Research is beginning to reveal how the first substances that enter a newborn’s gut can shape health for an entire lifetime. In 2017, two technicians at Queen’s Hospital in London waited each morning for tightly wrapped parcels carrying tiny samples of newborn stool. Parents scraped these samples from nappies and posted them to the Baby Biome study. Over two years, the team analysed more than 3,500 samples. It was a large effort, but the findings changed how scientists understand early development.

Experts now believe the first thousand days of life form a crucial window when microbes leave long-lasting marks on the immune system. According to Nigel Field of University College London, babies are born almost entirely free of microbes. Over the first few days, their bodies experience a sudden wave of new bacteria, fungi and viruses. These organisms begin building the complex microbiome that adults rely on to digest fibre, produce vitamins and fend off dangerous pathogens.

Recent studies show the benefits stretch far beyond digestion. A balanced microbiome may help protect against anxiety, depression and even diseases linked to ageing. On the other hand, adults with disrupted or weak microbial communities often face increased risks of cardiovascular disease, kidney problems, diabetes, inflammatory bowel disease and obesity. For years, scientists focused mainly on adults. Now childhood microbiomes are becoming a major research frontier. BBC reporting has highlighted how these early microbial shifts may shape lifelong resilience.

Researchers have found that the microbes arriving in the first months of life act like early architects of the immune system. They teach the body how to respond to threats and how to tolerate harmless microbes and food. These early communities influence allergy risk, vaccine response and the strength of the gut barrier. Evidence increasingly suggests that these early microbial changes can last for decades.

Scientists now think babies inherit most of their microbes from their mother’s digestive tract, not the vagina. The infant’s position during birth makes it likely they encounter the mother’s gut bacteria first. This helps explain the difference between babies born vaginally and by caesarean section. Field’s team found that babies born via C-section often miss out on beneficial bacteria, which may raise their chances of respiratory infections later on.

The study identified three main early bacterial pioneers. Babies tended to develop one of three patterns: Bifidobacterium longum, Bifidobacterium breve or Enterococcus faecalis. Vaginally born babies were far more likely to carry the Bifidobacterium species, while C-section babies often ended up with E. faecalis, a bacterium more commonly linked to hospital environments. Although these differences usually faded by the end of the first year, the early variations still mattered. Babies with B. longum were half as likely to be admitted to hospital with respiratory infections within two years.

Scientists believe these protective effects may come from how Bifidobacterium breaks down complex sugars in breast milk. These microbes produce short chain fatty acids, which appear to help regulate the immune system. These compounds help the infant recognise harmless substances and avoid unnecessary inflammation. Bifidobacterium also reduces oxygen in the newborn gut and lowers the pH, creating conditions that discourage harmful bacteria.

Even so, researchers stress that the picture is more nuanced than simply praising one birth method over another. Not all vaginal births deliver the most beneficial microbes, and not all C-section babies face serious risks. The next challenge is figuring out how to safely support babies who miss out on helpful microbes early in life.

Some parents are turning to practices like vaginal seeding, but experts warn it can carry dangerous infections and that the beneficial bacteria do not come from the vagina anyway. Faecal transplants have also been tested in small studies, but they are not considered safe or reliable enough for infants. Many scientists argue that probiotics remain the safest option for now, although it is still unclear which strains work best for different babies.

Researchers believe future treatments will rely on personalised microbial medicine. Doctors may one day tailor microbial support to each infant’s diet, genes and immune profile. For now, the science is still developing, but the message is becoming clearer. What enters a baby’s gut in the first days of life matters more than anyone once imagined.