Mark Sloan, MD

Unintended Consequences: Cesarean Birth, Gut Microbiota, and Child Health

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When I first learned some years ago that cesarean birth was associated with an increased risk of childhood asthma and eczema, I eagerly awaited the rest of the story. What could the link possibly be? Epidurals? Anesthetics? Antibiotics? Something strange and exotic was afoot, I was certain.

Imagine my surprise, then, when a growing body of evidence pointed to an unexpected source: the newborn gastrointestinal tract and the microorganisms that live there.

How might intestinal bacteria play such a major role in the health and well being of newborns and children? The answer lies in an ancient, mutually beneficial relationship between humans and bacteria, one that modern birth technology has dramatically altered.

Gut Microbiota

“Microbiota” is the term used to describe the community of microorganisms—bacteria, viruses, and fungi—that normally live in or on a given organ in the body. There’s a unique microbiota that inhabits the mouth, for example, another that lives on the skin, and still another that populates the intestine, or gut. Given an intestinal surface area of about 2,700 square feet—more or less the size of a tennis court—the microbiota inhabiting the gut is the largest and most diverse in the body.

How large and diverse? The gut microbiota contains roughly one quadrillion cells—at least ten times as many cells as there are in the entire human body. More than 1,000 bacterial species having been identified to date, with unknown numbers yet to be discovered.

The cells of the gut microbiota perform a number of critical functions for their human hosts: they promote intestinal cell growth, protect against infection, manufacture vitamin K, and even extract extra nutrients from otherwise indigestible food. A laboratory mouse bred without a gut microbiota will be scrawny, weak, and infection-prone; the same would be true for humans if not for our legion of microscopic fellow travelers.

The Bacterial Colonization of the Infant Gut

How do all those bacteria find their way to the newborn’s intestine?

The colonization of the infant gut occurs in five distinct phases: 1) prenatal; 2) intrapartum; 3) introduction of oral feedings; 4) weaning to solids; and 5) complete adult colonization, which under typical circumstances occurs by 12-18 months of age. The intrapartum and introduction of oral feeding phases—phases 2 and 3—will be discussed here, as mode of delivery and type of initial feeding are the most critical determinants of final gut microbiota makeup.

Intrapartum phase: For vaginally born babies the vast majority of bacteria destined to colonize the gut originate in the maternal birth canal and rectum. Once swallowed by the fetus/newborn during birth, they travel through the stomach and colonize the upper and lower intestine, a complicated process that evolves rapidly over the first hours and days of ex-utero life. Cesarean-born babies, particularly those delivered electively, encounter a very different scenario which will be discussed below.

Introduction of oral feedings: The type of feeding a mother chooses for her baby greatly influences the makeup of the gut microbiota. Breast milk is perfectly designed to promote the growth of healthy, “probiotic” bacteria in the gut. Breast milk contains not only the very probiotic bacteria the infant needs, but also oligosaccharides—small carbohydrate molecules that promote the growth of probiotic bacteria. These oligosaccharides—which are essentially “germ food,” as the newborn can’t digest them—make up 8% of the nutritive content of breast milk.

In other words, the initial colonization of the infant gut during birth is continually augmented by breastfeeding, which “seeds and feeds” the gut with health-promoting bacteria, such as Bifidobacteria, Lactobacillus and Bacteroides species, and bacteria-specific nourishment.

Disrupting an Ancient Process: How Cesarean Birth, Formula Feeding, and Antibiotics Impact Gut Colonization

Humans co-evolved over millions of years with the bacteria that populate our intestines. Our bodies have come to expect the arrival of probiotic bacteria at birth, and to prepare a bacteria-friendly environment in which they flourish. Two very recent technological advances—cesarean birth and artificial infant formula feeding—have radically changed this ancient relationship. We’re just now beginning to understand the unintended consequences of these changes.

Infants born by cesarean section—particularly cesareans performed before labor begins—typically don’t encounter the bacteria of the birth canal and maternal rectum. (If a cesarean is performed after rupture of membranes the infant may be exposed to these bacteria, but to a lesser degree than in vaginal birth.) Instead, skin bacteria and those from the hospital environment enter the newborn’s nose and throat and quickly populate the bowel. As a result, the bacteria inhabiting the lower intestine following a cesarean birth can differ significantly from those found in the vaginally born baby.

The gut microbiota in cesarean-born babies is less diverse than that seen with vaginal births. Probiotic bacteria species are slow to arrive and reduced in number. Abnormal bacteria, such as Clostridium difficile, are commonly found. Final colonization, which is completed between 12 and 18 months of age in vaginally born babies, can be delayed by months, even years.

Today’s commercial infant formulas can’t match breast milk for promoting a healthy gut microbiota. Unlike breast milk, formulas do not contain probiotic bacteria, and although prebiotic oligosaccharides are now added to some formulas, there is no convincing evidence that this promotes a healthy gut microbiota.

A third disruptor of gut colonization is the use of antibiotics during pregnancy, labor, and birth. Ample evidence has shown the microbiota-altering properties of antibiotics given to older infants for ear infections, pneumonia and the like. But, surprisingly, there hasn’t yet been much research on the effects of maternal antibiotics on the formation of the gut microbiota, or how maternal antibiotics might impact the probiotic content of breast milk. What studies there are suggest that antibiotics do change the gut microbiota in the immediate newborn period, but to what extent, and for how long, remain unclear.

Why Gut Microbiota Matter: Development of the Newborn Immune System

The dramatic first steps in immune system development take place at the same time the gut microbiota is being formed, and the bacteria acquired during birth and early feeding play critical roles in that process. In fact, they actually direct it.

Mark Sloan M.D. is a pediatrician, writer, and medical educator living in Santa Rosa, California. His book, Birth Day: A Pediatrician Explores the Science, the History, and the Wonder of Childbirth, has been praised by the Washington Post, the New England Journal of Medicine, and the Journal of Midwifery and Women’s Health, and was named a 2010 Northern California Book Awards finalist. Published as Baby Science in Japan, Birth Day was named a ‘Top Ten Science Book of 2010′ by the Japan Economic Times. His websites include: and

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