Building Baby’s Gut
The Truth About Microbiomes in the First Year
The first year of a baby’s life is filled with growth and discovery not just for them but for their tiny microbiome, the unseen world of bacteria and microorganisms that help shape their health. If you have been listening to the Baby Tribe Podcast, you’ll know that I am a bit obsessed with the microbiome because I truly believe that it has the power to determine our health, and even influence how genes are expressed!
It goes without saying that as a parent, you want to give your baby the best start. But with so much information out there, it can feel overwhelming. Does the way a baby is born affect their microbiome forever? (some would certainly lead you to believe so). How much do breastfeeding, antibiotics, or even the family dog play a role in building a healthy gut?
Those questions can weigh on us as parents because we know how important those first few months are, and we are now recognising how important the microbiome is in sharping our long-term health. The stakes feel high, and every decision can feel like a turning point. But here’s the truth: babies are resilient. Their microbiome is not only adaptable but also shaped by many factors: some can be out of our control (like the mode of delivery and even how we feed our babies), and some can he fully in our control. While birth mode matters in those first weeks, by six months, its impact fades. By one year, it is almost irrelevant. Instead, the focus shifts to what we, as parents, can control, feeding choices, exposure to a variety of environments, and avoiding unnecessary antibiotics. These small, everyday decisions build the foundation for a strong and thriving microbiome.
When we understand how it all works, it doesn’t weigh us down, it gives us a sense of control. Amid all the competing voices and advice, it reassures us that simple, caring steps can truly shape our babies’ future health. In doing so, we’re not just fostering a strong gut; we’re setting them on a path toward a lifetime of well-being.
What is The Microbiome?
The microbiome is a big part of who we are. Populated by bacteria, fungi, viruses, and more, it’s a crucial player in keeping our bodies running smoothly. We host different microbiomes in various spots—on our skin, in our mouths, even in our lungs—but the gut microbiome stands out for its influence and the depth of research behind it. Think of the gut as a bustling metropolis teeming with trillions of microbes, each contributing something unique. They help break down what we eat, generate vital nutrients, and keep harmful invaders at bay by maintaining internal harmony. They’re even involved in guiding our immune system, showing it how to distinguish friend from foe and potentially preventing autoimmune disorders. As scientists keep exploring, they uncover new ways in which these microbial communities shape our biology. It’s clear the microbiome is no bystander—it’s an active participant in our well-being.
Microbiome and Chronic Disease
Over time, the makeup of the gut microbiome can sway our odds of facing chronic conditions. If that delicate balance tilts—what experts call dysbiosis—it can be associated with obesity, type 2 diabetes, heart disease, and inflammatory bowel issues like Crohn’s and ulcerative colitis. There’s also emerging evidence suggesting the microbiome may impact neurological conditions such as Alzheimer’s, Parkinson’s, and even mood disorders like depression and anxiety. What’s going on here? Microbes craft important metabolites, like short-chain fatty acids (SCFAs), that have anti-inflammatory perks and help regulate metabolism. When beneficial bacteria dwindle, chronic low-grade inflammation can settle in, setting a stage for various modern health problems. The microbiome, in short, doesn’t just affect the gut; it resonates throughout the entire body.
Microbiome and Gene Expression
This microbial universe reaches right down to the genetic level, fine-tuning how certain genes behave. Through epigenetic mechanisms, gut microbes release molecules that signal our cells to switch specific genes on or off. SCFAs, for instance, can influence genes involved in immune responses or inflammation. They can also sway genes linked to how we store energy, process fats, and grow cells, shaping our health risks in subtle but meaningful ways. The relationship goes both ways: our lifestyle choices—diet, exercise, stress, medications—alter our gut communities, and these communities in turn modify how genes are expressed. It’s a delicate dance between our environment, our microbial partners, and the blueprint we carry in our DNA.
The Gut-Brain Connection
The gut microbiome also chats closely with our brain via what’s often called the gut-brain axis. This two-way communication involves nerves, hormones, and immune signals, and it has far-reaching effects on mood, cognition, and mental well-being. Certain gut bacteria produce neurotransmitters like serotonin and dopamine, which help regulate our emotions and behaviour. When our gut is off-balance, conditions like anxiety and depression may arise. It’s another reminder that the microbiome’s reach extends beyond digestion.
The Microbiome as a Partner in Health
The microbiome isn’t an idle passenger—it’s an active collaborator within our biology. By nourishing a healthy microbial community with fibre-rich foods, limiting unnecessary antibiotics, and adding probiotics or prebiotics, we can tap into its power. In doing so, we protect against chronic disease, better regulate gene expression, and support our mental and physical health. This amazing ecosystem serves as a reminder of how interconnected we truly are with the microbial world. Rather than being something separate, our microbiome is woven into our identity, guiding everything from our immune defences to the very genes that shape us.
Determinants of Microbiome Evolution in Your Baby
Now that we got what a microbiome is out of the way, lets learn about what influences its development in the newborn. When a baby is born, their microbiome starts to develop right away. This collection of bacteria, fungi, and other microorganisms plays a big role in their health.
The way a baby is born can have an impact, initially. Babies born vaginally are exposed to their mother’s microbes during delivery. These include bacteria like Bifidobacterium, which are known to support gut health. I’ve touched on this before in a previous article: Babies born by C-section miss this initial exposure, so their microbiome starts off differently. Early on, this difference is noticeable, but by the time they reach six months, those differences are much smaller. By one year, the microbiomes of babies born by C-section and those born vaginally look very similar. The reason for this stems from the compensatory mechanism present to ensure that essential microbes still colonize the baby’s microbiome. Breastfeeding plays a crucial role, with breast milk becoming a primary source of beneficial bacteria like Bifidobacterium and other gut-supporting microbes. Skin-to-skin contact also contributes, allowing maternal skin microbes to transfer to the baby. These alternative pathways help restore microbial diversity, ensuring that C-section-born babies develop a robust microbiome. This adaptability underscores the resilience of nature’s design, ensuring that no single pathway is indispensable for healthy microbial colonization.
Feeding plays a much bigger role in shaping a baby’s microbiome than the mode of delivery. Breastfeeding provides beneficial bacteria and supports their growth. It also helps protect against harmful bacteria. Babies who are breastfed tend to have a microbiome rich in Bifidobacterium, which is linked to a healthy gut. As babies grow, the introduction of solid foods, especially plant-based foods, further shapes their gut health. Foods like fruits, vegetables, and legumes support beneficial microbes, helping the microbiome mature.
Antibiotics can affect the microbiome too. When a baby receives antibiotics, it can reduce the number of good bacteria in their gut. This effect is temporary, but avoiding unnecessary antibiotics can help maintain balance.
The environment also plays a role. In the first months, a baby’s microbiome comes mostly from their mother and close family. Later, interactions with other people, pets, and even daycare can add to this diversity. For babies, having siblings or living in a home with pets can boost exposure to different microbes, helping to create a more diverse microbiome. The graph below shows the relative contributions of various factors on the baby’s microbiome at 6 and 12 months.
What About Vaginal Seeding and FMT?
Many parents wonder about vaginal seeding, a practice where a mother’s vaginal fluid is applied to a newborn delivered by C-section. The idea is to expose the baby to bacteria they would normally encounter during a vaginal birth, which some believe might improve gut health. While a few small studies suggest it may slightly change the baby’s gut bacteria, there is no strong evidence that it leads to long-term health benefits. Larger, more reliable studies are needed.
Experts and medical organizations do not recommend vaginal seeding because of potential risks. Harmful bacteria or viruses could be passed to the baby, and there are no safety guidelines in place to prevent this. For now, vaginal seeding is considered experimental, and parents are encouraged to focus on proven methods, like breastfeeding, until more research is available.
Maternal faecal microbiota transplantation (FMT) is another experimental approach aimed at restoring the microbiome of cesarean-born babies. By giving a small dose of the mother’s stool—usually mixed with breast milk—shortly after birth, FMT seeks to mimic the microbial transfer that happens during vaginal delivery. Early studies suggest it can contribute to microbial diversity, reduce harmful bacteria, and help cesarean-born infants develop a microbiome closer to those delivered vaginally.
Despite its promise, maternal FMT isn’t ready for widespread use. The process carries risks, such as the potential for transmitting pathogens, even with thorough screening. There’s no standardized method for preparing or administering FMT, and long-term effects remain unknown. Ethical and practical challenges, including safety concerns and the complexity of the procedure, further limit its readiness. For now, FMT remains in the research realm. Proven practices like breastfeeding and skin-to-skin contact continue to be the best ways to support a healthy microbiome for cesarean-born babies.
Do Fathers Play a Role?
It turns out that dads play a significant role in shaping their baby’s microbiome, and their influence is both unique and complementary to that of mothers. By the time a baby reaches their first birthday, the cumulative contribution of microbes from the father is comparable to that of the mother. This doesn’t replace maternal seeding but adds to it, providing diversity and resilience to the baby’s microbiome.
Interestingly, the strains provided by fathers don’t overlap much with those from mothers. Fathers contribute distinct microbes that expand the overall diversity of the infant’s gut. This is especially important in cases where maternal seeding is disrupted, such as with cesarean deliveries or when antibiotics are used during birth. In these situations, the father’s microbiota becomes an essential backup, helping to fill the gaps and ensure the baby gets a broad range of beneficial bacteria. The father’s role in microbiome seeding highlights just how interconnected the family unit is in supporting an infant’s health. It reminds us that gut health is not just a product of birth mode or maternal factors—it’s a collective effort. For dads, this is a powerful reminder of the impact they have from the very beginning, in ways that go far beyond genetics and caregiving. They, too, are active participants in shaping their child’s foundation for lifelong health.
Final Thoughts
Raising a child is a series of choices that weave together into the fabric of their inner world. A nurturing environment, breastfeeding or a nourishing formula, a balanced introduction to solid foods, and the warm comfort of holding, talking, and playing all steer the growth of a strong microbiome. No single decision sets your baby’s path in stone; each careful, loving step you take helps that inner ecosystem flourish, preparing them for the world ahead. The first year is just the start of this quiet miracle unfolding inside your baby. Though invisible, it’s always at work, evolving and enriching their health with every passing day.