Key Takeaways
- The microbiome starts developing before birth and is influenced by birth mode, nutrition, environment, and lifestyle.
- Breastfeeding plays a crucial role in shaping a healthy gut microbiome.
- Pets, antibiotics, stress, and household environments all impact microbial diversity.
- The microbiome is dynamic, adapting and evolving throughout life.
What Is the Microbiome?
The microbiome is a community of trillions of microorganisms—bacteria, fungi, viruses, and more—residing on and within the human body. Roughly 38 trillion bacteria alone contribute to vital functions, including digestion, immunity, and metabolism. These microbes inhabit various body parts, like the mouth, skin, but most of them reside in your gut.¹
Where Does the Microbiome Come From?
An infant’s microbiome originates from the mother, beginning in the womb and continuing through birth and early infancy. Factors such as birth mode, nutrition, environment, family members, pets, and antibiotics influence microbiome composition.
Microbiome Development Timeline
- Birth (0 months): Microbial seeding begins.¹
- 0-3 years: Rapid changes and evolution of the microbiome.²
- 3+ years: The gut microbiome is stabilizing, but still “under construction” and starts to resemble an adult’s microbiome.³
Are Babies Born with a Microbiome?
For years, scientists believed babies were born sterile.² However, new research suggests otherwise. Studies have found bacteria in:
- The placenta (connecting mother and baby)³
- The meconium (baby's first stool)⁴
- The amniotic fluid (surrounding the baby in the womb)⁵
Despite these findings, some scientists argue that the presence of bacteria does not necessarily mean a fully developed microbiome.⁶ Instead, these microbes may be passing through rather than forming a resident community.
What is certain is that even if babies lack an established microbiome before birth, they are exposed to maternal microbial byproducts that help prepare their immune system and metabolism for life outside the womb.⁷
Birth: The First Major Microbial Encounter
Birth is the first major microbial colonization, shaping an infant's lifelong microbiome.⁷ The birth mode plays a crucial role in determining the composition of this early microbial community.⁸,⁹
Vaginal Birth vs. Cesarean Section
Vaginal Birth: Babies acquire beneficial gut bacteria from exposure to the mother's vaginal microbiota during natural childbirth. This process introduces a diverse and rich array of microbes, promoting a rich and diverse gut environment compared to cesarean deliveries.
Cesarean Section: Babies are exposed to microbes from the skin, mouth, and operating room environment, which alters their early microbiome development.
Studies suggest that cesarean-born children have a higher risk of immune-related disorders, including asthma, allergies, inflammatory bowel disease, and obesity. However, birth mode is just one of many factors influencing the microbiome, and various strategies exist to support microbial health in cesarean-born infants.
Breastfeeding and the Infant Microbiome
Before solid foods are introduced, an infant’s microbiome is dynamic and heavily influenced by nutrition. Breastfeeding plays a key role in this process by directly supplying beneficial bacteria.
How Breastfeeding Shapes the Microbiome
- Provides Beneficial Bacteria: Breast milk contains live bacteria that colonize the infant’s gut.¹⁶
- Contains Human Milk Oligosaccharides (HMOs): These prebiotics feed beneficial gut bacteria, particularly Bifidobacteria.⁹
- Encourages Skin-to-Skin Transfer: Close contact during breastfeeding exposes infants to the mother’s skin microbes, further shaping their microbiome.²²
While formula aims to replicate the nutritional components of breast milk, it lacks the same bioactive elements, including live bacteria and HMOs.²³
Factors Affecting the Microbiome from Birth to Age 3
Several environmental and lifestyle factors continue shaping the infant microbiome beyond nutrition.
- Pets and Household Environment: Studies show that early-life exposure to pets can enhance microbial diversity. Infants raised in homes with pets exhibit increased beneficial gut bacteria and a reduced risk of allergies, asthma, and obesity.²⁵
- Antibiotics and Their Impact: While antibiotics are essential in treating infections, they indiscriminately kill both harmful and beneficial bacteria. Early antibiotic exposure has been linked to disruptions in microbiome development, which may contribute to allergies and metabolic conditions.²⁷
- Early Life Adversity Stress: and trauma in early childhood may impact microbial diversity, potentially leading to long-term health consequences. Some research suggests that individuals with irritable bowel syndrome (IBS) and early-life trauma exhibit distinct microbiome differences compared to healthy individuals.³⁰,³¹
- Sanitisation Products: Increased use of antimicrobial cleaning products may negatively impact the microbiome. Studies indicate that infants exposed to household disinfectants may have altered gut bacteria and a higher body mass index (BMI) by age three.³²
The Microbiome Beyond Age 3
Although the microbiome stabilizes around age three, it continues evolving throughout life.³³ No two people (not even twins) share the same microbial makeup. In this way, there is no fixed state, no universal endpoint, no one “perfect” microbiome. Factors such as diet, lifestyle, environment, and antibiotic use contribute to ongoing microbial shifts. Importantly, no two people share the same microbiome—it’s as unique as a fingerprint.
