If I were to ask you to rank the organs and parts of your body on their importance for human functioning, the brain would almost certainly be top of the list. I imagine the heart and lungs would also rank highly, followed by a long list of body parts that would probably end with the appendix (which we can actually do without).

Brain, heart, and lungs aside, I wonder how many of you placed the microbiome on your list of most treasured body parts. Indeed, I wonder how many of you consider the microbiome an organ at all.

The microbiome is the collection of bacteria, archaea, fungi, and other organisms that populate the length of your gastrointestinal tract, and nearly every surface of your body. Although very different from your other body tissues and structures, it does behave very much like an organ. It performs many essential duties, which we cannot do ourselves; it makes vitamins, helps digest our food, and trains our immune system, building our resilience to infection and disease.

So important are these microorganisms that some have suggested we redefine humans as a ‘superorganism’ or ‘holobiont’, acknowledging the wide variety of species (human, bacterial, viral) that make up each person.

So where do these important microbes come from? If they are so essential for us humans, we must be born with them, or at least get them very early in life, right?

Well, the jury is out on whether bacteria exist in the womb before birth, but evidence is clear that our passage into the world through the vaginal canal is our first large scale exposure to microbes. These bacteria take up residence in our guts and start a population that will be added to throughout our lives. For those people born through a caesarian section, a slightly different set of bacteria develop, at least initially.

After birth, we see that the microbiome is related to an extraordinary range of human functions, including toddler temperament, as well as the development of language abilities in infants. Studies in rats and mice have revealed that microbes are critical for emotional health as well as the development of the brain itself; growing up without germs results in different emotional behaviors and altered maturation of several brain regions critical for emotion processing, such as the amygdala, prefrontal cortex, and hippocampus. Finally, the microbiome has been shown to be related to learning and memory in both young and adult rodents.

The brain and the microbiome develop over similar timescales, with many of the largest changes happening in the first few years of life. Periods of rapid development are also times when the environment can have the biggest impact, and are often called ‘sensitive periods’ for that reason. Studies in rats and monkeys have shown that stressful early environments can change the microbiome in ways that are associated with anxiety. Importantly, those studies have not yet been carried out in humans.

“Microbes are critical for emotional health as well as the development of the brain itself.”

To determine how the microbiome, brain, and anxiety are impacted by early stress in young humans, my colleagues at Columbia University and I have been collecting stool samples (that’s how we measure the microbiome) from about 70 children that have been exposed to early stress, in this case a time-limited period of early caregiving adversity due to institutional or orphanage care before international adoption.

In addition, to test how the microbiome is related to learning and memory in those children, I have collected brain scans while children play a learning game. Finally, I have interviewed the parents about the children’s emotional health, and the children have answered emotion questionnaires.

In an earlier small (pilot) study, we showed that early stress was associated with differences in bacteria, and those bacteria were related to brain activity in regions like the prefrontal cortex, which has been implicated in anxiety and cognitive functioning. Analyses are currently underway to see whether those associations exist in the bigger group of children. If they do, it could have important implications for the ways we think about, and treat, stress.

So next time someone asks you to make a list of important body parts, I hope you will consider the microbiome in your top 5, as without it, you would most likely be quite a different person.


The purpose of the annual Flux Congress is to advance the understanding of human brain development by serving as a forum for professional and student scientists, physicians, and educators to: exchange information and educate the next generation of developmental cognitive neuroscience researchers; make widely available scientific research findings on brain development; encourage translational research to clinical populations, and encourage further progress in the field of developmental cognitive neuroscience. This year’s Flux Congress took place in Berlin, Germany.

Bridget Callaghan was among the speakers at the congress.

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