THE HUMAN MICROBIOME
The Trillions of You
3 Years Old - Adulthood
By age three, a child's microbiome looks a lot like an adult's, and it becomes much more stable. It still continues to change in response to events like illness, disease, antibiotic treatment, fever, stress, injury, and changes in diet. But the population still tends to shift back to a "baseline" state.
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Major life events—like puberty, pregnancy, and menopause—can cause larger shifts. For example, puberty affects skin microbes by causing changes in skin oils. And pregnancy brings on changes in the vaginal microbiome: species start to grow that will colonize and benefit the baby as it's born.
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Senior citizens have a distinct microbial profile, with certain species becoming more common and others becoming less common. After age 65, the number of microbial species decreases, and the microbial populations become more similar among individuals. [5]
Characterized by new sequencing technologies methods, the human microbiome plays a critical role in maternal and child health outcomes: as a person develops, so does their microbiome. The development begins in the womb, and continues throughout life until the person dies. Before birth, we have no microbes. Even as adults and senior citizens, our microbiota continues to shift and adapt.
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Growth and Development
Until recently, it was thought that the uterus and placenta were germ-free and completely sterile in order to keep the baby safe from infections. But babies have a complex collection of microbes by the time they are just one week old, where do those bacteria come from?
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Our first dose of microbes comes from our mother. Babies delivered vaginally are covered in a film of microbes as they pass through the birth canal, whereas babies delivered by cesarean section are colonized mainly by skin microbes—a very different set of species.
The Human Microbiome is composed of the microbes (as well as their genes and genomes), that live in and on the human body. These communities consist of a variety of microorganisms including eukaryotes, archaea, bacteria and viruses.
Unique to every individual, humans contain a wide diversity of microorganisms. These microbes contribute to our health by regulating nutrition, immune responses, and much more.
By studying the link between our microbes to the wide spectrum of diseases, such as infectious and inflammatory diseases like malaria, autism, cancer, and depression, researches will be able to diagnosis and develop a better understanding of the human body. We can then take this knowledge and apply it to biotechnology to further develop human health care by manipulating microbes to our advantage- launching the limitless possibilities that will save the lives of many for years to come.
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General Overview of the Human Microbiome
[2,3,4]
How We Study the Human Microbiome
To understand how microbes influence human disease, we first need to understand the microbial make up of a healthy person- what types of microbes are present, and what are they doing?
"We know the microbiome is important for maintaining human health, and when things go wrong it can contribute to disease. In order to understand how microbes influence human disease, we first need to understand the microbial make up of a healthy person—what types of microbes are present, and what are they doing?"
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Early research techniques involved taking a sample from a patient and growing it in the lab, where it could be studied using a combination of culture, microscopy, and staining techniques. This works well for microbes that grow easily in culture, like e. coli, but most microbes can’t be grown in culture. New technologies, like DNA sequencing, can be done using samples taken directly from patients, so these methods are especially important for learning about microbes that can’t be cultured. [1]
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However, microbial communities can vary from one healthy person to another, and even from a different from one location to another on the same individual.
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In order to reach the placenta, Fusobacterium Nucleatum alters blood vessels so that microbes can infiltrate the blood stream. But not only do babies get microbes from their mothers, but also from what they contact. Thus, babies who are born at home are exposed to different types of microbes than babies born in hospitals. Within weeks, babies pick up more microbes from their family members and surroundings, and the types of microbes living in different parts of the body start to specialize.
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Difference Between Vaginal vs. C-section Birth:
As a baby is born through the vagina, it breaths in all of the bacteria on the mother. This includes bacteria such as Lactobacillus, Prevotella and Sneathia, which are important to the gut/intestines, and are located in the vaginal flora.
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Babies who are born through Cesarean Section (C-section), are mainly exposed to the skin microbes of the mother and bacteria from the environment; most commonly being Staphylococcus. However, these babies have been shown to have less Bifidobacterium, a bacteria in the intestines that is used to treat diseases or conditions in the gastrointestinal tract. These babies' microbial diversity is not as diverse; thus, doctors are now working towards a solution in increasing microbial diversity to infants and experimenting with ways to rub bacteria collected from the mother's vagina into the baby's mouth and on its body.
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Variation of microbes is occurs most during childhood, and decreases with age. Events like a fever, antibiotics, or new foods can cause sudden shifts in the microbiome, with effects that may last for years or even a lifetime. [3]
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Kjersti Aagaard, an obstretrician and associate professor of gynecology at Baylor and Texas Children's Hospital, collected tissue samples from 320 placentas and isolated the bacteria. Aagaard and her team focused on collecting DNA from the placentas, and then sequenced the genetic material to reveal the identity of the microbes present. Their findings conclude: "the placental microbes with those in the mouth, nose, skin, vagina and gut of non-pregnant women, they found they most closely resembled the microbes that lived in the mouth"; showing that humans first receive microbes from the placenta through the blood stream thanks to the oral microbe called, Fusobacterium Nucleatum.
During and After Birth
THE HUMAN MICROBIOME: BACKGROUND
General Information Concerning the Microbiome
Breast Fed vs Bottle Fed
Colonizing bacteria within babies derive from the mother (mainly vaginal and intestinal microflora), breast milk, and their surrounding environment. When a baby is breastfed, they are getting the best possible nutrients and bacteria sent to the gut. Of these include oligosaccarides, which promotes the growth of new bacteria. Recent studies revealed that human milk contains higher concentrations of proteins that support gastrointestinal system, immune system, and neurological development.
A baby who is fed formula is getting vitamins and nutrients that are important, but they are not exposed to their mother's bacteria, which can affect the rate of development of the microbiome, and increase risk for infections and disorders such as allergies, neonatal diarrhea, necrotizing enterocolitis (NEC), obesity, and type 2 diabetes.
When put together, all of these factors create different ecosystems in the child. For example, one study found that delivering a baby vaginally at home, then exclusively breastfed creates the most "beneficial" microbiome. [4]
"Left: C-section babies get a microbiome (small red rods) upon delivery. Right: Swabbing the babies with gauze that has been in the mother's vagina transfers her vaginal microbiome (small blue rods) to her baby, resulting in a mixture of both types." [4]