The Second Genome: Bacteria We Receive from Our Family Shape Our Health

breastfeeding_namibiaThe genes we get from our parents are important for building and maintaining our cells and also predispose us to certain health disorders that are known to have a hereditary component. It was long believed that it was the human genes that shaped us, but we’re now learning that the trillions of microorganisms that inhabit the human body encode 100-fold more unique genes than the genome of the human host, which essentially means that we are more than 99% microbe from a genetic perspective (1). Just like our human genome, this “second genome” in our bodies is largely inherited from our parents. Recent research which shows that the microbiome impacts most aspects of our health is now changing our perspective on heredity and genetic predisposition to disease.

We receive microbial DNA from parents and close family

The Human Microbiome consists of trillions of microorganisms from thousands of different species. While the microbiome changes throughout life to reflect changes in environment and lifestyle, the basic structure of bacteria arrives from our mother, father, and other close relatives.

It was long considered a scientific dogma that the womb was a sterile environment, but we’re now learning that the human microbiome is probably seeded before birth. This is actually not surprising considering that most animals are inoculated with bacteria in the womb.

Father and baby

Children pick up bacteria from close relatives.

Infants also receive a mix of microorganisms when they pass through the birth canal, and this exposure seems to be especially important for establishing healthy bacteerial communities in the body. Children who are born through caesarean section acquire different bacteria and also have an increased risk of developing type 1 diabetes and autoimmune disease later in life (2,3).

After birth, breast milk quickly becomes the major source of beneficial bacteria and prebiotic fibers. Since breast milk contains over 700 species of bacteria, it’s no surprise that bottle-feeding dramatically jeopardizes the growth and immunity of the baby (4).

Newborn children also pick up plenty of bugs from family members through kissing, pre-chewed food, and other types of close contact. The microorganisms we pick up during these first days and months of life become the foundation of our microbiome.

The “second genome” has a significant impact on our health

If you’re a regular reader of this site or have been following the recent research on the human microbiome, you know that microbial imbalances in the body have been linked to all sorts of different diseases. E.g., lung diseases such as chronic obstructive pulmonary disease is associated with an altered lung microbiome, bacterial vaginosis is associated with changes to the microbiome in the vagina, and type-2 diabetes is associated with gut dysbiosis (5,6,7). Although we know that certain health disorders in itself can initiate changes to the microbiome, it’s well established that it also can happen the other way around – that dysbiosis drives inflammation and disease.

So, the question that comes to mind is: Do we receive the combination of microbes that our mother – and to a certain degree other family members – carries, or do we inherit a subset of the microbial communities? Let’s look at the different ways we receive microbes from close family:

  • The womb
    It’s still unclear which types of bacteria that live in the womb, and whether they play a role in seeding the microbiome of the fetus.
  • Birth canal
    The vaginal microbiome certainly impacts which types of bacteria that colonize the newborn during birth.
  • Breast milk
    We don’t know a lot about the factors that impact the composition of the human milk microbiome, but one recent study showed that “milk from obese mothers tended to contain a different and less diverse bacterial community compared with milk from normal-weight mothers” (8). Although it seems that the microbiome in the rest of our body affects the composition of microbes in breast milk, there just aren’t enough data to say for sure at this point.
  • Pre-chewed food, kissing/cuddling, etc.
    Health is contagious in the sense that we pick up bacteria from other humans and animals, and a newborn child certainly obtains microorganisms from the skin and mouth of mum, dad, and other close relatives.

Although more studies on the subject are needed, it’s clear that the organisms we receive reflects the microbiome of our parents and that part of the hereditary component of a lot of health disorders has to do with the second genome we inherit from our mother and other family members.

We have the ability to alter our genome to an extent never previously thought possible

Prokaryote cell

“The second genome” is comprised of the DNA of the trillions of microorganisms in our body.

The microorganisms that live in and on our bodies are sometimes referred to as “the forgotten organ”, because it’s only recently that we’re starting to understand the wide spectrum of metabolic functions that the microbiome provides. We also know that microbes are able to exchange DNA between each other through lateral gene transfers, and recent research even shows that bacteria occasionally transfer DNA into human genomes (9,10). Since microbial DNA has such a significant impact on our health, it seems that the microbiome isn’t just a forgotten organ, but also a forgotten genome.

Although we know that diet and lifestyle can impact gene expression, our human genome is more or less fixed, and we’re about 99% similar to other people in terms of our human DNA (11). However, the genome of our microbiome can vary significantly from one person to another and can also be altered fairly rapidly. Antibiotics, probiotics, prebiotics, antibacterial gels and lotions, smoking, and diet are just some of the factors that impact the second genome in our bodies.

The fact that we can alter the second genome also suggests that although we inherit a poor mix of bacteria from a diseased mother, we have the ability to manipulate the microbiome to our advantage.

Western lifestyle perturbs the second genome

A lot of the progress in modern medicine, such as antibiotics, have long unforeseen consequences to the human superorganism.

Antibiotics alter the balance of bacteria in our body and decrease microbial diversity.

While it’s estimated that the genome of the human host changes very slowly, we know that the trillions of microbes in our body are sensitive to external input. Increased use of antibiotics, low intake of prebiotic fiber, and reduced exposure to soil microbes are just some of the factors that seem to disrupt the microbiome, and therefore it’s no surprise that westerners typically have microbiota that is less diverse and likely contains lower quantities of beneficial bacteria like lactobacillus and bifidobacteria compared to healthy hunter-gatherers and non-westernized people (11).

All of the non-starch complex carbohydrates, some disaccharides, and certain proteins are all broken down by gut bacteria, and different types of gut bugs – and their genes – are needed to fully metabolize these food ingredients. Intolerance essentially comes from absence of genes in the gut microbiome, and the increased incidence of food intolerance and food allergy is just one of the symptoms of changes to the second genome in our bodies.

Microbial DNA: A new frontier in genetics and heredity

To summarize, there are five primary reasons why the second genome is interesting in terms of heredity and genetics:

  1. The genetic repertoire of the microbiome is at least 100 times greater than that of the human host.
  2. We receive microbes from parents and other close relatives.
  3. The microbiome plays an essential role in health and disease.
  4. We can manipulate the second genome.
  5. Western lifestyle perturbs the microbiome.

Since we essentially receive the microbiome our mother carries, we have to be healthy not for our own benefit, but also for the children we might bring into life…


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