The evidence is growing. Another recent study found that exposure to dirt and animals in the first year of life is beneficial for development of a a rich and diverse gut microbiome - that is, for greater species "richness" as well as more beneficial microbes. This is linked to lower levels of allergies and asthma in children.
So don't worry about children being exposed to animal "germs" and getting dirty! Instead, consider the microbes as having health benefits, such as developing a "robust immune system". In summary, it now appears that in the first year of life the immune system needs lots of exposure to all sorts of microbes (e.g. from pets, animals, dirt) to "train it" to develop normally.
The Ohio State University researchers compared 5 healthy rural Amish infants to 5 healthy non-Amish urban infants in Ohio, also found that all of the rural (Amish) children were breastfed, while 2 of the urban (non-Amish) children were only formula fed (some microbial differences there). The Amish households had farm animals (cattle, sheep, and/or horses) and pets (dogs and/or cats), while the non-Amish households had no contact with livestock, but did have a pet dog or cat. Just like in other studies, one pet doesn't seem to be enough - even more animal exposure in early childhood is best for the gut microbiome. [One study found a dose-dependent effect with exposure to 5 furry pets in early childhood was needed to prevent all allergies.]
Studies find that rural (Amish) children have a low incidence of allergies and asthma, while urban children have a high incidence of allergies and asthma. In this study, an example of microbial differences in the 2 groups of children was that Bifidobacterium bacteria were "enriched" in non-Amish (urban) infants, while Roseburia species were "enriched" in Amish (rural, farm-raised) infants. Similar gut microbe differences have been observed in other studies comparing rural and urban children, and both dietary differences (e.g. farm raised children eat lots of homegrown produce) and environmental differences (animal exposure) are thought to be responsible for the differences.
From Science Daily: Keeping livestock in the yard just might help your baby's immune system
Getting up close -- and a little dirty -- with farm animals just might help us fend off illness, say researchers who've further demonstrated the benefits of early exposure to a wide variety of environmental bacteria. Scientists from The Ohio State University found that bacteria and other microbes from rural Amish babies was far more diverse -- in a beneficial way -- than what was found in urban babies' intestines. And, in a first-of-its-kind experiment, they found evidence of how a healthier gut microbiome might lead to more robust development of the respiratory immune system.
"Good hygiene is important, but from the perspective of our immune systems, a sanitized environment robs our immune systems of the opportunity to be educated by microbes. Too clean is not necessarily a good thing," said the study's co-lead author Zhongtang Yu, a professor of microbiology in Ohio State's Department of Animal Sciences and a member of the university's Food Innovation Center.
The research team collected fecal samples from 10 Ohio babies who were around 6 months to a year old. The five Amish babies all lived in rural homes with farm animals. The other five babies lived in or near Wooster, a midsize Ohio city, and had no known contact with livestock.
The samples revealed important differences -- particularly a wide variation in microbes and an abundance of beneficial bacteria in the Amish babies' guts that wasn't found in their city-dwelling counterparts. The researchers expected this, based on the infants' exposure to the livestock and the fact that the Amish tend to live a relatively less-sanitized lifestyle than most other Americans.
What they really wanted to know was how these differences might affect development of the immune system, setting the groundwork for a body's ability to identify and attack diseases and its resistance to allergies and other immune-system problems. Previous studies in the U.S. Amish population and to comparable populations throughout the world have drawn a clear connection between rural life and a decrease in allergies and asthma, Gourapura said.
This connection has led to a theory called the "hygiene hypothesis," which is built on the idea that hyper-clean modern life -- think antibacterial soap, ubiquitous hand sanitizer and scrubbed-clean homes and workplaces -- has led to an increase in autoimmune and allergic diseases.
Given that the trillions of microbes in the human gut are known to play an important role in health and disease progression, the Ohio State researchers wanted to explore how different gut microbiomes might contribute to immune system development. To do this, they used fecal transplants from the babies in the study to colonize the guts of newborn pigs.
"We wanted to see what happens in early immune system development when newborn pigs with 'germ-free' guts are given the gut microbes from human babies raised in different environments," Gourapura said. "From the day of their birth, these Amish babies were exposed to various microbial species inside and outside of their homes." The researchers saw a connection between the diverse Amish gut microbes and a more-robust development of immune cells, particularly lymphoid and myeloid cells in the intestines.