cells in the human immune system—engulf and destroy hostile bacteria. He was always working on the idea that harmful processes in the body could be stopped by natural microorganisms.

After Mechnikov, research around probiotics was quiet for a while. But in Japan, around 1920, the researcher Minoru Shirota became inspired by Mechnikov’s work. Wanting to find a way to get live, intact bacteria into the intestinal gut, he developed Yakult, a drink that contains the bacterial strain Lactobacillus casei Shirota. This drink appeared on the market in Japan in 1953 but didn’t reach Europe and the United States until the 1990s.

Commercial Western companies quickly saw an opportunity for lucrative business in this type of drink, and a wave of probiotic products flooded the market. “Suddenly people started asking about gut health,” Reid remembers. Probiotics, according to Reid, do four things in our intestines: They break down food remnants that our own body’s bacteria have trouble dealing with (such as lactose), they reinforce the intestinal lining, they fight off harmful bacteria in the large intestine and they stimulate the immune system in the small intestine.

And all of this became a welcome target for the probiotics producers. “One year in America in the 2000s, there were about 300 probiotics that came on the market,” said Reid, with slight dismay. Most of these products were never tested and weren’t true probiotics, he explains.

There are still many unproven probiotics products making the rounds, said Reid. He lists several problems. First, there are many drinks and yogurts on the market containing Bifidobacteria and Lactobacilli. These may very well be beneficial bacterial strains, but since many have never been scientifically tested, it is hard to say if they will have any benefits. The body has various Lactobacilli of its own, so it is hard to know whether merely adding a few more makes a difference.

But that doesn’t mean Reid has only a few strains of probiotics to recommend. There has been extensive research on hundreds of strains by now, resulting in evidence for many specific health benefits. Probiotic drops with Lactobacillus reuteri DSM 17938, for example: “They help treat colicky babies.” He mentioned probiotic strains that prevent and treat urogenital infections and diarrhea, and others that relieve abdominal pain and bloating in patients with irritable bowel syndrome. He also listed probiotics that prevent pouchitis and are being used to treat ulcerative colitis.

Canada is a forerunner in the field of probiotics. In Europe and the U.S., the authorities are extremely cautious. They forbid producers of probiotics from listing their health benefits. Reid finds this terribly frustrating because, he said, this pushes probiotics off into a corner when so many people could benefit from them.

Hospitals aren’t taking probiotics seriously enough yet, either, in Reid’s opinion. He suggests that in the future, patients should be able to come to the hospital to submit a stool sample. “Within a few hours, you get your profile and they will see if there’s something wrong with the bacteria in there, and if there’s dysbiosis”—a microbial imbalance. The next step, according to Reid, would be to offer a variety of probiotics to match the patient’s microbiome profile and pathology.

That day still lies far in the future, but Reid continues to work on proving the benefits of probiotics and their importance to our health. He eats probiotic yogurt every day and sometimes a probiotic supplement, and enjoys a good health. “As a scientist, I need to try and find out what works, why it works in some people and not in others,” he said.

But it is clear to him that probiotics are a key to good health. “The sky’s the limit,” he said. “We came from these organisms, and so they’re integral to everything that we do. They affect every part of us.” 

Sidebar: Dishwashing as medicine

To say children don’t love washing dishes is an understatement. But recent studies show that children who live in houses where dishes are washed by hand have fewer allergies than children in homes with dishwashers. Swedish researchers at the University of Gothenburg reached this conclusion after studying hundreds of families. Their research was published this spring in Pediatrics.

The researchers carried out the study with the so-called hygiene hypothesis in the back of their minds. According to the hygiene hypothesis, exposure to diverse bacteria promotes the development of a strong immune system. This would explain the increase in allergies in countries where hygiene has improved substantially in recent decades. The Netherlands is one such country, where an increasing number of children are extremely sensitive to allergens. People who live in less hygienic circumstances, however, don’t suffer as much from hay fever, eczema and asthma.

The Swedish researchers wanted to find out how much influence lifestyle factors have on the development of allergies. Washing dishes by hand is probably less hygienic than putting the dirty plates and cutlery in the dishwasher. So they decided to study that. They put together questionnaires for the families of 1,029 children aged 8 to 9. They asked if the children suffered from eczema or asthma, for instance. They also took into account other factors that may influence the development of allergies, such as having been breastfed or owning pets.

Only 12 percent of the families still wash dishes by hand. But these families did report considerably fewer allergies. Of the dishwasher-using families, 38 percent reported eczema and 7 percent asthma. In families where dishes are still washed by hand, only 23 percent reported eczema and fewer than 2 percent asthma.

Also noteworthy was that families with the fewest allergies had three things in common: they wash dishes by hand, eat fermented food on a regular basis and buy food from a local farm. But the researchers don’t want to go so far as to recommend that everyone get rid of their dishwasher. They think more research is necessary first. | E.B.

Sidebar: Probiotics: Nine facts and tips

1 – The word probiotics comes from ancient Greek, meaning “good for life.” The World Health Organization defines probiotics as “live microorganisms which when administered in adequate amounts confer a health benefit.”

2 – Probiotics come in various forms: as drinks or as supplements such as capsules, tablets, pills, potions and powders. If you are buying a probiotic and want to assure yourself it has scientifically proven health benefits, check which bacterial strains were used and look them up online, for example in the academic medical database PubMed.

3 – That said, as Liz Lipski points out, “there’s still only bits and pieces that we know about probiotic supplements.” This is why she rotates her probiotic products. “The different strains have different properties, and we simply don’t know enough yet about each and every one of them.”

4 – Yakult, the Japanese probiotic dairy product, is drunk daily by millions of people around the world. The bacterial strain used to make it has been tested and has been proven to arrive in the intestines and improve slow digestion. According to its manufacturer, Yakult also strengthens the immune system by adding more Lactobacilli to the intestines.

5 – It is no simple matter for probiotics to actually reach the intestines, says Irma Kromhout-van Cappelle, a Dutch orthomolecular nutritional therapist and author of Probiotica: op zoek naar bacteriële balans (“Probiotics: In Search of a Bacterial Balance”). The stomach environment is often too acidic for probiotics because of our modern diet. It causes the probiotics to get killed in the stomach and not even reach the intestines. There are special supplements with a so-called enteric coating that doesn’t dissolve in the stomach, so that the organisms can be delivered to the intestinal tract.

6 – When purchasing supplements, Kromhout-van Cappelle always pays attention to the percentage of bacteria contained in them and makes sure there are many different strains. She says, “Everyone has different gut bacteria, so if you make use of diverse bacterial strains, you have a better chance that it will be effective and the supplement will take hold.”

7 – If you really want to make a drastic change in your microbiome, merely taking probiotics may not be enough. Currently, fecal microbiota transplants are being done all over the world, as a way to completely change the intestinal environment.

8 – After reading this article, you too might be interested in kefir. You can make your own with a base of water or milk, and you can find lots of information on how to do this online. The special thing about the kefir from De Anne Hoeve is that it is made from raw milk that still contains many enzymes, vitamins and minerals.

9 –  Finally, “putting more probiotic-rich foods into our lives is foundational,” as Lipski says. Yogurt, sauerkraut, kimchi (a Korean pickled cabbage), tempeh, sourdough bread and cultured pickles are all good options.