The role of nutrition in the development of the infant microbiome

The first 1000 days is an important period for a child’s development and for the development of the child’s microbiome. The role of nutrition is significant in that process, explains Dr. Maciej Chichlowski of Reckitt Benckiser in an interview with Dr. Radhika Bongoni, business developer at BaseClear.

Reckitt Benckiser is a large producer of cleaning, food and personal care products, including infant milk formulas and dietary supplements. Dr. Maciej Chichlowski, Principal Scientist in Reckitt Benckiser’s Global Nutrition Science department, is working on preclinical studies involving the microbiome, mostly in regard to pediatric nutrition, such as baby and infant formula.

Dr. Chichlowski was one of the speakers in the expert meeting on infant and pregnancy microbiome that BaseClear organized on May 14 2020. “The role of nutrition is significant in the development of an infant’s microbiome,” he says. “There are many factors involved in the development of the microbiome during the first thousand days. More and more links are being discovered for this ‘window of opportunity’. This refers to the first months of life when shaping of the infant microbiome takes place. This process can be influenced by type of feeding, for example breastmilk or infant formula. For babies who cannot be breastfed, designing a formula inspired by the composition of breast milk is important. However, we still don’t fully know whether the microbiome is reactive or a driver of the observed changes. Many of the involved factors cannot be influenced, such as the occurrence of a preterm birth. Nutrition, on the other hand, is a factor that we can control. In fact, the nutrition for babies is unique, since either breast milk or formula milk is the only type of food a baby receives during the first six months of its life or longer. Therefore, formula manufacturers’ have a huge responsibility to make the formula milk as similar to breast milk as possible. Interestingly, it has been shown that some of the components of breast milk are not the nutrients that baby is absorbing, but rather are there to stimulate the intestinal microbiome. Since evolution is very efficient and it eliminates anything that is useless, we can conclude that the microbiome must be very important for infant development.”

Higher or lower diversity

Still, there are many questions left in relation to microbiome development and the role of breast or formula milk. Dr. Chichlowski notes: “Historically, our mantra was that more biodiversity in the microbiome is better, but in fact we see that breast-fed infants have a lower alpha diversity than formula-fed infants. Breastfed infants have a smaller number of the dominating types of bacteria, which are the ones that can metabolize the breast milk complex sugars (human milk oligosaccharides, HMO). This is changing when breast fed infants are switching to solid food and no longer receive HMO.”

Dr. Chichlowski continues: “Published studies suggest that the microbiome of formula-fed infants, especially without prebiotics, is changing sooner to an adult-like composition. They skip the low-diversity profile that is observed in breast-fed infants and move sooner to a more diverse adult-like microbiome. Although we might argue that a higher diversity is good, this is not necessarily desirable during the first months of life. The microbiome in breast-fed infants supports certain functions, to train the immune system, to provide protection and educate immune responses in the baby. Therefore, this highlights in importance of breast-feeding baby as long as you can, or for formula fed infants choosing a formula that has bioactives that demonstrate similar effects to breast milk if possible.”

Different measures

The question is whether other aspects of the microbiome might be of more importance than the biodiversity, especially during the first period of development of the microbiome. Dr. Chichlowski agrees with that, stating, “Indeed, it might well be that the microbial diversity is not sufficient as a measure for the microbiomal health of infants. It might be better to look at the functionality of the microbes that are present instead of looking at diversity. That is a very big possibility. The metabolites might also be interesting to look at.”

Measuring microbiomal diversity is mostly done via 16S microbiomal profiling. “This is an important technology, but it is very difficult to draw conclusions based on these data,” Dr. Chichlowski says. Dr. Bongoni, business developer at BaseClear, suggests that metagenomics could help in such case. “Shotgun metagenomics not only generates profiles, but it also gives extra information, for example about the interplay between microbes, the function of genes and links between microbe communities. In fact, we see that more and more of our clients are moving from microbial profiling to shotgun metagenomics. However, shotgun metagenomics comes with higher costs which not always are not in favour of research budgets. We have developed a new bioinformatics pipeline which has curated databases from public/literature information for genomes specific to infant gut microbiome. These curated databases enable us to make the most of the minimal sequencing data generated. Currently we can deliver species level microbial taxonomic classifications at a sequencing depth of up to 300MB per sample. At this sequencing depth, we are also able to offer basic functional profiles. Of course, with every analysed sample, the database is curated each time.”


BaseClear would like to thank Dr. Maciej Chichlowski for his time and input for this interview. For Maciej’s contributions to this research field see

Get in touch