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Research is accumulating that the microbial exposure from a vaginal birth, breastfeeding, and pets in the first year of life are all good for a baby's developing immune system and the gut microbiome.

From Science Daily: Breastfeeding, other factors help shape immune system early in life

Researchers say that breastfeeding and other factors influence a baby's immune system development and susceptibility to allergies and asthma by what's in their gut. The striking findings from a series of studies further advance the so-called hygiene hypothesis theory that early childhood exposure to microorganisms affects the immune system's development and onset of allergies, says Christine Cole Johnson, Ph.D., MPH, chair of Henry Ford's Department of Public Health Sciences and principal research investigator.

The gut microbiome is the collection of microorganisms in the gastrointestional, or GI, tract, and the human body has billions of these microbes... The gut microbiome is known to play an important role in immune system development, and is thought to contribute to a host of diseases like obesity, autoimmune diseases, circulating disorders and pediatric allergies and infection.

"For years now, we've always thought that a sterile environment was not good for babies. Our research shows why. Exposure to these microorganisms, or bacteria, in the first few months after birth actually help stimulate the immune system," Dr. Johnson says."The immune system is designed to be exposed to bacteria on a grand scale. If you minimize those exposures, the immune system won't develop optimally."

In six separate studies, researchers sought to evaluate whether breastfeeding and maternal and birth factors had any effect on a baby's gut microbiome and allergic and asthma outcomes. Using data collected from the WHEALS birth cohort, researchers analyzed stool samples from infants taken at one month and six months after birth. They also looked at whether the gut microbiome impacted the development of regulatory T-cells, or Treg, which are known to regulate the immune system. Highlights:

Breastfed babies at one month and six months had distinct microbiome compositions compared to non-breastfed babies. These distinct compositions may influence immune system development.Breastfed babies at one month were at decreased risk of developing allergies to pets. • Asthmatic children who had nighttime coughing or flare-ups had a distinct microbiome composition during the first year of life. • For the first time, gut microbiome composition was shown to be associated with increasing Treg cells.

Researchers found that a baby's gut microbiome patterns vary by: • A mother's race/ethnicity. • A baby's gestational age at birth. • Prenatal and postnatal exposure to tobacco smoke. • Caesarean section versus vaginal delivery.• Presence of pets in the home.

Henry Ford's landmark 2002 study found exposure to dogs or cats in the first year of a baby's life reduced their risk for allergies.

More long-term benefits from breastfeeding. The first study finds that long-term it's as good or better than statins! From Science Daily:

Birthweight and breastfeeding have implications for children's health decades later

Young adults who were breastfed for three months or more as babies have a significantly lower risk of chronic inflammation associated with cardiovascular and metabolic diseases, according to research from the Brown School at Washington University in St. Louis.

"This study shows that birthweight and breastfeeding both have implications for children's health decades later," said Molly W. Metzger, PhD, assistant professor at the Brown School and a co-author of the study with Thomas W. McDade, PhD, of Northwestern University.

"Specifically, we are looking at the effects of these early factors on later levels of C-reactive protein (CRP), a biomarker associated with risk for cardiovascular and metabolic disease," Metzger said. "Comparing the long-term effects of breastfeeding to the effects of clinical trials of statin therapy, we find breastfeeding to exert effects that are as large or larger."

The researchers used data from the U.S. National Longitudinal Study of Adolescent Health, including parent surveys, and blood samples providing measurements of CRP. These findings held up in a series of sibling models, in which one sibling was breastfed and the other was not. Such models provide improved confidence in the results by implicitly controlling for genetic factors for elevated CRP.

This study was published a year ago (Aug. 2013) and shows a long-term benefit to the mother (reduced Alzheimer's risk) of breastfeeding. From Science Daily:

Breastfeeding may reduce Alzheimer's risk

Mothers who breastfeed their children may have a lower risk of developing Alzheimer's Disease, with longer periods of breastfeeding also lowering the overall risk, a new study suggests.

The report, newly published in the Journal of Alzheimer's Disease, suggests that the link may be to do with certain biological effects of breastfeeding. For example, breastfeeding restores insulin tolerance which is significantly reduced during pregnancy, and Alzheimer's is characterised by insulin resistance in the brain.

Another reason to breastfeed infants. From Medical Xpress:

Breastfeeding promotes the growth of beneficial bacteria in the gut

A number of studies have shown that breastfed babies grow slightly slower and are slightly slimmer than children who are fed with infant formula. Children who are breastfed also have a slightly lower incidence of obesity, allergies, diabetes and inflammatory bowel disease later in life. According to a new study by the National Food Institute and the University of Copenhagen this may be due to the fact that breastfeeding promotes the development of beneficial bacteria in the baby's gut.

"We have become increasingly aware of how crucially important a healthy gut microbial population is for a well-functioning immune system. Babies are born without bacteria in the gut, and so it is interesting to identify the influence dietary factors have on gut microbiota development in children's first three years of life," research manager at the National Food Institute Tine Rask Licht says.

The study shows that there are significant changes in the intestinal bacterial composition from nine to 18 months following cessation of breastfeeding and other types of food being introduced. However, a child's gut microbiota continues to evolve right up to the age of three, as it becomes increasingly complex and also more stable.

"The results help to support the assumption that the gut microbiota is not - as previously thought - stable from the moment a child is a year old. According to our study important changes continue to occur right up to the age of three.

More information: The study has been described in a scientific article in Applied and Environmental Microbiology: Establishment of intestinal microbiota during early life: A longitudinal, explorative study of a large cohort of Danish infants:www.ncbi.nlm.nih.gov/pubmed/24584251

Breast milk contains hundreds of species of bacteria.From the December 8, 2013 Scientific American:

The bacteria in breast milk

Several recent studies have found that breast milk contains a healthy dose of commensal bacteria; all the staphylococci, streptococci, and lactic acid bacteria that are found in the infant gut. This isn’t just bacteria from the skin which have contaminated the samples, but bacteria that have come from inside the breast as an integral component of the milk.

In a study of 16 women it was found that while each milk sample contained hundreds of different bacterial species, around half of the microbiotic community was made up of nine species present in all samples. The other half varied from person to person. This pattern is also found in human gut microbes; a core set present in all individuals along with a large diversity of separate species to make up a unique individual microbiome.

So how do bacteria get into breast milk? Some of them may come from the mouth of the baby. During feeding the skin of both the mother and baby will be in contact with the baby’s open mouth and a certain amount of flow-back can occur between the mouth and nipple. More excitingly it’s been suggested that immune cells in the mothers gut may be able to pick up bacteria and carry them around the body using the lymphatic system. The lymphatic system is a network of vessels used to transport blood plasma. It’s a main highway for immune cells inside the body and is also involved in the absorption and transports of fats.

Like all humans, infants have a range of bacteria within their gut. It looks like these bacteria are initially supplied from the mother’vaginal and skin bacteria, before being replaced by bacteria from the breast milk. Researchers also found that when babies started eating solid food a whole new range of bacteria was introduced, forming the gut microbiome that persisted into adulthood.