Case study: a baby microbiome

Molly is a healthy infant whose first-time parents are interested in the microbiome and have tried to do everything they can to optimize their baby’s microbial health. Molly was born vaginally, has never had antibiotics, is exclusively breast-fed by a mother who tries to eat nutritious, organic food. They live in the country, surrounded by nature, including pets and other animals that will become more of her life when she starts to move around.

But how can you tell whether their healthy lifestyle is helping? To find out, her parents gave Molly an $89 uBiome gut kit for her one-month birthday. As any parent on diaper duty knows, collecting the, um, sample is pretty easy. They mailed a tiny swab to the lab and a few weeks later they received this list of the kinds of bacteria found along with a breakdown of their percentage abundances:

Phylum (Baby)


Bacteroidetes 84.59% Actinobacteria 9.18% Proteobacteria 3.97% Firmicutes 2.26%

What does this all mean? Well, the first thing to notice about Molly's microbiome is the dominance of a group of bacteria called Bacteroidetes, and the much lower levels of another type called Firmicutes. In most westerners, the abundance of these two is exactly reversed, as you can see in a similar breakdown we have of Molly’s mom:

Phylum (Mom)


Firmicutes 50.40% Bacteroidetes 23.04% Verrucomicrobia 8.66% Actinobacteria 7.78% Proteobacteria 1.59% Nitrospirae 0.02%

Figure 2: Mom's microbiome

The bacterial kingdom is extremely old and diverse, much more so than the other types of living things around us. The categories Firmicutes and Bacteroidetes are therefore very broad, a bit like discussing “vertebrates” and lumping in everything from fish to people as one kind of life. Even at this high level, they have some distinctive features – Firmicutes tends to eat fats, whereas Bacteroidetes likes sugars – but to understand the difference between Molly and her mother, let’s dig more deeply into exactly the types of Firmicutes we see.

In adults like Molly’s Mom, we generally find that more than 99% of Firmicutes come from a group of inter-related bacteria called Clostridiales. But not Molly’s. Hers is almost entirely a single species, Phascolarctobacterium faecium. What does it do? Without comparing her to other babies, we don’t really know. How little we understand is just one of the frustrating recurring themes as we study the microbiome.

The next big bunch in Molly’s gut is Actinobacteria, of which nearly all is a well-studied species called Bifidobacterium longum. This one is so closely associated with good health that many supplement makers sell it as a prebiotic pill, and Molly has enough to fill a factory: it makes up more than 8% of her entire sample, nearly 100 times more than her mother.

Bifidobacteria like milk, and Molly’s are fortunate that she is breastfed. One clue about the importance of breast milk to baby microbes is human milk oligosaccharide (HMO), which despite being the most abundant component of milk, after fat and lactose1, has a chemical structure too complex for the baby to digest! Some early designers of infant formula assumed Nature had made a mistake and tried somewhat arrogantly to market their wares as "scientifically" better because it was simple enough for a baby. But HMOs aren't there to feed the baby; they nourish the abundant microbes in the infant gut, mostly the Bifidobacteria, and later the Bacteroides that will play a role when it comes time for the baby to begin eating solid foods. At that point, Molly’s microbiota will undergo a big transformation until, by three years old, her gut will look like an adult’s.

Turning to the other big phyla, Bacteroidetes, we see here too Molly’s is almost exclusively one species: Bacteroides fragilis, of which her mom (but not her dad) has a tiny bit as well. That makes sense because this particular bacterium is a well-known early infant colonizer, transmitted from mother to child. Some Norwegian scientists, surveying the research, noted its well-known immune system modulating properties:

B. fragilis are higher in children with high specific IgE (sIgE). IgE plays a central role in asthma and allergy. Other studies have shown a correlation of B. fragilis with asthma and pollen allergy.2

Now that doesn't mean Molly herself is predisposed to any of these conditions -- in fact, it may mean the exact opposite depending on the amounts or the presence or absence of other species. Again, without studying a lot more babies, we just don’t know.

Interestingly, when I looked closely at the broadest levels of bacteria, I couldn't find a single phylum of microbes that was present in Molly but not in her parents, while I found plenty of examples of the opposite. I guess that's one more way Molly is dependent on her mommy. Bottle-fed babies, by the way, tend to have more diversity; though my guess is those extra bacteria aren’t all good.

One microbe that doesn't appear in Molly's sample is Lactobacillus, which is often missing in collicky babies3. Fortunately, Molly seems completely normal for now but this is something to watch for in future tests. There may be an easy fix anyway: get her a sibling. Babies who grow up in homes with other small children tend to have better microbiomes. 4

Thanks to the surging interest in gut health, many parents are taking steps to ensure their babies have the best possible microbiome, but until the recent development of low-cost test kits, it was difficult to tell how well it was working. Now Molly’s parents have a new tool, and if you’re changing diapers regularly anyway, why not test your own baby too and share your results with others so that we can all learn more and contribute to the scientific understanding of the baby biome.

1. It takes up to 500 calories per day for a mother to produce enough breastmilk to feed a child (pregnancy takes only an extra 300), so nature is apparently very serious about getting this right.↩
2. Bjerke, G A, R Wilson, O Storrø, T Øyen, R Johnsen, and K Rudi. 2011. “Mother-to-Child Transmission of and Multiple-Strain Colonization by Bacteroides Fragilis in a Cohort of Mothers and Their Children.” Applied and Environmental Microbiology 77 (23): 8318–24. doi:10.1128/AEM.05293-11.
3. de Weerth, C., S. Fuentes, P. Puylaert, and W. M. de Vos. 2013. “Intestinal Microbiota of Infants With Colic: Development and Specific Signatures.” PEDIATRICS 131 (2): e550–58. doi:10.1542/peds.2012-1449.
4. Penders, John, Kerstin Gerhold, Ellen E Stobberingh, Carel Thijs, Kurt Zimmermann, Susanne Lau, and Eckard Hamelmann. 2013. “Establishment of the Intestinal Microbiota and Its Role for Atopic Dermatitis in Early Childhood.” The Journal of Allergy and Clinical Immunology 132 (3): 601–7.e8. doi:10.1016/j.jaci.2013.05.043.

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