It has generally been considered that an infant’s gut microbial composition resembles that of an adult by the age of about 12 months. Gut bacterial composition during the first year of life is in flux, with great variation seen between infants and even within the same infant over time. A recent study is changing how we view the early establishment of gut microbes, however. In a recent study published in the journal Applied Environmental Microbiology, researchers determined that microbes in the infant gut continue to transform over the first three years of life.1

The infant gut microbial composition is dependent on a number of factors, including mode of delivery, antibiotic use, and diet (breastfeeding or formula feeding). It is known that vaginal birth, as well as breastfeeding, promotes the growth of beneficial Bifidobacteria—well-known to be protective of infant health, while suppressing the growth of harmful bacteria.

Most studies of infant microbial composition have focused on colonization right after birth, during weaning, or up to one year of age. In this new study, the researchers analyzed changes in gut microbiota of Danish infants between ages 9 to 18 months and from 18 to 36 months. They noted clear changes during both periods, but particular between ages 9 and 18 months.

During the period between 9 to 18 months, they observed an increase in Bacteroidetes species, consistent with the introduction of food. At the same time, they observed a decrease in the abundance of Bifidobacterium. Specifically, B. longum and B. breve decreased while B. adolescentis increased. This makes sense when you consider that B. longum, B. breve utilize prebiotics found in breast milk as food, while B. adolescentis does not. Lactobacillus species and Enterobacteriaceae also decreased during the period between 9 to 18 months, also consistent with cessation of breastfeeding and introduction to formula or cow’s milk.

Interestingly, changes continued between 18 to 36 months, suggesting that a change toward adult-like stability was still occurring during this period. This is in line with another recent study that found a similar occurrence.2 These studies are shaking up what we thought we knew about infant microbial development.

Infants who were breastfed at 9 months had higher amounts of Lactobacillus and Bifidobacterium and lower amounts of other bacteria in the Clostridium and Eubacterium taxa, changes that were still evident at 18 months, but disappeared by 36 months. The researchers also looked at physiological parameters such as measures of growth and body composition and found a correlation between duration of breast milk consumption and overall energy intake—those infants who breast fed longest had lower energy intake. They also found a link between body mass index and an increase in Firmicutes bacteria, a group of bacteria that has been linked to body fat accumulation in a number of studies.

Lastly, the researchers found considerable changes between bacterial composition during the 9 to 18 month period and again during the 18 to 36 month period. They noted two distinct enterotypes, or dominant gut bacterial types, by 36 months of age, which is in accordance with findings of two or three enterotypes in adults. The two enterotypes observed in these infants were made up of Prevotella species in one and Bacteroides species in another. These enterotypes were able to change over time, which is in contrast to findings in adults.

It would be interesting to compare the gut microbiomes of these Danish children with those of the infants in Burkina Faso Africa, where they have found bacteria in children that are non-existent in Western cultures due to dietary differences. Many of these bacteria are very good at breaking down fiber due to the high-fiber diet of this culture. In many parts of the world, children are breastfed until at least age 3 or 4. Comparing Western children to these children would help us to learn more about the benefits of breastfeeding.

More studies will be needed to better determine gut microbial changes in infants, what factors affect these changes, and how these changes relate to health outcomes. One day, we will have available bioidentical breastmilk for women unable to breast feed. Until then, probiotics during infancy may be the best bet for babies unable to be breastfed.



  1. Bergstrom A, Skov TH, Bahl MI, et al., “Establishment of intestinal microbiota during early life: A longitudinal, explorative study of a large cohort of Danish infants.” Appl Environ Microbiol. 2014 Feb 28.
  2. Yatsunenko T, Rey FE, Manary MJ, et al., “Human gut microbiome viewed across age and geography.” Nature. 2012 May 9;486(7402):222-7.