As conscientious new parents, Erica and Justin Sonnenburg took a natural birth class and other steps to ensure their daughter a healthy start in life. But things didn't go as planned. After 30 hours of labor, Erica needed a C-section.
Mother and daughter came through fine. But when Claire was 3, she began to experience painful bouts of constipation, which led her scientist parents to wonder if the C-section, though medically necessary, also undermined her chance for that optimal healthy start. What the Sonnenburgs discovered about the likely source of their daughter's digestive distress not only inspired them to overhaul their family's diet, it informed their research into one of the hottest areas of medical science and human health.
The Sonnenburgs, who run their eponymous lab in Stanford's department of microbiology and immunology, have since become leading researchers in the field that studies gut health. They research how bacteria and other single-celled organisms -- the ecological community known as the microbiota -- are key to maintaining the health of our gastrointestinal systems.
But as suggested by the title of their 2015 book, "The Good Gut: Taking Control of Your Weight, Your Mood and Your Long-Term Health," the premise of their research is that a healthy GI tract does a lot more than prevent digestive disorders. It appears to be linked to all aspects of biology and to have far-reaching influence on health and wellness.
Among other things, the composition of micobiota in the large intestine may shed light on why a growing number of children and adults in Western countries have allergies, asthma, inflammatory bowel diseases, even autism. Improving gut health, they say, also could help prevent cancer, heart disease, diabetes and possibly cure obesity. As a bonus, they believe it could even help with such mental health issues as depression and schizophrenia.
Much of gut health research focuses on how our Western diets are much worse for us than we thought. The theory is that overprocessed, calorie-dense foods, along with the overuse of antibiotics and our super-hygenic foods and homes, have upset the diversity of microbes that have existed in human bodies for thousands of years. This disruption is making us sicker than we need to be.
"The field of microbiota studies has really exploded in the last 10 years," said Erica Sonnenburg, who is a senior research scientist in the lab.
Are we our bacteria?
Some may be familiar with the concept of gut health after coming across the word "probiotics" on the labels of fermented foods and supplements at health food stores.
Probiotics contain live bacteria that the Sonnenburgs believe nurture healthy gut bacteria and protect against illness. Yogurt, fermented pickles and kefir drinks are among the staples of the Sonnenburg family diet.
What's less familiar to most of us is the extent to which we are made up of bacteria. Our skin and orifices are covered in microbes, but most -- more than 100 trillion bacteria -- live in the large intestine, which is best known for absorbing water and vitamins and converting digested food into feces.
But the colon looks to be involved in much more, the Sonnenburgs say. It has a direct connection, via neurons and chemical pipelines, to the brain, which in part explains why we usually feel stress in our bellies. The gut microbes also are in constant communication with the immune system, "operating a dial" that controls immune response to disease-causing pathogens.
But the gut-immune system link also bolsters the idea that poor eating causes inflammation in our bodies, which, in turn leads, to chronic illnesses.
That idea was pioneered by Andrew Weil, the Harvard-educated expert in integrative medicine who wrote the introduction to "The Good Gut." He found a talk about new research Justin gave at a 2013 conference exciting because it offered possible explanations to "puzzling questions I had about health conditions on the rise," he said.
It all starts at birth
The Sonnenburgs say their older daughter's experience highlighted how good gut health starts from the very beginning.
Until birth, the human body is sterile, they say. During delivery, a baby picks up the microbes that will seed her gut microbiota from contact with her mother's vaginal area.
Babies born by C-section, like both the Sonnenburgs' daughters, may miss out on these mother-approved bacteria, which could be one reason C-section babies are more likely to become obese or have allergies, asthma and celiac disease.
With their older daughter, the Sonnenburgs believe the C-section allowed the wrong microbes to get into her body and mess with her developing microbiota. An added complication was the fact that she received a dose of antibiotics at birth. While it's generally known that the overuse of antibiotics has given rise to deadly antibiotic-resistant bacteria, it's less known that gut microbiota suffers "tremendous collateral damage" whenever we get a dose of antibiotics, said Justin. That's because most antibiotics are "broad spectrum," meaning they don't just kill the bad bacteria, they also kill the good microbes. While the gut usually recovers from a round of antibiotics, "it may never be the same," he said.
Boosting gut health
More than anyone, the Sonnenburgs understand that C-sections and antibiotics save lives. And they say there are things people can do to repair damage to the microbiota.
For a baby born by C-section, for example, parents can talk to the doctor about exposing the newborn to a swab from the mother's vagina.
The Sonnenburgs are also strong advocates of breast-feeding. Not only does breast milk contain super nutrients evolutionarily programmed for human survival, it's also packed with complex carbohydrates that feed the gut's microbiota.
For older kids -- and for the rest of us -- a healthy plant-based diet, similar to Mediterranean or Japanese diets, can help a lot. To address their oldest daughter's constipation, the Sonnenburgs took a careful look at what the family was eating.
While they say they weren't constantly feeding her Chicken McNuggets, they realized she was eating too much macaroni and cheese and too few vegetables.
So they went to what many might consider extremes. They emptied their kitchen of white rice, flour and pasta and filled it up with ancient grains like quinoa, as well as lots and lots of vegetables. The older girl's constipation disappeared and has never returned.
Today, the family follows that mostly plant-based diet, which includes some meat, and they regularly consume probiotic foods.
A long-term vision
"The Good Gut" is filled with examples of interventions for many puzzling health conditions. Fecal transplants are a promising treatment. In a 2013 Dutch study, stool samples from healthy donors were injected into people with debilitating colitis caused by the bacteria C. difficile. After the first treatment, 81 percent of patients were cured.
In the Sonnenburgs' lab, Justin has directed a graduate student to invent a device that would allow people to collect a stool sample at home, suspend it in a solution and use an app on their smartphone to regularly measure their gut bacteria and see if they need to adjust what they eat.
"That's one of the long-term kinds of things we're thinking about in our lab," he said. Other future possibilities? It may become routine to map the genes of one's intestinal bacteria to target treatment.
Said Erica: "We're at the point of understanding a lot of the basic principles of how gut bacteria work and how that translates into understanding other aspects of our biology that you wouldn't think would be at all related."