Human bodies are composed of approximately equal numbers of bacteria (and other foreign microbes) and our own cells. The bacteria living inside of us are often referred to as our microbiome. Maintaining the health of the human microbiome is complicated and a point of contentious debate; even defining what a healthy microbiome looks like has been challenging for scientists. Wellness companies have long promoted fermented foods as a holy grail for regulating gut health; their actual health benefits, however, remain to be uncovered. 

The microbiome itself is a complicated component of the human body. “Within our bodies we have microorganisms, [such as] bacteria, that live primarily in our gut,” said Mary Murphy, Infectious Disease teacher. “What we know is that often when someone has a disease we can see a disruption in the health of the microbiome.” The disruption could be in the diversity of the microbiome—how many different species are represented—or, a type of bacterium (singular type of bacteria) outcompeting other bacteria. 

However, what is considered to be a healthy microbiome also remains to be defined. Matthew Medeiros, an evolutionary biologist at the University of Hawaii, Manoa, said in an interview with The Urban Legend, “I would say that someone who eats lots of fruits and vegetables and doesn’t take antibiotics often probably has a nice diversity of healthy microbes that can help digest our food, regulate our appetites and even help us have an improved mood.” A nutrient-rich diet promotes the growth of bacteria that can further digest nutrient-rich foods. “[Likewise,] when we eat less-healthy foods, the microbes that like those foods multiply and even cause us to crave more junk food,” said Medeiros. 

Attaining a diverse gut microbiome is also dependent on environmental factors. “The diversity really is this feedback effect between you and the environment,” said Cole Larsen, a science teacher. “If you live in a more sterile or bacterially homogenous environment, you’ll probably have a more sterile, more bacterially homogenous microbiome.” 

There is some evidence that there are certain microbiome profiles that might be associated with certain health conditions. However, Larsen said, “I don’t think we know of a universal way to define [a microbiome] that’s healthy. We generally look for diversity [in bacteria types present within the microbiome].” 

With the development and increased use of efficient sequencing technologies and metagenomic approaches—both of which allow scientists to process large amounts of genetic data—scientists have been able to define the complexity of the microbiome without culturing—propagating bacteria within a laboratory setting—all bacterial species within the gut. “We can take a sample from their stool (poop) and then just sequence the DNA there without having to worry about actually ever seeing the bacteria that produced the DNA,” said Larsen. “So it basically allows us to take a genetic snapshot of a population.” This has been a critical advance because most bacteria in our guts cannot be cultured using standard techniques.

Additional advances in sequencing technology and bioinformatics approaches are enabling scientists to study the effects of individual genes within bacteria that may have an impact on human health. “If we can look at [a bacterial] genome, we can maybe try to find out why it’s beneficial,” said Larsen. Scientists can now move beyond correlational studies that focus on comparing the diversities of people’s microbiomes to understand what a healthy microbiome may look like. Instead, scientists can move towards understanding what the bacteria within human microbiomes may be doing based on their individual genes. 

The proven benefits of improving gut microbiome health are still a frontier of scientific research. Although there is no conclusive scientific evidence that proves that the consumption of foods high in probiotics—often called good bacteria—or high in antioxidants are beneficial to the human gut microbiome, they are not considered to be harmful either. Fermented foods such as yogurt, kimchi, some cheeses, sauerkraut and kombucha are all good sources of probiotics.  “[Still,] at least some of the marketing and promotion regarding probiotics is based on hope, not on science,” said Medeiros. 

That being said, consumption of food high in probiotics is not harmful to human health either. “I do think that fermented foods, in general, are probably good for us in the sense that they help increase beneficial microbes in our guts,” said Medeiros. “But I also think we’ll know a lot more in another 10 years or so.”